US20170037363A1 - Ammonia-oxidizing nitrosomonas eutropha strain d23 - Google Patents

Abstract

This disclosure provides, inter alia, an optimized strain of Nitrosomonas eutropha (N. eutropha) designated D23, D23-100, or AOB D23-100. N. eutropha bacteria disclosed in this application have desirable properties, e.g., optimized properties, such as the ability to suppress growth of pathogenic bacteria, and an enhanced ability to produce nitric oxide and nitric oxide precursors. The N. eutropha herein may be used, for instance, to treat diseases associated with low nitrite levels, skin diseases, and diseases caused by pathogenic bacteria.

Description

• This application claims priority to Greek Patent Application Number 20140100217, filed Apr. 15, 2014, U.S. Provisional Application No. 62/002,084, filed May 22, 2014, U.S. Provisional Application No. 62/012,811, filed Jun. 16, 2014, U.S. Provisional Application No. 62/053,588, filed Sep. 22, 2014, and Greek Patent Application Number 20150100115, filed Mar. 13, 2015, the contents of which are incorporated herein by reference in their entireties.
SEQUENCE LISTING
• The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Apr. 13, 2015, is named N2060-7001WO.txt and is 3,590,980 bytes in size.
BACKGROUND
• Beneficial bacteria can be used to suppress the growth of pathogenic bacteria. Bacteria and other microorganisms are ubiquitous in the environment. The discovery of pathogenic bacteria and the germ theory of disease have had a tremendous effect on health and disease states. Bacteria are a normal part of the environment of all living things. In the gut, these bacteria are not pathogenic under normal conditions, and in fact improve health by rendering the normal intestinal contents less hospitable for disease causing organisms. Disease prevention is accomplished in a number of ways: nutrients are consumed, leaving less for pathogens; conditions are produced, such as pH and oxygen tension, which are not hospitable for pathogens; compounds are produced that are toxic to pathogens; pathogens are consumed as food by these microorganisms; less physical space remains available for pathogens; and specific binding sites are occupied leaving fewer binding sites available for pathogens. The presence of these desirable bacteria is seen as useful in preventing disease states.
• There is a need in the art for improved beneficial bacteria that can suppress the growth of pathogenic bacteria.
SUMMARY
• This disclosure provides, inter alia, an optimized strain of Nitrosomonas eutropha (N. eutropha) designated D23, D23-100 or AOB D23-100, the terms which may be used interchangeably throughout the disclosure.
• Ammonia oxidizing bacterial of the genus Nitrosomonas are ubiquitous Gram-negative obligate chemolithoautotrophic bacteria with a unique capacity to generate energy exclusively from the conversion of ammonia to nitrite.
• N. eutropha bacteria disclosed in this application have desirable, e.g. optimized, properties such as the ability to suppress growth of pathogenic bacteria, and an enhanced ability to produce nitric oxide (NO) and nitric oxide (NO₂ ⁻) precursors. The N. eutropha, e.g., optimized N. eutropha, e.g., purified preparations of optimized N. eutropha herein may be used, for instance, to treat diseases, e.g., diseases associated with low nitrite levels, skin disorders, and diseases caused by pathogenic bacteria. When referring to N. eutropha throughout the disclosure, it may be referring to an optimized strain of N. eutropha or a purified preparation of optimized N. eutropha.
• The present disclosure provides, inter alia, a Nitrosomonas eutropha (N. eutropha) bacterium, e.g., an optimized N. eutropha, e.g., a purified preparation of optimized N. eutropha, having at least one property selected from:
• • an optimized growth rate;
  • an optimized NH₄ ⁺ oxidation rate; and
  • an optimized resistance to ammonium ion (NH₄ ⁺).
• The bacterium is optionally axenic.
• In embodiments, the optimized growth rate is a rate allowing a continuous culture of N. eutropha at an OD600 (optical density at 600 nm) of about 0.15-0.18 to reach an OD600 of about 0.5-0.6 in about 1-2 days. In embodiments, optimized growth rate is a doubling time of about 8 hours when cultured under batch culture conditions. In embodiments, the optimized NH₄ ⁺ oxidation rate is a rate of at least about 125 micromoles per minute of oxidizing NH₄ ⁺ to NO₂ ⁻. In embodiments, the optimized resistance to NH₄ ⁺ is an ability to grow in medium comprising about 200 mM NH₄ ⁺ for at least about 48 hours.
• In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) has at least two properties selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺. In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) has an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺. In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises a chromosome that hybridizes under very high stringency to SEQ ID NO: 1.
• In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises an AmoA protein having an identity to SEQ ID NO: 6 or 12 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an AmoB protein having an identity to SEQ ID NO: 8 or 14 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an amoC gene having an identity to SEQ ID NO: 4, 10, or 16 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a hydroxylamine oxidoreductase protein having an identity to SEQ ID NO: 18, 20, or 22 selected from at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a cytochrome c554 protein having an identity to SEQ ID NO: 24, 26, or 28 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, or a cytochrome c_M552 protein having an identity to SEQ ID NO: 30 or 32 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical.
• In some embodiments, the purified preparation of optimized N. eutropha bacterium (which is optionally axenic) comprises 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or all of the sequence characteristics of Table 2. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167. In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 33, e.g., a V at position 33. In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 165, e.g., an I at position 165. In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 79, e.g., an A at position 79. In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 271, e.g., a V at position 271. In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85. In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163. In some embodiments, the bacterium or preparation comprises a c554 CycA1, c554 CycA2, or c554 CycA3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 65, e.g., a T at position 65. In some embodiments, the bacterium or preparation comprises a c554 CycA1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 186, e.g., a T at position 186. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 63, e.g., a V at position 63. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 189, e.g., a P at position 189. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 206, e.g., an insE at position 206. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 207, e.g., an insE at position 207. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 195, e.g., an insD at position 195. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 196, e.g., an insD at position 196. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 197, e.g., an insD at position 197.
• Combinations of two or more sequence characteristics of Table 2 are also described. The two or more sequence characteristics may be in the same gene or different genes. The two or more sequence characteristics may be in the same protein or different proteins. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167. In some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160 and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167.
• In some embodiments, the bacterium or preparation comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 33, e.g., a V at position 33 and a mutation relative to N. eutropha strain C91 at position 165, e.g., an I at position 165.
• In some embodiments, the bacterium or preparation comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 79, e.g., an A at position 79 and a mutation relative to N. eutropha strain C91 at position 271, e.g., a V at position 271.
• In some embodiments, the bacterium or preparation comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163. In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312 and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163.
• In some embodiments, the bacterium or preparation comprises a c554 CycA1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 65, e.g., a T at position 65 and a mutation relative to N. eutropha strain C91 at position 186, e.g., a T at position 186.
• In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) mutations at any two or more of the following amino acid positions: 63, 189, 194, 195, 196, 197, 206, and 207. For instance, the two or more amino acid positions may comprise: 63 and 189, 63 and 194, 63 and 195, 63 and 196, 63 and 197, 63 and 206, 63 and 207, 189 and 194, 189 and 195, 189 and 196, 189 and 194, 189 and 195, 189 and 196, 189 and 197, 189 and 206, 189 and 207, 194 and 195, 194 and 196, 194 and 197, 194 and 206, 194 and 207, 195 and 196, 195 and 197, 195 and 206, 195 and 207, 196 and 197, 196 and 206, 196 and 207, 197 and 206, 197 and 207, or 206 and 207. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) any two or more mutations selected from the group consisting of: I63V, S189P, D194G, 195insD, 196insD, 197insD, 206insE, and 207insE. For instance, the two or more mutations can be selected from the group consisting of: I63V and S189P, I63V and D194G, I63V and 195insD, I63V and 196insD, I63V and 197insD, I63V and 206insE, I63V and 207insE, S189P and D194G, S189P and 195insD, S189P and 196insD, S189P and 197insD, S189P and 206insE, S189P and 207insE, D194G and 195insD, D194G and 196insD, D194G and 197insD, D194G and 206insE, D194G and 207insE, 195insD and 196insD, 195insD and 197insD, 195insD and 206insE, 195insD and 207insE, 196insD and 197insD, 196insD and 206insE, 196insD and 207insE, 197insD and 206insE, 197insD and 207insE, and 206insE and 207insE.
• In some embodiments, the bacterium or preparation comprises a c_M552 CycB2 protein having (or gene encoding) mutations at any two or more of the following amino acid positions: 63, 189, 206, and 207. For instance, the two or more amino acid positions may comprise: 63 and 189, 63 and 206, 63 and 207, 189 and 206, 189 and 207, or 206 and 207. In some embodiments, the bacterium or preparation comprises a c_M552 CycB2 protein having (or gene encoding) any two or more mutations selected from the group consisting of: I63V, S189P, 206insE, and 207insE. For instance, the two or more mutations can be selected from the group consisting of: I63V and S189P, I63V and 206insE, I63V and 207insE, S189P and 206insE, S189P and 207insE, and 206insE and 207insE.
• Combinations of three or more sequence characteristics of Table 2 are also described. For instance, in some embodiments, the bacterium or preparation comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1 and a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160, and a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167.
• In some embodiments, the bacterium or preparation comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85 and a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312, and a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163.
• In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) mutations at any three or more (e.g., 4, 5, 6, 7, or all) of the following amino acid positions: 63, 189, 194, 195, 196, 197, 206, and 207. For instance, the three mutations may be at positions 195, 196, and 197. In some embodiments, the bacterium or preparation comprises a c_M552 CycB1 protein having (or gene encoding) any three or more (e.g., 4, 5, 6, 7, or all) mutations selected from the group consisting of: I63V, S189P, D194G, 195insD, 196insD, 197insD, 206insE, and 207insE. For instance, the three mutations may be 195insD, 196insD, and 197insD.
• In some embodiments, the bacterium or preparation comprises a c_M552 CycB2 protein having (or gene encoding) mutations at any three or more (e.g., all) of the following amino acid positions: 63, 189, 206, and 207. In some embodiments, the bacterium or preparation comprises a c_M552 CycB2 protein having (or gene encoding) any three or more (e.g., all) mutations selected from the group consisting of: I63V, S189P, 206insE, and 207insE.
• In some embodiments, the bacterium or preparation comprises mutations relative to N. eutropha strain C91 in at least two genes, e.g., at least two genes listed in Table 2. The two genes may be, for instance, AmoA1 and AmoA2, AmoA1 and AmoB1, AmoA1 and AmoB2, AmoA1 and AmoC1, AmoA1 and AmoC2, AmoA1 and AmoC3, AmoA1 and Hao1, AmoA1 and Hao2, AmoA1 and Hao3, AmoA1 and c554 CycA1, AmoA1 and c554 CycA2, AmoA1 and c554 CycA3, AmoA1 and cM552 CycB1, AmoA1 and cM552 CycB2, AmoA2 and AmoB1, AmoA2 and AmoB2, AmoA2 and AmoC1, AmoA2 and AmoC2, AmoA2 and AmoC3, AmoA2 and Hao1, AmoA2 and Hao2, AmoA2 and Hao3, AmoA2 and c554 CycA1, AmoA2 and c554 CycA2, AmoA2 and c554 CycA3, AmoA2 and cM552 CycB1, AmoA2 and cM552 CycB2, AmoB1 and AmoB2, AmoB1 and AmoC1, AmoB1 and AmoC2, AmoB1 and AmoC3, AmoB1 and Hao1, AmoB1 and Hao2, AmoB1 and Hao3, AmoB1 and c554 CycA1, AmoB1 and c554 CycA2, AmoB1 and c554 CycA3, AmoB1 and cM552 CycB1, AmoB1 and cM552 CycB2, AmoB2 and AmoC1, AmoB2 and AmoC2, AmoB2 and AmoC3, AmoB2 and Hao1, AmoB2 and Hao2, AmoB2 and Hao3, AmoB2 and c554 CycA1, AmoB2 and c554 CycA2, AmoB2 and c554 CycA3, AmoB2 and cM552 CycB1, AmoB2 and cM552 CycB2, AmoC1 and AmoC2, AmoC1 and AmoC3, AmoC1 and Hao1, AmoC1 and Hao2, AmoC1 and Hao3, AmoC1 and c554 CycA1, AmoC1 and c554 CycA2, AmoC1 and c554 CycA3, AmoC1 and cM552 CycB1, AmoC1 and cM552 CycB2, AmoC2 and AmoC3, AmoC2 and Hao1, AmoC2 and Hao2, AmoC2 and Hao3, AmoC2 and c554 CycA1, AmoC2 and c554 CycA2, AmoC2 and c554 CycA3, AmoC2 and cM552 CycB1, AmoC2 and cM552 CycB2, AmoC3 and Hao1, AmoC3 and Hao2, AmoC3 and Hao3, AmoC3 and c554 CycA1, AmoC3 and c554 CycA2, AmoC3 and c554 CycA3, AmoC3 and cM552 CycB1, AmoC3 and cM552 CycB2, Hao1 and Hao2, Hao1 and Hao3, Hao1 and c554 CycA1, Hao1 and c554 CycA2, Hao1 and c554 CycA3, Hao1 and cM552 CycB1, Hao1 and cM552 CycB2, Hao2 and Hao3, Hao2 and c554 CycA1, Hao2 and c554 CycA2, Hao2 and c554 CycA3, Hao2 and cM552 CycB1, Hao2 and cM552 CycB2, Hao3 and c554 CycA1, Hao3 and c554 CycA2, Hao3 and c554 CycA3, Hao3 and cM552 CycB1, Hao3 and cM552 CycB2, c554 CycA1 and c554 CycA2, c554 CycA1 and c554 CycA3, c554 CycA1 and cM552 CycB1, c554 CycA1 and cM552 CycB2, c554 CycA2 and c554 CycA3, c554 CycA2 and cM552 CycB1, c554 CycA2 and cM552 CycB2, c554 CycA3 and cM552 CycB1, c554 CycA3 and cM552 CycB2, or cM552 CycB1 and cM552 CycB2.
• In some embodiments, the bacterium or preparation comprises mutations relative to N. eutropha strain C91 in at least three genes, e.g., at least three (e.g., 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all) genes listed in Table 2. The three genes may be, for instance AmoA1 and AmoA2 and AmoA3; AmoC1 and AmoC2 and AmoC3; or Hao1 and Hao2 and Hao3.
• In some embodiments, the bacterium or preparation comprises at least one structural difference, e.g., at least one mutation, relative to a wild-type bacterium such as N. eutropha strain C91. In some embodiments, the bacterium or preparation comprises a nucleic acid that can be amplified using a pair of primers described herein, e.g., a primer comprising a sequence of SEQ ID NO: 64 and a primer comprising a sequence of SEQ ID NO: 65. In some embodiments, the bacterium or preparation comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a gene of FIG. 6, 7, or 8, or a protein encoded by a gene of FIG. 6, 7, or 8. In some embodiments, the bacterium or preparation comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a sequence of any of SEQ ID NOS: 64-66 or a protein encoded by a sequence of any of SEQ ID NOS: 64-66.
• In some aspects, the present disclosure provides, inter alia, an N. eutropha bacterium, or a purified preparation thereof, comprising a mutation in an ammonia monooxygenase gene, a hydroxylamine oxidoreductase gene, a cytochrome c554 gene, or a cytochrome c_M552 gene. The mutation may be relative to a wild-type bacterium such as N. eutropha strain C91. The mutation may be in one or more of the amoA1 gene, the amoA2 gene, amoB1 gene, the amoB2 gene, and the amoC3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
• In some embodiments, the mutation may be in one or more of the hao1 gene, the hao2 gene, or the hao3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
• In some embodiments, the mutation may be in one or more of the c554 cycA1 gene, the c554 cycA2 gene, and the c554 cycA3 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
• In some embodiments, the mutation may be in one or more of the c_M552 cycB1 gene and the c_M552 cycB2 gene. The N. eutropha bacterium, or a purified preparation thereof may have a mutation at a position described herein, e.g., in Table 2. The N. eutropha bacterium, or a purified preparation thereof may have a mutation wherein said mutation is a mutation described herein, e.g., in Table 2.
• In certain aspects the N. eutropha bacterium, or a purified preparation thereof, described in the preceding four paragraphs may be based on a N. eutropha bacterium, e.g., an optimized N. eutropha, e.g., a purified preparation of optimized N. eutropha, having at least one property selected from:
• • an optimized growth rate;
  • an optimized NH₄ ⁺ oxidation rate; and
  • an optimized resistance to ammonium ion (NH₄ ⁺).
• In certain aspects, the N. eutropha bacterium, or a purified preparation thereof, described in the preceding five paragraphs may have a mutation in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 positions of one or more of amoA1 gene, amoA2 gene, amoB1 gene, amoB2 gene, amoC3 gene, hao1 gene, hao2 gene, hao3 gene, c554 cycA1 gene, c554 cycA2 gene, c554 cycA3 gene, c_M552 cycB1 gene, and c554 cycB2 gene.
• In some embodiments, the N. eutropha bacterium has an optimized growth rate, e.g., an optimized growth rate described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2. In some embodiments, the N. eutropha bacterium has an optimized NH₄ ⁺ oxidation rate, e.g., an optimized NH₄ ⁺ oxidation rate described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2. In some embodiments, the N. eutropha bacterium has an optimized resistance to NH₄ ⁺, e.g., an optimized resistance to NH₄ ⁺ described herein, and a structural difference such as a mutation (e.g., relative to a wild-type strain such as N. eutropha strain C91), e.g., a mutation described herein, e.g., a mutation of Table 2.
• In some embodiments, the N. eutropha bacterium comprises a nucleic acid that can be amplified using a pair of primers described herein, e.g., a primer comprising a sequence of SEQ ID NO: 64 and a primer comprising a sequence of SEQ ID NO: 65.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising a chromosome that hybridizes at high stringency to SEQ ID NO: 1.
• In embodiments, the chromosome hybridizes at very high stringency to SEQ ID NO: 1. In embodiments, the N. eutropha bacterium (which is optionally axenic) comprises a gene that is at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identical to one or more genes of FIGS. 6-8 (e.g., 10, 20, 30, 40, 50, 100, or all genes of any one or more of FIGS. 6, 7, and 8).
• In embodiments, the N. eutropha bacterium (which is optionally axenic) lacks any plasmid that is at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% identical to SEQ ID NO: 2 (pNeut1) or SEQ ID NO: 3 (pNeut2), as described by Stein et al. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental Microbiology (2007) 9(12), 2993-3007. In embodiments, the N. eutropha (which is optionally axenic) lacks one or more genes present on the plasmids of SEQ ID NO: 2 or SEQ ID NO: 3. For instance, the N. eutropha (which is optionally axenic) may lack at least 2, 3, 4, 5, 10, 15, or 20 genes present on one or both of pNeut1 and pNeut2. pNeut1 contains 55 protein-coding sequences while pNeutP2 contains 52 protein-coding sequences. In embodiments, the N. eutropha bacterium (which is optionally axenic) lacks any plasmid.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7 and an amoA2 gene at least about 98.8% identical to SEQ ID NO: 13.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9 and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 or amoA2 gene at least about 98.9% identical to SEQ ID NO: 7 or 13.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8 and an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, and an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, or an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a cycB1 gene at least about 96.8% identical to SEQ ID NO: 31 and a cycB2 gene at least about 97.2% identical to SEQ ID NO: 33.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, a hao3 gene at least about 99.3% identical to SEQ ID NO: 23, a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more of a CycB1 protein at least about 97.2% identical to SEQ ID NO: 30 or a CycB2 protein at least about 98.8% identical to SEQ ID NO: 32.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) further comprises one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22, a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more genes according to SEQ ID NOS: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, and 33.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising one or more proteins according to SEQ ID NOS: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, and 32.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising a protein that is mutant relative to N. eutropha strain C91 at at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the amino acid positions listed in Table 2.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) comprising proteins that are mutant relative to N. eutropha strain C91 at all of the amino acid positions listed in Table 2.
• In certain aspects, this disclosure provides an N. eutropha bacterium (which is optionally axenic) of strain D23, 25 vials of said bacterium, designated AOB D23-100, having been deposited with the ATCC patent depository on Apr. 8, 2014 under ATCC accession number PTA-121157.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) is transgenic.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) has at least one property selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) has at least two properties selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.
• In embodiments, the N. eutropha bacterium (which is optionally axenic) has an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.
• In embodiments, the N. eutropha bacterium as described herein (e.g., strain D23) is substantially free of bacteria, other ammonia oxidizing bacteria, fungi, viruses, or pathogens (e.g., animal pathogens, e.g., human pathogens), or any combination thereof.
• In certain aspects, this disclosure provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23), wherein the composition is substantially free of other organisms.
• In certain aspects, this disclosure provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising a second organism (e.g., a second strain or species), wherein the composition is substantially free of other organisms (e.g., strains or species). In embodiments, the second organism is an ammonia oxidizing bacterium. In embodiments, the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus, and Bifidobacter, and combinations thereof.
• This disclosure also provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising a second and a third organism (e.g., of other strains or species), wherein the composition is substantially free of other organisms (e.g., strains or species). This disclosure also provides a composition comprising the N. eutropha bacterium as described herein (e.g., strain D23) and further comprising 2, 3, 4, 5, 6, 7, 8, 9, or 10 other organisms (e.g., of other strains or species), wherein the composition is substantially free of other organisms (e.g., strains or species).
• In some aspects, this disclosure provides a composition comprising a cell suspension of an actively dividing culture of N. eutropha bacteria having an OD600 of at least about 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.6, 0.7, or 0.8, wherein the composition is substantially free of other organisms.
• In some aspects, this disclosure provides a composition for topical administration, comprising the N. eutropha bacterium as described herein (e.g., strain D23) and a pharmaceutically or cosmetically acceptable excipient suitable for topical administration. In embodiments, the composition is substantially free of other organisms. In embodiments, the composition further comprises a second organism (e.g., of another strain or specie). In embodiments, the composition further comprises 2, 3, 4, 5, 6, 7, 8, 9, or 10 other organisms (e.g., of other strains or species). The second organism may be, for example, an ammonia oxidizing bacterium. In embodiments, the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus, and Bifidobacter, and combinations thereof.
• In embodiments, the composition is a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage. In embodiments, the composition further comprises a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent. In embodiments, the excipient is an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener. In embodiments, the concentration of N. eutropha in the composition is about 10¹¹-10¹³ CFU/L. In embodiments, the concentration of N. eutropha in the composition is about 10⁹ CFU/ml. In embodiments, the mass ratio of N. eutropha to pharmaceutical excipient may be about 0.1 gram per liter to about 100 grams per liter. In some embodiments, the mass ratio of N. eutropha to pharmaceutical excipient is 1 gram per liter.
• In some aspects the composition and/or excipient may be in the form of one or more of a liquid, a solid, or a gel. For example, liquid suspensions may include, but are not limited to, water, saline, phosphate-buffered saline, or an ammonia oxidizing storage buffer. Gel formulations may include, but are not limited to agar, silica, polyacrylic acid (for example Carbopol®), carboxymethyl cellulose, starch, guar gum, alginate or chitosan. In some embodiments, the formulation may be supplemented with an ammonia source including, but not limited to ammonium chloride or ammonium sulfate.
• In some aspects, this disclosure provides a composition comprising at least about 10, 20, 50, 100, 200, 500, 1,000, 2,000, or 10,000 L, e.g., at about 10¹¹ CFU/L, 10¹² CFU/L, 10¹³ CFU/L of the N. eutropha bacterium as described herein (e.g., strain D23). In some embodiments, the composition is at a concentration of at least about 10⁹ CFU/L, 10¹⁰ CFU/L, 10¹¹ CFU/L, or 10¹² CFU/L. In some aspects, this disclosure provides a composition comprising at least about 1, 2, 5, 10, 20, 50, 100, 200, or 500 g of the N. eutropha bacterium described herein, e.g., as a dry formulation such as a powder.
• In some aspects, this disclosure provides an article of clothing comprising the N. eutropha as described herein (e.g., strain D23). In embodiments, the article of clothing is packaged. In embodiments, the article of clothing is packaged in a material that is resistant to gaseous exchange or resistant to water. The article of clothing may be provided, e.g., at a concentration that provides one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth.
• In some aspects, this disclosure provides a cloth comprising the N. eutropha as described herein (e.g., strain D23).
• In some aspects, this disclosure provides a yarn comprising the N. eutropha as described herein (e.g., strain D23).
• In some aspects, this disclosure provides a thread comprising the N. eutropha as described herein (e.g., strain D23).
• In some aspects, this disclosure provides a method of obtaining, e.g., manufacturing, an (optionally axenic) N. eutropha bacterium having an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, comprising:
• (a) culturing the bacterium under conditions that select for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, thereby producing a culture;
• (b) testing a sample from the culture for an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺; and
• (c) repeating the culturing and testing steps until a bacterium having an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺ is obtained.
• In embodiments, the method comprises a step of obtaining an N. eutropha bacterium from a source, such as soil or the skin of an individual. In embodiments, culturing the bacterium under conditions that select for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺ comprises culturing the bacterium in N. europaea medium that comprises about 200 mM NH₄ ⁺. In embodiments, the method comprises a step of creating an axenic culture. In embodiments, the method comprises a step of co-culturing the N. eutropha together with at least one other type of ammonia oxidizing bacteria. In embodiments, the N. eutropha of step (a) lack an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺ In embodiments, step (c) comprises repeating the culturing and testing steps until a bacterium having at least two of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺ is obtained.
• In some aspects, this disclosure provides an N. eutropha bacterium as described herein (e.g., strain D23), produced by the methods described above.
• In some aspects, this disclosure provides a method of testing a preparation of (optionally axenic) N. eutropha, comprising:
• assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺; and
• if the N. eutropha has one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, classifying the N. eutropha as accepted.
• In embodiments, the method further comprises a step of testing the preparation for contaminating organisms. In embodiments, the method further comprises a step of removing a sample from the preparation and conducting testing on the sample. In embodiments, the method further comprises testing medium in which the N. eutropha is cultured. In embodiments, the method further comprises packaging N. eutropha from the preparation into a package. In embodiments, the method further comprises placing N. eutropha from the preparation into commerce.
• In some aspects, this disclosure provides a method of producing, e.g., manufacturing N. eutropha, comprising contacting N. eutropha with culture medium and culturing the N. eutropha until an OD600 of at least about 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 is reached. In some embodiments, the method comprises culturing the N. eutropha until an OD600 of at about 0.3-0.4, 0.4-0.5, 0.5-0.6, 0.6-0.7, or 0.7-0.8 is reached.
• In embodiments, the method further comprises assaying the N. eutropha and culture medium for contaminating organisms. In embodiments, the method further comprises assaying the N. eutropha for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺ In embodiments, the method comprises producing at least at least about 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, or 10,000 L per day of N. eutropha, e.g., at about 10¹² CFUs/L. In some embodiments, the N. eutropha is at a concentration of about 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, or 10¹⁴ CFUs/L. In some embodiments, the N. eutropha is at a concentration of least about 10⁹, 10¹⁰, 10¹¹, 10¹², 10¹³, or 10¹⁴ CFUs/L.
• In some aspects, this disclosure provides a method of producing, e.g., manufacturing, N. eutropha, comprising contacting N. eutropha with culture medium and culturing the N. eutropha until about at least about 1,000 L at about 10¹² CFU/L N. eutropha are produced.
• In embodiments, the method further comprises a step of assaying the N. eutropha for one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.
• In embodiments, the method further comprises a step of testing the N. eutropha or culture medium for contaminating organisms. In embodiments, the N. eutropha brought into contact with the culture medium is an N. eutropha having one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.
• In some aspects, this disclosure provides a method of producing, e.g., manufacturing N. eutropha, comprising:
• (a) contacting N. eutropha with a culture medium; and
• (b) culturing the N. eutropha for 1-2 days, thereby creating a culture, until the culture reaches an OD600 of about 0.5-0.6.
• In embodiments, the method further comprises a step of assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺. In embodiments, the method further comprises a step of testing the culture for contaminating organisms, e.g., bacteria, viruses, fungi, or pathogens, or a combination thereof. In embodiments, the N. eutropha of step (a) is an N. eutropha having one or more (e.g., 2 or 3) of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺. In embodiments, the method comprises producing at least at least about 1,000 L per day at about 10¹² CFUs/L of N. eutropha.
• In some aspects, this disclosure provides a N. eutropha bacterium produced by the methods described above.
• In embodiments, a preparation of N. eutropha made by the methods described above. In some aspects, the preparation may comprise about 0.1 milligrams to about 100 milligrams (mg) of N. eutropha.
• In some aspects, a reaction mixture may be provided comprising N. eutropha at an optical density of about 0.5 to about 0.6. In some aspects, this disclosure provides a method of producing N. eutropha-bearing clothing, comprising contacting an article of clothing with of the N. eutropha as described herein (e.g., strain D23).
• In embodiments, the method comprises producing at least 10, 100, or 1000 articles of clothing. In embodiments, the method comprises contacting the article of clothing with at least 10¹⁰ CFUs of N. eutropha. In embodiments, the method further comprises packaging the clothing.
• In certain aspects, the present disclosure provides a method of obtaining a formulation of N. eutropha, combining contacting N. eutropha described herein (e.g., strain D23) with a pharmaceutically or cosmetically acceptable excipient.
• In embodiments, the method further comprises mixing the N. eutropha and the excipient. In embodiments, the method is performed under conditions that are substantially free of contaminating organisms, e.g., bacteria, viruses, fungi, or pathogens.
• In certain aspects, the present disclosure provides a method of packaging N. eutropha, comprising assembling N. eutropha described herein (e.g., strain D23) into a package.
• In embodiments, the package is resistant to gaseous exchange or resistant to water. In embodiments, the package is permeable to gaseous exchange, NH₃, NH₄ ⁺, or NO₂ ⁻.
• In certain aspects, the present disclosure provides a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
• In embodiments, the effective dose is approximately 1×10⁹ CFU, 2×10⁹ CFU, 5×10⁹ CFU, 1×10¹⁰ CFU, 1.5×10¹⁰ CFU, 2×10¹⁰ CFU, 5×10¹⁰ CFU, or 1×10¹¹ CFU. In embodiments, the effective dose is at least about 1×10⁹ CFU, 2×10⁹ CFU, 5×10⁹ CFU, 1×10¹⁰ CFU, 1.5×10¹⁰ CFU, 2×10¹⁰ CFU, 5×10¹⁰ CFU, or 1×10¹¹ CFU. In embodiments, the effective dose is approximately 1×10⁹ CFU-2×10⁹ CFU, 2×10⁹ CFU-5×10⁹ CFU, 5×10⁹ CFU-1×10¹⁰ CFU, 1×10¹⁰ CFU-1.5×10¹⁰ CFU, 1×10¹⁰ CFU-2×10¹⁰ CFU 1.5×10¹⁰ CFU-2×10¹⁰ CFU, 2×10¹⁰ CFU-5×10¹⁰ CFU, or 5×10¹⁰ CFU-1×10¹¹ CFU. In embodiments, the bacterium is administered at a concentration of about 1×10⁸, 2×10⁸, 5×10⁸, 1×10⁹, 2×10⁹, 5×10⁹, or 1×10¹⁰ CFU/ml. In embodiments, the bacterium is administered at a concentration of at least about 1×10⁸, 2×10⁸, 5×10⁸, 1×10⁹, 2×10⁹, 5×10⁹, or 1×10¹⁰ CFU/ml. In embodiments, the bacterium is administered at a concentration of about 1×10⁸-2×10⁸, 2×10⁸-5×10⁸, 5×10⁸-1×10⁹, 1×10⁹-2×10⁹, 2×10⁹-5×10⁹, or 5×10⁹-1×10¹⁰ CFU/ml. In embodiments, the administration is performed twice per day. In embodiments, the subject is a human. In embodiments, the microbial growth to be inhibited is growth of Pseudomonas aeruginosa or Staphylococcus aureus (S. aureus or SA), Streptococcus pyogenes (S. pyogenes or SP), or Acinetobacter baumannii (A. baumannii or AB).
• In certain aspects, the present disclosure provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of the N. eutropha bacteria described herein (e.g., strain D23) in close proximity to the subject.
• In certain aspects, the present disclosure provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
• In certain aspects, the present disclosure provides a method of treating a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria described herein (e.g., strain D23).
• In embodiments, the disease is HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, or cancer.
• In certain aspects, the present disclosure provides a method of treating a skin disorder, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria as described herein (e.g., strain D23). In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for treating a disorder such as a skin disorder. In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for the manufacture of a medicament, e.g., a medicament for treating a skin disorder.
• In embodiments, the skin disorder is acne, e.g., acne vulgaris, rosacea, eczema, or psoriasis. In some embodiments, the skin disorder is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer. In some embodiments, topically administering comprises pre-treating the subject with N. eutropha, e.g., an N. eutropha described herein. In some embodiments, topically administering comprises topically administering prior to occurrence of the skin disorder. In some embodiments, topically administering comprises topically administering subsequent to occurrence of the skin disorder.
• In certain aspects, the present disclosure provides a method of promoting wound healing or closure, comprising administering to a wound an effective dose of the N. eutropha bacteria as described herein (e.g., strain D23). In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for promoting wound healing. In related aspects, the disclosure provides an N. eutropha bacteria as described herein (e.g., strain D23) for the manufacture of a medicament, e.g., a medicament for promoting wound healing.
• In embodiments, the wound comprises one or more undesirable bacteria, e.g., pathogenic bacteria. In embodiments, the wound comprises S. aureus, P. aeruginosa, P. aeroginosa, or A. baunannii.
• In embodiments, the N. eutropha is administered to the subject prior to occurrence of the wound. In embodiments, administering to the wound comprises administering to the subject prior to occurrence of the wound. In embodiments, the method further comprises administering N. eutropha (e.g., an N. eutropha described herein, e.g., strain D23) to the wound subsequent to occurrence of the wound. In some aspects, the disclosure provides a method of killing or inhibiting growth of pathogenic bacteria comprising contacting, e.g., applying, N. eutropha bacteria (e.g., N. eutropha described herein, e.g., strain D23) to the skin.
• In embodiments, the pathogenic bacteria contribute to one or more of the following conditions: HIV dermatitis, an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
• In embodiments, the condition is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer. In embodiments, the condition is a venous leg ulcer. In embodiments, the condition is acne, e.g., acne vulgaris. In embodiments, the condition is acne vulgaris. In embodiments, the pathogenic bacteria is one or more of Propionibacterium acnes, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, or Acinetobacter baumannii. In embodiments, the method further comprises determining whether the subject is in need of killing or inhibiting growth of pathogenic bacteria, e.g., determining that the subject is in need of killing or inhibiting growth of pathogenic bacteria. In embodiments, the method further comprises selecting the subject in need of killing or inhibiting growth of pathogenic bacteria.
• In some embodiments, the N. eutropha catalyze the following reactions.
• At a neutral pH, ammonia generated from ammonium around neutral pH conditions is the substrate of the initial reaction. The conversion of ammonia to nitrite takes place in two steps catalyzed respectively by ammonia monooxygenase (Amo) and hydroxylamine oxidoreductase (Hao), as follows:
• 
  NH₃+2H⁺+2e−+O₂→NH₂OH+H₂O  (A)
• 
  NH₂OH+H₂O→NO₂ ⁻+4e−+5H⁺  (B)
• In some instances, reaction B is reported as follows, to indicate nitrous acid (HNO₂) formation at low pH:
• 
  NH₂OH+H₂O→HNO₂+4e−+4H⁺
• In certain embodiments, the N. eutropha has a doubling time of less than 4, 5, 6, 7, 8, 9, or 10 hours, for instance about 8 hours, e.g., 7-9 hours or 6-10 hours, when grown under batch culture conditions. In some embodiments, the doubling time is at least 3, 4, 5, or 6 hours under batch culture conditions. In some embodiments, the N. eutropha has a doubling time of less than 16, 18, 20, 22, 24, or 26 hours, for instance about 20 hours, e.g., 19-21 hours or 18-22 hours, when grown under chemostat (i.e., continuous culture) conditions. In some embodiments, the doubling time is at least 10, 12, 14, 16, or 18 hours under chemostat conditions.
• In certain embodiments, a continuous culture of N. eutropha at an OD600 of about 0.15-0.18 is capable of reaching an OD600 of about 0.5-0.6 in about 1-2 days. For instance, in some embodiments, a continuous culture of N. eutropha may grow from an OD600 of about 0.15 to at least 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 1 day; in embodiments the culture may reach an OD in range of 0.4-0.6 or 0.3-0.7 over about 1 day. In embodiments, the continuous culture of N. eutropha may grow from an OD600 of about 0.15 to at least 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 2 days; in embodiments the culture may reach an OD in the range of 0.4-0.6 or 0.3-0.7 over about 2 days. In some embodiments, the continuous culture conditions comprise growth in a bioreactor in N. europaea medium, optionally comprising about 200 mM NH₄ ⁺. In some embodiments, the continuous culture conditions are conditions set out in Example 2.
• In certain embodiments, the N. eutropha are capable of converting NH₄ ⁺ (e.g., at about 200 mM) to nitrite (e.g., reaching up to about 180 mM) at a rate of at least about 50, 75, 125, or 150 micromoles NO₂ ⁻ per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO₂ ⁻ per minute. In some embodiments, the reaction rates are measured in an about 1 L chemostat culture of about 10⁹ CFU/ml over the course of 24 hours.
• In certain embodiments, the N. eutropha are capable of growing in medium comprising at least 50 mM, 75 mM, 100 mM, 125 mM, 150 mM, 175 mM, 200 mM, 225 mM, 250 mM, 275 mM, or 300 mM NH₄ ⁺ (or NH₃), e.g., about 150-200, 175-225, 200-250, 225-275, 250-300 mM, e.g., about 200 or about 250 mM. In certain embodiments, the N. eutropha is grown in a bioreactor under these concentrations of ammonium. In some embodiments, when the N. eutropha is grown under these concentrations of ammonium, the concentration of nitrate or nitrite is capable of reaching at least 60, 80, 100, 120, 140, 160, or 180 mM, e.g., about 140-180, 160-200, or 140-200 mM, e.g., about 160 or 180 mM.
• In certain aspects, the present disclosure provides high density cultures of N. eutropha, e.g., N. eutropha strain D23. For instance, the high density culture composition may comprise a cell suspension of an actively dividing culture of N. eutropha bacteria having an OD600 of at least about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, or 0.7, e.g., about 0.2-0.6, 0.3-0.6, 0.4-0.6, 0.5-0.6, or 0.4-0.7, wherein the composition is substantially free of other organisms
• In some embodiments, the N. eutropha are stable for at least 2 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months when stored at 4° C. In some embodiments, the method of storage comprises resuspending the cells in a buffer comprising one or more of Na₂HPO₄ and MgCl₂, for instance 50 mM Na₂HPO₄ and 2 mM MgCl₂, for instance the storage buffer described in Example 2. For example, the storage conditions may be those specified in Example 2. In some embodiments, the N. eutropha are continuously cultured at 200 mM NH₄ ⁺ at a pH of 6-8, e.g., 7, before storage at 4°. Stability can include one or more of 1) retaining viability, 2) retaining a relevant property such as the ability to produce a given level of nitrite.
• In certain embodiments, NH₄ ⁺ and NH₃ may be used interchangeably throughout the disclosure.
• This disclosure provides, inter alia, a method of changing a composition of a skin microbiome of a subject. The method comprises administering, e.g., applying, a preparation comprising ammonia oxidizing bacteria to a surface of the skin, wherein the amount and frequency of administration, e.g., application, is sufficient to reduce the proportion of pathogenic bacteria on the surface of the skin.
• Ammonia oxidizing bacteria are, in some embodiments, ubiquitous Gram-negative obligate chemolithoautotrophic bacteria with a unique capacity to generate energy exclusively from the conversion of ammonia to nitrite.
• In some embodiments, the method may further comprise, selecting the subject on the basis of the subject being in need of a reduction in the proportion of pathogenic bacteria on the surface of the skin.
• In some embodiments, the preparation comprising ammonia oxidizing bacteria comprises at least one of ammonia, ammonium salts, and urea.
• In some embodiments, the preparation comprising ammonia oxidizing bacteria comprises a controlled release material, e.g., slow release material.
• In some embodiments, the preparation of ammonia oxidizing bacteria, comprises an excipient, e.g., one of a pharmaceutically acceptable excipient or a cosmetically acceptable excipient. The excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient, may be suitable for one of topical, nasal, pulmonary, and gastrointestinal administration. The excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient may be a surfactant. The surfactant may be selected from the group consisting of cocamidopropyl betaine (ColaTeric COAB), polyethylene sorbitol ester (e.g., Tween 80), ethoxylated lauryl alcohol (RhodaSurf 6 NAT), sodium laureth sulfate/lauryl glucoside/cocamidopropyl betaine (Plantapon 611 L UP), sodium laureth sulfate (e.g., RhodaPex ESB 70 NAT), alkyl polyglucoside (e.g., Plantaren 2000 N UP), sodium laureth sulfate (Plantaren 200), Dr. Bronner's Castile soap, lauramine oxide (ColaLux Lo), sodium dodecyl sulfate (SDS), polysulfonate alkyl polyglucoside (PolySufanate 160 P), sodium lauryl sulfate (Stepanol-WA Extra K), and any combination thereof. Dr. Bronner's Castile soap comprises water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol. In some embodiments, the excipient comprises one or more of, e.g., all of, water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol.
• In some embodiments, the preparation may be substantially free of other organisms.
• In some embodiments, the preparation may be disposed in a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage. The preparation may be provided as a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.
• In some embodiments, the preparation may comprise a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.
• In some embodiments, the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient may comprise an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener.
• In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise between about 10⁸ and about 10¹⁴ CFU/L. In certain aspects, the preparation may comprise between about 1×10⁹ CFU/L and about 10×10⁹ CFU/L.
• In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise between about 50 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria.
• In some embodiments, the mass ratio of ammonia oxidizing bacteria to the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient is in a range of about 0.1 grams per liter to about 1 gram per liter.
• In some embodiments, the preparation of ammonia oxidizing bacteria are useful in the treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth, e.g., pathogenic bacterial growth.
• In some embodiments, the ammonia oxidizing bacteria is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, and combinations thereof. The preparation may further comprise an organism selected from the group consisting of Lactobacillus, Streptococcus, Bifidobacter, and combinations thereof. In certain aspects, the preparation is substantially free of organisms other than ammonia oxidizing bacteria.
• In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a growth state. In some embodiments, the preparation comprising ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a storage state.
• In some embodiments, the methods of the present disclosure may be used to deliver a cosmetic product. In some embodiments, the methods of the present disclosure may be used to deliver a therapeutic product. The preparation may be useful for treatment of at least one of HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
• In certain aspects, the preparation may be useful for treatment of at least one of acne, e.g., acne vulgaris, eczema, psoriasis, uticaria, rosacea, and skin infections.
• In some embodiments, the preparation may be provided in a container, the preparation and the container having a weight of less than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 grams.
• In some embodiments, the preparation has less than about 0.1% to about 10% of surfactant. In certain aspects, the preparation may be substantially free of surfactant.
• In some embodiments, the preparation may comprise a chelator. In some embodiments, the preparation may be substantially free of a chelator.
• In some embodiments, the method may comprise applying the preparation about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 times per day. In certain aspects, the preparation may be applied one time per day. In certain other aspects, the preparation may be applied two times per day.
• In some embodiments, the preparation may be applied for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, or 84-91 days. In certain aspects, the preparation may be applied for about 16 days.
• In some embodiments, the method may further comprise obtaining a sample from the surface of the skin. In certain aspects, the method may further comprise isolating DNA of bacteria in the sample. In certain aspects, the method may further comprise sequencing DNA of bacteria in the sample.
• In some embodiments, administering the ammonia oxidizing bacteria provides for an increase in the proportion of non-pathogenic bacteria on the surface. In certain aspects, the non-pathogenic bacteria may be commensal non-pathogenic bacteria. In certain aspects, the non-pathogenic bacteria is commensal non-pathogenic bacteria of a genus of Staphylococcus. In certain aspects, the non-pathogenic bacteria may be commensal non-pathogenic bacteria Staphylococcus epidermidis.
• In some embodiments, the proportion of non-pathogenic bacteria Staphylococcus is, or is identified as being, increased after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks. In certain aspects, the proportion of non-pathogenic bacteria Staphylococcus epidermidis Staphylococcus is, or is identified as being, increased after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
• In some embodiments, potentially pathogenic or disease associated Propionibacteria is, or is identified as being, reduced after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
• In some embodiments, potentially pathogenic or disease associated Stenotrophomonas is, or is identified as being, reduced after about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 weeks.
• In some embodiments, the surface of the skin comprises a wound.
• In some embodiments, a method of treating acne e.g., acne vulgaris, may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating eczema may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating psoriasis may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating uticaria may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating rosacea may be provided by one or more methods of the present disclosure. In some embodiments, a method of treating skin infection may be provided by one or more methods of the present disclosure. In some embodiments, a method of reducing an amount of undesirable bacteria on a surface of a subject is provided.
• In some embodiments, the method herein (e.g., a method of administering a N. eutropha bacterium, e.g., a bacterium of strain D23 to a subject in need thereof), further comprise treating the subject with an antibiotic. In embodiments, the antibiotic is Tetracycline, a Lincosamide such as Clindamycin, a Macrolide such as Erythromycin, an Aminoglycoside such as Gentamicin, a β-lactam such as Piperacillin, β-lactamase inhibitor such as Tazobactam, or any combination thereof (such as a combination of a β-lactam such as Piperacillin and a β-lactamase inhibitor such as Tazobactam). In some embodiments, the antibiotic is an antibiotic to which the bacterium is sensitive. In embodiments, the antibiotic is administered after the bacterium has achieved the desired therapeutic effect. In embodiments, the antibiotic is an antibiotic to which the bacterium is resistant. In embodiments, the antibiotic is administered before or during the period in which the bacterium is producing its therapeutic effect.
• It is understood that compositions and methods herein involving a bacterium can also involve a plurality of bacteria. For instance, a method of administering a N. eutropha bacterium can also involve administering a plurality of N. eutropha bacteria.
• The present disclosure also provides, in certain aspects, a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within the D23 genome, e.g., a sequence of a gene provided herein, e.g., a gene described in Table 1, FIG. 6-8 or Supplementary Table 1, or SEQ ID NO: 66, or a reverse complement of any of the foregoing. In a related aspect, the present disclosure provides a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within SEQ ID NO: 1 or a reverse complement thereof. In a related aspect, the present disclosure provides a nucleic acid comprising a sequence of consecutive nucleotides (e.g., 15-100 nucleotides) from within a gene of Table 1 (e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof.
• In some embodiments, the nucleic acid has a non-naturally occurring sequence or another modification such as a label, or both. In some embodiments, the sequence of consecutive nucleotides is not a sequence found in N. Eutropha strain C91. In some embodiments, the nucleic acid comprises a heterologous sequence 5′ to the sequence of 15-100 consecutive nucleotides, or a heterologous sequence 3′ to the sequence of 15-100 consecutive nucleotides, or both. In some embodiments, the nucleic acid has a length of 10-15, 15-20, 20-25, 25-30, 30-24, 35-40 nucleotides. In some embodiments, the nucleic acid is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label. In some embodiments, the nucleic acid comprises 10-15, 15-20, 20-25, 25-30, 30-24, 35-40, 40-50, 50-60, 60-70, 70-80, 80-90, or 90-100 consecutive nucleotides from within the D23 genome. In some embodiments, the nucleic acid comprises at least about 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 consecutive nucleotides from within the D23 genome. In some embodiments, the nucleic acid is DNA.
• In some aspects, the disclosure provides a composition or a kit comprising a first nucleic acid and a second nucleic acid. In some embodiments, the first nucleic acid comprises consecutive nucleotides (e.g., 15-100) from within SEQ ID NO: 1, SEQ ID NO: 66, a gene of FIGS. 6-8, or a gene of Table 1, or a reverse complement thereof. In some embodiments, the second nucleic acid comprises consecutive nucleotides (e.g., 15-100) from within SEQ ID NO: 1, SEQ ID NO: 66, a gene of FIGS. 6-8, or a gene of Table 1, or a reverse complement thereof. In some embodiments, the nucleic acid has a non-naturally occurring sequence, e.g., a sequence not found in N. eutropha strain C91. In some embodiments, the first nucleic acid and the second nucleic acid define an amplicon in a gene of Table 1, e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof.
• In some embodiments, the first nucleic acid has a sequence that corresponds to a first region of SEQ ID NO: 1, and the reverse complement of the second nucleic acid has a sequence that corresponds to a second region of SEQ ID NO: 1, and the first and second regions are separated by a distance suitable for PCR. In some embodiments, the reverse complement of the first nucleic acid has a sequence that corresponds to a first region of SEQ ID NO: 1, and the second nucleic acid has a sequence that corresponds to a second region of SEQ ID NO: 1, and the first and second regions are separated by a distance suitable for PCR. In an embodiment, the distance suitable for PCR is no more than 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, or 1000 nucleotides of SEQ ID NO: 1. In some embodiments, the first nucleic acid and second nucleic acid delineate an amplicon in SEQ ID NO: 1. In some embodiments, the first nucleic acid and second nucleic acid each has a melting temperature (Tm) suitable for PCR, e.g., about 55-65° or about 60-65° C. In some embodiments, the Tm of the first nucleic acid is within 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1° C. of the Tm of the second nucleic acid.
• In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 5′ to the sequence of consecutive nucleotides. Alternatively or in combination, in some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 3′ to the sequence of consecutive nucleotides from within SEQ ID NO: 1 or SEQ ID NO: 66. In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid has a length of 15-20, 20-25, 25-30, 30-24, or 35-40 nucleotides. In some embodiments, the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label. In some embodiments, the first nucleic acid comprises, or consists of, a sequence of SEQ ID NO: 64. In some embodiments, the second nucleic acid comprises, or consists of, a sequence of SEQ ID NO: 65. In some embodiments, the first nucleic acid, the second nucleic acid, or both, are DNA.
• In some embodiments, the composition or kit comprises at least two (e.g., 3, 4, 5, 6, 7, 8, 9, or 10) pairs of primers, each pair recognizing an amplicon in a gene of Table 1 (e.g., a sequence of SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, or 33) or a reverse complement thereof. In some embodiments, a first pair of primers recognizes an amplicon in an Amo gene (e.g., AmoA1, AmoA2, AmoB1, AmoB2, AmoC1, AmoC2, or AmoC3) and the second pair of primers recognizes an amplicon in an Amo gene (e.g., AmoA1, AmoA2, AmoB1, AmoB2, AmoC1, AmoC2, or AmoC3). In some embodiments, a first pair of primers recognizes an amplicon in an AmoA gene (e.g., AmoA1 or AmoA2). In some embodiments, a second pair of primers recognizes an amplicon in an AmoB gene (e.g., AmoB1 or AmoB2). In some embodiments, a third pair of primers recognizes an amplicon in an AmoC gene (e.g., AmoC1, AmoC2, or AmoC3).
• In some embodiments, the kit comprises a first container in which the first nucleic acid is disposed and a second container in which the second nucleic acid is disposed. The kit may comprise additional containers, e.g., for a third, fourth, fifth, or sixth nucleic acid. In some embodiments, a pair of primers recognizing an amplicon is stored in a single container.
• The present disclosure also provides, in some aspects, a nucleic acid comprising, or consisting of, the sequence of SEQ ID NO: 64. The present disclosure also provides, in some aspects, a nucleic acid comprising, or consisting of, the sequence of SEQ ID NO: 65. The present disclosure also provides, in some aspects, the present disclosure provides a molecule comprising a nucleic acid described herein and a detectable label, e.g., a fluorescent label. The nucleic acid may consist of a sequence of SEQ ID NO: 64 or SEQ ID NO: 65, for example.
• The present disclosure provides, in some aspects, a composition comprising a first molecule and a second molecule. In some embodiments, the first molecule comprises a nucleic acid described herein, e.g., a nucleic acid consisting of the sequence of SEQ ID NO: 64, and optionally comprises a detectable label, e.g., a fluorescent label. In some embodiments, the second molecule comprises a nucleic acid described herein, e.g., a nucleic acid consisting of the sequence of SEQ ID NO: 65, and optionally comprises a detectable label, e.g., a fluorescent label.
• In some embodiments, the kit comprises a first container in which the first molecule is disposed and a second container in which the second molecule is disposed.
• In some embodiments, a kit described herein further comprises one or more of a buffer, an enzyme (e.g., a polymerase such as a thermostable polymerase such as Taq), nucleotides (e.g., dNTPs), and chain-terminating nucleotides (e.g., dideoxy nucleotides) which are optionally dye-labeled; these components may be provided separately or as part of a single composition.
• In certain aspects, this disclosure provides a method of detecting whether a D23 N. eutropha nucleic acid is present in a sample, comprising: performing a polymerase chain reaction (PCR) on the sample using primers specific to D23 N. eutropha, and determining whether a PCR product is produced, wherein the presence of a PCR product indicates that the D23 N. eutropha nucleic acid was present in the sample. In embodiments, at least two PCR reactions are performed, e.g., 3, 4, 5, 6, 7, 8, 9 or 10 PCR reactions. In embodiments, the PCR reactions are performed in separate reaction volumes. In embodiments, two or more PCR reactions are performed in multiplex.
• In some embodiments, the primers specific to D23 N. eutropha are a first nucleic acid and second nucleic acid described herein, e.g., a first and second nucleic acid from a composition or kit described herein. In some embodiments, the first primer comprises or consists of a sequence of SEQ ID NO: 65, and the second primer comprises or consists of a sequence of SEQ ID NO: 66.
• In some embodiments, the PCR reaction is a quantitative or real-time PCR reaction. In some embodiments, the PCR reaction comprises a TaqMan reaction. In some embodiments, the PCR reaction comprises cycling the temperature of a reaction mixture between a denaturing temperature (e.g., about 95° C.), an annealing temperature (e.g., 45-68, 55-65, or 60-65° C.), and an elongation temperature (e.g., about 68° C.) for a number of cycles sufficient to produce a detectable PCR product, e.g., about 10, 15, 20, 25, or 30 cycles. In some embodiments, detecting the PCR product comprises detecting fluorescence from the PCR product. In some embodiments, a positive control is performed, e.g., using a known D23 N. eutropha nucleic acid as a template. In some embodiments, a negative control is used, e.g., using no template or using another bacterial nucleic acid as a template.
• In certain aspects, the disclosure provides a method of detecting whether a D23 N. eutropha nucleic acid is present in a sample, comprising detecting binding of a nucleic acid described herein to a sample, wherein the presence of binding indicates that the D23 N. eutropha nucleic acid was present in the sample. In some embodiments, binding is detected by primer extension or RNase protection.
• In some embodiments of the methods herein, the sample comprises at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 strains of bacteria. In some embodiments, the sample is from the skin of a subject, e.g., a human subject. In some embodiments, the methods herein comprise detecting one or more additional types of bacterium in the sample, e.g., Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, or Acinetobacter baumannii.
• The disclosure contemplates all combinations of any one or more of the foregoing aspects and/or embodiments, as well as combinations with any one or more of the embodiments set forth in the detailed description and examples.
BRIEF DESCRIPTION OF THE DRAWINGS
• FIG. 1 shows the growth of a mixed culture of bacteria comprising N. eutropha strain D23. The optical density at a 600 nm wavelength is plotted relative to time.
• FIG. 2A shows the nitrite production of a mixed culture of bacteria comprising N. eutropha strain D23. The nitrite concentration is plotted relative to time.
• FIG. 2B-I shows the nitrite production kinetics by N. eutropha D23 in batch culture. The nitrite concentration is plotted relative to time.
• FIG. 2B-II shows the nitrite production kinetics by N. eutropha D23 in vitro. The nitrite concentration is plotted relative to time.
• FIG. 2C shows N. eutropha D23 stability upon storage at 4° C. The nitrite concentration is plotted relative to time.
• FIG. 3A shows the N. eutropha D23's ability to inhibit the growth of P. aeruginosa (left panel) and S. aureus (right panel) in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
• FIG. 3B shows the N. eutropha D23's ability to inhibit the growth of Streptococcus pyogenes (left panel) and Acinetobacter baumannii (right panel) in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
• FIG. 3C shows the N. eutropha D23's ability to inhibit the growth of Propionibacterium acnes in co-culture experiments. The amount of each type of undesirable bacteria (in CFU/ml) is plotted relative to time. In this figure, “AOB” refers to strain D23.
• FIG. 4A (top panel) plots the NO₂ ⁻ concentration over time in a co-culture experiment. The bottom panel plots pH over time in a co-culture experiment.
• FIG. 4B (top panels) plots the CFU/ml of the indicated bacteria over time in a co-culture experiment. The center panels plot the NO₂ ⁻ concentration over time in a co-culture experiment.
• The bottom panels plot pH over time in a co-culture experiment.
• FIG. 4C plots the microbicidal activity of D23 against skin pathogens.
• FIG. 4D plots the microbicidal activity of D23 against skin pathogens.
• FIG. 4E shows an alternative plot of microbicidal activity of D23 against skin pathogens.
• FIG. 5A plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
• FIG. 5B plots CT₅₀ for various D23 treatments.
• FIG. 5C plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
• FIG. 5D plots the percent wound closure over time in an experiment testing D23's ability to improve wound healing.
• FIG. 5E plots CT₅₀ for various D23 treatments.
• FIG. 5F shows images of D23 enhanced wound healing in diabetic mice at Day 1, Day 11, and Day 15.
• FIG. 5G shows blood glucose measurements for various concentrations of D23.
• FIG. 5H shows body weight of test subjects over the course of testing.
• FIG. 5I shows body weight of test subjects over the course of testing.
• FIG. 5J shows PCR scores for a scalp test of subjects. AOB refers to D23 in this Figure.
• FIG. 5K shows a schematic of a human volunteer study for an evaluation of a Nitrosomonas-containing topical suspension (AOB-001).
• FIG. 5L (left panel) shows PCR analyses of scalp swabs collected during the study. Percent-positive samples for AOB-specific three-gene signature (amoA, amoB, amoC). The right panel shows PCR analyses of scalp swabs collected during the study. Composite PCR scores for a total of six samples collected from each of 23 volunteers. The scoring scheme used for the positive samples collected at each of six sampling points is indicated.
• FIG. 5M shows genus-level bacterial diversity as determined by 16S rDNA sequencing in skin swab samples collected before and after topical application of AOB-001. The percentage of the total sequence reads representing each of twelve bacterial genera in samples collected at baseline prior to application (Day 0) and immediately after the one week application (Day 8), or one week after stopping topical application (Day 14), are shown. The proportions of Acinetobacter, Burkholderia, Enterobacter, Escherichia Shigella, Klebsiella, Nitrosomonas, Pantoea, Propionibacterium, Pseudomonas, Serratia, Staphylococcus, and Stenotrophomonas are shown.
• FIG. 5N-A shows changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. The percentages of the total 16S rDNA sequence reads representing Nitrosomonas prior to application (Day 0), immediately after the one-week application (Day 8), or one week after terminating application (Day 14) are shown.
• FIG. 5N-B shows changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. Changed patterns in abundance of species were detected by 16S rDNA sequencing in Day 0 versus Day 8 samples collected from AOB users.
• FIG. 5O shows user evaluation of AOB-001. Assessment of AOB-001 cosmetic effects as provided by 23 volunteers upon completion of the one week application to their scalp and face. Subjects were plotted in order of increasing composite PCT scores. (2=agree strongly; 0=no change; −2=disagree strongly).
• FIG. 6 is a table displaying unique D23 genes that have either an assigned open reading frame (ORF) number and a function based on sequence analysis, or a hypothetical gene above 200 base pairs in length. The column headers signify as follows: Feature.ID=a unique identifier for the gene; Type=type of gene, where CDS indicates a protein-coding DNA sequence; Start=starting position of gene in the genome sequence of SEQ ID NO: 1; Stop=end of gene in the genome sequence of SEQ ID NO: 1; Frame=reading frame; Length=length of gene in base pairs; Function=gene or protein function based on sequence analysis; Subsystem=category of gene function; D23GbkId=a gene identifier.
• FIG. 7 is a table displaying unique D23 genes below 200 base pairs that have an assigned ORF number. Column headers are as described in FIG. 6.
• FIG. 8 is a table displaying unique D23 genes with no assigned ORF number. Column headers are as described in FIG. 6.
• FIG. 9 lists unique C91 genes that do not have a homolog in D23.
• FIG. 10 is a sequence alignment between the AmoA1 and AmoA2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 10 discloses SEQ ID NOS 6, 12, 36 and 42, respectively, in order of appearance.
• FIG. 11 is a sequence alignment between the AmoB1 and AmoB2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 11 discloses SEQ ID NOS 8, 14, 38 and 44, respectively, in order of appearance.
• FIG. 12 is a sequence alignment between the AmoC1 and AmoC2 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 12 discloses SEQ ID NOS 34, 40, 10 and 4, respectively, in order of appearance.
• FIG. 13 is a sequence alignment between the AmoC3 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 13 discloses SEQ ID NOS 46 and 16, respectively, in order of appearance.
• FIG. 14 A and FIG. 14 B show a sequence alignment between the Hao1, Hao2, and Hao3 proteins in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 14 discloses SEQ ID NOS 20, 22, 18, 50, 52 and 48, respectively, in order of appearance.
• FIG. 15 is a sequence alignment between the cycA1, cycA2, and cycA3 genes in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 15 discloses SEQ ID NOS 26, 28, 24, 58, 56 and 54, respectively, in order of appearance.
• FIG. 16 is a sequence alignment between the cycB1 and cycB2 genes in N. eutropha strains D23 and C91. The SEQ ID of each protein is listed in Table 1. FIG. 16 discloses SEQ ID NOS 30, 32, 60 and 62, respectively, in order of appearance.
• FIG. 17 shows a bar graph of proportion of bacteria, by genus versus day.
• FIG. 18 shows a bar graph of proportion of bacteria, by genus versus bacteria genus, for day 0, day 1, day 8, day 14, and day 16.
• Supplementary Table 1 displays the genome annotation of 2,777 genes identified in strain D23 using sequence analysis. Column headers are as described in FIG. 6. “C91 Alias” refers to a homolog in strain C91. Supplementary Table 1 is appended to the end of the Detailed Description and Examples.
• Supplementary Table 2 displays the sequences of selected proteins genes identified in strain D23. Supplementary Table 2 is appended to the end of the Detailed Description and Examples.
DETAILED DESCRIPTION
• Ammonia-oxidizing bacteria (AOB) of the genus Nitrosomonas are Gram-negative obligate autotrophic bacteria with a unique capacity to generate nitrite and nitric oxide exclusively from ammonia as an energy source. They are widely present both in soil and water environments and are essential components of environmental nitrification processes. Due to the roles of nitrite and nitric oxide on human skin as important components of several physiological functions, such as vasodilation, skin inflammation and wound healing, these bacteria may have beneficial properties for both healthy and immunopathological skin conditions. These bacteria may be safe for use in humans because they are slow-growing, cannot grow on organic carbon sources, may be sensitive to soaps and antibiotics, and have never been associated with any disease or infection in animals or humans.
1. DEFINITIONS
• An ammonia oxidizing bacterium refers to a bacterium capable of oxidizing ammonia or ammonium to nitrite at a rate, e.g., a substantial rate, e.g., a pre-determined rate, e.g., at least the rate depicted in any one of FIG. 2A, 2B, 2C, 4A, 4B, or 5 or at least 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, or 10% of that rate. In some embodiments, the substantial rate refers to the conversion of ammonium ions (NH₄ ⁺)(e.g., at about 200 mM) to nitrite (NO₂ ⁻) at a rate of at least 50, 75, 125, or 150 micromoles NO₂ ⁻ per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO₂ ⁻ per minute. Examples of ammonia oxidizing bacteria include N. eutropha strains D23 and C91, and other bacteria in the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus, and Nitrosovibrio. D23 Nitrosomonas eutropha strain refers to the strain, designated AOB D23-100, deposited with the American Tissue Culture Collection (ATCC) on Apr. 8, 2014 having accession number PTA-121157. The D23 Nitrosomonas eutropha of accession number PTA-121157 has a genome sequence as set out in SEQ ID NO: 1 herein. The nucleic acid sequence(s), e.g., genome sequence, of accession number PTA-121157 are hereby incorporated by reference in their entireties.
• Optimized Nitrosomonas eutropha (N. eutropha), as that term is used herein, refers to an N. eutropha having an optimized growth rate; an optimized NH₄ ⁺ oxidation rate; or optimized resistance to NH₄ ⁺. In an embodiment it differs from naturally occurring N. eutropha by at least one nucleotide, e.g., a nucleotide in a gene selected from ammonia monooxygenase, hydroxylamine oxidoreductase, cytochrome c554, and cytochrome c_M552. The difference can arise, e.g., through selection of spontaneously arising mutation, induced mutation, or directed genetic engineering, of the N. eutropha. In an embodiment it differs from a naturally occurring N. eutropha in that it has a constellation of alleles, not present together in nature. These differences may provide for one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, and a treatment to inhibit microbial growth.
• As used herein, “axenic” refers to a composition comprising an organism that is substantially free of other organisms. For example, an axenic culture of ammonia oxidizing bacteria is a culture that is substantially free of organisms other than ammonia oxidizing bacteria. For example, an axenic culture of N. eutropha is a culture that is substantially free of organisms other than N. eutropha. In some embodiments, “substantially free” denotes undetectable by a method used to detect other organisms, e.g., plating the culture and examining colony morphology, or PCR for a conserved gene such as 16S RNA. An axenic composition may comprise elements that are not organisms, e.g., it may comprise nutrients or excipients. Any embodiment, preparation, composition, or formulation of ammonia oxidizing bacteria discussed herein may comprise, consist essentially of, or consist of optionally axenic ammonia oxidizing bacteria.
• Throughout this disclosure, formulation may refer to a composition or preparation.
• As used herein, an “autotroph”, e.g., an autotrophic bacterium, is any organism capable of self-nourishment by using inorganic materials as a source of nutrients and using photosynthesis or chemosynthesis as a source of energy. Autotrophic bacteria may synthesize organic compounds from carbon dioxide and ATP derived from other sources, oxidation of ammonia to nitrite, oxidation of hydrogen sulfide, and oxidation of Fe²⁺ to Fe³⁺ Autotrophic bacteria of the present disclosure are incapable of causing infection.
• Administered “in combination,” as used herein, means that two (or more) different treatments are delivered to the subject during the course of the subject's affliction with the disorder, e.g., the two or more treatments are delivered after the subject has been diagnosed with the disorder and before the disorder has been cured or eliminated. In some embodiments, the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap. This is sometimes referred to herein as “simultaneous” or “concomitant” or “concurrent delivery”. In other embodiments, the delivery of one treatment ends before the delivery of the other treatment begins. This is sometimes referred to herein as “successive” or “sequential delivery.” In embodiments of either case, the treatment is more effective because of combined administration. For example, the second treatment is a more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment, or the analogous situation is seen with the first treatment. In some embodiments, delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other. The effect of the two treatments can be partially additive, wholly additive, or greater than additive (i.e., synergistic). The delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered.
• Complete N. europaea medium refers to the N. europaea growth medium described in Ensign et al., “In vitro activation of ammonia monooxygenase from Nitrosomonas europaea by copper.” J Bacteriol. 1993 April; 175(7):1971-80.
• To “culture” refers to a process of placing an amount of a desired bacterium under conditions that promote its growth, i.e., promoting cell division. The conditions can involve a specified culture medium, a set temperature range, and/or an agitation rate. Bacteria can be cultured in a liquid culture or on plates, e.g., agar plates.
• The term “isolated,” as used herein, refers to material that is removed from its original or native environment (e.g., the natural environment if it is naturally occurring). For example, a naturally-occurring polynucleotide or polypeptide present in a living animal is not isolated, but the same polynucleotide or polypeptide, separated by human intervention from some or all of the co-existing materials in the natural system, is isolated. Such polynucleotides could be part of a vector and/or such polynucleotides or polypeptides could be part of a composition, and still be isolated in that such vector or composition is not part of the environment in which it is found in nature.
• The terms “nucleic acid,” “nucleic acid sequence,” “nucleotide sequence,” or “polynucleotide sequence,” and “polynucleotide” are used interchangeably. They refer to a polymeric form of nucleotides of any length, e.g., deoxyribonucleotides or ribonucleotides, or analogs thereof. The polynucleotide may be either single-stranded or double-stranded, and if single-stranded may be the coding strand or non-coding (antisense) strand. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.
• The nucleic acid may be a recombinant polynucleotide, or a polynucleotide of genomic, cDNA, semisynthetic, or synthetic origin which either does not occur in nature or is linked to another polynucleotide in a nonnatural arrangement.
• As used herein, the term “optimized growth rate” refers to one or more of: a doubling time of less than about 4, 5, 6, 7, 8, 9, or 10 hours when cultured under batch conditions as described herein in Example 2; a doubling time of less than about 16, 18, 20, 22, 24, or 26 hours, when grown under chemostat conditions as described herein in Example 2; or growing from an OD600 of about 0.15 to at least about 0.3, 0.4, 0.5, 0.6, 0.7, or 0.8 over about 1 or 2 days. In an embodiment, optimized growth rate is one having a doubling time that it is at least 10, 20, 30, 40, or 50% shorter than that of a naturally occurring N. eutropha.
• As used herein, “optimized NH₄ ⁺ oxidation rate” refers to a rate of at least about 50, 75, 125, or 150 micromoles per minute of converting NH₃ or NH₄ ⁺ into NO₂ ⁻. For instance, the rate may be at least about 50, 75, 125, or 150 micromoles per minute of converting NH₄ ⁺ (e.g., at about 200 mM) to NO₂ ⁻. In an embodiment, an optimized NH₄ ⁺ oxidation rate is one in which NH₃ or NH₄ ⁺ is converted into NO₂ ⁻′ at least 10, 20, 30, 40, or 50% more rapidly than is seen with a naturally occurring N. eutropha.
• Percent (%) amino acid sequence identity, with respect to the amino acid sequences here (e.g., proteins expressed by N. eutropha D23) is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the reference sequence, which may be a naturally-occurring N. eutropha sequence or an N. eutropha D23 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the means of those skilled in the art, for instance, using publicly available computer software such as BLAST, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For instance, the WU-BLAST-2 software may be used to determine amino acid sequence identity (Altschul et al, Methods in Enzymology 266, 460-480 (1996); http://blast.wustl/edu/blast/README.html). WU-BLAST-2 uses several search parameters, most of which are set to the default values. The adjustable parameters are set with the following values: overlap span=1, overlap fraction=0.125, world threshold (T)=I 1. HSP score (S) and HSP S2 parameters are dynamic values and are established by the program itself, depending upon the composition of the particular sequence, however, the minimum values may be adjusted as appropriate.
• Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements. Typical but not limiting conservative substitutions are the replacements, for one another, among the aliphatic amino acids Ala, Val, Leu and Ile; interchange of Ser and Thr containing hydroxy residues, interchange of the acidic residues Asp and Glu, interchange between the amide-containing residues Asn and Gln, interchange of the basic residues Lys and Arg, interchange of the aromatic residues Phe and Tyr, and interchange of the small-sized amino acids Ala, Ser, Thr, Met and Gly. Additional conservative substitutions include the replacement of an amino acid by another of similar spatial or steric configuration, for example the interchange of Asn for Asp, or Gln for Glu. Amino acid substitutions can also be the result of replacing one amino acid with another amino acid having dis-similar structural and/or chemical properties, i.e., non-conservative amino acid replacements. Insertions or deletions may optionally be in the range of 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity in the in vivo or in vitro assays for, e.g., metabolizing urea or ammonia.
• Percent (%) sequence identity with respect to the nucleic acid sequences here (e.g., the N. eutropha D23 genome and portions thereof) is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the reference sequence, which may be a naturally-occurring N. eutropha sequence or an N. eutropha D23 sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleotide sequence identity can be achieved in various ways that are within the means of those skilled in the art, for instance, using publicly available computer software such as BLAST. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
• The terms “polypeptide”, “peptide” and “protein” (if single chain) are used interchangeably herein to refer to amino acid polymers. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. The polypeptide can be isolated from natural sources, can be a produced by recombinant techniques from a eukaryotic or prokaryotic host, or can be a product of synthetic procedures.
• As used herein, “optimized resistance to NH₄ ⁺” refers to an ability to grow in conditions of greater than 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, or 300 mM NH₃ or NH₄ ⁺ for at least about 24 or 48 hours. In an embodiment, an optimized resistance to NH₄ ⁺ refers to the ability to grow at least 10, 20, 30, 40, or 50% more rapidly, or at least 10, 20, 30, 40, or 50% longer, in the presence of a selected concentration of NH₃ or NH₄ ⁺ than can a naturally occurring N. eutropha.
• As used herein with respect to a comparison between nucleic acid or protein sequences, “similar” means having homology. A similar gene or protein may comprise, e.g., substitutions (such as conservative or non-conservative substitutions), insertions (e.g., of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30 amino acids, and for example up to 2, 3, 4, 5, 10, 15, 20, 25, 30, or 50 amino acids, or any positive combination thereof, or the number of nucleotides necessary to encode said amino acids), or deletions (e.g., of at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30 amino acids, and for example up to 2, 3, 4, 5, 10, 15, 20, 25, 30, or 50 amino acids, or any positive combination thereof, or the number of nucleotides necessary to encode said amino acids), or any combination thereof. Each of substitutions, insertions, and deletions may be positioned at the N-terminus, C-terminus, or a central region of the protein or gene. In embodiments, a conservative substitution is one that does not alter the charge and/or polarity and/or approximate size and/or geometry at the substituted position.
• As used herein, “transgenic” means comprising one or more exogenous portions of DNA. The exogenous DNA is derived from another organism, e.g., another bacterium, a bacteriophage, an animal, or a plant.
• As used herein, treatment of a disease or condition refers to reducing the severity or frequency of at least one symptom of that disease or condition, compared to a similar but untreated patient. Treatment can also refer to halting, slowing, or reversing the progression of a disease or condition, compared to a similar but untreated patient. Treatment may comprise addressing the root cause of the disease and/or one or more symptoms.
• As used herein a therapeutically effective amount refers to a dose sufficient to prevent advancement, or to cause regression of a disease or condition, or which is capable of relieving a symptom of a disease or condition, or which is capable of achieving a desired result. A therapeutically effective dose can be measured, for example, as a number of bacteria or number of viable bacteria (e.g., in CFUs) or a mass of bacteria (e.g., in milligrams, grams, or kilograms), or a volume of bacteria (e.g., in mm³).
• As used herein, the term “viability” refers to the autotrophic bacteria's, e.g., ammonia oxidizing bacteria's, ability to oxidize ammonia, ammonium, or urea to nitrite at a pre-determined rate. In some embodiments, the rate refers to the conversion of ammonium ions (NH₄ ⁺) (e.g., at about 200 mM) to nitrite (NO₂ ⁻) at a rate of at least 50, 75, 125, or 150 micromoles NO₂ ⁻ per minute, e.g., about 100-150, 75-175, 75-125, 100-125, 125-150, or 125-175 micromoles/minute, e.g., about 125 micromoles NO₂ ⁻ per minute.
• “Growth media” or “AOB media,” as referred to herein comprises the following components of Table 3 or Table 4 herein.
• In some embodiments, the states most relevant to the present disclosure are the state of growth, e.g., maximal growth, characterized by a pH of at least about 7.6, ammonia, trace minerals, oxygen and carbon dioxide. Another state may be characterized by a pH of about 7.4 or less and characterized by an absence of carbon dioxide. Under low carbon dioxide conditions, ammonia oxidizing bacteria, e.g., Nitrosomonas, continues to oxidize ammonia into nitrite and generates ATP, but lacking carbon dioxide, e.g., lacking sufficient carbon dioxide, to fix and generate protein, it instead generates polyphosphate, which it uses as an energy storage medium. This may allow the ammonia oxidizing bacteria to remain in a “storage state” for a period of time, e.g., a pre-determined period of time, for example, at least 1, 2, 3, 4, 5, 6, 7, days, 1, 2, 3, 4 weeks, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months, 1, 2, 3, 4, or 5 years. In some embodiments, the ammonia oxidizing bacteria may remain in a storage state for at least about 6 months to about 1 year.
• As used herein, “growth state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, that may have a pH of at least about 7.6. Levels of at least one of ammonia, ammonium ions, and urea may be between about 1 micromolar and 1000 millimolar. Levels of trace materials are between about 0.01 micromolar iron and 200 micromolar iron. Levels of oxygen are between about 5% and 100% oxygen saturation (e.g., of media). Levels of carbon dioxide are between about 20 ppm and 10% saturation (e.g., of media). In certain aspects, levels of at least one of ammonia, ammonium ions, and urea may be between about 10 micromolar and 100 millimolar. Levels of trace materials are between about 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen are between about 5% and 100% oxygen saturation. Levels of carbon dioxide are between about 200 ppm and 5% saturation (e.g., of media).
• As used herein, “polyphosphate loading state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, that may have a pH of about 7.4, or less. Levels of at least one of ammonia, ammonium ions, and urea are between about 1 micromolar and 2000 millimolar. Levels of trace materials are between 0.01 micromolar iron and 200 micromolar iron. Levels of oxygen are between about 0% and 100% 02 saturation (e.g., of media). Levels of carbon dioxide are between/less than about zero and 400 ppm, and phosphate levels greater than about 1 micromolar. In certain aspects, levels of at least one of ammonia, ammonium ions, and urea are between about 10 micromolar and 200 millimolar. Levels of trace materials are between 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen are between about 5% and 100% 02 saturation. Levels of carbon dioxide are between/less than about zero and 200 ppm, and phosphate levels greater than about 10 micromolar.
• The polyphosphate loading state may be induced for a period of time, e.g., a pre-determined period of time. The pre-determined period of time may the time period that allows sufficient polyphosphate accumulation in the ammonia oxidizing bacteria. This pre-determined period of time is the period of time suitable to provide for sufficient polyphosphate loading to allow for the ammonia oxidizing bacteria to be stored for an extended period of time. The pre-determined period of time may be at least partially based on a period of time of about 0.2-10 times, 0.3-5 times, 0.5-3 times, 0.5-1.5 times, or 0.5 to 1 times the doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be at least partially based on a period of time of about one doubling time for the ammonia oxidizing bacteria. In some embodiments, the pre-determined period of time is between about 8 hours and 12 hours. In some embodiments, the pre-determined period of time is about 10 hours. In some embodiments, the pre-determined period of time is about 24 hours.
• A purpose of the polyphosphate loading state may be to provide AOB with sufficient ammonia, ammonium ions, and/or urea, and O₂ such that ATP can be produced, but to deny them CO₂ and carbonate such that they are unable to use that ATP to fix CO₂ and instead use that ATP to generate polyphosphate which may be stored by the bacteria.
• As used herein, the term “storage state” refers to autotrophic bacteria, e.g., ammonia oxidizing bacteria, in a state or in an environment, e.g., a media, e.g., a culture media, e.g., a growth media, having a pH of about 7.4 or less (in some embodiments, the pH may be 7.6 or less). Levels of at least one of ammonia, ammonium ions, and urea are between about _1 and 1000 micromolar. Levels of trace materials are between about 0.1 and 100 micromolar. Levels of oxygen are between about 0 and 100% saturation (e.g., of media). Levels of carbon dioxide are between about 0 and 800 ppm. In certain aspects, levels of at least one of ammonia, ammonium ions, and urea are between about _10 and 100 micromolar. Levels of trace materials are between about 1 and 10 micromolar. Levels of oxygen are between about 0 and 100% saturation (e.g., of media). Levels of carbon dioxide are between about 0 and 400 ppm.
• AOB are produced according to some embodiments of the present disclosure by generating AOB biomass during a growth state, then exposing the AOB to a polyphosphate loading state and then removing the media and resuspending the AOB in a buffer, e.g., a storage buffer (i.e., the storage state).
• The ammonia oxidizing bacteria may remain in a “storage state” for a period of time, e.g., a pre-determined period of time, for example, at least 1, 2, 3, 4, 5, 6, 7, days, 1, 2, 3, 4 weeks, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months, 1, 2, 3, 4, or 5 years. In some embodiments, the ammonia oxidizing bacteria may remain in a storage state for at least about 6 months to about 1 year. Upon revival, the viability of the ammonia oxidizing bacteria is at least about 50%, 60%, 70%, 80%, 90%, or 100% of the viability as of the ammonia oxidizing bacteria prior to storage e.g., in a growth state). In some embodiments, the preparation of ammonia oxidizing bacteria may be prepared, such that no more than 10%, 20%, 30%, 40%, 50%, 60%, or 70% of the ability to oxidize NH₄ ⁺ is lost upon storage at selected conditions.
• The time that it takes to revive the ammonia oxidizing bacteria from a storage state (or a polyphosphate loading state) may be a pre-determined period of time. For example, the pre-determined period of time may be less than about 75 hours, or less than about 72 hours. The pre-determined period of time may at least partially based on a period time of about 0.2-10 times, 0.3-5 times, 0.5-3 times, 0.5-1.5 times, or 0.5 to 1 times the doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be at least partially based on a period of time of about one doubling time for the ammonia oxidizing bacteria. The pre-determined period of time may be between about 8 hours and 12 hours. The pre-determined period of time may be about 10 hours. The pre-determined time may be less than about 75 hours, 72 hours, 70 hours, 68 hours, 65 hours, 60 hours, 55 hours, 50 hours, 45 hours, 40 hours, 35 hours, 30 hours, 25 hours, 20 hours, 15 hours, 10 hours, 5 hours, 4 hours, 3, hours, 2 hours, or 1 hour. The pre-determined period of time may be between about 5 minutes and 5 hours. The pre-determined period of time may be about 5-10 minutes, 10-15 minutes, 15-20 minutes, 20-25 minutes, 25-30 minutes, 30-45 minutes, 45-60 minutes, 60 minutes-1.5 hours, 1.5 hours-2 hours, 2 hours-2.5 hours, 2.5 hours-3 hours, 3 hours-3.5 hours, 3.5 hours-4 hours, 4 hours-4.5 hours, 4.5 hours-5 hours. In some embodiments, the pre-determined period of time may be about 2 hours. The pre-determined period of time, e.g., may be the time it may take to achieve revival of the ammonia oxidizing bacteria, e.g., achieve viability of the ammonia oxidizing bacteria as compared to the viability of the bacteria prior to storage (e.g., in a growth state), e.g., at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, or 100% viability.
2. AMMONIA OXIDIZING BACTERIA (AOBS), N. EUTROPHA STRAIN D23 AND SIMILAR BACTERIA
• Autotrophic ammonia oxidizing bacteria, which may be referred to herein as AOBs or AOB, are obligate autotrophic bacteria as noted by Alan B. Hooper and A. Krummel at al. Alan B. Hooper, Biochemical Basis of Obligate Autotrophy in Nitrosomonas europaea, Journal of Bacteriology, February 1969, p. 776-779. Antje Krummel et al., Effect of Organic Matter on Growth and Cell Yield of Ammonia-Oxidizing Bacteria, Arch Microbiol (1982) 133: 50-54. These bacteria derive all metabolic energy only from the oxidation of ammonia to nitrite with nitric oxide (NO) as an intermediate product in their respiration chain and derive virtually all carbon by fixing carbon dioxide. They are incapable of utilizing carbon sources other than a few simple molecules.
• Ammonia oxidizing bacteria (AOB) are widely found in the environment, and in the presence of ammonia, oxygen and trace metals will fix carbon dioxide and proliferate. AOB may be slow growing and toxic levels of ammonia may kill fish and other organisms before AOB can proliferate and reduce ammonia to non-toxic levels. Slow growth of AOB also may delay the health benefits of the NO and nitrite the AOB produce when applied to the skin.
• Supplementing the aquarium, skin, or process with sufficient viable AOB grown and stored for that purpose is desired. AOB do not form spores, so storage in the dry state with high viability is difficult, and storage in the wet state leaves them metabolically active. Decay of nitrifying capacity during storage of AOB for wastewater treatment has been studied, as for example (Munz G, Lubello C, Oleszkiewicz J A. Modeling the decay of ammonium oxidizing bacteria. Water Res. 2011 January; 45(2): 557-64. Oi: 10.1016/j.watres.2010.09.022.)
• Growth, prolonged storage, and restoration of activity of Nitrosomonas is discussed by Cassidy et al. (U.S. Pat. No. 5,314,542) where they disclose growing Nitrosomonas, removing toxic waste products, storing in sterile water of appropriate salinity for periods of time up to one year, and then reviving by adding buffer (CaCO₃) and 200 ppm, of ammonium, which reviving takes 72 hours.
• As obligate autotrophs, AOB synthesize protein via the fixing of CO₂ using the energy and reducing equivalents generated by the oxidation of ammonia to nitrite. Growth requires ammonia, oxygen, minerals and carbon dioxide.
• Nitrosomonas may exist in several metabolic states, according to “Polyphosphate and Orthophosphate Content of Nitrosomonas europaea as a Function of Growth” by K. R. Terry and A. B. Hooper, Journal of Bacteriology, July 1970, p. 199-206, Vol. 103, No. I.
• In certain embodiments of the disclosure, the ammonia oxidizing bacteria may be axenic. The preparation (formulation or composition) of ammonia oxidizing bacteria may comprise, consist essentially of, or consist of axenic ammonia oxidizing bacteria. The ammonia oxidizing bacteria may be from a genus selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, and combinations thereof.
• This disclosure provides, inter alia, N. eutropha strain D23, a unique, e.g., optimized strain of ammonia oxidizing bacteria that can increase production of nitric oxide and nitric oxide precursors on the surface of a subject, e.g., a human subject. This disclosure also provides methods of using the bacteria and articles comprising the bacteria.
• In embodiments, the N. eutropha is non-naturally occurring. For instance, it may have accumulated desirable mutations during a period of selection. In other embodiments, desirable mutations may be introduced by an experimenter. In some embodiments, the N. eutropha may be a purified preparation, and may be an optimized N. eutropha.
• In preferred embodiments, the N. eutropha strain is autotrophic and so incapable of causing infection. A preferred strain utilizes urea as well as ammonia, so that hydrolysis of the urea in sweat would not be necessary prior to absorption and utilization by the bacteria. Also, in order to grow at low pH, the bacteria may either absorb NH₄ ⁺ ions or urea. The selected strain should also be capable of living on the external skin of a subject, e.g., a human, and be tolerant of conditions there.
• Although this disclosure refers to N. eutropha strain D23 in detail, the preparations, methods, compositions, treatments, wearable articles, and articles of clothing may be used with one or more of: one or more other strains of N. eutropha, one or more other species of Nitrosomonas, and one or more other ammonia oxidizing bacteria. Autotrophic AOBs are obligate autotrophic bacteria as noted by Alan B. Hooper and A. Krummel at al. Alan B. Hooper, Biochemical Basis of Obligate Autotrophy in Nitrosomonas europaea, Journal of Bacteriology, February 1969, p. 776-779. Antje Krummel et al., Effect of Organic Matter on Growth and Cell Yield of Ammonia-Oxidizing Bacteria, Arch Microbiol (1982) 133: 50-54. These bacteria derive all metabolic energy only from the oxidation of ammonia to nitrite with nitric oxide (NO) as an intermediate product in their respiration chain and derive virtually all carbon by fixing carbon dioxide. They are incapable of utilizing carbon sources other than a few simple molecules.
• In certain embodiments, the N. eutropha is the strain deposited with the American Tissue Culture Collection (ATCC) on Apr. 8, 2014, designated AOB D23-100 (25 vials) under accession number PTA-121157.
• In certain embodiments, the N. eutropha comprises a chromosome having a sequence at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1 (the strain D23 whole-genome sequence).
• In certain embodiments, a bacterium with the above-mentioned sequence characteristics has one or more of (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH₄ ⁺ oxidation rate, (4) an optimized resistance to NH₄ ⁺, and (4) an optimized resistance to NO₂ ⁻. Particular sub-combinations of these properties are specified in the following paragraph.
• In some embodiments, the N. eutropha described herein has one or more of: (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH₄ ⁺ oxidation rate, (4) an optimized resistance to, NH₄ ⁺, and (4) an optimized resistance to, NO₂ ⁻. For instance, the bacterium may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the bacterium may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the bacterium may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the bacterium has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph.
• This disclosure also provides an axenic composition of N. eutropha having one or more of: (1) an optimized growth rate as measured by doubling time, (2) an optimized growth rate as measured by OD600, (3) an optimized NH₄ ⁺ oxidation rate, (4) an optimized resistance to, NH₄ ⁺, and (4) an optimized resistance to, NO₂ ⁻. For instance, the axenic N. eutropha composition may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the axenic N. eutropha composition may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the axenic N. eutropha composition may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the axenic N. eutropha composition has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph.
• N. eutropha strain D23, as deposited in the form of 25 vials on Apr. 8, 2014, in the ATCC patent depository, designated AOB D23-100, under accession number PTA-121157, comprises a circular genome having SEQ ID NO: 1 or its complement. Accordingly, in some embodiments, an N. eutropha strain described herein comprises a nucleic acid sequence, e.g., a genome, that is similar to SEQ ID NO: 1 or its complement.
• For instance, the N. eutropha may comprise a nucleic acid sequence having a 1,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 1,000 base pair portion of SEQ ID NO: 1 or its complement. The 1,000 base pair portion may span, e.g., nucleotides (n*1,000)+1 to (n+1)*1,000, where n=0, 1, 2, 3 . . . 2538, e.g., nucleotides 1-1,000, 1,001-2,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 2,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 2,000 base pair portion of SEQ ID NO: 1 or its complement. The 2,000 base pair portion may span, e.g., nucleotides (n*2,000)+1 to (n+1)*2,000, where n=0, 1, 2, 3 . . . 1269, e.g., nucleotides 1-2,000, 2,001-4,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 5,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 5,000 base pair portion of SEQ ID NO: 1 or its complement. The 5,000 base pair portion may span, e.g., nucleotides (n*5,000)+1 to (n+1)*5,000, where n=0, 1, 2, 3 . . . 508, e.g., nucleotides 1-5,000, 5,001-10,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 10,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 10,000 base pair portion of SEQ ID NO: 1 or its complement. The 10,000 base pair portion may span, e.g., nucleotides (n*10,000)+1 to (n+1)*10,000, where n=0, 1, 2, 3 . . . 254, e.g., nucleotides 1-10,000, 10,001-20,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 20,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 20,000 base pair portion of SEQ ID NO: 1 or its complement. The 20,000 base pair portion may span, e.g., nucleotides (n*20,000)+1 to (n+1)*20,000, where n=0, 1, 2, 3 . . . 127, e.g., nucleotides 1-20,000, 20,001-40,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 50,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 50,000 base pair portion of SEQ ID NO: 1 or its complement. The 50,000 base pair portion may span, e.g., nucleotides (n*50,000)+1 to (n+1)*50,000, where n=0, 1, 2, 3 . . . 51, e.g., nucleotides 1-50,000, 50,001-100,000, and so on through the end of SEQ ID NO: 1.
• In embodiments, the N. eutropha comprises a nucleic acid sequence having a 100,000 base pair portion having at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to a 100,000 base pair portion of SEQ ID NO: 1 or its complement. The 100,000 base pair portion may span, e.g., nucleotides (n*100,000)+1 to (n+1)*100,000, where n=0, 1, 2, 3 . . . 26, e.g., nucleotides 1-100,000, 100,001-20,000, and so on through the end of SEQ ID NO: 1.
• In some aspects, the present disclosure provides a composition of N. eutropha comprising a chromosome at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1. In some aspects, the present disclosure provides an axenic composition of N. eutropha comprising a chromosome at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1.
• In certain embodiments, the N. eutropha strain comprises a nucleic acid sequence, e.g., a genome, that hybridizes to SEQ ID NO: 1, or to the genome of the D23 strain deposited in the form of 25 vials with the ATCC patent depository on Apr. 8, 2014, designated AOB D23-100, under accession number PTA-121157, or their complements, under low stringency, medium stringency, high stringency, or very high stringency, or other hybridization condition described herein. As used herein, the term “hybridizes under low stringency, medium stringency, high stringency, or very high stringency conditions” describes conditions for hybridization and washing. Guidance for performing hybridization reactions can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6, which is incorporated by reference. Aqueous and nonaqueous methods are described in that reference and either can be used. Specific hybridization conditions referred to herein are as follows: 1) low stringency hybridization conditions in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at least at 50° C. (the temperature of the washes can be increased to 55° C. for low stringency conditions); 2) medium stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 60° C.; 3) high stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C.; 4) very high stringency hybridization conditions are 0.5M sodium phosphate, 7% SDS at 65° C., followed by one or more washes at 0.2×SSC, 1% SDS at 65° C. Very high stringency conditions (4) are suitable conditions and the ones that should be used unless otherwise specified.
• The genome of strain D23 (SEQ ID NO: 1) was compared with the genome of N. eutropha C91. An annotation of the D23 genome is shown in Supplementary Table 1, which lists the positions of 2,777 genes in SEQ ID NO: 1 as identified by sequence analysis. In certain embodiments, the N. eutropha described herein comprises one or more genes or proteins listed in Supplementary Table 1, or a gene or protein similar to one of said genes or proteins.
• Accordingly, in some embodiments, the N. eutropha comprises a gene of Supplementary Table 1, or a protein encoded by said gene. In certain embodiments, the N. eutropha comprises a gene that is similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to a gene of Supplementary Table 1, or a protein encoded by said gene. In embodiments, the N. eutropha comprises genes or proteins that are identical or similar to at least 2, 3, 4, 5, 10, 20, 30, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 1000, 1500, 2000, 2500, or all the genes of Supplementary Table 1, or a protein encoded by said genes.
• In some embodiments, the N. eutropha described herein (e.g., strain D23) comprises one or more genes or proteins that are absent from strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIG. 6-8 and are described in more detail in Example 4 herein.
• Accordingly, with respect to FIG. 6, in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the genes in FIG. 6. In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 6.
• With respect to FIG. 7, in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the genes in FIG. 7. In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 7.
• With respect to FIG. 8, in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the genes in FIG. 8. In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the proteins encoded by the genes listed in FIG. 8.
• With respect to FIGS. 6-8 collectively, in some embodiments, the N. eutropha comprises genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the genes in FIGS. 6-8. In some embodiments, the N. eutropha comprises proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the proteins encoded by genes listed in FIGS. 6-8.
• In some embodiments, the N. eutropha described herein (e.g., strain D23) lacks one or more genes or proteins that are unique to strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIG. 9 and are described in more detail in Example 4 herein. Accordingly, in some embodiments, the N. eutropha described herein lacks at least 1, 2, 3, 4, 5, 10, 20, 50, 100, 150, 200, 250, or all of the genes of FIG. 9. In some embodiments, the N. eutropha described herein lacks up to 2, 3, 4, 5, 10, 20, 50, 100, 150, 200, 250, or all of the genes of FIG. 9. In embodiments, the N. eutropha described herein lacks about 1-5, 5-10, 10-20, 20-50, 50-100, 100-150, 150-200, 200-250, or 250-all of the genes of FIG. 9.
• Sequencing of the D23 genome revealed several genes of potential interest, including genes involved in ammonia metabolism (e.g., ammonia monooxygenase, hydroxylamine oxidoreductase, cytochrome c554, and cytochrome c_M552). All of these genes are present in multiple copies, and in general the copies are not identical to each other. One set of genes of interest is the ammonia monooxygenase synthesis operon amoCAB, which is present in two copies, along with a third copy of amoC. The operons have homologs in C91, i.e., Neut_2078/7/6 and Neut_2319/8/7. Another set of genes of interest is hydroxylamine oxidoreductase (hao), which is present in three copies. The hao homologs in C91 are designated Neut_1672, 1793, and 2335. A third set of genes of interest is the cytochrome c554 gene encoded by cycA, which is present in three copies. The corresponding C91 genes are designated Neut_1670, 1791, and 2333. A fourth set of genes of interest is the cytochrome c_M552 genes encoded by cycB, which are present in two copies. The homologous C91 genes are designated Neut_1790 and 2332. Each group of genes is summarized in Table 1 and is discussed in more detail below.

• TABLE 1
  Sequences of ammonia metabolism genes in N. eutropha
  strain D23.

  	SEQ ID in	SEQ ID in
  	strain D23	strain C91	Type	Gene name

  1. ammonia monooxygenase

  	4	34	Protein	amoC1
  	5	35	DNA	amoC1
  	6	36	Protein	amoA1
  	7	37	DNA	amoA1
  	8	38	Protein	amoB1
  	9	39	DNA	amoB1
  	10	40	Protein	amoC2
  	11	41	DNA	amoC2
  	12	42	Protein	amoA2
  	13	43	DNA	amoA2
  	14	44	Protein	amoB2
  	15	45	DNA	amoB2
  	16	46	Protein	amoC3
  	17	47	DNA	amoC3

  2. hydroxylamine oxidoreductase

  	18	48	Protein	hao1
  	19	49	DNA	hao1
  	20	50	Protein	hao2
  	21	51	DNA	hao2
  	22	52	Protein	hao3
  	23	53	DNA	hao3

  3. cytochrome c554

  	24	54	Protein	c554 cycA1
  	25	55	DNA	c554 cycA1
  	26	56	Protein	c554 cycA2
  	27	57	DNA	c554 cycA2
  	28	58	Protein	c554 cycA3
  	29	59	DNA	c554 cycA3

  4. cytochrome cM552

  	30	60	Protein	cM552 cycB1
  	31	61	DNA	cM552 cycB1
  	32	62	Protein	cM552 cycB2
  	33	63	DNA	cM552 cycB2

• In some aspects, the N. eutropha described herein comprises genes identical to or similar to the genes and proteins of Table 1.
• More particularly, in certain aspects, this disclosure provides a composition of N. eutropha, e.g., a purified preparation of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising nucleic acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c_M552 sequence of Table 1.
• In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.4%, 99.5%, 99.6%, or 99.7% identical to hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.5%, 99.6%, or 99.7% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides a composition of N. eutropha comprising amino acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.1%, 97.2%, 97.5%, 98%, 98.5%, 98.6%, 98.7%, 98.8%, 99%, or 99.5% identical to a cytochrome c_M552 sequence of Table 1.
• In some embodiments, the N. eutropha are present in an axenic composition, and e.g., in the form of a purified preparation of optimized N. eutropha.
• More particularly, in certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 98.5%, 98.8%, 98.9%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising nucleic acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a cytochrome c_M552 sequence of Table 1.
• In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 98.5%, 98.8%, 98.9%, 99%, 99.2%, 99.3%, 99.4%, 99.5%, or 99.6% identical to an ammonia monooxygenase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.4%, 99.5%, 99.6%, or 99.7% identical to hydroxylamine oxidoreductase sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.5%, 99.6%, or 99.7% identical to a cytochrome c554 sequence of Table 1. In certain aspects, this disclosure provides an axenic composition of N. eutropha comprising amino acid sequences at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.1%, 97.2%, 97.5%, 98%, 98.5%, 98.6%, 98.7%, 98.8%, 99%, or 99.5% identical to a cytochrome c_M552 sequence of Table 1.
• In some embodiments, the N. eutropha comprises a gene or protein comprising a sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to a strain D23 sequence of Table 1, e.g., any of SEQ IDs 4-33. Substitutions may be conservative or non-conservative; also, insertions and deletions are contemplated. In some embodiments, the N. eutropha comprises a gene or protein comprising a sequence of Table 1, e.g., any of SEQ IDs 4-33. In some embodiments, the protein has an N-terminal and/or C-terminal extension or deletion of up to about 1, 2, 3, 4, 5, 6, 8, 10, 15, 20, 25, 50, or 100 amino acids.
• Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The following paragraphs discuss this percent identity and describe various genes having homology to the D23 genes of Table 1.
• More specifically, the amoA1 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA1 gene.
• The amoA2 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA2 gene.
• The amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB1 gene.
• The amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB2 gene.
• The amoC1 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.8%, 99.9%, or 100% identical to the D23 amoC1 gene.
• The amoC2 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.8%, 99.9%, or 100% identical to the D23 amoC2 gene.
• The amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoC3 gene.
• The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao1 gene.
• The hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao2 gene.
• The hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao3 gene.
• The cycA1 genes are about 98.0% identical (i.e., at 694/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.0%, 98.2%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA1 gene.
• The cycA2 genes are about 98.7% identical (i.e., at 699/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 98.7%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA2 gene.
• The cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 99.3%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA3 gene.
• The cycB1 genes are about 96.7% identical (i.e., at 696/720 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 96.7%, 96.8%, 97.0%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB1 gene.
• The cycB2 genes are about 97.1% identical (i.e., at 702/723 positions). Accordingly, in some embodiments, the N. eutropha described herein comprise D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the N. eutropha described herein comprise a gene at least about 97.1%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB2 gene.
• The following four paragraphs describe genes and proteins of Table 1 in more detail.
• Ammonia monooxygenase is an enzyme involved in ammonia oxidation, that catalyzes the reaction NH₃+O₂+2e⁻+2H⁺

  

  NH₂OH+H₂O (Ensign et al., 1993). In N. eutropha strain D23, the ammonia monooxygenase operon comprises three genes designated amoA, amoB, and amoC. Strain D23 comprises two copies of the entire operon, and a third copy of amoC. These genes and the corresponding proteins are listed in Table 1 above. In certain embodiments, the N. eutropha described herein comprise 1 or 2 ammonia monooxygenase subunit A genes and/or protein of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In some embodiments, the N. eutropha described herein comprise 1 or 2 ammonia monooxygenase subunit B genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In certain embodiments, the N. eutropha described herein comprise 1, 2, or 3 ammonia monooxygenase subunit C genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. In some embodiments, the N. eutropha described herein comprise at least one or two each of (a) an ammonia monooxygenase subunit A gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1), (b) an ammonia monooxygenase subunit B gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1), and (c) an ammonia monooxygenase subunit C gene and/or protein of Table 1 (e.g., the D23 sequences of Table 1). For instance, the N. eutropha may comprise all of the ammonia monooxygenase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 ammonia monooxygenase genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 ammonia monooxygenase proteins of Table 1. Hydroxylamine oxidoreductases catalyze the general reaction NH₂OH+O₂ NO₂ ⁻+H₂O. They typically use heme as a cofactor. N. eutropha strain D23 comprises three hydroxylamine oxidoreductases, designated hao1, hao2, and hao3. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1, 2, or 3 hydroxylamine oxidoreductase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise all of the hydroxylamine oxidoreductase genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 hydroxylamine oxidoreductase genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 hydroxylamine oxidoreductase proteins of Table 1.
• The capacity of D23 to aerobically catabolize ammonia as the sole source of energy and reductant requires two specialized protein complexes, Amo and Hao as well as the cytochromes c554 and c_m552, which relay the electrons to the quinone pool. The NO reductase activity of c554 is important during ammonia oxidation at low oxygen concentrations. N. eutropha strain D23 comprises three cytochrome c554 genes, designated cycA1, cycA2, and cycA3. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1, 2, or 3 cytochrome c554 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise all of the cytochrome c554 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises all of the D23 cytochrome c554 genes of Table 1. In some embodiments, the N. eutropha comprises all of the D23 cytochrome c554 proteins of Table 1.
• The capacity of D23 to aerobically catabolize ammonia as the sole source of energy and reductant requires two specialized protein complexes, Amo and Hao as well as the Cytochromes c554 and c_M552, which relay the electrons to the quinone pool. Cytochrome c_M552 reduces quinones, with electrons originating from Hao. N. eutropha strain D23 comprises two cytochrome c_M552 genes, designated cycB1 and cycB2. These genes and the corresponding proteins are listed in Table 1 above. In some embodiments, the N. eutropha described herein comprise 1 or 2 cytochrome c_M552 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. For instance, the N. eutropha may comprise both of the cytochrome c_M552 genes and/or proteins of Table 1 (e.g., the D23 sequences of Table 1), or genes and/or proteins similar thereto. Even more specifically, in some embodiments, the N. eutropha comprises both of the D23 cytochrome c_M552 genes of Table 1. In some embodiments, the N. eutropha comprises both of the D23 Cytochrome c_M552 proteins of Table 1.
• In some embodiments, the N. eutropha described herein comprises a combination of genes and/or proteins selected from Table 1. This combination may comprise, for instance, genes and/or proteins listed in the preceding four paragraphs. For instance, the combination may comprise genes and/or proteins from two classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c_M552 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs. In embodiments, the N. eutropha comprises one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c_M552 genes and/or proteins as described in Table 1, or as described in the preceding four paragraphs.
• The combination may also comprise genes and/or proteins from three classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c_M552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more one or more ammonia monooxygenase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c_M552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs. In embodiments, the N. eutropha comprises one or more one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c_M552 genes and/or proteins as described in Table 1, or as described in the aforementioned four paragraphs.
• The combination may comprise genes and/or proteins from all four classes within Table 1. Accordingly, in some embodiments, the N. eutropha comprises one or more ammonia monooxygenase genes and/or proteins and one or more hydroxylamine oxidoreductase genes and/or proteins and one or more cytochrome c554 genes and/or proteins and/or one or more cytochrome c_M552 genes as described in Table 1, or as described in the aforementioned four paragraphs.
• Table 2 (below) lists sequence differences between the D23 and C91 proteins of Table 1. For example, AmoA1 has M at position 1 in C91 but V at position 1 in D23, and this difference is abbreviated as M1V in Table 2. As another example, the D23 CycB1 has an insertion of DDD between residues 194 and 195 of the C91 protein, so that the added residues are residues number 195, 196, and 197 of the D23 protein and this difference is abbreviated as 195insD, 196insD, and 197insD respectively in Table 2. The sequence alignments that form the basis for Table 2 are shown in FIGS. 10-16.

• TABLE 2
  Amino acid sequence differences between N. eutropha
  strains D23 and C91

  Protein	Sequence characteristics of D23 compared to C91

  1. ammonia monooxygenase

  AmoA1	M1V, M160L, P167A
  AmoA2	M1V, M160L, P167A
  AmoB1	I33V, V165I
  AmoB2	I33V, V165I
  AmoC1	N/A
  AmoC2	N/A
  AmoC3	V79A, I271V

  2. hydroxylamine oxidoreductase

  Hao1	N85S, V163A, G312E
  Hao2	N85S, G312E
  Hao3	N85S, G312E

  3. cytochrome c554

  c554 CycA1	A65T, A186T
  c554 CycA2	A65T
  c554 CycA3	A65T

  4. cytochrome cM552

  cM552 CycB1	I63V, S189P, D194G, 195insD, 196insD,
  	197insD, 206insE, 207insE
  cM552 CycB2	I63V, S189P, 206insE, 207insE

• Accordingly, the N. eutropha described herein may comprise one or more of the sequence characteristics listed in Table 2. For instance, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the sequence characteristics of Table 2. In some embodiments, the N. eutropha comprises no more than 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the sequence characteristics of Table 2. In embodiments, the N. eutropha comprises 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or all of the sequence characteristics of Table 2. The N. eutropha may also comprise fragments of said proteins.
• As to individual categories of genes or proteins, in some embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the sequence characteristics of Table 2, Section 1 (which describes ammonia monooxygenases). In embodiments, the N. eutropha comprises 1-5, 3-7, 4-8, or 5-10 of the sequence characteristics of Table 2, Section 1. For instance, in some embodiments, the N. eutropha comprises at least 1, 2, or 3 sequence characteristics of an amoA gene or protein as listed in Table 2, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise at least 1 or 2 sequence characteristics of an amoB gene or protein as listed in Table 2. In addition, the N. eutropha may comprise at least 1 or 2 sequence characteristics of the amoC3 gene as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
• With respect to hao genes and proteins, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, or all of the sequence characteristics of Table 2, Section 2 (which describes hydroxylamine oxidoreductases). In embodiments, the N. eutropha comprises 1-4, 2-5, 3-6, or 4-8 of the sequence characteristics of Table 2, Section 2. The N. eutropha may also comprise at least 1, 2 or 3 sequence characteristics of Hao1 as listed in Table 1, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise at least 1 or 2 sequence characteristics of Hao2 or Hao3 as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
• Turning now to cytochrome c554, the N. eutropha may comprise at least 1, 2, 3, 4, or all of the sequence characteristics of Table 2, Section 3 (which describes cytochrome c554). In embodiments, the N. eutropha comprises at most 2, 3, 4, or all of the sequence characteristics of Table 2 Section 3. In embodiments, the N. eutropha comprises at least 1 or 2 sequence characteristics of cytochrome c554 CycA1 as listed in Table 2. The N. eutropha may also comprise at least 1 sequence characteristic of c554 CycA2 or c554 CycA3 as listed in Table 2. The N. eutropha may also comprise fragments of said proteins.
• With respect to the c_M552 genes and proteins, the N. eutropha may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the sequence characteristics of Table 2, Section 4 (which describes cytochrome c_M552). In embodiments, the N. eutropha comprises at most 2, 3, 4, 5, 6, 7, 8, 9, 10, or all the sequence characteristics of Table 2, Section 4. For instance, in embodiments the N. eutropha comprises 1-5, 2-7, 3-8, or 5-10 sequence characteristics of Table 2, Section 4. In embodiments, at least 1, 2, 3, 4, 5, 6, or 7 sequence characteristics of c_M552 CycB1 as listed in Table 2, and/or no more than 2, 3, 4, 5, 6, or 7 of these characteristics. The N. eutropha may also comprise at least 1, 2, or 3 sequence characteristics of c_M552 CycB2 as listed in Table 2, and/or no more than 2 or 3 of these characteristics. The N. eutropha may also comprise fragments of said proteins.
• It is understood that the paragraphs above, which refer to sequence characteristics of various N. eutropha proteins, also describe the sequences of nucleic acids that encode these proteins.
• The sequencing analysis described herein revealed that strain D23 lacks plasmids. Consequently, in some embodiments, the N. eutropha bacterium lacks plasmids, i.e., all of its DNA is contained in the chromosome. In some embodiments, the N. eutropha bacterium lacks endogenous plasmids, but carries one or more transgenic plasmids.
• This D23 strain is not believed to be a product of nature, but rather has acquired certain mutations and characteristics during an extended period of culture and selection in the laboratory. For instance, D23 has an ability to grow in conditions of greater than about 200 or 250 mM NH₄ ⁺ for more than 24 hours.
• In some embodiments, the N. eutropha disclosed herein differ from naturally occurring bacteria in the abundance of siderophores. For instance, the N. eutropha may have elevated or reduced levels of siderophores compared to N. eutropha C91. Generally, siderophores are secreted iron-chelating compounds that help bacteria scavenge iron from their environment. Some siderophores are peptides, and others are small organic molecules.
• The AOBs, for example, N. eutropha contemplated in this disclosure may comprise mutations relative to wild-type N. eutropha and/or the N. eutropha sequences disclosed herein. These mutations may, e.g., occur spontaneously, be introduced by random mutagenesis, or be introduced by targeted mutagenesis. For instance, the N. eutropha may lack one or more genes or regulatory DNA sequences that wild-type N. eutropha typically comprises. The N. eutropha may also comprise point mutations, substitutions, insertions, deletions, and/or rearrangements relative to the sequenced strain or a wild-type strain. The N. eutropha may be a purified preparation of optimized N. eutropha.
• In certain embodiments, the N. eutropha is transgenic. For instance, it may comprise one or more genes or regulatory DNA sequences that wild-type N. eutropha D23 lacks. More particularly, the N. eutropha may comprise, for instance, a reporter gene, a selective marker, a gene encoding an enzyme, or a promoter (including an inducible or repressible promoter). In some embodiments the additional gene or regulatory DNA sequence is integrated into the bacterial chromosome; in some embodiments the additional gene or regulatory DNA sequence is situated on a plasmid, for instance a plasmid related to a plasmid found in N. eutropha N91.
• In some preferred embodiments, the N. eutropha differs by at least one nucleotide from naturally occurring bacteria. For instance, the N. eutropha may differ from naturally occurring bacteria in a gene or protein that is part of a relevant pathway, e.g., an ammonia metabolism pathway, a urea metabolism pathway, or a pathway for producing nitric oxide or nitric oxide precursors. More particularly, the N. eutropha may comprise a mutation that elevates activity of the pathway, e.g., by increasing levels or activity of an element of that pathway.
• The above-mentioned mutations can be introduced using any suitable technique. Numerous methods are known for introducing mutations into a given position. For instance, one could use site-directed mutagenesis, oligonucleotide-directed mutagenesis, or site-specific mutagenesis. Non-limiting examples of specific mutagenesis protocols are described in, e.g., Mutagenesis, pp. 13.1-13.105 (Sambrook and Russell, eds., Molecular Cloning A Laboratory Manual, Vol. 3, 3.sup.rd ed. 2001). In addition, non-limiting examples of well-characterized mutagenesis protocols available from commercial vendors include, without limitation, Altered Sites® II in vitro Mutagenesis Systems (Promega Corp., Madison, Wis.); Erase-a-Base® System (Promega, Madison, Wis.); GeneTailor™ Site-Directed Mutagenesis System (Invitrogen, Inc., Carlsbad, Calif.); QuikChange® II Site-Directed Mutagenesis Kits (Stratagene, La Jolla, Calif.); and Transformer™ Site-Directed Mutagenesis Kit (BD-Clontech, Mountain View, Calif.).
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise a concentration or amount of ammonia oxidizing bacteria in order to at least partially treat a condition or disease. The preparation of ammonia oxidizing bacteria may comprise a concentration or amount of ammonia oxidizing bacteria in order to alter, e.g., reduce or increase, an amount, concentration or proportion of a bacterium, or genus of bacteria, on a surface, e.g., a skin surface. The bacteria may be non-pathogenic or pathogenic, or potentially pathogenic.
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 10⁸ to about 10¹⁴ CFU/L. The preparation may comprise at least 10⁸, 10⁹, 10¹⁰, 10¹¹, 2×10¹¹, 5×10¹¹, 10¹², 2×10¹², 5×10¹², 10¹³, 2×10¹³, 5×10¹³, or 10¹⁴; or about 10⁸-10⁹, 10⁹-10¹⁰, 10¹¹-10¹¹, 10¹¹-10¹², 10¹²-10¹³, or 10¹³-10¹⁴ CFU/L. In certain aspects, the preparation may comprise between about 1×10⁹ CFU/L to about 10×10⁹ CFU/L. In certain aspects, the preparation may comprise between about 1×10⁹ CFU to about 10×10⁹ CFU.
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 0.1 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria. In certain aspects, the preparation may comprise between about 50 mg and about 1000 mg of ammonia oxidizing bacteria. The preparation may comprise between about 0.1-0.5 mg, 0.2-0.7 mg, 0.5-1.0 mg, 0.5-2 mg, 0.5-5 mg, 2.5-5 mg, 2.5-7.0 mg, 5.0-10 mg, 7.5-15 mg, 10-15 mg, 15-20 mg, 15-25 mg, 20-30 mg, 25-50 mg, 25-75 mg, 50-75 mg, 50-100 mg, 75-100 mg, 100-200 mg, 200-300 mg, 300-400 mg, 400-500 mg, 500-600 mg, 600-700 mg, 700-800 mg, 800-900 mg, 900-1000 mg, 100-250 mg, 250-500 mg, 100-500 mg, 500-750 mg, 750-1000 mg, or 500-1000 mg.
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise a mass ratio of ammonia oxidizing bacteria to an excipient, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient in a range of about 0.1 grams per liter to about 1 gram per liter. The preparation may comprise a mass ratio of ammonia oxidizing bacteria to an excipient in a range of about 0.1-0.2, 0.2-0.3, 0.1-0.5, 0.2-0.7, 0.5-1.0, or 0.7-1.0 grams per liter.
• In some embodiments, the preparation of ammonia oxidizing bacteria may be in a growth state. A growth state may be provided by exposing ammonia oxidizing bacteria to an environment that may promote growth. The growth state may be a state, e.g., ammonia oxidizing bacteria in an environment that allows immediate availability of ammonia oxidizing bacteria to convert ammonium ions (NH₄ ⁺) to nitrite (NO₂ ⁻). The growth state may comprise providing ammonia oxidizing bacteria in an environment having a pH of greater than about 7.6. The growth state may also comprise providing ammonia oxidizing bacteria in an environment having ammonia, ammonium salts, and/or urea, trace minerals and sufficient oxygen and carbon dioxide, as described above in Section 1.
• In some embodiments, the preparation of ammonia oxidizing bacteria may be in a polyphosphate loading state, wherein the state or the environment, e.g., a media, e.g., a culture media, e.g., a growth media, may have a pH of less than about 7.4. Levels of at least one of ammonia, ammonium ions, and urea may be between about 10 micromolar and 200 millimolar. Levels of trace materials may be between 0.1 micromolar iron and 20 micromolar iron. Levels of oxygen may be between about 5% and 100% oxygen saturation. Levels of carbon dioxide may be between/less than about zero and 200 ppm, and phosphate levels greater than about 10 micromolar. The purpose of the polyphosphate loading state is to provide AOB with ammonia and oxygen such that ATP can be produced, but to deny them carbon dioxide and carbonate such that they are unable to use that ATP to fix carbon dioxide and instead use that ATP to generate polyphosphate which may be stored.
• In some embodiments, the preparation of ammonia oxidizing bacteria may be in a storage state. A storage state may be defined as ammonia oxidizing bacteria in an environment in which they may be stored to be later revived. The storage state may be a state, e.g., ammonia oxidizing bacteria in an environment that allows availability of ammonia oxidizing bacteria after being revived, e.g., after being place in an environment promoting a growth state for a pre-determined period of time.
• The storage state may comprise providing ammonia oxidizing bacteria in an environment having a pH of less than about 7.4. The storage state may also comprise providing ammonia oxidizing bacteria in an environment having ammonia, ammonia salts, and/or urea, trace minerals, oxygen, and low concentrations of carbon dioxide, as described above in Section 1.
• Storage may also be accomplished by storing at 4° C. for up to several months. The storage buffer in some embodiments may comprise 50 mM Na₂HPO₄-2 mM MgCl₂ (pH 7.6).
• In some embodiments, ammonia oxidizing bacteria may be cyropreserved. A 1.25 ml of ammonia oxidizing bacteria mid-log culture may be added to a 2 ml cryotube and 0.75 ml of sterile 80% glycerol. Tubes may be shaken gently, and incubate at room temperature for 15 min to enable uptake of the cryoprotective agents by the cells. The tubes may be directly stored in a −80° C. freezer for freezing and storage.
• For resuscitation of cultures, frozen stocks may be thawed on ice for 10-20 minutes, and then centrifuged at 8,000×g for 3 minutes at 4° C. The pellet may be washed by suspending it in 2 ml AOB medium followed by another centrifugation at 8,000×g for 3 minutes at 4° C. to reduce potential toxicity of the cryoprotective agents. The pellet may be resuspended in 2 ml of AOB medium, inoculated into 50 ml of AOB medium containing 50 mM NH₄ ⁺, and incubated in dark at 30° C. by shaking at 200 rpm.
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise ammonia oxidizing bacteria in a storage state and/or ammonia oxidizing bacteria in a polyphosphate loading state and/or ammonia oxidizing bacteria in a growth state.
• Without wishing to be bound by theory, by maintaining ammonia oxidizing bacteria under conditions or in an environment of low carbon dioxide, with sufficient oxygen and ammonia, they may accumulate polyphosphate for a pre-determined period, e.g., for a period of about one doubling time, e.g., for about 8-12 hours, e.g., for about 10 hours. The ammonia oxidizing bacteria may accumulate sufficient polyphosphate to extend their storage viability, storage time, and accelerate their revival. This may occur with or without the addition of buffer and ammonia.
• The presence of sufficient stored polyphosphate may allow the ammonia oxidizing bacteria the ATP resources to maintain metabolic activity even in the absence of ammonia and oxygen, and to survive insults that would otherwise be fatal.
• The process of oxidation of ammonia to generate ATP has two steps. The first step is the oxidation of ammonia to hydroxylamine by ammonia monoxoygenase (Amo), followed by the conversion of hydroxylamine to nitrite by hydroxylamine oxidoreductase (Hao). Electrons from the second step (conversion of hydroxylamine to nitrite) are used to power the first step (oxidation of ammonia to hydroxylamine).
• If an ammonia oxidizing bacteria does not have hydroxylamine to generate electrons for Amo, then hydroxylamine is not available for Hao. For example, acetylene irreversibly inhibits the enzyme crucial for the first step in the oxidation of ammonia to nitrite, the oxidation of ammonia to hydroxylamine. Once AOB are exposed to acetylene, Amo is irreversibly inhibited and new enzyme must be synthesized before hydroxylamine can be generated. In a normal consortium biofilm habitat, AOB may share and receive hydroxylamine form other AOB (even different strains with different susceptibilities to inhibitors) and so the biofilm tends to be more resistant to inhibitors such as acetylene than an individual organism. AOB can use stored polyphosphate to synthesize new Amo, even in the absence of hydroxylamine.
• Any embodiment, preparation, composition, or formulation of ammonia oxidizing bacteria discussed herein may comprise, consist essentially of, or consist of optionally axenic ammonia oxidizing bacteria.
3. METHODS OF PRODUCING N. EUTROPHA
• Methods of culturing various Nitrosomonas species are known in the art. N. eutropha may be cultured, for example, using N. europaea medium as described in Example 2 below. Ammonia oxidizing bacteria may be cultured, for example, using the media described in Table 3 or Table 4, above.
• N. eutropha may be grown, for example, in a liquid culture or on plates. Suitable plates include 1.2% R2A agar, 1.2% agar, 1.2% agarose, and 1.2% agarose with 0.3 g/L pyruvate.
• In some embodiments, ammonia oxidizing bacteria, such as N. eutropha is cultured in organic free media. One advantage of using organic free media is that it lacks substrate for heterotrophic bacteria to metabolize except for that produced by the autotrophic bacteria. Another advantage of using the as-grown culture is that substantial nitrite accumulates in the culture media, and this nitrite is also inhibitory of heterotrophic bacteria and so acts as a preservative during storage.
• In some embodiments, ammonia oxidizing bacteria such as an N. eutropha strain with improved, e.g. optimized, properties is produced by an iterative process of propagation and selecting for desired properties. In some embodiments, the selection and propagation are carried out simultaneously. In some embodiments, the selection is carried out in a reaction medium (e.g., complete N. europaea medium) comprising 50 mM, 75 mM, 100 mM, 125 mM, 150 mM, 175 mM, 200 mM, 225 mM, 250 mM, 275 mM, or 300 mM NH₄ ⁺, e.g., at least 200 mM NH₄ ⁺. In some embodiments, the period of propagation and/or selection is at least 1, 2, 3, or 6 months. In embodiments, the period of propagation and/or selection is at least 1, 2, 4, 6, 8, or 10 years.
• In some aspects, the ammonia oxidizing bacteria, such as the N. eutropha are manufactured on a commercial scale. In some embodiments, commercial scale refers to a liquid culturing method with a culture medium volume of at least 10,000, 20,000, 30,000, 50,000, or 100,000 liters (L). In some embodiments, the bacteria are produced in a bioreactor. The bioreactor may maintain the bacteria at a constant temperature, e.g., about 26-30 degrees Celsius using, for example a thermal jacket for insulation, a temperature sensor, and a heating or cooling element. The bioreactor may have an apparatus for stirring the culture to improve distribution of nutrients like ammonia, urea, oxygen, carbon dioxide, and various minerals. The bioreactor may also have an inlet tube for addition of new medium, and an outlet tube for collection of cells. The bioreactor may also have an aerator for distributing oxygen and/or carbon dioxide to the culture. The bioreactor may be, e.g., a batch reactor, a fed batch reactor, or a continuous reactor. In some embodiments, commercial scale production of N. eutropha yields a batch of 1,000 to 100,000 L per day at about 10¹² CFU/liter and 1,000 to 100,000. The commercial scale production may yield e.g., a batch of 1,000-5,000, 5,000-10,000, 10,000-50,000, or 50,000-100,000 L/day. The commercial scale production may yield e.g., a batch of 1,000-5,000, 5,000-10,000, 10,000-50,000, or 50,000-100,000 L per batch. In some embodiments, the yield is at a concentration of at least 10¹⁰, 10¹¹, 2×10¹¹, 5×10¹¹, or 10¹², or about 10¹⁰-10¹¹, 10¹¹-10¹², 10¹²-10¹³, or 10¹³-10¹⁴ CFU/L
• In some embodiments, typically including commercial scale production, quality control (QC) testing steps are carried out. The general steps of QC typically comprise, 1) culturing N. eutropha, 2) performing a testing step on the culture or an aliquot thereof, and 3) obtaining a value from the testing step, and optionally: 4) comparing the obtained value to a reference value or range of acceptable values, and 5) if the obtained value meets the acceptable reference value or range, then classifying the culture as acceptable, and if the obtained value does not meet the acceptable reference value or range, then classifying the culture as unacceptable. If the culture is classified as acceptable, the culture may, e.g., be allowed to continue growing and/or may be harvested and added to a commercial product. If the culture is classified as unacceptable, the culture may, e.g., be safely disposed of or the defect may be remedied.
• The testing step may comprise measuring the optical density (OD) of the culture. OD is measured in a spectrophotometer, and provides information on the amount of light transmitted through the sample as distinguished from light absorbed or scattered. In some embodiments, the OD600 (e.g., optical density of light with a wavelength of 600 nm) may be determined. This measurement typically indicates the concentration of cells in the medium, where a higher optical density corresponds to a higher cell density.
• The testing step may comprise measuring the pH of the culture. The pH of an N. eutropha culture indicates the rate of nitrogen oxidation, and can also indicate whether the culture comprises a contaminating organism. pH may be measured using, e.g., a pH-sensing device comprising a electrode (such as a hydrogen electrode, quinhydron-Electrode, antimony electrode, glass electrode), a pH-sensing device comprising a semiconductor, or a color indicator reagent such as pH paper.
• In certain embodiments, producing the ammonia oxidizing bacteria such as N. eutropha comprises carrying out various quality control steps. For instance, one may test the medium in which the N. eutropha is grown, e.g., to determine whether it has an appropriate pH, whether it has a sufficiently low level of waste products, and/or whether it has a sufficiently high level or nutrients. One may also test for the presence of contaminating organisms. A contaminating organism is typically an organism other than an ammonia oxidizing bacteria such as N. eutropha, for instance an organism selected Microbacterium sp., Alcaligenaceae bacterium, Caulobacter sp., Burkodelia multivorans, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. One may test for contaminants by, e.g., extracting DNA, amplifying it, and sequencing a conserved gene such as 16S rRNA. One may also test for contaminants by plating culture on agar plates and observing colony morphology. N. eutropha typically forms red colonies, so non-red colonies are often indicative of contaminating organisms.
4. COMPOSITIONS COMPRISING AMMONIA OXIDIZING BACTERIA; COMPOSITIONS COMPRISING N. EUTROPHA
• The present disclosure provides, inter alia, compositions comprising ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, or a purified preparation of ammonia oxidizing bacteria e.g., a natural product, or a fortified natural product. The compositions comprising ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, or a purified preparation of ammonia oxidizing bacteria may be provided in a cosmetic product or a therapeutic product. The preparation may comprise, inter alia, at least one of ammonia, ammonium salts, and urea.
• The present disclosure provides, inter alia, compositions comprising N. eutropha, e.g., a purified preparation of an optimized N. eutropha. In some embodiments, the N. eutropha in the compositions has at least one property selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.
• In some aspects, the present disclosure provides compositions with a defined number of species. For instance, this disclosure provides a composition having N. eutropha and one other type of organism, and no other types of organism. In other examples, the composition has N. eutropha and 2, 3, 4, 5, 6, 7, 8, 9, or 10 other types of organism, and no other types of organism. The other type of organism in this composition may be, for instance, a bacterium, such as an ammonia-oxidizing bacterium. Suitable ammonia-oxidizing bacteria for this purpose include those in the genera Nitrosomonas, Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus, or Nitrosovibrio.
• In some embodiments, the composition comprising N. eutropha provides conditions that support N. eutropha viability. For instance, the composition may promote N. eutropha growth and metabolism or may promote a dormant state (e.g., freezing) from which viable N. eutropha can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that N. eutropha consumes, e.g., as ammonium, ammonia, urea, oxygen, carbon dioxide, or trace minerals. In some embodiments, the composition comprising ammonia oxidizing bacteria provides conditions that support ammonia oxidizing bacteria viability. For instance, the composition may promote ammonia oxidizing bacteria growth and metabolism or may promote a dormant state (e.g., freezing) or storage state as described herein, from which viable ammonia oxidizing bacteria can be recovered. When the composition promotes growth or metabolism, it may contain water and/or nutrients that ammonia oxidizing bacteria consumes, e.g., as ammonium ions, ammonia, urea, oxygen, carbon dioxide, or trace minerals.
• In some embodiments, one or more other organisms besides ammonia oxidizing bacteria may be included in the preparation of ammonia oxidizing bacteria. For example, an organism of the genus selected from the group consisting of Lactobacillus, Streptococcus, Bifidobacter, and combinations thereof, may be provided in the preparation of ammonia oxidizing bacteria. In some embodiments, the preparation may be substantially free of other organisms.
• Preparations of ammonia oxidizing bacteria may comprise between about between about 10⁸ to about 10¹⁴ CFU/L. The preparation may comprise at least about 10⁸, 10⁹, 10¹⁰, 10¹¹, 2×10¹¹, 5×10¹¹, 10¹², 2×10¹², 5×10¹², 10¹³, 2×10¹³, 5×10¹³, or 10¹⁴; or about 10⁸-10⁹, 10⁹-10¹⁰, 10¹⁰-10¹¹, 10¹¹-10¹², 10¹²-10¹³, or 10¹³-10¹⁴ CFU/L.
• In some embodiments, the preparation may comprise at least 10⁸, 10⁹, 10¹⁰, 10¹¹, 2×10¹¹, 5×10¹¹, 10¹², 2×10¹², 5×10¹², 10¹³, 2×10¹³, 5×10¹³, or 10¹⁴; or about 10⁸-10⁹, 10⁹-10¹⁰, 10¹⁰-10¹¹, 10¹¹-10¹², 10¹²-10¹³, or 10¹³-10¹⁴ CFU/ml.
• In some embodiments, the preparation may comprise between about 1×10⁹ to about 10×10⁹ CFU/L. In some embodiments, the preparation may comprise about 3×10¹⁰ CFU, e.g., 3×10¹⁰ CFU per day. In some embodiments, the preparation may comprise about 1×10⁹ to about 10×10⁹ CFU, e.g., about 1×10⁹ to about 10×10⁹ CFU per day.
• In some embodiments, the preparation of ammonia oxidizing bacteria may comprise between about 0.1 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria. In certain aspects, the preparation may comprise between about 50 mg and about 1000 mg of ammonia oxidizing bacteria. The preparation may comprise between about 0.1-0.5 mg, 0.2-0.7 mg, 0.5-1.0 mg, 0.5-2 mg, 0.5-5 mg, 2.5-5 mg, 2.5-7.0 mg, 5.0-10 mg, 7.5-15 mg, 10-15 mg, 15-20 mg, 15-25 mg, 20-30 mg, 25-50 mg, 25-75 mg, 50-75 mg, 50-100 mg, 75-100 mg, 100-200 mg, 200-300 mg, 300-400 mg, 400-500 mg, 500-600 mg, 600-700 mg, 700-800 mg, 800-900 mg, 900-1000 mg, 100-250 mg, 250-500 mg, 100-500 mg, 500-750 mg, 750-1000 mg, or 500-1000 mg.
• In some embodiments, the preparation of ammonia oxidizing bacteria my comprise a mass ratio of ammonia oxidizing bacteria to an excipient, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient in a range of about 0.1 grams per liter to about 1 gram per liter. The preparation may comprise a mass ratio of ammonia oxidizing bacteria to an excipient in a range of about 0.1-0.2, 0.2-0.3, 0.1-0.5, 0.2-0.7, 0.5-1.0, or 0.7-1.0 grams per liter.
• Advantageously, a formulation may have a pH that promotes AOB, e.g., N. eutropha viability, e.g., metabolic activity. Urea would hydrolyze to ammonia and would raise the pH to 7 to 8. AOB are very active at this pH range and would lower the pH to about 6 where the NH3 converts to ammonium and is unavailable. Lower pH levels, e.g. about pH 4, are also acceptable. The ammonia oxidizing bacteria, e.g., N. eutropha may be combined with one or more pharmaceutically or cosmetically acceptable excipients. In some embodiments, “pharmaceutically acceptable excipient” refers to a pharmaceutically-acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material. In some embodiments, each excipient is “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of a pharmaceutical formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit/risk ratio. See, Remington: The Science and Practice of Pharmacy, 21st ed.; Lippincott Williams & Wilkins: Philadelphia, Pa., 2005; Handbook of Pharmaceutical Excipients, 6th ed.; Rowe et al., Eds.; The Pharmaceutical Press and the American Pharmaceutical Association: 2009; Handbook of Pharmaceutical Additives, 3rd ed.; Ash and Ash Eds.; Gower Publishing Company: 2007; Pharmaceutical Preformulation and Formulation, 2nd ed.; Gibson Ed.; CRC Press LLC: Boca Raton, Fla., 2009.
• In some embodiments, a cosmetically acceptable excipient refers to a cosmetically acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material. In some embodiments, each excipient is cosmetically acceptable in the sense of being compatible with the other ingredients of a cosmetic formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit/risk ratio.
• While it is possible for the active ingredient, e.g., ammonia oxidizing bacteria, e.g., N. eutropha, to be administered alone, in many embodiments it present in a pharmaceutical formulation or composition. Accordingly, this disclosure provides a pharmaceutical formulation comprising ammonia oxidizing bacteria, for example, N. eutropha and a pharmaceutically acceptable excipient. Pharmaceutical compositions may take the form of a pharmaceutical formulation as described below.
• The pharmaceutical formulations described herein include those suitable for oral, parenteral (including subcutaneous, intradermal, intramuscular, intravenous, and intraarticular), inhalation (including fine particle dusts or mists which may be generated by means of various types of metered doses, pressurized aerosols, nebulizers or insufflators, and including intranasally or via the lungs), rectal and topical (including dermal, transdermal, transmucosal, buccal, sublingual, and intraocular) administration, although the most suitable route may depend upon, for example, the condition and disorder of the recipient.
• The formulations may conveniently be presented in unit dosage form and may be prepared by any of the methods known in the art of pharmacy. Typically, methods include the step of bringing the active ingredient (e.g., ammonia oxidizing bacteria, e.g., N. eutropha) into association with a pharmaceutical carrier which constitutes one or more accessory ingredients. In general the formulations are prepared by uniformly and intimately bringing into association the active ingredient with liquid carriers or finely divided solid carriers or both and then, if necessary, shaping the product into the desired formulation.
• Formulations may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of, e.g., N. eutropha; as a powder or granules; as a solution or a suspension in an aqueous liquid or a non-aqueous liquid; or as an oil-in-water liquid emulsion or a water-in-oil liquid emulsion. The active ingredient may also be presented as a bolus, electuary or paste. Various pharmaceutically acceptable carriers and their formulation are described in standard formulation treatises, e.g., Remington's Pharmaceutical Sciences by E. W. Martin. See also Wang, Y. J. and Hanson, M. A., Journal of Parenteral Science and Technology, Technical Report No. 10, Supp. 42:2 S, 1988.
• The ammonia oxidizing bacteria, e.g., N. eutropha compositions can, for example, be administered in a form suitable for immediate release or extended release. Suitable examples of sustained-release systems include suitable polymeric materials, for example semi-permeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules; suitable hydrophobic materials, for example as an emulsion in an acceptable oil; or ion exchange resins. Sustained-release systems may be administered orally; rectally; parenterally; intracisternally; intravaginally; intraperitoneally; topically, for example as a powder, ointment, gel, drop or transdermal patch; bucally; or as a spray.
• Preparations for administration can be suitably formulated to give controlled release of ammonia oxidizing bacteria, e.g., N. eutropha. For example, the pharmaceutical compositions may be in the form of particles comprising one or more of biodegradable polymers, polysaccharide jellifying and/or bioadhesive polymers, or amphiphilic polymers. These compositions exhibit certain biocompatibility features which allow a controlled release of an active substance. See U.S. Pat. No. 5,700,486.
• Exemplary compositions include suspensions which can contain, for example, microcrystalline cellulose for imparting bulk, alginic acid or sodium alginate as a suspending agent, methylcellulose as a viscosity enhancer, dicalcium phosphate, starch, magnesium stearate and/or lactose and/or other excipients, binders, extenders, disintegrants, diluents and lubricants, mannitol, lactose, sucrose and/or cyclodextrins. Also included in such formulations may be high molecular weight excipients such as celluloses (avicel) or polyethylene glycols (PEG). Such formulations can also include an excipient to aid mucosal adhesion such as hydroxy propyl cellulose (HPC), hydroxy propyl methyl cellulose (HPMC), sodium carboxy methyl cellulose (SCMC), maleic anhydride copolymer (e.g., Gantrez), and agents to control release such as polyacrylic copolymer (e.g. Carbopol 934). Lubricants, glidants, flavors, coloring agents and stabilizers may also be added for ease of fabrication and use. The surfactant may be a zwitterionic surfactant, a non-ionic surfactant, or an anionic surfactant.
• Excipients, such as surfactants that may be used with embodiments of the present disclosure may include one or more of cocamidopropyl betaine (ColaTeric COAB), polyethylene sorbitol ester (e.g., Tween 80), ethoxylated lauryl alcohol (RhodaSurf 6 NAT), sodium laureth sulfate/lauryl glucoside/cocamidopropyl betaine (Plantapon 611 L UP), sodium laureth sulfate (e.g., RhodaPex ESB 70 NAT), alkyl polyglucoside (e.g., Plantaren 2000 N UP), sodium laureth sulfate (Plantaren 200), Dr. Bronner's Castile soap, Dr. Bronner's Castile baby soap, Lauramine oxide (ColaLux Lo), sodium dodecyl sulfate (SDS), polysulfonate alkyl polyglucoside (PolySufanate 160 P), sodium lauryl sulfate (Stepanol-WA Extra K). and combinations thereof. Dr. Bronner's Castile soap and Dr. Bronner's baby soap comprises water, organic coconut oil, potassium hydroxide, organic olive oil, organic fair deal hemp oil, organic jojoba oil, citric acid, and tocopherol.
• In some embodiments, surfactants may be used with ammonia oxidizing bacteria in amounts that allow nitrite production to occur. In some embodiments, the preparation may have less than about 0.0001% to about 10% of surfactant. In some embodiments, the preparation may have between about 0.1% and about 10% surfactant. In some embodiments, the concentration of surfactant used may be between about 0.0001% and about 10%. In some embodiments, the preparation may be substantially free of surfactant.
• In some embodiments, the formulation, e.g., preparation, may include other components that may enhance effectiveness of ammonia oxidizing bacteria, or enhance a treatment or indication.
• In some embodiments, a chelator may be included in the preparation. A chelator may be a compound that may bind with another compound, e.g., a metal. The chelator may provide assistance in removing an unwanted compound from an environment, or may act in a protective manner to reduce or eliminate contact of a particular compound with an environment, e.g., ammonia oxidizing bacteria, e.g. a preparation of ammonia oxidizing bacteria, e.g., an excipient. In some embodiments, the preparation may be substantially free of chelator.
• Formulations may also contain anti-oxidants, buffers, bacteriostats that prevent the growth of undesired bacteria, solutes, and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example sealed ampoules and vials, and may be stored in a freeze-dried (lyophilised) condition requiring only the addition of a sterile liquid carrier, for example saline or water-for-injection, immediately prior to use. Extemporaneous solutions and suspensions may be prepared from powders, granules and tablets of the kind previously described. Exemplary compositions include solutions or suspensions which can contain, for example, suitable non-toxic, pharmaceutically acceptable diluents or solvents, such as mannitol, 1,3-butanediol, water, Ringer's solution, an isotonic sodium chloride solution, or other suitable dispersing or wetting and suspending agents, including synthetic mono- or diglycerides, and fatty acids, including oleic acid, or Cremaphor. An aqueous carrier may be, for example, an isotonic buffer solution at a pH of from about 3.0 to about 8.0, a pH of from about 3.5 to about 7.4, for example from 3.5 to 6.0, for example from 3.5 to about 5.0. Useful buffers include sodium citrate-citric acid and sodium phosphate-phosphoric acid, and sodium acetate/acetic acid buffers. The composition in some embodiments does not include oxidizing agents.
• Excipients that can be included are, for instance, proteins, such as human serum albumin or plasma preparations. If desired, the pharmaceutical composition may also contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate. In some embodiments, excipients, e.g., a pharmaceutically acceptable excipient or a cosmetically acceptable excipient, may comprise an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener. In some embodiments, the preparation may be substantially free of excipients.
• In some embodiments, the preparation may be substantially free of one or more of the compounds or substances listed in the disclosure.
• Exemplary compositions for aerosol administration include solutions in saline, which can contain, for example, benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, and/or other solubilizing or dispersing agents. Conveniently in compositions for aerosol administration the ammonia oxidizing bacteria, e.g., N. eutropha is delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoro-methane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin can be formulated to contain a powder mix of the N. eutropha and a suitable powder base, for example lactose or starch. In certain embodiments, N. eutropha is administered as an aerosol from a metered dose valve, through an aerosol adapter also known as an actuator. Optionally, a stabilizer is also included, and/or porous particles for deep lung delivery are included (e.g., see U.S. Pat. No. 6,447,743).
• Formulations may be presented with carriers such as cocoa butter, synthetic glyceride esters or polyethylene glycol. Such carriers are typically solid at ordinary temperatures, but liquefy and/or dissolve at body temperature to release the ammonia oxidizing bacteria, e.g., N. eutropha.
• Exemplary compositions for topical administration include a topical carrier such as Plastibase (mineral oil gelled with polyethylene). In some aspects, the composition and/or excipient may be in the form of one or more of a liquid, a solid, or a gel. For example, liquid suspensions may include, but are not limited to, water, saline, phosphate-buffered saline, or an ammonia oxidizing storage buffer. Gel formulations may include, but are not limited to agar, silica, polyacrylic acid (for example Carbopol®), carboxymethyl cellulose, starch, guar gum, alginate or chitosan. In some embodiments, the formulation may be supplemented with an ammonia source including, but not limited to ammonium chloride or ammonium sulfate.
• In some embodiments, an ammonia oxidizing bacteria, e.g., N. eutropha composition is formulated to improve NO penetration into the skin. A gel-forming material such as KY jelly or various hair gels would present a diffusion barrier to NO loss to ambient air, and so improve the skin's absorption of NO. The NO level in the skin will generally not greatly exceed 20 nM/L because that level activates GC and would cause local vasodilatation and oxidative destruction of excess NO.
• It should be understood that in addition to the ingredients particularly mentioned above, the formulations as described herein may include other agents conventional in the art having regard to the type of formulation in question.
• The formulation, e.g., preparation, e.g., composition may be provided in a container, delivery system, or delivery device, having a weight, including or not including the contents of the container, that may be less than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 grams.
• Suitable unit dosage formulations are those containing an effective dose, as hereinbefore recited, or an appropriate fraction thereof, of ammonia oxidizing bacteria, e.g., N. eutropha.
• A therapeutically effective amount of ammonia oxidizing bacteria, e.g., N. eutropha may be administered as a single pulse dose, as a bolus dose, or as pulse doses administered over time. Thus, in pulse doses, a bolus administration of ammonia oxidizing bacteria, e.g., N. eutropha is provided, followed by a time period wherein ammonia oxidizing bacteria, e.g., N. eutropha is administered to the subject, followed by a second bolus administration. In specific, non-limiting examples, pulse doses are administered during the course of a day, during the course of a week, or during the course of a month.
• In some embodiments, a preparation of ammonia oxidizing bacteria, e.g., a formulation, e.g., a composition, may be applied for a pre-determined number of days. This may be based, for example, at least in part, on the severity of the condition or disease, the response to the treatment, the dosage applied and the frequency of the dose. For example, the preparation may be applied for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days, for about 1 month, for about 2 months, for about 3 months. In some embodiments, the ammonia oxidizing bacteria is administered for an indefinite period of time, e.g., greater than one year, greater than 5 years, greater than 10 years, greater than 15 years, greater than 30 years, greater than 50 years, greater than 75 years. In certain aspects, the preparation may be applied for about 16 days.
• In some embodiments, a preparation of ammonia oxidizing bacteria, e.g., a formulation, e.g., a composition, may be applied a pre-determined number of times per day. This may be based, for example, at least in part, on the severity of the condition or disease, the response to the treatment, the dosage applied and the frequency of the dose. For example, the preparation may be applied 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 times per day.
• In some embodiments, the preparation may be applied one time per day. In other embodiments, the preparation may be applied two times per day. In some embodiments, the preparation may be applied a first pre-determined amount for a certain number of days, and a second pre-determined amount for a certain subsequent number of days. In some embodiments, the preparation may be applied for about 16 days.
• Consumer Products
• Ammonia oxidizing bacteria, e.g., N. eutropha may be associated with a variety of consumer products, and examples of such products are set out below. In some embodiments, the ammonia oxidizing bacteria, e.g., N. eutropha associated with a product is admixed with the product, for example, spread evenly throughout the product, and in some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha associated with a product is layered on the product.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a powder. Powders are typically small particulate solids that are not attached to each other and that can flow freely when tilted. Exemplary powders for consumer use include talcum powder and some cosmetics (e.g., powder foundation).
• In some embodiments, the ammonia oxidizing bacteria is associated with a cosmetic. The cosmetic may be a substance for topical application intended to alter a person's appearance, e.g., a liquid foundation, a powder foundation, blush, or lipstick. The cosmetic may be any substance recited in the Food and Drug Administration regulations, e.g., under 21 C.F.R. §720.4.
• The cosmetic may be at least one of a baby product, e.g., a baby shampoo, a baby lotion, a baby oil, a baby powder, a baby cream; a bath preparation, e.g., a bath oil, a tablet, a salt, a bubble bath, a bath capsule; an eye makeup preparation, e.g., an eyebrow pencil, an eyeliner, an eye shadow, an eye lotion, an eye makeup remover, a mascara; a fragrance preparation, e.g., a colognes, a toilet water, a perfume, a powder (dusting and talcum), a sachet; hair preparations, e.g., hair conditioners, hair sprays, hair straighteners, permanent waves, rinses, shampoos, tonics, dressings, hair grooming aids, wave sets; hair coloring preparations, e.g., hair dyes and colors, hair tints, coloring hair rinses, coloring hair shampoos, hair lighteners with color, hair bleaches; makeup preparations, e.g., face powders, foundations, leg and body paints, lipstick, makeup bases, rouges, makeup fixatives; manicuring preparations, e.g., basecoats and undercoats, cuticle softeners, nail creams and lotions, nail extenders, nail polish and enamel, nail polish and enamel removers; oral hygiene products, e.g., dentrifices, mouthwashes and breath fresheners; bath soaps and detergents, deodorants, douches, feminine hygiene deodorants; shaving preparations, e.g., aftershave lotions, beard softeners, talcum, preshave lotions, shaving cream, shaving soap; skin care preparations, e.g., cleansing, depilatories, face and neck, body and hand, foot powders and sprays, moisturizing, night preparations, paste masks, skin fresheners; and suntan preparations, e.g., gels, creams, and liquids, and indoor tanning preparations.
• In some embodiments, the formulations, compositions, or preparations described herein, may comprise, be provided as, or disposed in at least one of a baby product, e.g., a baby shampoo, a baby lotion, a baby oil, a baby powder, a baby cream; a bath preparation, e.g., a bath oil, a tablet, a salt, a bubble bath, a bath capsule; a powder (dusting and talcum), a sachet; hair preparations, e.g., hair conditioners, rinses, shampoos, tonics, face powders, cuticle softeners, nail creams and lotions, oral hygiene products, mouthwashes, bath soaps, douches, feminine hygiene deodorants; shaving preparations, e.g., aftershave lotions, skin care preparations, e.g., cleansing, face and neck, body and hand, foot powders and sprays, moisturizing, night preparations, paste masks, skin fresheners; and suntan preparations, e.g., gels, creams, and liquids.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a cosmetic. The cosmetic may be a substance for topical application intended to alter a person's appearance, e.g., a liquid foundation, a powder foundation, blush, or lipstick. Other components may be added to these cosmetic preparations as selected by one skilled in the art of cosmetic formulation such as, for example, water, mineral oil, coloring agent, perfume, aloe, glycerin, sodium chloride, sodium bicarbonate, pH buffers, UV blocking agents, silicone oil, natural oils, vitamin E, herbal concentrates, lactic acid, citric acid, talc, clay, calcium carbonate, magnesium carbonate, zinc oxide, starch, urea, and erythorbic acid, or any other excipient known by one of skill in the art, including those disclosed herein.
• In some embodiments, the preparation may be disposed in, or provided as, a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a cream. The cream may be a fluid comprising a thickening agent, and generally has a consistency that allows it to be spread evenly on the skin. Exemplary creams include moisturizing lotion, face cream, and body lotion.
• In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a stick. A stick is typically a solid that, when placed in contact with a surface, transfers some of the stick contents to the surface. Exemplary sticks include deodorant stick, lipstick, lip balm in stick form, and sunscreen applicator sticks.
• In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with an aerosol. An aerosol is typically a colloid of fine solid particles or fine liquid droplets, in a gas such as air. Aerosols may be created by placing the N. eutropha (and optionally carriers) in a vessel under pressure, and then opening a valve to release the contents. The container may be designed to only exert levels of pressure that are compatible with N. eutropha viability. For instance, the high pressure may be exerted for only a short time, and/or the pressure may be low enough not to impair viability. Examples of consumer uses of aerosols include for sunscreen, deodorant, perfume, hairspray, and insect repellant.
• In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a salve. A salve may be a topically applied agent with a liquid or cream-like consistency, intended to protect the skin or promote healing. Examples of salves include burn ointments and skin moisturizers.
• In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is associated with a wipe. A wipe may be a flexible material suitable for topically applying a liquid or cream onto skin. The wipe may be, e.g., paper-based or cloth based. Exemplary wipes include tissues and wet wipes.
• The compositions comprising ammonia oxidizing bacteria, e.g., N. eutropha may also comprise one or more of a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.
• For instance, the moisturizing agent may be an agent that reduces or prevents skin dryness. Exemplary moisturizing agents include humectants (e.g., urea, glycerin, alpha hydroxy acids and dimethicone) and emollients (e.g., lanolin, mineral oil and petrolatum). Moisturizing agents may be included, e.g., in ammonia oxidizing bacteria, e.g., N. eutropha-containing creams, balms, lotions, or sunscreen.
• A deodorizing agent may be an agent that reduces unwanted odors. A deodorizing agent may work by directly neutralizing odors, preventing perspiration, or preventing the growth of odor-producing bacteria. Exemplary deodorizing agents include aluminum salts (e.g., aluminum chloride or aluminum chlorohydrate), cyclomethicone, talc, baking soda, essential oils, mineral salts, hops, and witch hazel. Deodorizing agents are typically present in spray or stick deodorants, and can also be found in some soaps and clothing.
• An insect repellant may be an agent that can be applied to surfaces (e.g., skin) that discourage insects and other arthropods from lighting on the surface. Insect repellants include DEET (N,N-diethyl-m-toluamide), p-menthane-3,8-diol (PMD), icaridin, nepetalactone, citronella oil, neem oil, bog myrtle, dimethyl carbate, Tricyclodecenyl allyl ether, and IR3535 (3-[N-Butyl-N-acetyl]-aminopropionic acid, ethyl ester).
• A cleansing agent may be an agent that removes dirt or unwanted bacteria from a surface like skin. Exemplary cleansing agents include bar soaps, liquid soaps, and shampoos.
• A UV-blocking agent may be an agent that can be applied to a surface to reduce the amount of ultraviolet light the surface receives. A UV-blocking agent may block UV-A and/or UV-B rays. A UV blocking agent can function by absorbing, reflecting, or scattering UV. Exemplary UV-blocking agents include absorbers, e.g., homosalate, octisalate (also called octyl salicylate), octinoxate (also called octyl methoxycinnamate or OMC), octocrylene, oxybenzone, and avobenzone, and reflectors (e.g., titanium dioxide and zinc oxide). UV-blocking agents are typically presents in sunscreens, and can also be found in skin creams and some cosmetics.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with a conditioner. Conditioner generally refers to a substance with cream-like consistency that can be applied to hair to improve its appearance, strength, or manageability.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with cloth. Cloth generally refers to a flexible material suitable to be made into clothing, e.g., having enough material strength to withstand everyday motion by a wearer. Cloth can be fibrous, woven, or knit; it can be made of a naturally occurring material or a synthetic material. Exemplary cloth materials include cotton, flax, wool, ramie, silk, denim, leather, nylon, polyester, and spandex, and blends thereof.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with yarn. Yarn generally refers to a long, thin spun flexible material that is suitable for knitting or weaving. Yarn can be made of, e.g., wool, cotton, polyester, and blends thereof.
• In some embodiments, ammonia oxidizing bacteria, e.g., N. eutropha is associated with thread. Thread generally refers to a long, thin spun flexible material that is suitable for sewing. Thread generally has a thinner diameter than yarn. Thread can be made of, e.g., cotton, polyester, nylon, silk, and blends thereof.
• Articles of clothing such as, for example, shoes, shoe inserts, pajamas, sneakers, belts, hats, shirts, underwear, athletic garments, helmets, towels, gloves, socks, bandages, and the like, may also be treated with ammonia oxidizing bacteria, e.g., N. eutropha. Bedding, including sheets, pillows, pillow cases, and blankets may also be treated with ammonia oxidizing bacteria, e.g., N. eutropha. In some embodiments, areas of skin that cannot be washed for a period of time may also be contacted with ammonia oxidizing bacteria, e.g., N. eutropha. For example, skin enclosed in orthopedic casts which immobilize injured limbs during the healing process, and areas in proximity to injuries that must be kept dry for proper healing such as stitched wounds may benefit from contact with the ammonia oxidizing bacteria, e.g., N. eutropha.
• In some aspects, the present disclosure provides a wearable article comprising an N. eutropha strain as described herein. A wearable article may be a light article that can be closely associated with a user's body, in a way that does not impede ambulation. Examples of wearable articles include a wristwatch, wristband, headband, hair elastic, hair nets, shower caps, hats, hairpieces, and jewelry. The wearable article comprising an ammonia oxidizing bacteria, e.g., N. eutropha strain described herein may provide, e.g., at a concentration that provides one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth.
• In some embodiments, the ammonia oxidizing bacteria, e.g., N. eutropha is associated with a product intended to contact the hair, for example, a brush, comb, shampoo, conditioner, headband, hair elastic, hair nets, shower caps, hats, and hairpieces. Nitric oxide formed on the hair, away from the skin surface, may be captured in a hat, scarf or face mask and directed into inhaled air.
• Articles contacting the surface of a human subject, such as a diaper, may be associated with ammonia oxidizing bacteria, e.g., N. eutropha. Because diapers are designed to hold and contain urine and feces produced by incontinent individuals, the urea in urine and feces can be hydrolyzed by skin and fecal bacteria to form free ammonia which is irritating and may cause diaper rash. Incorporation of bacteria that metabolize urea into nitrite or nitrate, such as ammonia oxidizing bacteria, e.g., N. eutropha, may avoid the release of free ammonia and may release nitrite and ultimately NO which may aid in the maintenance of healthy skin for both children and incontinent adults. The release of nitric oxide in diapers may also have anti-microbial effects on disease causing organisms present in human feces. This effect may continue even after disposable diapers are disposed of as waste and may reduce the incidence of transmission of disease through contact with soiled disposable diapers
• In some embodiments, the product comprising ammonia oxidizing bacteria, e.g., N. eutropha is packaged. The packaging may serve to compact the product or protect it from damage, dirt, or degradation. The packaging may comprise, e.g., plastic, paper, cardboard, or wood. In some embodiments the packaging is impermeable to bacteria. In some embodiments the packaging is permeable to oxygen and/or carbon dioxide.
5. METHODS OF TREATMENT WITH N. EUTROPHA
• The present disclosure provides various methods of treating diseases and conditions using ammonia oxidizing bacteria, e.g., N. eutropha. The ammonia oxidizing bacteria, e.g., N. eutropha that may be used to treat diseases and conditions include all the ammonia oxidizing bacteria, e.g., N. eutropha compositions described in this application, e.g. a purified preparation of optimized ammonia oxidizing bacteria, e.g., N. eutropha, e.g. those in Section 2 above, for instance strain D23.
• For instance, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), an optionally axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to SEQ ID NO: 1; an optionally axenic composition of N. eutropha comprising a nucleic acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to any one of the strain D23 nucleic acids of Table 1. In embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the strain D23 nucleic acids of Table 1. In embodiments, the N. eutropha comprises one or more nucleic acids of FIGS. 6-8. As a further example, this disclosure provides uses, for treating a condition or disease, an optionally axenic composition of N. eutropha comprising an amino acid sequence at least about 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 99.5% identical to any one of the strain D23 protein sequences of Table 1. In embodiments, the N. eutropha comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the strain D23 protein sequences of Table 1. In embodiments, the N. eutropha comprises one or more proteins encoded by the nucleic acids of FIGS. 6-8. The N. eutropha of this paragraph may be used to treat, e.g., diabetic ulcers, e.g., diabetic foot ulcers, chronic wounds, acne, rosacea, eczema, or psoriasis.
• In certain embodiments, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), an optionally axenic composition of N. eutropha having one or more of: (1) an optimized growth rate, (2) an optimized NH₄ ⁺ oxidation rate, (3) an optimized resistance to NH₃, (4) an optimized resistance to, NH₄ ⁺, and (5) an optimized resistance to, NO₂ ⁻. For instance, the axenic N. eutropha composition may have properties (1) and (2); (2) and (3); (3) and (4); or (4) and (5) from the list at the beginning of this paragraph. As another example, the axenic N. eutropha composition may have properties (1), (2), and (3); (1), (2), and (4); (1), (2), and (5); (1), (3), and (4); (1), (3), and (5); (1), (4), and (5); (2), (3), and (4); (2), (3), and (5), or (3), (4), and (5) from the list at the beginning of this paragraph. As a further example, the optionally axenic N. eutropha composition may have properties (1), (2), (3), and (4); (1), (2), (3), and (5); (1), (2), (4), and (5); (1), (3), (4), and (5); or (2), (3), (4), and (5) from the list at the beginning of this paragraph. In some embodiments, the axenic N. eutropha composition has properties (1), (2), (3), (4), and (5) from the list at the beginning of this paragraph. The N. eutropha of this paragraph may be used to treat, e.g., diabetic ulcers, e.g., diabetic foot ulcers, chronic wounds, acne, rosacea, eczema, or psoriasis.
• In some embodiments, optionally axenic N. eutropha (e.g., strain D23) are used to treat a subject. Subjects may include an animal, a mammal, a human, a non-human animal, a livestock animal, or a companion animal.
• In some embodiments, optionally axenic N. eutropha described herein (e.g., the N. eutropha described in this Section and in Section 2 above, e.g., strain D23) are used to inhibit the growth of other organisms. For instance, N. eutropha D23 is well-adapted for long-term colonization of human skin, and in some embodiments it out-competes other bacteria that are undesirable on the skin. Undesirable skin bacteria include, e.g., those that can infect wounds, raise the risk or severity of a disease, or produce odors. Certain undesirable skin bacteria include S. aureus, P. aeruginosa, S. pyogenes, and A. baumannii. The N. eutropha described herein may out-compete other organisms by, e.g., consuming scarce nutrients, or generating byproducts that are harmful to other organisms, e.g., changing the pH of the skin to a level that is not conducive to the undesirable organism's growth.
• Accordingly, the present disclosure provides, inter alia, a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a human in need thereof an effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in inhibiting microbial growth on a subject's skin. Likewise, the present disclosure provides a use of optionally axenic N. eutropha (e.g., strain D23) in the manufacture of a medicament for inhibiting microbial growth on a subject's skin.
• The present disclosure also provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23) in close proximity to the subject. Similarly, the present disclosure provides optionally axenic N. eutropha (e.g., strain D23) as described herein for use in supplying nitric oxide to a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha (e.g., strain D23) in the manufacture of a medicament or composition suitable for position in close proximity to a subject.
• The present disclosure also provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in reducing body odor in a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament or composition for reducing body odor.
• The present disclosure also provides a method of treating or preventing a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of optionally axenic N. eutropha bacteria described herein (e.g., strain D23). Similarly, the present disclosure provides a topical formulation of optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a disease associated with low nitrite levels. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a topical medicament for treating a disease associated with low nitrite levels.
• The present disclosure also provides a method of treating or preventing a skin disorder or skin infection, comprising topically administering to a subject in need thereof a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a skin disorder in a subject. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament for treating skin disorder. In embodiments, the skin disorder is acne, rosacea, eczema, psoriasis, or urticaria; the skin infection is impetigo.
• While not wishing to be bound by theory, it is proposed that treatment of acne with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve the downregulation of inflammation due to NO generation; and/or limiting and/or inhibiting the spread and proliferation of Propionibacterium acnes associated with acne vulgaris through acidified nitrite and NO production.
• For instance, the disclosure provides uses, for treating a condition or disease (e.g., inhibiting microbial growth on a subject's skin), a composition of ammonia oxidizing bacteria. In embodiments, the ammonia oxidizing bacteria may be used to treat, e.g., chronic wounds, acne, rosacea, eczema, psoriasis, uticaria, skin infections, or diabetic ulcers, e.g., diabetic foot ulcers.
• The systems and methods of the present disclosure may provide for, or contain contents, to be useful for treating or preventing a skin disorder, treating or preventing a disease or condition associated with low nitrite levels, a treating or preventing body odor, treating to supply nitric oxide to a subject, or treating to inhibit microbial growth.
• The systems and methods of the present disclosure may provide for reducing an amount of undesirable bacteria from an environment, e.g., a surface of a subject.
• The systems and methods of the present disclosure may provide for, or contain contents, to be useful in a treatment of at least one of HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.
• The systems and methods of the present disclosure may provide for, or contain contents, to be useful in a treatment of at least one of acne, eczema, psoriasis, uticaria, rosacea, skin infections and wounds, e.g., an infected wound.
• In some embodiments, ammonia oxidizing bacteria may be used to treat a subject. Subjects may include an animal, a mammal, a human, a non-human animal, a livestock animal, or a companion animal.
• In some embodiments, ammonia oxidizing bacteria described herein are used to inhibit the growth of other organisms. For instance, ammonia oxidizing bacteria may be well-adapted for long-term colonization of human skin, and in some embodiments it out-competes other bacteria that are undesirable on the skin. Undesirable skin bacteria include, e.g., those that can infect wounds, raise the risk or severity of a disease, or produce odors. Undesirable bacteria may be referred to as pathogenic bacteria. Certain undesirable skin bacteria include Staphylococcus aureus (S. aureus), e.g., methicillin resistant Staphylococcus aureus Pseudomonas aeruginosa (P. aeruginosa), Streptococcus pyogenes (S. pyogenes), Acinetobacter baumannii (A. baumannii), Propionibacteria, and Stenotrophomonas. The ammonia oxidizing bacteria described herein may out-compete other organisms by, e.g., consuming scarce nutrients, or generating byproducts that are harmful to other organisms, e.g., changing the pH of the skin to a level that is not conducive to the undesirable organism's growth.
• Accordingly, the present disclosure provides, inter alia, a method of inhibiting microbial growth on a subject's skin, comprising topically administering to a human in need thereof an effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in inhibiting microbial growth on a subject's skin. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria in the manufacture of a medicament for inhibiting microbial growth on a subject's skin.
• The present disclosure provides, inter alia, a method of changing a composition of a skin microbiome, e.g., modulating a composition of a skin microbiome, e.g., modulating or changing the proportions of the skin microbiome, in an environment, e.g., a surface, e.g., a surface of a subject. The method may comprise administering, e.g., applying, a preparation comprising ammonia oxidizing bacteria to an environment, e.g., a surface, e.g., a surface of a subject. In some embodiments, the amount and frequency of administration, e.g., application, may be sufficient to reduce the proportion of pathogenic bacteria on the surface of the skin. In some embodiments, the subject may be selected on the basis of the subject being in need of a reduction in the proportion of pathogenic bacteria on the surface of the skin.
• The present disclosure may further provide obtaining a sample from the surface of the skin, and isolating DNA of bacteria in the sample. Sequencing of the DNA of bacteria in the sample may also be performed to determine or monitor the amount or proportion of bacteria in a sample of a subject.
• The present disclosure may also provide for increasing the proportion of non-pathogenic bacteria on the surface. In some embodiments, the non-pathogenic bacteria may be commensal non-pathogenic bacteria. In some embodiments, the non-pathogenic bacteria may be of the Staphylococcus genus. In some embodiments, the non-pathogenic bacteria may be Staphylococcus epidermidis. In some embodiments, the non-pathogenic bacteria that is increased in proportion may be of the Staphylococcus genus, comprising at least about 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% Staphylococcus epidermidis.
• The increase in the proportion of non-pathogenic bacteria may occur with a pre-determined period of time, e.g., in less than 1 day, 2 days, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, or 4 weeks, or in less than 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days.
• The increase in the proportion of Staphylococcus bacteria, e.g., Staphylococcus epidermidis, may be observed in less than about 3 weeks, e.g., about 16 days, e.g., about 2 weeks.
• The present disclosure may provide for decreasing the proportion of pathogenic bacteria, e.g., potentially pathogenic bacteria, e.g., disease-associated bacteria on the surface. In some embodiments, the pathogenic bacteria may be Propionibacteria. In some embodiments, the pathogenic bacteria may be Stenotrophomonas.
• The decrease in the proportion of pathogenic bacteria may occur with a pre-determined period of time, e.g., in less than 1 day, 2 days, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, or 4 weeks, or in less than 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days.
• The decrease in the proportion of Propionibacteria bacteria and/or Stenotrophomonas may be observed in less than about 3 weeks, e.g., about 16 days, e.g., about 2 weeks.
• The present disclosure also provides a method of supplying nitric oxide to a subject, comprising positioning an effective dose of ammonia oxidizing bacteria described herein in close proximity to the subject. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in supplying nitric oxide to a subject. Likewise, the present disclosure provides a use of in the manufacture of a medicament or composition suitable for position in close proximity to a subject.
• The present disclosure also provides a method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of ammonia oxidizing bacteria described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in reducing body odor in a subject. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament or composition for reducing body odor.
• The present disclosure also provides a method of treating or preventing a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of ammonia oxidizing bacteria described herein. Similarly, the present disclosure provides a topical formulation of ammonia oxidizing bacteria as described herein for use in treating a disease associated with low nitrite levels. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a topical medicament for treating a disease associated with low nitrite levels.
• The present disclosure also provides a method of treating or preventing a skin disorder or skin infection, comprising topically administering to a subject in need thereof a therapeutically effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in treating a skin disorder in a subject. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament for treating skin disorder. In embodiments, the skin disorder is acne, rosacea, eczema, psoriasis, or urticaria; the skin infection is impetigo.
• While not wishing to be bound by theory, it is proposed that treatment of rosacea with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation due to NO generation. This may be due to expression of Kazal-type KLK5/KLK7 inhibitor(s) that may reduce formation of the human cathelicidin peptide LL-37 from its precursor propeptide hCAP18.
• While not wishing to be bound by theory, it is proposed that treatment of eczema and/or atopic dermatitis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation; and/or limiting and/or inhibiting the spread and proliferation of S. aureus and other skin pathogens often associated with very high colonization rates and skin loads in atopic dermatitis through acidified nitrite and NO production.
• While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation and reduction in formation of human cathelicidin peptide LL-37.
• While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve downregulation of inflammation due to NO generation.
• While not wishing to be bound by theory, it is proposed that treatment of impetigo or other skin and soft tissue infections with a therapeutically effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23) may involve limiting and/or inhibiting the spread and proliferation of S. aureus and S. pyogenes.
• The present disclosure also provides a method of promoting wound healing, comprising administering to a wound an effective dose of optionally axenic N. eutropha bacteria as described herein (e.g., strain D23). Similarly, the present disclosure provides optionally axenic N. eutropha as described herein (e.g., strain D23) for use in treating a wound. Likewise, the present disclosure provides a use of optionally axenic N. eutropha as described herein (e.g., strain D23) in the manufacture of a medicament or a composition for treating a wound.
• Optionally axenic N. eutropha as described herein (e.g., strain D23) may be used to promote wound healing in a patient that has an impaired healing ability, e.g., a diabetic patient.
• In some embodiments, this disclosure provides methods of using optionally axenic N. eutropha as described herein (e.g., strain D23) to prevent a disease or disorder, e.g., a skin disorder. Prevention, in certain embodiments, means reducing the risk of a subject developing a disease, compared to a similar untreated subject. The risk need not be reduced to zero.
• Individuals having a reduced bathing frequency, such as astronauts, submarine crew members, military personnel during a campaign, civilian workers in remote locations, refugees, bedridden individuals and many others may maintain healthier skin by maintaining N. eutropha on the skin. With regard to bedridden individuals, the N. eutropha in some embodiments reduces the frequency or severity of bed sores by augmenting inadequate circulation.
• It is appreciated that many modern degenerative diseases may be caused by a lack of NO species, and that AOB on the external skin can supply those species by diffusion, and that application of AOB to the skin resolves long standing medical conditions. In certain embodiments, AOB are applied to a subject to offset modern bathing practices, especially with anionic detergents remove AOB from the external skin.
• One suitable method of topical application to apply sufficient N. eutropha and then wear sufficient clothing so as to induce sweating. However, many people will want to derive the benefits of AOB while maintaining their current bathing habits, in which case, a culture of the bacteria can be applied along with sufficient substrate for them to produce NO. A nutrient solution approximating the inorganic composition of human sweat can be used for this purpose. Using bacteria adapted to media approximating human sweat minimizes the time for them to adapt when applied. Since sweat evaporates once excreted onto the skin surface, using a culture media that has a higher ionic strength is desirable. A concentration approximately twice that of human sweat is suitable, but other conditions are also contemplated. AOB's nutritional needs are typically met with NH₃ or urea, O₂, CO₂, and minerals. In some embodiments, the substrate comprises trace minerals including iron, copper, zinc, cobalt, molybdenum, manganese, sodium, potassium, calcium, magnesium, chloride, phosphate, sulfate, or any combination thereof.
• In some embodiments, the present disclosure provides a method of treating a wound by applying a bandage comprising N. eutropha to the wound. Also provided are methods of producing such a bandage. The bandage may comprise, for example, an adhesive portion to affix the bandage to undamaged skin near the wound and a soft, flexible portion to cover or overlay the wound. In some embodiments, the bandage contains no other organisms but N. eutropha. The bandage may be made of a permeable material that allows gasses like oxygen and carbon dioxide to reach the N. eutropha when the bandage is applied to the wound. In certain embodiments, the bandage comprises nutrients for N. eutropha such as ammonium, ammonia, urea, or trace minerals. In certain embodiments, the bandage comprises an antibiotic to which the N. eutropha is resistant. The antibiotic resistance may arise from one or more endogenous resistance gene or from one or more transgenic.
• In some embodiments, the N. eutropha is administered at a dose of about 10⁸-10⁹ CFU, 10⁹-10¹⁰ CFU, 10¹⁰-10¹¹ CFU, or 10¹¹-10¹² CFU per application. In some embodiments, the N. eutropha is administered topically at a dose of about 10¹⁰-10¹¹ CFU, e.g., about 1×10¹⁰-5×10¹⁰, 1×10¹⁰-3×10¹⁰, or 1×10¹⁰-2×10¹⁰ CFU.
• In some embodiments, the N. eutropha is administered in a volume of about 1-2, 2-5, 5-10, 10-15, 12-18, 15-20, 20-25, or 25-50 ml per dose. In some embodiments, the solution is at a concentration of about 10⁸-10⁹, 10⁹-10¹⁰, or 10¹⁰-10¹¹ CFUs/ml. In some embodiments, the N. eutropha is administered as two 15 ml doses per day, where each dose is at a concentration of 10⁹ CFU/ml.
• In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered once, twice, three, or four times per day. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered once, twice, three, four, five, or six times per week. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered shortly after bathing. In some embodiments, ammonia oxidizing bacteria, e.g., the N. eutropha is administered shortly before sleep.
• In certain aspects, the present disclosure provides combination therapies comprising ammonia oxidizing bacteria, e.g., a N. eutropha and a second therapeutic. For instance, the disclosure provides physical admixtures of the two (or more) therapies are physically admixed. In other embodiments, the two (or more) therapies are administered in combination as separate formulation. The second therapy may be, e.g., a pharmaceutical agent, surgery, or any other medical approach that treats the relevant disease or disorder. The following paragraphs describe combination therapies capable of treating diabetic ulcers, chronic wounds, acne, rosacea, eczema, and psoriasis.
• For instance, in a combination therapy capable of treating diabetic ulcers, the second therapy may comprise, e.g., a wound dressing (e.g., absorptive fillers, hydrogel dressings, or hydrocolloids), angiotensin, angiotensin analogues, platelet-rich fibrin therapy, hyperbaric oxygen therapy, negative pressure wound therapy, debridement, drainage, arterial revascularization, hyperbaric oxygen therapy, low level laser therapy, and gastrocnemius recession. The combination therapy may comprise one or more of the above-mentioned treatments.
• In a combination therapy capable of treating chronic wounds, the second therapy may comprise, e.g., an antibiotic (e.g., topical or systemic, and bacteriocidal or bacteriostatic) such as Penicillins, cephalosporins, polymyxins, rifamycins, lipiarmycins, quinolones, sulfonamides, macrolides, lincosamides, tetracyclines, cyclic lipopeptides, glycylcyclines, oxazolidinones, and lipiarmycins; angiotensin, angiotensin analogues; debridement; drainage; wound irrigation; negative pressure wound therapy; application of heat; arterial revascularization; hyperbaric oxygen therapy; antioxidants such as ascorbic acid, glutathione, lipoic acid, carotenes, α-tocopherol, or ubiquinol; low level laser therapy; gastrocnemius recession; growth factors such as vascular endothelial growth factor, insulin-like growth factor 1-2, platelet derived growth factor, transforming growth factor-β, or epidermal growth factor; application of autologous platelets such as those that secrete one or more growth factors such as vascular endothelial growth factor, insulin-like growth factor 1-2, platelet derived growth factor, transforming growth factor-β, or epidermal growth factor; implantation of cultured keratinocytes; allograft; collagen, for instance a dressing comprising collagen; or protease inhibitors such as SLPI. The combination therapy may comprise one or more of the above-mentioned treatments.
• In a combination therapy capable of treating acne, the second therapy may comprise, e.g., a medication (e.g., systemic or topical) such as Benzoyl peroxide, antibiotics (such as erythromycin, clindamycin, or a tetracycline), Salicylic acid, hormones (e.g., comprising a progestin such as desogestrel, norgestimate or drospirenone), retinoids such as tretinoin, adapalene, tazarotene, or isotretinoin. The second therapy may also be a procedure such as comedo extraction, corticosteroid injection, or surgical lancing. The combination therapy may comprise one or more of the above-mentioned treatments.
• In a combination therapy capable of treating rosacea, the second therapy may comprise, e.g., an antibiotic, e.g., an oral tetracycline antibiotic such as tetracycline, doxycycline, or minocycline, or a topical antibiotic such as metronidazole; azelaic acid; alpha-hydroxy acid; isotretinoin can be prescribed; sandalwood oil; clonidine; beta-blockers such as nadolol and propranolol; antihistamines (such as loratadine); mirtazapine; methylsulfonylmethane or silymarin, optionally in combination with each other; lasers such as dermatological vascular laser or CO₂ laser; or light therapies such as intense pulsed light, low-level light therapy or photorejuvenation. The combination therapy may comprise one or more of the above-mentioned treatments.
• In a combination therapy capable of treating eczema, the second therapy may comprise, e.g., a corticosteroid such as hydrocortisone or clobetasol propionate, immunosuppressants (topical or systemic) such as pimecrolimus, tacrolimus, ciclosporin, azathioprine or methotrexate, or light therapy such as with ultraviolet light. The combination therapy may comprise one or more of the above-mentioned treatments.
• In a combination therapy capable of treating psoriasis, the second therapy may comprise, e.g., a corticosteroid such as desoximetasone; a retinoid; coal tar; Vitamin D or an analogue thereof such as paricalcitol or calcipotriol; moisturizers and emollients such as mineral oil, vaseline, calcipotriol, decubal, or coconut oil; dithranol; or fluocinonide. The combination therapy may comprise one or more of the above-mentioned treatments.
• While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of ammonia oxidizing bacteria described herein may involve downregulation of inflammation due to NO generation and reduction in formation of human cathelicidin peptide LL-37.
• While not wishing to be bound by theory, it is proposed that treatment of psoriasis with a therapeutically effective dose of ammonia oxidizing bacteria as described herein may involve downregulation of inflammation due to NO generation.
• While not wishing to be bound by theory, it is proposed that treatment of impetigo or other skin and soft tissue infections with a therapeutically effective dose of ammonia oxidizing bacteria as described herein may involve limiting and/or inhibiting the spread and proliferation of Staphylococcus aureus (S. aureus), e.g., methicillin resistant Staphylococcus aureus, Pseudomonas aeruginosa (P. aeruginosa), Streptococcus pyogenes (S. pyogenes), Acinetobacter baumannii (A. baumannii), Propionibacteria, and Stenotrophomonas.
• The present disclosure also provides a method of promoting wound healing, comprising administering to a wound an effective dose of ammonia oxidizing bacteria as described herein. Similarly, the present disclosure provides ammonia oxidizing bacteria as described herein for use in treating a wound. Likewise, the present disclosure provides a use of ammonia oxidizing bacteria as described herein in the manufacture of a medicament or a composition for treating a wound.
• Ammonia oxidizing bacteria as described herein may be used to promote wound healing in a patient that has an impaired healing ability, e.g., a diabetic patient.
• In some embodiments, this disclosure provides methods of using ammonia oxidizing bacteria as described herein to prevent a disease or disorder, e.g., a skin disorder. Prevention, in certain embodiments, means reducing the risk of a subject developing a disease, compared to a similar untreated subject. The risk need not be reduced to zero.
• Individuals having a reduced bathing frequency, such as astronauts, submarine crew members, military personnel during a campaign, civilian workers in remote locations, refugees, bedridden individuals and many others may maintain healthier skin by maintaining ammonia oxidizing bacteria on the skin. With regard to bedridden individuals, the ammonia oxidizing bacteria in some embodiments reduces the frequency or severity of bed sores by augmenting inadequate circulation.
• It is appreciated that many modern degenerative diseases may be caused by a lack of NO species, and that ammonia oxidizing bacteria on the external skin can supply those species by diffusion, and that application of ammonia oxidizing bacteria to the skin resolves long standing medical conditions. In certain embodiments, ammonia oxidizing bacteria are applied to a subject to offset modern bathing practices, especially with anionic detergents remove ammonia oxidizing bacteria from the external skin.
• One suitable method of topical application to apply sufficient ammonia oxidizing bacteria and then wear sufficient clothing so as to induce sweating. However, many people will want to derive the benefits of ammonia oxidizing bacteria while maintaining their current bathing habits, in which case, a culture of the bacteria can be applied along with sufficient substrate for them to produce NO. A nutrient solution approximating the inorganic composition of human sweat can be used for this purpose. Using bacteria adapted to media approximating human sweat minimizes the time for them to adapt when applied. Since sweat evaporates once excreted onto the skin surface, using a culture media that has a higher ionic strength is desirable. A concentration approximately twice that of human sweat is suitable, but other conditions are also contemplated. Ammonia oxidizing bacteria's nutritional needs are typically met with NH₃ or urea, O₂, CO₂, and minerals. In some embodiments, the substrate comprises trace minerals including iron, copper, zinc, cobalt, molybdenum, manganese, sodium, potassium, calcium, magnesium, chloride, phosphate, sulfate, or any combination thereof.
• In some embodiments, the present disclosure provides a method of treating a wound by applying a bandage comprising ammonia oxidizing bacteria to the wound. Also provided are methods of producing such a bandage. The bandage may comprise, for example, an adhesive portion to affix the bandage to undamaged skin near the wound and a soft, flexible portion to cover or overlay the wound. In some embodiments, the bandage contains no other organisms but ammonia oxidizing bacteria. The bandage may made of a permeable material that allows gasses like oxygen and carbon dioxide to reach the ammonia oxidizing bacteria when the bandage is applied to the wound. In certain embodiments, the bandage comprises nutrients for ammonia oxidizing bacteria such as ammonium, ammonia, urea, or trace minerals. In certain embodiments, the bandage comprises an antibiotic to which the ammonia oxidizing bacteria is resistant. The antibiotic resistance may arise from one or more endogenous resistance gene or from one or more transgenes.
• In some embodiments, the ammonia oxidizing bacteria, e.g., a preparation of ammonia oxidizing bacteria, is administered at a dose of about 10⁸-10⁹ CFU, 10⁹-10¹⁰ CFU, 10¹⁰-10¹¹ CFU, or 10¹¹-10¹² CFU per application or per day. In some embodiments, the ammonia oxidizing bacteria is administered topically at a dose of about 10⁹-10¹⁰ CFU, e.g., about 1×10⁹-5×10⁹, 1×10⁹-3×10⁹, or 1×10⁹-10×10⁹ CFU.
• In some embodiments, the ammonia oxidizing bacteria is administered in a volume of about 1-2, 2-5, 5-10, 10-15, 12-18, 15-20, 20-25, or 25-50 ml per dose. In some embodiments, the solution is at a concentration of about 10⁸-10⁹, 10⁹-10¹⁰, or 10¹⁰-10¹¹ CFU/ml. In some embodiments, the ammonia oxidizing bacteria is administered as two 15 ml doses per day, where each dose is at a concentration of 10⁹ CFU/ml.
• In some embodiments, the ammonia oxidizing bacteria is administered once, twice, three, or four times per day. In some embodiments, the ammonia oxidizing bacteria is administered once, twice, three, four, five, or six times per week. In some embodiments, the ammonia oxidizing bacteria is administered shortly after bathing. In some embodiments, the ammonia oxidizing bacteria is administered shortly before sleep.
• In some embodiments, the ammonia oxidizing bacteria is administered for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, 84-91 days, e.g., for about 1 month, for about 2 months, for about 3 months. In some embodiments, the ammonia oxidizing bacteria is administered for an indefinite period of time, e.g., greater than one year, greater than 5 years, greater than 10 years, greater than 15 years, greater than 30 years, greater than 50 years, greater than 75 years.
6. EXPERIMENTAL MODELS FOR REFINING D23 TREATMENTS
• Treatments comprising ammonia oxidizing bacteria as described herein (optionally in combination with another therapy) can be refined using a number of model systems. These model systems can be used to determine suitable doses and timing of administration.
• For instance, with respect to chronic wounds and diabetic ulcers, one may use the mouse skin puncture model. Other models for these disorders include controlled cutaneous ischemia in a guinea pig model, rabbit ear ulcer model, application of calcium to a wound, or topical application of doxorubicin.
• With respect to acne, one may use (for example) the Mexican hairless dog model, the Rhino mouse model, or the rabbit ear assay. With respect to rosacea, one may use (for example) intradermal injection of LL-37 into mouse skin or the Syrian hamster model. With respect to eczema, one may use (for example) application of a crude extract of Dermatophagoides farina, application of dinitrochlorobenzene to the ears of sensitized guinea pigs, or NC/Nga mice. With respect to psoriasis, one may use (for example) xenograft models in which involved and uninvolved psoriatic skin are transplanted onto immunodeficient mice, application of an antibody directed against interleukin 15 to the skin of SCID mice, and the Sharpin^cpdm/Sharpin^cpdm mouse model.
• Treatments comprising ammonia oxidizing bacteria, e.g., N. eutropha as described herein (e.g., strain D23) (optionally in combination with another therapy) can be refined using a number of model systems. These model systems can be used to determine suitable doses and timing of administration.
• For instance, with respect to chronic wounds and diabetic ulcers, one may use the mouse skin puncture model described herein in Example 6. Other models for these disorders include controlled cutaneous ischemia in a guinea pig model, rabbit ear ulcer model, application of calcium to a wound, or topical application of doxorubicin.
• With respect to acne, one may use (for example) the Mexican Hairless Dog model, the Rhino mouse model, or the rabbit ear assay. With respect to rosacea, one may use (for example) intradermal injection of LL-37 into mouse skin or the Syrian hamster model. With respect to eczema, one may use (for example) application of a crude extract of Dermatophagoides farina, application of dinitrochlorobenzene to the ears of sensitized guinea pigs, or NC/Nga mice. With respect to psoriasis, one may use (for example) xenograft models in which involved and uninvolved psoriatic skin are transplanted onto immunodeficient mice, application of an antibody directed against interleukin 15 to the skin of SCID mice, and the Sharpin^cpdm/Sharpin^cpdm mouse model.
7. MECHANISM OF THERAPEUTIC BENEFIT
• While not wishing to be bound by theory, it is believed that one or more of the following mechanisms contributes to the beneficial effect of ammonia oxidizing bacteria, e.g., N. eutropha in treating the diseases and conditions discussed herein. Additional mechanistic details are found in International Application WO/2005/030147, which is herein incorporated by reference in its entirety.
• In order to understand the beneficial aspects of these bacteria, it is helpful to understand angiogenesis. All body cells, except those within a few hundred microns of the external air, receive all metabolic oxygen from the blood supply. The oxygen is absorbed by the blood in the lung, is carried by red blood cells as oxygenated hemoglobin to the peripheral tissues, where it is exchanged for carbon dioxide, which is carried back and exhaled from the lung. Oxygen must diffuse from the erythrocyte, through the plasma, through the endothelium and through the various tissues until it reached the mitochondria in the cell which consumes it. The human body contains about 5 liters of blood, so the volume of the circulatory system is small compared to that of the body. Oxygen is not actively transported. It passively diffuses down a concentration gradient from the air to the erythrocyte, from the erythrocyte to the cell, and from the cell to cytochrome oxidase where it is consumed. The concentration of oxygen at the site of consumption is the lowest in the body, and the O₂ flux is determined by the diffusion resistance and the concentration gradient. Achieving sufficient oxygen supply to all the peripheral tissues requires exquisite control of capillary size and location. If the spacing between capillaries were increased, achieving the same flux of oxygen would require a larger concentration difference and hence a lower O₂ concentration at cytochrome oxidase. With more cells between capillaries, the O₂ demand would be greater. If the spacing between capillaries were decreased, there would be less space available for the cells that perform the metabolic function of the organ.
• In certain aspects, it is appreciated that NO from ammonia oxidizing bacteria is readily absorbed by the outer skin and converted into S-nitrosothiols since the outer skin is free from hemoglobin. M. Stucker et al. have shown that the external skin receives all of its oxygen from the external air in “The cutaneous uptake of atmospheric oxygen contributes significantly to the oxygen supply of human dermis and epidermis. (Journal of Physiology (2002), 538.3, pp. 985-994.) This is readily apparent, because the external skin can be seen to be essentially erythrocyte free. There is circulation of plasma through these layers because they are living and do require the other nutrients in blood, just not the oxygen. S-nitrosothiols formed are stable, can diffuse throughout the body, and constitute a volume source of authentic NO and a source of NO to transnitrosate protein thiols.
• In some aspects, it is appreciated that capillary rarefaction may be one of the first indications of insufficient levels of NO. F. T. Tarek et al. have shown that sparse capillaries, or capillary rarefaction, is commonly seen in people with essential hypertension. (Structural Skin Capillary Rarefaction in Essential Hypertension. Hypertension. 1999; 33:998-1001
• A great many conditions are associated with the capillary density becoming sparser. Hypertension is one, and researchers reported that sparse capillaries are also seen in the children of people with essential hypertension, and also in people with diabetes. Significant complications of diabetes are hypertension, diabetic nephropathy, diabetic retinopathy, and diabetic neuropathy. R. Candido et al. have found that the last two conditions are characterized by a reduction in blood flow to the affected areas prior to observed symptoms. (Haemodynamics in microvascular complications in type 1 diabetes. Diabetes Metab Res Rev 2002; 18: 286-304.) Reduced capillary density is associated with obesity, and simple weight loss increases capillary density as shown by A Philip et al. in “Effect of Weight Loss on Muscle Fiber Type, Fiber Size, Capilarity, and Succinate Dehydrogenase Activity in Humans. The Journal of Clinical Endocrinology & Metabolism Vol. 84, No. 11 4185-4190, 1999.
• Researchers have shown that in primary Raynaud's phenomena (PRP), the nailfold capillaries are sparser (slightly) than in normal controls, and more abundant than in patients that have progressed to systemic sclerosis (SSc). M. Bukhari, Increased Nailfold Capillary Dimensions In Primary Raynaud's Phenomenon And Systemic Sclerosis. British Journal of Rheumatology, Vol. 24 No 35: 1127-1131, 1996. They found that the capillary density decreased from 35 loops/mm² (normal controls) to 33 (PRP), to 17 (SSc). The average distance between capillary limbs was 18μ, 18μ, and 30μ for controls, PRP and SSc, respectively.
• In certain aspects, it is appreciated that the mechanism that the body normally uses to sense “hypoxia” may affect the body's system that regulates capillary density. According to this aspect of the invention, a significant component of “hypoxia” is sensed, not by a decrease in O2 levels, but rather by an increase in NO levels. Lowering of basal NO levels interferes with this “hypoxia” sensing, and so affects many bodily functions regulated through “hypoxia.” For Example, anemia is commonly defined as “not enough hemoglobin,” and one consequence of not enough hemoglobin is “hypoxia”, which is defined as “not enough oxygen.” According to some aspects, these common definitions do not account for the nitric oxide mediated aspects of both conditions.
• At rest, acute isovolemic anemia is well tolerated. A ⅔ reduction in hematocrit has minimal effect on venous return PvO2, indicating no reduction in either O₂ tension or delivery throughout the entire body. Weiskopf et al. Human cardiovascular and metabolic response to acute, severe isovolemic anemia. JAMA 1998, vol 279, No. 3, 217-221. At 50% reduction (from 140 to 70 g Hb/L), the average PvO2 (over 32 subjects) declined from about 77% to about 74% (of saturation). The reduction in O₂ capacity of the blood is compensated for by vasodilatation and tachycardia with the heart rate increasing from 63 to 85 bpm. That the compensation is effective is readily apparent, however, the mechanism is not. A typical explanation is that “hypoxia” sensors detected “hypoxia” and compensated with vasodilatation and tachycardia. However, there was no “hypoxia” to detect. There was a slight decrease in blood lactate (a marker for anaerobic respiration) from 0.77 to 0.62 mM/L indicating less anaerobic respiration and less “hypoxia.” The 3% reduction in venous return PvO2 is the same level of “hypoxia” one would get by ascending 300 meters in altitude (which typically does not produce tachycardia). With the O₂ concentration in the venous return staying the same, and the O₂ consumption staying the same, there is no place in the body where there is a reduction in O₂ concentration. Compensation during isovolemic anemia may not occur because of O₂ sensing.
• Thus the vasodilatation that is observed in acute isovolemic anemia may be due to the increased NO concentration at the vessel wall. NO mediates dilatation of vessels in response to shear stress and other factors. No change in levels of NO metabolites would be observed, because the production rate of NO is unchanged and continues to equal the destruction rate. The observation of no “hypoxic” compensation with metHb substitution can be understood because metHb binds NO just as Hb does, so there is no NO concentration increase with metHb substitution as there is with Hb withdrawal.
• Nitric oxide plays a role in many metabolic pathways. It has been suggested that a basal level of NO exerts a tonal inhibitory response, and that reduction of this basal level leads to a dis-inhibition of those pathways. Zanzinger et al. have reported that NO has been shown to inhibit basal sympathetic tone and attenuate excitatory reflexes. (Inhibition of basal and reflex-mediated sympathetic activity in the RVLM by nitric oxide. Am. J. Physiol. 268 (Regulatory Integrative Comp. Physiol. 37): R958-R962, 1995.)
• In some aspects, it is appreciated that one component of a volume source of NO is low molecular weight S-nitrosothiols produced in the erythrocyte free skin from NO produced on the external skin by ammonia oxidizing bacteria. These low molecular weight S-nitrosothiols are stable for long periods, and can diffuse and circulate freely in the plasma. Various enzymes can cleave the NO from various S-nitrosothiols liberating NO at the enzyme site. It is the loss of this volume source of NO from AOB on the skin that leads to disruptions in normal physiology. The advantage to the body of using S-nitrosothiols to generate NO far from a capillary is that O₂ is not required for NO production from S-nitrosothiols. Production of NO from nitric oxide synthase (NOS) does require O₂. With a sufficient background of S-nitrosothiols, NO can be generated even in anoxic regions. Free NO is not needed either since NO only exerts effects when attached to another molecule, such as the thiol of a cysteine residue or the iron in a heme, so the effects of NO can be mediated by transnitrosation reactions even in the absence of free NO provided that S-nitrosothiols and transnitrosation enzymes are present.
• Frank et al. have shown that the angiogenesis that accompanies normal wound healing is produced in part by elevated VEGF which is induced by increased nitric oxide. (Nitric oxide triggers enhanced induction of vascular endothelial growth factor expression in cultured keratinocytes (HaCaT) and during cutaneous wound repair. FASEB J. 13, 2002-2014 (1999).)
• NO has a role in the development of cancer, indicating that the bacteria described herein may be used in methods of cancer treatment and prevention. According to certain aspects, it is appreciated that the presence of NO during hypoxia may prevent cells from dividing while under hypoxic stress, when cells are at greater risk for errors in copying DNA. One relevant cell function is the regulation of the cell cycle. This is the regulatory program which controls how and when the cell replicates DNA, assembles it into duplicate chromosomes, and divides. The regulation of the cell cycle is extremely complex, and is not fully understood. However, it is known that there are many points along the path of the cell cycle where the cycle can be arrested and division halted until conditions for doing so have improved. The p53 tumor suppressor protein is a key protein in the regulation of the cell cycle, and it serves to initiate both cell arrest and apoptosis from diverse cell stress signals including DNA damage and p53 is mutated in over half of human cancers as reported by Ashcroft et al. in “Stress Signals Utilize Multiple Pathways To Stabilize p53.” (Molecular And Cellular Biology, May 2000, p. 3224-3233.) Hypoxia does initiate accumulation of p53, and while hypoxia is important in regulating the cell cycle, hypoxia alone fails to induce the downstream expression of p53 mRNA effector proteins and so fails to cause arrest of the cell cycle. Goda et al. have reported that hypoxic induction of cell arrest requires hypoxia-inducing factor-1 (HIF-1α). (Hypoxia-Inducible Factor 1α Is Essential for Cell Cycle Arrest during Hypoxia. Molecular And Cellular Biology, January 2003, p. 359-369.) Britta et al. have reported that NO is one of the main stimuli for HIF-1α. (Accumulation of HIF-1α under the influence of nitric oxide. Blood, 15 Feb. 2001, Volume 97, Number 4.) In contrast, NO does cause the accumulation of transcriptionally active p53 and does cause arrest of the cell cycle and does cause apoptosis. Wang et al., P53 Activation By Nitric Oxide Involves Down-Regulation Of Mdm2. THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 277, No. 18, Issue Of May 3, Pp. 15697-15702, 2002.
• In certain aspect of the invention, it is appreciated that preventing the necrotic death of cells by preventing the capillary rarefaction that leads to their hypoxic death may prevent autoimmune disorders. When cells are exposed to chronic hypoxia, the production of reactive oxygen species (ROS) is increased, and there is increased damage to the cells metabolic machinery and ultimately to the cells' DNA. Decreased metabolic capacity will decrease capacity for repair of damage due to ROS and due to exogenous carcinogen exposure. Over time, the damage accumulates and increases the chance of three events: the cell will undergo deletion of cancer-preventing genes and the cell will become cancerous, the cell will die through necrosis, or the cell will die through apoptosis. When cells die, either through necrosis or apoptosis, the cell debris must be cleared from the site. Dead cells are phagocytosed by immune cells, including dendritic cells and macrophages. When these cells phagocytose a body, it is digested by various proteolytic enzymes into antigenic fragments, and then these antigens are attached to the major histocompatibility complex (MHC1, MHC2) and the antigen-MHC complex is moved to the surface of the cell where it can interact with T cells and activate the T cells in various ways. Any cell injury releases adjuvants which stimulate the immune system in various ways. In general, cells that undergo necrosis stimulate a greater immune response than cells that undergo apoptosis. Chronic exposure of immune cells to dead and dying cells is therefore likely to lead to autoimmune disorders.
• In certain aspects, it is appreciated that low basal NO leads to fibrotic hypertrophy. Once a dead cell has been cleared, a new cell cannot easily take its place, because there is insufficient O₂ to support it. Any such new cell would suffer the same fate. The space can remain empty, in which case the organ shrinks, the capillaries draw closer together, new cells are now deprived of the VEGF formerly produced by the now-missing cell, so capillaries ablate and the hypoxic zone reforms. This could result in a general shrinkage of the affected tissues. In tissues that support fibrosis, relatively inert collagen fibers can fill the space. Since the metabolic requirements of the body for the particular organ in question are not reduced, the organ may attempt to grow larger, but now with a significant fibrous content. This may result in fibrotic hypertrophy, such as of the heart and liver. Some organs, such as the brain, cannot grow larger or smaller because the three-dimensional connectivity of nerves and blood vessels are important, and cannot be continuously and simultaneously mapped onto an asymmetrically shrinking brain. The space must be filled with something, and β-amyloid might be the (not so inert) space filler. The kidney cannot grow larger because of the renal capsule, so the number of living cells becomes smaller and they are replaced with fibrotic tissue. If the dead cells are cleared, the tissue shrinks, and the ratio of NO/O₂ goes down again, and the capillaries again become sparser. This may set up the vicious circle of end stage renal disease, congestive heart failure/cardiac hypertrophy, primary biliary cirrhosis, Alzheimer's disease, atherosclerosis, inflammatory bowel disease, hypertrophic scar formation, and the multiple connective tissue diseases starting with Raynaud's phenomena and ending with Systemic Sclerosis and primary Sjogren's syndrome where capillary rarefaction is also observed. Ferrini et al, have shown that a reduction in basal NO levels through chronic inhibition of NOS with L-NAME leads to generalized fibrosis of the heart and kidneys. (Antifibrotic Role of Inducible Nitric Oxide Synthase. Nitric Oxide: Biology and Chemistry Vol. 6, No. 3, pp. 283-294 (2002).) It may be that low basal NO leads to fibrotic hypertrophy.
• In certain aspects, it is appreciated that capillary rarefaction affects a subject's ability to control their appetite. Capillary rarefaction is observed in the brains of aged humans and animals. Capillary rarefaction is associated with declines in circulating growth factors including insulin like growth factor-1. Neurogenesis in the adult brain is coordinated with angiogenesis. Since the brain regulates many homeostatic functions, increased diffusion lengths between capillaries to control elements of the brain might be “interpreted” as inadequate blood concentrations of those species. The flux of glucose in the brain is quite close to normal metabolic needs, where glucose flux is only 50 to 75% greater than glucose consumption and the glucose transporters across the blood brain barrier are saturable, stereospecific and independent of energy or ion gradients. A large part of the regulation of appetite is mediated through the brain, and capillary rarefaction may cause an adequate blood concentration of “nutrients” (or marker compounds proportional to “nutrients”) to be interpreted as insufficient. This may be one cause of obesity.
• According to certain aspects, it is appreciated that capillary rarefaction may be a cause of non-insulin dependent diabetes. Non-insulin dependent diabetes (NIDDM) is also known as the Metabolic Syndrome or Diabetes type 2, and is characterized by insulin resistance. The sensitivity of the body to insulin is reduced, and insulin levels increase People with NIDDM have high blood glucose, high blood triglycerides, are typically obese, hypertensive, and typically have significant visceral fat.
• Other symptoms accompany NIDDM, which may point to capillary rarefaction as the cause. In a study of 40 men, with and without NIDDM, obese (BMI 29) and lean (BMI 24) (10 of each), Konrad et al. report that blood lactate levels at rest were 1.78, 2.26, 2.42, and 2.76 (mM/L) for lean men without, obese men without, lean men with NIDDM, obese men with NIDDM respectively. (A-Lipoic acid treatment decreases serum lactate and pyruvate concentrations and improves glucose effectiveness in lean and obese patients with type 2 diabetes. Diabetes Care 22:280-287, 1999.) Lactate is a measure of anaerobic glycolysis. When O₂ is insufficient to generate ATP through oxidative phosphorylation, cells can produce ATP through anaerobic glycolysis. One of the products of anaerobic glycolysis is lactate, which must be exported from the cells, otherwise the pH drops and function is compromised. Blood lactate is commonly measured in exercise studies, where an increase indicates the work load at which maximum oxidative work can be done. Higher levels of lactate at rest would indicate increased anaerobic glycolysis at rest, which is consistent with capillary rarefaction.
• Primary biliary cirrhosis is associated with Raynaud's phenomena, pruritus, sicca syndrome, osteoporosis, portal hypertension, neuropathy, and pancreatic insufficiency, and liver abnormalities are associated with rheumatic diseases. Elevated liver enzymes are a symptom of liver inflammation, and elevated liver enzymes are observed as an early symptom of “asymptomatic” primary biliary cirrhosis. Accordingly, the bacteria described herein may be used to treat liver inflammation.
• Torre et al have reported that Alzheimer's disease (AD) is a microvascular disorder with neurological degeneration secondary to hypoperfusion, resulting in part from insufficient nitric oxide. (Review: Evidence that Alzheimer's disease is a microvascular disorder: the role of constitutive nitric oxide, Brain Research Reviews 34 (2000) 119-136.) Accordingly, the bacteria described herein may be used to treat AD.
• Adverse health effects that are associated with hypertension may also be consequences of low basal NO. The decreased response to vasodilatation is also consistent with low basal NO. NO is a diffusible molecule that diffuses from a source to a sensor site where it has the signaling effect. With low NO levels, every NO source must produce more NO to generate an equivalent NO signal of a certain intensity a certain distance away. NO diffuses in three dimensions and the whole volume within that diffusion range must be raised to the level that will give the proper signal at the sensor location. This may result in higher NO levels at the source and between the source and the sensor. Adverse local effects of elevated NO near a source may then arise from too low a NO background. There is some evidence that this scenario actual occurs. In rat pancreatic islets, Henningsson et al have reported that inhibition of NOS with L-NAME increases total NO production through the induction of iNOS. (Chronic blockade of NO synthase paradoxically increases islet NO production and modulates islet hormone release. Am J Physiol Endocrinol Metab 279: E95-E107, 2000.) Increasing NO by increasing NOS activity will only work up to some limit. When NOS is activated but is not supplied with sufficient tetrahydrobiopterin (BH4) or L-arginine, it becomes “uncoupled” and generates superoxide (O2−) instead of NO. This O₂ ⁻ may then destroy NO. Attempting to produce NO at a rate that exceeds the supply of BH4 or L-arginine may instead decrease NO levels. This may result in positive feedback where low NO levels are made worse by stimulation of NOS, and uncoupled NOS generates significant O₂ ⁻ which causes local reactive oxygen species (ROS) damage such as is observed in atherosclerosis, end stage renal disease, Alzheimer's, and diabetes.
• The bacteria described herein may also be used to delay the signs of aging. Caloric restriction extends lifespan, and Holloszy reported that restricting food intake to 70% of ad lib controls, prolongs life in sedentary rats from 858 to 1,051 days, almost 25%. (Mortality rate and longevity of food restricted exercising male rats: a reevaluation. J. Appl. Physiol. 82(2): 399-403, 1997.) The link between calorie restriction and prolonged life is well established, however, the causal mechanism is not. Lopez-Torres et al. reported that the examination of liver mitochondrial enzymes in rats indicates a reduction in H₂O₂ production due to reduced complex I activity associated with calorie restriction. (Influence Of Aging And Long-Term Caloric Restriction On Oxygen Radical Generation And Oxidative DNA Damage In Rat Liver Mitochondria. Free Radical Biology & Medicine Vol. 32 No 9 pp 882-8899, 2002.) H₂O₂ is produced by dismutation of O₂ ⁻, which is a major ROS produced by the mitochondria during respiration. The main source of O₂ ⁻ has been suggested by Kushareva et al. and others to be complex I which catalyzes the NAD/NADH redox couple by reverse flow of electrons from complex III, the site of succinate reduction. The free radical theory, proposed by Beckman, of aging postulates, that free radical damage to cellular DNA, antioxidant systems and DNA repair systems accumulates with age and when critical systems are damaged beyond repair, death ensues. (The Free Radical Theory of Aging Matures. Physiol. Rev. 78: 547-581, 1998.)
• As an additional mechanism, NO has been demonstrated by Vasa et al. to activate telomerase and to delay senescence of endothelial cells. (Nitric Oxide Activates Telomerase and Delays Endothelial Cell Senescence. Circ Res. 2000; 87:540-542.) Low basal NO will increase basal metabolic rate by disinhibition of cytochrome oxidase. Increased basal metabolism will also increase cell turn-over and growth rate. Capillary rarefaction, by inducing chronic hypoxia may increase free radical damage and may also increase cell turn-over, and so accelerate aging by both mechanisms.
• In some aspects, it is appreciated that autotrophic ammonia-oxidizing bacteria may produce protective aspects for allergies and autoimmune disorders. The best known autoimmune disease is perhaps Diabetes Type 1, which results from the destruction of the insulin producing cells in the pancreas by the immune system. Recurrent pregnancy loss is also associated with autoimmune disorders where the number of positive autoimmune antibodies correlated positively with numbers recurrent pregnancy losses. Systemic Sclerosis, Primary Biliary Cirrhosis, autoimmune hepatitis, and the various rheumatic disorders are other examples of autoimmune disorders. Application of AOB was observed to reduce an allergy, hay fever, as described in WO/2005/030147.
• One mechanism by which AOB may exert their protective effect on allergies and autoimmune disorders is through the production of nitric oxide, primarily through the regulatory inhibition of NF-κB and the prevention of activation of immune cells and the induction of inflammatory reactions. NF-κB is a transcription factor that up-regulates gene expression and many of these genes are associated with inflammation and the immune response including genes which cause the release of cytokines, chemokines, and various adhesion factors. These various immune factors cause the migration of immune cells to the site of their release resulting in the inflammation response. Constitutive NO production has been shown to inhibit NF-κB by stabilizing IκBα (an inhibitor of NF-κB) by preventing IκBα degradation.
• Administration of an NO donor has been shown by Xu et al. to prevent the development of experimental allergic encephalomyelitis in rats. (SIN-1, a Nitric Oxide Donor, Ameliorates Experimental Allergic Encephalomyelitis in Lewis Rats in the Incipient Phase: The Importance of the Time Window. The Journal of Immunology, 2001, 166: 5810-5816.) In this study, it was demonstrated that administering an NO donor, reduced the infiltration of macrophages into the central nervous system, reduced the proliferation of blood mononuclear cells, and increased apoptosis of blood mononuclear cells. All of these results are expected to reduce the extent and severity of the induced autoimmune response.
• Low basal NO may lead to autism via the mechanism that new connections in the brain are insufficiently formed as a result of insufficient basal nitric oxide. While not wishing to be bound in theory, in some embodiments, formation of neural connections is modulated by NO. In these cases, any condition that lowers the range of NO diffusion may decrease the volume size of brain elements that can undergo connections. A brain which developed under conditions of low basal NO levels may be arranged in smaller volume elements because the reduced effective range of NO.
• Additional symptoms exhibited in autistic individuals may also point to low NO as a cause, including increased pitch discrimination, gut disturbances, immune system dysfunction, reduced cerebral blood flow, increased glucose consumption of the brain, increased plasma lactate, attachment disorders, and humming. Each of these symptoms may be attributed to a low basal NO level.
• Takashi Ohnishi et al. have reported that autistic individuals show decreased blood flow. Takashi Ohnishi et al., Abnormal regional cerebral blood flow in childhood autism. Brain (2000), 123, 1838-1844. J. M. Rumsey et al. have reported that autistic individuals have increased glucose consumption. Rumsey J M, Duara R, Grady C, Rapoport J L, Margolin R A, Rapoport S I, Cutler N R. Brain metabolism in autism. Resting cerebral glucose utilization rates as measured with positron emission tomography. Arch Gen Psychiatry, 1985 May; 42(5):448-55 (abstract). D. C. Chugani has reported that autistic individuals have an increased plasma lactate levels. Chugani D C, et al., Evidence of altered energy metabolism in autistic children. Prog Neuropsychopharmacol Biol Psychiatry. 1999 May; 23(4):635-41. The occurrence of these effects may be a result of capillary rarefaction in the brain, which may reduce blood flow and O₂ supply, such that some of the metabolic load of the brain may be produced through glycolysis instead of oxidative phosphorylation.
• Nitric oxide has been demonstrated by B. A. Klyachko et al. to increase the excitability of neurons by increasing the after hyperpolarization through cGMP modification of ion channels. Vitaly A. Klyachko et al., cGMP-mediated facilitation in nerve terminals by enhancement of the spike after hyperpolarization. Neuron, Vol. 31, 1015-1025, Sep. 27, 2001. C. Sandie et al. have shown that inhibition of NOS reduces startle. Carmen Sandi et al., Decreased spontaneous motor activity and startle response in nitric oxide synthase inhibitor-treated rats. European journal of pharmacology 277 (1995) 89-97. Attention-Deficit Hyperactivity Disorder (ADHD) has been modeled using the spontaneously hypertensive rat (SHR) and the Naples high-excitability (NHE) rat. Both of these models have been shown by Raffaele Aspide et al, to show increased attention deficits during periods of acute NOS inhibition. Raffaele Aspide et al., Non-selective attention and nitric oxide in putative animal models of attention-deficit hyperactivity disorder. Behavioral Brain Research 95 (1998) 123-133. Accordingly, the bacteria herein may be used in the treatment of ADHD.
• Inhibition of NOS has also been shown by M. R. Dzoljic to inhibit sleep. M. R. Dzoljic, R. de Vries, R. van Leeuwen. Sleep and nitric oxide: effects of 7-nitro indazole, inhibitor of brain nitric oxide synthase. Brain Research 718 (1996) 145-150. G. Zoccoli has reported that a number of the physiological effects seen during sleep are altered when NOS is inhibited, including rapid eye movement and sleep-wake differences in cerebral circulation. G. Zoccoli, et al., Nitric oxide inhibition abolishes sleep-wake differences in cerebral circulation. Am. J. Physiol. Heart Circ Physiol 280: H2598-2606, 2001. NO donors have been shown by L. Kapas et al. to promote non-REM sleep, however, these increases persisted much longer than the persistence of the NO donor, suggesting perhaps a rebound effect. Levente Kapas et al. Nitric oxide donors SIN-1 and SNAP promote nonrapid-eye-movement sleep in rats. Brain Research Bullitin, vol 41, No 5, pp. 293-298, 1996. M. Rosaria et al., Central NO facilitates both penile erection and yawning. Maria Rosaria Melis and Antonio Argiolas. Role of central nitric oxide in the control of penile erection and yawning. Prog Neuro-Psychopharmacol & Biol. Phychiat. 1997, vol 21, pp 899-922. P. Tani et al, have reported that insomnia is a frequent finding in adults with Asperger's. Pekka Tani et al., Insomnia is a frequent finding in adults with Asperger's syndrome. BMC Psychiatry 2003, 3:12. Y. Hoshino has also observed sleep disturbances in autistic children. Hoshino Y, Watanabe H, Yashima Y, Kaneko M, Kumashiro H. An investigation on sleep disturbance of autistic children. Folia Psychiatr Neurol Jpn. 1984; 38(1):45-51. (abstract) K. A. Schreck et al. has observed that the severity of sleep disturbances correlates with severity of autistic symptoms. Schreck K A, et al., Sleep problems as possible predictors of intensified symptoms of autism. Res Dev Disabil. 2004 Jan.-Feb.; 25(1):57-66. (abstract). Accordingly, the bacteria herein may be used in the treatment of insomnia.
• W. D. Ratnasooriya et al reported that inhibition of NOS in male rats reduces pre-coital activity, reduces libido, and reduces fertility. W. D. Ratnasooriya et al., Reduction in libido and fertility of male rats by administration of the nitric oxide (NO) synthase inhibitor N-nitro-L-arginine methyl ester. International journal of andrology, 23: 187-191 (2000).
• It may be that a number of seemingly disparate disorders, characterized by ATP depletion and eventual organ failure are actually “caused” by nitropenia, caused by a global deficiency in basal nitric oxide. When this occurs in the heart, the result is dilative cardiomyopathy. When this occurs in the brain, the result is white matter hyperintensity, Alzheimer's, vascular depression, vascular dementia, Parkinson's, and the Lewy body dementias. When this occurs in the kidney, the result is end stage renal disease, when this occurs in the liver, the result is primary biliary cirrhosis. When this occurs in muscle, the consequence is fibromyaligia, Gulf War Syndrome, or chronic fatigue syndrome. When this occurs in the bowel, the consequence is ischemic bowel disease. When this occurs in the pancreas, the consequence is first type 2 diabetes, followed by chronic inflammation of the pancreas, followed by autoimmune attack of the pancreas (or pancreatic cancer), followed by type 1 diabetes. When this occurs in the connective tissue, the consequence is systemic sclerosis.
• In the remnant kidney model of end stage renal disease, part of the kidney is removed, (either surgically or with a toxin) which increases the metabolic load on the remainder. Superoxide is generated to decrease NO and increase O₂ diffusion to the kidney mitochondria. Chronic overload results in progressive kidney capillary rarefaction and progressive kidney failure. In acute kidney failure, putting people in dialysis can give the kidney a “rest”, and allows it to recover. In acute renal failure induced by rhabdomyolysis (muscle damage which releases myoglobin into the blood stream) kidney damage is characterized by ischemic damage. Myoglobin scavenges NO, just as hemoglobin does, and would cause vasoconstriction in the kidney leading to ischemia. Myoglobin would also induce local nitropenia and the cascade of events leading to further ATP depletion.
• In some aspects, low NO levels lead to reduced mitochondrial biogenesis. Producing the same ATP at a reduced mitochondria density will result in an increase in O₂ consumption, or an accelerated basal metabolic rate. An accelerated basal metabolic rate is observed in a number of conditions, including: Sickle cell anemia, Congestive heart failure, Diabetes, Liver Cirrhosis, Crohn's disease, Amyotrophic lateral sclerosis, Obesity, End stage renal disease, Alzheimer's, and chronic obstructive pulmonary disease.
• While some increased O₂ consumption might be productively used, in many of these conditions uncoupling protein is also up-regulated, indicating that at least part of the increased metabolic rate is due to inefficiency. Conditions where uncoupling protein is known to be up-regulated include obesity and diabetes.
• With fewer mitochondria consuming O₂ to a lower O₂ concentration, the O₂ gradient driving O₂ diffusion is greater, so the O₂ diffusion path length can increase resulting in capillary rarefaction, which is observed in dilative cardiomyopathy, hypertension, diabetes type 2, and renal hypertension.
• Copper, either as Cu2+ or as ceruloplasmin (CP) (the main Cu containing serum protein which is present at 0.38 g/L in adult sera and which is 0.32% Cu and contains 94% of the serum copper) catalyzes the formation of S—NO-thiols from NO and thiol containing groups (RSH). The Cu content of plasma is variable and is increased under conditions of infection. Berger et al. reported that the Cu and Zn content of burn-wound exudates is considerable with patients with ⅓ of their skin burned, losing 20 to 40% of normal body Cu and 5 to 10% of Zn content in 7 days. (Cutaneous copper and zinc losses in burns. Burns. 1992 October; 18(5):373-80.) If the patients skin were colonized by AOB, wound exudates which contains urea and Fe, Cu, and Zn that AOB need, would be converted into NO and nitrite, greatly supplementing the local production of NO by iNOS, without consuming resources (such as O₂ and L-arginine) in the metabolically challenged wound. A high production of NO and nitrite by AOB on the surface of a wound would be expected to inhibit infection, especially by anaerobic bacteria such as the Clostridia which cause tetanus, gas gangrene, and botulism.
• The practice of the present invention may employ, unless otherwise indicated, conventional methods of immunology, molecular biology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, et al. Molecular Cloning: A Laboratory Manual (Current Edition); and Current Protocols in Molecular Biology (F. M. Ausubel, et al. eds., current edition).
8. NUCLEIC ACIDS AND PROTEINS FROM N. EUTROPHA
• This disclosure provides, among other things, proteins and nucleic acids (optionally, isolated proteins and nucleic acids) that are identical to or similar to those found in strain D23. While not wishing to be bound by theory, it is believed that the sequenced strain of D23 has non-naturally occurring protein and nucleic acid sequences due to an extended period of culture and selection in the laboratory.
• These nucleic acids and proteins have numerous uses. For instance, the proteins may be used to generate antibodies or other binding molecules that detect strain D23 or related strains. The proteins may also be used to carry out reactions under high-NH₄ ⁺ conditions, because D23 is adapted for growth and metabolism under these conditions. As another example, the nucleic acids may be used to produce proteins for generating antibodies or carrying out reactions as described above. The nucleic acids may also be used to detect strain D23 or related strains, e.g., using a microarray or another hybridization-based assay.
• The genome of strain D23 is provided as SEQ ID NO: 1. The genome annotation (including the position and orientation of genes within SEQ ID NO: 1) is provided as Supplementary Table 1. Accordingly, this disclosure provides genes and proteins identical or similar to the genes listed in Supplementary Table 1.
• Accordingly, this disclosure provides a nucleic acid (e.g., an isolated nucleic acid) comprising a sequence of a gene of Supplementary Table 1, as well as a protein encoded by said gene. In certain embodiments, the nucleic acid comprises a sequence that is similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to a gene of Supplementary Table 1, or a protein encoded by said gene. The disclosure also provides a composition comprising a nucleic acid that is at least 1, 2, 3, 4, 5, 10, 15, 20, 50, 100, 200, 500, 1,000, 1,500, 2,000, 2,500, or all of the sequences of Supplementary Table 1, or a sequence that is similar thereto (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical), or one or more proteins encoded by said nucleic acids. Also provided are fragments of said nucleic acids and proteins.
• The present disclosure also provides, inter alia, one or more genes or proteins that are present in strain D23 and absent from strain C91, or a gene or protein similar to one of said genes or proteins. Examples of these genes are set out in FIGS. 6-8 and are described in more detail in Example 4 herein. Examples of these genes and proteins, as well as genes and proteins similar thereto, are described below.
• Accordingly, with respect to FIG. 6, this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the sequences in FIG. 6. This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 6. Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
• With respect to FIG. 7, this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the sequences in FIG. 7. This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, or all of the proteins encoded by the genes listed in FIG. 7. Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
• With respect to FIG. 8, this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the sequences in FIG. 8. This application also discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 200, or all of the proteins encoded by the genes listed in FIG. 8. Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 0-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
• With respect to FIGS. 6-8 collectively, this application discloses nucleic acids that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the sequences in FIGS. 6-8. This application discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identical) to 1, 2, 3, 4, 5, 10, 20, 40, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or all of the proteins encoded by genes listed in FIGS. 6-8. Furthermore, the application discloses fragments of these genes and proteins, e.g., fragments of 1-20, 20-50, 50-100, 100-200, 200-500, 500-1000, or greater than 1000 nucleotides or amino acids. In some embodiments, a plurality of the above-mentioned genes or proteins are affixed to a solid support, e.g., to form a microarray.
• This disclosure also provides nucleic acid sequences that are fragments of SEQ ID NO: 1. The fragments may be, e.g., 1-20, 20-50, 50-100, 100-200, 200-500, 500-1000, 1,000-2,000, 2,000-5,000, or 10,000 or more nucleotides in length. The fragments may also be at least about 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 99.5% identity to the corresponding portion of SEQ ID NO: 1 or its complement. The fragment may also be a fragment that hybridizes to SEQ ID NO: 1, or to the genome of the D23 strain deposited with the ATCC patent depository on Apr. 8, 2014, designated AOB D23-100 with the ATCC under accession number PTA-121157, or their complements, under low stringency, medium stringency, high stringency, or very high stringency, or other hybridization condition described herein.
• The disclosure also provides nucleic acid sequences set out in Table 1 (which describes genes involved in ammonia metabolism). Accordingly, in some aspects, this application discloses genes that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.5%, 98%, 98.2%, 98.4%, 98.6%, 98.8%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the genes in Table 1. In embodiments, this application discloses proteins that are identical or similar (e.g., at least 70%, 80%, 85%, 90%, 95%, 96%, 97%, 97.5%, 98%, 98.2%, 98.4%, 98.6%, 98.8%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, or 100% identical) to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all of the proteins in Table 1.
• Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The following paragraphs discuss this percent identity and describe various nucleic acids having homology to the D23 genes of Table 1.
• More specifically, the amoA1 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the amoA1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA1 nucleic acid comprise D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA1 nucleic acid comprises a sequence at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA1 gene.
• The amoA2 genes are about 98.8% identical (i.e., at 821/831 positions). Accordingly, in some embodiments, the amoA2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoA2 nucleic acid comprises a sequence at least about 98.8%, 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoA2 gene.
• The amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions). Accordingly, in some embodiments, the amoB1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB1 nucleic acid comprises a sequence at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB1 gene.
• The amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions). Accordingly, in some embodiments, the amoB2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoB2 nucleic acid comprises a sequence at least about 99.1%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoB2 gene.
• The amoC1 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the amoC1 nucleic acid comprises D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC1 nucleic acid comprises D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC1 nucleic acid comprises a sequence at least about 99.8%, 99.9%, or 100% identical to the D23 amoC1 gene.
• The amoC2 genes are about 99.8% identical (i.e., at 814/816 positions). Accordingly, in some embodiments, the amoC2 nucleic acid comprises D23 nucleotides at at least 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC2 nucleic acid comprises D23 nucleotides at at most 1, 2, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC2 nucleic acid comprises a sequence at least about 99.8%, 99.9%, or 100% identical to the D23 amoC2 gene.
• The amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). Accordingly, in some embodiments, the amoC3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the amoC3 nucleic acid comprises a sequence at least about 98.9%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 amoC3 gene.
• The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions). Accordingly, in some embodiments, the hao1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao1 nucleic acid comprises a sequence at least about 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao1 gene.
• The hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions). Accordingly, in some embodiments, the hao2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao2 nucleic acid comprises a sequence at least about 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao2 gene.
• The hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Accordingly, in some embodiments, the hao3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the hao3 nucleic acid comprises a sequence at least about 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 hao3 gene.
• The cycA1 genes are about 98.0% identical (i.e., at 694/708 positions). Accordingly, in some embodiments, the cycA1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA1 nucleic acid comprises a sequence at least about 98.0%, 98.2%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA1 gene.
• The cycA2 genes are about 98.7% identical (i.e., at 699/708 positions). Accordingly, in some embodiments, the cycA2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA2 nucleic acid comprises a sequence at least about 98.7%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA2 gene.
• The cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Accordingly, in some embodiments, the cycA3 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA3 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycA3 nucleic acid comprises a sequence at least about 99.3%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycA3 gene.
• The cycB1 genes are about 96.7% identical (i.e., at 696/720 positions). Accordingly, in some embodiments, the cycB1 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB1 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB1 nucleic acid comprises a sequence at least about 96.7%, 96.8%, 97.0%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB1 gene.
• The cycB2 genes are about 97.1% identical (i.e., at 702/723 positions). Accordingly, in some embodiments, the cycB2 nucleic acid comprises D23 nucleotides at at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB2 nucleic acid comprises D23 nucleotides at at most 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or all of the positions that differ in this gene between strains C91 and D23. In embodiments, the cycB2 nucleic acid comprises a sequence at least about 97.1%, 97.2%, 97.4%, 97.6%, 97.8%, 98.0%, 98.2%, 98.4%, 98.4%, 98.6%, 98.8%, 99.0%, 99.2%, 99.4%, 99.6%, 99.8%, or 100% identical to the D23 cycB2 gene.
• Further provided herein are vectors comprising nucleotide sequences described herein. In some embodiments, the vectors comprise nucleotides encoding a protein described herein. The vectors include, but are not limited to, a virus, plasmid, cosmid, lambda phage or a yeast artificial chromosome (YAC). Such vectors may include a promoter, an open reading frame with or without introns, and a termination signal.
• The present disclosure also provides host cells comprising a nucleic acid as described herein, or a nucleic acid encoding a protein as described herein.
• In certain embodiments, the host cells are genetically engineered by using an expression cassette. The phrase “expression cassette,” refers to nucleotide sequences, which are capable of affecting expression of a gene in hosts compatible with such sequences. Such cassettes may include a promoter, an open reading frame with or without introns, and a termination signal. Additional factors necessary or helpful in effecting expression may also be used, such as, for example, an inducible promoter.
• The disclosure also provides host cells comprising the vectors described herein.
• The cell can be, but is not limited to, a eukaryotic cell, a bacterial cell, an insect cell, or a human cell. If the cell is a bacterial cell, it may be, e.g., E. coli or an ammonia-oxidizing bacterium such as Nitrosomonas (e.g., N. eutropha or N. europaea), Nitrosococcus, Nitrosospira, Nitrosocystis, Nitrosolobus, and Nitrosovibrio.
9. ADJUSTING THE SKIN MICROBIOME WITH AMMONIA OXIDIZING BACTERIA
• The present disclosure provides for systems and methods for changing the skin microbiome, e.g., the human skin microbiome. The systems and methods may provide treatment of infections or conditions, e.g., related to the skin, e.g., skin infections and/or skin conditions.
• Ammonia-oxidizing bacteria (AOB) of the genus Nitrosomonas are Gram-negative obligate autotrophic bacteria with a unique capacity to generate nitrite and nitric oxide exclusively from ammonia as an energy source. They are widely present both in soil and water environments and are essential components of environmental nitrification processes. Due to the roles of nitrite and nitric oxide on human skin as important components of several physiological functions, such as vasodilation, skin inflammation and wound healing, these bacteria may have beneficial properties for both healthy and immunopathological skin conditions. These bacteria may be safe for use in humans because they are slow-growing, cannot grow on organic carbon sources, may be sensitive to soaps and antibiotics, and have never been associated with any disease or infection in animals or humans.
• Topical application of ammonia oxidizing bacteria to a subject, e.g., a human subject may lead to unexpected changes in the skin microbiome, and more specifically it may lead to increases in the proportion of normal commensal non-pathogenic species and reductions in the proportion of potentially pathogenic, pathogenic, or disease causing organisms.
EXAMPLES Example 1 Initial Culturing of N. eutropha
• A soil-derived culture enriched in various ammonia oxidizing bacteria was applied to the skin of an adult male subject as described in WO/2003/057380. The period of growth on the human body selected for a strain with the capacity to colonize human skin for an extended period of time. After several months, the strain was re-isolated from the skin of the individual and cultured in laboratory conditions for a sustained period as described in the subsequent examples. While not wishing to be bound by theory, it is believed that the sustained laboratory culture selected for new mutations improving the strain properties, e.g., improved tolerance for high-ammonia conditions.
Example 2 Growing and Monitoring D23 or Mixtures of Strains that Comprise D23 Culture Conditions
• D23 can be grown in batches or by continuous cultivation in a bioreactor. Batch preparation uses the medium of Table 3.

• TABLE 3
  Growth Medium for Batch culturing:

  	Weight/Volume	Final Concentration
  	(in~1.5 L)	(in~1.5 L)

  (NH4)2SO4	4.95	g	50	mM NH4 +
  (MW 132.14)
  KH2PO4 (MW 136.1)	0.616	g	3.0	mM
  1M MgSO4	1.137	ml	0.76	mM
  1M CaCl2	0.3	ml	0.2	mM
  30 mM FeCl3/50 mM	0.5	ml	10	μM/16.7 μM
  EDTA
  50 mM CuSO 4	30	μl	1.0	μM

  Add 1400 ml ddH2O to flask. Autoclave. Store at room temperature.

  After autoclaving add:

  Phosphate Buffer	100	ml	32	mM KH2PO4/
  			2.7	mM NaH2PO4•H2O

  5% Na2CO3	12	ml	0.04%

• The medium of Table 3 is inoculated with ˜15 ml of a 3 day old culture of D23 (i.e. 1% volume). The cultures are incubated in the dark at 30° C. by shaking at 200 rpm.
• Often, a N. eutropha D23 mixed culture is grown on complete N. europaea media. The culture medium is described below, and additional details on culturing ammonia-oxidizing bacteria are available on the World Wide Web at nitrificationnetwork.org/Nerecipe.php, Ensign et al., 1993, and Stein & Arp, 1998.
Step 1.
• Add 900 ml of deionized water to a 2-liter Erlenmeyer flask.
• Add in sequence:
• 3.3 g (NH₄ ⁺)₂SO₄ (50 mM);
• 0.41 g KH₂PO₄
• 0.75 ml 1 M MgSO₄ stock solution
• 0.2 ml 1 M CaCl₂ stock solution
• 0.33 ml 30 mM FeSO₄/50 mM EDTA stock solution
• 0.01 ml 50 mM CuSO₄ stock solution
• Sterilize the solution by autoclaving.
Step 2.
• Add 400 ml of deionized water to a beaker. Add:
• 27.22 g KH₂PO₄
• 2.4 g NaH₂PO₄
• Adjust the pH to 8.0 with 10 N NaOH, and bring the final volume to 500 ml with deionized water.
• Sterilize 100 ml fractions of the solution by autoclaving in 250-500 ml Erlenmeyer flasks.
Step 3
• Prepare 500 ml of 5% (w/v) Na₂CO₃ (anhydrous)
• Sterilize the solution by autoclaving.
Step 4
• Add 1×100 ml aliquot of solution prepared in Step 2 to the flask prepared in Step 1.
Step 5
• Add 8 ml of the solution prepared in Step 3 to the flask prepared in Step 1.
• The D23 can also be cultured continuously in a bioreactor. Table 4 describes the appropriate media.

• TABLE 4
  Growth Medium for continuous culture:

  	Batch medium	Feeding solution
  	Weight/Volume (1 L)	Weight/Volume (1 L)
  	(Final concentration)	(Final concentration)

  (NH4)2SO4 (MW 132.14)

  3.3

  g

  13.2

  g

  (50 mM NH4 +)

  (200 mM NH4 +)

  KH2PO4 (MW 136.1)

  1.23

  g

  0.41

  g

  (9.0 mM)

  (3.0 mM)

  1M MgSO4

  0.758

  ml

  0.758

  ml

  (0.76 mM)

  (0.76 mM)

  1M CaCl2

  0.2

  ml

  0.2

  ml

  (0.2 mM)

  (0.2 mM)

  30 mM FeCl3/50 mM EDTA

  0.333

  ml

  0.333

  ml

  (10 μM/16.7 μM)

  (10 μM/16.7 μM)

  50 mM CuSO 4

  20

  μl

  20

  μl

  	(1.0 μM)	(1.0 μM)
  ddH2O	1000 ml	1000 ml
  Autoclave each solution and store at room temperature.

• The batch media, in a bioreactor vessel, is inoculated with ˜10 ml of a 3 day old N. eutropha D23 culture (i.e. 1% volume). The pH is adjusted to 7.6 using 7.5% Na₂CO₃ The bioreactor is run in batch mode with below parameters: pH: 7.6 (lower limit: 7.45 & upper limit: 7.8), Temperature: 28° C. (lower limit: 25° C. & upper limit: 32° C.), DO (dissolved oxygen): 45% (lower limit: 10%, upper limit: 100%), Stirrer: 550 rpm.
• The OD600 nm of the culture in the bioreactor reaches 0.15 to 0.18 in 3-4 days. At this point, the culture will consume most of the 50 mM NH₄+ present in the AOB growth media, and a user should start feeding the bioreactor with feeding solution at 0.59 ml/min (˜10%). The outflow pump should also be turned on at 0.59 ml/min (˜10%). The OD600 nm of the bioreactor reaches 0.5-0.6 in 1-2 days of continuous culture. The culture in the bioreactor is tested for heterotrophic contaminants by plating 1 ml of the bioreactor outflow on an LB plate.
• Monitoring Growth of N. eutropha D23
• Growth of N. eutropha D23 cells is monitored by measuring the OD600 nm of the culture. Typical growth in a batch culture as measured by OD600 nm is between 0.06 to 0.08.
• The AOB growth medium contains NH₄+ that is stoichiometrically converted to NO₂− by N. eutropha D23. Another way to monitor the growth of N. eutropha is to follow the release of nitrite (NO₂−) in the growth medium. NO₂− concentration is determined with Griess reagents, sulfanilamide and N-naphthylethylenediamine (also called NNEQ). Briefly, sulfanilamide and NNEQ are added to a sample and to known concentrations of sodium nitrite that make up a standard curve. Samples are incubated in the dark for 30 minutes. The absorbance is read at 540 nm.
• Another way to follow nitrite production is by using a spectrophotometer by monitoring the optical density (OD) difference between 352 nm and 400 nm. The nitrite concentration is determined using a millimolar extinction coefficient of 0.0225 mM⁻¹. This assay can be performed directly by sampling the medium with the cells.
• 
  NO₂− concentration (mM)=(OD₃₅₂−OD₄₀₀)/0.0225
• The growth of a mixed culture comprising D23 was monitored by measuring optical density at 600 nm (OD600 nm) and by measuring Nitrite (NO₂ ⁻), and the growth rate is shown in FIGS. 1 and 2. FIG. 1 shows that the optical density at a 600 nm wavelength plateaus slightly below 0.1, after 3 to 4 days. FIG. 2A shows that the amount of nitrite produced plateaus slightly below 25 mM after 3 to 4 days. NO₂ ⁻ concentrations in the cultures were determined colorimetrically by the Griess reagent (Hageman & Hucklesby, 1971), and is used as a second indicator for the growth rates and growth phases since the accumulation of NO₂ ⁻ is consistently proportional to the increase in cell mass during growth.
• In FIG. 2B-I, increasing densities of D23 harvested from continuous culture were suspended in medium supplemented with 50 mM NH₄ ⁺ and grown shaking at 30° C. for 48 hours. Nitrite production was measured in supernatant samples using the Griess assay at the time points indicated. Results shown are mean values±SD from three independent experiments.
• In FIG. 2B-II. Nitrite production by N. eutropha D23 in vitro is shown. Increasing densities of D23 were suspended in mineral salt medium supplemented with 50 mM NH₄ ⁺ and grown shaking at 30° C. for 24 hr. Nitrite production was measured in supernatant samples using the Griess assay at the time points indicated.
• Storage Conditions
• N. eutropha suspensions obtained from the continuous culture system showed remarkable stability upon storage at 4° C. for several months, as indicated by the highly consistent nitrite concentrations generated upon subculture under batch growth conditions. Protocols for storing and recovering N. eutropha are set out below.
• Obtain 500 ml of a N. eutropha D23 culture grown to late-exponential phase (OD600=0.5-0.6 in continuous culture). Centrifuge at 10,000×g for 15 min at 20° C. Remove supernatant and resuspend the pellet in 50 ml of AOB storage buffer. Spin as above. Remove supernatant and resuspend thoroughly in a total of 50 ml storage buffer. This would be the 10× AOB stock. Store upright at 4° C. in 50 ml polypropylene tubes.
• AOB Storage Buffer (for AOB storage at 4° C.): 50 mM Na₂HPO₄-2 mM MgCl₂ (pH 7.6) can be made as follows.
• In 1 Liter ddH2O: Na₂HPO₄-7.098 g
• MgCl₂-0.1904 g
• Adjust pH to 7.6. Filter-sterilize.
• N. eutropha may be cryopreserved as follows. Transfer 1.25 ml of N. eutropha D23 mid-log culture to a 2 ml cryotube and 0.75 ml of sterile 80% glycerol. Shake tubes gently, incubate at room temperature for 15 min to enable uptake of the cryoprotective agents by the cells. Then, put tubes directly in a −80oC freezer for freezing and storage. For resuscitation of cultures, thaw frozen stocks on ice for 10-20 minutes. Centrifuge, at 8,000×g for 3 minutes at 4° C. Discard supernatant and wash the pellet by suspending it in 2 ml AOB medium followed by another centrifugation at 8,000×g for 3 minutes at 4° C. to reduce potential toxicity of the cryoprotective agents in subsequent growth experiments. Discard the supernatant and resuspend the pellet in 2 ml of AOB medium, inoculate into 50 ml of AOB medium containing 50 mM NH₄ ⁺, and incubate in dark at 30° C. by shaking at 200 rpm.
• In FIG. 2C, stability upon storage at 4° C. was studied. N. eutropha D23 previously harvested from continuous culture and stored at 4° C. was inoculated at 10⁹ CFU/ml in mineral salt medium supplemented with 50 mM NH₄ ⁺ and grown shaking at 30° C. Nitrite production was determined at 24 and 48 hours post-incubation (left and right panel, respectively). Data shown are representative of a D23 suspension sampled repeatedly over a 6-month period.
Example 3 Creation of an Axenic D23 Culture
• To isolate N. eutropha D23 in pure culture, four types of media (described below) were made, autoclaved and poured in plates. Sterile nylon membranes were placed on the plates.
• N. europaea media+1.2% R₂A agar
  N. europaea media+1.2% agar
  N. europaea media+1.2% agarose
  N. europaea media+1.2% agarose+0.3 g/L pyruvate
• 3 day old N. eutropha D23 culture was streaked onto the nylon membranes and the plates were incubated at 30° C. The plates were monitored daily for growth of red colored N. eutropha cells. Nylon membranes were transferred to fresh plates once a week.
• Reddish colored colonies appeared on plates with R₂A agar or agar by end of 1 week. Single colonies were picked from plates with R2A agar and grown in N. europaea media. The cultures grew well in 6 days to 0.08 OD600 nm. Heterotrophic colonies appeared when the culture was plated on LB-Agar plates.
• Reddish colored colonies on plates with R₂A agar, agar, agarose, or agarose+pyruvate appeared by end of 2 weeks. Single colonies were picked from plates with agar or agarose and grown in N. europaea media. The cultures grew well in 6-8 days to 0.08 OD600 nm. Heterotrophic colonies appeared when the culture was plated on LB-Agar plates.
• Bright reddish colonies on plates with R₂A agar, agar, agarose, or agarose+pyruvate appeared by end of 4 weeks. Single colonies were picked from plates with agarose and grown in N. europaea media. The cultures grew well in 6-8 days to 0.08 OD600 nm. White colonies appeared when the culture was plated on LB-Agar plates.
• Contaminating bacteria (e.g., non-N. eutropha bacteria present in the mixed culture) were identified by culturing, amplifying 16S rRNA by PCR, and sequencing of the PCR products. Contaminants were identified as Microbacterium sp. and Alcaligenaceae bacterium.
• To create an axenic culture of D23 (i.e., free of contaminating bacteria) serial dilution was used. Eight single colonies (designated A-H) were picked, and each was placed into a 10 ml culture of N. europae medium. For each culture, five sequential 1:10 dilutions were created. For each culture A-H, growth was observed in the two or three most concentrated of the dilutions.
• A second serial dilution was carried out. 50 ml of media was inoculated with approximately 2×10⁸ N. eutropha cells, and sequential dilutions of 1:50 were made, such that after the fifth dilution, a flask was expected to have approximately one cell. Flasks that exhibited bacterial growth were plated on LB-agar to assay for contaminating bacteria, and no contaminating bacteria were observed. In addition, no contaminating gram positive cells were observed under the microscope.
• Accordingly, the serial dilution process yielded an axenic or substantially axenic culture of N. eutropha.
Example 4 Sequencing of the D23 Genome
• Strain D23 was obtained as described in Example 1, and was made axenic as described in Example 3.
• A 10 ml aliquot the bacterial sample was inoculated into approximately 1 L of N. europaea growth medium described in Example 2. The culture grew well to optical density of 0.08 at 600 nm in a batch culture in 3 days.
• Total DNA of the culture was prepared and sequenced using Illumina® technology and/or SMRT® DNA Sequencing System technology, Pacific Biosciences. The strain was identified as Nitrosomonas eutropha and was designated D23.
• The genome sequence of D23 was compared to that of N. eutropha C91, which is believed to be the only other sequenced strain of N. eutropha.
• The length of the D23 chromosome is 2,537,572 base pairs, which is shorter than the 2,661,057 base pair chromosome of N. eutropha strain C91 chromosome. Based on the 16S-23S operon, strain D23 has 99.46% identity to C91 and 95.38% identity to N. europaea. DNA sequencing of N. eutropha D23 indicated that this strain lacks plasmids. This contrasts with the sequence of strain C91, which has two plasmids.
• Protein-encoding regions and RNA-encoding sequences were identified by sequence analysis. Supplementary Table 1 is a table of annotations that lists the positions of 2,777 genes in the D23 genome (SEQ ID NO: 1).
• On the level of individual genes, several genes are present in D23 that are absent in C91. These genes are summarized in FIGS. 6-8. FIG. 6 is a table displaying unique D23 genes with an assigned ORF number and a function based on sequence analysis, or a hypothetical gene above 200 base pairs in length. There are 162 genes in this category. FIG. 7 is a table displaying unique D23 genes below 200 base pairs that have an assigned ORF number. There are 164 of these genes. FIG. 8 is a table displaying unique D23 genes with no assigned ORF number. There are 219 of these genes (of which 180 are below 200 bp in length).
• Strain D23 also lacks a number of genes that are present (or lack close homologs) in strain C91. These genes are sometimes referred to as unique C91 genes. These genes include the about 300 genes listed in FIG. 9.
• D23 contains several ammonia metabolism genes that differ from their homologs in C91. Certain of these genes are enumerated in Table 1 of the Detailed Description. Sequence alignments were performed between the D23 proteins and their homologs in strain C91. The sequence alignments are shown in FIGS. 10-16 and sequence differences between the two strains are shown in Table 2 of the Detailed Description.
• The sequence comparisons revealed the percent sequence identities between the C91 and D23 homologs of each protein. More specifically, FIG. 10 is an alignment between AmoA1 and AmoA2 of strains C91 and D23. Each protein is identical at 273/276 residues, and so each is about 98.9% identical between strains. FIG. 11 is an alignment between AmoB1 and AmoB2 of strains C91 and D23. Both proteins are identical at 419/421 positions, and so are about 99.5% identical between strains. FIG. 12 is an alignment between AmoC1 and AmoC2 of strains C91 and D23. Both proteins are identical throughout. FIG. 13 is an alignment between AmoC3 of strains C91 and D23. This protein is identical at 272/274 positions, and so are about 99.3% identical between strains.
• As to the Hao proteins, FIG. 14 (A and B) is an alignment between Hao1, Hao2, and Hao3 of strains C91 and D23. Hao1 is identical at 567/570 positions, and so each is about 99.5% identical between strains. Hao2 and Hao3 are each identical at 568/570 positions, and so are about 99.6% identical between strains.
• Turning now to cytochrome c554 proteins, FIG. 15 is an alignment between CycA1, CycA2, and CycA3 of strains C91 and D23. CycA1 is identical at 233/235 positions, and so is about 99.1% identical between strains. CycA2 and CycA3 are each identical at 234/235 positions, and so each is about 99.6% identical between strains.
• As to the cytochrome c_M552 proteins, FIG. 16 is an alignment between CycB1 and CycB2 of strains C91 and D23. CycB1 is identical at 232/239 positions, and so is about 97.1% identical between strains. CycB2 is identical at 236/239 positions, and so is about 98.7% identical between strains. Here, the length of the protein is considered 239 amino acids because that is its length in strain D23.
• Alignment of the nucleic acid sequences of Table 1 shows the percent identity between homologs in C91 and D23. The amoA1 genes are about 98.8% identical (i.e., at 821/831 positions), the amoA2 genes are about 98.8% identical (i.e., at 821/831 positions), the amoB1 genes are about 99.1% identical (i.e., at 1255/1266 positions), the amoB2 genes are about 99.1% identical (i.e., at 1254/1266 positions), the amoC1 genes are about 99.8% identical (i.e., at 814/816 positions), the amoC2 genes are about 99.8% identical (i.e., at 814/816 positions), and the amoC3 genes are about 98.9% identical (i.e., at 816/825 positions). The hao1 genes are about 99.0% identical (i.e., at 1696/1713 positions), the hao2 genes are about 99.4% identical (i.e., at 1702/1713 positions), and the hao3 genes are about 99.2% identical (i.e., at 1700/1713 positions). Of the cytochrome c554 genes, the cycA1 genes are about 98.0% identical (i.e., at 694/708 positions), the cycA2 genes are about 98.7% identical (i.e., at 699/708 positions), and the cycA3 genes are about 99.3% identical (i.e., at 703/708 positions). Of the cytochrome c_M552 genes, the cycB1 genes are about 96.7% identical (i.e., at 696/720 positions) and the cycB2 genes are about 97.1% identical (i.e., at 702/723 positions).
Example 5 Competitive Growth Studies
• A study was designed to determine whether N. eutropha strain D23 could inhibit the growth of undesirable bacteria such as Pseudomonas aeruginosa (P. aeruginosa or PA), Staphylococcus aureus (S. aureus or SA), Streptococcus pyogenes (S. pyogenes or SP), Acinetobacter baumannii (A. baumannii or AB), and Propionibacterium acnes, all of which are important pathogenic agents frequently isolated from either one or both of infected skin and wound sites. This protocol may also be used to test other N. eutropha strains for the ability to inhibit the growth of undesirable bacteria.
• Briefly, a suitable protocol can comprise the following steps. At t=0, a culture is inoculated with N. eutropha, and then the N. eutropha is incubated for 24 hours. Culture characteristics (e.g., pH and nitrite levels) are assayed. At t=24 hours, the undesirable bacterium is added to the culture. Immediately upon addition, samples are obtained for determining CFU/ml of the undesirable bacteria and optionally CFU/ml of N. eutropha, pH, and nitrite levels. Incubation is allowed to proceed for an additional 24 hours. At subsequent timepoints, e.g., t=30 and t=48, one can take the same measurements as at t=24. To determine CFU/ml, one can plate neat/−1/−2/−3/−4/−5 (or higher) to obtain accurate counts.
• A more detailed protocol is set out below.
Day 1
• 1. Mix the 10×AOB stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained.
• 2. Aliquot 10 ml of the suspension in 8×1.5 ml polypropylene tubes.
• 3. Centrifuge at 17,000×g for 3 min at room temperature.
• 4. Remove supernatant and any residual buffer from each pellet and resuspend all pellets thoroughly into a total of 10 ml complete AOB medium in a 50 ml polypropylene tube.
• 5. Pipet 5 ml of 10×AOB suspension in each of two 50 ml polypropylene tubes (Tube 1-2).
• 6. Prepare five additional tubes (Tube 4-8) containing 10×AOB suspensions in complete AOB medium/0.5× Phosphate Buffer. Aliquot 26 ml of the 10×AOB stock suspension in 16×1.5 ml polypropylene tubes. Obtain pellets as above and resuspend in a total of 26 ml complete AOB medium/0.5× Phosphate Buffer in a 50 ml polypropylene tube.
• 7. Pipet 5 ml of the 10×AOB suspension in each of five 50 ml polypropylene tubes (Tube 4-8).
• 8. Also, prepare two tubes with 10× Heat-killed AOB suspensions in either complete AOB medium (Tube 3) or complete AOB medium/0.5× Phosphate Buffer (Tube 9). Aliquot 10 ml of the Heat-killed suspension stored at 4° C. in 8×1.5 ml polypropylene tubes. Centrifuge at 17,000×g for 3 min at room temperature and remove supernatant, as described above for live AOB. Resuspend four pellets in a total of 5 ml complete AOB medium in one 50 ml polypropylene tube (Tube 3) and the remaining four pellets in a total of 5 ml complete AOB medium/0.5× Phosphate Buffer in a second 50 ml polypropylene tube (Tube 9).
• 9. Add 141 μl of 1 M ammonium sulfate to obtain 25 mM final concentration ( Tube 1, 3, 4, 5, 9). Add an equal volume of dH₂O to corresponding control tubes ( Tube 2, 6, 7).
• 10. To Tube 8, add 141 μl of fresh 1 M NaNO₂.
• 11. Swirl all tubes gently, but thoroughly, to mix.
• 12. Immediately after mixing each suspension, remove 0.5 ml from each tube and centrifuge all samples at 17,000×g, 3 min, RT. Transfer supernatants into fresh tubes after completing step 13, and measure both pH and nitrite levels using Griess Reagent to obtain TO values.
• 13. Incubate all 50 ml tubes at 30° C. with mixing on an orbital shaker at 150 rpm (upright position) for 24 hr.

• TABLE 5
  T0

  			10x				T24
  		10x	Killed	1M		1M	SA/PA
  		AOB	AOB	(NH4)2SO4	H2O	NaNO2	in saline
  SAMPLE	Tube	(ml)	(ml)	(μl)	(μl)	(μl)	(ml)

  Complete AOB medium

  10x AOB + NH 4 +	1	5	—	141	—	—	0.5
  10x AOB	2	5	—	—	141	—	0.5
  10x Killed AOB +	3	—	5	141	—	—	0.5
  NH4 +

  Complete AOB medium/0.5x Phosphate Buffer

  10x AOB + NH 4 +	4	5	—	141	—	—	0.5
  10x AOB + NH 4 +	5	5	—	141	—	—	0.5
  10x AOB	6	5	—	—	141	—	0.5
  10x AOB	7	5	—	—	141	—	0.5
  10x AOB + NaNO 2	8	5	—	—	—	141	0.5
  10x Killed AOB +	9	—	5	141	—	—	0.5
  NH4 +

Day 2
• 14. At 24 hr, prepare SA, PA, SP or AB inocula to add to the suspensions.
• 15. From an overnight (20-24 hr) SA or PA culture grown on Tryptic Soy Agar (TSA), or a SP or AB culture prepared on Brain Heart Infusion (BHI) Agar, prepare bacterial suspension in Tryptic Soy Broth (TSB) or BHI broth (BHIB) at ˜2×10⁸ CFU/ml.
• 16. Pipet 50 μl of the SA/PA/SP/AB suspension in 9.95 ml saline to obtain ˜10⁶ CFU/ml. Keep on ice, as needed.
• 17. Vortex SA/PA/SP/AB suspension and add 0.5 ml to Tube 1-9.
• 18. Swirl all tubes gently, but thoroughly, to mix.
• 19. Immediately after mixing each suspension, transfer 100 μl from each tube into 0.9 ml TSB or BHIB (10⁻¹ dilution) to neutralize samples for CFU determination. In addition, remove 0.5 ml from each tube and centrifuge at 17,000×g, 3 min, RT. Recover supernatants in fresh tubes after completing Step 20 and measure both pH and nitrite levels using Griess Reagent after Step 21 to obtain T24 values.
• 20. Incubate all 50 ml tubes at 30° C. with mixing on an orbital shaker (150 rpm) for an additional 24 hr.
• 21. Dilute T24 samples further in TSB or BHIB and plate −2/−3/−4 dilutions on TSA or BHI agar. Incubate plates at 37° C. for 24 hr to obtain SA, PA, SP, or AB viable counts.
• 22. At 6 and 24 hr post-mixing of SA/PA/SP/AB with AOB, vortex tubes and pipet 100 μl samples into 0.9 ml TSB. Dilute further in TSB or BHIB and plate neat through −5 dilutions on TSA or BHI agar. At each time point, also remove 0.5 ml from each tube and measure both pH and nitrite levels in each supernatant sample, as described above.
• 23. Incubate TSA or BHI agar plates at 37° C. for 24 hr to obtain T30 (6 hr) and T48 (24 hr) viable counts.
• 24. Count CFU to determine % killing rates for each time point
Griess Reagent Assay for Nitrite Quantification
• 1. Use the 0.5 ml supernatant samples obtained for pH determination at 0, 2, 6, and 24 hr.
  2. Serially dilute 56 μl of the supernatant in 0.5 ml dH2O to obtain 10-100- and 1000-fold dilutions, as needed. For TO samples, use 1/10 for Tube 1-6, 8, 9, and 1/1000 for Tube 7. For T24/T30/T48 samples, use 1/10, 1/100, 1/1000 for all tubes,
  3. To prepare sodium nitrite standards, dilute 10 μl of a fresh 1 M stock in 990 μl complete AOB medium-10% saline to obtain a 10 mM solution.
  4. Dilute 10 μl of the 10 mM stock in 990 μl dH₂O to obtain a 100 μM working solution.
  5. Prepare standards in dH₂O as shown below. Run standards only with TO samples.

• 	TABLE 6
  	100 μM		Nitrite
  	sodium nitrite	dH2O	conc	A540nm
  	(μl)	(μl)	(μM)	(indicative values)

  	0 (blank)	500	0	0
  	62.5	437.5	12.5	0.307
  	125	375	25	0.607
  	250	250	50	1.164
  	500	0	100	2.35

  
  6. To each 0.5 ml sample (or sodium nitrite standard), add 0.25 ml each of Reagent A (58 mM sulfanilamide in 1.5 N HCl) and Reagent B (0.77 mM n-(1-napthyl) ethylene diamine-2HCl in H₂O (light-sensitive; store in dark).
  7. Mix and let stand at room temperature for 30 min in the dark (or cover with foil). The color should change to a vivid pink/violet.
  8. Read absorbance at 540 nm and determine nitrite concentrations from standard curve.
• This protocol was used to test N. eutropha D23's ability to inhibit the growth of P. aeruginosa (PA), S. aureus (SA), S. pyogenes (SP), A. baumannii (AB), or P. acnes. The results of this experiment are shown in FIGS. 3A, 3B, and 3C.
• The left panel of FIG. 3A plots CFU/ml of PA versus time, when PA is co-cultured with live N. eutropha and ammonium (squares), live N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO₂ (inverted triangles). The right panel of FIG. 3A plots CFU/ml of SA versus time, under the same conditions. The left panel of FIG. 3B plots CFU/ml of SP versus time, under the same conditions. The right panel of FIG. 3B plots CFU/ml AB versus time, under the same conditions. FIG. 3C plots CFU/ml of P. acnes versus time, when P. acnes is co-cultured with live N. eutropha and ammonium (squares), live N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO₂ (inverted triangles). In all cases, live N. eutropha with ammonium results in declining numbers of PA, SA, SP, AB, or P. acnes whereas the other culture conditions allow the undesirable bacteria to grow. Without being bound by theory, these experiments suggest that nitrite generation from ammonia concurrently with medium acidification by D23 led to strong antibacterial effects, e.g., an approximately 100-fold reduction in viable counts of methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pyogenes, Acinetobacter baumannii, or P. acnes. By contrast, control co-cultures of pathogenic bacteria either with heat-killed D23 supplemented with ammonia, or with live D23 without ammonia, did not produce comparable antibacterial effects. The control comprising live N. eutropha culture without ammonium is consistent with the model that N. eutropha's ammonia oxidation activity contributes to its antibacterial effects. The control comprising killed N. eutropha and ammonium indicates that some biological activity of the N. eutropha (e.g., its ammonia oxidation activity) contributes to antibacterial activity. The control comprising live N. eutropha with NaNO₂ indicates that comparable nitrite levels at neutral pH (versus low pH when the bacteria use ammonia) do not have a strong antimicrobial effect, and is consistent with the model that N. eutropha's oxidation of ammonia, rather than nitrite alone, contributes to the antibacterial activity.
• The top panel of FIG. 4A plots the NO₂ ⁻ concentration over time in the co-cultures described in the paragraph above. NO₂ ⁻ concentration is an indication of the rate of NH₃ metabolism in the cultures. As above, PA is co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), or killed N. eutropha and ammonium (triangles). Live N. eutropha with ammonium produces dramatically higher NO₂ ⁻ levels than the two control cultures, indicating that the live N. eutropha converts ammonium into NO₂ ⁻ under the culture conditions.
• The bottom panel of FIG. 4A plots pH over time in the same co-culturing conditions. pH indicates the metabolic activity of the N. eutropha because the conversion of ammonia to nitrite produces hydrogen ions. PA is co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO₂ (inverted triangles). Live N. eutropha with ammonium acidifies the medium, in contrast to the three control cultures, indicating that the live N. eutropha metabolizes ammonium under the culture conditions.
• The top panels of FIG. 4B plot the NO₂ ⁻ concentration over time in the co-cultures described above. NO₂ ⁻ concentration is an indication of the rate of NH₃ metabolism in the cultures. As above, S. pyogenes (SP) and A. baumannii (AB) are co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), or killed N. eutropha and ammonium (triangles). Live N. eutropha with ammonium produces dramatically higher NO₂ levels than the two control cultures, indicating that the live N. eutropha converts ammonium into NO₂ ⁻ under the culture conditions.
• The bottom panels of FIG. 4B plot pH over time in the same co-culturing conditions. pH indicates the metabolic activity of the N. eutropha because the conversion of ammonia to nitrite produces hydrogen ions. SP and AB are co-cultured with N. eutropha and ammonium (squares), N. eutropha without ammonium (circles), killed N. eutropha and ammonium (triangles), or live N. eutropha with NaNO₂ (inverted triangles). Live N. eutropha with ammonium acidifies the medium, in contrast to the three control cultures, indicating that the live N. eutropha metabolizes ammonium under the culture conditions.
• FIG. 4E shows an alternative visualization the data of FIGS. 4A and 4B.
• The capacity of Nitrosomonas eutropha D23 to inhibit proliferation of pathogenic bacteria due to nitrite production concurrent with acidification (acidified nitrite) was assessed by testing the survival of 5 strains of pathogenic bacteria in co-culture studies with D23 in vitro. The five strains of pathogenic bacteria included Propionibacterium acnes, Streptococcus pyogenes, methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa, and multidrug-resistant Acinetobacter baumannii. Incubation of N. eutropha D23 (10¹⁰ cells/ml) in the presence of ammonium led to nitrite concentrations of 10 mM or higher and acidification to pH 6 or lower (FIG. 4B). The combination of increased nitrite concentration and lowering of pH led to bactericidal or bacteriostatic effects and a marked reduction (up to 965-fold) in viable counts of the pathogenic bacterial species tested. The results of these studies are summarized in FIG. 4D and Table 7, below. In contrast to the D23 co-cultures incubated in the presence of ammonium, control co-cultures of the five pathogenic agents with D23 without ammonium, or with heat-killed D23 (B244) supplemented with ammonium, did not lead to any inhibitory or antimicrobial effects.

• TABLE 7
  Effect of N. eutropha D23 (D23) on relative survival of pathogenic
  bacteria in vitro

  Relative Survival (Fold Change)

  			Heat-Killed
  Pathogen Tested	AOB + NH3	AOB − NH3	AOB + NH3

  Priopionibacterium acnes	−114	−19,067	−1.05
  ATCC 6919
  Staphylococcus aureus (MRSA)	−117.6	8.2	2.03
  ATCC BAA-1717
  Pseudomonas aeruginosa	−84.3	2.65	379
  ATCC 15442
  Streptococcus pyogenes	−965	−2.88	−3.81
  ATCC 19615
  Acinetobacter baumannii (MDR)	−5.43	92.4	89.8
  ATCC BAA-1605

Example 6 Wound Healing
• The effect of Nitrosomonas eutropha D23 (sometimes also called B244) on wound closure in diabetic mice was evaluated in two separate studies. In Study 1, db/db mice (8 mice/group) were pre-treated by body immersion daily for one week with 3 concentrations of D23 (10⁷, 10⁸ or 10⁹ cells/ml) supplemented with ammonium chloride, or with vehicle control suspension only. Subsequently, full-thickness wounds generated on the back of each animal were treated topically once daily for 14 days with vehicle alone or equal volumes of 3 concentrations of D23 (10⁷, 10⁸ or 10⁹ cells/ml) in PBS supplemented ammonium chloride. Of the three D23-treated groups, the group receiving the highest dose showed significant improvement in wound closure from day 5 to day 15, with the most pronounced improvement of 83% observed on day 9 post-wounding. The median time to 50% wound closure was significantly reduced (P<0.05) for the animals treated with 10⁹ cells/ml of D23, as compared to the animal group receiving vehicle treatment alone.
• Initial histopathology analyses of wound tissue samples collected on Day 15 upon study completion did not reveal any gross differences between vehicle- and D23-treated animals. Subsequently, a more in-depth examination of the tissue sections was performed according to the scoring system and parameters adapted and modified form Altavilla, et al (2001). This analysis suggested a trend of increased levels of angiogenesis and maturity of granulation tissue with decreased levels of dermal inflammation in animals treated with 10⁹ cells/ml of D23 versus the vehicle control group, which was consistent with the observed improvement in wound healing rates of the D23-treated animals
• N. eutropha strain D23 was tested for its ability to accelerate wound healing in a diabetic mouse model, using C57BLKS/J Iar−+Lepr^db/+Lepr^db male mice (non-GLP). A detailed protocol is set out below.
• Day −6 to Day 1: Whole-Body Immersion Pre-Treatment of Mice with Test Organism
• • 1. Mix the 10×D23 stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained.
  • 2. Pipet 2×29 ml of the 10× stock suspension into two 50 ml polypropylene centrifuge tubes.
  • 3. Centrifuge at 8,000×g for 15 min at 20° C.
  • 4. Remove supernatant and any residual buffer from the pellets and resuspend the two pellets gently but thoroughly into a total of 58 ml room-temperature Phosphate Buffered Saline, pH 7.4 (PBS). This is the 10×D23 (Test Organism) suspension to use for the following steps.
  • 5. Prepare 500 ml baths containing the Test Organism at 1×, 0.1× and 0.01× strength in pre-warmed PBS at 30° C. supplemented with 2 mM NH₄Cl, or a Vehicle control bath, as shown below. Prepare and use one bath at a time from the 10×D23 suspension kept at room temperature before continuing with the next bath. This will prevent keeping the Test Substance at 30° C. for long time periods without ammonium. To prevent contamination of the Vehicle control group with the Test Substance, begin with the Vehicle control group before proceeding with the D23 baths.
  • 6. Immerse each group of mice in corresponding baths for 60 sec daily for seven days.
  • 7. Use a fresh 500 ml baths for each daily immersion into the Test Organism or Vehicle control.

• 	TABLE 8
  		10× D23		1M
  		(room	PBS	NH4/
  	BATH/	temp.)	pH 7.4	Cl	CFU/
  	GROUP	(ml)	(ml)	(ml)	ml

  	Vehicle	—	500	1.0	0
  	(control)
  	1× D23	50	450	1.0	109
  	0.1× D23	5	495	1.0	108
  	0.01× D23	0.5	499	1.0	107

Day 1: Wounding of Mice by Skin Puncture
• • 1. Generate skin wounds on the back of each mouse by skin puncture after shaving of the back and shoulders.
  • 2. House each mouse separately for the remainder of the study.
    Day 1 to Day 15: Topical Treatment of Skin Wounds with Test Organism
  • 1. Mix the 10×D23 stock suspension stored at 4° C. by inverting several times until a homogenous suspension is obtained.
  • 2. Pipet 1 ml of the 10× stock suspension into a 1.5 ml polypropylene tube.
  • 3. Centrifuge at 17,000×g for 3 min at room temperature.
  • 4. Remove supernatant and any residual buffer from the pellet and resuspend pellet gently but thoroughly into a total of 10 ml pre-warmed Phosphate Buffered Saline, pH 7.4 (PBS) at 30° C. This is the 1×D23 (Test Organism) suspension to use for the following steps.
  • 5. Prepare 1×, 0.1× and 0.01× suspensions of the Test Organism in pre-warmed PBS supplemented with 2 mM NH₄Cl, or a Vehicle control solution, in 50 ml polypropylene tubes as shown below.
  • 6. Draw 2.0 ml of each suspension using a repetitive pipet.
  • 7. Drip slowly 0.2 ml of the Test Organism (1×, 0.1×, 0.01× groups), or an equal volume of Vehicle control, onto each wound and surrounding shaved skin area. Gently spread applied suspension onto the wound and the entire shaved skin area using a pipet tip.
  • 8. Repeat application of Test Organism or Vehicle control daily for a total of 14 days.
  • 9. Measure wound size by wound planimetry and obtain photo images of each wound on Day 1, 3, 5, 7, 9, 11, 13 and 15 using Image Analyzer (Image-pro plus version 4.5, Media Cybernetics Inc).
  • 10. Calculate % wound closure and wound half-closure time (CT₅₀) for each group.

• TABLE 9
  		PBS	1M
  	1× D23	pH 7.4	NH4Cl	CFU/	CFU/
  GROUP	(ml)	(ml)	(μl)	ml	wound

  Vehicle		5.0	10	0	0
  (control)
  1× D23	5.0	0	10	109	2 × 108
  0.1× D23	0.5	4.5	10	108	2 × 107
  0.01× D23	0.05	4.95	10	107	2 × 106

Day 15 (Upon Study Completion): Collection of Wound Tissues Samples and Histopathology Analyses
• • 1. Obtain half-wound tissue samples from four mice per group using aseptic technique to avoid cross-contamination of tissues.
  • 2. Proceed with histopathology analyses.
  • 3. Store temporarily at −70° C. the remainder half-wound samples and the additional four full-size wound tissues from each group for further evaluation.
• As shown in FIG. 5A, topical application of 10⁹ CFU/ml of strain D23 significantly (*p<0.05) accelerated wound healing. The sample size was N=8 animals/gp. The group receiving the highest doses showed significant improvement in would closure from day 5 to day 15, with the most pronounced improvement of 83% observed on day 9, post-wounding. This study demonstrates the potential therapeutic benefit of ammonia oxidizing bacteria, e.g., D23, to diabetic foot ulcers, chronic wounds, and other related indications.
• FIG. 5B is a plot showing CT₅₀ versus control (vehicle) and 10⁹ CFU/ml D23. CT50 is the time required to achieve a 50% wound closure. As shown in the plot, those wounds having application of D23 provided for lower CT₅₀ values.
• FIG. 5C is a plot of another experiment in which the protocol above was carried out to obtain wound closure measurements versus time. Control (vehicle) wounds were tested and compared to D23 at 10⁹ CFU/ml wounds. This plot shows the effects of D23 when immersion pre-treatment and topical application was carried out.
• FIG. 5D is a plot of another experiment in which the protocol above was carried out, without immersion pre-treatment, to obtain wound closure measurements versus time. Control (vehicle) wounds were tested and compared to applications of D23 at 10⁹ CFU/ml and 10¹⁰ CFU/ml to wounds. This plot shows the effects of D23 when topical application was carried out.
• FIG. 5E is a plot showing CT₅₀ versus control (vehicle) and 10⁹ CFU/ml D23, with and without immersion pre-treatment, and 10⁹ CFU/ml D23 without pre-treatment. As shown in the plot, those wounds having application of D23 provided for lower CT50 values.
• FIG. 5F are images of the wound healing experiments, at Day 1, Day 11, and Day 15. AOB represents D23.
• Possible modulation of inflammatory responses coupled with ant-infective action of D23 could prove an effective topical treatment against diabetic and other chronic wounds.
• FIG. 5G are plots of blood glucose levels in the mice tested for the control (vehicle) and various concentrations of D23. “IM” shown in the x-axis of the right-hand panel plot represents those tests down with an immersion pre-treatment of D23. FIG. 5H is a plot of body weight of the animals used in testing for the study including immersion pre-treatment, over the time of the study. FIG. 5I are plots of body weight of the animals used in testing for the study, including the immersion pre-treatment study, and the study done without immersion pre-treatment, over the time of the studies.
• In Study 2, the effect of pretreatment of db/db mice with 10⁹ cells/ml of B244 on wound closure was examined. Groups of seven mice were treated topically with 10⁹ cells/ml of B244 with and without prior body immersion. One additional group of seven mice was treated topically with 10¹⁰ cells/ml of D23 (B244). Corresponding vehicle groups (seven mice) were run in parallel with and without body immersion as negative controls. Wound surface area and photo images of each wound were obtained as before. These studies reproduced the findings of Study 1 suggesting improvement of wound closure with a B244 dose of approximately 10⁹ cells/ml. Moreover, topical treatment alone with 10⁹ cells/ml improved wound closure rates similar to the animals receiving topical treatments with immersion. Additional histopathology analyses by of H & E—stained wound tissue sections recovered on Day 5 did not reveal any differences between vehicle and D23 (B244)-treated wounds.
• Cytokine and growth factor expression in D23-treated diabetic animals was investigated using Luminex technology. Specifically, expression of growth-regulated oncogene/keratinocyte chemoattractant (Gro/KC), interleukin-1 (IL-1), interleukin-6 (IL-6), macrophage inflammatory protein-2 (MIP-2), tumor necrosis factor (TNF), and vascular endothelial growth factor (VEGF) was compared between D23-treated and control diabetic animals in serum samples obtained on Day 5 and Day 15 from four mice per group treated with or without prior body immersion. In similar Luminex analyses, lysates of tissues from D23-treated or Vehicle control animals obtained upon completion of the study (Day 15) were also analyzed. Abnormally high and sustained expression of inflammation markers, including MIP-2, TNFα and IL-1β, has been previously associated with a dysregulated inflammatory response and impaired wound healing processes in db/db mice (Wetzler, 2000). Analyses of Day 5 and Day 15 serum samples yielded very low signal for all six cytokines in both D23-treated and vehicle control animals, a result indicating the lack of systemic effects following wound treatment with high D23 doses. In wound tissue lysates obtained on Day 15, MIP-2 levels (1155-1516 pg/100 g total protein) were significantly higher than the remaining five cytokines, with IL-6 and Gro/KC measured at much lower levels (44-48 pg/100 g total protein) and both IL-1 and VEGF being close to undetectable (≦3.8 pg/100 g total protein). Overall, no difference was observed between D23-treated animals and vehicle control animals with or without full-body immersion in D23 suspensions. The levels of all six cytokines or growth factors measured in tissue lysates of all four groups of mice examined are summarized in Table 10 below.

• TABLE 10
  Cytokine levels measured in wound tissue lysates of D23-treated and vehicle
  control-treated db/db mice

  					MIP-2
  		Gro/KC	IL-1β	IL-6	(pg/	TNFα	VEGF
  		(pg/100 g	(pg/100 g	(pg/100 g	100 g	(pg/100 g	(pg/100 g
  Treatment	Animal	protein)	protein)	protein)	protein)	protein)	protein)

  Vehicle	1-1	49	2.4	78	1089	28.7	5.8
  (with prior	1-3	66	2.4	134	1335	31.2	4.5
  immersion)	1-5	59	2.7	128	1112	25.7	4.2
  	1-7	76	1.2	148	1013	9.4	4.1
  	MEAN	62	2.2	122	1137	23.7	4.7
  D23	3-1	49	2.1	66	1830	24.7	4.1
  109 cells/ml	3-3	75	1.8	162	1615	32.3	3.6
  (with prior	3-5	50	2.4	132	1896	23.9	4.3
  immersion)	3-7	17	1.5	28	720	9.0	3.4
  	MEAN	48	1.9	97	1516	22.5	3.8
  Vehicle	5-1	43	1.5	90	833	13.2	3.6
  (topical	5-3	55	2.2	104	1312	18.6	3.6
  only)	5-5	44	1.4	59	644	17.6	3.2
  	5-7	100	3.8	168	1308	48.6	4.0
  	MEAN	60	2.2	105	1024	24.5	3.6
  D23	6-1	82	2.2	105	1573	28.5	2.9
  109 cells/ml	6-3	18	0.8	36	943	8.0	2.5
  (topical	6-5	25	1.2	45	1027	9.5	2.2
  only)	6-7	49	1.5	92	1077	18.5	2.9
  	MEAN	44	1.4	69	1155	16.1	2.6

• Pharmacokinetic evaluation of D23 (B244) in rodents was conducted during a 28-day repeat dose toxicology study as described in the section below. No separate single dose pharmacokinetic studies were run for D23 (B244).
Example 7 Toxicology
• 28-Day Safety Study of Nitrosomonas eutropha D23 (B244) Application on Full-Thickness Wounds of Streptozotocin-Induced Diabetic Sprague-Dawley Rats
• The objectives of this study were to determine the potential toxicity of Nitrosomonas eutropha D23 (B244) in rats when given dermally on wounded skin for a minimum of 28 days, and to evaluate the potential reversibility of any findings. In addition, the toxicokinetic characteristics of D23 (B244) were determined.
Study Design and Methods
• The design was based on the study objectives, the overall product development strategy for the test article, and the following study design guidelines: OECD Guidelines 407 and 417, Committee for Human Medicinal Products (CHMP), and ICH Harmonised Tripartite Guidelines M3 (R2), S3a, and S6 (R1). The study design is outlined herein and results are shown in Table 11.

• TABLE 11
  28-Day Safety Study design

  	Dose
  	Volume	Dose	No. of Animals

  Group

  Test

  Dose Level

  (mL/kg)

  Conc.

  Main Study

  Recovery

  No.	Material	(CFU/kg/day)	Split	(CFU/mL)	M	F	M	F
  1	Control	0	0.8	0	10	10	5	5
  	Article
  2	AOB-D23-	6 × 107	0.8	8 × 107	10	10	0	0
  	100
  3	AOB-D23-	6 × 108	0.8	8 × 108	10	10	0	0
  	100
  4	AOB-D23-	6 × 109	0.8	8 × 109	10	10	5	5
  	100
  M = Male,
  F = Female,
  Conc. = Concentration,
  CFU = Colony Forming Unit.
  Control Article = 99.998% Phosphate Buffered Saline, pH 7.4 (PBS), 0.002% 1M NH4Cl

• For induction of diabetes, Streptozotocin was administered to Sprague Dawley rats via intraperitoneal injection on Day −4. Animals with blood glucose levels of >200 mg/dL were considered as responders to the Streptozotocin treatment and were used for the dosing phase of the study. Two full-thickness skin wounds were created per animal (1 on each side of the back of each anesthetized animal) using an 8-mm skin biopsy punch. The wounds were left uncovered during administration of the control and test article and also for the duration of the study. The test and control articles were administered to the appropriate animals dermally once daily (for 24 hours±1 hour) from Days 1 to 28. The end points evaluated in this study were the following: clinical signs, dermal findings, body weights, body weight changes, food consumption, ophthalmology, glucose analysis, clinical pathology parameters (hematology, coagulation, clinical chemistry, urinalysis, hemoglobin A1c, and methemoglobulin), C-reactive protein and serum ferritin analysis, toxicokinetic parameters, gross necropsy findings, organ weights, and wound histopathology.
Results
• The results for the endpoints evaluated in the 28-day GLP toxicology study are outlined below in Table 12.

• TABLE 12
  28-Day Safety Study-Results

  End points	Observations	Comments
  Mortality	No unscheduled deaths during the course of
  	the study were attributed to D23 (B244).
  	One control male was found dead on Day
  	41; the cause of death due to necrosis in the
  	kidney, liver, pancreas, and spleen
  Clinical	No test article D23 (B244)-related clinical	Similar clinical signs
  Observations	signs were observed during the study.	have been previously
  	Clinical signs including abdominal	associated with an
  	distension, prominent backbone, fur	uncontrolled diabetic
  	staining, soft stools and ungroomed	state in rats and other
  	appearance were related to the diabetic state	animal models
  	of the animals
  	Skin discoloration (red/black) was present
  	in both control and treated animals
  Dermal Scores	No dermal irritation occurred during the
  	study
  	No erythema or edema was observed
  	following dermal administration of the test
  	article
  Body Weights and	No D23 (B244)-related effects on body
  Body Weight	weight or body weight change were noted
  Changes	during the study.
  	Mean weight gain was observed throughout
  	the study interval, with isolated instances of
  	slight loss in individual animals across the
  	dose groups which did not follow specific
  	dose-related trends
  Food Consumption	There were no test article-related effects on
  	food consumption.
  Ophthalmic	There were no D23 (B244)-related	The appearance of
  Examinations	ophthalmologic changes during the study. The	cataracts is a known
  	majority of the animals on study developed	complication of
  	cataracts and there were no differences among	diabetes
  	dose groups.
  Hematology,	No test article-related changes were noted in
  Coagulation,	hematology, coagulation, hemoglobin A1c,
  Hemoglobin A1c,	and methemoglobin parameters on
  and Methemoglobin	Day 29 or 43.
  	Isolated statistically significant differences
  	were noted during the study; however, the
  	values were within the historical control
  	ranges and were not considered meaningful
  Clinical Chemistry	No test article-related changes were noted on
  	Days 29 or 43.
  	Isolated statistically significant differences
  	were noted during the study; however, the
  	values were within the historical control
  	ranges and not considered meaningful
  Urinalysis	No test article-related effects
  C-reactive Protein	No test article-related effects
  and Serum Ferritin
  Analysis
  Gross Pathology	No test article-related gross findings were	Any gross findings
  	noted on Day 29 or Day 43	observed were
  		considered to be related
  		to the diabetic
  		condition of the rats
  		and incidental in nature
  Organ Weights	There was an increase in adrenal weight in
  	females at ≧6 × 108 CFU/kg/day on Day 29,
  	whereas adrenal weight was decreased in
  	males and there were no associated gross
  	pathology findings making the association
  	of this finding to D23 (B244) administration
  	equivocal
  	Potential D23 (B244)-related organ weight
  	changes noted at the terminal euthanasia
  	(Day 29) were not observed at the end of the
  	recovery period (Day 43)
  Histopathology	No D23 (B244)-related microscopic findings
  Terminal	on Day 29.
  Euthanasia (Day 29)	Changes observed in the kidneys, large and
  	small intestine, and urinary bladder were
  	related to the diabetic state of the animals.
  	The incidence and severity of these
  	findings were similar in all study groups
  	including controls.
  	Changes at the administration/wound sites
  	included epidermal regeneration, fibrosis,
  	and granulomatous inflammation. The
  	incidence and severity of these findings
  	were similar in all groups including
  	controls
  Histopathology	Changes observed on Day 43 were similar
  Recovery	to those reported on Day 29
  Euthanasia (Day 43)

Conclusions
• • Once daily application of D23 (B244) on rat wounds was well tolerated at levels of 6×10⁷, 6×10⁸, and 6×10⁹ CFU/kg/day.
  • No D23 (B244)-related mortality observed during the study
  • Healing of full tissue thickness excisions was similar in all groups
  • No D23 (B244)-related clinical signs or dermal irritation were observed
  • No effects observed during the study on body weight, food consumption, clinical pathology parameters, c-reactive protein, or serum ferritin
  • No test article-related gross necropsy findings or histopathologic findings
  • The no-observed-adverse-effect level (NOAEL) was determined to be 6×10⁹ CFU/kg/day (8×10⁹ cells/ml)
  • No specific target organs were identified
• No D23 related mortality occurred during the study. There were no D23-related clinical signs or dermal irritation, and there were no effects on body weight, body weight changes, food consumption, clinical pathology parameters, C-reactive protein, or serum ferritin during the study. There were no test article-related gross necropsy findings or histopathologic findings. Increases in adrenal weights were noted in the >6×10⁸ CFU/kg/day females on Day 29; however, association with D23 was considered equivocal based on the lack of a similar effect in the males, the lack of corresponding gross findings, and the lack of microscopic evaluation of this tissue.
• All wound sites were completely covered by epidermis and appeared to be in the remodeling/resolution phase, which was characterized by stratification of the epidermis with keratinization and refinement of the dermal collagen (synthesis, bundling, and degradation) and capillaries to restore the normal architecture of the epidermis and dermis. The incidence and severity were similar in all groups, including controls.
Example 8 Antibiotic Susceptibility
• The activities of five antibiotics, each representing a different antibiotic class, were tested against Nitrosomonas eutropha D23. The antibiotics tested included clindamycin, erythromycin, gentamicin, piperacillin with or without the β-lactamase inhibitor Tazobactam, and tetracycline. These were chosen based on the Clinical and Laboratory Standards Institute (CLSI) recommendations for routine testing and reporting of phylogenetically-related proteobacteria (Pseudomonas aeruginosa) listed under Non-fastidious organisms and Non-Enterobacteriaceae in the CLSI 24th Informational Supplement (M100-524), and also included topical or systemic antimicrobial agents commonly used against acne, such as clindamycin or tetracycline. Studies with clindamycin were included even though this antibiotic was not expected to be very effective at inhibiting Nitrosomonas, as is the case for other aerobic Gram-negative bacteria.
• Minimal Inhibitory Concentrations (MICs) were determined by culturing N. eutropha D23 in decreasing concentrations of each of the five antibiotics. Bacterial growth at 30° C. was monitored for 48-72 hr by determining optical density (OD₆₀₀) values in samples collected at 24 hr intervals. MIC values were identified as the lowest antibiotic concentration from a two-fold dilution series leading to no increase in OD₆₀₀ measurements for the 2 or 3-day incubation period. The N. eutropha D23 phenotype in each antibiotic test was determined as Susceptible, Intermediate, or Resistant according to the MIC Interpretive Criteria provided by the CLSI. As summarized in Table 13, these studies demonstrated susceptibility of N. eutropha D23 to erythromycin and gentamicin and intermediate resistance to tetracycline and piperacillin suggesting the lack of strong antibiotic-resistance potential by the Drug Substance. Clindamycin resistance observed for N. eutropha D23 is in agreement with previous reports for natural resistance of aerobic Gram-negative bacteria to this antibiotic. In addition to testing the β-lactam antibiotic piperacillin alone, the broad range β-lactamase inhibitor Tazobactam was also tested in combination with piperacillin to assess the possible expression of β-lactamase(s) by N. eutropha D23. The results from this comparison showed no increase in N. eutropha D23 susceptibility, indicating the absence of β-lactamase expression by N. eutropha D23, at least under the conditions tested.

• TABLE 13
  MIC values for five antibiotics tested against N. eutropha
  D23 cultures in vitro

  		MIC	MIC Interpretive
  Antibiotic	Antibiotic Class	(μg/ml)	Criteria*

  Clindamycin	Lincosamide	>16	Resistant (≧4 μg/ml)
  Erythromycin	Macrolide	0.16	Susceptible (≦0.5 μg/ml)
  Gentamicin	Aminoglycoside	0.25	Susceptible (≦4 μg/ml)
  Piperacillin	β-lactam	64	Intermediate
  			(32-64 μg/ml)
  Piperacillin/	β-lactam/	64/4	Intermediate
  Tazobactam	β-lactamase		(32/4-64/4 μg/ml)
  	inhibitor
  Tetracycline	Tetracycline
  	8	Intermediate (8 μg/ml)
  *as recommended by the Clinical and Laboratory Standards Institute (values in parentheses represent MIC levels for corresponding Susceptible, Intermediate or Resistant outcomes)

Conclusions
• These studies demonstrate susceptibility of D23 (B244) to macrolide and aminoglycoside antibiotics and resistance to lincosamides, results that indicate the lack of strong antibiotic-resistance potential by the Drug Substance.
Example 9 Elucidation of Structure of N. eutropha
• N. eutropha was defined at the species and the strain level using PCR and gene sequencing methodologies. The species level was defined as N. eutropha by sequencing of the V1-V5 variable regions of the 16S rRNA gene. N. eutropha was defined as a novel N. eutropha strain D23 by identification of a unique gene from whole genome sequence analysis. N. eutropha was defined at the species level as N. eutropha by 16S rRNA gene sequencing using the MicroSeq 500 rDNA Bacterial Identification PCL and sequencing kit.
• Strain identity may be determined using custom primers, which correspond to the underlined portions of the following sequence and the D23 1c1355 sequence & primers Table 14 below. While not wishing to be bound by theory, it is believed that gene D23 1c1355 is unique to N. eutropha D23, and thus performing a PCR amplification reaction within gene D23 1c1355 will indicate whether N. eutropha D23 is present in a given sample.

• TABLE 14
  D23_1c1355 sequence & primers

  				Product
  		Tm	Posi-	size
  Primer	Sequence (5′-3′)	(° C.)	tion	(bp)
  D23_	AATCTGTCTCCACAGGCAGC	54	287-305	595
  1c1355-F	(SEQ ID NO: 64)
  D23_	TATACCCACCACCCACGCTA	54	881-862
  1c1355-R	(SEQ ID NO: 65)

• D23_1c1355 outer membrane autotransporter
  barrel domain-containing protein
  (SEQ ID NO: 66)
  TTGGTTGGTTTGAAACAGGTAAGGGAGAAGGAGGAAAATCGCCAGAATAT
  10        20        30        40        50
  CGTCGCCAAAGGTTATCGGATCACCATAGCTTATCCACTCAAAGGGGAGA
  60        70        80        90       100
  TTATCATGAGCAAGGTTCGTCGATTAAAAAAGAGTTTATATACGGTTACT
  110       120       130       140       150
  GCACTAACTCTCGGTTTCGGACCATTTGTGACAGCGAGTGGACAATCATT
  160       170       180       190       200
  CGAAGAAACACCCGTACAAACACCCGGACGAGCTTTTGCAGTGGACAATT
  210       220       230       240       250
  TAAAGGGTATCTGTGTACAAAACACAAGTGAAGACCCCTCATTAGCAATA
  260       270       280       290       300
  GCTTGCACCTTCGCACTGGGCGGGATAAATGATATTACCGCGCAGAATCT
  310       320       330       340       350
  GTCTCCACAGGCAGCGATTCAGGCCGAGTCGATCGCGATTACTTCTCCCT
  360       370       380       390       400
  ATCAGTTTATTCGCAGCACGAATGAAAGCATACAGCGGCTAACAGGTCGC
  410       420       430       440       450
  TCTGCTGAGAAACGTCAGCAACAATCCTCTTTTTTACTACAAAGCTCAGC
  460       470       480       490       500
  GTCGGTAGCAGGCACGCCATCATTTGGCACTTCTGGTTTTATAGGGCCTG
  510       520       530       540       550
  TAGGGGTTTCGCTGAGCGGTGGCGGGAGCTTTGGTGAACGCAATACCGCT
  560       570       580       590       600
  GAAGGGCAGACCGGTTTTCAATTGAATACCCGGCAAACCAGCCTGATGAT
  610       620       630       640       650
  CGATTATTCATTTAATCAAAAATTGATTGGCGGCTTTTCCTTTAATTATC
  660       670       680       690       700
  TGGGGACAGATCGTAATTTGAGATTGGCGAGTGGGGACTTGAATTCCGAT
  710       720       730       740       750
  AGCTATCGGTTTGCACCCTTTGTGCTTTTCAGACCAACTACCAATAGCTA
  760       770       780       790       800
  CTTAACTCTGATGGGAGGGTATGCTTTGGTTAATTATCGTTCCACGCGCA
  810       820       830       840       850
  GCGTTTCGAGTCAAAATGACATCACGTTTGATAACGCCACAGCCAACTAT
  860       870       880       890       900
  GATGCTAATCAGTTTTTTGCTAGCGTGGGTGGTGGGTATACCTTTACTTT
  910       920       930       940       950
  AATGGATGGATGGAATCTGCGAGGATATGGTCGCGGGGACTTTAGTGATA
  960       970       980       990      1000
  TTAGTATCCAGAGCTTTCAGGAAAAAGGTGGCGTTGCTCATAGTGGGAAC
  1010      1020      1030      1040      1050
  GATAGTTTATCTCTTGCTATGTCTGTGAATAAACAAACCATACGCTCGGT
  1060      1070      1080      1090      1100
  TACCAGTACATTAGGCGTTGAACTTAGTCATGCAATTAGCACCAGAACTT
  1110      1120      1130      1140      1150
  TTATTCCCGTCATTATCCCGAGACTGCGTGCAGAATGGGTGCATGAATTT
  1160      1170      1180      1190      1200
  GAAAACAATGCCAGAACTATCACGGCCGGTTTCACTGGCCAGAACTATAG
  1210      1220      1230      1240      1250
  TCCCACTTCTGCATCAATGGCAGTTGCAAGCTCAGTGCGTAATTGGGCAA
  1260      1270      1280      1290      1300
  ACCTGGGGGTTGGAGTGCAAATGCTGTTTGCCCGCTCGATTATCGGGTAC
  1310      1320      1330      1340      1350
  ATTAATTACGACAGATTAATTATCAAGCACGCGGAGAACAATATCATTTC
  1360      1370      1380
  TGGTGGGATTCGTATGAATTTCTAA

Example 10 Administering Ammonia Oxidizing Bacteria to the Back of the Head to Change the Skin Microbiome
• Ammonia oxidizing bacteria (N. eutropha D23) was applied topically to the back of the head of a subject for over 2 weeks. The dose was 3×10¹⁰ CFU applied per day. The product concentration was 1×10⁹ CFU/ml (15 ml, two times a day) in a phosphate buffer with magnesium chloride. On each day a skin swab was taken to isolate and sequence all the bacterial DNA that was present, using isolation and sequencing protocols known in the art.
• Ammonia oxidizing bacteria of the genus Nitrosomonas was not present in the Day 0 sample, and was detected and present in the Day 7, 14, and 16 skin swabs.
• As shown in FIGS. 17 and 18, which plots the proportion versus bacterial genus for Day 0, 1, 8, 14, and 16, the application of ammonia oxidizing bacteria led to proportional increases in commensal non-pathogenic Staphylococcus (which was at least 98% Staphylococcus epidermidis) from close to 0% on day 0 to approximately 50% on day 16. Additionally, application of ammonia oxidizing bacteria led to a proportional reduction in potentially pathogenic or disease associated Propionibacteria over the time period tested (from over 75% on day 0 to less than 50% on day 16). Application of ammonia oxidizing bacteria also led to reductions in potentially pathogenic or disease associated Stenotrophomonas over the time period tested (from 0.1% on day 0 to less than 0.01% on day 16.)
• Some of the data shown in FIGS. 1 and 2 is also presented below in Table 15.

• TABLE 15
  Genera by Day

  		Proportion	Proportion	Proportion
  		by genus:	by genus:	by genus:
  	Day	Propionibacteria	Staphylococci	Stenotrophomonas

  	0	0.78	0.01	0.13
  	1	0.79	0.1	0
  	8	0.8	0.15	0
  	14	0.55	0.45	0.001
  	16	0.48	0.49	0

• As shown in Table 15, the proportion of Propionibacteria was reduced after about 14 days (compare data for Day 0, 1, and 8 with Day 14 and 16 in Table 15). The proportion of Staphylococci increased after about two weeks (compare data for Day 0, 1, and 8 with Day 14 and 16 in Table 15). The proportion of Stenotrophomonas decreased after about 1 day (compare data for Day 0 with Day 1, 8, 14, and 16 in Table 15).
• These changes in the skin microbiome composition to a less pathogenic state indicate that application of ammonia oxidizing bacteria would be useful in treatment of dermatologic diseases including but not limited to acne, eczema, skin infections, and rosacea.
Example 11 Studies with Ammonia-Oxidizing Bacteria for the Human Skin: Cosmetic Effects, Safety, Detection and Skin Metagenomics
• A blinded, placebo-controlled 24 human volunteer study randomized 4:1 AOB to placebo control was performed. Subjects applied a Nitrosomonas suspension (10⁹ CFU/ml, 2 times per day, for a total of 3×10¹⁰ CFU per day) to their face and scalp twice daily for one week and were followed for two additional weeks post-application. Volunteers were instructed to refrain from using hair products during the one-week AOB application as well as the week following application, then returned to regular shampoo use for the third week. Scalp swabs were obtained on Day 0 as baseline controls and on Day 1, 3, 8, 14 and 21 to assess presence/absence of AOB by PCR and 16S rRNA sequencing analyses.
• No serious adverse events were associated with AOB application for one week and the product was deemed safe. AOB users reported a clear improvement in skin condition and quality, as indicated by self-assessment reports completed after the seven-day application period. Using AOB-specific PCR analyses of the skin samples, we could demonstrate presence of the bacteria in 83-100% of AOB users during the application period, whereas no AOB were detected in the placebo control samples. All subjects lacked AOB from baseline swabs obtained prior to study initiation, consistent with the predicted sensitivity of these bacteria to soaps and other commercial products. Amplification of the 16S rRNA gene and sequencing of a subset of samples confirmed presence of AOB in corresponding samples and suggested potential trends in modulating the skin microbiome by topical AOB application. In summary, live AOB-based products are safe and could hold great promise as novel self-regulating topical delivery agents of nitrite and nitric oxide to the human skin.
• As shown in Table 16, below, the proportion of Nitrosomonas (AOB) went up when comparing Day 0 versus Day 8. The proportion of other bacteria, Propionibacterium, Enterobacter, and Citrobacter went down, when comparing Day 0 versus Day 8. The p-values indicated in Table 16 demonstrate that the most significant change between Day 0 and Day 8 was observed with Nitrosomonas (AOB) followed by Propionibacterium. Enterobacter and Citrobacter also showed changes between Day 0 and Day 8 to a lesser degree.

• TABLE 16
  Trends in microbiome composition following AOB application
  (Day 0 versus Day 8)

  	Genus	P-value (unadjusted)	Trend
  	Nitrosomonas (AOB)	0.0039	Up
  	Propionibacterium	0.0078	Down
  	Enterobacter	0.0346	Down
  	Citrobacter	0.036	Down

• Because nitrite and nitric oxide have been implicated in critical physiological functions, such as vasodilation, skin inflammation and wound healing, we have hypothesized that AOB may have beneficial effects on both healthy and immunopathological skin conditions by metabolizing ammonia from sweat while concurrently driving skin acidification. We reasoned that Nitrosomonas would be safe for human use because they are slow-growing and incapable of utilizing organic carbon sources, they are sensitive to antibiotics, and they have never been linked to animal or human disease. Here we describe a blinded, placebo-controlled 24 human volunteer study where subjects applied a live Nitrosomonas suspension to their face and scalp twice daily for one week and were subsequently followed for two additional weeks. Volunteers did not use hair products during the first and second week, then they returned to their regular routine for the third week. Scalp swabs were obtained on Day 0 as baseline controls and on Day 1, 3, 8, 14 and 21 to assess presence/absence of Nitrosomonas and to examine microbial diversity. Importantly, no adverse events were associated with topical application. PCR analyses demonstrated presence of the bacteria in 83%-100% of skin swabs obtained from AOB users during or immediately after completion of the one-week application period ( Day 1, 3 or 8) and in 60% of the users on Day 14, but not in any of the placebo control samples. All subjects lacked AOB from baseline swabs obtained prior to study initiation. Increased levels of AOB during the one-week application period correlated with a qualitative improvement in skin condition, in contrast to no improvement reported by placebo control subjects. Sequencing of the 16S rRNA gene amplification product obtained from a subset of subjects verified the presence of AOB in corresponding samples and suggested potential modulation of the skin microbiome composition. In summary, live Nitrosomonas are well tolerated and may hold promise as novel self-regulating topical delivery agents of nitrite and nitric oxide to the human skin.
• Here, we present the results from preliminary studies in humans where we have begun evaluating topical application of a Nitrosomonas suspension to the human skin and the potential of using AOB as natural delivery systems of NO/NO₂ ⁻ in vivo. We have explored methodologies for AOB detection in skin specimens and the possible effects of AOB in skin microbial communities, as well as collected important user feedback from the early adopters of our topical cosmetic.
• Methods
• Culture Conditions.
• N. eutropha D23 was propagated in batch culture at 28-30° C. in mineral salt medium supplemented with 20-50 mM NH₄ ⁺ and sodium carbonate as the carbon source [Ensign et al, 1993]. For continuous culture, D23 was grown at ˜10⁹ cells/ml in a 1 liter mini-Bioreactor (Applikon Biotechnology) at 28° C. using sodium carbonate for both pH neutralization and the carbon source.
• Nitrite Quantification.
• Nitrite concentrations in culture supernatants were determined using the Griess colorimetric assay [Hageman and Kucklesby, 1971] and sodium nitrite as standards.
• DNA Extraction from Skin Swabs.
• Samples were maintained in 1 ml of 10% AssayAssure Bioservative (Thermo Scientific) diluted in PBS. Biomass was centrifuged and cells were lysed using a method developed for skin specimens [Grice, 2009] with modifications to the buffer designed to maintain long DNA integrity. DNA was then purified using the PowerLyzer UltraClean microbial DNA isolation kit (Mo Bio Laboratories). N. eutropha D23 was identified using a 3-gene PCR signature amplifying the ammonia monooxygenase encoding locus amoCAB.
• PCR and Library Preparation.
• Full-length 16S rRNA genes were amplified in duplicate reactions using a cocktail of primers and AccuPrime DNA polymerase SuperMix kit (Life Technologies). All PCR products were directly treated with the SMRTbell Template Prep Kit followed by the DNA/Polymerase Binding Kit P4 (Pacific Biosciences).
• 16S rDNA Sequencing and Analysis.
• PCR products were sequenced using the Pacific Biosciences RS instrument [Eid, 2009]. Raw base calls were transformed to consensus DNA sequences using the Pacific Biosciences Consensus Tools package and then processed with the Whole Biome Microbiome Profiling Platform to obtain phylum-genus and strain-level frequency measures for each sample.
• Human Volunteer Study.
• A total of 24 male volunteers were included in a blinded, placebo-controlled, study each for a total of three weeks according to a protocol for topical AOB-001 use approved by the Allendale Institutional Review Board (Old Lyme, Conn.). Written informed consent was obtained from each study participant. Subjects applied 15 ml of an aqueous suspension of N. eutropha (AOB-001), or placebo (vehicle), twice daily containing ˜10⁹ cells/ml.
• The human volunteer study design for the preliminary evaluation of a Nitrosomonas-containing topical suspension (AOB-001) is shown in FIG. 5K. Detection of AOB was performed by PCR in scalp swab samples. FIG. 5L shows PCR analyses of scalp swabs collected during the study. The left panel indicates the percent-positive samples for AOB-specific three-gene signature (amoA, amoB, amoC). The right panel indicates the Composite PCR scores for a total of six samples collected from each of 23 volunteers. The scoring scheme used for the positive samples collected at each of six sampling points is indicated.
• Skin microbiome composition prior and during AOB-001 application were obtained by 16S rDNA sequencing. FIG. 5M indicates that genus-level bacterial diversity as determined by 16S rDNA sequencing in skin swab samples collected before and after topical application of AOB-001.
• The percentage of the total sequence reads representing each of twelve bacterial genera in samples collected at baseline prior to application (Day 0) and immediately after the one week application (Day 8), or one week after stopping topical application (Day 14), are shown.
• FIG. 5N indicates changes in abundance of Nitrosomonas and other species in skin samples collected before and after AOB-001 application. Panel A shows percentages of the total 16S rDNA sequence reads representing Nitrosomonas prior to application (Day 0), immediately after the one-week application (Day 8), or one week after terminating application (Day 14) are shown. Panel B shows a change in patterns in abundance of species detected by 16S rDNA sequencing in Day 0 versus Day 8 samples collected from AOB users.
• AOB-001 users report an improvement in skin condition. FIG. 5O shows a user evaluation of AOB-001. Assessment of AOB-001 cosmetic effects was provided by 23 volunteers upon completion of the one week application to their scalp and face. Subjects were plotted in order of increasing composite PCR scores. (The responses were categorized as 2=agree strongly; 0=no change; −2=disagree strongly). In summary, AOB-001 is well-tolerated. The user responses in a blind study indicate improved skin/scalp condition. AOB (Nitrosomonas) are readily detectable in skin microbiome samples by PCR and 16S rRNA gene sequencing. Preliminary microbiome analyses indicate modulation of skin microbiota by AOB.

• SUPPLEMENTARY TABLE 1
  Annotation of genes in SEQ ID NO: 1.

  Feature						Length			D23	C91
  ID	Type	Start	Stop	Frame	Strand	(bp)	Function	Subsystem	Gbkld	Alias

  fig|6666666.60966.peg.1	CDS	35	1414	2	+	1380	Chromosomal	Cell Division Subsystem	D23_1c0001	Neut_0001
  							replication initiator	including YidCD;
  							protein DnaA	<br>DNA replication
  								cluster 1
  fig|6666666.60966.peg.2	CDS	1619	2740	2	+	1122	DNA polymerase III beta	Cell Division Subsystem	D23_1c0002	Neut_0002
  							subunit (EC 2.7.7.7)	including YidCD;
  								<br>DNA replication
  								cluster 1
  fig|6666666.60966.peg.3	CDS	2798	5227	2	+	2430	DNA gyrase subunit B	Cell Division Subsystem	D23_1c0003	Neut_0003
  							(EC 5.99.1.3)	including YidCD;
  								<br>DNA gyrase
  								subunits; <br>DNA
  								replication cluster 1;
  								<br>DNA
  								topoisomerases, Type II,
  								ATP-dependent;
  								<br>Resistance to
  								fluoroquinolones
  fig|6666666.60966.peg.4	CDS	5248	5691	1	+	444	FIG039061:	-none-	D23_1c0004	Neut_0004
  							hypothetical protein
  							related to heme
  							utilization
  fig|6666666.60966.peg.5	CDS	5748	6479	3	+	732	tRNA pseudouridine	Colicin V and Bacteriocin	D23_1c0005	Neut_0005
  							synthase A (EC 4.2.1.70)	Production Cluster;
  								<br>RNA pseudouridine
  								syntheses; <br>tRNA
  								modification Bacteria;
  								<br>tRNA processing
  fig|6666666.60966.peg.6	CDS	7261	7518	1	+	258	4Fe—4S ferredoxin, iron-	Inorganic Sulfur	D23_1c0009	Neut_0127
  							sulfur binding	Assimilation
  fig|6666666.60966.peg.7	CDS	7584	7946	3	+	363	FIG00858425:	-none-	D23_1c0010	Neut_0128
  							hypothetical protein
  fig|6666666.60966.peg.8	CDS	11430	7966	−3	−	3465	Transcription-repair	Transcription factors	D23_1c0011	Neut_0129
  							coupling factor	bacterial;
  								<br>Transcription repair
  								cluster
  fig|6666666.60966.peg.9	CDS	12737	11457	−2	−	1281	InterPro IPR003416	-none-	D23_1c0012	Neut_0130
  							COGs COG3174
  fig|6666666.60966.peg.10	CDS	14499	12730	−3	−	1770	Single-stranded-DNA-	DNA Repair Base	D23_1c0013	Neut_0131
  							specific exonuclease	Excision
  							RecJ (EC 3.1.—.—)
  fig|6666666.60966.peg.11	CDS	15277	14681	−1	−	597	InterPro IPR000345	-none-	D23_1c0014	Neut_0132
  fig|6666666.60966.peg.12	CDS	16285	15365	−1	−	921	Indole-3-glycerol	Chorismate:	D23_1c0015	Neut_0133
  							phosphate synthase (EC	Intermediate for
  							4.1.1.48)	synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.13	CDS	17321	16296	−2	−	1026	Anthranilate	Auxin biosynthesis;	D23_1c0016	Neut_0134
  							phosphoribosyltransferase	<br>Chorismate:
  							(EC 2.4.2.18)	Intermediate for
  								synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.14	CDS	17920	17318	−1	−	603	Anthranilate synthase,	Chorismate:	D23_1c0017	Neut_0135
  							amidotransferase	Intermediate for
  							component (EC	synthesis of Tryptophan,
  							4.1.3.27)	PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.15	CDS	18046	19545	1	+	1500	Putative sensor-like	-none-	D23_1c0018	Neut_0136
  							histidine kinase YfhK
  fig|6666666.60966.peg.16	CDS	19644	20081	3	+	438	FIG00858754:	-none-	D23_1c0019	Neut_0137
  							hypothetical protein
  fig|6666666.60966.peg.17	CDS	20101	21465	1	+	1365	Putative sensory	-none-	D23_1c0020	Neut_0138
  							histidine kinase YfhA
  fig|6666666.60966.peg.18	CDS	22742	21474	−2	−	1269	PDZ/DHR/GLGF domain	-none-	D23_1c0021	Neut_0139
  							protein
  fig|6666666.60966.peg.19	CDS	26700	22798	−3	−	3903	Phosphoribosylformylglycinamidine	De Novo Purine	D23_1c0022	Neut_0140
  							synthase,	Biosynthesis; <br>De
  							synthetase subunit (EC	Novo Purine
  							6.3.5.3)/	Biosynthesis
  							Phosphoribosylformylglycinamidine
  							synthase,
  							glutamine
  							amidotransferase
  							subunit (EC 6.3.5.3)
  fig|6666666.60966.peg.20	CDS	26942	28510	2	+	1569	hypothetical protein	-none-	D23_1c0023	Neut_0141
  fig|6666666.60966.peg.22	CDS	28682	28867	2	+	186	hypothetical protein	-none-	D23_1c0024	NA
  fig|6666666.60966.peg.23	CDS	29060	28851	−2	−	210	Death on curing	Phd-Doc, YdcE-YdcD	D23_1c0025	NA
  							protein, Doc toxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.24	CDS	29367	29227	−3	−	141	Prevent host death	Phd-Doc, YdcE-YdcD	D23_1c0026	Neut_0143
  							protein, Phd antitoxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.25	CDS	29726	30082	2	+	357	blr1219; hypothetical	-none-	D23_1c0028	Neut_0144
  							protein
  fig|6666666.60966.peg.26	CDS	30113	31672	2	+	1560	NAD(P)HX epimerase/	YjeE; <br>YjeE	D23_1c0029	Neut_0145
  							NAD(P)HX dehydratase
  fig|6666666.60966.peg.29	CDS	31959	32078	3	+	120	hypothetical protein	-none-	D23_1c0030	NA
  fig|6666666.60966.peg.30	CDS	32096	32914	2	+	819	O-antigen export	-none-	D23_1c0031	Neut_0146
  							system permease
  							protein RfbD
  fig|6666666.60966.peg.31	CDS	33063	33266	3	+	204	hypothetical protein	-none-	D23_1c0032	Neut_0147
  fig|6666666.60966.peg.32	CDS	33441	33995	3	+	555	hypothetical protein	-none-	D23_1c0033	Neut_0148
  fig|6666666.60966.peg.33	CDS	34044	34424	3	+	381	hypothetical protein	-none-	D23_1c0034	NA
  fig|6666666.60966.peg.34	CDS	34530	35588	3	+	1059	putative transposase	-none-	D23_1c0035	Neut_0149
  fig|6666666.60966.peg.36	CDS	36348	36064	−3	−	285	HigA protein (antitoxin	Toxin-antitoxin replicon	D23_1c0037	Neut_0150
  							to HigB)	stabilization systems
  fig|6666666.60966.peg.37	CDS	36621	36379	−3	−	243	HigB toxin protein	Toxin-antitoxin replicon	D23_1c0038	Neut_0151
  								stabilization systems
  fig|6666666.60966.peg.38	CDS	36580	36750	1	+	171	hypothetical protein	-none-	D23_1c0039	NA
  fig|6666666.60966.peg.39	CDS	36747	38108	3	+	1362	Teichoic acid export	Rhamnose containing	D23_1c0040	Neut_0152
  							ATP-binding protein	glycans
  							TagH (EC 3.6.3.40)
  fig|6666666.60966.peg.40	CDS	38105	42433	2	+	4329	Glycosyl transferase,	-none-	D23_1c0041	Neut_0153
  							group 2 family protein
  fig|6666666.60966.peg.41	CDS	42537	43733	3	+	1197	glycosyl transferase,	-none-	D23_1c0042	NA
  							group 1/2 family
  							protein
  fig|6666666.60966.peg.42	CDS	43945	44838	1	+	894	Alpha-L-Rha alpha-1,3-	Rhamnose containing	D23_1c0043	Neut_0166
  							L-rhamnosyltransferase	glycans
  							(EC 2.4.1.—)
  fig|6666666.60966.peg.43	CDS	45457	45140	−1	−	318	HigA protein (antitoxin	Toxin-antitoxin replicon	D23_1c0044	Neut_0167
  							to HigB)	stabilization systems
  fig|6666666.60966.peg.44	CDS	45610	45470	−1	−	141	HigB toxin protein	Toxin-antitoxin replicon	D23_1c0045	Neut_0168
  								stabilization systems
  fig|6666666.60966.peg.45	CDS	45950	46279	2	+	330	Glycosyl transferase,	-none-	D23_1c0046	Neut_0169
  							group 2 family protein
  fig|6666666.60966.peg.47	CDS	47082	46804	−3	−	279	hypothetical protein	-none-	D23_1c0047	NA
  fig|6666666.60966.peg.49	CDS	48719	47757	−2	−	963	Mobile element protein	-none-	D23_1c0049	Neut_0978
  fig|6666666.60966.peg.50	CDS	48899	48777	−2	−	123	Mobile element protein	-none-	D23_1c0050	Neut_0357
  fig|6666666.60966.peg.51	CDS	49218	48970	−3	−	249	Mobile element protein	-none-	D23_1c0051	Neut_2405
  fig|6666666.60966.peg.52	CDS	49615	49502	−1	−	114	hypothetical protein	-none-	D23_1c0052	NA
  fig|6666666.60966.peg.53	CDS	49842	50255	3	+	414	Nucleotidyltransferase	-none-	D23_1c0053	Neut_0172
  							(EC 2.7.7.—)
  fig|6666666.60966.peg.54	CDS	50257	50622	1	+	366	Nucleotidyltransferase	-none-	D23_1c0054	Neut_0173
  							(EC 2.7.7.—)
  fig|6666666.60966.peg.55	CDS	51293	50880	−2	−	414	Mobile element protein	-none-	D23_1c0056	NA
  fig|6666666.60966.peg.56	CDS	51432	51253	−3	−	180	hypothetical protein	-none-	D23_1c0057	Neut_0176
  fig|6666666.60966.peg.57	CDS	51530	52492	2	+	963	Mobile element protein	-none-	D23_1c0058	Neut_1746
  fig|6666666.60966.peg.58	CDS	52657	52908	1	+	252	Mobile element protein	-none-	D23_1c0059	Neut_0884
  fig|6666666.60966.peg.59	CDS	52964	53326	2	+	363	Mobile element protein	-none-	D23_1c0060	Neut_2499
  fig|6666666.60966.peg.60	CDS	54452	53361	−2	−	1092	putative transposase	-none-	D23_1c0061	Neut_0177
  fig|6666666.60966.peg.61	CDS	54765	54430	−3	−	336	FIG00859125:	-none-	D23_1c0062	Neut_0178
  							hypothetical protein
  fig|6666666.60966.peg.62	CDS	55016	55774	2	+	759	dTDP-Rha:A-D-GlcNAc-	dTDP-rhamnose	D23_1c0063	Neut_0179
  							diphosphoryl	synthesis
  							polyprenol, A-3-L-
  							rhamnosyl transferase
  							WbbL
  fig|6666666.60966.peg.63	CDS	56735	55788	−2	−	948	UDP-glucose 4-	CBSS-	D23_1c0064	Neut_0180
  							epimerase (EC 5.1.3.2)	296591.1.peg.2330;
  								<br>N-linked
  								Glycosylation in
  								Bacteria; <br>Rhamnose
  								containing glycans
  fig|6666666.60966.peg.64	CDS	56874	56746	−3	−	129	hypothetical protein	-none-	D23_1c0065	NA
  fig|6666666.60966.peg.65	CDS	60470	57075	−2	−	3396	Adenylate cyclase (EC	cAMP signaling in	D23_1c0066	Neut_0181
  							4.6.1.1)/Guanylate	bacteria
  							cyclase (EC 4.6.1.2)
  fig|6666666.60966.peg.66	CDS	60633	60755	3	+	123	hypothetical protein	-none-	D23_1c0067	NA
  fig|6666666.60966.peg.67	CDS	62853	60769	−3	−	2085	Ubiquinone	Ubiquinone	D23_1c0068	Neut_0182
  							biosynthesis	Biosynthesis;
  							monooxygenase UbiB	<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.68	CDS	63084	63821	3	+	738	hypothetical protein	-none-	D23_1c0069	Neut_0183
  fig|6666666.60966.peg.69	CDS	64515	66023	3	+	1509	CBSS-	-none-	D23_1c0070	NA
  							498211.3.peg.1514:
  							hypothetical protein
  fig|6666666.60966.peg.70	CDS	66074	66751	2	+	678	FIG039767:	-none-	D23_1c0071	NA
  							hypothetical protein
  fig|6666666.60966.peg.71	CDS	66741	70157	3	+	3417	FIG007317:	-none-	D23_1c0072	NA
  							hypothetical protein
  fig|6666666.60966.peg.72	CDS	70190	71326	2	+	1137	FIG005429:	-none-	D23_1c0073	Neut_0184
  							hypothetical protein
  fig|6666666.60966.peg.73	CDS	71379	71939	3	+	561	Lipid carrier: UDP-N-	CBSS-	D23_1c0074	Neut_0185
  							acetylgalactosaminyltransferase	296591.1.peg.2330;
  							(EC 2.4.1.—)	<br>N-linked
  								Glycosylation in Bacteria
  fig|6666666.60966.peg.74	CDS	71949	73931	3	+	1983	Nucleoside-diphosphate	CBSS-296591.1.peg.2330	D23_1c0075	Neut_0186
  							sugar
  							epimerase/dehydratase
  fig|6666666.60966.peg.75	CDS	74467	73949	−1	−	519	cytidine and	-none-	D23_1c0076	Neut_0187
  							deoxycytidylate
  							deaminase family
  							protein
  fig|6666666.60966.peg.76	CDS	74956	74594	−1	−	363	Mobile element protein	-none-	D23_1c0077	Neut_2499
  fig|6666666.60966.peg.77	CDS	75263	75012	−2	−	252	Mobile element protein	-none-	D23_1c0078	Neut_0884
  fig|6666666.60966.peg.78	CDS	75586	76446	1	+	861	Flagellar motor rotation	Flagellar motility;	D23_1c0079	Neut_0188
  							protein MotA	<br>Flagellum
  fig|6666666.60966.peg.79	CDS	76489	77433	1	+	945	Flagellar motor rotation	Flagellar motility;	D23_1c0080	Neut_0189
  							protein MotB	<br>Flagellum
  fig|6666666.60966.peg.80	CDS	77408	78205	2	+	798	FIG00858624:	-none-	D23_1c0081	Neut_0190
  							hypothetical protein
  fig|6666666.60966.peg.81	CDS	79621	78218	−1	−	1404	Cysteinyl-tRNA	Zinc regulated enzymes;	D23_1c0082	Neut_0191
  							synthetase (EC 6.1.1.16)	<br>tRNA
  								aminoacylation, Cys
  fig|6666666.60966.peg.83	CDS	79830	80384	3	+	555	Peptidyl-prolyl cis-trans	Peptidyl-prolyl cis-trans	D23_1c0083	Neut_0192
  							isomerase PpiB (EC	isomerase;
  							5.2.1.8)	<br>Queuosine-
  								Archaeosine
  								Biosynthesis
  fig|6666666.60966.peg.84	CDS	80403	80894	3	+	492	Peptidyl-prolyl cis-trans	Peptidyl-prolyl cis-trans	D23_1c0084	Neut_0193
  							isomerase PpiB (EC	isomerase;
  							5.2.1.8)	<br>Queuosine-
  								Archaeosine
  								Biosynthesis
  fig|6666666.60966.peg.85	CDS	80972	81424	2	+	453	Rhodanese-related	-none-	D23_1c0085	Neut_0194
  							sulfurtransferase
  fig|6666666.60966.peg.86	CDS	82260	81439	−3	−	822	Undecaprenyl-	-none-	D23_1c0086	Neut_0195
  							diphosphatase (EC
  							3.6.1.27)
  fig|6666666.60966.peg.87	CDS	84206	82308	−2	−	1899	Thiamin biosynthesis	Thiamin biosynthesis	D23_1c0087	Neut_0196
  							protein ThiC
  fig|6666666.60966.peg.88	CDS	84412	85068	1	+	657	Protein-L-isoaspartate	Protein-L-isoaspartate O-	D23_1c0088	Neut_0197
  							O-methyltransferase	methyltransferase;
  							(EC 2.1.1.77)	<br>Stationary phase
  								repair cluster; <br>Ton
  								and Tol transport
  								systems
  fig|6666666.60966.peg.90	CDS	85216	86493	1	+	1278	Type I secretion outer	Multidrug Resistance	D23_1c0089	Neut_0198
  							membrane protein,	Efflux Pumps; <br>Ton
  							TolC precursor	and Tol transport
  								systems
  fig|6666666.60966.peg.91	CDS	89009	86556	−2	−	2454	ATP-dependent	Proteasome bacterial;	D23_1c0090	Neut_0199
  							protease La (EC	<br>Proteolysis in
  							3.4.21.53) Type II	bacteria, ATP-dependent
  fig|6666666.60966.peg.92	CDS	89253	89375	3	+	123	hypothetical protein	-none-	D23_1c0091	NA
  fig|6666666.60966.peg.93	CDS	89433	89579	3	+	147	hypothetical protein	-none-	D23_1c0092	NA
  fig|6666666.60966.peg.94	CDS	90769	89555	−1	−	1215	Serine--pyruvate	Photorespiration	D23_1c0093	Neut_0200
  							aminotransferase (EC	(oxidative C2 cycle);
  							2.6.1.51)/L-	<br>Pyruvate Alanine
  							alanine:glyoxylate	Serine Interconversions
  							aminotransferase (EC
  							2.6.1.44)
  fig|6666666.60966.peg.95	CDS	93514	91088	−1	−	2427	ATP-dependent	Proteasome bacterial;	D23_1c0095	Neut_0201
  							protease La (EC	<br>Proteolysis in
  							3.4.21.53) Type I	bacteria, ATP-dependent
  fig|6666666.60966.peg.96	CDS	94903	93620	−1	−	1284	ATP-dependent Clp	Proteasome bacterial;	D23_1c0096	Neut_0202
  							protease ATP-binding	<br>Proteolysis in
  							subunit ClpX	bacteria, ATP-dependent
  fig|6666666.60966.peg.97	CDS	95607	94963	−3	−	645	ATP-dependent Clp	Proteasome bacterial;	D23_1c0097	Neut_0203
  							protease proteolytic	<br>Proteolysis in
  							subunit (EC 3.4.21.92)	bacteria, ATP-
  								dependent; <br>cAMP
  								signaling in bacteria
  fig|6666666.60966.peg.98	CDS	96907	95591	−1	−	1317	Cell division trigger	Bacterial Cell Division	D23_1c0098	Neut_0204
  							factor (EC 5.2.1.8)
  fig|6666666.60966.peg.99	CDS	97996	97241	−1	−	756	Short-chain	Transcription repair	D23_1c0100	Neut_0205
  							dehydrogenase/reductase	cluster
  							SDR
  fig|6666666.60966.peg.100	CDS	99750	98107	−3	−	1644	Heat shock protein 60	GroEL GroES	D23_1c0101	Neut_0206
  							family chaperone GroEL
  fig|6666666.60966.peg.101	CDS	100080	99790	−3	−	291	Heat shock protein 60	GroEL GroES	D23_1c0102	Neut_0207
  							family co-chaperone
  							GroES
  fig|6666666.60966.peg.102	CDS	100244	101554	2	+	1311	Adenosylmethionine-8-	Biotin biosynthesis;	D23_1c0103	Neut_0208
  							amino-7-oxononanoate	<br>Biotin biosynthesis
  							aminotransferase (EC	Experimental; <br>Biotin
  							2.6.1.62)	synthesis cluster
  fig|6666666.60966.peg.103	CDS	101561	102967	2	+	1407	Metallo-beta-lactamase	Bacterial RNA-	D23_1c0104	Neut_0209
  							family protein, RNA-	metabolizing Zn-
  							specific	dependent hydrolases;
  								<br>Ribonucleases in
  								Bacillus
  fig|6666666.60966.peg.104	CDS	103374	103066	−3	−	309	Cytochrome c, class I	-none-	D23_1c0105	Neut_0210
  fig|6666666.60966.peg.105	CDS	103536	104300	3	+	765	Exodeoxyribonuclease	DNA repair, bacterial	D23_1c0106	Neut_0211
  							III (EC 3.1.11.2)
  fig|6666666.60966.peg.106	CDS	104347	105459	1	+	1113	Alanine dehydrogenase	Pyruvate Alanine Serine	D23_1c0107	Neut_0212
  							(EC 1.4.1.1)	Interconversions
  fig|6666666.60966.peg.107	CDS	106118	105597	−2	−	522	Conserved	Tolerance to colicin E2	D23_1c0108	Neut_0213
  							uncharacterized protein
  							CreA
  fig|6666666.60966.peg.109	CDS	107425	106253	−1	−	1173	Permeases of the major	-none-	D23_1c0109	Neut_0214
  							facilitator superfamily
  fig|6666666.60966.peg.110	CDS	108032	107454	−2	−	579	Uncharacterized protein	-none-	D23_1c0110	Neut_0215
  							family UPF0016
  fig|6666666.60966.peg.112	CDS	108821	109603	2	+	783	Ribulose-5-phosphate	-none-	D23_1c0113	Neut_0218
  							4-epimerase and
  							related epimerases and
  							aldolases
  fig|6666666.60966.peg.113	CDS	109609	113274	1	+	3666	InterPro	-none-	D23_1c0114	Neut_0219
  							IPR000014:IPR001789:IPR002106:
  							IPR002570:IPR003594:
  							IPR003660:
  							IPR003661:IPR004358:IPR005467
  							COGs
  							COG0642
  fig|6666666.60966.peg.114	CDS	113292	114485	3	+	1194	Succinyl-CoA ligase	TCA Cycle	D23_1c0115	Neut_0220
  							[ADP-forming] beta
  							chain (EC 6.2.1.5)
  fig|6666666.60966.peg.115	CDS	114489	115364	3	+	876	Succinyl-CoA ligase	TCA Cycle	D23_1c0116	Neut_0221
  							[ADP-forming] alpha
  							chain (EC 6.2.1.5)
  fig|6666666.60966.peg.116	CDS	115402	115722	1	+	321	FIG00858523:	-none-	D23_1c0117	Neut_0222
  							hypothetical protein
  fig|6666666.60966.peg.117	CDS	115750	117177	1	+	1428	D-alanyl-D-alanine	CBSS-84588.1.peg.1247;	D23_1c0118	Neut_0223
  							carboxypeptidase (EC	<br>Metallocarboxypeptidases
  							3.4.16.4)	(EC 3.4.17.—);
  								<br>Murein Hydrolases;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.118	CDS	117265	118227	1	+	963	Mobile element protein	-none-	D23_1c0119	Neut_1278
  fig|6666666.60966.peg.119	CDS	120193	120056	−1	−	138	hypothetical protein	-none-	D23_1c0120	NA
  fig|6666666.60966.rna.5	RNA	118725	120255	3	+	1531	Small Subunit
  							Ribosomal RNA;	-none-	D23_1c0120
  							ssuRNA; SSU rRNA
  fig|6666666.60966.peg.121	CDS	122376	122495	3	+	120	hypothetical protein	-none-	D23_1c0124	NA
  fig|6666666.60966.peg.120	CDS	121863	121994	3	+	132	hypothetical protein	-none-	D23_1c0124	NA
  fig|6666666.60966.rna.8	RNA	120652	123535	1	+	2884	Large Subunit	-none-	D23_1c0124
  							Ribosomal RNA;
  							IsuRNA; LSU rRNA
  fig|6666666.60966.rna.9	RNA	123600	123716	3	+	117	5S RNA	-none-	D23_1c0126
  fig|6666666.60966.peg.123	CDS	124878	124708	−3	−	171	hypothetical protein	-none-	D23_1c0127	NA
  fig|6666666.60966.peg.124	CDS	125317	125496	1	+	180	hypothetical protein	-none-	D23_1c0129	Neut_0547
  fig|6666666.60966.peg.125	CDS	125792	126799	2	+	1008	NAD-dependent	CBSS-296591.1.peg.2330	D23_1c0130	Neut_0225
  							epimerase/dehydratase
  fig|6666666.60966.peg.126	CDS	126808	128082	1	+	1275	UDP-glucose	-none-	D23_1c0131	Neut_0226
  							dehydrogenase (EC
  							1.1.1.22)
  fig|6666666.60966.peg.127	CDS	128985	128089	−3	−	897	Permeases of the	-none-	D23_1c0132	Neut_0227
  							drug/metabolite
  							transporter (DMT)
  							superfamily
  fig|6666666.60966.peg.128	CDS	129078	130283	3	+	1206	N-succinyl-L,L-	Lysine Biosynthesis DAP	D23_1c0133	Neut_0228
  							diaminopimelate	Pathway, GJO scratch
  							aminotransferase
  							alternative (EC 2.6.1.17)
  fig|6666666.60966.peg.129	CDS	130311	131132	3	+	822	2,3,4,5-	Lysine Biosynthesis DAP	D23_1c0134	Neut_0229
  							tetrahydropyridine-2,6-	Pathway, GJO scratch
  							dicarboxylate N-
  							succinyltransferase (EC
  							2.3.1.117)
  fig|6666666.60966.peg.130	CDS	131322	131693	3	+	372	FIG00858507:	-none-	D23_1c0135	Neut_0230
  							hypothetical protein
  fig|6666666.60966.peg.131	CDS	131801	132127	2	+	327	FIG00858507:	-none-	D23_1c0136	Neut_0231
  							hypothetical protein
  fig|6666666.60966.peg.132	CDS	132190	132312	1	+	123	hypothetical protein	-none-	D23_1c0137	NA
  fig|6666666.60966.peg.133	CDS	132314	133303	2	+	990	Biotin operon repressor/	Biotin biosynthesis;	D23_1c0138	Neut_0232
  							Biotin-protein ligase	<br>Biotin biosynthesis;
  							(EC 6.3.4.15)	<br>Biotin synthesis
  								cluster; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.134	CDS	133331	134104	2	+	774	Pantothenate kinase	Coenzyme A	D23_1c0139	Neut_0233
  							type III, CoaX-like (EC	Biosynthesis;
  							2.7.1.33)	<br>Coenzyme A
  								Biosynthesis cluster
  fig|6666666.60966.peg.135	CDS	134123	134794	2	+	672	GTP-binding protein	Universal GTPases	D23_1c0140	Neut_0234
  							EngB
  fig|6666666.60966.peg.136	CDS	134938	135945	1	+	1008	Porphobilinogen	Heme and Siroheme	D23_1c0141	Neut_0235
  							synthase (EC 4.2.1.24)	Biosynthesis; <br>Zinc
  								regulated enzymes
  fig|6666666.60966.peg.137	CDS	136861	136064	−1	−	798	Phosphate transport	High affinity phosphate	D23_1c0142	Neut_0236
  							ATP-binding protein	transporter and control
  							PstB (TC 3.A.1.7.1)	of PHO regulon;
  								<br>Phosphate
  								metabolism
  fig|6666666.60966.peg.138	CDS	137797	136871	−1	−	927	Phosphate transport	High affinity phosphate	D23_1c0143	Neut_0237
  							system permease	transporter and control
  							protein PstA (TC	of PHO regulon;
  							3.A.1.7.1)	<br>Phosphate
  								metabolism
  fig|6666666.60966.peg.139	CDS	138817	137876	−1	−	942	Phosphate transport	High affinity phosphate	D23_1c0144	Neut_0238
  							system permease	transporter and control
  							protein PstC (TC	of PHO regulon;
  							3.A.1.7.1)	<br>Phosphate
  								metabolism
  fig|6666666.60966.peg.140	CDS	139048	139299	1	+	252	FIG00858998:	-none-	D23_1c0146	Neut_0239
  							hypothetical protein
  fig|6666666.60966.peg.141	CDS	140580	139432	−3	−	1149	Cell division protein	Bacterial Cell Division;	D23_1c0147	Neut_0240
  							FtsZ (EC 3.4.24.—)	<br>Bacterial
  								Cytoskeleton; <br>cell
  								division cluster
  								containing FtsQ; <br>cell
  								division core of larger
  								cluster
  fig|6666666.60966.peg.142	CDS	141909	140650	−3	−	1260	Cell division protein	Bacterial Cell Division;	D23_1c0149	Neut_0241
  							FtsA	<br>Bacterial
  								Cytoskeleton; <br>cell
  								division cluster
  								containing FtsQ; <br>cell
  								division core of larger
  								cluster
  fig|6666666.60966.peg.143	CDS	142678	141950	−1	−	729	Cell division protein	Bacterial Cell Division;	D23_1c0150	Neut_0242
  							FtsQ	<br>Bacterial
  								Cytoskeleton; <br>cell
  								division cluster
  								containing FtsQ; <br>cell
  								division core of larger
  								cluster
  fig|6666666.60966.peg.144	CDS	143654	142734	−2	−	921	D-alanine--D-alanine	Peptidoglycan	D23_1c0152	Neut_0243
  							ligase (EC 6.3.2.4)	Biosynthesis;
  								<br>Peptidoglycan
  								biosynthesis--gjo;
  								<br>cell division cluster
  								containing FtsQ
  fig|6666666.60966.peg.145	CDS	144649	143651	−1	−	999	UDP-N-	Peptidoglycan	D23_1c0153	Neut_0244
  							acetylenolpyruvoylglucosamine	Biosynthesis; <br>UDP-
  							reductase (EC	N-acetylmuramate from
  							1.1.1.158)	Fructose-6-phosphate
  								Biosynthesis
  fig|6666666.60966.peg.146	CDS	146080	144659	−1	−	1422	UDP-N-	Peptidoglycan	D23_1c0154	Neut_0245
  							acetylmuramate--	Biosynthesis;
  							alanine ligase (EC	<br>Peptidoglycan
  							6.3.2.8)	biosynthesis--gjo;
  								<br>cell division cluster
  								containing FtsQ
  fig|6666666.60966.peg.147	CDS	147159	146077	−3	−	1083	UDP-N-	Peptidoglycan	D23_1c0155	Neut_0246
  							acetylglucosamine--N-	Biosynthesis; <br>cell
  							acetylmuramyl-	division core of larger
  							(pentapeptide)	cluster
  							pyrophosphoryl-
  							undecaprenol N-
  							acetylglucosamine
  							transferase (EC
  							2.4.1.227)
  fig|6666666.60966.peg.148	CDS	148372	147212	−1	−	1161	Cell division protein	Bacterial Cell Division;	D23_1c0156	Neut_0247
  							FtsW	<br>Bacterial
  								Cytoskeleton; <br>cell
  								division cluster
  								containing FtsQ
  fig|6666666.60966.peg.149	CDS	149789	148377	−2	−	1413	UDP-N-	Peptidoglycan	D23_1c0157	Neut_0248
  							acetylmuramoylalanine--	Biosynthesis;
  							D-glutamate ligase (EC	<br>Peptidoglycan
  							6.3.2.9)	biosynthesis--gjo
  fig|6666666.60966.peg.150	CDS	150871	149786	−1	−	1086	Phospho-N-	Peptidoglycan	D23_1c0158	Neut_0249
  							acetylmuramoyl-	Biosynthesis
  							pentapeptide-
  							transferase (EC
  							2.7.8.13)
  fig|6666666.60966.peg.151	CDS	152316	150943	−3	−	1374	UDP-N-	Peptidoglycan	D23_1c0159	Neut_0250
  							acetylmuramoylalanyl-	Biosynthesis;
  							D-glutamyl-2,6-	<br>Peptidoglycan
  							diaminopimelate--D-	biosynthesis--gjo
  							alanyl-D-alanine ligase
  							(EC 6.3.2.10)
  fig|6666666.60966.peg.152	CDS	153875	152313	−2	−	1563	UDP-N-	Peptidoglycan	D23_1c0160	Neut_0251
  							acetylmuramoylalanyl-	Biosynthesis;
  							D-glutamate--2,6-	<br>Peptidoglycan
  							diaminopimelate ligase	biosynthesis--gjo
  							(EC 6.3.2.13)
  fig|6666666.60966.peg.153	CDS	155545	153872	−1	−	1674	Cell division protein Ftsl	16S rRNA modification	D23_1c0161	Neut_0252
  							[Peptidoglycan	within P site of
  							synthetase] (EC	ribosome; <br>Bacterial
  							2.4.1.129)	Cell Division;
  								<br>Bacterial
  								Cytoskeleton; <br>CBSS-
  								83331.1.peg.3039;
  								<br>Flagellum in
  								Campylobacter;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.155	CDS	155895	155608	−3	−	288	Cell division protein FtsL	16S rRNA modification	D23_1c0162	Neut_0253
  								within P site of
  								ribosome; <br>Bacterial
  								Cell Division;
  								<br>Bacterial
  								Cytoskeleton;
  								<br>Stationary phase
  								repair cluster
  fig|6666666.60966.peg.156	CDS	156845	155892	−2	−	954	rRNA small subunit	16S rRNA modification	D23_1c0163	Neut_0254
  							methyltransferase H	within P site of
  								ribosome; <br>Bacterial
  								Cell Division
  fig|6666666.60966.peg.157	CDS	157094	156861	−2	−	234	Cell division protein	16S rRNA modification	D23_1c0164	Neut_0255
  							MraZ	within P site of
  								ribosome; <br>Bacterial
  								Cell Division;
  								<br>Bacterial
  								Cytoskeleton
  fig|6666666.60966.peg.158	CDS	157584	157859	3	+	276	DNA-3-methyladenine	DNA Repair Base	D23_1c0165	NA
  							glycosylase II (EC	Excision
  							3.2.2.21)
  fig|6666666.60966.peg.159	CDS	158202	158420	3	+	219	Rho-specific inhibitor of	Transcription factors	D23_1c0166	Neut_0257
  							transcription	bacterial
  							termination (YaeO)
  fig|6666666.60966.peg.160	CDS	159328	158561	−1	−	768	InterPro IPR001173	-none-	D23_1c0167	Neut_0258
  							COGs COG0463
  fig|6666666.60966.peg.161	CDS	159475	159924	1	+	450	InterPro IPR000086	-none-	D23_1c0168	Neut_0259
  							COGs COG0494
  fig|6666666.60966.peg.162	CDS	160257	160814	3	+	558	possible (U92432) ORF4	-none-	D23_1c0169	Neut_0260
  							[Nitrosospira sp. NpAV]
  fig|6666666.60966.peg.164	CDS	160969	161451	1	+	483	FIG00859298:	-none-	D23_1c0170	Neut_0261
  							hypothetical protein
  fig|6666666.60966.peg.165	CDS	161593	162063	1	+	471	Adenine	Purine conversions;	D23_1c0171	Neut_0262
  							phosphoribosyltransferase	<br>cAMP signaling in
  							(EC 2.4.2.7)	bacteria
  fig|6666666.60966.peg.166	CDS	162260	163573	2	+	1314	Seryl-tRNA synthetase	CBSS-	D23_1c0172	Neut_0263
  							(EC 6.1.1.11)	326442.4.peg.1852;
  								<br>Glycine and Serine
  								Utilization; <br>tRNA
  								aminoacylation, Ser
  fig|6666666.60966.peg.167	CDS	163620	164306	3	+	687	FIG00858527:	-none-	D23_1c0173	Neut_0264
  							hypothetical protein
  fig|6666666.60966.peg.168	CDS	165061	164351	−1	−	711	Phosphoglycerate	Glycolysis and	D23_1c0174	Neut_0265
  							mutase (EC 5.4.2.1)	Gluconeogenesis;
  								<br>Phosphoglycerate
  								mutase protein family
  fig|6666666.60966.peg.169	CDS	166178	165111	−2	−	1068	InterPro IPR001225	-none-	D23_1c0175	Neut_0266
  fig|6666666.60966.peg.170	CDS	166643	166200	−2	−	444	FIG00858776:	-none-	D23_1c0176	Neut_0267
  							hypothetical protein
  fig|6666666.60966.peg.171	CDS	167465	166659	−2	−	807	CTP:Inositol-1-	-none-	D23_1c0177	Neut_0268
  							phosphate
  							cytidylyltransferase
  							(2.7.7.—)
  fig|6666666.60966.peg.172	CDS	168669	167509	−3	−	1161	Cysteine desulfurase	Alanine biosynthesis;	D23_1c0178	Neut_0269
  							(EC 2.8.1.7)	<br>CBSS-
  								84588.1.peg.1247;
  								<br>mnm5U34
  								biosynthesis bacteria;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.174	CDS	169251	169631	3	+	381	FIG048548: ATP	-none-	D23_1c0180	Neut_0270
  							synthase protein I2
  fig|6666666.60966.peg.175	CDS	169720	170472	1	+	753	ATP synthase A chain	-none-	D23_1c0181	Neut_0271
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.176	CDS	170516	170788	2	+	273	ATP synthase C chain	-none-	D23_1c0182	Neut_0272
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.177	CDS	170900	171301	2	+	402	ATP synthase B chain	-none-	D23_1c0183	Neut_0273
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.178	CDS	171302	171838	2	+	537	ATP synthase delta	-none-	D23_1c0184	Neut_0274
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.179	CDS	171851	173392	2	+	1542	ATP synthase alpha	-none-	D23_1c0185	Neut_0275
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.180	CDS	173396	174280	2	+	885	ATP synthase gamma	-none-	D23_1c0186	Neut_0276
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.181	CDS	174311	175693	2	+	1383	ATP synthase beta chain	-none-	D23_1c0187	Neut_0277
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.182	CDS	175842	176141	3	+	300	ATP synthase epsilon	-none-	D23_1c0188	Neut_0278
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.183	CDS	176389	177765	1	+	1377	N-acetylglucosamine-1-	Peptidoglycan	D23_1c0189	Neut_0279
  							phosphate	Biosynthesis;
  							uridyltransferase (EC	<br>Peptidoglycan
  							2.7.7.23)/	Biosynthesis; <br>Sialic
  							Glucosamine-1-	Acid Metabolism;
  							phosphate N-	<br>Sialic Acid
  							acetyltransferase (EC	Metabolism;
  							2.3.1.157)	<br>Transcription repair
  								cluster;
  								<br>Transcription repair
  								cluster; <br>UDP-N-
  								acetylmuramate from
  								Fructose-6-phosphate
  								Biosynthesis; <br>UDP-
  								N-acetylmuramate from
  								Fructose-6-phosphate
  								Biosynthesis
  fig|6666666.60966.peg.184	CDS	177805	179652	1	+	1848	Glucosamine-fructose-	Sialic Acid Metabolism;	D23_1c0190	Neut_0280
  							6-phosphate	<br>UDP-N-
  							aminotransferase	acetylmuramate from
  							[isomerizing] (EC	Fructose-6-phosphate
  							2.6.1.16)	Biosynthesis
  fig|6666666.60966.peg.185	CDS	179795	180520	2	+	726	FIG000859:	Riboflavin, FMN and FAD	D23_1c0191	Neut_0281
  							hypothetical protein	metabolism in plants;
  							YebC	<br>RuvABC plus a
  								hypothetical
  fig|6666666.60966.peg.186	CDS	180523	181059	1	+	537	Crossover junction	RuvABC plus a	D23_1c0192	Neut_0282
  							endodeoxyribonuclease	hypothetical
  							RuvC (EC 3.1.22.4)
  fig|6666666.60966.peg.187	CDS	181056	181640	3	+	585	Holliday junction DNA	RuvABC plus a	D23_1c0193	Neut_0283
  							helicase RuvA	hypothetical
  fig|6666666.60966.peg.188	CDS	181659	182699	3	+	1041	Holliday junction DNA	RuvABC plus a	D23_1c0194	Neut_0284
  							helicase RuvB	hypothetical
  fig|6666666.60966.peg.189	CDS	182760	183173	3	+	414	4-hydroxybenzoyl-CoA	Ton and Tol transport	D23_1c0195	Neut_0285
  							thioesterase family	systems
  							active site
  fig|6666666.60966.peg.190	CDS	183166	183870	1	+	705	MotA/TolQ/ExbB	Ton and Tol transport	D23_1c0196	Neut_0286
  							proton channel family	systems
  							protein
  fig|6666666.60966.peg.191	CDS	183867	184283	3	+	417	Tol biopolymer	Ton and Tol transport	D23_1c0197	Neut_0287
  							transport system, TolR	systems
  							protein
  fig|6666666.60966.peg.192	CDS	184304	185200	2	+	897	TolA protein	Ton and Tol transport	D23_1c0198	Neut_0288
  								systems
  fig|6666666.60966.peg.193	CDS	185239	186510	1	+	1272	tolB protein precursor,	Ton and Tol transport	D23_1c0199	Neut_0289
  							periplasmic protein	systems
  							involved in the tonb-
  							independent uptake of
  							group A colicins
  fig|6666666.60966.peg.194	CDS	186565	187086	1	+	522	18K peptidoglycan-	Ton and Tol transport	D23_1c0200	Neut_0290
  							associated outer	systems
  							membrane lipoprotein;
  							Peptidoglycan-
  							associated lipoprotein
  							precursor; Outer
  							membrane protein P6;
  							OmpA/MotB precursor
  fig|6666666.60966.peg.195	CDS	187086	187907	3	+	822	TPR repeat containing	Ton and Tol transport	D23_1c0201	Neut_0291
  							exported protein;	systems
  							Putative periplasmic
  							protein contains a
  							protein
  							prenylyltransferase
  							domain
  fig|6666666.60966.peg.196	CDS	188060	188644	2	+	585	Queuosine Biosynthesis	Queuosine-Archaeosine	D23_1c0202	Neut_0292
  							QueE Radical SAM	Biosynthesis; <br>tRNA
  								modification Bacteria
  fig|6666666.60966.peg.197	CDS	188666	189346	2	+	681	Queuosine Biosynthesis	Queuosine-Archaeosine	D23_1c0203	Neut_0293
  							QueC ATPase	Biosynthesis; <br>tRNA
  								modification Bacteria
  fig|6666666.60966.peg.198	CDS	189700	189347	−1	−	354	Dihydroneopterin	Folate Biosynthesis	D23_1c0204	Neut_0294
  							aldolase (EC 4.1.2.25)
  fig|6666666.60966.peg.199	CDS	189786	190388	3	+	603	Acyl-	Glycerolipid and	D23_1c0205	Neut_0295
  							phosphate:glycerol-3-	Glycerophospholipid
  							phosphate O-	Metabolism in Bacteria
  							acyltransferase PlsY
  fig|6666666.60966.peg.200	CDS	191422	190406	−1	−	1017	TsaD/Kae1/Qri7	Bacterial RNA-	D23_1c0206	Neut_0296
  							protein, required for	metabolizing Zn-
  							threonylcarbamoyladenosine	dependent hydrolases;
  							t(6)A37 formation	<br>Macromolecular
  							in tRNA	synthesis operon;
  								<br>YgjD and YeaZ
  fig|6666666.60966.peg.201	CDS	191698	191910	1	+	213	SSU ribosomal protein	Macromolecular	D23_1c0207	Neut_0297
  							S21p	synthesis operon
  fig|6666666.60966.peg.202	CDS	191984	192391	2	+	408	Transamidase GatB	Macromolecular	D23_1c0208	Neut_0298
  							domain protein	synthesis operon
  fig|6666666.60966.peg.203	CDS	192486	194279	3	+	1794	DNA primase (EC 2.7.7.—)	CBSS-	D23_1c0209	Neut_0299
  								349161.4.peg.2417;
  								<br>Macromolecular
  								synthesis operon
  fig|6666666.60966.peg.204	CDS	194461	196710	1	+	2250	RNA polymerase sigma	CBSS-	D23_1c0210	Neut_0300
  							factor RpoD	349161.4.peg.2417;
  								<br>Flagellum;
  								<br>Macromolecular
  								synthesis operon;
  								<br>Transcription
  								initiation, bacterial
  								sigma factors
  fig|6666666.60966.peg.206	CDS	197605	197180	−1	−	426	Mobile element protein	-none-	D23_1c0212	Neut_0357
  fig|6666666.60966.peg.207	CDS	198088	198819	1	+	732	Mobile element protein	-none-	D23_1c0213	NA
  fig|6666666.60966.peg.209	CDS	200235	199564	−3	−	672	transposase and	-none-	D23_1c0214	Neut_2192
  							inactivated derivatives
  fig|6666666.60966.peg.210	CDS	200398	200210	−1	−	189	hypothetical protein	-none-	D23_1c0215	NA
  fig|6666666.60966.peg.211	CDS	200852	200995	2	+	144	Mobile element protein	-none-	D23_1c0216	Neut_0978
  fig|6666666.60966.peg.212	CDS	201848	200970	−2	−	879	Mobile element protein	-none-	D23_1c0217	Neut_1720
  fig|6666666.60966.peg.213	CDS	202240	201947	−1	−	294	Mobile element protein	-none-	D23_1c0218	Neut_1719
  fig|6666666.60966.peg.214	CDS	202367	203209	2	+	843	Mobile element protein	-none-	D23_1c0219	Neut_1524
  fig|6666666.60966.peg.215	CDS	203592	203461	−3	−	132	Phage Rha protein	-none-	D23_1c0220	NA
  fig|6666666.60966.peg.216	CDS	203906	203571	−2	−	336	Mobile element protein	-none-	D23_1c0221	Neut_2450
  fig|6666666.60966.peg.218	CDS	204442	204113	−1	−	330	hypothetical protein	-none-	D23_1c0222	Neut_2449
  fig|6666666.60966.peg.219	CDS	205381	204746	−1	−	636	Cytochrome c4	Soluble cytochromes	D23_1c0223	Neut_0305
  								and functionally related
  								electron carriers
  fig|6666666.60966.peg.220	CDS	205494	206096	3	+	603	FIG00859469:	-none-	D23_1c0224	Neut_0306
  							hypothetical protein
  fig|6666666.60966.peg.221	CDS	206204	207016	2	+	813	Methionine	CBSS-	D23_1c0225	Neut_0307
  							aminopeptidase (EC	312309.3.peg.1965;
  							3.4.11.18)	<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.222	CDS	207076	207840	1	+	765	Ribonuclease PH (EC	Heat shock dnaK gene	D23_1c0226	Neut_0308
  							2.7.7.56)	cluster extended;
  								<br>tRNA processing
  fig|6666666.60966.peg.223	CDS	207825	208439	3	+	615	Xanthosine/inosine	CBSS-630.2.peg.3360;	D23_1c0227	Neut_0309
  							triphosphate	<br>Heat shock dnaK
  							pyrophosphatase;	gene cluster extended
  							HAM1-like protein
  fig|6666666.60966.peg.224	CDS	208474	209709	1	+	1236	Radical SAM family	CBSS-630.2.peg.3360;	D23_1c0228	Neut_0310
  							enzyme, similar to	<br>Heat shock dnaK
  							coproporphyrinogen III	gene cluster extended;
  							oxidase, oxygen-	<br>Heme and Siroheme
  							independent, clustered	Biosynthesis;
  							with nucleoside-	<br>Queuosine-
  							triphosphatase RdgB	Archaeosine
  								Biosynthesis
  fig|6666666.60966.peg.225	CDS	209741	211540	2	+	1800	Multicopper oxidase	Copper homeostasis	D23_1c0229	Neut_0311
  fig|6666666.60966.peg.226	CDS	211537	212352	1	+	816	Copper resistance	Copper homeostasis	D23_1c0230	Neut_0312
  							protein B
  fig|6666666.60966.peg.227	CDS	213327	212398	−3	−	930	hypothetical protein	-none-	D23_1c0231	Neut_0313
  fig|6666666.60966.peg.228	CDS	213918	213340	−3	−	579	LemA PROTEIN	-none-	D23_1c0232	Neut_1392
  fig|6666666.60966.peg.229	CDS	214368	214553	3	+	186	Mobile element protein	-none-	D23_1c0233	Neut_2500
  fig|6666666.60966.peg.230	CDS	214610	215206	2	+	597	Mobile element protein	-none-	D23_1c0234	Neut_1375
  fig|6666666.60966.peg.231	CDS	215510	215623	2	+	114	hypothetical protein	-none-	D23_1c0235	NA
  fig|6666666.60966.peg.232	CDS	215668	215847	1	+	180	hypothetical protein	-none-	D23_1c0236	Neut_0314
  fig|6666666.60966.peg.233	CDS	217943	216069	−2	−	1875	Glutathione-regulated	Glutathione-regulated	D23_1c0237	Neut_0315
  							potassium-efflux system	potassium-efflux system
  							ATP-binding protein	and associated
  								functions;
  								<br>Potassium
  								homeostasis
  fig|6666666.60966.peg.234	CDS	218233	219195	1	+	963	Mobile element protein	-none-	D23_1c0238	Neut_1862
  fig|6666666.60966.peg.235	CDS	219960	219271	−3	−	690	InterPro IPR001687	-none-	D23_1c0239	NA
  fig|6666666.60966.peg.236	CDS	220560	222266	3	+	1707	Glutathione-regulated	Glutathione-regulated	D23_1c0241	Neut_0318
  							potassium-efflux system	potassium-efflux system
  							protein KefB	and associated functions
  fig|6666666.60966.peg.237	CDS	222848	223903	2	+	1056	SAM-dependent	-none-	D23_1c0242	Neut_0320
  							methyltransferase
  							SCO3452 (UbiE paralog)
  fig|6666666.60966.peg.238	CDS	223971	224243	3	+	273	Phosphate transport	High affinity phosphate	D23_1c0244	Neut_0321
  							system permease	transporter and control
  							protein PstA (TC	of PHO regulon;
  							3.A.1.7.1)	<br>Phosphate
  								metabolism
  fig|6666666.60966.peg.239	CDS	225095	224421	−2	−	675	tRNA (guanine46-N7-)-	RNA methylation;	D23_1c0245	Neut_0322
  							methyltransferase (EC	<br>tRNA modification
  							2.1.1.33)	Bacteria
  fig|6666666.60966.peg.240	CDS	225934	225128	−1	−	807	Thiazole biosynthesis	Thiamin biosynthesis	D23_1c0246	Neut_0323
  							protein ThiG
  fig|6666666.60966.peg.241	CDS	226194	225994	−3	−	201	Sulfur carrier protein	Thiamin biosynthesis	D23_1c0247	Neut_0324
  							ThiS
  fig|6666666.60966.peg.242	CDS	226421	227008	2	+	588	FIG008443:	CBSS-208964.1.peg.1768	D23_1c0249	Neut_0325
  							hypothetical protein
  fig|6666666.60966.peg.243	CDS	227005	228537	1	+	1533	FIG139976:	CBSS-208964.1.peg.1768	D23_1c0250	Neut_0326
  							hypothetical protein
  fig|6666666.60966.peg.244	CDS	228587	229492	2	+	906	FIG002781: Alpha-L-	CBSS-208964.1.peg.1768	D23_1c0251	Neut_0327
  							glutamate ligase family
  							protein
  fig|6666666.60966.peg.245	CDS	231155	229677	−2	−	1479	Cardiolipin synthetase	Cardiolipin synthesis;	D23_1c0252	Neut_0328
  							(EC 2.7.8.—)	<br>Glycerolipid and
  								Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.246	CDS	231229	231411	1	+	183	hypothetical protein	-none-	D23_1c0253	NA
  fig|6666666.60966.peg.248	CDS	232352	231813	−2	−	540	Urea channel Urel	Urea decomposition	D23_1c0255	Neut_0329
  fig|6666666.60966.peg.249	CDS	232767	232585	−3	−	183	hypothetical protein	-none-	D23_1c0256	NA
  fig|6666666.60966.peg.251	CDS	233588	234748	2	+	1161	FIG00855934:	-none-	D23_1c0259	Neut_0331
  							hypothetical protein
  fig|6666666.60966.peg.252	CDS	235271	234831	−2	−	441	Mobile element protein	-none-	D23_1c0260	Neut_0332
  fig|6666666.60966.peg.253	CDS	235792	235397	−1	−	396	NAD-dependent	Calvin-Benson cycle;	D23_1c0261	Neut_0333
  							glyceraldehyde-3-	<br>Glycolysis and
  							phosphate	Gluconeogenesis;
  							dehydrogenase (EC	<br>Pyridoxin (Vitamin
  							1.2.1.12)	B6) Biosynthesis
  fig|6666666.60966.peg.254	CDS	235832	236260	2	+	429	hypothetical protein	-none-	D23_1c0261	Neut_0333
  fig|6666666.60966.peg.255	CDS	237167	236592	−2	−	576	Flagellar basal-body P-	Flagellum	D23_1c0262	Neut_0334
  							ring formation protein
  							FlgA
  fig|6666666.60966.peg.256	CDS	237299	237415	2	+	117	hypothetical protein	-none-	D23_1c0264	NA
  fig|6666666.60966.peg.257	CDS	237436	237924	1	+	489	Flagellar basal-body rod	Flagellum; <br>Flagellum	D23_1c0265	Neut_0335
  							protein FlgB	in Campylobacter
  fig|6666666.60966.peg.258	CDS	237930	238334	3	+	405	Flagellar basal-body rod	Flagellum; <br>Flagellum	D23_1c0266	Neut_0336
  							protein FlgC	in Campylobacter
  fig|6666666.60966.peg.259	CDS	238347	239021	3	+	675	Flagellar basal-body rod	Flagellar motility;	D23_1c0267	Neut_0337
  							modification protein	<br>Flagellum
  							FlgD
  fig|6666666.60966.peg.260	CDS	239037	240296	3	+	1260	Flagellar hook protein	Flagellum	D23_1c0268	Neut_0338
  							FlgE
  fig|6666666.60966.peg.261	CDS	240337	241080	1	+	744	Flagellar basal-body rod	Flagellum	D23_1c0269	Neut_0339
  							protein FlgF
  fig|6666666.60966.peg.262	CDS	241119	241901	3	+	783	Flagellar basal-body rod	Flagellum	D23_1c0270	Neut_0340
  							protein FlgG
  fig|6666666.60966.peg.263	CDS	242034	242828	3	+	795	Flagellar L-ring protein	Flagellar motility;	D23_1c0271	Neut_0341
  							FlgH	<br>Flagellum
  fig|6666666.60966.peg.264	CDS	242850	243977	3	+	1128	Flagellar P-ring protein	Flagellum	D23_1c0272	Neut_0342
  							FlgI
  fig|6666666.60966.peg.265	CDS	243991	244998	1	+	1008	Flagellar protein FlgJ	Flagellum	D23_1c0273	Neut_0343
  							[peptidoglycan
  							hydrolase] (EC 3.2.1.—)
  fig|6666666.60966.peg.266	CDS	245257	246660	1	+	1404	Flagellar hook-	Flagellum	D23_1c0274	Neut_0344
  							associated protein FlgK
  fig|6666666.60966.peg.267	CDS	246638	247588	2	+	951	Flagellar hook-	Flagellum	D23_1c0275	Neut_0345
  							associated protein FlgL
  fig|6666666.60966.peg.268	CDS	247665	248210	3	+	546	FIG00859049:	-none-	D23_1c0276	Neut_0346
  							hypothetical protein
  fig|6666666.60966.peg.269	CDS	249330	248200	−3	−	1131	FIG00859091:	-none-	D23_1c0277	Neut_0347
  							hypothetical protein
  fig|6666666.60966.peg.270	CDS	249439	249960	1	+	522	FIG00859511:	-none-	D23_1c0278	Neut_0348
  							hypothetical protein
  fig|6666666.60966.peg.271	CDS	249932	250513	2	+	582	GCN5-related N-	-none-	D23_1c0279	Neut_0349
  							acetyltransferase
  fig|6666666.60966.peg.272	CDS	250589	250861	2	+	273	FIG001341: Probable	Heat shock dnaK gene	D23_1c0280	Neut_0350
  							Fe(2+)-trafficking	cluster extended
  							protein YggX
  fig|6666666.60966.peg.273	CDS	250912	253038	1	+	2127	Polyphosphate kinase	High affinity phosphate	D23_1c0281	Neut_0351
  							(EC 2.7.4.1)	transporter and control
  								of PHO regulon;
  								<br>Phosphate
  								metabolism;
  								<br>Polyphosphate;
  								<br>Purine conversions
  fig|6666666.60966.peg.274	CDS	254786	253059	−2	−	1728	Sulfate permease	Cysteine Biosynthesis	D23_1c0282	Neut_0352
  fig|6666666.60966.peg.275	CDS	255133	254783	−1	−	351	Transcriptional	-none-	D23_1c0283	Neut_0353
  							regulator, ArsR family
  fig|6666666.60966.peg.277	CDS	256153	255827	−1	−	327	hypothetical protein	-none-	D23_1c0285	Neut_0355
  fig|6666666.60966.peg.278	CDS	256608	257603	3	+	996	hypothetical protein	-none-	D23_1c0286	Neut_0356
  fig|6666666.60966.peg.279	CDS	258986	257739	−2	−	1248	Mobile element protein	-none-	D23_1c0287	Neut_0357
  fig|6666666.60966.peg.280	CDS	259004	259126	2	+	123	patatin family protein	-none-	D23_1c0288	Neut_1317
  fig|6666666.60966.peg.281	CDS	259254	259123	−3	−	132	cAMP-binding proteins-	cAMP signaling in	D23_1c0289	NA
  							catabolite gene	bacteria
  							activator and regulatory
  							subunit of cAMP-
  							dependent protein
  							kinases
  fig|6666666.60966.peg.282	CDS	259543	260031	1	+	489	Cytochrome c&#39;	-none-	D23_1c0291	NA
  fig|6666666.60966.peg.283	CDS	260060	260947	2	+	888	Putative diheme	Soluble cytochromes	D23_1c0292	Neut_1381
  							cytochrome c-553	and functionally related
  								electron carriers
  fig|6666666.60966.peg.285	CDS	261917	261708	−2	−	210	hypothetical protein	-none-	D23_1c0294	Neut_0363
  fig|6666666.60966.peg.288	CDS	262640	262440	−2	−	201	Mobile element protein	-none-	D23_1c0296	Neut_1696
  fig|6666666.60966.peg.289	CDS	263106	264041	3	+	936	hypothetical protein	-none-	D23_1c0297	NA
  fig|6666666.60966.peg.290	CDS	264137	265633	2	+	1497	SII1503 protein	-none-	D23_1c0298	NA
  fig|6666666.60966.peg.294	CDS	266897	266760	−2	−	138	hypothetical protein	-none-	D23_1c0300	NA
  fig|6666666.60966.peg.295	CDS	267026	267370	2	+	345	COGs COG3339	-none-	D23_1c0301	Neut_0371
  fig|6666666.60966.peg.297	CDS	268862	267765	−2	−	1098	L-lactate	Lactate utilization;	D23_1c0302	Neut_0372
  							dehydrogenase (EC	<br>Respiratory
  							1.1.2.3)	dehydrogenases 1
  fig|6666666.60966.peg.298	CDS	269655	268972	−3	−	684	Iron-uptake factor PiuC	-none-	D23_1c0303	Neut_0373
  fig|6666666.60966.peg.299	CDS	271893	269683	−3	−	2211	TonB-dependent	Ton and Tol transport	D23_1c0304	Neut_0374
  							siderophore receptor	systems
  fig|6666666.60966.peg.301	CDS	272682	273740	3	+	1059	protein of unknown	-none-	D23_1c0306	Neut_0377
  							function DUF81
  fig|6666666.60966.peg.302	CDS	273758	274108	2	+	351	hypothetical protein	-none-	D23_1c0307	NA
  fig|6666666.60966.peg.303	CDS	274775	274182	−2	−	594	InterPro IPR001226	-none-	D23_1c0308	Neut_0379
  							COGs COG0790
  fig|6666666.60966.peg.304	CDS	274944	274792	−3	−	153	hypothetical protein	-none-	D23_1c0309	NA
  fig|6666666.60966.peg.305	CDS	276110	274986	−2	−	1125	dNTP	Purine conversions;	D23_1c0310	Neut_0380
  							triphosphohydrolase,	<br>dNTP
  							broad substrate	triphosphohydrolase
  							specificity, subgroup 2	protein family
  fig|6666666.60966.peg.306	CDS	277212	276103	−3	−	1110	3-dehydroquinate	Chorismate Synthesis;	D23_1c0311	Neut_0381
  							synthase (EC 4.2.3.4)	<br>Common Pathway
  								For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.308	CDS	277726	277896	1	+	171	hypothetical protein	-none-	D23_1c0312	Neut_0382
  fig|6666666.60966.peg.307	CDS	277692	277261	−3	−	432	Shikimate kinase I (EC	Chorismate Synthesis;	D23_1c0312	Neut_0382
  							2.7.1.71)	<br>Common Pathway
  								For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.309	CDS	279343	277982	−1	−	1362	Putative protease	-none-	D23_1c0313	Neut_0383
  fig|6666666.60966.peg.310	CDS	279362	282934	2	+	3573	DNA polymerase III	Phage replication	D23_1c0314	Neut_0384
  							alpha subunit (EC
  							2.7.7.7)
  fig|6666666.60966.peg.311	CDS	283139	282948	−2	−	192	putative	-none-	D23_1c0315	Neut_0385
  							transmembrane protein
  fig|6666666.60966.peg.312	CDS	283290	284243	3	+	954	tRNA	tRNA modification	D23_1c0316	Neut_0386
  							dimethylallyltransferase	Bacteria; <br>tRNA
  							(EC 2.5.1.75)	processing
  fig|6666666.60966.peg.313	CDS	284258	284401	2	+	144	hypothetical protein	-none-	D23_1c0317	NA
  fig|6666666.60966.peg.314	CDS	286041	284776	−3	−	1266	Two component,	-none-	D23_1c0320	Neut_0387
  							sigma54 specific,
  							transcriptional
  							regulator, Fis family
  fig|6666666.60966.peg.315	CDS	286328	286191	−2	−	138	hypothetical protein	-none-	D23_1c0321	NA
  fig|6666666.60966.peg.316	CDS	288462	286330	−3	−	2133	Nitrogen regulation	Possible RNA	D23_1c0322	Neut_0388
  							protein NtrY (EC 2.7.3.—)	degradation cluster
  fig|6666666.60966.peg.317	CDS	289077	288514	−3	−	564	Probable proline rich	-none-	D23_1c0323	Neut_0389
  							signal peptide protein
  fig|6666666.60966.peg.318	CDS	290401	289121	−1	−	1281	16S rRNA	RNA methylation	D23_1c0324	Neut_0390
  							(cytosine(967)-C(5))-
  							methyltransferase (EC
  							2.1.1.176) ## SSU rRNA
  							m5C967
  fig|6666666.60966.peg.319	CDS	291388	290414	−1	−	975	Methionyl-tRNA	Translation initiation	D23_1c0325	Neut_0391
  							formyltransferase (EC	factors bacterial
  							2.1.2.9)
  fig|6666666.60966.peg.320	CDS	291933	291427	−3	−	507	Peptide deformylase	Bacterial RNA-	D23_1c0326	Neut_0392
  							(EC 3.5.1.88)	metabolizing Zn-
  								dependent hydrolases;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.321	CDS	292108	293136	1	+	1029	Uncharacterized protein	-none-	D23_1c0327	Neut_0393
  							with LysM domain,
  							COG1652
  fig|6666666.60966.peg.322	CDS	293235	294356	3	+	1122	Rossmann fold	-none-	D23_1c0328	Neut_0394
  							nucleotide-binding
  							protein Smf possibly
  							involved in DNA uptake
  fig|6666666.60966.peg.323	CDS	294438	294896	3	+	459	Protein of unknown	-none-	D23_1c0329	Neut_0395
  							function Smg
  fig|6666666.60966.peg.324	CDS	295024	297522	1	+	2499	DNA topoisomerase III,	DNA topoisomerases,	D23_1c0330	Neut_0396
  							Burkholderia type (EC	Type I, ATP-independent
  							5.99.1.2)
  fig|6666666.60966.peg.325	CDS	297826	297575	−1	−	252	FIG00858730:	-none-	D23_1c0331	Neut_0397
  							hypothetical protein
  fig|6666666.60966.peg.326	CDS	298176	299477	3	+	1302	5-Enolpyruvylshikimate-	Chorismate Synthesis;	D23_1c0333	Neut_0398
  							3-phosphate synthase	<br>Common Pathway
  							(EC 2.5.1.19)	For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.327	CDS	299557	300228	1	+	672	Cytidylate kinase (EC	-none-	D23_1c0335	Neut_0399
  							2.7.4.14)
  fig|6666666.60966.peg.328	CDS	300339	302051	3	+	1713	SSU ribosomal protein	-none-	D23_1c0336	Neut_0400
  							S1p
  fig|6666666.60966.peg.329	CDS	302061	302378	3	+	318	Integration host factor	DNA structural proteins,	D23_1c0337	Neut_0401
  							beta subunit	bacterial
  fig|6666666.60966.peg.330	CDS	302493	302368	−3	−	126	hypothetical protein	-none-	D23_1c0338	NA
  fig|6666666.60966.peg.33 1	CDS	302902	303597	1	+	696	Orotidine 5&#39;-	De Novo Pyrimidine	D23_1c0339	Neut_0402
  							phosphate	Synthesis; <br>Riboflavin
  							decarboxylase (EC	synthesis cluster
  							4.1.1.23)
  fig|6666666.60966.peg.332	CDS	304632	303592	−3	−	1041	Squalene synthase (EC	Hopanes	D23_1c0340	Neut_0403
  							2.5.1.21)
  fig|6666666.60966.peg.333	CDS	305907	304654	−3	−	1254	Diaminopimelate	Lysine Biosynthesis DAP	D23_1c0341	Neut_0404
  							decarboxylase (EC	Pathway, GJO scratch
  							4.1.1.20)
  fig|6666666.60966.peg.334	CDS	306026	305904	−2	−	123	hypothetical protein	-none-	D23_1c0342	NA
  fig|6666666.60966.peg.335	CDS	306654	306052	−3	−	603	Probable lipoprotein	-none-	D23_1c0343	Neut_0405
  fig|6666666.60966.peg.336	CDS	307556	306651	−2	−	906	ABC-type transport	-none-	D23_1c0344	Neut_0406
  							system involved in
  							resistance to organic
  							solvents, periplasmic
  							component
  fig|6666666.60966.peg.337	CDS	308341	307583	−1	−	759	Inositol-1-	-none-	D23_1c0345	Neut_0407
  							monophosphatase (EC
  							3.1.3.25)
  fig|6666666.60966.peg.339	CDS	308500	309207	1	+	708	tRNA:Cm32/Um32	RNA methylation;	D23_1c0346	Neut_0408
  							methyltransferase	<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.340	CDS	309905	309291	−2	−	615	Glutathione S-	Glutathione: Non-redox	D23_1c0347	Neut_0409
  							transferase family	reactions; <br>Scaffold
  							protein	proteins for [4Fe-4S]
  								cluster assembly (MRP
  								family)
  fig|6666666.60966.peg.341	CDS	310042	311418	1	+	1377	Adenylosuccinate lyase	De Novo Purine	D23_1c0348	Neut_0410
  							(EC 4.3.2.2)	Biosynthesis; <br>Purine
  								conversions
  fig|6666666.60966.peg.342	CDS	311556	312146	3	+	591	Heat shock protein	GroEL GroES; <br>Heat	D23_1c0349	Neut_0411
  							GrpE	shock dnaK gene cluster
  								extended; <br>Protein
  								chaperones
  fig|6666666.60966.peg.343	CDS	312210	314153	3	+	1944	Chaperone protein	GroEL GroES; <br>Heat	D23_1c0350	Neut_0412
  							DnaK	shock dnaK gene cluster
  								extended; <br>Protein
  								chaperones
  fig|6666666.60966.peg.344	CDS	314344	315453	1	+	1110	Chaperone protein DnaJ	GroEL GroES; <br>Heat	D23_1c0351	Neut_0413
  								shock dnaK gene cluster
  								extended; <br>Protein
  								chaperones
  fig|6666666.60966.peg.345	CDS	318894	315550	−3	−	3345	Potassium efflux system	Potassium homeostasis	D23_1c0352	Neut_0414
  							KefA protein/Small-
  							conductance
  							mechanosensitive
  							channel
  fig|6666666.60966.peg.346	CDS	319923	319357	−3	−	567	Transcriptional	-none-	D23_1c0353	Neut_0415
  							regulator, TetR family
  fig|6666666.60966.peg.347	CDS	321174	319990	−3	−	1185	InterPro IPR001327	-none-	D23_1c0354	Neut_0416
  							COGs COG2072
  fig|6666666.60966.peg.348	CDS	321778	321236	−1	−	543	hypothetical protein	-none-	D23_1c0355	Neut_0417
  fig|6666666.60966.peg.349	CDS	322196	322363	2	+	168	hypothetical protein	-none-	D23_1c0356	NA
  fig|6666666.60966.peg.350	CDS	325140	322522	−3	−	2619	Membrane alanine	Aminopeptidases (EC	D23_1c0357	Neut_0418
  							aminopeptidase N (EC	3.4.11.—)
  							3.4.11.2)
  fig|6666666.60966.peg.351	CDS	325139	325255	2	+	117	hypothetical protein	-none-	D23_1c0358	NA
  fig|6666666.60966.peg.352	CDS	326547	325213	−3	−	1335	Peptide methionine	Peptide methionine	D23_1c0359	Neut_0419
  							sulfoxide reductase	sulfoxide reductase;
  							MsrA (EC 1.8.4.11)/	<br>Peptide methionine
  							Thiol:disulfide	sulfoxide reductase;
  							oxidoreductase	<br>Peptide methionine
  							associated with MetSO	sulfoxide reductase
  							reductase/Peptide
  							Methionine sulfoxide
  							reductase MsrB (EC
  							1.8.4.12)
  fig|6666666.60966.peg.354	CDS	326909	329791	2	+	2883	Diguanylate	-none-	D23_1c0360	Neut_0422
  							cyclase/phosphodiesterase
  							domain 2 (EAL)
  fig|6666666.60966.peg.355	CDS	331130	329874	−2	−	1257	FIG00858721:	-none-	D23_1c0361	Neut_0423
  							hypothetical protein
  fig|6666666.60966.peg.356	CDS	331369	332730	1	+	1362	O-acetylhomoserine	Methionine	D23_1c0363	Neut_0424
  							sulfhydrylase (EC	Biosynthesis;
  							2.5.1.49)/O-	<br>Methionine
  							succinylhomoserine	Biosynthesis
  							sulfhydrylase (EC
  							2.5.1.48)
  fig|6666666.60966.peg.357	CDS	334115	332718	−2	−	1398	NnrS protein involved in	Denitrification;	D23_1c0364	Neut_0425
  							response to NO	<br>Nitrosative stress;
  								<br>Oxidative stress
  fig|6666666.60966.peg.358	CDS	334992	334066	−3	−	927	Serine acetyltransferase	Cysteine Biosynthesis;	D23_1c0365	Neut_0426
  							(EC 2.3.1.30)	<br>Methionine
  								Biosynthesis
  fig|6666666.60966.peg.360	CDS	335392	336399	1	+	1008	Glucokinase (EC 2.7.1.2)	Glycolysis and	D23_1c0367	Neut_0427
  								Gluconeogenesis
  fig|6666666.60966.peg.361	CDS	336414	337073	3	+	660	Probable	-none-	D23_1c0368	Neut_0428
  							transmembrane protein
  fig|6666666.60966.peg.362	CDS	337412	337101	−2	−	312	FIG00858769:	-none-	D23_1c0369	Neut_0429
  							hypothetical protein
  fig|6666666.60966.peg.363	CDS	338169	337483	−3	−	687	6-	Pentose phosphate	D23_1c0370	Neut_0430
  							phosphogluconolactonase	pathway
  							(EC 3.1.1.31),
  							eukaryotic type
  fig|6666666.60966.peg.364	CDS	338807	338151	−2	−	657	hydrolase, haloacid	-none-	D23_1c0371	Neut_0431
  							dehalogenase-like
  							family
  fig|6666666.60966.peg.365	CDS	339746	338814	−2	−	933	NAD-dependent	CBSS-296591.1.peg.2330	D23_1c0372	Neut_0432
  							epimerase/dehydratase
  fig|6666666.60966.peg.366	CDS	340674	339739	−3	−	936	D-3-phosphoglycerate	Glycine and Serine	D23_1c0373	Neut_0433
  							dehydrogenase (EC	Utilization;
  							1.1.1.95)	<br>Pyridoxin (Vitamin
  								B6) Biosynthesis;
  								<br>Serine Biosynthesis
  fig|6666666.60966.peg.367	CDS	341432	340671	−2	−	762	2,4-dihydroxyhept-2-	-none-	D23_1c0374	Neut_0434
  							ene-1,7-dioic acid
  							aldolase (EC 4.1.2.—)
  fig|6666666.60966.peg.368	CDS	342202	341444	−1	−	759	3-deoxy-manno-	KDO2-Lipid A	D23_1c0375	Neut_0435
  							octulosonate	biosynthesis cluster 2
  							cytidylyltransferase (EC
  							2.7.7.38)
  fig|6666666.60966.peg.370	CDS	342384	342509	3	+	126	hypothetical protein	-none-	D23_1c0376	NA
  fig|6666666.60966.peg.371	CDS	342506	343585	2	+	1080	Glycosyl transferase,	-none-	D23_1c0377	Neut_0436
  							group 2 family protein
  fig|6666666.60966.peg.372	CDS	343660	344931	1	+	1272	O-antigen ligase	-none-	D23_1c0378	Neut_0437
  fig|6666666.60966.peg.373	CDS	344931	345620	3	+	690	O-methyltransferase	-none-	D23_1c0379	Neut_0438
  							family protein [C1]
  fig|6666666.60966.peg.374	CDS	345673	345930	1	+	258	FIG00859064:	-none-	D23_1c0380	Neut_0439
  							hypothetical protein
  fig|6666666.60966.peg.375	CDS	345980	346498	2	+	519	Mlr4354 like protein	-none-	D23_1c0381	Neut_0440
  fig|6666666.60966.peg.376	CDS	346511	346858	2	+	348	Arsenate reductase (EC	Anaerobic respiratory	D23_1c0382	Neut_0441
  							1.20.4.1)	reductases;
  								<br>Transcription repair
  								cluster
  fig|6666666.60966.peg.377	CDS	347305	346916	−1	−	390	LSU ribosomal protein	-none-	D23_1c0383	Neut_0442
  							L19p
  fig|6666666.60966.peg.378	CDS	348122	347277	−2	−	846	tRNA (Guanine37-N1)-	RNA methylation;	D23_1c0384	Neut_0443
  							methyltransferase (EC	<br>Ribosome
  							2.1.1.31)	biogenesis bacterial;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.379	CDS	348636	348130	−3	−	507	16S rRNA processing	Ribosome biogenesis	D23_1c0385	Neut_0444
  							protein RimM	bacterial
  fig|6666666.60966.peg.381	CDS	349157	350437	2	+	1281	Glycolate	Glycolate, glyoxylate	D23_1c0386	Neut_0446
  							dehydrogenase (EC	interconversions;
  							1.1.99.14), iron-sulfur	<br>Photorespiration
  							subunit GlcF	(oxidative C2 cycle)
  fig|6666666.60966.peg.382	CDS	350492	351118	2	+	627	Uncharacterized	Ubiquinone Biosynthesis-	D23_1c0387	Neut_0447
  							hydroxylase PA0655	gjo
  fig|6666666.60966.peg.383	CDS	351152	351712	2	+	561	UPF0301 protein YqgE	-none-	D23_1c0388	Neut_0448
  fig|6666666.60966.peg.384	CDS	351705	352178	3	+	474	Putative Holliday	-none-	D23_1c0389	Neut_0449
  							junction resolvase (EC
  							3.1.—.—)
  fig|6666666.60966.peg.385	CDS	352165	352668	1	+	504	Uracil	De Novo Pyrimidine	D23_1c0390	Neut_0450
  							phosphoribosyltransferase	Synthesis; <br>De Novo
  							(EC 2.4.2.9)/	Pyrimidine Synthesis;
  							Pyrimidine operon	<br>pyrimidine
  							regulatory protein PyrR	conversions
  fig|6666666.60966.peg.386	CDS	352856	353806	2	+	951	Aspartate	De Novo Pyrimidine	D23_1c0391	Neut_0451
  							carbamoyltransferase	Synthesis
  							(EC 2.1.3.2)
  fig|6666666.60966.peg.387	CDS	353822	355093	2	+	1272	Dihydroorotase (EC	De Novo Pyrimidine	D23_1c0392	Neut_0452
  							3.5.2.3)	Synthesis; <br>Zinc
  								regulated enzymes
  fig|6666666.60966.peg.388	CDS	355217	357322	2	+	2106	Oligopeptidase A (EC	Protein degradation	D23_1c0393	Neut_0453
  							3.4.24.70)
  fig|6666666.60966.peg.389	CDS	357558	358709	3	+	1152	Carbamoyl-phosphate	De Novo Pyrimidine	D23_1c0394	Neut_0454
  							synthase small chain	Synthesis;
  							(EC 6.3.5.5)	<br>Macromolecular
  								synthesis operon
  fig|6666666.60966.peg.390	CDS	358735	361932	1	+	3198	Carbamoyl-phosphate	De Novo Pyrimidine	D23_1c0395	Neut_0455
  							synthase large chain (EC	Synthesis;
  							6.3.5.5)	<br>Macromolecular
  								synthesis operon
  fig|6666666.60966.peg.391	CDS	362117	362593	2	+	477	Transcription	Transcription factors	D23_1c0396	Neut_0456
  							elongation factor GreA	bacterial
  fig|6666666.60966.peg.392	CDS	363579	362608	−3	−	972	ErfK/YbiS/YcfS/YnhG	-none-	D23_1c0397	Neut_0457
  							family protein
  fig|6666666.60966.peg.393	CDS	364226	366052	2	+	1827	Long-chain-fatty-acid--	Biotin biosynthesis;	D23_1c0398	Neut_0458
  							CoA ligase (EC 6.2.1.3)	<br>Biotin synthesis
  								cluster; <br>Fatty acid
  								metabolism cluster
  fig|6666666.60966.peg.394	CDS	366141	367064	3	+	924	FIG010773: NAD-	-none-	D23_1c0399	Neut_0459
  							dependent
  							epimerase/dehydratase
  fig|6666666.60966.peg.395	CDS	367176	367430	3	+	255	phosphopantetheine-	-none-	D23_1c0400	Neut_0460
  							binding
  fig|6666666.60966.peg.396	CDS	367430	368617	2	+	1188	Aminotransferase class	-none-	D23_1c0401	Neut_0461
  							II, serine
  							palmitoyltransferase
  							like (EC 2.3.1.50)
  fig|6666666.60966.peg.397	CDS	368669	369427	2	+	759	COG1496:	-none-	D23_1c0402	Neut_0462
  							Uncharacterized
  							conserved protein
  fig|6666666.60966.peg.398	CDS	369615	370427	3	+	813	Zinc transporter, ZIP	-none-	D23_1c0403	Neut_0463
  							family
  fig|6666666.60966.peg.399	CDS	373049	370434	−2	−	2616	Dolichyl-phosphate	-none-	D23_1c0404	Neut_0464
  							beta-D-
  							mannosyltransferase
  							(EC: 2.4.1.83)
  fig|6666666.60966.peg.400	CDS	374173	373157	−1	−	1017	FIG004453: protein	CBSS-	D23_1c0405	Neut_0465
  							YceG like	323097.3.peg.2594;
  								<br>Cluster containing
  								Alanyl-tRNA synthetase;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.401	CDS	374277	374140	−3	−	138	hypothetical protein	-none-	D23_1c0406	NA
  fig|6666666.60966.peg.402	CDS	375542	374301	−2	−	1242	3-oxoacyl-[acyl-carrier-	Fatty Acid Biosynthesis	D23_1c0407	Neut_0466
  							protein] synthase, KASII	FASII
  							(EC 2.3.1.41)
  fig|6666666.60966.peg.403	CDS	375822	375577	−3	−	246	Acyl carrier protein	Fatty Acid Biosynthesis	D23_1c0408	Neut_0467
  								FASII; <br>Glycerolipid
  								and Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.405	CDS	376731	375988	−3	−	744	3-oxoacyl-[acyl-carrier	Fatty Acid Biosynthesis	D23_1c0409	Neut_0468
  							protein] reductase (EC	FASII
  							1.1.1.100)
  fig|6666666.60966.peg.406	CDS	377726	376788	−2	−	939	Malonyl CoA-acyl	Fatty Acid Biosynthesis	D23_1c0410	Neut_0469
  							carrier protein	FASII
  							transacylase (EC
  							2.3.1.39)
  fig|6666666.60966.peg.407	CDS	378692	377730	−2	−	963	3-oxoacyl-[acyl-carrier-	Fatty Acid Biosynthesis	D23_1c0411	Neut_0470
  							protein] synthase,	FASII
  							KASIII (EC 2.3.1.41)
  fig|6666666.60966.peg.408	CDS	379722	378703	−3	−	1020	Phosphate:acyl-ACP	Glycerolipid and	D23_1c0412	Neut_0471
  							acyltransferase PlsX	Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.409	CDS	379982	379800	−2	−	183	LSU ribosomal protein	-none-	D23_1c0414	Neut_0472
  							L32p
  fig|6666666.60966.peg.410	CDS	380510	380007	−2	−	504	COG1399 protein,	-none-	D23_1c0415	Neut_0473
  							clustered with
  							ribosomal protein L32p
  fig|6666666.60966.peg.411	CDS	380534	381175	2	+	642	FIG146278:	-none-	D23_1c0416	Neut_0474
  							Maf/YceF/YhdE family
  							protein
  fig|6666666.60966.peg.412	CDS	381292	381684	1	+	393	FIG00858587:	-none-	D23_1c0417	Neut_0475
  							hypothetical protein
  fig|6666666.60966.peg.413	CDS	381793	383217	1	+	1425	Heavy metal RND efflux	Cobalt-zinc-cadmium	D23_1c0418	Neut_0476
  							outer membrane	resistance
  							protein, CzcC family
  fig|6666666.60966.peg.414	CDS	383214	384710	3	+	1497	Cobalt/zinc/cadmium	Cobalt-zinc-cadmium	D23_1c0419	Neut_0477
  							efflux RND transporter,	resistance
  							membrane fusion
  							protein, CzcB family
  fig|6666666.60966.peg.415	CDS	384811	388020	1	+	3210	Cobalt-zinc-cadmium	Cobalt-zinc-cadmium	D23_1c0421	Neut_0478
  							resistance protein CzcA;	resistance; <br>Cobalt-
  							Cation efflux system	zinc-cadmium resistance
  							protein CusA
  fig|6666666.60966.peg.416	CDS	388294	388731	1	+	438	FIG00858457:	-none-	D23_1c0423	Neut_0479
  							hypothetical protein
  fig|6666666.60966.peg.417	CDS	388756	389043	1	+	288	FIG00858508:	-none-	D23_1c0424	Neut_0480
  							hypothetical protein
  fig|6666666.60966.peg.418	CDS	389040	389948	3	+	909	FIG00858931:	-none-	D23_1c0425	Neut_0481
  							hypothetical protein
  fig|6666666.60966.peg.419	CDS	389941	391068	1	+	1128	hypothetical protein	-none-	D23_1c0426	Neut_0482
  fig|6666666.60966.peg.420	CDS	392521	391079	−1	−	1443	Mg/Co/Ni transporter	Magnesium transport	D23_1c0427	Neut_0483
  							MgtE/CBS domain
  fig|6666666.60966.peg.424	CDS	394723	393761	−1	−	963	Mobile element protein	-none-	D23_1c0430	Neut_1746
  fig|6666666.60966.peg.425	CDS	394947	394834	−3	−	114	hypothetical protein	-none-	D23_1c0431	NA
  fig|6666666.60966.peg.426	CDS	394946	395251	2	+	306	hypothetical protein	-none-	D23_1c0432	Neut_0486
  fig|6666666.60966.peg.427	CDS	395968	395309	−1	−	660	COG1272: Predicted	-none-	D23_1c0433	Neut_0487
  							membrane protein
  							hemolysin III homolog
  fig|6666666.60966.peg.428	CDS	396481	396179	−1	−	303	hypothetical protein	-none-	D23_1c0434	Neut_0488
  fig|6666666.60966.peg.430	CDS	397189	396863	−1	−	327	hypothetical protein	-none-	D23_1c0435	Neut_0490
  fig|6666666.60966.peg.433	CDS	397653	398393	3	+	741	cAMP-binding proteins-	cAMP signaling in	D23_1c0436	Neut_0491
  							catabolite gene	bacteria
  							activator and regulatory
  							subunit of cAMP-
  							dependent protein
  							kinases
  fig|6666666.60966.peg.434	CDS	398690	398424	−2	−	267	Putative lipoprotein	-none-	D23_1c0437	Neut_0492
  fig|6666666.60966.peg.435	CDS	399146	398973	−2	−	174	hypothetical protein	-none-	D23_1c0438	NA
  fig|6666666.60966.peg.436	CDS	399498	399373	−3	−	126	hypothetical protein	-none-	D23_1c0439	NA
  fig|6666666.60966.peg.437	CDS	400841	399609	−2	−	1233	hypothetical protein	-none-	D23_1c0440	Neut_0494
  fig|6666666.60966.peg.438	CDS	401592	400858	−3	−	735	Monofunctional	Peptidoglycan	D23_1c0441	Neut_0495
  							biosynthetic	Biosynthesis
  							peptidoglycan
  							transglycosylase (EC
  							2.4.2.—)
  fig|6666666.60966.peg.439	CDS	402422	401589	−2	−	834	Shikimate 5-	Chorismate Synthesis;	D23_1c0442	Neut_0496
  							dehydrogenase I alpha	<br>Cluster containing
  							(EC 1.1.1.25)	Alanyl-tRNA synthetase;
  								<br>Common Pathway
  								For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.440	CDS	403340	402456	−2	−	885	TonB protein	-none-	D23_1c0443	Neut_0497
  fig|6666666.60966.peg.441	CDS	405237	403378	−3	−	1860	Exoribonuclease II (EC	RNA processing and	D23_1c0444	Neut_0498
  							3.1.13.1)	degradation, bacterial
  fig|6666666.60966.peg.443	CDS	405594	406985	3	+	1392	Glutamyl-tRNA	Heme and Siroheme	D23_1c0445	Neut_0499
  							synthetase (EC 6.1.1.17)	Biosynthesis; <br>tRNA
  								aminoacylation, Glu and
  								Gln
  fig|6666666.60966.peg.444	CDS	407045	410752	2	+	3708	5-	Methionine Biosynthesis	D23_1c0446	Neut_0500
  							methyltetrahydrofolate--
  							homocysteine
  							methyltransferase (EC
  							2.1.1.13)
  fig|6666666.60966.peg.445	CDS	410924	412267	2	+	1344	NADP-specific	Arginine and Ornithine	D23_1c0447	Neut_0501
  							glutamate	Degradation;
  							dehydrogenase (EC	<br>Glutamate
  							1.4.1.4)	dehydrogenases;
  								<br>Glutamine,
  								Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis;
  								<br>Proline Synthesis
  fig|6666666.60966.peg.446	CDS	412461	414368	3	+	1908	Soluble lytic murein	Murein Hydrolases	D23_1c0449	Neut_0502
  							transglycosylase
  							precursor (EC 3.2.1.—)
  fig|6666666.60966.peg.447	CDS	414379	415617	1	+	1239	tRNA	A cluster relating to	D23_1c0450	Neut_0503
  							nucleotidyltransferase	Tryptophanyl-tRNA
  							(EC 2.7.7.21) (EC	synthetase;
  							2.7.7.25)	<br>Polyadenylation
  								bacterial; <br>tRNA
  								nucleotidyltransferase
  fig|6666666.60966.peg.448	CDS	417316	415592	−1	−	1725	Phospholipid-	N-linked Glycosylation in	D23_1c0451	Neut_0504
  							lipopolysaccharide ABC	Bacteria
  							transporter
  fig|6666666.60966.peg.449	CDS	418171	417335	−1	−	837	Diaminopimelate	CBSS-84588.1.peg.1247;	D23_1c0452	Neut_0505
  							epimerase (EC 5.1.1.7)	<br>Lysine Biosynthesis
  								DAP Pathway, GJO
  								scratch
  fig|6666666.60966.peg.450	CDS	418345	418193	−1	−	153	hypothetical protein	-none-	D23_1c0453	NA
  fig|6666666.60966.peg.451	CDS	418574	419011	2	+	438	Predicted secretion	Predicted secretion	D23_1c0454	Neut_0506
  							system X protein GspG-	system X
  							like 3
  fig|6666666.60966.peg.452	CDS	419030	420214	2	+	1185	Predicted secretion	Predicted secretion	D23_1c0455	Neut_0507
  							system X protein GspF-	system X
  							like
  fig|6666666.60966.peg.453	CDS	420211	421905	1	+	1695	Predicted secretion	Predicted secretion	D23_1c0456	Neut_0508
  							system X protein GspE-	system X
  							like
  fig|6666666.60966.peg.454	CDS	421910	422731	2	+	822	Predicted secretion	Predicted secretion	D23_1c0457	Neut_0509
  							system X FIG084745:	system X
  							hypothetical protein
  fig|6666666.60966.peg.455	CDS	422772	423260	3	+	489	Predicted secretion	Predicted secretion	D23_1c0458	Neut_0510
  							system X	system X
  							transmembrane protein
  1
  fig|6666666.60966.peg.472	CDS	440367	440753	3	+	387	Mobile element protein	-none-	D23_1c0476	Neut_0884
  fig|6666666.60966.peg.473	CDS	440716	441171	1	+	456	Mobile element protein	-none-	D23_1c0477	Neut_2502
  fig|6666666.60966.peg.474	CDS	441829	441158	−1	−	672	Gluconate 2-	D-gluconate and	D23_1c0478	NA
  							dehydrogenase (EC	ketogluconates
  							1.1.99.3), membrane-	metabolism
  							bound, gamma subunit
  fig|6666666.60966.peg.475	CDS	444093	441973	−3	−	2121	diguanylate	-none-	D23_1c0479	Neut_0525
  							cyclase/phosphodiesterase
  							(GGDEF & EAL
  							domains) with PAS/PAC
  							sensor(s)
  fig|6666666.60966.peg.476	CDS	444457	444311	−1	−	147	hypothetical protein	-none-	D23_1c0480	NA
  fig|6666666.60966.peg.478	CDS	444629	445810	2	+	1182	NAD(FAD)-utilizing	-none-	D23_1c0481	Neut_0526
  							dehydrogenases
  fig|6666666.60966.peg.479	CDS	446569	445952	−1	—	618	Methionine	-none-	D23_1c0482	Neut_0527
  							biosynthesis protein
  							MetW
  fig|6666666.60966.peg.480	CDS	447733	446600	−1	−	1134	Homoserine O-	Methionine Biosynthesis	D23_1c0483	Neut_0528
  							acetyltransferase (EC
  							2.3.1.31)
  fig|6666666.60966.peg.481	CDS	449559	447832	−3	−	1728	Phosphoenolpyruvate-	-none-	D23_1c0484	Neut_0529
  							protein
  							phosphotransferase of
  							PTS system (EC 2.7.3.9)
  fig|6666666.60966.peg.482	CDS	449825	449556	−2	−	270	Phosphocarrier protein,	-none-	D23_1c0485	Neut_0530
  							nitrogen regulation
  							associated
  fig|6666666.60966.peg.483	CDS	450219	449815	−3	−	405	Sugar transport PTS	-none-	D23_1c0486	Neut_0531
  							system IIa component
  fig|6666666.60966.peg.484	CDS	450568	451605	1	+	1038	Phosphatidylglycerophosphatase	Glycerolipid and	D23_1c0488	Neut_0532
  							B (EC 3.1.3.27)	Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.485	CDS	451971	451705	−3	−	267	HrgA protein	-none-	D23_1c0489	Neut_2454
  fig|6666666.60966.peg.486	CDS	452384	453631	2	+	1248	Mobile element protein	-none-	D23_1c0490	Neut_0357
  fig|6666666.60966.peg.487	CDS	455203	454049	−1	−	1155	hypothetical protein	-none-	D23_1c0491	NA
  fig|6666666.60966.peg.488	CDS	455538	455371	−3	−	168	hypothetical protein	-none-	D23_1c0492	NA
  fig|6666666.60966.peg.489	CDS	455581	456603	1	+	1023	Lipolytic enzyme, G-D-S-L	-none-	D23_1c0493	Neut_0534
  fig|6666666.60966.peg.490	CDS	457214	456669	−2	−	546	N-acetylmuramoyl-L-	Recycling of	D23_1c0494	Neut_0535
  							alanine amidase (EC	Peptidoglycan Amino
  							3.5.1.28) AmpD	Acids
  fig|6666666.60966.peg.491	CDS	457304	457951	2	+	648	Thymidylate kinase (EC	pyrimidine conversions	D23_1c0495	Neut_0536
  							2.7.4.9)
  fig|6666666.60966.peg.492	CDS	461332	458087	−1	−	3246	Type I restriction-	Restriction-Modification	D23_1c0496	Neut_0537
  							modification system,	System; <br>Type I
  							restriction subunit R (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.493	CDS	462292	461345	−1	−	948	Putative DNA-binding	Restriction-Modification	D23_1c0497	NA
  							protein in cluster with	System
  							Type I restriction-
  							modification system
  fig|6666666.60966.peg.494	CDS	462416	462285	−2	−	132	hypothetical protein	-none-	D23_1c0498	NA
  fig|6666666.60966.peg.495	CDS	463405	462413	−1	−	993	hypothetical protein	-none-	D23_1c0499	NA
  fig|6666666.60966.peg.496	CDS	464694	463405	−3	−	1290	Type I restriction-	Restriction-Modification	D23_1c0500	Neut_0540
  							modification system,	System; <br>Type I
  							specificity subunit S (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.497	CDS	466246	464684	−1	−	1563	Type I restriction-	Restriction-Modification	D23_1c0501	Neut_0541
  							modification system,	System; <br>Type I
  							DNA-methyltransferase	Restriction-Modification
  							subunit M (EC 2.1.1.72)
  fig|6666666.60966.peg.498	CDS	467880	466453	−3	−	1428	Na+/H+ antiporter	-none-	D23_1c0502	Neut_0542
  							NhaC
  fig|6666666.60966.peg.499	CDS	468057	467896	−3	−	162	hypothetical protein	-none-	D23_1c0503	NA
  fig|6666666.60966.peg.500	CDS	468126	469190	3	+	1065	DNA polymerase III	-none-	D23_1c0504	Neut_0543
  							delta prime subunit (EC
  							2.7.7.7)
  fig|6666666.60966.peg.501	CDS	469691	469194	−2	−	498	hypothetical protein	-none-	D23_1c0505	Neut_0544
  fig|6666666.60966.peg.502	CDS	469703	469870	2	+	168	hypothetical protein	-none-	D23_1c0506	NA
  fig|6666666.60966.peg.503	CDS	470025	471155	3	+	1131	Magnesium and cobalt	Magnesium transport	D23_1c0508	Neut_0545
  							transport protein CorA
  fig|6666666.60966.peg.504	CDS	471202	471447	1	+	246	Mobile element protein	-none-	D23_1c0509	Neut_0884
  fig|6666666.60966.peg.505	CDS	471504	471617	3	+	114	hypothetical protein	-none-	D23_1c0510	Neut_0547
  fig|6666666.60966.peg.506	CDS	471862	473013	1	+	1152	conserved hypothetical	-none-	D23_1c0511	Neut_0548
  							protein
  fig|6666666.60966.peg.507	CDS	473412	473957	3	+	546	Uncharacterized protein	-none-	D23_1c0512	Neut_0550
  							conserved in bacteria
  fig|6666666.60966.peg.508	CDS	474111	474269	3	+	159	Mobile element protein	-none-	D23_1c0513	NA
  fig|6666666.60966.peg.510	CDS	474450	474653	3	+	204	hypothetical protein	-none-	D23_1c0514	NA
  fig|6666666.60966.peg.512	CDS	475553	476005	2	+	453	SSU ribosomal protein	Mycobacterium	D23_1c0515	Neut_0554
  							S7p (S5e)	virulence operon
  								involved in protein
  								synthesis (SSU ribosomal
  								proteins)
  fig|6666666.60966.peg.513	CDS	476121	478166	3	+	2046	Translation elongation	Mycobacterium	D23_1c0516	Neut_0555
  							factor G	virulence operon
  								involved in protein
  								synthesis (SSU ribosomal
  								proteins);
  								<br>Translation
  								elongation factor G
  								family; <br>Translation
  								elongation factors
  								bacterial; <br>Universal
  								GTPases
  fig|6666666.60966.peg.514	CDS	478196	479386	2	+	1191	Translation elongation	Mycobacterium	D23_1c0517	Neut_0556
  							factor Tu	virulence operon
  								involved in protein
  								synthesis (SSU ribosomal
  								proteins);
  								<br>Translation
  								elongation factors
  								bacterial; <br>Universal
  								GTPases
  fig|6666666.60966.peg.515	CDS	479569	479775	1	+	207	SSU ribosomal protein	-none-	D23_1c0518	Neut_0557
  							S10p (S20e)
  fig|6666666.60966.peg.516	CDS	479823	480476	3	+	654	LSU ribosomal protein	-none-	D23_1c0519	Neut_0558
  							L3p (L3e)
  fig|6666666.60966.peg.517	CDS	480494	481114	2	+	621	LSU ribosomal protein	-none-	D23_1c0520	Neut_0559
  							L4p (L1e)
  fig|6666666.60966.peg.518	CDS	481111	481446	1	+	336	LSU ribosomal protein	-none-	D23_1c0521	Neut_0560
  							L23p (L23Ae)
  fig|6666666.60966.peg.519	CDS	481446	482279	3	+	834	LSU ribosomal protein	-none-	D23_1c0522	Neut_0561
  							L2p (L8e)
  fig|6666666.60966.peg.520	CDS	482948	483595	2	+	648	SSU ribosomal protein	-none-	D23_1c0523	Neut_0564
  							S3p (S3e)
  fig|6666666.60966.peg.521	CDS	483680	484096	2	+	417	LSU ribosomal protein	-none-	D23_1c0524	Neut_0565
  							L16p (L10e)
  fig|6666666.60966.peg.524	CDS	485008	485331	1	+	324	LSU ribosomal protein	-none-	D23_1c0525	Neut_0569
  							L24p (L26e)
  fig|6666666.60966.peg.525	CDS	485458	485886	1	+	429	LSU ribosomal protein	-none-	D23_1c0526	Neut_0570
  							L5p (L11e)
  fig|6666666.60966.peg.526	CDS	486881	487222	2	+	342	LSU ribosomal protein	-none-	D23_1c0527	Neut_0573
  							L6p (L9e)
  fig|6666666.60966.peg.527	CDS	487678	488151	1	+	474	SSU ribosomal protein	-none-	D23_1c0528	Neut_0575
  							S5p (S2e)
  fig|6666666.60966.peg.528	CDS	488796	490118	3	+	1323	Preprotein translocase	-none-	D23_1c0530	Neut_0578
  							secY subunit (TC
  							3.A.5.1.1)
  fig|6666666.60966.peg.530	CDS	491337	491963	3	+	627	SSU ribosomal protein	-none-	D23_1c0531	Neut_0582
  							S4p (S9e)
  fig|6666666.60966.peg.531	CDS	492065	492997	2	+	933	DNA-directed RNA	RNA polymerase	D23_1c0532	Neut_0583
  							polymerase alpha	bacterial
  							subunit (EC 2.7.7.6)
  fig|6666666.60966.peg.532	CDS	494213	493998	−2	−	216	Putative oligoketide	Possible RNA	D23_1c0534	Neut_0586
  							cyclase/dehydratase or	degradation cluster
  							lipid transport protein
  							YfjG
  fig|6666666.60966.peg.533	CDS	494546	494995	2	+	450	tmRNA-binding protein	Heat shock dnaK gene	D23_1c0535	Neut_0587
  							SmpB	cluster extended;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.534	CDS	495005	496075	2	+	1071	Heme A synthase,	Biogenesis of	D23_1c0536	Neut_0588
  							cytochrome oxidase	cytochrome c oxidases
  							biogenesis protein
  							Cox15-CtaA
  fig|6666666.60966.peg.535	CDS	496163	496582	2	+	420	Probable	-none-	D23_1c0537	Neut_0589
  							transmembrane protein
  fig|6666666.60966.peg.537	CDS	496945	498528	1	+	1584	DNA polymerase III	DNA processing cluster	D23_1c0538	Neut_0590
  							subunits gamma and
  							tau (EC 2.7.7.7)
  fig|6666666.60966.peg.538	CDS	498545	498868	2	+	324	FIG000557:	DNA processing cluster	D23_1c0539	Neut_0591
  							hypothetical protein co-
  							occurring with RecR
  fig|6666666.60966.peg.539	CDS	498922	499740	1	+	819	Pseudouridine synthase	-none-	D23_1c0540	Neut_0592
  							family protein
  fig|6666666.60966.peg.540	CDS	500690	499770	−2	−	921	Protein-N(5)-glutamine	-none-	D23_1c0541	Neut_0593
  							methyltransferase
  							PrmB, methylates LSU
  							ribosomal protein L3p
  fig|6666666.60966.peg.541	CDS	500738	501241	2	+	504	tRNA-specific	tRNA modification	D23_1c0542	Neut_0594
  							adenosine-34	Bacteria; <br>tRNA
  							deaminase (EC 3.5.4.—)	processing
  fig|6666666.60966.peg.542	CDS	501238	501717	1	+	480	Conserved domain	-none-	D23_1c0543	Neut_0595
  							protein
  fig|6666666.60966.peg.543	CDS	501779	503389	2	+	1611	NAD-dependent malic	Pyruvate metabolism I:	D23_1c0544	Neut_0596
  							enzyme (EC 1.1.1.38)	anaplerotic reactions,
  								PEP
  fig|6666666.60966.peg.544	CDS	504268	503438	−1	−	831	Phosphoserine	Glycine and Serine	D23_1c0545	Neut_0597
  							phosphatase (EC	Utilization; <br>Serine
  							3.1.3.3)	Biosynthesis; <br>Serine
  								Biosynthesis
  fig|6666666.60966.peg.545	CDS	505831	504356	−1	−	1476	FIG00858790:	-none-	D23_1c0546	Neut_0598
  							hypothetical protein
  fig|6666666.60966.peg.547	CDS	506088	507581	3	+	1494	Cytosol aminopeptidase	Aminopeptidases (EC	D23_1c0547	Neut_0599
  							PepA (EC 3.4.11.1)	3.4.11.—);
  								<br>Dehydrogenase
  								complexes
  fig|6666666.60966.peg.548	CDS	507615	508043	3	+	429	DNA polymerase III chi	-none-	D23_1c0548	Neut_0600
  							subunit (EC 2.7.7.7)
  fig|6666666.60966.peg.549	CDS	508116	508517	3	+	402	FIG00859089:	-none-	D23_1c0549	Neut_0601
  							hypothetical protein
  fig|6666666.60966.peg.550	CDS	508581	511334	3	+	2754	Valyl-tRNA synthetase	tRNA aminoacylation,	D23_1c0550	Neut_0602
  							(EC 6.1.1.9)	Val
  fig|6666666.60966.peg.551	CDS	511430	512500	2	+	1071	Uroporphyrinogen III	Heme and Siroheme	D23_1c0551	Neut_0603
  							decarboxylase (EC	Biosynthesis
  							4.1.1.37)
  fig|6666666.60966.peg.552	CDS	513466	512660	−1	−	807	Maebl	-none-	D23_1c0552	Neut_0604
  fig|6666666.60966.peg.553	CDS	514503	513616	−3	−	888	Succinyl-CoA ligase	TCA Cycle	D23_1c0553	Neut_0605
  							[ADP-forming] alpha
  							chain (EC 6.2.1.5)
  fig|6666666.60966.peg.554	CDS	515705	514533	−2	−	1173	Succinyl-CoA ligase	TCA Cycle	D23_1c0554	Neut_0606
  							[ADP-forming] beta
  							chain (EC 6.2.1.5)
  fig|6666666.60966.peg.555	CDS	516828	515878	−3	−	951	Malyl-CoA lyase (EC	Photorespiration	D23_1c0555	Neut_0607
  							4.1.3.24)	(oxidative C2 cycle)
  fig|6666666.60966.peg.557	CDS	518554	517079	−1	−	1476	Glycogen synthase,	Glycogen metabolism	D23_1c0557	Neut_0608
  							ADP-glucose
  							transglucosylase (EC
  							2.4.1.21)
  fig|6666666.60966.peg.558	CDS	520242	518608	−3	−	1635	Glucose-6-phosphate	Glycolysis and	D23_1c0558	Neut_0609
  							isomerase (EC 5.3.1.9)	Gluconeogenesis
  fig|6666666.60966.peg.559	CDS	521449	520271	−1	−	1179	3-ketoacyl-CoA thiolase	Acetyl-CoA fermentation	D23_1c0559	Neut_0610
  							(EC 2.3.1.16) @ Acetyl-	to Butyrate; <br>Biotin
  							CoA acetyltransferase	biosynthesis; <br>Biotin
  							(EC 2.3.1.9)	synthesis cluster;
  								<br>Butanol
  								Biosynthesis;
  								<br>Butyrate
  								metabolism cluster;
  								<br>Fatty acid
  								metabolism cluster;
  								<br>Isoprenoid
  								Biosynthesis;
  								<br>Polyhydroxybutyrate
  								metabolism;
  								<br>Polyhydroxybutyrate
  								metabolism
  fig|6666666.60966.peg.560	CDS	522790	521459	−1	−	1332	ATP-dependent hsl	Proteasome bacterial;	D23_1c0560	Neut_0611
  							protease ATP-binding	<br>Proteolysis in
  							subunit HslU	bacteria, ATP-dependent
  fig|6666666.60966.peg.561	CDS	523346	522825	−2	−	522	ATP-dependent	Proteasome bacterial;	D23_1c0561	Neut_0612
  							protease HslV (EC	<br>Proteolysis in
  							3.4.25.—)	bacteria, ATP-dependent
  fig|6666666.60966.peg.563	CDS	523758	523555	−3	−	204	DNA-directed RNA	RNA polymerase	D23_1c0562	Neut_0613
  							polymerase omega	bacterial
  							subunit (EC 2.7.7.6)
  fig|6666666.60966.peg.564	CDS	524414	523809	−2	−	606	Guanylate kinase (EC	CBSS-	D23_1c0563	Neut_0614
  							2.7.4.8)	323097.3.peg.2594;
  								<br>Purine conversions
  fig|6666666.60966.peg.565	CDS	525166	524684	−1	−	483	Dihydroneopterin	Folate Biosynthesis	D23_1c0565	Neut_0615
  							triphosphate
  							pyrophosphohydrolase
  							type 2 (nudB)
  fig|6666666.60966.peg.566	CDS	526961	525180	−2	−	1782	Aspartyl-tRNA	tRNA aminoacylation,	D23_1c0566	Neut_0616
  							synthetase (EC 6.1.1.12)	Asp and Asn; <br>tRNA
  							@ Aspartyl-tRNA(Asn)	aminoacylation, Asp and
  							synthetase (EC 6.1.1.23)	Asn
  fig|6666666.60966.peg.567	CDS	527054	527206	2	+	153	hypothetical protein	-none-	D23_1c0567	NA
  fig|6666666.60966.peg.568	CDS	528907	527456	−1	−	1452	Mannose-1-phosphate	Mannose Metabolism;	D23_1c0569	Neut_0618
  							guanylyltransferase	<br>Mannose
  							(GDP) (EC 2.7.7.22)/	Metabolism
  							Mannose-6-phosphate
  							isomerase (EC 5.3.1.8)
  fig|6666666.60966.peg.569	CDS	530083	528971	−1	−	1113	UDP-N-	CMP-N-	D23_1c0570	Neut_0619
  							acetylglucosamine 2-	acetylneuraminate
  							epimerase (EC 5.1.3.14)	Biosynthesis; <br>Sialic
  								Acid Metabolism
  fig|6666666.60966.peg.570	CDS	530171	530284	2	+	114	hypothetical protein	-none-	D23_1c0571	NA
  fig|6666666.60966.peg.571	CDS	530407	530535	1	+	129	hypothetical protein	-none-	D23_1c0572	NA
  fig|6666666.60966.peg.572	CDS	530637	531041	3	+	405	Truncated hemoglobins	-none-	D23_1c0573	Neut_0620
  fig|6666666.60966.peg.573	CDS	531034	532257	1	+	1224	NnrS protein involved in	Denitrification;	D23_1c0574	Neut_0621
  							response to NO	<br>Nitrosative stress;
  								<br>Oxidative stress
  fig|6666666.60966.peg.574	CDS	532298	532738	2	+	441	putative membrane	-none-	D23_1c0575	Neut_0622
  							protein
  fig|6666666.60966.peg.575	CDS	532841	533326	2	+	486	FIG001943:	Broadly distributed	D23_1c0576	Neut_0623
  							hypothetical protein	proteins not in
  							YajQ	subsystems
  fig|6666666.60966.peg.576	CDS	534972	533485	−3	−	1488	FIG00859034:	-none-	D23_1c0577	Neut_0624
  							hypothetical protein
  fig|6666666.60966.peg.577	CDS	535028	535240	2	+	213	hypothetical protein	-none-	D23_1c0578	NA
  fig|6666666.60966.peg.578	CDS	536092	535289	−1	−	804	FIG00858513:	-none-	D23_1c0579	Neut_0626
  							hypothetical protein
  fig|6666666.60966.peg.579	CDS	537497	536616	−2	−	882	hypothetical protein	-none-	D23_1c0581	NA
  fig|6666666.60966.peg.580	CDS	538547	537726	−2	−	822	hypothetical protein	-none-	D23_1c0582	NA
  fig|6666666.60966.peg.581	CDS	539856	538789	−3	−	1068	Conserved domain	-none-	D23_1c0583	NA
  							protein
  fig|6666666.60966.peg.582	CDS	540712	539849	−1	−	864	Conserved domain	-none-	D23_1c0584	NA
  							protein
  fig|6666666.60966.peg.583	CDS	541704	540841	−3	−	864	possible long-chain N-	-none-	D23_1c0585	Neut_0638
  							acyl amino acid
  							synthase
  fig|6666666.60966.peg.584	CDS	541934	541812	−2	−	123	hypothetical protein	-none-	D23_1c0586	NA
  fig|6666666.60966.peg.586	CDS	542270	542467	2	+	198	conserved hypothetical	-none-	D23_1c0587	Neut_0639
  							protein
  fig|6666666.60966.peg.587	CDS	542451	542618	3	+	168	hypothetical protein	-none-	D23_1c0588	Neut_0640
  fig|6666666.60966.peg.588	CDS	542602	542724	1	+	123	hypothetical protein	-none-	D23_1c0589	Neut_0641
  fig|6666666.60966.peg.590	CDS	543111	544673	3	+	1563	Putative inner	-none-	D23_1c0590	Neut_0642
  							membrane protein
  fig|6666666.60966.peg.591	CDS	544721	544834	2	+	114	hypothetical protein	-none-	D23_1c0591	NA
  fig|6666666.60966.peg.592	CDS	545193	546098	3	+	906	Membrane-bound lytic	CBSS-228410.1.peg.134;	D23_1c0592	Neut_0643
  							murein transglycosylase	<br>CBSS-
  							D precursor (EC 3.2.1.—)	342610.3.peg.1536;
  								<br>Murein Hydrolases
  fig|6666666.60966.peg.593	CDS	546933	546274	−3	−	660	Endonuclease III (EC	DNA Repair Base	D23_1c0593	Neut_0644
  							4.2.99.18)	Excision
  fig|6666666.60966.peg.594	CDS	547586	546930	−2	−	657	Electron transport	-none-	D23_1c0594	Neut_0645
  							complex protein RnfB
  fig|6666666.60966.peg.595	CDS	548604	547576	−3	−	1029	Dihydroorotate	De Novo Pyrimidine	D23_1c0595	Neut_0646
  							dehydrogenase (EC	Synthesis
  							1.3.3.1)
  fig|6666666.60966.peg.596	CDS	549246	548605	−3	−	642	Arginine-tRNA-protein	Protein degradation	D23_1c0596	Neut_0647
  							transferase (EC 2.3.2.8)
  fig|6666666.60966.peg.597	CDS	550041	549343	−3	−	699	Leucyl/phenylalanyl-	Protein degradation	D23_1c0597	Neut_0648
  							tRNA-protein
  							transferase (EC 2.3.2.6)
  fig|6666666.60966.peg.598	CDS	550783	550328	−1	−	456	Mobile element protein	-none-	D23_1c0598	Neut_2502
  fig|6666666.60966.peg.599	CDS	551132	550746	−2	−	387	Mobile element protein	-none-	D23_1c0599	Neut_0884
  fig|6666666.60966.peg.600	CDS	551404	551517	1	+	114	hypothetical protein	-none-	D23_1c0600	NA
  fig|6666666.60966.peg.601	CDS	551625	552500	3	+	876	FIG00859053:	-none-	D23_1c0601	Neut_0650
  							hypothetical protein
  fig|6666666.60966.peg.602	CDS	554066	552684	−2	−	1383	UDP-N-	Peptidoglycan	D23_1c0602	Neut_0651
  							acetylmuramate:L-	biosynthesis--gjo;
  							alanyl-gamma-D-	<br>Recycling of
  							glutamyl-meso-	Peptidoglycan Amino
  							diaminopimelate ligase	Acids
  							(EC 6.3.2.—)
  fig|6666666.60966.peg.603	CDS	554191	555363	1	+	1173	NADH dehydrogenase	Respiratory	D23_1c0603	Neut_0652
  							(EC 1.6.99.3)	dehydrogenases 1;
  								<br>Riboflavin synthesis
  								cluster
  fig|6666666.60966.peg.604	CDS	556325	555387	−2	−	939	Mutator mutT protein	Nudix proteins	D23_1c0604	Neut_0653
  							(7,8-dihydro-8-	(nucleoside triphosphate
  							oxoguanine-	hydrolases); <br>Nudix
  							triphosphatase) (EC	proteins (nucleoside
  							3.6.1.—)/Thiamin-	triphosphate hydrolases)
  							phosphate
  							pyrophosphorylase-like
  							protein
  fig|6666666.60966.peg.605	CDS	557210	556338	−2	−	873	putative ATP/GTP-	-none-	D23_1c0605	Neut_0654
  							binding protein
  fig|6666666.60966.peg.606	CDS	558441	557212	−3	−	1230	Glutamate N-	Arginine Biosynthesis--	D23_1c0607	Neut_0655
  							acetyltransferase (EC	gjo; <br>Arginine
  							2.3.1.35)/N-	Biosynthesis--gjo;
  							acetylglutamate	<br>Arginine
  							synthase (EC 2.3.1.1)	Biosynthesis extended;
  								<br>Arginine
  								Biosynthesis extended
  fig|6666666.60966.peg.607	CDS	558602	559015	2	+	414	FIG136845: Rhodanese-	Glutaredoxin 3	D23_1c0608	Neut_0656
  							related	containing cluster
  							sulfurtransferase
  fig|6666666.60966.peg.608	CDS	559045	559302	1	+	258	Glutaredoxin 3 (Grx3)	Glutaredoxin 3	D23_1c0609	Neut_0657
  								containing cluster;
  								<br>Glutaredoxins;
  								<br>Glutathione: Redox
  								cycle
  fig|6666666.60966.peg.609	CDS	559377	559862	3	+	486	Protein export	Glutaredoxin 3	D23_1c0610	Neut_0658
  							cytoplasm chaperone	containing cluster
  							protein (SecB,
  							maintains protein to be
  							exported in unfolded
  							state)
  fig|6666666.60966.peg.610	CDS	559866	560345	3	+	480	FIG00859406:	-none-	D23_1c0611	Neut_0659
  							hypothetical protein
  fig|6666666.60966.peg.611	CDS	560342	561331	2	+	990	Glycerol-3-phosphate	Glutaredoxin 3	D23_1c0612	Neut_0660
  							dehydrogenase	containing cluster;
  							[NAD(P)+] (EC 1.1.1.94)	<br>Glycerol and
  								Glycerol-3-phosphate
  								Uptake and Utilization;
  								<br>Glycerolipid and
  								Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.612	CDS	561519	561791	3	+	273	DNA-binding protein	DNA structural proteins,	D23_1c0613	Neut_0661
  							HU-beta	bacterial
  fig|6666666.60966.peg.614	CDS	562230	564023	3	+	1794	Peptidyl-prolyl cis-trans	Peptidyl-prolyl cis-trans	D23_1c0616	Neut_0662
  							isomerase PpiD (EC	isomerase
  							5.2.1.8)
  fig|6666666.60966.peg.615	CDS	564844	564050	−1	−	795	Enoyl-[acyl-carrier-	Fatty Acid Biosynthesis	D23_1c0617	Neut_0663
  							protein] reductase	FASII
  							[NADH] (EC 1.3.1.9)
  fig|6666666.60966.peg.616	CDS	565168	564959	−1	−	210	hypothetical protein	-none-	D23_1c0618	NA
  fig|6666666.60966.peg.617	CDS	565170	567587	3	+	2418	Transcription accessory	CBSS-243265.1.peg.198;	D23_1c0619	Neut_0664
  							protein (S1 RNA-binding	<br>Transcription
  							domain)	factors bacterial
  fig|6666666.60966.peg.618	CDS	567598	567975	1	+	378	hypothetical protein	-none-	D23_1c0620	Neut_0682
  fig|6666666.60966.peg.619	CDS	567977	568255	2	+	279	hypothetical protein	-none-	D23_1c0621	Neut_0682
  fig|6666666.60966.peg.621	CDS	568500	568871	3	+	372	hypothetical protein	-none-	D23_1c0622	Neut_0683
  fig|6666666.60966.peg.622	CDS	569150	568989	−2	−	162	hypothetical protein	-none-	D23_1c0623	Neut_0684
  fig|6666666.60966.peg.623	CDS	570485	569238	−2	−	1248	Mobile element protein	-none-	D23_1c0624	Neut_0357
  fig|6666666.60966.peg.624	CDS	571236	570577	−3	−	660	N-hydroxyarylamine O-	-none-	D23_1c0626	Neut_0684
  							acetyltransferase (EC
  							2.3.1.118)
  fig|6666666.60966.peg.625	CDS	572209	571295	−1	−	915	Permease of the	Queuosine-Archaeosine	D23_1c0627	Neut_0685
  							drug/metabolite	Biosynthesis
  							transporter (DMT)
  							superfamily
  fig|6666666.60966.peg.626	CDS	573622	572339	−1	−	1284	TRAP dicarboxylate	TRAP Transporter	D23_1c0628	Neut_0686
  							transporter, DctM	unknown substrate 6
  							subunit, unknown
  							substrate
  6
  fig|6666666.60966.peg.627	CDS	574259	573705	−2	−	555	TRAP dicarboxylate	TRAP Transporter	D23_1c0629	Neut_0687
  							transporter, DctQ	unknown substrate 6
  							subunit, unknown
  							substrate
  6
  fig|6666666.60966.peg.628	CDS	575698	574334	−1	−	1365	TldE protein, part of	Putative TldE-TldD	D23_1c0630	Neut_0688
  							TldE/TldD proteolytic	proteolytic complex
  							complex
  fig|6666666.60966.peg.629	CDS	575950	576474	1	+	525	FIG138315: Putative	Putative TldE-TldD	D23_1c0632	Neut_0689
  							alpha helix protein	proteolytic complex
  fig|6666666.60966.peg.630	CDS	576475	576609	1	+	135	hypothetical protein	-none-	D23_1c0633	NA
  fig|6666666.60966.peg.631	CDS	576740	577006	2	+	267	FIG00859002:	-none-	D23_1c0635	Neut_0690
  							hypothetical protein
  fig|6666666.60966.peg.632	CDS	577046	577804	2	+	759	Exodeoxyribonuclease	DNA repair, bacterial	D23_1c0636	Neut_0691
  							III (EC 3.1.11.2)
  fig|6666666.60966.peg.633	CDS	577801	579195	1	+	1395	AmpG permease	Recycling of	D23_1c0637	Neut_0692
  								Peptidoglycan Amino
  								Acids
  fig|6666666.60966.peg.636	CDS	580217	579867	−2	−	351	Cytochrome O	Terminal cytochrome O	D23_1c0638	Neut_0694
  							ubiquinol oxidase	ubiquinol oxidase;
  							subunit IV (EC 1.10.3.—)	<br>Terminal
  								cytochrome oxidases
  fig|6666666.60966.peg.637	CDS	580885	580214	−1	−	672	Cytochrome O	Terminal cytochrome O	D23_1c0639	Neut_0695
  							ubiquinol oxidase	ubiquinol oxidase;
  							subunit III (EC 1.10.3.—)	<br>Terminal
  								cytochrome oxidases
  fig|6666666.60966.peg.638	CDS	582993	580882	−3	−	2112	Cytochrome O	Terminal cytochrome O	D23_1c0640	Neut_0696
  							ubiquinol oxidase	ubiquinol oxidase;
  							subunit 1 (EC 1.10.3.—)	<br>Terminal
  								cytochrome oxidases
  fig|6666666.60966.peg.639	CDS	583998	582997	−3	−	1002	Cytochrome O	Terminal cytochrome O	D23_1c0641	Neut_0697
  							ubiquinol oxidase	ubiquinol oxidase;
  							subunit II (EC 1.10.3.—)	<br>Terminal
  								cytochrome oxidases
  fig|6666666.60966.peg.640	CDS	585484	584237	−1	−	1248	Mobile element protein	-none-	D23_1c0642	Neut_0357
  fig|6666666.60966.peg.641	CDS	585502	585633	1	+	132	patatin family protein	-none-	D23_1c0643	Neut_1317
  fig|6666666.60966.peg.642	CDS	585643	586530	1	+	888	UTP--glucose-1-	-none-	D23_1c0644	Neut_0698
  							phosphate
  							uridylyltransferase (EC
  							2.7.7.9)
  fig|6666666.60966.peg.643	CDS	586705	587817	1	+	1113	FIG00859666:	-none-	D23_1c0645	Neut_0699
  							hypothetical protein
  fig|6666666.60966.peg.644	CDS	587837	589201	2	+	1365	Succinate-semialdehyde	-none-	D23_1c0646	Neut_0700
  							dehydrogenase [NAD]
  							(EC 1.2.1.24); Succinate-
  							semialdehyde
  							dehydrogenase
  							[NADP+] (EC 1.2.1.16)
  fig|6666666.60966.peg.645	CDS	589224	590942	3	+	1719	InterPro IPR001440	-none-	D23_1c0647	Neut_0701
  							COGs COG0457
  fig|6666666.60966.peg.646	CDS	592871	591033	−2	−	1839	Long-chain-fatty-acid--	Biotin biosynthesis;	D23_1c0648	Neut_0702
  							CoA ligase (EC 6.2.1.3)	<br>Biotin synthesis
  								cluster; <br>Fatty acid
  								metabolism cluster
  fig|6666666.60966.peg.647	CDS	595204	592868	−1	−	2337	Butyryl-CoA	-none-	D23_1c0649	Neut_0703
  							dehydrogenase (EC
  							1.3.99.2)
  fig|6666666.60966.peg.648	CDS	595489	595223	−1	−	267	hypothetical protein	-none-	D23_1c0650	Neut_0704
  fig|6666666.60966.peg.649	CDS	596053	595673	−1	−	381	Putative membrane	-none-	D23_1c0651	Neut_0705
  							protein
  fig|6666666.60966.peg.650	CDS	596962	596099	−1	−	864	Pirin	-none-	D23_1c0652	Neut_0706
  fig|6666666.60966.peg.651	CDS	597098	598030	2	+	933	Transcriptional	-none-	D23_1c0653	Neut_0707
  							regulator, LysR family
  fig|6666666.60966.peg.652	CDS	598202	599338	2	+	1137	hypothetical protein	-none-	D23_1c0655	Neut_0708
  fig|6666666.60966.peg.653	CDS	599418	599657	3	+	240	Flavodoxin reductases	Anaerobic respiratory	D23_1c0656	Neut_0709
  							(ferredoxin-NADPH	reductases
  							reductases) family 1
  fig|6666666.60966.peg.654	CDS	599689	600114	1	+	426	Flavodoxin reductases	Anaerobic respiratory	D23_1c0657	Neut_0709
  							(ferredoxin-NADPH	reductases
  							reductases) family 1
  fig|6666666.60966.peg.655	CDS	601243	600251	−1	−	993	Multicopper oxidase	Copper homeostasis	D23_1c0658	Neut_0710
  fig|6666666.60966.peg.656	CDS	602188	601454	−1	−	735	FIG00859807:	-none-	D23_1c0659	Neut_0711
  							hypothetical protein
  fig|6666666.60966.peg.657	CDS	602534	602346	−2	−	189	hypothetical protein	-none-	D23_1c0660	Neut_0712
  fig|6666666.60966.peg.658	CDS	602837	602700	−2	−	138	Putative NAD(P)-	-none-	D23_1c0661	Neut_0990
  							dependent
  							oxidoreductase EC-
  							YbbO
  fig|6666666.60966.peg.659	CDS	603148	602882	−1	−	267	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c0662	Neut_0713
  							transport system,
  							permease component
  fig|6666666.60966.peg.660	CDS	603362	605239	2	+	1878	1,4-alpha-glucan	-none-	D23_1c0663	Neut_0714
  							branching enzyme (EC
  							2.4.1.18)
  fig|6666666.60966.peg.661	CDS	605497	605619	1	+	123	Glutathione peroxidase	Glutathione: Redox cycle	D23_1c0664	Neut_0715
  							(EC 1.11.1.9)
  fig|6666666.60966.peg.662	CDS	607768	605882	−1	−	1887	TonB-dependent hemin,	Ton and Tol transport	D23_1c0665	Neut_0716
  							ferrichrome receptor	systems
  fig|6666666.60966.peg.663	CDS	609583	607862	−1	−	1722	hypothetical protein	-none-	D23_1c0666	Neut_0717
  fig|6666666.60966.peg.664	CDS	610957	609656	−1	−	1302	Membrane protein	-none-	D23_1c0667	Neut_0718
  							involved in colicin
  							uptake
  fig|6666666.60966.peg.665	CDS	611184	612413	3	+	1230	FIG00858430:	-none-	D23_1c0668	Neut_0719
  							hypothetical protein
  fig|6666666.60966.peg.666	CDS	612533	615022	2	+	2490	TonB-dependent	Ton and Tol transport	D23_1c0669	Neut_0720
  							receptor	systems
  fig|6666666.60966.peg.667	CDS	615143	615012	−2	−	132	hypothetical protein	-none-	D23_1c0670	NA
  fig|6666666.60966.peg.668	CDS	615337	617457	1	+	2121	TonB-dependent	Ton and Tol transport	D23_1c0672	Neut_0721
  							receptor	systems
  fig|6666666.60966.peg.669	CDS	617524	618762	1	+	1239	putative signal peptide	-none-	D23_1c0673	Neut_0722
  							protein
  fig|6666666.60966.peg.670	CDS	618762	619262	3	+	501	InterPro IPR000063	-none-	D23_1c0674	Neut_0723
  							COGs COG0526
  fig|6666666.60966.peg.671	CDS	619459	621978	1	+	2520	Enoyl-CoA hydratase	Acetyl-CoA fermentation	D23_1c0675	Neut_0724
  							(EC 4.2.1.17)/3,2-	to Butyrate; <br>Acetyl-
  							trans-enoyl-CoA	CoA fermentation to
  							isomerase (EC 5.3.3.8)/	Butyrate; <br>Butanol
  							3-hydroxyacyl-CoA	Biosynthesis;
  							dehydrogenase (EC	<br<Butyrate
  							1.1.1.35)	metabolism cluster;
  								<br>Butyrate
  								metabolism cluster;
  								<br>Fatty acid
  								metabolism cluster;
  								<br>Fatty acid
  								metabolism cluster;
  								<br>Polyhydroxybutyrate
  								metabolism;
  								<br>Polyhydroxybutyrate
  								metabolism
  fig|6666666.60966.peg.672	CDS	622043	623245	2	+	1203	3-ketoacyl-CoA thiolase	Acetyl-CoA fermentation	D23_1c0676	Neut_0725
  							(EC 2.3.1.16) @ Acetyl-	to Butyrate; <br>Biotin
  							CoA acetyltransferase	biosynthesis; <br>Biotin
  							(EC 2.3.1.9)	synthesis cluster;
  								<br>Butanol
  								Biosynthesis;
  								<br>Butyrate
  								metabolism cluster;
  								<br>Fatty acid
  								metabolism cluster;
  								<br>Isoprenoid
  								Biosynthesis;
  								<br>Polyhydroxybutyrate
  								metabolism;
  								<br>Polyhydroxybutyrate
  								metabolism
  fig|6666666.60966.peg.673	CDS	623639	623301	−2	−	339	FIG00859796:	-none-	D23_1c0677	Neut_0726
  							hypothetical protein
  fig|6666666.60966.peg.674	CDS	623711	623827	2	+	117	hypothetical protein	-none-	D23_1c0678	NA
  fig|6666666.60966.peg.675	CDS	624186	624479	3	+	294	Mobile element protein	-none-	D23_1c0680	Neut_1719
  fig|6666666.60966.peg.676	CDS	624578	625456	2	+	879	Mobile element protein	-none-	D23_1c0681	Neut_1720
  fig|6666666.60966.peg.677	CDS	626009	625605	−2	−	405	hypothetical protein	-none-	D23_1c0682	NA
  fig|6666666.60966.peg.678	CDS	626270	628669	2	+	2400	Predicted hydrolase of	-none-	D23_1c0684	Neut_0728
  							the metallo-beta-
  							lactamase superfamily,
  							clustered with KDO2-
  							Lipid A biosynthesis
  							genes
  fig|6666666.60966.peg.679	CDS	628866	629183	3	+	318	Flagellar transcriptional	Flagellum	D23_1c0685	Neut_0729
  							activator FlhD
  fig|6666666.60966.peg.680	CDS	629210	629785	2	+	576	Flagellar transcriptional	Flagellum	D23_1c0686	Neut_0730
  							activator FlhC
  fig|6666666.60966.peg.681	CDS	630020	631549	2	+	1530	Proposed peptidoglycan	Peptidoglycan lipid II	D23_1c0687	Neut_0731
  							lipid II flippase MurJ	flippase
  fig|6666666.60966.peg.683	CDS	633437	632277	−2	−	1161	Outer membrane	Lipopolysaccharide	D23_1c0688	Neut_0732
  							protein NlpB,	assembly
  							lipoprotein component
  							of the protein assembly
  							complex (forms a
  							complex with YaeT,
  							YfiO, and YfgL);
  							Lipoprotein-34
  							precursor
  fig|6666666.60966.peg.684	CDS	634289	633447	−2	−	843	Dihydrodipicolinate	-none-	D23_1c0689	Neut_0733
  							synthase (EC 4.2.1.52)
  fig|6666666.60966.peg.685	CDS	637007	634416	−2	−	2592	ClpB protein	Protein chaperones;	D23_1c0690	Neut_0734
  							<br>Proteolysis in
  							bacteria, ATP-dependent
  fig|6666666.60966.peg.686	CDS	637484	637326	−2	−	159	hypothetical protein	-none-	D23_1c0693	NA
  fig|6666666.60966.peg.687	CDS	638994	637501	−3	−	1494	Ferredoxin-dependent	Ammonia assimilation;	D23_1c0694	Neut_0735
  							glutamate synthase (EC	<br>Glutamine,
  							1.4.7.1)	Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.688	CDS	639034	639930	1	+	897	Quinolinate	Mycobacterium	D23_1c0695	NA
  							phosphoribosyltransferase	virulence operon
  							[decarboxylating]	possibly involved in
  							(EC 2.4.2.19)	quinolinate biosynthesis;
  								<br>NAD and NADP
  								cofactor biosynthesis
  								global
  fig|6666666.60966.peg.689	CDS	641903	640635	−2	−	1269	Flagellar hook-length	Flagellum	D23_1c0696	Neut_0740
  							control protein FliK
  fig|6666666.60966.peg.690	CDS	642413	641961	−2	−	453	Flagellar protein FliJ	Flagellum	D23_1c0697	Neut_0741
  fig|6666666.60966.peg.691	CDS	643836	642430	−3	−	1407	Flagellum-specific ATP	Flagellar motility;	D23_1c0698	Neut_0742
  							synthase Flil	<br>Flagellum
  fig|6666666.60966.peg.692	CDS	644577	643858	−3	−	720	Flagellar assembly	Flagellum	D23_1c0699	Neut_0743
  							protein FliH
  fig|6666666.60966.peg.693	CDS	645764	644769	−2	−	996	Flagellar motor switch	Flagellum	D23_1c0700	Neut_0744
  							protein FliG
  fig|6666666.60966.peg.694	CDS	647397	645754	−3	−	1644	Flagellar M-ring protein	Flagellum	D23_1C0701	Neut_0745
  							FliF
  fig|6666666.60966.peg.695	CDS	647548	647402	−1	−	147	hypothetical protein	-none-	D23_1c0702	NA
  fig|6666666.60966.peg.696	CDS	647628	648872	3	+	1245	Flagellar sensor	Flagellum	D23_1c0703	Neut_0746
  							histidine kinase FleS
  fig|6666666.60966.peg.697	CDS	648876	650189	3	+	1314	InterPro	-none-	D23_1c0704	Neut_0747
  							IPR001789:IPR002078:IPR002197:
  							IPR003593
  							COGs COG2204
  fig|6666666.60966.peg.698	CDS	650217	650546	3	+	330	Flagellar hook-basal	Flagellum; <br>Flagellum	D23_1c0705	Neut_0748
  							body complex protein	in Campylobacter
  							FliE
  fig|6666666.60966.peg.699	CDS	650581	651390	1	+	810	FIG00858443:	-none-	D23_1c0706	Neut_0749
  							hypothetical protein
  fig|6666666.60966.peg.700	CDS	651752	651411	−2	−	342	Flagellar biosynthesis	Flagellar motility;	D23_1c0707	Neut_0750
  							protein FlhB	<br>Flagellum
  fig|6666666.60966.peg.701	CDS	652764	651739	−3	−	1026	FIG00726091:	-none-	D23_1c0708	Neut_0751
  							hypothetical protein
  fig|6666666.60966.peg.702	CDS	652766	652948	2	+	183	hypothetical protein	-none-	D23_1c0709	NA
  fig|6666666.60966.peg.703	CDS	653125	653517	1	+	393	hypothetical protein	-none-	D23_1c0710	Neut_2449
  fig|6666666.60966.peg.704	CDS	653664	653810	3	+	147	Mobile element protein	-none-	D23_1c0711	Neut_1756
  fig|6666666.60966.peg.705	CDS	654316	653858	−1	−	459	Cytochrome c family	-none-	D23_1c0712	Neut_0754
  							protein
  fig|6666666.60966.peg.706	CDS	654869	654345	−2	−	525	CopG protein	Copper homeostasis	D23_1c0713	Neut_0755
  fig|6666666.60966.peg.707	CDS	655268	656209	2	+	942	tRNA(Cytosine32)-2-	CBSS-	D23_1c0714	Neut_0756
  							thiocytidine synthetase	326442.4.peg.1852;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.708	CDS	657180	656236	−3	−	945	Lipoate synthase	Lipoic acid metabolism;	D23_1c0715	Neut_0757
  								<br>Lipoic acid synthesis
  								cluster; <br>Possible
  								RNA degradation cluster
  fig|6666666.60966.peg.709	CDS	657847	657170	−1	−	678	Octanoate-[acyl-carrier-	Lipoic acid metabolism;	D23_1c0716	Neut_0758
  							protein]-protein-N-	<br>Lipoic acid synthesis
  							octanoyltransferase	cluster
  fig|6666666.60966.peg.710	CDS	658198	657935	−1	−	264	Proposed lipoate	Lipoicacid metabolism;	D23_1c0717	Neut_0759
  							regulatory protein YbeD	<br>Lipoic acid synthesis
  								cluster
  fig|6666666.60966.peg.711	CDS	659068	658208	−1	−	861	D-alanine	Pyruvate Alanine Serine	D23_1c0718	Neut_0760
  							aminotransferase (EC	Interconversions
  							2.6.1.21)
  fig|6666666.60966.peg.712	CDS	660251	659088	−2	−	1164	D-alanyl-D-alanine	CBSS-84588.1.peg.1247;	D23_1c0719	Neut_0761
  							carboxypeptidase (EC	<br>Metallocarboxypeptidases
  							3.4.16.4)	(EC 3.4.17.—);
  								<br>Murein Hydrolases;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.713	CDS	660353	660787	2	+	435	LSU ribosomal protein	-none-	D23_1c0720	Neut_0762
  							L13p (L13Ae)
  fig|6666666.60966.peg.714	CDS	660799	661191	1	+	393	SSU ribosomal protein	-none-	D23_1c0721	Neut_0763
  							S9p (S16e)
  fig|6666666.60966.peg.715	CDS	661324	662352	1	+	1029	N-acetyl-gamma-	Arginine Biosynthesis--	D23_1c0722	Neut_0764
  							glutamyl-phosphate	gjo; <br>Arginine
  							reductase (EC 1.2.1.38)	Biosynthesis extended
  fig|6666666.60966.peg.716	CDS	662454	663221	3	+	768	putative integral	-none-	D23_1c0723	Neut_0765
  							membrane protein
  fig|6666666.60966.peg.717	CDS	663202	663627	1	+	426	Integral membrane	-none-	D23_1c0724	Neut_0766
  							protein CcmA involved
  							in cell shape
  							determination
  fig|6666666.60966.peg.718	CDS	665316	663655	−3	−	1662	DNA repair protein	DNA repair, bacterial	D23_1c0725	Neut_0767
  							RecN
  fig|6666666.60966.peg.719	CDS	666357	665326	−3	−	1032	NAD kinase (EC	NAD and NADP cofactor	D23_1c0726	Neut_0768
  							2.7.1.23)	biosynthesis global
  fig|6666666.60966.peg.720	CDS	666433	667449	1	+	1017	Heat-inducible	GroEL GroES; <br>Heat	D23_1c0727	Neut_0769
  							transcription repressor	shock dnaK gene cluster
  							HrcA	extended
  fig|6666666.60966.peg.721	CDS	667469	668566	2	+	1098	Ferrochelatase,	Heme and Siroheme	D23_1c0728	Neut_0770
  							protoheme ferro-lyase	Biosynthesis
  							(EC 4.99.1.1)
  fig|6666666.60966.peg.722	CDS	668678	669469	2	+	792	Zn-dependent protease	-none-	D23_1c0729	Neut_0771
  							with chaperone
  							function PA4632
  fig|6666666.60966.peg.723	CDS	669589	670461	1	+	873	Phosphoribulokinase	Calvin-Benson cycle	D23_1c0730	Neut_0772
  							(EC 2.7.1.19)
  fig|6666666.60966.peg.724	CDS	670525	672771	1	+	2247	ATP-dependent DNA	DNA repair, bacterial	D23_1c0731	Neut_0773
  							helicase UvrD/PcrA	UvrD and related
  								helicases
  fig|6666666.60966.peg.725	CDS	673569	672778	−3	−	792	Possible	-none-	D23_1c0732	Neut_0774
  							transmembrane protein
  fig|6666666.60966.peg.726	CDS	674610	673660	−3	−	951	Homoserine kinase (EC	CBSS-	D23_1c0733	Neut_0775
  							2.7.1.39)	269482.1.peg.1294;
  								<br>Methionine
  								Biosynthesis;
  								<br>Threonine and
  								Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.727	CDS	674585	674716	2	+	132	hypothetical protein	-none-	D23_1c0734	NA
  fig|6666666.60966.peg.728	CDS	675030	674704	−3	−	327	FIG00858562:	-none-	D23_1c0735	Neut_0776
  							hypothetical protein
  fig|6666666.60966.peg.729	CDS	675190	674996	−1	−	195	hypothetical protein	-none-	D23_1c0736	NA
  fig|6666666.60966.peg.730	CDS	675866	675147	−2	−	720	FIG00859241:	-none-	D23_1c0737	Neut_0777
  							hypothetical protein
  fig|6666666.60966.peg.731	CDS	675882	678602	3	+	2721	DNA polymerase I (EC	DNA Repair Base	D23_1c0738	Neut_0778
  							2.7.7.7)	Excision
  fig|6666666.60966.peg.732	CDS	678725	679912	2	+	1188	Fatty acid desaturase	-none-	D23_1c0739	Neut_0779
  							(EC 1.14.19.1); Delta-9
  							fatty acid desaturase
  							(EC 1.14.19.1)
  fig|6666666.60966.peg.733	CDS	680149	679994	−1	−	156	LSU ribosomal protein	-none-	D23_1c0740	Neut_0780
  							L33p @ LSU ribosomal
  							protein L33p, zinc-
  							independent
  fig|6666666.60966.peg.734	CDS	680390	680190	−2	−	201	LSU ribosomal protein	-none-	D23_1c0741	Neut_0781
  							L28p
  fig|6666666.60966.peg.735	CDS	681169	680495	−1	−	675	DNA repair protein	Bacterial cell division	D23_1c0742	Neut_0782
  							RadC	cluster; <br>DNA repair,
  								bacterial
  fig|6666666.60966.peg.736	CDS	681339	682508	3	+	1170	Phosphopantothenoylcysteine	Coenzyme A	D23_1c0743	Neut_0783
  							decarboxylase	Biosynthesis;
  							(EC 4.1.1.36)/	<br>Coenzyme A
  							Phosphopantothenoylcysteine	Biosynthesis
  							synthetase (EC
  							6.3.2.5)
  fig|6666666.60966.peg.737	CDS	682518	682967	3	+	450	Deoxyuridine 5&#39;-	Housecleaning	D23_1c0744	Neut_0784
  							triphosphate	nucleoside triphosphate
  							nucleotidohydrolase (EC	pyrophosphatases;
  							3.6.1.23)	<br>Nudix proteins
  								(nucleoside triphosphate
  								hydrolases)
  fig|6666666.60966.peg.738	CDS	682961	683386	2	+	426	exported protein	-none-	D23_1c0745	Neut_0785
  fig|6666666.60966.peg.739	CDS	685816	683759	−1	−	2058	Pyrophosphate-	Phosphate metabolism	D23_1c0746	Neut_0786
  							energized proton pump
  							(EC 3.6.1.1)
  fig|6666666.60966.peg.740	CDS	687229	685970	−1	−	1260	6-phosphofructokinase	Glycolysis and	D23_1c0747	Neut_0787
  							(EC 2.7.1.11)	Gluconeogenesis
  fig|6666666.60966.peg.741	CDS	687933	687400	−3	−	534	Adenylate kinase (EC	Purine conversions	D23_1c0748	NA
  							2.7.4.3)
  fig|6666666.60966.peg.742	CDS	688328	689359	2	+	1032	RecA protein	DNA repair, bacterial;	D23_1c0749	Neut_0789
  								<br>DNA repair system
  								including RecA, MutS
  								and a hypothetical
  								protein; <br>RecA and
  								RecX
  fig|6666666.60966.peg.743	CDS	689362	689802	1	+	441	Regulatory protein RecX	DNA repair system	D23_1c0750	Neut_0790
  								including RecA, MutS
  								and a hypothetical
  								protein; <br>RecA and
  								RecX
  fig|6666666.60966.peg.744	CDS	689820	692411	3	+	2592	Alanyl-tRNA synthetase	Cluster containing	D23_1c0751	Neut_0791
  							(EC 6.1.1.7)	Alanyl-tRNA synthetase;
  								<br>tRNA
  								aminoacylation, Ala
  fig|6666666.60966.peg.745	CDS	692450	693403	2	+	954	Thioredoxin reductase	Thioredoxin-disulfide	D23_1c0752	Neut_0792
  							(EC 1.8.1.9)	reductase;
  								<br>pyrimidine
  								conversions
  fig|6666666.60966.peg.746	CDS	693409	6939991	1	+	591	Smr domain	-none-	D23_1c0753	Neut_0793
  fig|6666666.60966.peg.747	CDS	694203	694349	3	+	147	Carbonic anhydrase (EC	Zinc regulated enzymes	D23_1c0754	Neut_0794
  							4.2.1.1)
  fig|6666666.60966.peg.750	CDS	695056	695208	1	+	153	hypothetical protein	-none-	D23_1c0755	Neut_1255
  fig|6666666.60966.peg.751	CDS	695216	695383	2	+	168	hypothetical protein	-none-	D23_1c0756	Neut_2449
  fig|6666666.60966.peg.752	CDS	695522	695986	2	+	465	Mobile element protein	-none-	D23_1c0758	Neut_1256
  fig|6666666.60966.peg.753	CDS	696281	696072	−2	−	210	Chemotaxis regulator-	Flagellar motility	D23_1c0759	Neut_0796
  							transmits
  							chemoreceptor signals
  							to flagelllar motor
  							components CheY
  fig|6666666.60966.peg.754	CDS	696491	696619	2	+	129	hypothetical protein	-none-	D23_1c0760	Neut_0797
  fig|6666666.60966.peg.755	CDS	696639	696812	3	+	174	Mobile element protein	-none-	D23_1c0760	Neut_0797
  fig|6666666.60966.peg.756	CDS	696806	696934	2	+	129	Mobile element protein	-none-	D23_1c0761	NA
  fig|6666666.60966.peg.757	CDS	697179	698426	3	+	1248	Mobile element protein	-none-	D23_1c0762	Neut_0357
  fig|6666666.60966.peg.758	CDS	698760	700454	3	+	1695	NADH dehydrogenase,	Respiratory Complex I	D23_1c0763	Neut_0799
  							subunit
  5
  fig|6666666.60966.peg.759	CDS	700473	701258	3	+	786	hypothetical protein	-none-	D23_1c0765	Neut_0800
  fig|6666666.60966.peg.760	CDS	701243	704371	2	+	3129	Hypothetical	CO2 uptake,	D23_1c0766	Neut_0801
  							transmembrane protein	carboxysome;
  							coupled to NADH-	<br>Respiratory
  							ubiquinone	Complex I
  							oxidoreductase chain 5
  							homolog
  fig|6666666.60966.peg.761	CDS	704368	704694	1	+	327	Nitrogen regulatory	Ammonia assimilation	D23_1c0767	Neut_0802
  							protein P-II
  fig|6666666.60966.peg.762	CDS	704850	705059	3	+	210	hypothetical protein	-none-	D23_1c0768	Neut_0800
  fig|6666666.60966.peg.763	CDS	705044	708184	2	+	3141	Hypothetical	CO2 uptake,	D23_1c0769	Neut_0801
  							transmembrane protein	carboxysome;
  							coupled to NADH-	<br>Respiratory
  							ubiquinone	Complex I
  							oxidoreductase chain 5
  							homolog
  fig|6666666.60966.peg.764	CDS	708181	708507	1	+	327	Nitrogen regulatory	Ammonia assimilation	D23_1c0770	Neut_0802
  							protein P-II
  fig|6666666.60966.peg.765	CDS	709429	708509	−1	−	921	RuBisCO operon	CO2 uptake,	D23_1c0771	Neut_0803
  							transcriptional	carboxysome
  							regulator CbbR
  fig|6666666.60966.peg.766	CDS	709628	711049	2	+	1422	Ribulose bisphosphate	CO2 uptake,	D23_1c0772	Neut_0804
  							carboxylase large chain	carboxysome;
  							(EC 4.1.1.39)	<br>Calvin-Benson cycle;
  								<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.767	CDS	711134	711460	2	+	327	Ribulose bisphosphate	CO2 uptake,	D23_1c0773	Neut_0805
  							carboxylase small chain	carboxysome;
  							(EC 4.1.1.39)	<br>Calvin-Benson cycle;
  								<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.768	CDS	711860	711645	−2	−	216	hypothetical protein	-none-	D23_1c0774	Neut_0806
  fig|6666666.60966.peg.769	CDS	711868	714264	1	+	2397	carboxysome shell	CO2 uptake,	D23_1c0774	Neut_0806
  							protein CsoS2	carboxysome
  fig|6666666.60966.peg.770	CDS	714275	715804	2	+	1530	carboxysome shell	CO2 uptake,	D23_1c0775	Neut_0807
  							protein CsoS3	carboxysome
  fig|6666666.60966.peg.771	CDS	715825	716082	1	+	258	putative carboxysome	CO2 uptake,	D23_1c0776	Neut_0808
  							peptide A	carboxysome
  fig|6666666.60966.peg.772	CDS	716082	716330	3	+	249	putative carboxysome	CO2 uptake,	D23_1c0777	Neut_0809
  							peptide B	carboxysome
  fig|6666666.60966.peg.773	CDS	716439	716735	3	+	297	carboxysome shell	CO2 uptake,	D23_1c0778	Neut_0810
  							protein CsoS1	carboxysome
  fig|6666666.60966.peg.774	CDS	716777	717124	2	+	348	carboxysome shell	CO2 uptake,	D23_1c0779	Neut_0811
  							protein CsoS1	carboxysome
  fig|6666666.60966.peg.775	CDS	717145	717567	1	+	423	bacterioferritin possible	-none-	D23_1c0780	Neut_0812
  							associated with
  							carboxysome
  fig|6666666.60966.peg.776	CDS	717576	717842	3	+	267	Possible pterin-4 alpha-	CO2 uptake,	D23_1c0781	Neut_0813
  							carbinolamine	carboxysome
  							dehydratase-like
  							protein
  fig|6666666.60966.peg.777	CDS	717911	718483	2	+	573	Chromosome (plasmid)	Bacterial Cell Division;	D23_1c0782	Neut_0814
  							partitioning protein	<br>Bacterial
  							ParA	Cytoskeleton; <br>Cell
  								Division Subsystem
  								including YidCD;
  								<br>RNA modification
  								and chromosome
  								partitioning cluster
  fig|6666666.60966.peg.778	CDS	718480	718674	1	+	195	hypothetical protein	-none-	D23_1c0783	NA
  fig|6666666.60966.peg.779	CDS	718681	719631	1	+	951	Rubisco activation	CO2 uptake,	D23_1c0784	Neut_0815
  							protein CbbQ	carboxysome
  fig|6666666.60966.peg.780	CDS	719654	722014	2	+	2361	Rubisco activation	CO2 uptake,	D23_1c0785	Neut_0816
  							protein CbbO	carboxysome
  fig|6666666.60966.peg.781	CDS	722027	722659	2	+	633	FIG00852745:	-none-	D23_1c0786	Neut_0817
  							hypothetical protein
  fig|6666666.60966.peg.782	CDS	722704	723528	1	+	825	FIG00853400:	-none-	D23_1c0787	Neut_0818
  							hypothetical protein
  fig|6666666.60966.peg.783	CDS	723822	723676	−3	−	147	Mobile element protein	-none-	D23_1c0788	NA
  fig|6666666.60966.peg.784	CDS	723900	724055	3	+	156	hypothetical protein	-none-	D23_1c0790	NA
  fig|6666666.60966.peg.785	CDS	724125	724304	3	+	180	Rubisco activation	CO2 uptake,	D23_1c0791	NA
  							protein CbbO	carboxysome
  fig|6666666.60966.peg.786	CDS	724415	724621	2	+	207	Rubisco activation	CO2 uptake,	D23_1c0792	Neut_0816
  							protein CbbO	carboxysome
  fig|6666666.60966.peg.787	CDS	724700	724975	2	+	276	Nitric oxide reductase	Denitrification;	D23_1c0793	Neut_0816
  							activation protein NorD	<br>Denitrifying
  								reductase gene clusters
  fig|6666666.60966.peg.788	CDS	724985	725104	2	+	120	hypothetical protein	-none-	D23_1c0794	Neut_0816
  fig|6666666.60966.peg.789	CDS	725079	725336	3	+	258	Nitric oxide reductase	Denitrification;	D23_1c0794	Neut_0816
  							activation protein NorD	<br>Denitrifying
  								reductase gene clusters
  fig|6666666.60966.peg.790	CDS	725493	725657	3	+	165	hypothetical protein	-none-	D23_1c0795	Neut_0821
  fig|6666666.60966.peg.791	CDS	727182	725782	−3	−	1401	FIG00861154:	-none-	D23_1c0796	Neut_1550
  							hypothetical protein
  fig|6666666.60966.peg.792	CDS	727830	727411	−3	−	420	FIG00859219:	-none-	D23_1c0797	Neut_0823
  							hypothetical protein
  fig|6666666.60966.peg.793	CDS	729449	728481	−2	−	969	Octaprenyl diphosphate	Isoprenoid Biosynthesis;	D23_1c0800	Neut_0825
  							synthase (EC 2.5.1.90)/	<br>Isoprenoid
  							Dimethylallyltransferase	Biosynthesis;
  							(EC 2.5.1.1)/(2E,6E)-	<br>Isoprenoid
  							farnesyl diphosphate	Biosynthesis:
  							synthase (EC 2.5.1.10)/	Interconversions;
  							Geranylgeranyl	<br>Isoprenoinds for
  							diphosphate synthase	Quinones;
  							(EC 2.5.1.29)	<br>Isoprenoinds for
  								Quinones;
  								<br>Isoprenoinds for
  								Quinones;
  								<br>Isoprenoinds for
  								Quinones;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis
  fig|6666666.60966.peg.795	CDS	729633	730886	3	+	1254	Glutamyl-tRNA	A Gammaproteobacteria	D23_1c0801	Neut_0826
  							reductase (EC 1.2.1.70)	Cluster Relating to
  								Translation; <br>Heme
  								and Siroheme
  								Biosynthesis
  fig|6666666.60966.peg.796	CDS	730883	731962	2	+	1080	Peptide chain release	A Gammaproteobacteria	D23_1c0802	Neut_0827
  							factor
  1	Cluster Relating to
  								Translation; <br>CBSS-
  								216600.3.peg.802;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.797	CDS	731959	732840	1	+	882	Protein-N(5)-glutamine	A Gammaproteobacteria	D23_1c0803	Neut_0828
  							methyltransferase	Cluster Relating to
  							PrmC, methylates	Translation; <br>CBSS-
  							polypeptide chain	216600.3.peg.802;
  							release factors RF1 and	<br>Translation
  							RF2	termination factors
  								bacterial
  fig|6666666.60966.peg.798	CDS	732995	733303	2	+	309	Glutaredoxin-related	Glutaredoxins	D23_1c0805	Neut_0829
  							protein
  fig|6666666.60966.peg.799	CDS	733743	733324	−3	−	420	Putative membrane	-none-	D23_1c0806	Neut_0830
  							protein
  fig|6666666.60966.peg.800	CDS	734018	734161	2	+	144	hypothetical protein	-none-	D23_1c0807	NA
  fig|6666666.60966.peg.801	CDS	734194	734826	1	+	633	Glutathione S-	Glutathione: Non-redox	D23_1c0808	Neut_0831
  							transferase (EC	reactions
  							2.5.1.18)
  fig|6666666.60966.peg.802	CDS	735097	735381	1	+	285	conserved hypothetical	-none-	D23_1c0809	Neut_0832
  							protein
  fig|6666666.60966.peg.803	CDS	735730	736488	1	+	759	hypothetical protein	-none-	D23_1c0810	Neut_0833
  fig|6666666.60966.peg.804	CDS	737600	736485	−2	−	1116	COGs COG1502	-none-	D23_1c0811	Neut_0834
  fig|6666666.60966.peg.805	CDS	738943	737585	−1	−	1359	hypothetical protein	-none-	D23_1c0812	Neut_0835
  fig|6666666.60966.peg.806	CDS	739386	739240	−3	−	147	hypothetical protein	-none-	D23_1c0813	NA
  fig|6666666.60966.peg.807	CDS	740790	739585	−3	−	1206	DnaJ domain protein	-none-	D23_1c0814	Neut_0836
  fig|6666666.60966.peg.809	CDS	742340	741159	−2	−	1182	Putative	-none-	D23_1c0815	Neut_0837
  							aminotransferase
  fig|6666666.60966.peg.810	CDS	744454	742337	−1	−	2118	Conserved domain	-none-	D23_1c0816	Neut_0838
  							protein
  fig|6666666.60966.peg.811	CDS	744823	744647	−1	−	177	hypothetical protein	-none-	D23_1c0817	NA
  fig|6666666.60966.peg.812	CDS	745953	745228	−3	−	726	hypothetical protein	-none-	D23_1c0818	Neut_0840
  fig|6666666.60966.peg.814	CDS	748473	746350	−3	−	2124	InterPro IPR000209	-none-	D23_1c0820	Neut_0841
  							COGs COG1404
  fig|6666666.60966.peg.815	CDS	748862	749245	2	+	384	ApaG protein	EC49-61	D23_1c0822	Neut_0842
  fig|6666666.60966.peg.816	CDS	749258	749992	2	+	735	Tetrapyrrole methylase	-none-	D23_1c0823	Neut_0843
  							family protein
  fig|6666666.60966.peg.817	CDS	751297	750077	−1	−	1221	Proton/glutamate	Glutamate and	D23_1c0824	Neut_0844
  							symport protein @	Aspartate uptake in
  							Sodium/glutamate	Bacteria
  							symport protein
  fig|6666666.60966.peg.818	CDS	752156	751611	−2	−	546	Cytochrome c-type	Biogenesis of c-type	D23_1c0825	Neut_0845
  							biogenesis protein ResA	cytochromes
  fig|6666666.60966.peg.819	CDS	754247	752304	−2	−	1944	Cytochrome c-type	Biogenesis of c-type	D23_1c0826	Neut_0846
  							biogenesis protein	cytochromes;
  							DsbD, protein-disulfide	<br>Periplasmic disulfide
  							reductase (EC 1.8.1.8)	interchange
  fig|6666666.60966.peg.820	CDS	754631	754260	−2	−	372	Periplasmic divalent	Copper homeostasis:	D23_1c0827	Neut_0847
  							cation tolerance protein	copper tolerance
  							CutA
  fig|6666666.60966.peg.821	CDS	754715	754909	2	+	195	FIG00859483:	-none-	D23_1c0828	Neut_0848
  							hypothetical protein
  fig|6666666.60966.peg.822	CDS	754952	755695	2	+	744	FIG00859295:	-none-	D23_1c0829	Neut_0849
  							hypothetical protein
  fig|6666666.60966.peg.823	CDS	756608	755733	−2	−	876	Staphylococcus	-none-	D23_1c0830	Neut_0850
  							nuclease (SNase)
  							domain
  fig|6666666.60966.peg.824	CDS	756650	757549	2	+	900	Methionine ABC	Methionine	D23_1c0831	Neut_0851
  							transporter ATP-binding	Biosynthesis;
  							protein	<br>Methionine
  								Degradation
  fig|6666666.60966.peg.825	CDS	757674	758384	3	+	711	Uncharacterized ABC	Lipopolysaccharide	D23_1c0832	Neut_0852
  							transporter, permease	assembly
  							component YrbE
  fig|6666666.60966.peg.826	CDS	758396	758863	2	+	468	Uncharacterized ABC	Lipopolysaccharide	D23_1c0833	Neut_0853
  							transporter, periplasmic	assembly
  							component YrbD
  fig|6666666.60966.peg.827	CDS	758879	759496	2	+	618	Uncharacterized ABC	Lipopolysaccharide	D23_1c0834	Neut_0854
  							transporter, auxiliary	assembly
  							component YrbC
  fig|6666666.60966.peg.828	CDS	759503	759817	2	+	315	STAS domain	-none-	D23_1c0835	Neut_0855
  fig|6666666.60966.peg.829	CDS	759879	760793	3	+	915	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c0836	Neut_0856
  							transport system,
  							ATPase component
  fig|6666666.60966.peg.830	CDS	760790	761545	2	+	756	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c0837	Neut_0857
  							transport system,
  							permease component
  fig|6666666.60966.peg.831	CDS	761590	761844	1	+	255	YrbA protein	Broadly distributed	D23_1c0838	Neut_0858
  								proteins not in
  								subsystems
  fig|6666666.60966.peg.832	CDS	763192	761900	−1	−	1293	Dihydrolipoamide	Dehydrogenase	D23_1c0839	Neut_0859
  							succinyltransferase	complexes; <br>TCA
  							component (E2) of 2-	Cycle
  							oxoglutarate
  							dehydrogenase
  							complex (EC 2.3.1.61)
  fig|6666666.60966.peg.833	CDS	766072	763214	−1	−	2859	2-oxoglutarate	Dehydrogenase	D23_1c0840	Neut_0860
  							dehydrogenase E1	complexes; <br>TCA
  							component (EC 1.2.4.2)	Cycle
  fig|6666666.60966.peg.834	CDS	767529	766234	−3	−	1296	Citrate synthase (si) (EC	TCA Cycle	D23_1c0841	Neut_0861
  							2.3.3.1)
  fig|6666666.60966.peg.835	CDS	767808	767575	−3	−	234	YgfY COG2938	-none-	D23_1c0842	Neut_0862
  fig|6666666.60966.peg.836	CDS	768500	767805	−2	−	696	Succinate	5-FCL-like protein;	D23_1c0843	Neut_0863
  							dehydrogenase iron-	<br>Succinate
  							sulfur protein (EC	dehydrogenase;
  							1.3.99.1)	<br>TCA Cycle
  fig|6666666.60966.peg.837	CDS	770059	768629	−1	−	1431	Threonine synthase (EC	Threonine and	D23_1c0844	Neut_0864
  							4.2.3.1)	Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.839	CDS	771500	770184	−2	−	1317	Homoserine	Methionine	D23_1c0845	Neut_0865
  							dehydrogenase (EC	Biosynthesis;
  							1.1.1.3)	<br>Threonine and
  								Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.840	CDS	772833	771607	−3	−	1227	Aspartate	CBSS-216591.1.peg.168;	D23_1c0846	Neut_0866
  							aminotransferase (EC	<br>Glutamine,
  							2.6.1.1)	Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis;
  								<br>Threonine and
  								Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.841	CDS	773025	773147	3	+	123	hypothetical protein	-none-	D23_1c0847	NA
  fig|6666666.60966.peg.842	CDS	773125	773508	1	+	384	Membrane protein	-none-	D23_1c0848	Neut_0867
  fig|6666666.60966.peg.843	CDS	773605	775980	1	+	2376	Phosphoenolpyruvate	A Hypothetical that	D23_1c0849	Neut_0868
  							synthase (EC 2.7.9.2)	Clusters with PEP
  								Synthase; <br>Glycolysis
  								and Gluconeogenesis;
  								<br>Pyruvate
  								metabolism I:
  								anaplerotic reactions,
  								PEP
  fig|6666666.60966.peg.844	CDS	775985	776812	2	+	828	FIG137360:	A Hypothetical that	D23_1c0850	Neut_0869
  							hypothetical protein	Clusters with PEP
  								Synthase
  fig|6666666.60966.peg.845	CDS	777372	776854	−3	−	519	NLP/P60	-none-	D23_1c0851	Neut_0870
  fig|6666666.60966.peg.846	CDS	779204	777507	−2	−	1698	Glutaminyl-tRNA	tRNA aminoacylation,	D23_1c0852	Neut_0871
  							synthetase (EC 6.1.1.18)	Glu and Gln
  fig|6666666.60966.peg.847	CDS	779394	779245	−3	−	150	hypothetical protein	-none-	D23_1c0853	NA
  fig|6666666.60966.peg.848	CDS	779393	780991	2	+	1599	Lysyl-tRNA synthetase	tRNA aminoacylation,	D23_1c0854	Neut_0872
  							(class II) (EC 6.1.1.6)	Lys
  fig|6666666.60966.peg.849	CDS	781093	781749	1	+	657	FIG00858849:	-none-	D23_1c0855	Neut_0873
  							hypothetical protein
  fig|6666666.60966.peg.850	CDS	781999	782385	1	+	387	hypothetical protein	-none-	D23_1c0856	NA
  fig|6666666.60966.peg.851	CDS	782415	782747	3	+	333	Mobile element protein	-none-	D23_1c0857	NA
  fig|6666666.60966.peg.852	CDS	782952	783485	3	+	534	hypothetical protein	-none-	D23_1c0858	Neut_0875
  fig|6666666.60966.peg.853	CDS	783597	783767	3	+	171	hypothetical protein	-none-	D23_1c0859	NA
  fig|6666666.60966.peg.854	CDS	784671	784048	−3	−	624	Trp repressor binding	-none-	D23_1c0860	Neut_0876
  							protein
  fig|6666666.60966.peg.855	CDS	785041	784757	−1	−	285	Mobile element protein	-none-	D23_1c0861	NA
  fig|6666666.60966.peg.857	CDS	787300	785558	−1	−	1743	Beta-glucosidase (EC	-none-	D23_1c0862	Neut_0879
  							3.2.1.21)
  fig|6666666.60966.peg.858	CDS	788430	787327	−3	−	1104	Mobile element protein	-none-	D23_1c0863	Neut_1278
  fig|6666666.60966.peg.859	CDS	789557	789045	−2	−	513	Mobile element protein	-none-	D23_1c0864	Neut_1624
  fig|6666666.60966.peg.860	CDS	789894	789589	−3	−	306	Mobile element protein	-none-	D23_1c0865	Neut_1371
  fig|6666666.60966.peg.861	CDS	790136	789951	−2	−	186	Mobile element protein	-none-	D23_1c0866	Neut_2500
  fig|6666666.60966.peg.863	CDS	792236	790869	−2	−	1368	ATP-dependent RNA	ATP-dependent RNA	D23_1c0869	Neut_0889
  							helicase RhlE	helicases, bacterial
  fig|6666666.60966.peg.865	CDS	794169	792502	−3	−	1668	ATPase components of	-none-	D23_1c0871	Neut_0890
  							ABC transporters with
  							duplicated ATPase
  							domains
  fig|6666666.60966.peg.867	CDS	794389	794568	1	+	180	hypothetical protein	-none-	D23_1c0872	NA
  fig|6666666.60966.peg.868	CDS	795019	795636	1	+	618	FIG123464:	Cell wall related cluster	D23_1c0873	Neut_0891
  							Polysaccharide export
  							protein
  fig|6666666.60966.peg.869	CDS	795679	797223	1	+	1545	Lipopolysaccharide	Cell wall related cluster	D23_1c0874	Neut_0892
  							biosynthesis chain
  							length determinant
  							protein
  fig|6666666.60966.peg.870	CDS	797305	798243	1	+	939	Protein-tyrosine kinase	Cell wall related cluster	D23_1c0875	Neut_0893
  							(EC 2.7.1.112)
  fig|6666666.60966.peg.871	CDS	798243	799823	3	+	1581	Glycine-rich cell wall	Cell wall related cluster	D23_1c0876	Neut_0894
  							structural protein
  							precursor
  fig|6666666.60966.peg.872	CDS	799837	800670	1	+	834	FIG022606: AAA ATPase	Cell wall related cluster	D23_1c0877	Neut_0895
  fig|6666666.60966.peg.873	CDS	800676	801515	3	+	840	FIG004655:	Cell wall related cluster	D23_1c0878	Neut_0896
  							Polysaccharide
  							deacetylase
  fig|6666666.60966.peg.875	CDS	801827	802591	2	+	765	FIG070318:	Cell wall related cluster	D23_1c0879	Neut_0897
  							hypothetical protein
  fig|6666666.60966.peg.876	CDS	802597	803808	1	+	1212	FIG137776:	Cell wall related cluster	D23_1c0880	Neut_0898
  							Glycosyltransferase
  fig|6666666.60966.peg.877	CDS	803877	805457	3	+	1581	Eight transmembrane	Cell wall related cluster;	D23_1c0881	Neut_0899
  							protein EpsH/EpsI	<br>Cell wall related
  							protein	cluster
  fig|6666666.60966.peg.878	CDS	805493	806635	2	+	1143	FIG040338: Glycosyl	Cell wall related cluster	D23_1c0882	Neut_0900
  							transferase
  fig|6666666.60966.peg.879	CDS	806677	808611	1	+	1935	Asparagine synthetase	Cell wall related cluster;	D23_1c0884	Neut_0901
  							[glutamine-hydrolyzing]	<br>Glutamine,
  							(EC 6.3.5.4) AsnH	Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.880	CDS	808662	809654	3	+	993	FIG00859061:	-none-	D23_1c0885	Neut_0902
  							hypothetical protein
  fig|6666666.60966.peg.881	CDS	809654	810592	2	+	939	FIG00859041:	-none-	D23_1c0886	Neut_0903
  							hypothetical protein
  fig|6666666.60966.peg.882	CDS	810623	811849	2	+	1227	hypothetical protein	-none-	D23_1c0887	Neut_0903
  fig|6666666.60966.peg.883	CDS	812814	811852	−3	−	963	Mobile element protein	-none-	D23_1c0888	Neut_1746
  fig|6666666.60966.peg.884	CDS	813957	813094	−3	−	864	Mobile element protein	-none-	D23_1c0889	Neut_2192
  fig|6666666.60966.peg.885	CDS	814250	813954	−2	−	297	hypothetical protein	-none-	D23_1c0890	Neut_2193
  fig|6666666.60966.peg.887	CDS	814624	815706	1	+	1083	glycosyltransferase	-none-	D23_1c0891	NA
  fig|6666666.60966.peg.888	CDS	817016	816339	−2	−	678	hypothetical protein	-none-	D23_1c0892	NA
  fig|6666666.60966.peg.889	CDS	818253	817114	−3	−	1140	hypothetical protein	-none-	D23_1c0893	Neut_0906
  fig|6666666.60966.peg.890	CDS	819313	818282	−1	−	1032	hypothetical protein	-none-	D23_1c0894	Neut_2116
  fig|6666666.60966.peg.891	CDS	820446	819313	−3	−	1134	hypothetical protein	-none-	D23_1c0895	Neut_0905
  fig|6666666.60966.peg.892	CDS	821935	820481	−1	−	1455	hypothetical protein	-none-	D23_1c0896	Neut_0909
  fig|6666666.60966.peg.893	CDS	823840	822074	−1	−	1767	Asparagine synthetase	Cyanophycin	D23_1c0897	Neut_0910
  							[glutamine-hydrolyzing]	Metabolism;
  							(EC 6.3.5.4)	<br>Glutamate and
  								Aspartate uptake in
  								Bacteria; <br>Glutamine,
  								Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.895	CDS	824361	825170	3	+	810	hypothetical protein	-none-	D23_1c0898	Neut_0911
  fig|6666666.60966.peg.896	CDS	825186	826454	3	+	1269	hypothetical protein	-none-	D23_1c0899	Neut_0912
  fig|6666666.60966.peg.897	CDS	827356	826457	−1	−	900	hypothetical protein	-none-	D23_1c0900	Neut_0913
  fig|6666666.60966.peg.898	CDS	827907	827404	−3	−	504	Low molecular weight	LMPTP YfkJ cluster;	D23_1c0901	Neut_0914
  							protein tyrosine	<br>Protein deglycation
  							phosphatase (EC
  							3.1.3.48)
  fig|6666666.60966.peg.899	CDS	828032	829777	2	+	1746	ABC transporter, fused	-none-	D23_1c0902	Neut_0915
  							permease and ATPase
  							domains
  fig|6666666.60966.peg.900	CDS	830559	829798	−3	−	762	Sulfur carrier protein	Thiamin biosynthesis	D23_1c0903	Neut_0916
  							adenylyltransferase
  							ThiF
  fig|6666666.60966.peg.901	CDS	832018	830588	−1	−	1431	Carboxyl-terminal	Phosphoglycerate	D23_1c0904	Neut_0917
  							protease (EC	mutase protein family
  							3.4.21.102)
  fig|6666666.60966.peg.902	CDS	833380	832100	−1	−	1281	Lipoprotein NlpD	Stationary phase repair	D23_1c0905	Neut_0918
  								cluster
  fig|6666666.60966.peg.903	CDS	834129	833380	−3	−	750	Phosphoglycerate	Glycolysis and	D23_1c0906	Neut_0919
  							mutase (EC 5.4.2.1)	Gluconeogenesis;
  								<br>Phosphoglycerate
  								mutase protein family
  fig|6666666.60966.peg.904	CDS	834328	835086	1	+	759	Triosephosphate	CBSS-	D23_1c0907	Neut_0920
  							isomerase (EC 5.3.1.1)	331978.3.peg.2915;
  								<br>Calvin-Benson cycle;
  								<br>Glycolysis and
  								Gluconeogenesis
  fig|6666666.60966.peg.905	CDS	835105	835470	1	+	366	Preprotein translocase	CBSS-331978.3.peg.2915	D23_1c0908	Neut_0921
  							subunit SecG (TC
  							3.A.5.1.1)
  fig|6666666.60966.peg.906	CDS	835677	836045	3	+	369	NADH ubiquinone	NADH ubiquinone	D23_1c0910	Neut_0922
  							oxidoreductase chain A	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.907	CDS	836049	836525	3	+	477	NADH-ubiquinone	NADH ubiquinone	D23_1c0911	Neut_0923
  							oxidoreductase chain B	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.908	CDS	836535	837155	3	+	621	NADH-ubiquinone	NADH ubiquinone	D23_1c0912	Neut_0924
  							oxidoreductase chain C	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.909	CDS	837213	838466	3	+	1254	NADH-ubiquinone	NADH ubiquinone	D23_1c0913	Neut_0925
  							oxidoreductase chain D	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.910	CDS	838475	838951	2	+	477	NADH-ubiquinone	NADH ubiquinone	D23_1c0914	Neut_0926
  							oxidoreductase chain E	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.911	CDS	838948	840225	1	+	1278	NADH-ubiquinone	NADH ubiquinone	D23_1c0915	Neut_0927
  							oxidoreductase chain F	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.912	CDS	840287	842692	2	+	2406	NADH-ubiquinone	NADH ubiquinone	D23_1c0917	Neut_0928
  							oxidoreductase chain G	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.913	CDS	842717	843814	2	+	1098	NADH-ubiquinone	NADH ubiquinone	D23_1c0918	Neut_0929
  							oxidoreductase chain H	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.914	CDS	843832	844320	1	+	489	NADH-ubiquinone	NADH ubiquinone	D23_1c0919	Neut_0930
  							oxidoreductase chain I	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.915	CDS	844339	844944	1	+	606	NADH-ubiquinone	NADH ubiquinone	D23_1c0920	Neut_0931
  							oxidoreductase chain J	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.916	CDS	845000	845305	2	+	306	NADH-ubiquinone	NADH ubiquinone	D23_1c0921	Neut_0932
  							oxidoreductase chain K	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.917	CDS	845366	847312	2	+	1947	NADH-ubiquinone	NADH ubiquinone	D23_1c0922	Neut_0933
  							oxidoreductase chain L	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.918	CDS	847401	848882	3	+	1482	NADH-ubiquinone	NADH ubiquinone	D23_1c0923	Neut_0934
  							oxidoreductase chain M	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.919	CDS	848945	850390	2	+	1446	NADH-ubiquinone	NADH ubiquinone	D23_1c0924	Neut_0935
  							oxidoreductase chain N	oxidoreductase;
  							(EC 1.6.5.3)	<br>Respiratory
  								Complex I
  fig|6666666.60966.peg.920	CDS	851362	850412	−1	−	951	L-sorbosone	-none-	D23_1c0925	Neut_0936
  							dehydrogenase
  fig|6666666.60966.peg.921	CDS	851619	853541	3	+	1923	Chaperone protein	Protein chaperones	D23_1c0926	Neut_0937
  							HtpG
  fig|6666666.60966.peg.922	CDS	853878	854918	3	+	1041	WD40 domain protein	-none-	D23_1c0927	Neut_0938
  							beta Propeller
  fig|6666666.60966.peg.924	CDS	855176	855598	2	+	423	Mobile element protein	-none-	D23_1c0929	Neut_0939
  fig|6666666.60966.peg.925	CDS	855805	858447	1	+	2643	Hopanoid-associated	Hopanes	D23_1c0930	Neut_0940
  							RND transporter, HpnN
  fig|6666666.60966.peg.926	CDS	859079	858483	−2	−	597	DedA protein	Colicin V and Bacteriocin	D23_1c0931	Neut_0941
  								Production Cluster;
  								<br>DedA family of inner
  								membrane proteins;
  								<br>Uptake of selenate
  								and selenite
  fig|6666666.60966.peg.928	CDS	861652	859424	−1	−	2229	Probable	-none-	D23_1c0933	Neut_0942
  							transmembrane protein
  fig|6666666.60966.peg.929	CDS	861629	861754	2	+	126	hypothetical protein	-none-	D23_1c0934	NA
  fig|6666666.60966.peg.930	CDS	861857	861720	−2	−	138	hypothetical protein	-none-	D23_1c0935	NA
  fig|6666666.60966.peg.931	CDS	861928	862341	1	+	414	Protoporphyrinogen IX	Heme and Siroheme	D23_1c0936	Neut_0943
  							oxidase, novel form,	Biosynthesis
  							HemJ (EC 1.3.—.—)
  fig|6666666.60966.peg.932	CDS	862893	862363	−3	−	531	Peptide deformylase	Bacterial RNA-	D23_1c0937	Neut_0944
  							(EC 3.5.1.88)	metabolizing Zn-
  								dependent hydrolases;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.933	CDS	863632	862886	−1	−	747	5&#39;-	-none-	D23_1c0938	Neut_0945
  							methylthioadenosine
  							phosphorylase (EC
  							2.4.2.28)
  fig|6666666.60966.peg.934	CDS	865800	863752	−3	−	2049	DNA ligase (EC 6.5.1.2)	DNA Repair Base	D23_1c0939	Neut_0946
  								Excision
  fig|6666666.60966.peg.935	CDS	865959	866654	3	+	696	hypothetical protein	-none-	D23_1c0940	Neut_0947
  fig|6666666.60966.peg.936	CDS	867392	867021	−2	−	372	Flagellar biosynthesis	Flagellum	D23_1c0941	Neut_0948
  							protein FliT
  fig|6666666.60966.peg.937	CDS	867859	867389	−1	−	471	Flagellar biosynthesis	Flagellum	D23_1c0942	Neut_0949
  							protein FliS
  fig|6666666.60966.peg.938	CDS	869359	867917	−1	−	1443	Flagellar hook-	Flagellum	D23_1c0943	Neut_0950
  							associated protein FliD
  fig|6666666.60966.peg.939	CDS	870186	869716	−3	−	471	hypothetical protein	-none-	D23_1c0944	Neut_0951
  fig|6666666.60966.peg.940	CDS	870616	870891	1	+	276	hypothetical protein	-none-	D23_1c0945	Neut_0952
  fig|6666666.60966.peg.941	CDS	871905	870955	−3	−	951	Glutathione synthetase	Glutathione:	D23_1c0946	Neut_0953
  							(EC 6.3.2.3)	Biosynthesis and
  								gamma-glutamyl cycle;
  								<br>Heat shock dnaK
  								gene cluster extended
  fig|6666666.60966.peg.942	CDS	873212	871902	−2	−	1311	Glutamate--cysteine	Glutathione:	D23_1c0947	Neut_0954
  							ligase (EC 6.3.2.2),	Biosynthesis and
  							divergent, of Alpha- and	gamma-glutamyl cycle
  							Beta-proteobacteria
  							type
  fig|6666666.60966.peg.944	CDS	873411	873722	3	+	312	LSU ribosomal protein	CBSS-176279.3.peg.868	D23_1c0949	Neut_0955
  							L21p
  fig|6666666.60966.peg.945	CDS	873734	873991	2	+	258	LSU ribosomal protein	CBSS-176279.3.peg.868	D23_1c0950	Neut_0956
  							L27p
  fig|6666666.60966.peg.946	CDS	873991	874104	1	+	114	hypothetical protein	-none-	D23_1c0951	NA
  fig|6666666.60966.peg.947	CDS	874121	875152	2	+	1032	GTP-binding protein	CBSS-176279.3.peg.868;	D23_1c0952	Neut_0957
  							Obg	<br>Universal GTPases
  fig|6666666.60966.peg.948	CDS	875158	876279	1	+	1122	Glutamate 5-kinase (EC	Proline Synthesis;	D23_1c0953	Neut_0958
  							2.7.2.11)/RNA-binding	<br>Proline Synthesis
  							C-terminal domain PUA
  fig|6666666.60966.peg.949	CDS	876330	877331	3	+	1002	InterPro IPR000379	-none-	D23_1c0954	Neut_0959
  							COGs COG0429
  fig|6666666.60966.peg.950	CDS	877428	878744	3	+	1317	Phosphate regulon	High affinity phosphate	D23_1c0955	Neut_0960
  							sensor protein PhoR	transporter and control
  							(SphS) (EC 2.7.13.3)	of PHO regulon;
  								<br>PhoR-PhoB two-
  								component regulatory
  								system; <br>Phosphate
  								metabolism
  fig|6666666.60966.peg.951	CDS	879101	879343	2	+	243	RNA-binding protein	Hfl operon;	D23_1c0957	Neut_0961
  							Hfq	<br>Polyadenylation
  								bacterial; <br>Possible
  								RNA degradation cluster
  fig|6666666.60966.peg.952	CDS	879345	880478	3	+	1134	GTP-binding protein	Hfl operon; <br>Possible	D23_1c0958	Neut_0962
  							HflX	RNA degradation cluster;
  								<br>Universal GTPases
  fig|6666666.60966.peg.953	CDS	880535	881725	2	+	1191	HflK protein	Hfl operon; <br>Scaffold	D23_1c0959	Neut_0963
  								proteins for [4Fe—4S]
  								cluster assembly (MRP
  								family)
  fig|6666666.60966.peg.954	CDS	881725	882603	1	+	879	HflC protein	Hfl operon; <br>Scaffold	D23_1c0960	Neut_0964
  								proteins for [4Fe—4S]
  								cluster assembly (MRP
  								family)
  fig|6666666.60966.peg.955	CDS	882732	882917	3	+	186	Putative inner	Hfl operon	D23_1c0961	Neut_0965
  							membrane protein YjeT
  							(clustered with HflC)
  fig|6666666.60966.peg.956	CDS	882992	884164	2	+	1173	ATP	Histidine Biosynthesis	D23_1c0962	Neut_0966
  							phosphoribosyltransferase
  							regulatory subunit
  							(EC 2.4.2.17)
  fig|6666666.60966.peg.957	CDS	884298	885596	3	+	1299	Adenylosuccinate	Purine conversions	D23_1c0963	Neut_0967
  							synthetase (EC 6.3.4.4)
  fig|6666666.60966.peg.958	CDS	885982	885665	−1	−	318	FIG00858510:	-none-	D23_1c0964	Neut_0968
  							hypothetical protein
  fig|6666666.60966.peg.959	CDS	886361	886164	−2	−	198	FIG00859475:	-none-	D23_1c0966	Neut_0969
  							hypothetical protein
  fig|6666666.60966.peg.961	CDS	889010	886635	−2	−	2376	ATP-dependent	Proteasome bacterial;	D23_1c0967	Neut_0970
  							protease La (EC	<br>Proteolysis in
  							3.4.21.53) Type I	bacteria, ATP-dependent
  fig|6666666.60966.peg.962	CDS	889609	889160	−1	−	450	CBS domain protein	-none-	D23_1c0968	Neut_0971
  fig|6666666.60966.peg.963	CDS	890160	889657	−3	−	504	hypothetical protein	-none-	D23_1c0969	Neut_0972
  fig|6666666.60966.peg.964	CDS	890193	890345	3	+	153	hypothetical protein	-none-	D23_1c0970	NA
  fig|6666666.60966.peg.965	CDS	890326	890442	1	+	117	hypothetical protein	-none-	D23_1c0971	NA
  fig|6666666.60966.peg.966	CDS	890503	891663	1	+	1161	ABC-transporter	-none-	D23_1c0972	Neut_0973
  							permease protein
  fig|6666666.60966.peg.967	CDS	891663	892352	3	+	690	ABC transporter, ATP-	-none-	D23_1c0973	Neut_0974
  							binding protein
  fig|6666666.60966.peg.968	CDS	892533	893492	3	+	960	Membrane protein	-none-	D23_1c0974	Neut_0975
  fig|6666666.60966.peg.969	CDS	895517	893706	−2	−	1812	Sodium/hydrogen	-none-	D23_1c0976	Neut_0976
  							exchanger family
  							protein
  fig|6666666.60966.peg.970	CDS	895888	896574	1	+	687	FIG00859851:	-none-	D23_1c0978	Neut_0977
  							hypothetical protein
  fig|6666666.60966.peg.971	CDS	897991	897029	−1	−	963	Mobile element protein	-none-	D23_1c0979	Neut_0978
  fig|6666666.60966.peg.972	CDS	899539	898112	−1	−	1428	Pyruvate kinase (EC	Glycerate metabolism;	D23_1c0980	Neut_0979
  							2.7.1.40)	<br>Glycolysis and
  								Gluconeogenesis;
  								<br>Pyruvate
  								metabolism I:
  								anaplerotic reactions,
  								PEP
  fig|6666666.60966.peg.973	CDS	899838	899563	−3	−	276	hypothetical protein	-none-	D23_1c0981	Neut_0980
  fig|6666666.60966.peg.974	CDS	900234	900398	3	+	165	hypothetical protein	-none-	D23_1c0982	NA
  fig|6666666.60966.peg.975	CDS	903871	900686	−1	−	3186	TonB-dependent	Ton and Tol transport	D23_1c0983	Neut_1076
  							receptor	systems
  fig|6666666.60966.peg.976	CDS	904856	903873	−2	−	984	hypothetical protein	-none-	D23_1c0984	Neut_1077
  fig|6666666.60966.peg.977	CDS	906168	904861	−3	−	1308	putative helicase	-none-	D23_1c0985	Neut_1078
  fig|6666666.60966.peg.978	CDS	908497	906392	−1	−	2106	sucrose synthase	-none-	D23_1c0988	Neut_1079
  fig|6666666.60966.peg.979	CDS	910925	908787	−2	−	2139	Sucrose phosphate	-none-	D23_1c0989	Neut_1080
  							synthase
  fig|6666666.60966.peg.980	CDS	911865	910936	−3	−	930	Fructokinase (EC	-none-	D23_1c0990	Neut_1081
  							2.7.1.4)
  fig|6666666.60966.peg.981	CDS	914147	912060	−2	−	2088	Excinuclease ABC	DNA repair, UvrABC	D23_1c0991	Neut_1082
  							subunit B	system
  fig|6666666.60966.peg.982	CDS	914226	915419	3	+	1194	Aspartate	CBSS-216591.1.peg.168;	D23_1c0992	Neut_1083
  							aminotransferase (EC	<br>Glutamine,
  							2.6.1.1)	Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis;
  								<br>Threonine and
  								Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.983	CDS	915551	915688	2	+	138	hypothetical protein	-none-	D23_1c0993	NA
  fig|6666666.60966.peg.984	CDS	915891	916277	3	+	387	Mobile element protein	-none-	D23_1c0994	Neut_0884
  fig|6666666.60966.peg.985	CDS	916240	916695	1	+	456	Mobile element protein	-none-	D23_1c0995	Neut_2502
  fig|6666666.60966.peg.986	CDS	916764	917726	3	+	963	Mobile element protein	-none-	D23_1c0996	Neut_1862
  fig|6666666.60966.peg.987	CDS	918535	918419	−1	−	117	hypothetical protein	-none-	D23_1c0997	NA
  fig|6666666.60966.peg.988	CDS	919358	918504	−2	−	855	DNA-directed RNA	RNA polymerase	D23_1c0998	NA
  							polymerase alpha	bacterial
  							subunit (EC 2.7.7.6)
  fig|6666666.60966.peg.989	CDS	919525	919409	−1	−	117	hypothetical protein	-none-	D23_1c0999	Neut_1085
  fig|6666666.60966.peg.990	CDS	919587	919787	3	+	201	Glutathione synthetase	Glutathione:	D23_1c0999	Neut_1085
  							(EC 6.3.2.3)	Biosynthesis and
  								gamma-glutamyl cycle;
  								<br>Heat shock dnaK
  								gene cluster extended
  fig|6666666.60966.peg.991	CDS	919919	920287	2	+	369	FIG00858546:	-none-	D23_1c1000	Neut_1086
  							hypothetical protein
  fig|6666666.60966.peg.992	CDS	920496	921119	3	+	624	bacteriocin resistance	-none-	D23_1c1001	Neut_1087
  							protein, putative
  fig|6666666.60966.peg.993	CDS	921168	921644	3	+	477	FIG00859915:	-none-	D23_1c1002	Neut_1088
  							hypothetical protein
  fig|6666666.60966.peg.994	CDS	921659	923050	2	+	1392	FIG00858837:	-none-	D23_1c1003	Neut_1089
  							hypothetical protein
  fig|6666666.60966.peg.995	CDS	923533	923105	−1	−	429	Zn-dependent	-none-	D23_1c1004	Neut_1090
  							hydrolases, including
  							glyoxylases
  fig|6666666.60966.peg.996	CDS	923845	924936	1	+	1092	Diaminohydroxyphosphoribosylaminopyrimidine	Riboflavin, FMN and FAD	D23_1c1005	Neut_1091
  							deaminase (EC	metabolism;
  							3.5.4.26)/5-amino-6-	<br>Riboflavin, FMN and
  							(5-	FAD metabolism;
  							phosphoribosylamino)uracil	<br>Riboflavin, FMN and
  							reductase (EC	FAD metabolism in
  							1.1.1.193)	plants; <br>Riboflavin,
  								FMN and FAD
  								metabolism in plants;
  								<br>Riboflavin synthesis
  								cluster; <br>Riboflavin
  								synthesis cluster
  fig|6666666.60966.peg.997	CDS	925042	926262	1	+	1221	Glycosyl transferase,	-none-	D23_1c1006	Neut_1092
  							group 1
  fig|6666666.60966.peg.998	CDS	926363	927685	2	+	1323	UDP-glucose	-none-	D23_1c1007	Neut_1093
  							dehydrogenase (EC
  							1.1.1.22)
  fig|6666666.60966.peg.999	CDS	928127	928318	2	+	192	hypothetical protein	-none-	D23_1c1009	Neut_1095
  fig|6666666.60966.peg.1000	CDS	928500	928315	−3	−	186	hypothetical protein	-none-	D23_1c1010	NA
  fig|6666666.60966.peg.1002	CDS	929085	930362	3	+	1278	InterPro IPR001296	-none-	D23_1c1011	Neut_1096
  							COGs COG0438
  fig|6666666.60966.peg.1003	CDS	930467	931729	2	+	1263	Coenzyme F390	-none-	D23_1c1012	Neut_1097
  							synthetase
  fig|6666666.60966.peg.1004	CDS	932351	931731	−2	−	621	exopolysaccharide	-none-	D23_1c1013	Neut_1098
  							synthesis protein ExoD-
  							related protein
  fig|6666666.60966.peg.1005	CDS	932631	933110	3	+	480	FIG00859304:	-none-	D23_1c1014	Neut_1099
  							hypothetical protein
  fig|6666666.60966.peg.1006	CDS	933200	934357	2	+	1158	FIG010505:	-none-	D23_1c1015	Neut_1100
  							hypothetical protein
  fig|6666666.60966.peg.1007	CDS	934409	935224	2	+	816	FIG00858774:	-none-	D23_1c1016	Neut_1101
  							hypothetical protein
  fig|6666666.60966.peg.1008	CDS	935243	936316	2	+	1074	Probable	-none-	D23_1c1017	Neut_1102
  							transmembrane protein
  fig|6666666.60966.peg.1009	CDS	936361	937383	1	+	1023	FIG000906: Predicted	-none-	D23_1c1018	Neut_1103
  							Permease
  fig|6666666.60966.peg.1010	CDS	937391	938608	2	+	1218	CDP-alcohol	-none-	D23_1c1019	Neut_1104
  							phosphatidyltransferase
  fig|6666666.60966.peg.1011	CDS	938637	939593	3	+	957	FIG00480695:	-none-	D23_1c1020	Neut_1105
  							hypothetical protein
  fig|6666666.60966.peg.1012	CDS	939607	940575	1	+	969	FIG00859274:	-none-	D23_1c1021	Neut_1106
  							hypothetical protein
  fig|6666666.60966.peg.1013	CDS	940636	941283	1	+	648	FIG00859276:	-none-	D23_1c1022	Neut_1107
  							hypothetical protein
  fig|6666666.60966.peg.1014	CDS	941749	941294	−1	−	456	Zn-ribbon-containing,	DNA replication cluster 1	D23_1c1023	Neut_1108
  							possibly RNA-binding
  							protein and truncated
  							derivatives
  fig|6666666.60966.peg.1016	CDS	942037	942186	1	+	150	hypothetical protein	-none-	D23_1c1024	NA
  fig|6666666.60966.peg.1017	CDS	942242	944971	2	+	2730	Protein export	-none-	D23_1c1025	Neut_1109
  							cytoplasm protein SecA
  							ATPase RNA helicase
  							(TC 3.A.5.1.1)
  fig|6666666.60966.peg.1018	CDS	945151	945756	1	+	606	Ubiquinol-cytochrome C	Ubiquinone	D23_1c1026	Neut_1110
  							reductase iron-sulfur	Menaquinone-
  							subunit (EC 1.10.2.2)	cytochrome c reductase
  								complexes
  fig|6666666.60966.peg.1019	CDS	945758	947005	2	+	1248	Ubiquinol--cytochrome	Ubiquinone	D23_1c1027	Neut_1111
  							c reductase,	Menaquinone-
  							cytochrome B subunit	cytochrome c reductase
  							(EC 1.10.2.2)	complexes
  fig|6666666.60966.peg.1020	CDS	947002	947706	1	+	705	ubiquinol cytochrome C	Ubiquinone	D23_1c1028	Neut_1112
  							oxidoreductase,	Menaquinone-
  							cytochrome C1 subunit	cytochrome c reductase
  								complexes
  fig|6666666.60966.peg.1021	CDS	947758	948357	1	+	600	Stringent starvation	Carbon Starvation	D23_1c1029	Neut_1113
  							protein A
  fig|6666666.60966.peg.1023	CDS	949015	949215	1	+	201	hypothetical protein	-none-	D23_1c1031	Neut_2449
  fig|6666666.60966.peg.1024	CDS	949203	949682	3	+	480	Mobile element protein	-none-	D23_1c1032	Neut_2417
  fig|6666666.60966.peg.1025	CDS	950361	950651	3	+	291	Mobile element protein	-none-	D23_1c1034	Neut_2190
  fig|6666666.60966.peg.1026	CDS	951943	950696	−1	−	1248	Mobile element protein	-none-	D23_1c1035	Neut_0357
  fig|6666666.60966.peg.1027	CDS	952378	952208	−1	−	171	hypothetical protein	-none-	D23_1c1036	NA
  fig|6666666.60966.peg.1028	CDS	953114	952689	−2	−	426	C4-type zinc finger	Zinc regulated enzymes	D23_1c1037	Neut_1117
  							protein, DksA/TraR
  							family
  fig|6666666.60966.peg.1029	CDS	955194	953479	−3	−	1716	Adenylate cyclase (EC	cAMP signaling in	D23_1c1038	Neut_1118
  							4.6.1.1)	bacteria
  fig|6666666.60966.peg.1030	CDS	956008	955157	−1	−	852	HD domain	-none-	D23_1c1039	Neut_1119
  fig|6666666.60966.peg.1032	CDS	956563	957111	1	+	549	InterPro IPR000345	-none-	D23_1c1042	Neut_1126
  fig|6666666.60966.peg.1033	CDS	958663	957200	−1	−	1464	3-polyprenyl-4-	Ubiquinone	D23_1c1043	Neut_1127
  							hydroxybenzoate	Biosynthesis;
  							carboxy-lyase (EC	<br>Ubiquinone
  							4.1.1.—)	Biosynthesis-gjo
  fig|6666666.60966.peg.1034	CDS	959616	958756	−3	−	861	4-hydroxybenzoate	Ubiquinone	D23_1c1045	Neut_1128
  							polyprenyltransferase	Biosynthesis;
  							(EC 2.5.1.39)	<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.1035	CDS	960159	959695	−3	−	465	Chorismate--pyruvate	Ubiquinone	D23_1c1046	Neut_1129
  							lyase (EC 4.1.3.40)	Biosynthesis;
  								<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.1036	CDS	960706	960299	−1	−	408	twitching motility	-none-	D23_1c1047	Neut_1130
  							protein PilG
  fig|6666666.60966.peg.1037	CDS	962283	960874	−3	−	1410	Potassium uptake	Hyperosmotic potassium	D23_1c1048	Neut_1131
  							protein TrkH	uptake; <br>Potassium
  								homeostasis;
  								<br>Potassium
  								homeostasis
  fig|6666666.60966.peg.1038	CDS	963803	962355	−2	−	1449	Trk system potassium	Bacterial RNA-	D23_1c1049	Neut_1132
  							uptake protein TrkA	metabolizing Zn-
  								dependent hydrolases;
  								<br>Hyperosmotic
  								potassium uptake;
  								<br>Possible RNA
  								degradation cluster;
  								<br>Potassium
  								homeostasis;
  								<br>Potassium
  								homeostasis
  fig|6666666.60966.peg.1039	CDS	965344	964070	−1	−	1275	FIG00858490:	-none-	D23_1c1050	Neut_1133
  							hypothetical protein
  fig|6666666.60966.peg.1040	CDS	965355	965495	3	+	141	hypothetical protein	-none-	D23_1c1051	NA
  fig|6666666.60966.peg.1041	CDS	965968	965477	−1	−	492	Starvation lipoprotein	Carbon Starvation	D23_1c1052	Neut_1134
  							Slp paralog
  fig|6666666.60966.peg.1042	CDS	966371	967021	2	+	651	Septum site-	Bacterial Cell Division;	D23_1c1054	Neut_1135
  							determining protein	<br>Bacterial
  							MinC	Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>Septum site-
  								determining cluster Min
  fig|6666666.60966.peg.1043	CDS	967047	967856	3	+	810	Septum site-	Bacterial Cell Division;	D23_1c1055	Neut_1136
  							determining protein	<br>Bacterial
  							MinD	Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>Septum site-
  								determining cluster Min
  fig|6666666.60966.peg.1044	CDS	967856	968152	2	+	297	Cell division topological	Bacterial Cell Division;	D23_1c1056	Neut_1137
  							specificity factor MinE	<br>Bacterial
  								Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>Septum site-
  								determining cluster Min
  fig|6666666.60966.peg.1045	CDS	968284	968895	1	+	612	Outer membrane	A Gammaproteobacteria	D23_1c1057	Neut_1138
  							lipoprotein LolB	Cluster Relating to
  								Translation;
  								<br>Lipopolysaccharide
  								assembly;
  								<br>Lipoprotein sorting
  								system
  fig|6666666.60966.peg.1046	CDS	968920	969756	1	+	837	4-diphosphocytidyl-2-C-	A Gammaproteobacteria	D23_1c1058	Neut_1139
  							methyl-D-erythritol	Cluster Relating to
  							kinase (EC 2.7.1.148)	Translation;
  								<br>Isoprenoid
  								Biosynthesis;
  								<br>Nonmevalonate
  								Branch of Isoprenoid
  								Biosynthesis
  fig|6666666.60966.peg.1047	CDS	969932	970882	2	+	951	Ribose-phosphate	A Gammaproteobacteria	D23_1c1060	Neut_1140
  							pyrophosphokinase (EC	Cluster Relating to
  							2.7.6.1)	Translation; <br>De
  								Novo Purine
  								Biosynthesis;
  								<br>Pentose phosphate
  								pathway;
  								<br>Transcription repair
  								cluster
  fig|6666666.60966.peg.1048	CDS	970936	971544	1	+	609	LSU ribosomal protein	Transcription repair	D23_1c1061	Neut_1141
  							L25p	cluster
  fig|6666666.60966.peg.1049	CDS	971667	972236	3	+	570	Peptidyl-tRNA	Sporulation-associated	D23_1c1062	Neut_1142
  							hydrolase (EC 3.1.1.29)	proteins with broader
  								functions;
  								<br>Transcription repair
  								cluster; <br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.1050	CDS	972291	973382	3	+	1092	GTP-binding and nucleic	Universal GTPases	D23_1c1063	Neut_1143
  							acid-binding protein
  							YchF
  fig|6666666.60966.peg.1051	CDS	973589	973461	−2	−	129	hypothetical protein	-none-	D23_1c1064	NA
  fig|6666666.60966.peg.1052	CDS	973891	975303	1	+	1413	3-isopropylmalate	Branched-Chain Amino	D23_1c1066	Neut_1144
  							dehydratase large	Acid Biosynthesis;
  							subunit (EC 4.2.1.33)	<br>Leucine
  								Biosynthesis
  fig|6666666.60966.peg.1053	CDS	975336	975464	3	+	129	FIG00858504:	-none-	D23_1c1067	Neut_1145
  							hypothetical protein
  fig|6666666.60966.peg.1054	CDS	975470	976108	2	+	639	3-isopropylmalate	Branched-Chain Amino	D23_1c1068	Neut_1146
  							dehydratase small	Acid Biosynthesis;
  							subunit (EC 4.2.1.33)	<br>Leucine
  								Biosynthesis
  fig|6666666.60966.peg.1055	CDS	976133	977203	2	+	1071	3-isopropylmalate	Branched-Chain Amino	D23_1c1069	Neut_1147
  							dehydrogenase (EC	Acid Biosynthesis;
  							1.1.1.85)	<br>Leucine
  								Biosynthesis
  fig|6666666.60966.peg.1056	CDS	977333	978457	2	+	1125	Aspartate-	Lysine Biosynthesis DAP	D23_1c1070	Neut_1148
  							semialdehyde	Pathway, GJO scratch;
  							dehydrogenase (EC	<br>Threonine and
  							1.2.1.11)	Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.1057	CDS	978574	980970	1	+	2397	hypothetical protein	-none-	D23_1c1071	Neut_1149
  fig|6666666.60966.peg.1058	CDS	981084	981917	3	+	834	tRNA pseudouridine	Colicin V and Bacteriocin	D23_1c1072	Neut_1150
  							synthase A (EC 4.2.1.70)	Production Cluster;
  								<br>RNA pseudouridine
  								syntheses; <br>tRNA
  								modification Bacteria;
  								<br>tRNA processing
  fig|6666666.60966.peg.1059	CDS	981929	982555	2	+	627	Phosphoribosylanthranilate	Auxin biosynthesis;	D23_1c1073	Neut_1151
  							isomerase (EC	<br>Chorismate:
  							5.3.1.24)	Intermediate for
  								synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.1060	CDS	982542	983741	3	+	1200	Tryptophan synthase	Auxin biosynthesis;	D23_1c1074	Neut_1152
  							beta chain (EC 4.2.1.20)	<br>Chorismate:
  								Intermediate for
  								synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.1061	CDS	983794	984618	1	+	825	Tryptophan synthase	Auxin biosynthesis;	D23_1c1075	Neut_1153
  							alpha chain (EC	<br>Chorismate:
  							4.2.1.20)	Intermediate for
  								synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.1062	CDS	984623	985513	2	+	891	Acetyl-coenzyme A	Colicin V and Bacteriocin	D23_1c1076	Neut_1154
  							carboxyl transferase	Production Cluster;
  							beta chain (EC 6.4.1.2)	<br>Fatty Acid
  								Biosynthesis FASII
  fig|6666666.60966.peg.1063	CDS	985642	986925	1	+	1284	Dihydrofolate synthase	Colicin V and Bacteriocin	D23_1c1077	Neut_1155
  							(EC 6.3.2.12)/	Production Cluster;
  							Folylpolyglutamate	<br>Colicin V and
  							synthase (EC 6.3.2.17)	Bacteriocin Production
  								Cluster; <br>Folate
  								Biosynthesis; <br>Folate
  								Biosynthesis
  fig|6666666.60966.peg.1064	CDS	986945	987616	2	+	672	DedD protein	Colicin V and Bacteriocin	D23_1c1078	Neut_1156
  								Production Cluster
  fig|6666666.60966.peg.1065	CDS	987613	988107	1	+	495	Colicin V production	Colicin V and Bacteriocin	D23_1c1079	Neut_1157
  							protein	Production Cluster
  fig|6666666.60966.peg.1066	CDS	988214	989731	2	+	1518	Amidophosphoribosyltransferase	Colicin V and Bacteriocin	D23_1c1080	Neut_1158
  							(EC 2.4.2.14)	Production Cluster;
  								<br>De Novo Purine
  								Biosynthesis
  fig|6666666.60966.peg.1067	CDS	989748	990923	3	+	1176	O-acetylhomoserine	Methionine	D23_1c1081	Neut_1159
  							sulfhydrylase (EC	Biosynthesis;
  							2.5.1.49)/O-	<br>Methionine
  							succinylhomoserine	Biosynthesis
  							sulfhydrylase (EC
  							2.5.1.48)
  fig|6666666.60966.peg.1068	CDS	991043	992554	2	+	1512	Threonine dehydratase	Branched-Chain Amino	D23_1c1082	Neut_1160
  							biosynthetic (EC	Acid Biosynthesis
  							4.3.1.19)
  fig|6666666.60966.peg.1069	CDS	992670	992536	−3	−	135	hypothetical protein	-none-	D23_1c1083	NA
  fig|6666666.60966.peg.1070	CDS	993016	994950	1	+	1935	twitching motility	-none-	D23_1c1084	Neut_1161
  							protein PilJ
  fig|6666666.60966.peg.1071	CDS	995179	995054	−1	−	126	hypothetical protein	-none-	D23_1c1085	Neut_1162
  fig|6666666.60966.peg.1072	CDS	995174	1000177	2	+	5004	Signal transduction	Flagellar motility	D23_1c1085	Neut_1162
  							histidine kinase CheA
  							(EC 2.7.3.—)
  fig|6666666.60966.peg.1073	CDS	1000248	1002095	3	+	1848	ParB-like nuclease	-none-	D23_1c1086	Neut_1163
  							domain
  fig|6666666.60966.peg.1074	CDS	1003717	1002203	−1	−	1515	Ubiquinone	Ubiquinone	D23_1c1087	Neut_1164
  							biosynthesis	Biosynthesis;
  							monooxygenase UbiB	<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.1075	CDS	1004439	1003807	−3	−	633	Protein YigP (COG3165)	Ubiquinone	D23_1c1088	Neut_1165
  							clustered with	Biosynthesis;
  							ubiquinone biosynthetic	<br>Ubiquinone
  							genes	Biosynthesis-gjo
  fig|6666666.60966.peg.1076	CDS	1004959	1004528	−1	−	432	FIG00858586:	-none-	D23_1c1089	Neut_1166
  							hypothetical protein
  fig|6666666.60966.peg.1077	CDS	1005165	1004962	−3	−	204	hypothetical protein	-none-	D23_1c1090	NA
  fig|6666666.60966.peg.1078	CDS	1005185	1007323	2	+	2139	Signal transduction	Flagellar motility	D23_1c1091	Neut_1167
  							histidine kinase CheA
  							(EC 2.7.3.—)
  fig|6666666.60966.peg.1079	CDS	1007395	1007916	1	+	522	Positive regulator of	-none-	D23_1c1092	Neut_1168
  							CheA protein activity
  							(CheW)
  fig|6666666.60966.peg.1080	CDS	1008003	1010258	3	+	2256	Methyl-accepting	-none-	D23_1c1093	Neut_1169
  							chemotaxis protein I
  							(serine chemoreceptor
  							protein)
  fig|6666666.60966.peg.1082	CDS	1010399	1012744	2	+	2346	Methyl-accepting	-none-	D23_1c1094	Neut_1170
  							chemotaxis protein I
  							(serine chemoreceptor
  							protein)
  fig|6666666.60966.peg.1083	CDS	1012932	1013807	3	+	876	Chemotaxis protein	-none-	D23_1c1095	Neut_1171
  							methyltransferase CheR
  							(EC 2.1.1.80)
  fig|6666666.60966.peg.1084	CDS	1013887	1014471	1	+	585	Chemotaxis protein	-none-	D23_1c1096	Neut_1172
  							CheD
  fig|6666666.60966.peg.1085	CDS	1014502	1015569	1	+	1068	Chemotaxis response	-none-	D23_1c1097	Neut_1173
  							regulator protein-
  							glutamate
  							methylesterase CheB
  							(EC 3.1.1.61)
  fig|6666666.60966.peg.1087	CDS	1017858	1016338	−3	−	1521	Ferredoxin reductase	Anaerobic respiratory	D23_1c1099	Neut_1175
  								reductases
  fig|6666666.60966.peg.1088	CDS	1018141	1019145	1	+	1005	Fructose-1,6-	Calvin-Benson cycle;	D23_1c1100	Neut_1176
  							bisphosphatase, type I	<br>Glycolysis and
  							(EC 3.1.3.11)	Gluconeogenesis
  fig|6666666.60966.peg.1089	CDS	1020142	1019183	−1	−	960	Glutathione S-	Glutathione: Non-redox	D23_1c1101	Neut_1177
  							transferase, omega (EC	reactions
  							2.5.1.18)
  fig|6666666.60966.peg.1090	CDS	1020604	1020146	−1	−	459	Membrane protein,	-none-	D23_1c1102	Neut_1178
  							distant similarity to
  							thiosulphate:quinone
  							oxidoreductase DoxD
  fig|6666666.60966.peg.1091	CDS	1020710	1020862	2	+	153	hypothetical protein	-none-	D23_1c1103	NA
  fig|6666666.60966.peg.1092	CDS	1022088	1021138	−3	−	951	COGs COG0726	-none-	D23_1c1104	Neut_1179
  fig|6666666.60966.peg.1093	CDS	1022664	1022212	−3	−	453	Phosphohistidine	-none-	D23_1c1105	Neut_1180
  							phosphatase SixA
  fig|6666666.60966.peg.1094	CDS	1023442	1022753	−1	−	690	COGs COG1814	-none-	D23_1c1106	Neut_1181
  fig|6666666.60966.peg.1095	CDS	1024149	1023445	−3	−	705	probable	-none-	D23_1c1107	Neut_1182
  							carboxylesterase
  fig|6666666.60966.peg.1096	CDS	1024228	1025334	1	+	1107	InterPro IPR002931	-none-	D23_1c1108	Neut_1183
  							COGs COG1305
  fig|6666666.60966.peg.1097	CDS	1027262	1025541	−2	−	1722	Sulfite reductase	Cysteine Biosynthesis;	D23_1c1109	Neut_1184
  							[NADPH] hemoprotein	<br>Inorganic Sulfur
  							beta-component (EC	Assimilation
  							1.8.1.2)
  fig|6666666.60966.peg.1098	CDS	1029106	1027271	−1	−	1836	Sulfite reductase	Cysteine Biosynthesis;	D23_1c1110	Neut_1185
  							[NADPH] flavoprotein	<br>Inorganic Sulfur
  							alpha-component (EC	Assimilation
  							1.8.1.2)
  fig|6666666.60966.peg.1100	CDS	1030580	1029651	−2	−	930	Cys regulon	Cysteine Biosynthesis;	D23_1c1111	Neut_1186
  							transcriptional activator	<br>LysR-family proteins
  							CysB	in Escherichia coli
  fig|6666666.60966.peg.1101	CDS	1030815	1031513	3	+	699	Phosphoadenylyl-	Cysteine Biosynthesis;	D23_1c1112	Neut_1187
  							sulfate reductase	<br>Inorganic Sulfur
  							[thioredoxin] (EC	Assimilation;
  							1.8.4.8)/Adenylyl-	<br>Inorganic Sulfur
  							sulfate reductase	Assimilation
  							[thioredoxin] (EC
  							1.8.4.10)
  fig|6666666.60966.peg.1102	CDS	1031599	1032447	1	+	849	Sulfate	Cysteine Biosynthesis;	D23_1c1113	Neut_1188
  							adenylyltransferase	<br>Inorganic Sulfur
  							subunit 2 (EC 2.7.7.4)	Assimilation
  fig|6666666.60966.peg.1103	CDS	1032508	1033791	1	+	1284	Sulfate	Cysteine Biosynthesis;	D23_1c1114	Neut_1189
  							adenylyltransferase	<br>Inorganic Sulfur
  							subunit 1 (EC 2.7.7.4)	Assimilation
  fig|6666666.60966.peg.1105	CDS	1033967	1037446	2	+	3480	Glutamate synthase	Ammonia assimilation;	D23_1c1115	Neut_1190
  							[NADPH] small chain	<br>Glutamine,
  							(EC 1.4.1.13)	Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.1106	CDS	1037596	1038723	1	+	1128	NAD(P)	Phosphate metabolism	D23_1c1116	Neut_1191
  							transhydrogenase alpha
  							subunit (EC 1.6.1.2)
  fig|6666666.60966.peg.1107	CDS	1038778	1039086	1	+	309	NAD(P)	Phosphate metabolism	D23_1c1117	Neut_1192
  							transhydrogenase alpha
  							subunit (EC 1.6.1.2)
  fig|6666666.60966.peg.1108	CDS	1039087	1040466	1	+	1380	NAD(P)	Phosphate metabolism	D23_1c1118	Neut_1193
  							transhydrogenase
  							subunit beta (EC
  							1.6.1.2)
  fig|6666666.60966.peg.1109	CDS	1041147	1040488	−3	−	660	FIG00858826:	-none-	D23_1c1119	Neut_1194
  							hypothetical protein
  fig|6666666.60966.peg.1110	CDS	1042046	1041582	−2	−	465	Bacterioferritin	-none-	D23_1c1120	Neut_1195
  fig|6666666.60966.peg.1112	CDS	1043119	1043253	1	+	135	hypothetical protein	-none-	D23_1c1121	NA
  fig|6666666.60966.peg.1113	CDS	1043368	1043511	1	+	144	hypothetical protein	-none-	D23_1c1122	NA
  fig|6666666.60966.peg.1115	CDS	1043900	1043736	−2	−	165	hypothetical protein	-none-	D23_1c1123	NA
  fig|6666666.60966.peg.1116	CDS	1043900	1044847	2	+	948	2,3-	-none-	D23_1c1124	Neut_1198
  							bisphosphoglycerate-
  							independent
  							phosphoglycerate
  							mutase
  fig|6666666.60966.peg.1117	CDS	1044958	1045530	1	+	573	InterPro	-none-	D23_1c1125	Neut_1199
  							IPR000014:IPR001633
  							COGs COG2200
  fig|6666666.60966.peg.1118	CDS	1045566	1045859	3	+	294	Mobile element protein	-none-	D23_1c1126	Neut_1719
  fig|6666666.60966.peg.1119	CDS	1045958	1046836	2	+	879	Mobile element protein	-none-	D23_1c1127	Neut_1720
  fig|6666666.60966.peg.1120	CDS	1046891	1047784	2	+	894	InterPro	-none-	D23_1c1128	Neut_1199
  							IPR000014:IPR001633
  							COGs COG2200
  fig|6666666.60966.peg.1121	CDS	1048688	1047801	−2	−	888	Phosphoribosylaminoimidazole-	De Novo Purine	D23_1c1129	Neut_1200
  							succinocarboxamide	Biosynthesis
  							synthase (EC 6.3.2.6)
  fig|6666666.60966.peg.1122	CDS	1049856	1048726	−3	−	1131	Phosphoribosylaminoimidazole	De Novo Purine	D23_1c1130	Neut_1201
  							carboxylase	Biosynthesis
  							ATPase subunit (EC
  							4.1.1.21)
  fig|6666666.60966.peg.1123	CDS	1050317	1049847	−2	−	471	Phosphoribosylaminoimidazole	De Novo Purine	D23_1c1131	Neut_1202
  							carboxylase	Biosynthesis
  							catalytic subunit (EC
  							4.1.1.21)
  fig|6666666.60966.peg.1124	CDS	1050521	1050955	2	+	435	Biopolymer transport	Ton and Tol transport	D23_1c1133	Neut_1203
  							protein ExbD/TolR	systems
  fig|6666666.60966.peg.1125	CDS	1050942	1051664	3	+	723	Superoxide dismutase	Oxidative stress;	D23_1c1134	Neut_1204
  							[Fe] (EC 1.15.1.1)	<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.1126	CDS	1051674	1052324	3	+	651	ATP	Histidine Biosynthesis;	D23_1c1135	Neut_1205
  							phosphoribosyltransferase	<br>Riboflavin synthesis
  							(EC 2.4.2.17)	cluster
  fig|6666666.60966.peg.1127	CDS	1052409	1053644	3	+	1236	Histidinol	Histidine Biosynthesis	D23_1c1136	Neut_1206
  							dehydrogenase (EC
  							1.1.1.23)
  fig|6666666.60966.peg.1128	CDS	1053708	1054883	3	+	1176	2-octaprenyl-6-	CBSS-87626.3.peg.3639;	D23_1c1137	Neut_1207
  							methoxyphenol	<br>Ubiquinone
  							hydroxylase (EC	Biosynthesis;
  							1.14.13.—)	<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.1129	CDS	1055047	1056060	1	+	1014	tRNA dihydrouridine	Possible RNA	D23_1c1138	Neut_1208
  							synthase B (EC 1.—.—.—)	degradation cluster;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1130	CDS	1056057	1056299	3	+	243	DNA-binding protein Fis	DNA structural proteins,	D23_1c1139	Neut_1209
  								bacterial
  fig|6666666.60966.peg.1131	CDS	1056309	1057871	3	+	1563	IMP cyclohydrolase (EC	5-FCL-like protein;	D23_1c1140	Neut_1210
  							3.5.4.10)/	<br>De Novo Purine
  							Phosphoribosylaminoimidazolecarboxamide	Biosynthesis; <br>De
  							formyltransferase (EC	Novo Purine
  							2.1.2.3)	Biosynthesis
  fig|6666666.60966.peg.1132	CDS	1057947	1059233	3	+	1287	Phosphoribosylamine-	De Novo Purine	D23_1c1141	Neut_1211
  							glycine ligase (EC	Biosynthesis
  							6.3.4.13)
  fig|6666666.60966.peg.1133	CDS	1059226	1060497	1	+	1272	FIG00858582:	-none-	D23_1c1142	Neut_1213
  							hypothetical protein
  fig|6666666.60966.peg.1134	CDS	1061025	1060582	−3	−	444	TPR repeat precursor	-none-	D23_1c1143	Neut_1214
  fig|6666666.60966.peg.1135	CDS	1061496	1061041	−3	−	456	Mobile element protein	-none-	D23_1c1144	Neut_2502
  fig|6666666.60966.peg.1136	CDS	1061839	1061459	−1	−	381	Mobile element protein	-none-	D23_1c1145	Neut_0884
  fig|6666666.60966.peg.1137	CDS	1062885	1061836	−3	−	1050	TPR repeat precursor	-none-	D23_1c1146	Neut_0701
  fig|6666666.60966.peg.1138	CDS	1064906	1062960	−2	−	1947	DinG family ATP-	DNA repair, bacterial	D23_1c1148	Neut_1215
  							dependent helicase	DinG and relatives
  							YoaA
  fig|6666666.60966.peg.1139	CDS	1065051	1064932	−3	−	120	hypothetical protein	-none-	D23_1c1149	NA
  fig|6666666.60966.peg.1140	CDS	1065126	1067303	3	+	2178	Outer membrane	EC49-61; <br>ECSIG4-	D23_1c1150	Neut_1216
  							protein Imp, required	SIG7;
  							for envelope biogenesis/	<br>Lipopolysaccharide
  							Organic solvent	assembly
  							tolerance protein
  							precursor
  fig|6666666.60966.peg.1141	CDS	1067300	1068643	2	+	1344	Survival protein SurA	EC49-61; <br>ECSIG4-	D23_1c1151	Neut_1217
  							precursor (Peptidyl-	SIG7;
  							prolyl cis-trans	<br>Lipopolysaccharide
  							isomerase SurA) (EC	assembly; <br>Peptidyl-
  							5.2.1.8)	prolyl cis-trans
  								isomerase;
  								<br>Periplasmic Stress
  								Response
  fig|6666666.60966.peg.1142	CDS	1068713	1069750	2	+	1038	4-hydroxythreonine-4-	EC49-61; <br>ECSIG4-	D23_1c1152	Neut_1218
  							phosphate	SIG7; <br>Pyridoxin
  							dehydrogenase (EC	(Vitamin B6)
  							1.1.1.262)	Biosynthesis
  fig|6666666.60966.peg.1143	CDS	1069754	1070524	2	+	771	SSU rRNA	EC49-61; <br>ECSIG4-	D23_1c1153	Neut_1219
  							(adenine(1518)-	SIG7; <br>RNA
  							N(6)/adenine(1519)-	methylation;
  							N(6))-	<br>Ribosome
  							dimethyltransferase (EC	biogenesis bacterial
  							2.1.1.182) ## SSU rRNA
  							m6,m6-A1518-1519
  fig|6666666.60966.peg.1144	CDS	1071020	1070517	−2	−	504	Methylated-DNA--	DNA repair, bacterial	D23_1c1154	Neut_1220
  							protein-cysteine
  							methyltransferase (EC
  							2.1.1.63)
  fig|6666666.60966.peg.1145	CDS	1071346	1071080	−1	−	267	ADA regulatory protein/	DNA repair, bacterial;	D23_1c1155	Neut_1221
  							Methylated-DNA--	<br>DNA repair,
  							protein-cysteine	bacterial
  							methyltransferase (EC
  							2.1.1.63)
  fig|6666666.60966.peg.1146	CDS	1072448	1071324	−2	−	1125	ADA regulatory protein/	DNA repair, bacterial;	D23_1c1156	Neut_1221
  							Methylated-DNA--	<br>DNA repair,
  							protein-cysteine	bacterial
  							methyltransferase (EC
  							2.1.1.63)
  fig|6666666.60966.peg.1149	CDS	1073291	1073809	2	+	519	Helix-turn-helix motif	-none-	D23_1c1157	Neut_1223
  fig|6666666.60966.peg.1150	CDS	1075783	1074353	−1	−	1431	Siroheme synthase/	Heme and Siroheme	D23_1c1159	Neut_1002
  							Precorrin-2 oxidase (EC	Biosynthesis; <br>Heme
  							1.3.1.76)/	and Siroheme
  							Sirohydrochlorin	Biosynthesis; <br>Heme
  							ferrochelatase (EC	and Siroheme
  							4.99.1.4)/	Biosynthesis
  							Uroporphyrinogen-III
  							methyltransferase (EC
  							2.1.1.107)
  fig|6666666.60966.peg.1151	CDS	1076939	1075926	−2	−	1014	Phosphate ABC	High affinity phosphate	D23_1c1160	Neut_1001
  							transporter, periplasmic	transporter and control
  							phosphate-binding	of PHO regulon;
  							protein PstS (TC	<br>PhoR-PhoB two-
  							3.A.1.7.1)	component regulatory
  								system; <br>Phosphate
  								metabolism
  fig|6666666.60966.peg.1152	CDS	1078435	1077059	−1	−	1377	Phosphoglucosamine	Sialic Acid Metabolism;	D23_1c1161	Neut_1000
  							mutase (EC 5.4.2.10)	<br>UDP-N-
  								acetylmuramate from
  								Fructose-6-phosphate
  								Biosynthesis
  fig|6666666.60966.peg.1153	CDS	1079505	1078603	−3	−	903	Dihydropteroate	Folate Biosynthesis	D23_1c1162	Neut_0999
  							synthase (EC 2.5.1.15)
  fig|6666666.60966.peg.1154	CDS	1081457	1079529	−2	−	1929	Cell division protein	Bacterial Cell Division	D23_1c1163	Neut_0998
  							FtsH (EC 3.4.24.—)
  fig|6666666.60966.peg.1155	CDS	1082161	1081541	−1	−	621	Cell division protein FtsJ/	Bacterial Cell Division;	D23_1c1164	Neut_0997
  							Ribosomal RNA large	<br>RNA methylation
  							subunit
  							methyltransferase E (EC
  							2.1.1.—) ## LSU rRNA
  							Um2552
  fig|6666666.60966.peg.1156	CDS	1082195	1082575	2	+	381	FIG004454: RNA	-none-	D23_1c1165	Neut_0996
  							binding protein
  fig|6666666.60966.peg.1157	CDS	1082674	1083084	1	+	411	CBS domain	-none-	D23_1c1166	Neut_0995
  fig|6666666.60966.peg.1158	CDS	1083081	1083464	3	+	384	tRNA	A cluster relating to	D23_1c1167	Neut_0994
  							nucleotidyltransferase,	Tryptophanyl-tRNA
  							A-adding (EC 2.7.7.25)	synthetase;
  								<br>Polyadenylation
  								bacterial; <br>tRNA
  								nucleotidyltransferase
  fig|6666666.60966.peg.1159	CDS	1084218	1083646	−3	−	573	DNA-3-methyladenine	DNA Repair Base	D23_1c1168	Neut_0993
  							glycosylase II (EC	Excision
  							3.2.2.21)
  fig|6666666.60966.peg.1160	CDS	1084717	1084241	−1	−	477	Glutathione peroxidase	Glutathione: Redox cycle	D23_1c1169	Neut_0992
  							(EC 1.11.1.9)
  fig|6666666.60966.peg.1161	CDS	1084748	1085341	2	+	594	Carbonic anhydrase,	Zinc regulated enzymes	D23_1c1170	Neut_0991
  							gamma class (EC
  							4.2.1.1)
  fig|6666666.60966.peg.1162	CDS	1085402	1086241	2	+	840	Putative NAD(P)-	-none-	D23_1c1171	Neut_0990
  							dependent
  							oxidoreductase EC-
  							YbbO
  fig|6666666.60966.peg.1163	CDS	1086401	1087885	2	+	1485	alpha amylase, catalytic	-none-	D23_1c1172	Neut_0989
  							region
  fig|6666666.60966.peg.1164	CDS	1090985	1087899	−2	−	3087	RND multidrug efflux	Multidrug Resistance	D23_1c1173	Neut_0988
  							transporter; Acriflavin	Efflux Pumps
  							resistance protein
  fig|6666666.60966.peg.1165	CDS	1092079	1090982	−1	−	1098	Membrane fusion	Multidrug Resistance	D23_1c1174	Neut_0987
  							protein of RND family	Efflux Pumps
  							multidrug efflux pump
  fig|6666666.60966.peg.1168	CDS	1092982	1092851	−1	−	132	hypothetical protein	-none-	D23_1c1175	NA
  fig|6666666.60966.peg.1169	CDS	1094042	1093413	−2	−	630	Nicotinamidase family	NAD and NADP cofactor	D23_1c1176	NA
  							protein YcaC	biosynthesis global
  fig|6666666.60966.peg.1170	CDS	1094408	1094223	−2	−	186	Mobile element protein	-none-	D23_1c1178	Neut_1984
  fig|6666666.60966.peg.1171	CDS	1094750	1094514	−2	−	237	Mobile element protein	-none-	D23_1c1179	Neut_1353
  fig|6666666.60966.peg.1172	CDS	1095334	1094984	−1	−	351	hypothetical protein	-none-	D23_1c1180	NA
  fig|6666666.60966.peg.1173	CDS	1095854	1095486	−2	−	369	Mobile element protein	-none-	D23_1c1181	Neut_2502
  fig|6666666.60966.peg.1175	CDS	1096049	1095933	−2	−	117	Mobile element protein	-none-	D23_1c1182	Neut_0884
  fig|6666666.60966.peg.1176	CDS	1096623	1096288	−3	−	336	putative (AJ245540)	-none-	D23_1c1183	Neut_1054
  							NrfJ [Wolinella
  							succinogenes]
  fig|6666666.60966.peg.1177	CDS	1098408	1096669	−3	−	1740	FIG00859793:	-none-	D23_1c1184	Neut_1053
  							hypothetical protein
  fig|6666666.60966.peg.1178	CDS	1098651	1100255	3	+	1605	Multicopper oxidase	Copper homeostasis	D23_1c1185	Neut_1052
  fig|6666666.60966.peg.1179	CDS	1101152	1100349	−2	−	804	Inositol-1-	-none-	D23_1c1186	Neut_1051
  							monophosphatase (EC
  							3.1.3.25)
  fig|6666666.60966.peg.1180	CDS	1101712	1101155	−1	−	558	Alkyl hydroperoxide	-none-	D23_1c1187	Neut_1050
  							reductase and/or thiol-
  							specific antioxidant
  							family (AhpC/TSA)
  							protein
  fig|6666666.60966.peg.1181	CDS	1101810	1102571	3	+	762	Ribosomal RNA small	Heat shock dnaK gene	D23_1c1188	Neut_1049
  							subunit	cluster extended;
  							methyltransferase E (EC	<br>RNA methylation
  							2.1.1.—)
  fig|6666666.60966.peg.1182	CDS	1102595	1103929	2	+	1335	N-acetylglutamate	Arginine Biosynthesis--	D23_1c1189	Neut_1048
  							synthase (EC 2.3.1.1)	gjo; <br>Arginine
  								Biosynthesis extended
  fig|6666666.60966.peg.1183	CDS	1104924	1104208	−3	−	717	FIG002842:	-none-	D23_1c1190	Neut_1046
  							hypothetical protein
  fig|6666666.60966.peg.1184	CDS	1105647	1105036	−3	−	612	Dephospho-CoA kinase	Coenzyme A	D23_1c1191	Neut_1045
  							(EC 2.7.1.24)	Biosynthesis
  fig|6666666.60966.peg.1185	CDS	1106511	1105651	−3	−	861	Leader peptidase	-none-	D23_1c1192	Neut_1044
  							(Prepilin peptidase) (EC
  							3.4.23.43)/N-
  							methyltransferase (EC
  							2.1.1.—)
  fig|6666666.60966.peg.1186	CDS	1107775	1106555	−1	−	1221	Type IV fimbrial	-none-	D23_1c1193	Neut_1043
  							assembly protein PilC
  fig|6666666.60966.peg.1187	CDS	1108692	1107835	−3	−	858	Nucleoside-	CBSS-296591.1.peg.2330	D23_1c1194	Neut_1042
  							diphosphate-sugar
  							epimerases
  fig|6666666.60966.peg.1189	CDS	1108961	1109818	2	+	858	2-polyprenylphenol	-none-	D23_1c1195	Neut_1041
  							hydroxylase and related
  							flavodoxin
  							oxidoreductases/CDP-
  							6-deoxy-delta-3,4-
  							glucoseen reductase-
  							like
  fig|6666666.60966.peg.1190	CDS	1111006	1109825	−1	−	1182	Homolog of E. coli	-none-	D23_1c1196	Neut_1040
  							HemY protein
  fig|6666666.60966.peg.1191	CDS	1112031	1111003	−3	−	1029	Uroporphyrinogen-III	Heme and Siroheme	D23_1c1197	Neut_1039
  							methyltransferase (EC	Biosynthesis
  							2.1.1.107)
  fig|6666666.60966.peg.1192	CDS	1112828	1112046	−2	−	783	Uroporphyrinogen-III	Heme and Siroheme	D23_1c1198	Neut_1038
  							synthase (EC 4.2.1.75)	Biosynthesis
  fig|6666666.60966.peg.1193	CDS	1113852	1112848	−3	−	1005	Porphobilinogen	Heme and Siroheme	D23_1c1199	Neut_1037
  							deaminase (EC 2.5.1.61)	Biosynthesis
  fig|6666666.60966.peg.1194	CDS	1113898	1116699	1	+	2802	Phosphoenolpyruvate	Pyruvate metabolism I:	D23_1c1200	Neut_1036
  							carboxylase (EC	anaplerotic reactions,
  							4.1.1.31)	PEP
  fig|6666666.60966.peg.1195	CDS	1116922	1118904	1	+	1983	FIG00858706:	-none-	D23_1c1201	Neut_1035
  							hypothetical protein
  fig|6666666.60966.peg.1196	CDS	1120329	1118899	−3	−	1431	probable integral	-none-	D23_1c1202	Neut_1034
  							membrane protein
  							NMA1898
  fig|6666666.60966.peg.1197	CDS	1121723	1120329	−2	−	1395	FIG00859415:	-none-	D23_1c1203	Neut_1033
  							hypothetical protein
  fig|6666666.60966.peg.1198	CDS	1121909	1121763	−2	−	147	hypothetical protein	-none-	D23_1c1204	NA
  fig|6666666.60966.peg.1199	CDS	1121985	1122698	3	+	714	COGs COG0518	-none-	D23_1c1205	Neut_1032
  fig|6666666.60966.peg.1200	CDS	1123590	1122748	−3	−	843	RNA polymerase sigma	Heat shock Cell division	D23_1c1206	Neut_1031
  							factor RpoH	Proteases and a
  								Methyltransferase;
  								<br>Heat shock dnaK
  								gene cluster extended;
  								<br>Transcription
  								initiation, bacterial
  								sigma factors
  fig|6666666.60966.peg.1201	CDS	1124005	1124823	1	+	819	Cytochrome c family	-none-	D23_1c1207	NA
  							protein
  fig|6666666.60966.peg.1203	CDS	1125802	1127289	1	+	1488	FIG00858881:	-none-	D23_1c1209	Neut_1029
  							hypothetical protein
  fig|6666666.60966.peg.1204	CDS	1127318	1128325	2	+	1008	Sulfate-binding protein	Inorganic Sulfur	D23_1c1210	Neut_1028
  							Sbp	Assimilation
  fig|6666666.60966.peg.1205	CDS	1128452	1128580	2	+	129	hypothetical protein	-none-	D23_1c1211	NA
  fig|6666666.60966.peg.1206	CDS	1128661	1129494	1	+	834	Sulfate transport	Cysteine Biosynthesis;	D23_1c1212	Neut_1026
  							system permease	<br>Inorganic Sulfur
  							protein CysT	Assimilation
  fig|6666666.60966.peg.1207	CDS	1129502	1130371	2	+	870	Sulfate transport	Cysteine Biosynthesis;	D23_1c1213	Neut_1025
  							system permease	<br>Inorganic Sulfur
  							protein CysW	Assimilation
  fig|6666666.60966.peg.1208	CDS	1130383	1131471	1	+	1089	Sulfate and thiosulfate	Cysteine Biosynthesis;	D23_1c1214	Neut_1024
  							import ATP-binding	<br>Inorganic Sulfur
  							protein CysA (EC	Assimilation;
  							3.6.3.25)	<br>Uptake of selenate
  								and selenite
  fig|6666666.60966.peg.1209	CDS	1131827	1131510	−2	−	318	possible lipase	-none-	D23_1c1215	Neut_1023
  fig|6666666.60966.peg.1210	CDS	1133403	1131859	−3	−	1545	Aminopeptidase PepA-	-none-	D23_1c1216	Neut_1022
  							related protein
  fig|6666666.60966.peg.1211	CDS	1133455	1134249	1	+	795	Thymidylate synthase	Folate Biosynthesis;	D23_1c1217	Neut_1021
  							(EC 2.1.1.45)	<br>pyrimidine
  								conversions
  fig|6666666.60966.peg.1212	CDS	1134246	1134776	3	+	531	Dihydrofolate reductase	5-FCL-like protein;	D23_1c1218	Neut_1020
  							(EC 1.5.1.3)	<br>EC49-61; <br>Folate
  								Biosynthesis
  fig|6666666.60966.peg.1213	CDS	1136053	1134809	−1	−	1245	Response regulator	-none-	D23_1c1219	Neut_1019
  fig|6666666.60966.peg.1215	CDS	1136321	1136785	2	+	465	Mobile element protein	-none-	D23_1c1220	Neut_0357
  fig|6666666.60966.peg.1216	CDS	1136808	1137512	3	+	705	Mobile element protein	-none-	D23_1c1221	Neut_1318
  fig|6666666.60966.peg.1217	CDS	1137576	1138703	3	+	1128	Catalase (EC 1.11.1.6)	Oxidative stress;	D23_1c1222	NA
  								<br>Photorespiration
  								(oxidative C2cycle);
  								<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.1218	CDS	1139453	1138773	−2	−	681	Mobile element protein	-none-	D23_1c1223	Neut_1318
  fig|6666666.60966.peg.1219	CDS	1139703	1139837	3	+	135	Mobile element protein	-none-	D23_1c1224	Neut_2500
  fig|6666666.60966.peg.1220	CDS	1139894	1140238	2	+	345	Mobile element protein	-none-	D23_1c1225	Neut_1375
  fig|6666666.60966.peg.1221	CDS	1141157	1140195	−2	−	963	Mobile element protein	-none-	D23_1c1226	Neut_1278
  fig|6666666.60966.peg.1222	CDS	1141250	1141762	2	+	513	Mobile element protein	-none-	D23_1c1227	Neut_1624
  fig|6666666.60966.peg.1223	CDS	1142310	1141846	−3	−	465	Mobile element protein	-none-	D23_1c1228	Neut_0357
  fig|6666666.60966.peg.1224	CDS	1142882	1142409	−2	−	474	Mobile element protein	-none-	D23_1c1229	Neut_0883
  fig|6666666.60966.peg.1225	CDS	1144087	1143419	−1	−	669	hypothetical protein	-none-	D23_1c1230	NA
  fig|6666666.60966.peg.1226	CDS	1144329	1144078	−3	−	252	ABC-type antimicrobial	-none-	D23_1c1231	NA
  							peptide transport
  							system, permease
  							component
  fig|6666666.60966.peg.1227	CDS	1144623	1145231	3	+	609	Transcriptional	-none-	D23_1c1232	Neut_1011
  							regulator, TetR family
  fig|6666666.60966.peg.1228	CDS	1145317	1146351	1	+	1035	Predicted membrane	ATP-dependent efflux	D23_1c1233	Neut_1010
  							fusion protein (MFP)	pump transporter Ybh
  							component of efflux
  							pump, membrane
  							anchor protein YbhG
  fig|6666666.60966.peg.1229	CDS	1146341	1148125	2	+	1785	ABC transporter	ATP-dependent efflux	D23_1c1234	Neut_1009
  							multidrug efflux pump,	pump transporter Ybh
  							fused ATP-binding
  							domains
  fig|6666666.60966.peg.1230	CDS	1148122	1149270	1	+	1149	ABC transport system,	ATP-dependent efflux	D23_1c1235	Neut_1008
  							permease component	pump transporter Ybh
  							YbhS
  fig|6666666.60966.peg.1231	CDS	1149276	1150400	3	+	1125	ABC transport system,	ATP-dependent efflux	D23_1c1236	Neut_1007
  							permease component	pump transporter Ybh
  							YbhR
  fig|6666666.60966.peg.1232	CDS	1150415	1150546	2	+	132	hypothetical protein	-none-	D23_1c1237	NA
  fig|6666666.60966.peg.1233	CDS	1150719	1150507	−3	−	213	hypothetical protein	-none-	D23_1c1238	NA
  fig|6666666.60966.peg.1234	CDS	1150690	1150875	1	+	186	hypothetical protein	-none-	D23_1c1239	Neut_1006
  fig|6666666.60966.peg.1235	CDS	1150882	1151043	1	+	162	hypothetical protein	-none-	D23_1c1240	NA
  fig|6666666.60966.peg.1236	CDS	1151054	1151923	2	+	870	hypothetical protein	-none-	D23_1c1241	Neut_1006
  fig|6666666.60966.peg.1237	CDS	1151916	1152278	3	+	363	hypothetical protein	-none-	D23_1c1242	NA
  fig|6666666.60966.peg.1239	CDS	1152362	1152703	2	+	342	hypothetical protein	-none-	D23_1c1243	Neut_1005
  fig|6666666.60966.peg.1240	CDS	1153760	1152756	−2	−	1005	Mobile element protein	-none-	D23_1c1244	Neut_1862
  fig|6666666.60966.peg.1241	CDS	1153821	1154177	3	+	357	Putative transport	-none-	D23_1c1245	Neut_1004
  							system permease
  							protein
  fig|6666666.60966.peg.1242	CDS	1154289	1154441	3	+	153	FIG00626672:	-none-	D23_1c1246	Neut_1003
  							hypothetical protein
  fig|6666666.60966.peg.1243	CDS	1154607	1154476	−3	−	132	hypothetical protein	-none-	D23_1c1247	Neut_1226
  fig|6666666.60966.peg.1244	CDS	1156287	1154728	−3	−	1560	amino acid transporter	-none-	D23_1c1248	Neut_1227
  fig|6666666.60966.peg.1245	CDS	1157495	1156611	−2	−	885	DNA recombination-	DNA repair, bacterial	D23_1c1250	Neut_1228
  							dependent growth
  							factor C
  fig|6666666.60966.peg.1246	CDS	1158541	1157738	−1	−	804	Probable component of	Lipopolysaccharide	D23_1c1252	Neut_1229
  							the lipoprotein	assembly
  							assembly complex
  							(forms a complex with
  							YaeT, YfgL, and NlpB)
  fig|6666666.60966.peg.1247	CDS	1158543	1159571	3	+	1029	Ribosomal large subunit	RNA pseudouridine	D23_1c1253	Neut_1230
  							pseudouridine synthase	syntheses;
  							D (EC 4.2.1.70)	<br>Ribosome
  								biogenesis bacterial
  fig|6666666.60966.peg.1248	CDS	1159795	1161201	1	+	1407	Glutamine synthetase	Ammonia assimilation;	D23_1c1254	Neut_1231
  							type I (EC 6.3.1.2)	<br>Glutamine,
  								Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis;
  								<br>Glutamine
  								synthetases;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.1249	CDS	1161356	1161826	2	+	471	FIG00858905:	-none-	D23_1c1256	Neut_1232
  							hypothetical protein
  fig|6666666.60966.peg.1250	CDS	1161926	1161813	−2	−	114	hypothetical protein	-none-	D23_1c1257	NA
  fig|6666666.60966.peg.1251	CDS	1162096	1162263	1	+	168	hypothetical protein	-none-	D23_1c1258	NA
  fig|6666666.60966.peg.1252	CDS	1162260	1162415	3	+	156	hypothetical protein	-none-	D23_1c1259	NA
  fig|6666666.60966.peg.1253	CDS	1162412	1163191	2	+	780	Putative sulfate	Inorganic Sulfur	D23_1c1260	Neut_1235
  							permease	Assimilation
  fig|6666666.60966.peg.1254	CDS	1163827	1163267	−1	−	561	Iron-sulfur cluster	-none-	D23_1c1261	Neut_1236
  							assembly scaffold
  							protein IscU/NifU-like
  							for SUF system, SufE3
  fig|6666666.60966.peg.1255	CDS	1164319	1163837	−1	−	483	Putative iron-sulfur	-none-	D23_1c1262	Neut_1237
  							cluster assembly
  							scaffold protein for SUF
  							system, SufE2
  fig|6666666.60966.peg.1256	CDS	1165584	1164316	−3	−	1269	Cysteine desulfurase	Alanine biosynthesis;	D23_1c1263	Neut_1238
  							(EC 2.8.1.7), SufS	<br>mnm5U34
  							subfamily	biosynthesis bacteria;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1257	CDS	1166895	1165588	−3	−	1308	Iron-sulfur cluster	CBSS-	D23_1c1264	Neut_1239
  							assembly protein SufD	196164.1.peg.1690;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1258	CDS	1167683	1166892	−2	−	792	Iron-sulfur cluster	CBSS-	D23_1c1265	Neut_1240
  							assembly ATPase	196164.1.peg.1690;
  							protein SufC	<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1259	CDS	1169116	1167680	−1	−	1437	Iron-sulfur cluster	CBSS-	D23_1c1266	Neut_1241
  							assembly protein SufB	196164.1.peg.1690;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1260	CDS	1169465	1169136	−2	−	330	Iron binding protein	Alanine biosynthesis;	D23_1c1267	Neut_1242
  							IscA for iron-sulfur	<br>tRNA modification
  							cluster assembly	Bacteria
  fig|6666666.60966.peg.1261	CDS	1169958	1169491	−3	−	468	Iron-sulfur cluster	Alanine biosynthesis;	D23_1c1268	Neut_1243
  							regulator IscR	<br>Rrf2 family
  								transcriptional
  								regulators
  fig|6666666.60966.peg.1262	CDS	1170306	1171838	3	+	1533	2-isopropylmalate	Branched-Chain Amino	D23_1c1270	Neut_1244
  							synthase (EC 2.3.3.13)	Acid Biosynthesis;
  								<br>Leucine
  								Biosynthesis
  fig|6666666.60966.peg.1263	CDS	1171964	1172467	2	+	504	Cytochrome c-type	Biogenesis of c-type	D23_1c1271	Neut_1245
  							biogenesis protein ResA	cytochromes
  fig|6666666.60966.peg.1264	CDS	1173081	1172488	−3	−	594	FIG016425: Soluble lytic	-none-	D23_1c1272	Neut_1246
  							murein transglycosylase
  							and related regulatory
  							proteins (some contain
  							LysM/invasin domains)
  fig|6666666.60966.peg.1265	CDS	1174775	1173069	−2	−	1707	Prolyl-tRNA synthetase	tRNA aminoacylation,	D23_1c1273	Neut_1247
  							(EC 6.1.1.15), bacterial	Pro
  							type
  fig|6666666.60966.peg.1266	CDS	1175004	1175567	3	+	564	Adenosine (5&#39;)-	CBSS-	D23_1c1274	Neut_1248
  							pentaphospho-	364106.7.peg.3204;
  							(5&#39;&#39;)-	<br>Nudix proteins
  							adenosine	(nucleoside triphosphate
  							pyrophosphohydrolase	hydrolases);
  							(EC 3.6.1.—)	<br>Phosphoglycerate
  								mutase protein family
  fig|6666666.60966.peg.1267	CDS	1175673	1176677	3	+	1005	Cytochrome c551	Protection from Reactive	D23_1c1275	Neut_1249
  							peroxidase (EC 1.11.1.5)	Oxygen Species
  fig|6666666.60966.peg.1269	CDS	1176892	1178190	1	+	1299	Sensor histidine kinase	Global Two-component	D23_1c1276	Neut_1250
  							PrrB (RegB) (EC 2.7.3.—)	Regulator PrrBA in
  								Proteobacteria
  fig|6666666.60966.peg.1270	CDS	1178205	1178750	3	+	546	Dna binding response	Global Two-component	D23_1c1277	Neut_1251
  							regulator PrrA (RegA)	Regulator PrrBA in
  								Proteobacteria
  fig|6666666.60966.peg.1271	CDS	1181021	1178853	−2	−	2169	Ferrichrome-iron	-none-	D23_1c1278	Neut_1252
  							receptor
  fig|6666666.60966.peg.1272	CDS	1181355	1181558	3	+	204	hypothetical protein	-none-	D23_1c1279	NA
  fig|6666666.60966.peg.1273	CDS	1181609	1181776	2	+	168	hypothetical protein	-none-	D23_1c1280	NA
  fig|6666666.60966.peg.1274	CDS	1181748	1181981	3	+	234	Mobile element protein	-none-	D23_1c1281	NA
  fig|6666666.60966.peg.1275	CDS	1182136	1181990	−1	−	147	hypothetical protein	-none-	D23_1c1282	NA
  fig|6666666.60966.peg.1277	CDS	1182799	1182386	−1	−	414	hypothetical protein	-none-	D23_1c1283	Neut_1254
  fig|6666666.60966.peg.1278	CDS	1182892	1183920	1	+	1029	Mobile element protein	-none-	D23_1c1284	Neut_1746
  fig|6666666.60966.peg.1280	CDS	1185348	1184569	−3	−	780	CDP-diacylglycerol--	Glycerolipid and	D23_1c1285	Neut_1258
  							serine O-	Glycerophospholipid
  							phosphatidyltransferase	Metabolism in Bacteria
  							(EC 2.7.8.8)
  fig|6666666.60966.peg.1281	CDS	1186028	1185378	−2	−	651	Phosphatidylserine	Glycerolipid and	D23_1c1286	Neut_1259
  							decarboxylase (EC	Glycerophospholipid
  							4.1.1.65)	Metabolism in Bacteria
  fig|6666666.60966.peg.1282	CDS	1187049	1186033	−3	−	1017	Ketol-acid	Branched-Chain Amino	D23_1c1287	Neut_1260
  							reductoisomerase (EC	Acid Biosynthesis;
  							1.1.1.86)	<br>Coenzyme A
  								Biosynthesis
  fig|6666666.60966.peg.1283	CDS	1187629	1187138	−1	−	492	Acetolactate synthase	Acetolactate synthase	D23_1c1288	Neut_1261
  							small subunit (EC	subunits; <br>Branched-
  							2.2.1.6)	Chain Amino Acid
  								Biosynthesis
  fig|6666666.60966.peg.1284	CDS	1189337	1187634	−2	−	1704	Acetolactate synthase	Acetolactate synthase	D23_1c1289	Neut_1262
  							large subunit (EC	subunits; <br>Branched-
  							2.2.1.6)	Chain Amino Acid
  								Biosynthesis
  fig|6666666.60966.peg.1285	CDS	1189440	1189327	−3	−	114	hypothetical protein	-none-	D23_1c1290	NA
  fig|6666666.60966.peg.1287	CDS	1191111	1189663	−3	−	1449	TldD protein, part of	CBSS-316057.3.peg.563;	D23_1c1292	Neut_1263
  							TldE/TldD proteolytic	<br>CBSS-
  							complex	354.1.peg.2917;
  								<br>Putative TldE-TldD
  								proteolytic complex
  fig|6666666.60966.peg.1288	CDS	1192101	1191238	−3	−	864	FIG003879: Predicted	CBSS-354.1.peg.2917	D23_1c1293	Neut_1264
  							amidohydrolase/
  							Aliphatic amidase AmiE
  							(EC 3.5.1.4)
  fig|6666666.60966.peg.1289	CDS	1196193	1192303	−3	−	3891	FIG005080: Possible	CBSS-354.1.peg.2917	D23_1c1294	Neut_1265
  							exported protein
  fig|6666666.60966.peg.1290	CDS	1196421	1199210	3	+	2790	Glutamate-ammonia-	Ammonia assimilation;	D23_1c1295	Neut_1266
  							ligase	<br>CBSS-
  							adenylyltransferase (EC	316057.3.peg.3521
  							2.7.7.42)
  fig|6666666.60966.peg.1291	CDS	1200720	1200058	−3	−	663	FIG00859512:	-none-	D23_1c1300	Neut_1268
  							hypothetical protein
  fig|6666666.60966.peg.1292	CDS	1200901	1200761	−1	−	141	hypothetical protein	-none-	D23_1c1301	NA
  fig|6666666.60966.peg.1293	CDS	1200921	1202306	3	+	1386	Argininosuccinate lyase	Arginine Biosynthesis--	D23_1c1302	Neut_1269
  							(EC 4.3.2.1)	gjo; <br>Arginine
  								Biosynthesis extended
  fig|6666666.60966.peg.1294	CDS	1202336	1203241	2	+	906	Ribulosamine/erythrulosamine	Protein deglycation	D23_1c1303	Neut_1270
  							3-kinase
  							potentially involved in
  							protein deglycation
  fig|6666666.60966.peg.1295	CDS	1203386	1204876	2	+	1491	FIG00807778:	-none-	D23_1c1304	Neut_1271
  							hypothetical protein
  fig|6666666.60966.peg.1297	CDS	1205984	1205553	−2	−	432	hypothetical protein	-none-	D23_1c1305	Neut_1272
  fig|6666666.60966.peg.1298	CDS	1206313	1205987	−1	−	327	hypothetical protein	-none-	D23_1c1306	Neut_1273
  fig|6666666.60966.peg.1299	CDS	1206643	1206329	−1	−	315	CrcB protein	-none-	D23_1c1307	Neut_1274
  fig|6666666.60966.peg.1300	CDS	1206663	1206902	3	+	240	hypothetical protein	-none-	D23_1c1308	NA
  fig|6666666.60966.peg.1301	CDS	1207586	1206945	−2	−	642	Chemotaxis response-	-none-	D23_1c1309	Neut_1275
  							phosphatase CheZ
  fig|6666666.60966.peg.1302	CDS	1208030	1207635	−2	−	396	Chemotaxis regulator-	Flagellar motility	D23_1c1310	Neut_1276
  							transmits
  							chemoreceptor signals
  							to flagelllar motor
  							components CheY
  fig|6666666.60966.peg.1303	CDS	1209139	1208375	−1	−	765	Mobile element protein	-none-	D23_1c1311	NA
  fig|6666666.60966.peg.1305	CDS	1210466	1210134	−2	−	333	hypothetical protein	-none-	D23_1c1313	NA
  fig|6666666.60966.peg.1306	CDS	1210482	1210661	3	+	180	hypothetical protein	-none-	D23_1c1314	Neut_1280
  fig|6666666.60966.peg.1307	CDS	1212693	1210768	−3	−	1926	Cytochrome c, class I	-none-	D23_1c1315	Neut_1281
  fig|6666666.60966.peg.1308	CDS	1213523	1213044	−2	−	480	FIG00858481:	-none-	D23_1c1317	Neut_1282
  							hypothetical protein
  fig|6666666.60966.peg.1309	CDS	1213544	1214608	2	+	1065	Folate-dependent	-none-	D23_1c1318	Neut_1283
  							protein for Fe/S cluster
  							synthesis/repair in
  							oxidative stress
  fig|6666666.60966.peg.1310	CDS	1215290	1214631	−2	−	660	FOG: Ankyrin repeat	-none-	D23_1c1319	Neut_1284
  fig|6666666.60966.peg.1311	CDS	1215984	1215292	−3	−	693	Putative	YcfH	D23_1c1320	Neut_1285
  							deoxyribonuclease YcfH
  fig|6666666.60966.peg.1313	CDS	1216517	1216125	−2	−	393	Queuosine biosynthesis	Queuosine-Archaeosine	D23_1c1321	Neut_1286
  							QueD, PTPS-I	Biosynthesis; <br>Zinc
  								regulated enzymes;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1315	CDS	1216624	1217484	1	+	861	Radical SAM domain	-none-	D23_1c1322	Neut_1287
  							protein
  fig|6666666.60966.peg.1316	CDS	1217801	1217514	−2	−	288	FIG00858571:	-none-	D23_1c1323	Neut_1288
  							hypothetical protein
  fig|6666666.60966.peg.1318	CDS	1219170	1218214	−3	−	957	Cobalt-zinc-cadmium	Cobalt-zinc-cadmium	D23_1c1325	Neut_1289
  							resistance protein CzcD	resistance
  fig|6666666.60966.peg.1319	CDS	1221684	1219195	−3	−	2490	Lead, cadmium, zinc	Copper Transport	D23_1c1326	Neut_1290
  							and mercury	System; <br>Copper
  							transporting ATPase (EC	homeostasis
  							3.6.3.3) (EC 3.6.3.5);
  							Copper-translocating P-
  							type ATPase (EC 3.6.3.4)
  fig|6666666.60966.peg.1320	CDS	1223842	1221797	−1	−	2046	1,4-alpha-glucan	Glycogen metabolism	D23_1c1327	Neut_1291
  							(glycogen) branching
  							enzyme, GH-13-type (EC
  							2.4.1.18)
  fig|6666666.60966.peg.1321	CDS	1223815	1224054	1	+	240	hypothetical protein	-none-	D23_1c1328	NA
  fig|6666666.60966.peg.1322	CDS	1224141	1225418	3	+	1278	Glucose-1-phosphate	Glycogen metabolism	D23_1c1329	Neut_1292
  							adenylyltransferase (EC
  							2.7.7.27)
  fig|6666666.60966.peg.1323	CDS	1225484	1227202	2	+	1719	Amylopullulanase (EC	-none-	D23_1c1330	Neut_1293
  							3.2.1.1)/(EC 3.2.1.41)
  fig|6666666.60966.peg.1324	CDS	1227268	1229292	1	+	2025	Alpha-amylase (EC	-none-	D23_1c1331	Neut_1294
  							3.2.1.1)
  fig|6666666.60966.peg.1325	CDS	1229324	1232014	2	+	2691	hypothetical protein	-none-	D23_1c1332	Neut_1295
  fig|6666666.60966.peg.1326	CDS	1232973	1232236	−3	−	738	Uracil-DNA glycosylase,	Uracil-DNA glycosylase	D23_1c1334	Neut_1296
  							family
  4
  fig|6666666.60966.peg.1327	CDS	1233520	1233032	−1	−	489	Ribosomal-protein-	Bacterial RNA-	D23_1c1335	Neut_1297
  							S18p-alanine	metabolizing Zn-
  							acetyltransferase (EC	dependent hydrolases;
  							2.3.1.—)	<br>Ribosome
  								biogenesis bacterial
  fig|6666666.60966.peg.1328	CDS	1234194	1233523	−3	−	672	Inactive homolog of	-none-	D23_1c1336	Neut_1298
  							metal-dependent
  							proteases, putative
  							molecular chaperone
  fig|6666666.60966.peg.1329	CDS	1234742	1234209	−2	−	534	2&#39;-5&#39; RNA	RNA processing orphans	D23_1c1337	Neut_1299
  							ligase
  fig|6666666.60966.peg.1330	CDS	1235245	1234742	−1	−	504	2-C-methyl-D-erythritol	Isoprenoid Biosynthesis;	D23_1c1338	Neut_1300
  							2,4-cyclodiphosphate	<br>Nonmevalonate
  							synthase (EC 4.6.1.12)	Branch of Isoprenoid
  								Biosynthesis;
  								<br>Possible RNA
  								degradation cluster;
  								<br>Stationary phase
  								repair cluster
  fig|6666666.60966.peg.1331	CDS	1235544	1235356	−3	−	189	hypothetical protein	-none-	D23_1c1339	Neut_0314
  fig|6666666.60966.peg.1332	CDS	1235706	1235566	−3	−	141	hypothetical protein	-none-	D23_1c1340	Neut_0314
  fig|6666666.60966.peg.1335	CDS	1236565	1236008	−1	−	558	Translation elongation	Translation elongation	D23_1c1341	Neut_1302
  							factor P	factors bacterial
  fig|6666666.60966.peg.1336	CDS	1237794	1236640	−3	−	1155	hypothetical protein	-none-	D23_1c1342	Neut_1303
  fig|6666666.60966.peg.1337	CDS	1237927	1238928	1	+	1002	D-lactate	Fermentations: Lactate	D23_1c1343	Neut_1304
  							dehydrogenase (EC
  							1.1.1.28)
  fig|6666666.60966.peg.1338	CDS	1240296	1239037	−3	−	1260	putative membrane	-none-	D23_1c1344	Neut_1315
  							protein
  fig|6666666.60966.peg.1339	CDS	1241400	1240354	−3	−	1047	Peptide chain release	Programmed frameshift;	D23_1c1345	Neut_1316
  							factor 2; programmed	<br>Programmed
  							frameshift-containing	frameshift;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.1340	CDS	1243378	1241576	−1	−	1803	patatin family protein	-none-	D23_1c1346	Neut_1317
  fig|6666666.60966.peg.1341	CDS	1244736	1243531	−3	−	1206	Catalase (EC 1.11.1.6)	Oxidative stress;	D23_1c1348	NA
  								<br>Photorespiration
  								(oxidative C2 cycle);
  								<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.1342	CDS	1246268	1244739	−2	−	1530	Peroxidase (EC 1.11.1.7)	Oxidative stress;	D23_1c1349	NA
  								<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.1343	CDS	1247585	1246281	−2	−	1305	Peroxidase (EC 1.11.1.7)	Oxidative stress;	D23_1c1350	NA
  								<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.1344	CDS	1248078	1247623	−3	−	456	hypothetical protein	-none-	D23_1c1351	NA
  fig|6666666.60966.peg.1345	CDS	1248448	1251117	1	+	2670	FIG00860108:	-none-	D23_1c1352	Neut_0141
  							hypothetical protein
  fig|6666666.60966.peg.1346	CDS	1251218	1253155	2	+	1938	Choline dehydrogenase	-none-	D23_1c1353	NA
  							(EC 1.1.99.1)
  fig|6666666.60966.peg.1347	CDS	1256051	1253184	−2	−	2868	Peroxidase (EC 1.11.1.8)	-none-	D23_1c1354	NA
  fig|6666666.60966.peg.1348	CDS	1257505	1256081	−1	−	1425	Hemagglutinin	-none-	D23_1c1355	NA
  fig|6666666.60966.peg.1349	CDS	1258257	1257547	−3	−	711	hypothetical protein	-none-	D23_1c1356	NA
  fig|6666666.60966.peg.1350	CDS	1259233	1258262	−1	−	972	hypothetical protein	-none-	D23_1c1357	NA
  fig|6666666.60966.peg.1351	CDS	1261078	1259246	−1	−	1833	hypothetical protein	-none-	D23_1c1358	NA
  fig|6666666.60966.peg.1352	CDS	1262776	1261109	−1	−	1668	Arachidonate 15-	-none-	D23_1c1359	NA
  							lipoxygenase (EC
  							1.13.11.33)
  fig|6666666.60966.peg.1353	CDS	1264449	1262845	−3	−	1605	putative	-none-	D23_1c1360	NA
  							cyclooxygenase-2
  fig|6666666.60966.peg.1354	CDS	1266134	1264638	−2	−	1497	hypothetical protein	-none-	D23_1c1361	NA
  fig|6666666.60966.peg.1355	CDS	1266382	1266167	−1	−	216	hypothetical protein	-none-	D23_1c1362	NA
  fig|6666666.60966.peg.1356	CDS	1266704	1266444	−2	−	261	hypothetical protein	-none-	D23_1c1363	NA
  fig|6666666.60966.peg.1357	CDS	1267804	1266983	−1	−	822	Kazal-type serine	-none-	D23_1c1364	NA
  							protease inhibitor
  							domain
  fig|6666666.60966.peg.1358	CDS	1268650	1267970	−1	−	681	Kazal-type serine	-none-	D23_1c1365	NA
  							protease inhibitor
  							domain
  fig|6666666.60966.peg.1359	CDS	1268913	1268800	−3	−	114	hypothetical protein	-none-	D23_1c1366	NA
  fig|6666666.60966.peg.1360	CDS	1269830	1269126	−2	−	705	Mobile element protein	-none-	D23_1c1367	Neut_1318
  fig|6666666.60966.peg.1361	CDS	1270083	1269853	−3	−	231	Mobile element protein	-none-	D23_1c1368	Neut_1318
  fig|6666666.60966.peg.1362	CDS	1270317	1270111	−3	−	207	Mobile element protein	-none-	D23_1c1369	Neut_2405
  fig|6666666.60966.peg.1363	CDS	1271332	1270409	−1	−	924	alpha/beta hydrolase	-none-	D23_1c1370	NA
  							fold
  fig|6666666.60966.peg.1364	CDS	1271721	1271329	−3	−	393	hypothetical protein	-none-	D23_1c1371	NA
  fig|6666666.60966.peg.1365	CDS	1272160	1273251	1	+	1092	Putrescine transport	Polyamine Metabolism	D23_1c1372	Neut_1328
  							ATP-binding protein
  							PotA (TC 3.A.1.11.1)
  fig|6666666.60966.peg.1366	CDS	1273248	1274150	3	+	903	Spermidine Putrescine	Polyamine Metabolism	D23_1c1373	Neut_1329
  							ABC transporter
  							permease component
  							PotB (TC 3.A.1.11.1)
  fig|6666666.60966.peg.1367	CDS	1274170	1274955	1	+	786	Spermidine Putrescine	Polyamine Metabolism	D23_1c1374	Neut_1330
  							ABC transporter
  							permease component
  							potC (TC_3.A.1.11.1)
  fig|6666666.60966.peg.1368	CDS	1274952	1276061	3	+	1110	ABC transporter,	Polyamine Metabolism	D23_1c1375	Neut_1331
  							periplasmic spermidine
  							putrescine-binding
  							protein PotD (TC
  							3.A.1.11.1)
  fig|6666666.60966.peg.1369	CDS	1276066	1276374	1	+	309	Ferredoxin, 2Fe—2S	Alanine biosynthesis;	D23_1c1376	Neut_1332
  								<br>Soluble
  								cytochromes and
  								functionally related
  								electron carriers;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1370	CDS	1278030	1276423	−3	−	1608	Type I restriction-	Restriction-Modification	D23_1c1377	Neut_0541
  							modification system,	System; <br>Type I
  							DNA-methyltransferase	Restriction-Modification
  							subunit M (EC 2.1.1.72)
  fig|6666666.60966.peg.1371	CDS	1279031	1278027	−2	−	1005	Putative DNA-binding	Restriction-Modification	D23_1c1378	NA
  							protein in cluster with	System
  							Type I restriction-
  							modification system
  fig|6666666.60966.peg.1372	CDS	1282963	1279028	−1	−	3936	Type I restriction-	Restriction-Modification	D23_1c1379	Neut_0537
  							modification system,	System; <br>Type I
  							restriction subunit R (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.1373	CDS	1283272	1282982	−1	−	291	Type I restriction-	Restriction-Modification	D23_1c1380	NA
  							modification system,	System; <br>Type I
  							restriction subunit R (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.1374	CDS	1287342	1283581	−3	−	3762	macromolecule	-none-	D23_1c1381	Neut_1336
  							metabolism;
  							macromolecule
  							synthesis, modification;
  							dna-replication, repair,
  							restr./modif.
  fig|6666666.60966.peg.1375	CDS	1287828	1287349	−3	−	480	FIG00858549:	-none-	D23_1c1382	Neut_1337
  							hypothetical protein
  fig|6666666.60966.peg.1376	CDS	1288968	1287859	−3	−	1110	2-keto-3-deoxy-D-	Chorismate Synthesis;	D23_1c1383	Neut_1338
  							arabino-heptulosonate-	<br>Common Pathway
  							7-phosphate synthase I	For Synthesis of
  							alpha (EC 2.5.1.54)	Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.1377	CDS	1290768	1289113	−3	−	1656	MutS domain protein,	DNA repair, bacterial	D23_1c1384	Neut_1339
  							family
  6	MutL-MutS system
  fig|6666666.60966.peg.1378	CDS	1290915	1291493	3	+	579	FIG00858435:	-none-	D23_1c1385	Neut_1340
  							hypothetical protein
  fig|6666666.60966.peg.1379	CDS	1291506	1292660	3	+	1155	Probable Co/Zn/Cd	Cobalt-zinc-cadmium	D23_1c1386	Neut_1341
  							efflux system	resistance
  							membrane fusion
  							protein
  fig|6666666.60966.peg.1380	CDS	1292693	1293328	2	+	636	ABC transporter ATP-	-none-	D23_1c1387	Neut_1342
  							binding protein YvcR
  fig|6666666.60966.peg.1381	CDS	1293325	1294527	1	+	1203	ABC transporter	-none-	D23_1c1388	Neut_1343
  							permease protein
  fig|6666666.60966.peg.1382	CDS	1294533	1295732	3	+	1200	putative ABC	-none-	D23_1c1389	Neut_1344
  							transporter protein
  fig|6666666.60966.peg.1383	CDS	1296266	1295742	−2	−	525	FIG00859169:	-none-	D23_1c1390	Neut_1345
  							hypothetical protein
  fig|6666666.60966.peg.1385	CDS	1296862	1297086	1	+	225	ADA regulatory protein/	DNA repair, bacterial;	D23_1c1391	Neut_1346
  							Methylated-DNA--	<br>DNA repair,
  							protein-cysteine	bacterial
  							methyltransferase (EC
  							2.1.1.63)
  fig|6666666.60966.peg.1386	CDS	1297089	1297802	3	+	714	hypothetical protein	-none-	D23_1c1392	Neut_1347
  fig|6666666.60966.peg.1387	CDS	1298101	1297967	−1	−	135	hypothetical protein	-none-	D23_1c1393	NA
  fig|6666666.60966.peg.1389	CDS	1298212	1298838	1	+	627	Alkylated DNA repair	-none-	D23_1c1395	Neut_1349
  							protein
  fig|6666666.60966.peg.1390	CDS	1300170	1298923	−3	−	1248	Mobile element protein	-none-	D23_1c1396	Neut_0357
  fig|6666666.60966.peg.1391	CDS	1300681	1300355	−1	−	327	hypothetical protein	-none-	D23_1c1397	Neut_1350
  fig|6666666.60966.peg.1392	CDS	1301157	1300963	−3	−	195	Glutaredoxin	Glutaredoxins;	D23_1c1398	Neut_1351
  								<br>Glutathione: Redox
  								cycle; <br>Phage DNA
  								synthesis
  fig|6666666.60966.peg.1393	CDS	1302170	1301697	−2	−	474	Mobile element protein	-none-	D23_1c1399	Neut_1353
  fig|6666666.60966.peg.1394	CDS	1303008	1302400	−3	−	609	Glutathione S-	Glutathione: Non-redox	D23_1c1400	Neut_1354
  							transferase (EC	reactions
  							2.5.1.18)
  fig|6666666.60966.peg.1395	CDS	1303729	1303556	−1	−	174	hypothetical protein	-none-	D23_1c1402	NA
  fig|6666666.60966.peg.1396	CDS	1303948	1307514	1	+	3567	Exodeoxyribonuclease V	DNA repair, bacterial	D23_1c1403	Neut_1355
  							gamma chain (EC	RecBCD pathway
  							3.1.11.5)
  fig|6666666.60966.peg.1397	CDS	1307530	1311216	1	+	3687	Exodeoxyribonuclease V	DNA repair, bacterial	D23_1c1404	Neut_1356
  							beta chain (EC 3.1.11.5)	RecBCD pathway
  fig|6666666.60966.peg.1398	CDS	1311213	1313258	3	+	2046	Exodeoxyribonuclease V	DNA repair, bacterial	D23_1c1405	Neut_1357
  							alpha chain (EC	RecBCD pathway
  							3.1.11.5)
  fig|6666666.60966.peg.1399	CDS	1314581	1313277	−2	−	1305	Aspartyl	-none-	D23_1c1406	Neut_1358
  							aminopeptidase
  fig|6666666.60966.peg.1400	CDS	1315032	1314604	−3	−	429	PIN domain family	-none-	D23_1c1407	Neut_1359
  							protein
  fig|6666666.60966.peg.1401	CDS	1315334	1315032	−2	−	303	DNA-binding protein,	-none-	D23_1c1408	Neut_1360
  							CopG family
  fig|6666666.60966.peg.1402	CDS	1316699	1315362	−2	−	1338	Sensor protein PhoQ	-none-	D23_1c1409	Neut_1361
  							(EC 2.7.13.3)
  fig|6666666.60966.peg.1403	CDS	1317382	1316696	−1	−	687	DNA-binding response	-none-	D23_1c1410	Neut_1362
  							regulator
  fig|6666666.60966.peg.1404	CDS	1317741	1317451	−3	−	291	hypothetical protein	-none-	D23_1c1411	Neut_1363
  fig|6666666.60966.peg.1405	CDS	1318192	1317827	−1	−	366	Putative metal	G3E family of P-loop	D23_1c1412	NA
  							chaperone, involved in	GTPases (metallocenter
  							Zn homeostasis, GTPase	biosynthesis); <br>Zinc
  							of COG0523 family	regulated enzymes
  fig|6666666.60966.peg.1406	CDS	1318485	1319036	3	+	552	Protein of unknown	-none-	D23_1c1413	Neut_1365
  							function DUF924
  fig|6666666.60966.peg.1407	CDS	1320160	1319171	−1	−	990	Integron integrase	Integrons	D23_1c1414	Neut_1366
  							IntlPac
  fig|6666666.60966.peg.1408	CDS	1320314	1321651	2	+	1338	DNA modification	-none-	D23_1c1415	NA
  							methyltransferase
  fig|6666666.60966.peg.1409	CDS	1321654	1322532	1	+	879	hypothetical protein	-none-	D23_1c1416	NA
  fig|6666666.60966.peg.1410	CDS	1322665	1322880	1	+	216	hypothetical protein	-none-	D23_1c1417	NA
  fig|6666666.60966.peg.1411	CDS	1323474	1324154	3	+	681	ThiJ/Pfpl family protein	-none-	D23_1c1418	NA
  fig|6666666.60966.peg.1412	CDS	1324808	1324990	2	+	183	hypothetical protein	-none-	D23_1c1419	NA
  fig|6666666.60966.peg.1413	CDS	1325941	1324979	−1	−	963	Mobile element protein	-none-	D23_1c1420	Neut_1746
  fig|6666666.60966.peg.1415	CDS	1326558	1328531	3	+	1974	Monoamine oxidase	Auxin biosynthesis;	D23_1c1421	NA
  							(1.4.3.4)	<br>Glycine and Serine
  								Utilization;
  								<br>Threonine
  								degradation
  fig|6666666.60966.peg.1417	CDS	1328848	1328711	−1	−	138	Mobile element protein	-none-	D23_1c1422	Neut_2501
  fig|6666666.60966.peg.1418	CDS	1329144	1328821	−3	−	324	Mobile element protein	-none-	D23_1c1423	Neut_1624
  fig|6666666.60966.peg.1419	CDS	1329566	1329129	−2	−	438	Mobile element protein	-none-	D23_1c1424	Neut_1888
  fig|6666666.60966.peg.1420	CDS	1330200	1329892	−3	−	309	Death on curing	Phd-Doc, YdcE-YdcD	D23_1c1425	NA
  							protein, Doc toxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.1421	CDS	1330677	1330231	−3	−	447	Prevent host death	Phd-Doc, YdcE-YdcD	D23_1c1426	NA
  							protein, Phd antitoxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.1423	CDS	1331253	1331387	3	+	135	Mobile element protein	-none-	D23_1c1427	Neut_2500
  fig|6666666.60966.peg.1424	CDS	1331444	1332292	2	+	849	Mobile element protein	-none-	D23_1c1428	Neut_1888
  fig|6666666.60966.peg.1425	CDS	1332744	1333214	3	+	471	3-demethylubiquinone-	-none-	D23_1c1429	Neut_1376
  							9 3-methyltransferase
  fig|6666666.60966.peg.1426	CDS	1333410	1335026	3	+	1617	Dihydroxyacetone	Dihydroxyacetone	D23_1c1431	Neut_1377
  							kinase, ATP-dependent	kinases
  							(EC 2.7.1.29)
  fig|6666666.60966.peg.1427	CDS	1335644	1335210	−2	−	435	hypothetical protein	-none-	D23_1c1432	Neut_1378
  fig|6666666.60966.peg.1428	CDS	1339065	1335670	−3	−	3396	PDZ domain	-none-	D23_1c1433	Neut_1379
  fig|6666666.60966.peg.1429	CDS	1339241	1340350	2	+	1110	COGs COG0823	-none-	D23_1c1435	Neut_1380
  fig|6666666.60966.peg.1430	CDS	1341715	1340438	−1	−	1278	Putative diheme	Soluble cytochromes	D23_1c1436	Neut_1381
  							cytochrome c-553	and functionally related
  								electron carriers
  fig|6666666.60966.peg.1431	CDS	1342431	1341712	−3	−	720	Probable cytochrome c2	Soluble cytochromes	D23_1c1437	Neut_1382
  								and functionally related
  								electron carriers
  fig|6666666.60966.peg.1432	CDS	1342445	1342963	2	+	519	FIG00859968:	-none-	D23_1c1438	Neut_1383
  							hypothetical protein
  fig|6666666.60966.peg.1433	CDS	1344805	1342952	−1	−	1854	Cell division protein	Bacterial Cell Division	D23_1c1439	Neut_1384
  							FtsH (EC 3.4.24.—)
  fig|6666666.60966.peg.1434	CDS	1345012	1346118	1	+	1107	S-	Glutathione-dependent	D23_1c1440	Neut_1385
  							(hydroxymethyl)glutathione	pathway of
  							dehydrogenase (EC	formaldehyde
  							1.1.1.284)	detoxification
  fig|6666666.60966.peg.1435	CDS	1346131	1347000	1	+	870	S-formylglutathione	Glutathione-dependent	D23_1c1441	Neut_1386
  							hydrolase (EC 3.1.2.12)	pathway of
  								formaldehyde
  								detoxification
  fig|6666666.60966.peg.1436	CDS	1348436	1347264	−2	−	1173	Ornithine	Arginine and Ornithine	D23_1c1442	Neut_1387
  							decarboxylase (EC	Degradation;
  							4.1.1.17)/Arginine	<br>Arginine and
  							decarboxylase (EC	Ornithine Degradation;
  							4.1.1.19)	<br>Polyamine
  								Metabolism;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.1437	CDS	1348961	1349230	2	+	270	FIG00858492:	-none-	D23_1c1443	Neut_1388
  							hypothetical protein
  fig|6666666.60966.peg.1438	CDS	1349336	1349214	−2	−	123	hypothetical protein	-none-	D23_1c1444	NA
  fig|6666666.60966.peg.1439	CDS	1349660	1350622	2	+	963	Mobile element protein	-none-	D23_1c1446	Neut_1862
  fig|6666666.60966.peg.1440	CDS	1350742	1352079	1	+	1338	Ribosomal protein S12p	Methylthiotransferases;	D23_1c1447	Neut_1389
  							Asp88 (E. coli)	<br>Ribosomal protein
  							methylthiotransferase	S12p Asp
  								methylthiotransferase
  fig|6666666.60966.peg.1441	CDS	1353046	1352255	−1	−	792	hypothetical protein	-none-	D23_1c1448	Neut_1390
  fig|6666666.60966.peg.1442	CDS	1353301	1353618	1	+	318	Cell division protein	Bacterial Cell Division	D23_1c1449	Neut_1391
  							BolA
  fig|6666666.60966.peg.1443	CDS	1353569	1354282	2	+	714	LemA family protein	-none-	D23_1c1450	Neut_1392
  fig|6666666.60966.peg.1444	CDS	1354309	1355193	1	+	885	Beta-propeller domains	-none-	D23_1c1451	Neut_1393
  							of methanol
  							dehydrogenase type
  fig|6666666.60966.peg.1445	CDS	1355207	1355710	2	+	504	FIG004694:	-none-	D23_1c1452	Neut_1394
  							Hypothetical protein
  fig|6666666.60966.peg.1446	CDS	1356010	1356513	1	+	504	DNA-directed RNA	-none-	D23_1c1454	Neut_1395
  							polymerase specialized
  							sigma subunit, sigma24-
  							like
  fig|6666666.60966.peg.1447	CDS	1356510	1357232	3	+	723	FIG00859011:	-none-	D23_1c1455	Neut_1396
  							hypothetical protein
  fig|6666666.60966.peg.1448	CDS	1357326	1359644	3	+	2319	ABC transporter,	-none-	D23_1c1456	Neut_1397
  							transmembrane
  							region: ABC transporter
  							related
  fig|6666666.60966.peg.1449	CDS	1359641	1360108	2	+	468	DUF1854 domain-	-none-	D23_1c1457	Neut_1398
  							containing protein
  fig|6666666.60966.peg.1451	CDS	1360927	1362021	1	+	1095	hypothetical protein	-none-	D23_1c1458	Neut_1860
  fig|6666666.60966.peg.1452	CDS	1362049	1362342	1	+	294	Mobile element protein	-none-	D23_1c1459	Neut_1719
  fig|6666666.60966.peg.1453	CDS	1362441	1363319	3	+	879	Mobile element protein	-none-	D23_1c1460	Neut_1720
  fig|6666666.60966.peg.1454	CDS	1363397	1365250	2	+	1854	hypothetical protein	-none-	D23_1c1461	NA
  fig|6666666.60966.peg.1455	CDS	1365453	1365262	−3	−	192	Mobile element protein	-none-	D23_1c1462	Neut_2502
  fig|6666666.60966.peg.1456	CDS	1365648	1367945	3	+	2298	Cyanophycin synthase	Cyanophycin	D23_1c1463	Neut_1401
  							(EC 6.3.2.29)(EC	Metabolism
  							6.3.2.30)
  fig|6666666.60966.peg.1457	CDS	1367966	1370572	2	+	2607	Cyanophycin synthase	Cyanophycin	D23_1c1464	Neut_1402
  							(EC 6.3.2.29)(EC	Metabolism
  							6.3.2.30)
  fig|6666666.60966.peg.1458	CDS	1371664	1370720	−1	−	945	Copper-containing	Denitrification;	D23_1c1465	Neut_1403
  							nitrite reductase (EC	<br>Denitrifying
  							1.7.2.1)	reductase gene clusters
  fig|6666666.60966.peg.1459	CDS	1372091	1371708	−2	−	384	cytochrome c, class IC	-none-	D23_1c1466	Neut_1404
  fig|6666666.60966.peg.1460	CDS	1372789	1372091	−1	−	699	Cytochrome c, class I	-none-	D23_1c1467	Neut_1405
  fig|6666666.60966.peg.1461	CDS	1373888	1372827	−2	−	1062	Multicopper oxidase	Copper homeostasis	D23_1c1468	Neut_1406
  fig|6666666.60966.peg.1462	CDS	1374021	1374137	3	+	117	hypothetical protein	-none-	D23_1c1469	NA
  fig|6666666.60966.peg.1463	CDS	1374189	1374653	3	+	465	Nitrite-sensitive	Nitrosative stress;	D23_1c1470	Neut_1407
  							transcriptional	<br>Oxidative stress;
  							repressor NsrR	<br>Rrf2 family
  								transcriptional
  								regulators
  fig|6666666.60966.peg.1464	CDS	1378537	1374641	−1	−	3897	FIG00858660:	-none-	D23_1c1471	Neut_1408
  							hypothetical protein
  fig|6666666.60966.peg.1465	CDS	1380248	1378539	−2	−	1710	Outer membrane	-none-	D23_1c1472	Neut_1409
  							protein
  fig|6666666.60966.peg.1466	CDS	1380471	1380340	−3	−	132	hypothetical protein	-none-	D23_1c1473	NA
  fig|6666666.60966.peg.1467	CDS	1380491	1381141	2	+	651	Uracil-DNA glycosylase,	Uracil-DNA glycosylase	D23_1c1474	Neut_1410
  							family
  5
  fig|6666666.60966.peg.1468	CDS	1381162	1381350	1	+	189	putative isomerase	-none-	D23_1c1475	Neut_1411
  fig|6666666.60966.peg.1469	CDS	1381364	1383178	2	+	1815	Excinuclease ABC	DNA repair, UvrABC	D23_1c1476	Neut_1412
  							subunit C	system
  fig|6666666.60966.peg.1470	CDS	1383321	1384283	3	+	963	Mobile element protein	-none-	D23_1c1477	Neut_1746
  fig|6666666.60966.peg.1471	CDS	1384401	1384814	3	+	414	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c1478	NA
  							transport system,
  							permease component
  fig|6666666.60966.peg.1472	CDS	1384811	1385149	2	+	339	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c1479	NA
  							transport system,
  							permease component
  fig|6666666.60966.peg.1474	CDS	1385894	1388275	2	+	2382	Penicillin acylase II	-none-	D23_1c1480	Neut_1415
  fig|6666666.60966.peg.1475	CDS	1388559	1388395	−3	−	165	hypothetical protein	-none-	D23_1c1481	NA
  fig|6666666.60966.peg.1476	CDS	1388615	1389973	2	+	1359	Response regulatory	-none-	D23_1c1482	Neut_1416
  							protein
  fig|6666666.60966.peg.1477	CDS	1390014	1391603	3	+	1590	Long-chain-fatty-acid--	Biotin biosynthesis;	D23_1c1483	Neut_1417
  							CoAligase (EC 6.2.1.3)	<br>Biotin synthesis
  								cluster; <br>Fatty acid
  								metabolism cluster
  fig|6666666.60966.peg.1478	CDS	1391630	1392835	2	+	1206	Diaminopimelate	Lysine Biosynthesis DAP	D23_1c1484	Neut_1418
  							decarboxylase (EC	Pathway, GJO scratch
  							4.1.1.20)
  fig|6666666.60966.peg.1479	CDS	1392996	1394843	3	+	1848	Asparagine synthetase	Cyanophycin	D23_1c1485	Neut_1419
  							[glutamine-hydrolyzing]	Metabolism;
  							(EC 6.3.5.4)	<br>Glutamate and
  								Aspartate uptake in
  								Bacteria; <br>Glutamine,
  								Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.1480	CDS	1394795	1394911	2	+	117	hypothetical protein	-none-	D23_1c1486	NA
  fig|6666666.60966.peg.1482	CDS	1395163	1395975	1	+	813	FIG00858746:	-none-	D23_1c1488	Neut_1420
  							hypothetical protein
  fig|6666666.60966.peg.1483	CDS	1397102	1396140	−2	−	963	Mobile element protein	-none-	D23_1c1490	Neut_1746
  fig|6666666.60966.peg.1484	CDS	1397178	1397462	3	+	285	COGs COG0226	-none-	D23_1c1491	Neut_1423
  fig|6666666.60966.peg.1485	CDS	1397455	1398681	1	+	1227	FIG00859800:	-none-	D23_1c1492	Neut_1424
  							hypothetical protein
  fig|6666666.60966.peg.1486	CDS	1398693	1401635	3	+	2943	diguanylate	-none-	D23_1c1493	Neut_1425
  							cyclase/phosphodiesterase
  							(GGDEF & EAL
  							domains) with PAS/PAC
  							sensor(s)
  fig|6666666.60966.peg.1488	CDS	1402082	1401924	−2	−	159	hypothetical protein	-none-	D23_1c1494	NA
  fig|6666666.60966.peg.1489	CDS	1402531	1402115	−1	−	417	OsmC/Ohr family	-none-	D23_1c1495	Neut_1426
  							protein
  fig|6666666.60966.peg.1490	CDS	1403584	1402532	−1	−	1053	DNA polymerase III	CBSS-208964.1.peg.3988	D23_1c1496	Neut_1427
  							delta subunit (EC
  							2.7.7.7)
  fig|6666666.60966.peg.1491	CDS	1404106	1403612	−1	−	495	LPS-assembly	CBSS-	D23_1c1497	Neut_1428
  							lipoprotein RlpB	208964.1.peg.3988;
  							precursor (Rare	<br>Lipopolysaccharide
  							lipoprotein B)	assembly
  fig|6666666.60966.peg.1492	CDS	1406732	1404126	−2	−	2607	Leucyl-tRNA synthetase	CBSS-	D23_1c1498	Neut_1429
  							(EC 6.1.1.4)	208964.1.peg.3988;
  								<br>tRNA
  								aminoacylation, Leu
  fig|6666666.60966.peg.1493	CDS	1406756	1407925	2	+	1170	S-	CBSS-	D23_1c1499	Neut_1430
  							adenosylmethionine:tRNA	211586.1.peg.2832;
  							ribosyltransferase-	<br>Queuosine-
  							isomerase (EC 5.—.—.—)	Archaeosine
  								Biosynthesis;
  								<br>Scaffold proteins for
  								[4Fe—4S] cluster
  								assembly (MRP family);
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1494	CDS	1407922	1409007	1	+	1086	tRNA-guanine	CBSS-	D23_1c1500	Neut_1431
  							transglycosylase (EC	211586.1.peg.2832;
  							2.4.2.29)	<br>Queuosine-
  								Archaeosine
  								Biosynthesis;
  								<br>Scaffold proteins for
  								[4Fe—4S] cluster
  								assembly (MRP family);
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1495	CDS	1409072	1409536	2	+	465	Preprotein translocase	CBSS-211586.1.peg.2832	D23_1c1501	Neut_1432
  							subunit YajC (TC
  							3.A.5.1.1)
  fig|6666666.60966.peg.1496	CDS	1409575	1411470	1	+	1896	Protein-export	CBSS-211586.1.peg.2832	D23_1c1502	Neut_1433
  							membrane protein
  							SecD (TC 3.A.5.1.1)
  fig|6666666.60966.peg.1497	CDS	1411495	1412427	1	+	933	Protein-export	CBSS-211586.1.peg.2832	D23_1c1503	Neut_1434
  							membrane protein SecF
  							(TC 3.A.5.1.1)
  fig|6666666.60966.peg.1498	CDS	1412467	1412844	1	+	378	FIG028220:	-none-	D23_1c1504	Neut_1435
  							hypothetical protein co-
  							occurring with HEAT
  							repeat protein
  fig|6666666.60966.peg.1499	CDS	1412897	1413628	2	+	732	Ubiquinone/menaquinone	Menaquinone and	D23_1c1505	Neut_1436
  							biosynthesis	Phylloquinone
  							methyltransferase UbiE	Biosynthesis;
  							(EC 2.1.1.—)	<br>Ubiquinone
  								Biosynthesis;
  								<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.1500	CDS	1413802	1413680	−1	−	123	Agmatinase (EC	Arginine and Ornithine	D23_1c1506	Neut_1437
  							3.5.3.11)	Degradation;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.1501	CDS	1414650	1413808	−3	−	843	Agmatinase (EC	Arginine and Ornithine	D23_1c1507	Neut_1437
  							3.5.3.11)	Degradation;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.1502	CDS	1415255	1414815	−2	−	441	Lipoprotein signal	Lipoprotein Biosynthesis;	D23_1c1509	Neut_1438
  							peptidase (EC 3.4.23.36)	<br>Signal peptidase
  fig|6666666.60966.peg.1503	CDS	1415346	1415224	−3	−	123	hypothetical protein	-none-	D23_1c1510	NA
  fig|6666666.60966.peg.1504	CDS	1418173	1415339	−1	−	2835	Isoleucyl-tRNA	tRNA aminoacylation, Ile	D23_1c1511	Neut_1439
  							synthetase (EC 6.1.1.5)
  fig|6666666.60966.peg.1505	CDS	1418945	1418148	−2	−	798	Riboflavin kinase (EC	Riboflavin, FMN and FAD	D23_1c1512	Neut_1440
  							2.7.1.26)/FMN	metabolism;
  							adenylyltransferase (EC	<br>Riboflavin, FMN and
  							2.7.7.2)	FAD metabolism;
  								<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>Riboflavin,
  								FMN and FAD
  								metabolism in plants;
  								<br>riboflavin to FAD;
  								<br>riboflavin to FAD
  fig|6666666.60966.peg.1506	CDS	1419539	1419237	−2	−	303	possible sec-	-none-	D23_1c1513	Neut_1441
  							independent protein
  							translocase protein
  							TatC
  fig|6666666.60966.peg.1507	CDS	1420011	1419886	−3	−	126	hypothetical protein	-none-	D23_1c1514	Neut_1442
  fig|6666666.60966.peg.1508	CDS	1420112	1422079	2	+	1968	Dipeptide-binding ABC	ABC transporter	D23_1c1514	Neut_1442
  							transporter, periplasmic	dipeptide (TC 3.A.1.5.2)
  							substrate-binding
  							component (TC
  							3.A.1.5.2)
  fig|6666666.60966.peg.1509	CDS	1422089	1423066	2	+	978	Oligopeptide transport	ABC transporter	D23_1c1515	Neut_1443
  							system permease	oligopeptide (TC
  							protein OppB (TC	3.A.1.5.1)
  							3.A.1.5.1)
  fig|6666666.60966.peg.1511	CDS	1423196	1424851	2	+	1656	DnaJ-class molecular	Protein chaperones	D23_1c1516	Neut_1444
  							chaperone CbpA
  fig|6666666.60966.peg.1512	CDS	1424900	1425844	2	+	945	DnaJ-class molecular	Protein chaperones	D23_1c1517	Neut_1445
  							chaperone CbpA
  fig|6666666.60966.peg.1513	CDS	1425856	1426152	1	+	297	InterPro IPR000551	-none-	D23_1c1518	Neut_1446
  fig|6666666.60966.peg.1514	CDS	1426240	1427103	1	+	864	FIG00858431:	-none-	D23_1c1519	Neut_1447
  							hypothetical protein
  fig|6666666.60966.peg.1515	CDS	1427120	1427659	2	+	540	FAD pyrophosphatase	-none-	D23_1c1520	Neut_1448
  							(EC 3.6.1.18), projected
  							from PMID:18815383
  fig|6666666.60966.peg.1516	CDS	1428946	1428491	−1	−	456	Mobile element protein	-none-	D23_1c1522	Neut_2502
  fig|6666666.60966.peg.1517	CDS	1429295	1428909	−2	−	387	Mobile element protein	-none-	D23_1c1523	Neut_0884
  fig|6666666.60966.peg.1518	CDS	1430487	1429300	−3	−	1188	Mobile element protein	-none-	D23_1c1524	Neut_2405
  fig|6666666.60966.peg.1519	CDS	1430505	1430621	3	+	117	patatin family protein	-none-	D23_1c1525	Neut_1317
  fig|6666666.60966.peg.1520	CDS	1430834	1430670	−2	−	165	hypothetical protein	-none-	D23_1c1526	NA
  fig|6666666.60966.peg.1521	CDS	1431909	1431424	−3	−	486	hypothetical protein	-none-	D23_1c1527	Neut_1449
  fig|6666666.60966.peg.1522	CDS	1432156	1431899	−1	−	258	hypothetical protein	-none-	D23_1c1528	Neut_1450
  fig|6666666.60966.peg.1523	CDS	1432650	1432159	−3	−	492	phage-related	-none-	D23_1c1529	Neut_1451
  							hypothetical protein
  fig|6666666.60966.peg.1524	CDS	1432970	1432650	−2	−	321	hypothetical protein	-none-	D23_1c1530	Neut_1452
  fig|6666666.60966.peg.1525	CDS	1433143	1432967	−1	−	177	hypothetical protein	-none-	D23_1c1531	Neut_1453
  fig|6666666.60966.peg.1526	CDS	1434487	1433552	−1	−	936	hypothetical protein	-none-	D23_1c1533	Neut_1454
  fig|6666666.60966.peg.1527	CDS	1437226	1434497	−1	−	2730	hypothetical protein	-none-	D23_1c1534	Neut_1455
  fig|6666666.60966.peg.1528	CDS	1437449	1437267	−2	−	183	Phage protein	-none-	D23_1c1535	Neut_1456
  fig|6666666.60966.peg.1529	CDS	1437694	1437467	−1	−	228	hypothetical protein	-none-	D23_1c1536	Neut_1457
  fig|6666666.60966.peg.1530	CDS	1438472	1437702	−2	−	771	hypothetical protein	-none-	D23_1c1537	Neut_1458
  fig|6666666.60966.peg.1531	CDS	1439638	1438469	−1	−	1170	hypothetical protein	-none-	D23_1c1538	Neut_1459
  fig|6666666.60966.peg.1532	CDS	1441511	1439631	−2	−	1881	Phage tail length tape-	Phage tail proteins;	D23_1c1539	Neut_1460
  							measure protein	<br>Phage tail proteins 2
  fig|6666666.60966.peg.1533	CDS	1442755	1441508	−1	−	1248	Mobile element protein	-none-	D23_1c1540	Neut_0357
  fig|6666666.60966.peg.1534	CDS	1443390	1442854	−3	−	537	Phage protein	-none-	D23_1c1541	Neut_1460
  fig|6666666.60966.peg.1535	CDS	1443638	1443390	−2	−	249	hypothetical protein	-none-	D23_1c1542	Neut_1461
  fig|6666666.60966.peg.1536	CDS	1444027	1443677	−1	−	351	Phage protein	-none-	D23_1c1543	Neut_1462
  fig|6666666.60966.peg.1537	CDS	1444752	1444036	−3	−	717	major tail protein,	-none-	D23_1c1544	Neut_1463
  							putative
  fig|6666666.60966.peg.1538	CDS	1445120	1444758	−2	−	363	hypothetical protein	-none-	D23_1c1545	Neut_1464
  fig|6666666.60966.peg.1539	CDS	1445638	1445117	−1	−	522	FIG00959132:	-none-	D23_1c1546	Neut_1465
  							hypothetical protein
  fig|6666666.60966.peg.1540	CDS	1445985	1445650	−3	−	336	Phage protein	-none-	D23_1c1547	Neut_1466
  fig|6666666.60966.peg.1541	CDS	1446544	1445987	−1	−	558	Similar to Gene Transfer	-none-	D23_1c1548	Neut_1467
  							Agent (GTA) ORFG06
  fig|6666666.60966.peg.1542	CDS	1446900	1446601	−3	−	300	hypothetical protein	-none-	D23_1c1549	Neut_1468
  fig|6666666.60966.peg.1543	CDS	1448136	1446910	−3	−	1227	Phage major capsid	Phage capsid proteins	D23_1c1550	Neut_1469
  							protein
  fig|6666666.60966.peg.1544	CDS	1448949	1448218	−3	−	732	Prophage Clp protease-	cAMP signaling in	D23_1c1551	Neut_1470
  							like protein	bacteria
  fig|6666666.60966.peg.1545	CDS	1450207	1448915	−1	−	1293	Phage portal protein	Phage packaging	D23_1c1552	Neut_1471
  								machinery
  fig|6666666.60966.peg.1546	CDS	1451877	1450204	−3	−	1674	Phage terminase large	Phage packaging	D23_1c1553	Neut_1472
  							subunit	machinery
  fig|6666666.60966.peg.1547	CDS	1452346	1451882	−1	−	465	Phage terminase, small	Phage packaging	D23_1c1554	Neut_1473
  							subunit	machinery
  fig|6666666.60966.peg.1548	CDS	1452801	1452478	−3	−	324	Phage holin	-none-	D23_1c1555	Neut_1474
  fig|6666666.60966.peg.1549	CDS	1453267	1452887	−1	−	381	hypothetical protein	-none-	D23_1c1556	Neut_1475
  fig|6666666.60966.peg.1550	CDS	1453430	1453269	−2	−	162	hypothetical protein	-none-	D23_1c1557	NA
  fig|6666666.60966.peg.1551	CDS	1453630	1453451	−1	−	180	hypothetical protein	-none-	D23_1c1558	NA
  fig|6666666.60966.peg.1552	CDS	1453862	1453623	−2	−	240	hypothetical protein	-none-	D23_1c1559	Neut_1477
  fig|6666666.60966.peg.1553	CDS	1456504	1454171	−1	−	2334	DNA primase, phage	-none-	D23_1c1560	Neut_1478
  							associated # P4-type
  fig|6666666.60966.peg.1554	CDS	1456740	1456501	−3	−	240	hypothetical protein	-none-	D23_1c1561	NA
  fig|6666666.60966.peg.1555	CDS	1456744	1456887	1	+	144	Phage-related protein	-none-	D23_1c1562	Neut_1480
  fig|6666666.60966.peg.1556	CDS	1456894	1457172	1	+	279	Helix-turn-helix motif	-none-	D23_1c1563	Neut_1481
  fig|6666666.60966.peg.1557	CDS	1457678	1457277	−2	−	402	hypothetical protein	-none-	D23_1c1564	NA
  fig|6666666.60966.peg.1558	CDS	1458137	1458478	2	+	342	hypothetical protein	-none-	D23_1c1565	NA
  fig|6666666.60966.peg.1559	CDS	1458868	1459158	1	+	291	hypothetical protein	-none-	D23_1c1566	NA
  fig|6666666.60966.peg.1561	CDS	1459812	1459672	−3	−	141	hypothetical protein	-none-	D23_1c1567	NA
  fig|6666666.60966.peg.1563	CDS	1460270	1460563	2	+	294	Mobile element protein	-none-	D23_1c1568	Neut_1719
  fig|6666666.60966.peg.1564	CDS	1460662	1461540	1	+	879	Mobile element protein	-none-	D23_1c1569	Neut_1720
  fig|6666666.60966.peg.1565	CDS	1462142	1461954	−2	−	189	hypothetical protein	-none-	D23_1c1570	Neut_1489
  fig|6666666.60966.peg.1567	CDS	1462722	1462844	3	+	123	hypothetical protein	-none-	D23_1c1571	NA
  fig|6666666.60966.peg.1568	CDS	1463137	1463829	1	+	693	putative nuclease	-none-	D23_1c1572	Neut_1491
  fig|6666666.60966.peg.1569	CDS	1464806	1463826	−2	−	981	Abortive infection	-none-	D23_1c1573	NA
  							bacteriophage
  							resistance protein
  fig|6666666.60966.peg.1570	CDS	1466353	1465106	−1	−	1248	Mobile element protein	-none-	D23_1c1574	Neut_0357
  fig|6666666.60966.peg.1573	CDS	1466953	1467108	1	+	156	hypothetical protein	-none-	D23_1c1575	NA
  fig|6666666.60966.peg.1574	CDS	1467105	1467389	3	+	285	hypothetical protein	-none-	D23_1c1576	Neut_1493
  fig|6666666.60966.peg.1575	CDS	1467386	1467868	2	+	483	hypothetical protein	-none-	D23_1c1577	Neut_1494
  fig|6666666.60966.peg.1576	CDS	1467883	1468245	1	+	363	hypothetical protein	-none-	D23_1c1578	Neut_1495
  fig|6666666.60966.peg.1577	CDS	1468255	1468638	1	+	384	hypothetical protein	-none-	D23_1c1579	Neut_1496
  fig|6666666.60966.peg.1580	CDS	1469337	1470362	3	+	1026	Integrase	-none-	D23_1c1580	Neut_1498
  fig|6666666.60966.peg.1581	CDS	1470687	1470989	3	+	303	Exodeoxyribonuclease	DNA repair, bacterial;	D23_1c1582	Neut_1499
  							VII small subunit (EC	<br>Purine salvage
  							3.1.11.6)	cluster
  fig|6666666.60966.peg.1582	CDS	1470979	1471872	1	+	894	Octaprenyl diphosphate	Isoprenoid Biosynthesis;	D23_1c1583	Neut_1500
  							synthase (EC 2.5.1.90)/	<br>Isoprenoid
  							Dimethylallyltransferase	Biosynthesis;
  							(EC 2.5.1.1)/(2E,6E)-	<br>Isoprenoid
  							farnesyl diphosphate	Biosynthesis:
  							synthase (EC 2.5.1.10)/	Interconversions;
  							Geranylgeranyl	<br>Isoprenoinds for
  							diphosphate synthase	Quinones;
  							(EC 2.5.1.29)	<br>Isoprenoinds for
  								Quinones;
  								<br>Isoprenoinds for
  								Quinones;
  								<br>Isoprenoinds for
  								Quinones;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis
  fig|6666666.60966.peg.1583	CDS	1471935	1473779	3	+	1845	1-deoxy-D-xylulose 5-	Isoprenoid Biosynthesis;	D23_1c1584	Neut_1501
  							phosphate synthase (EC	<br>Nonmevalonate
  							2.2.1.7)	Branch of Isoprenoid
  								Biosynthesis;
  								<br>Pyridoxin (Vitamin
  								B6) Biosynthesis;
  								<br>Thiamin
  								biosynthesis
  fig|6666666.60966.peg.1584	CDS	1473895	1474698	1	+	804	GTP cyclohydrolase I	Folate Biosynthesis;	D23_1c1585	Neut_1502
  							(EC 3.5.4.16) type 2	<br>Queuosine-
  								Archaeosine
  								Biosynthesis; <br>Zinc
  								regulated enzymes
  fig|6666666.60966.peg.1585	CDS	1474865	1475485	2	+	621	InterPro IPR005134	-none-	D23_1c1586	Neut_1503
  							COGs COG2862
  fig|6666666.60966.peg.1586	CDS	1476254	1475514	−2	−	741	FolM Alternative	Folate Biosynthesis	D23_1c1587	Neut_1504
  							dihydrofolate reductase
  1
  fig|6666666.60966.peg.1587	CDS	1476327	1477502	3	+	1176	COG1565:	-none-	D23_1c1588	Neut_1505
  							Uncharacterized
  							conserved protein
  fig|6666666.60966.peg.1588	CDS	1478242	1477499	−1	−	744	5&#39;-	Adenosyl nucleosidases;	D23_1c1589	Neut_1506
  							methylthioadenosine	<br>Adenosyl
  							nucleosidase (EC	nucleosidases;
  							3.2.2.16)/S-	<br>CBSS-
  							adenosylhomocysteine	320388.3.peg.3759;
  							nucleosidase (EC	<br>CBSS-
  							3.2.2.9)	320388.3.peg.3759;
  								<br>Methionine
  								Biosynthesis;
  								<br>Methionine
  								Degradation;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.1589	CDS	1480269	1478239	−3	−	2031	Squalene--hopene	CBSS-	D23_1c1590	Neut_1507
  							cyclase (EC 5.4.99.17)	320388.3.peg.3759;
  								<br>Hopanes
  fig|6666666.60966.peg.1590	CDS	1481103	1480384	−3	−	720	Surface lipoprotein	-none-	D23_1c1591	Neut_1508
  fig|6666666.60966.peg.1591	CDS	1481997	1481389	−3	−	609	Ferric siderophore	Ton and Tol transport	D23_1c1592	Neut_1509
  							transport system,	systems
  							biopolymer transport
  							protein ExbB
  fig|6666666.60966.peg.1592	CDS	1482298	1483644	1	+	1347	Exodeoxyribonuclease	DNA repair, bacterial;	D23_1c1594	Neut_1510
  							VII large subunit (EC	<br>Purine salvage
  							3.1.11.6)	cluster
  fig|6666666.60966.peg.1593	CDS	1483709	1484089	2	+	381	COG2363	-none-	D23_1c1595	Neut_1511
  fig|6666666.60966.peg.1594	CDS	1484150	1485328	2	+	1179	23S rRNA (guanine-N-2-)-	RNA methylation	D23_1c1596	Neut_1512
  							methyltransferase
  							rlmL EC 2.1.1.—)
  fig|6666666.60966.peg.1595	CDS	1485345	1485833	3	+	489	Periplasmic	Biogenesis of c-type	D23_1c1597	Neut_1513
  							thiol:disulfide	cytochromes;
  							oxidoreductase DsbB,	<br>Periplasmic disulfide
  							required for DsbA	interchange
  							reoxidation
  fig|6666666.60966.peg.1596	CDS	1486114	1486503	1	+	390	Endoribonuclease L-PSP	CBSS-	D23_1c1598	Neut_1514
  								176299.4.peg.1996A
  fig|6666666.60966.peg.1598	CDS	1486998	1486651	−3	−	348	FIG016027: protein of	-none-	D23_1c1599	Neut_1515
  							unknown function YeaO
  fig|6666666.60966.peg.1599	CDS	1487053	1487727	1	+	675	AttE component of	AttEFGH ABC Transport	D23_1c1600	Neut_1516
  							AttEFGH ABC transport	System
  							system
  fig|6666666.60966.peg.1600	CDS	1487724	1490273	3	+	2550	AttF component of	AttEFGH ABC Transport	D23_1c1601	Neut_1517
  							AttEFGH ABC transport	System; <br>AttEFGH
  							system/AttG	ABC Transport System
  							component of AttEFGH
  							ABC transport system
  fig|6666666.60966.peg.1601	CDS	1490273	1491343	2	+	1071	AttH component of	AttEFGH ABC Transport	D23_1c1602	Neut_1518
  							AttEFGH ABC transport	System
  							system
  fig|6666666.60966.peg.1602	CDS	1491424	1491666	1	+	243	Molybdopterin	-none-	D23_1c1603	Neut_1519
  							biosynthesis protein B
  fig|6666666.60966.peg.1603	CDS	1491738	1491619	−3	−	120	hypothetical protein	-none-	D23_1c1604	NA
  fig|6666666.60966.peg.1605	CDS	1492158	1492982	3	+	825	Particulate methane	Particulate methane	D23_1c1605	Neut_1520
  							monooxygenase C-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.1607	CDS	1494238	1493309	−1	−	930	Cytochrome c551	Protection from Reactive	D23_1c1607	Neut_1521
  							peroxidase (EC 1.11.1.5)	Oxygen Species
  fig|6666666.60966.peg.1609	CDS	1494804	1495091	3	+	288	Mobile element protein	-none-	D23_1c1608	Neut_2502
  fig|6666666.60966.peg.1611	CDS	1495989	1495288	−3	−	702	2-C-methyl-D-erythritol	Isoprenoid Biosynthesis;	D23_1c1609	Neut_1525
  							4-phosphate	<br>Nonmevalonate
  							cytidylyltransferase (EC	Branch of Isoprenoid
  							2.7.7.60)	Biosynthesis;
  								<br>Possible RNA
  								degradation cluster;
  								<br>Stationary phase
  								repair cluster
  fig|6666666.60966.peg.1612	CDS	1496057	1496497	2	+	441	Inosine-5&#39;-	Purine conversions;	D23_1c1610	Neut_1526
  							monophosphate	<br>Purine salvage
  							dehydrogenase (EC	cluster
  							1.1.1.205)
  fig|6666666.60966.peg.1613	CDS	1497472	1496552	−1	−	921	Cell division protein	Bacterial Cell Division;	D23_1c1611	Neut_1527
  							FtsX	<br>Heat shock Cell
  								division Proteases and a
  								Methyltransferase
  fig|6666666.60966.peg.1614	CDS	1498131	1497469	−3	−	663	Cell division	Bacterial Cell Division;	D23_1c1612	Neut_1528
  							transporter, ATP-	<br>Heat shock Cell
  							binding protein FtsE (TC	division Proteases and a
  							3.A.5.1.1)	Methyltransferase
  fig|6666666.60966.peg.1615	CDS	1499195	1498158	−2	−	1038	Signal recognition	Bacterial Cell Division;	D23_1c1613	Neut_1529
  							particle receptor	<br>Bacterial signal
  							protein FtsY (=alpha	recognition particle
  							subunit) (TC 3.A.5.1.1)	(SRP); <br>Heat shock
  								Cell division Proteases
  								and a Methyltransferase;
  								<br>Universal GTPases
  fig|6666666.60966.peg.1616	CDS	1499262	1500653	3	+	1392	FIG015547: peptidase,	-none-	D23_1c1614	Neut_1530
  							M16 family
  fig|6666666.60966.peg.1617	CDS	1500780	1501865	3	+	1086	Alanine racemase (EC	Alanine biosynthesis;	D23_1c1615	Neut_1531
  							5.1.1.1)	<br>Pyruvate Alanine
  								Serine Interconversions
  fig|6666666.60966.peg.1618	CDS	1502688	1501894	−3	−	795	Peptidyl-prolyl cis-trans	Queuosine-Archaeosine	D23_1c1616	Neut_1532
  							isomerase (EC 5.2.1.8)	Biosynthesis
  fig|6666666.60966.peg.1619	CDS	1502854	1502738	−1	−	117	hypothetical protein	-none-	D23_1c1617	NA
  fig|6666666.60966.peg.1620	CDS	1503164	1502862	−2	−	303	YciL protein	Broadly distributed	D23_1c1618	Neut_1533
  								proteins not in
  								subsystems; <br>CBSS-
  								211586.9.peg.2729
  fig|6666666.60966.peg.1621	CDS	1504431	1503277	−3	−	1155	Rubredoxin-NAD(+)	Rubrerythrin	D23_1c1619	Neut_1534
  							reductase (EC 1.18.1.1)
  fig|6666666.60966.peg.1622	CDS	1504748	1505626	2	+	879	Probable protease htpX	-none-	D23_1c1620	Neut_1535
  							homolog (EC 3.4.24.—)
  fig|6666666.60966.peg.1623	CDS	1505626	1505739	1	+	114	hypothetical protein	-none-	D23_1c1621	NA
  fig|6666666.60966.peg.1624	CDS	1506477	1505698	−3	−	780	Surface lipoprotein	-none-	D23_1c1622	Neut_1536
  fig|6666666.60966.peg.1625	CDS	1507909	1506626	−1	−	1284	Glutamate-1-	CBSS-196164.1.peg.461;	D23_1c1623	Neut_1537
  							semialdehyde	<br>Heme and Siroheme
  							aminotransferase (EC	Biosynthesis
  							5.4.3.8)
  fig|6666666.60966.peg.1626	CDS	1508584	1507946	−1	−	639	Thiamin-phosphate	5-FCL-like protein;	D23_1c1624	Neut_1538
  							pyrophosphorylase (EC	<br>Thiamin
  							2.5.1.3)	biosynthesis
  fig|6666666.60966.peg.1627	CDS	1509419	1508577	−2	−	843	Phosphomethylpyrimidine	5-FCL-like protein;	D23_1c1625	Neut_1539
  							kinase (EC 2.7.4.7)	<br>Thiamin
  								biosynthesis
  fig|6666666.60966.peg.1628	CDS	1509508	1509660	1	+	153	Rubredoxin	Rubrerythrin	D23_1c1626	Neut_1540
  fig|6666666.60966.peg.1629	CDS	1509660	1510049	3	+	390	Lactoylglutathione lyase	Glutathione: Non-redox	D23_1c1627	Neut_1541
  							(EC 4.4.1.5)	reactions;
  								<br>Methylglyoxal
  								Metabolism
  fig|6666666.60966.peg.1630	CDS	1510238	1510603	2	+	366	probable iron binding	-none-	D23_1c1628	Neut_1542
  							protein from the
  							HesB_IscA_SufA family
  fig|6666666.60966.peg.1631	CDS	1511703	1510612	−3	−	1092	Anhydro-N-	Recycling of	D23_1c1629	Neut_1543
  							acetylmuramic acid	Peptidoglycan Amino
  							kinase (EC 2.7.1.—)	Sugars
  fig|6666666.60966.peg.1632	CDS	1513070	1511739	−2	−	1332	Peptidase, M23/M37	-none-	D23_1c1630	Neut_1544
  							family
  fig|6666666.60966.peg.1633	CDS	1513163	1514383	2	+	1221	Tyrosyl-tRNA	tRNA aminoacylation,	D23_1c1631	Neut_1545
  							synthetase (EC 6.1.1.1)	Tyr
  fig|6666666.60966.peg.1634	CDS	1514577	1515674	3	+	1098	Myo-inositol 2-	-none-	D23_1c1632	Neut_1547
  							dehydrogenase (EC
  							1.1.1.18)
  fig|6666666.60966.peg.1635	CDS	1515687	1516748	3	+	1062	N-Acetylneuraminate	CMP-N-	D23_1c1633	Neut_1548
  							cytidylyltransferase (EC	acetylneuraminate
  							2.7.7.43)	Biosynthesis; <br>Sialic
  								Acid Metabolism
  fig|6666666.60966.peg.1636	CDS	1516926	1518425	3	+	1500	N-acetylneuraminate	CMP-N-	D23_1c1634	Neut_1549
  							synthase (EC 2.5.1.56)	acetylneuraminate
  								Biosynthesis; <br>Sialic
  								Acid Metabolism
  fig|6666666.60966.peg.1637	CDS	1518919	1518437	−1	−	483	Ribonucleotide	Ribonucleotide	D23_1c1635	Neut_1551
  							reductase	redcution
  							transcriptional
  							regulator NrdR
  fig|6666666.60966.peg.1638	CDS	1520246	1518996	−2	−	1251	Serine	5-FCL-like protein;	D23_1c1636	Neut_1552
  							hydroxymethyltransferase	<br>Glycine
  							(EC 2.1.2.1)	Biosynthesis;
  								<br>Glycine and Serine
  								Utilization;
  								<br>Photorespiration
  								(oxidative C2 cycle);
  								<br>Serine Biosynthesis
  fig|6666666.60966.peg.1639	CDS	1520440	1521180	1	+	741	PqqC-like protein	Folate Biosynthesis	D23_1c1638	Neut_1553
  fig|6666666.60966.peg.1640	CDS	1522218	1521283	−3	−	936	Transcriptional	LysR-family proteins in	D23_1c1639	Neut_1554
  							activator MetR	Escherichia coli;
  								<br>LysR-family proteins
  								in Salmonella enterica
  								Typhimurium;
  								<br>Methionine
  								Biosynthesis
  fig|6666666.60966.peg.1641	CDS	1522318	1524594	1	+	2277	5-	Methionine Biosynthesis	D23_1c1640	Neut_1555
  							methyltetrahydropteroyltriglutamate--
  							homocysteine
  							methyltransferase (EC
  							2.1.1.14)
  fig|6666666.60966.peg.1643	CDS	1526020	1524767	−1	−	1254	UDP-N-	Peptidoglycan	D23_1c1641	Neut_1556
  							acetylglucosamine 1-	Biosynthesis; <br>UDP-
  							carboxyvinyltransferase	N-acetylmuramate from
  							(EC 2.5.1.7)	Fructose-6-phosphate
  								Biosynthesis
  fig|6666666.60966.peg.1644	CDS	1526108	1526497	2	+	390	Putative translation	-none-	D23_1c1642	Neut_1557
  							initiation inhibitor, yjgF
  							family
  fig|6666666.60966.peg.1645	CDS	1526528	1528585	2	+	2058	ATP-dependent DNA	-none-	D23_1c1643	Neut_1558
  							helicase RecG (EC
  							3.6.1.—)
  fig|6666666.60966.peg.1646	CDS	1529436	1528588	−3	−	849	Hypothetical ATP-	-none-	D23_1c1644	Neut_1559
  							binding protein
  							UPF0042, contains P-
  							loop
  fig|6666666.60966.peg.1647	CDS	1529521	1530072	1	+	552	Transcription	CBSS-243265.1.peg.198;	D23_1c1645	Neut_1560
  							elongation factor GreB	<br>Transcription
  								factors bacterial
  fig|6666666.60966.peg.1648	CDS	1532787	1530136	−3	−	2652	Malto-oligosyltrehalose	-none-	D23_1c1646	NA
  							synthase (EC 5.4.99.15)
  fig|6666666.60966.peg.1649	CDS	1533038	1532850	−2	−	189	hypothetical protein	-none-	D23_1c1647	NA
  fig|6666666.60966.peg.1650	CDS	1534716	1533031	−3	−	1686	Malto-oligosyltrehalose	-none-	D23_1c1648	Neut_1291
  							trehalohydrolase (EC
  							3.2.1.141)
  fig|6666666.60966.peg.1651	CDS	1535327	1534896	−2	−	432	Trehalose synthase,	-none-	D23_1c1649	NA
  							nucleoside diphosphate
  							glucose dependent
  fig|6666666.60966.peg.1652	CDS	1535502	1535386	−3	−	117	hypothetical protein	-none-	D23_1c1650	NA
  fig|6666666.60966.peg.1653	CDS	1535501	1536028	2	+	528	Sensory histidine kinase	-none-	D23_1c1651	Neut_1565
  							QseC
  fig|6666666.60966.peg.1654	CDS	1535992	1536651	1	+	660	Sensory histidine kinase	-none-	D23_1c1652	Neut_1565
  							QseC
  fig|6666666.60966.peg.1655	CDS	1537148	1537849	2	+	702	Protein of unknown	-none-	D23_1c1653	Neut_1566
  							function DUF484
  fig|6666666.60966.peg.1656	CDS	1537833	1538798	3	+	966	Tyrosine recombinase	-none-	D23_1c1654	Neut_1567
  							XerC
  fig|6666666.60966.peg.1657	CDS	1539747	1538845	−3	−	903	Arogenate	Chorismate Synthesis;	D23_1c1655	Neut_1568
  							dehydrogenase (EC	<br>Phenylalanine and
  							1.3.1.43)	Tyrosine Branches from
  								Chorismate
  fig|6666666.60966.peg.1658	CDS	1540893	1539775	−3	−	1119	Biosynthetic Aromatic	Phenylalanine and	D23_1c1656	Neut_1569
  							amino acid	Tyrosine Branches from
  							aminotransferase beta	Chorismate
  							(EC 2.6.1.57)
  fig|6666666.60966.peg.1659	CDS	1541973	1540915	−3	−	1059	Chorismate mutase I	Chorismate Synthesis;	D23_1c1657	Neut_1570
  							(EC 5.4.99.5)/	<br>Chorismate
  							Prephenate	Synthesis;
  							dehydratase (EC	<br>Phenylalanine and
  							4.2.1.51)	Tyrosine Branches from
  								Chorismate;
  								<br>Phenylalanine and
  								Tyrosine Branches from
  								Chorismate
  fig|6666666.60966.peg.1660	CDS	1543230	1542013	−3	−	1218	D-3-phosphoglycerate	Glycine and Serine	D23_1c1658	Neut_1571
  							dehydrogenase (EC	Utilization;
  							1.1.1.95)	<br>Pyridoxin (Vitamin
  								B6) Biosynthesis;
  								<br>Serine Biosynthesis
  fig|6666666.60966.peg.1661	CDS	1544329	1543223	−1	−	1107	Phosphoserine	Glycine and Serine	D23_1c1659	Neut_1572
  							aminotransferase (EC	Utilization;
  							2.6.1.52)	<br>Pyridoxin (Vitamin
  								B6) Biosynthesis;
  								<br>Serine Biosynthesis
  fig|6666666.60966.peg.1662	CDS	1546893	1544347	−3	−	2547	DNA gyrase subunit A	Cell Division Subsystem	D23_1c1660	Neut_1573
  							(EC 5.99.1.3)	including YidCD;
  								<br>DNA gyrase
  								subunits; <br>DNA
  								replication cluster
  1;
  								<br>DNA
  								topoisomerases, Type II,
  								ATP-dependent;
  								<br>Resistance to
  								fluoroquinolones
  fig|6666666.60966.peg.1663	CDS	1547556	1546963	−3	−	594	COGs COG2854	-none-	D23_1c1661	Neut_1574
  fig|6666666.60966.peg.1664	CDS	1548691	1547573	−1	−	1119	Glycosyl transferase,	-none-	D23_1c1662	Neut_1575
  							family 2
  fig|6666666.60966.peg.1665	CDS	1549918	1548755	−1	−	1164	Possible Fe—S	-none-	D23_1c1663	Neut_1576
  							oxidoreductase
  fig|6666666.60966.peg.1666	CDS	1550134	1550247	1	+	114	hypothetical protein	-none-	D23_1c1664	NA
  fig|6666666.60966.peg.1668	CDS	1550439	1552481	3	+	2043	Transketolase (EC	Calvin-Benson cycle;	D23_1c1666	Neut_1577
  							2.2.1.1)	<br>Pentose phosphate
  								pathway
  fig|6666666.60966.peg.1669	CDS	1552544	1553551	2	+	1008	NADPH-dependent	Calvin-Benson cycle;	D23_1c1667	Neut_1578
  							glyceraldehyde-3-	<br>Calvin-Benson cycle;
  							phosphate	<br>Glycolysis and
  							dehydrogenase (EC	Gluconeogenesis;
  							1.2.1.13)/NAD-	<br>Glycolysis and
  							dependent	Gluconeogenesis;
  							glyceraldehyde-3-	<br>Pyridoxin (Vitamin
  							phosphate	B6) Biosynthesis
  							dehydrogenase (EC
  							1.2.1.12)
  fig|6666666.60966.peg.1670	CDS	1553775	1553659	−3	−	117	hypothetical protein	-none-	D23_1c1668	NA
  fig|6666666.60966.peg.1671	CDS	1553870	1555048	2	+	1179	Phosphoglycerate	Calvin-Benson cycle;	D23_1c1669	Neut_1579
  							kinase (EC 2.7.2.3)	<br>Glycolysis and
  								Gluconeogenesis
  fig|6666666.60966.peg.1672	CDS	1555083	1556573	3	+	1491	Pyruvate kinase (EC	Glycerate metabolism;	D23_1c1670	Neut_1580
  							2.7.1.40)	<br>Glycolysis and
  								Gluconeogenesis;
  								<br>Pyruvate
  								metabolism I:
  								anaplerotic reactions,
  								PEP
  fig|6666666.60966.peg.1673	CDS	1556682	1557746	3	+	1065	Fructose-bisphosphate	Calvin-Benson cycle;	D23_1c1671	Neut_1581
  							aldolase class II (EC	<br>Glycolysis and
  							4.1.2.13)	Gluconeogenesis
  fig|6666666.60966.peg.1674	CDS	1558432	1560090	1	+	1659	Cytochrome c oxidases	Terminal cytochrome C	D23_1c1672	Neut_1582
  							subunit CcoN (EC	oxidases
  							1.9.3.1)
  fig|6666666.60966.peg.1675	CDS	1560080	1560688	2	+	609	Cytochrome c oxidase	Terminal cytochrome C	D23_1c1673	Neut_1583
  							subunit CcoO (EC	oxidases
  							1.9.3.1)
  fig|6666666.60966.peg.1676	CDS	1560753	1561364	3	+	612	Copper-containing	Denitrification;	D23_1c1674	Neut_1584
  							nitrite reductase (EC	<br>Denitrifying
  							1.7.2.1)	reductase gene clusters
  fig|6666666.60966.peg.1677	CDS	1561404	1562054	3	+	651	Cytochrome oxidase	Biogenesis of	D23_1c1675	Neut_1585
  							biogenesis protein	cytochrome c oxidases
  							Sco1/SenC/PrrC,
  							putative copper
  							metallochaperone
  fig|6666666.60966.peg.1678	CDS	1562150	1562635	2	+	486	hypothetical	-none-	D23_1c1676	Neut_1586
  							cytochrome oxidase
  							associated membrane
  							protein
  fig|6666666.60966.peg.1679	CDS	1563699	1562746	−3	−	954	Rare lipoprotein A	Peptidoglycan	D23_1c1677	Neut_1587
  							precursor	Biosynthesis
  fig|6666666.60966.peg.1680	CDS	1564813	1563704	−1	−	1110	Rod shape-determining	Bacterial Cytoskeleton;	D23_1c1678	Neut_1588
  							protein RodA	<br>Bacterial cell
  								division cluster;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.1681	CDS	1566713	1564836	−2	−	1878	Penicillin-binding	16S rRNA modification	D23_1c1679	Neut_1589
  							protein 2 (PBP-2)	within P site of
  								ribosome; <br>Bacterial
  								cell division cluster;
  								<br>CBSS-
  								83331.1.peg.3039;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.1682	CDS	1567261	1566710	−1	−	552	Rod shape-determining	Bacterial Cell Division;	D23_1c1680	Neut_1590
  							protein MreD	<br>Bacterial
  								Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>CBSS-
  								354.1.peg.2917
  fig|6666666.60966.peg.1683	CDS	1568123	1567233	−2	−	891	Rod shape-determining	Bacterial Cell Division;	D23_1c1681	Neut_1591
  							protein MreC	<br>Bacterial
  								Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>CBSS-
  								354.1.peg.2917
  fig|6666666.60966.peg.1684	CDS	1569547	1568486	−1	−	1062	Rod shape-determining	Bacterial Cell Division;	D23_1c1682	Neut_1592
  							protein MreB	<br>Bacterial
  								Cytoskeleton;
  								<br>Bacterial cell
  								division cluster
  fig|6666666.60966.peg.1685	CDS	1569665	1569997	2	+	333	Aspartyl-tRNA(Asn)	tRNA aminoacylation,	D23_1c1683	Neut_1593
  							amidotransferase	Asp and Asn; <br>tRNA
  							subunit C (EC 6.3.5.6) @	aminoacylation, Glu and
  							Glutamyl-tRNA(Gln)	Gln
  							amidotransferase
  							subunit C (EC 6.3.5.7)
  fig|6666666.60966.peg.1686	CDS	1570062	1571522	3	+	1461	Aspartyl-tRNA(Asn)	tRNA aminoacylation,	D23_1c1684	Neut_1594
  							amidotransferase	Asp and Asn; <br>tRNA
  							subunit A (EC 6.3.5.6) @	aminoacylation, Glu and
  							Glutamyl-tRNA(Gln)	Gln
  							amidotransferase
  							subunit A (EC 6.3.5.7)
  fig|6666666.60966.peg.1687	CDS	1571587	1573023	1	+	1437	Aspartyl-tRNA(Asn)	tRNA aminoacylation,	D23_1c1685	Neut_1595
  							amidotransferase	Asp and Asn; <br>tRNA
  							subunit B (EC 6.3.5.6) @	aminoacylation, Glu and
  							Glutamyl-tRNA(Gln)	Gln
  							amidotransferase
  							subunit B (EC 6.3.5.7)
  fig|6666666.60966.peg.1688	CDS	1573150	1573001	−1	−	150	hypothetical protein	-none-	D23_1c1686	NA
  fig|6666666.60966.peg.1689	CDS	1573320	1573129	−3	−	192	FIG00859257:	-none-	D23_1c1687	NA
  							hypothetical protein
  fig|6666666.60966.peg.1691	CDS	1574140	1573703	−1	−	438	heat shock protein,	-none-	D23_1c1688	Neut_1596
  							Hsp20 family
  fig|6666666.60966.peg.1692	CDS	1574662	1574802	1	+	141	Integrase	-none-	D23_1c1690	Neut_1498
  fig|6666666.60966.peg.1693	CDS	1575055	1574942	−1	−	114	hypothetical protein	-none-	D23_1c1692	NA
  fig|6666666.60966.peg.1694	CDS	1575572	1575369	−2	−	204	hypothetical protein	-none-	D23_1c1693	NA
  fig|6666666.60966.peg.1696	CDS	1575911	1575753	−2	−	159	Mobile element protein	-none-	D23_1c1694	Neut_1094
  fig|6666666.60966.peg.1697	CDS	1576265	1578433	2	+	2169	GTP pyrophosphokinase	Stringent Response,	D23_1c1695	Neut_1601
  							(EC 2.7.6.5), (p)ppGpp	(p)ppGpp metabolism;
  							synthetase II/	<br>Stringent Response,
  							Guanosine-	(p)ppGpp metabolism
  							3&#39;,5&#39;-
  							bis(diphosphate)
  							3&#39;-
  							pyrophosphohydrolase
  							(EC 3.1.7.2)
  fig|6666666.60966.peg.1698	CDS	1578452	1579135	2	+	684	FIG00858669:	-none-	D23_1c1696	Neut_1602
  							hypothetical protein
  fig|6666666.60966.peg.1699	CDS	1579798	1579145	−1	−	654	Periplasmic	Biogenesis of c-type	D23_1c1697	Neut_1603
  							thiol:disulfide	cytochromes;
  							interchange protein	<br>Periplasmic disulfide
  							DsbA	interchange
  fig|6666666.60966.peg.1700	CDS	1580580	1579915	−3	−	666	Cell division protein	-none-	D23_1c1698	Neut_1604
  fig|6666666.60966.peg.1701	CDS	1582304	1580604	−2	−	1701	Arginyl-tRNA synthetase	tRNA aminoacylation,	D23_1c1699	Neut_1605
  							(EC 6.1.1.19)	Arg
  fig|6666666.60966.peg.1702	CDS	1582613	1583272	2	+	660	FIG00859197:	-none-	D23_1c1700	Neut_1606
  							hypothetical protein
  fig|6666666.60966.peg.1703	CDS	1583410	1584297	1	+	888	Methylenetetrahydrofolate	5-FCL-like protein;	D23_1c1701	Neut_1607
  							dehydrogenase	<br>One-carbon
  							(NADP+) (EC 1.5.1.5)/	metabolism by
  							Methenyltetrahydrofolate	tetrahydropterines;
  							cyclohydrolase (EC	<br>One-carbon
  							3.5.4.9)	metabolism by
  								tetrahydropterines
  fig|6666666.60966.peg.1704	CDS	1584339	1586999	3	+	2661	Pyruvate	5-FCL-like protein;	D23_1c1702	Neut_1608
  							dehydrogenase E1	<br>Dehydrogenase
  							component (EC 1.2.4.1)	complexes;
  								<br>Methionine
  								Degradation;
  								<br>Pyruvate
  								metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.1705	CDS	1587072	1588421	3	+	1350	Dihydrolipoamide	5-FCL-like protein;	D23_1c1703	Neut_1609
  							acetyltransferase	<br>Dehydrogenase
  							component of pyruvate	complexes;
  							dehydrogenase	<br>Pyruvate
  							complex (EC 2.3.1.12)	metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.1706	CDS	1588457	1589170	2	+	714	Nicotinate-nucleotide	NAD and NADP cofactor	D23_1c1704	Neut_1610
  							adenylyltransferase (EC	biosynthesis global
  							2.7.7.18)
  fig|6666666.60966.peg.1707	CDS	1589167	1589532	1	+	366	Iojap protein	-none-	D23_1c1705	Neut_1611
  fig|6666666.60966.peg.1708	CDS	1589624	1590091	2	+	468	LSU m3Psi1915	RNA methylation;	D23_1c1706	Neut_1612
  							methyltransferase RlmH	<br>Ribosome
  								biogenesis bacterial;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.1709	CDS	1590169	1590792	1	+	624	Septum formation	Bacterial Cell Division;	D23_1c1707	Neut_1613
  							protein Maf	<br>Bacterial
  								Cytoskeleton;
  								<br>Bacterial cell
  								division cluster;
  								<br>CBSS-
  								354.1.peg.2917
  fig|6666666.60966.peg.1710	CDS	1590825	1592276	3	+	1452	Cytoplasmic axial	Bacterial Cell Division;	D23_1c1708	Neut_1614
  							filament protein CafA	<br>CBSS-
  							and Ribonuclease G (EC	354.1.peg.2917;
  							3.1.4.—)	<br>RNA processing and
  								degradation, bacterial
  fig|6666666.60966.peg.1711	CDS	1592500	1593222	1	+	723	Ferric siderophore	Ton and Tol transport	D23_1c1709	Neut_1615
  							transport system,	systems
  							periplasmic binding
  							protein TonB
  fig|6666666.60966.peg.1712	CDS	1593226	1594023	1	+	798	MotA/TolQ/ExbB	Ton and Tol transport	D23_1c1710	Neut_1616
  							proton channel family	systems
  							protein
  fig|6666666.60966.peg.1713	CDS	1594023	1594448	3	+	426	Biopolymer transport	Ton and Tol transport	D23_1c1711	Neut_1617
  							protein ExbD/TolR	systems
  fig|6666666.60966.peg.1714	CDS	1595300	1594518	−2	−	783	23S rRNA (guanosine-	RNA methylation	D23_1c1712	Neut_1618
  							2&#39;-O-)-
  							methyltransferase rlmB
  							(EC 2.1.1.—)
  fig|6666666.60966.peg.1715	CDS	1597532	1595328	−2	−	2205	3&#39;-to-5&#39;	RNA processing and	D23_1c1713	Neut_1619
  							exoribonuclease RNase R	degradation, bacterial
  fig|6666666.60966.peg.1717	CDS	1598152	1599303	1	+	1152	DNA polymerase IV (EC	DNA repair, bacterial	D23_1c1715	Neut_1620
  							2.7.7.7)
  fig|6666666.60966.peg.1718	CDS	1599507	1599391	−3	−	117	hypothetical protein	-none-	D23_1c1716	NA
  fig|6666666.60966.peg.1719	CDS	1599639	1601015	3	+	1377	Flagellar regulatory	Flagellum	D23_1c1717	Neut_1621
  							protein FleQ
  fig|6666666.60966.peg.1720	CDS	1601809	1601045	−1	−	765	hypothetical protein	-none-	D23_1c1718	Neut_1622
  fig|6666666.60966.peg.1721	CDS	1604085	1601893	−3	−	2193	hypothetical protein	-none-	D23_1c1719	Neut_1623
  fig|6666666.60966.peg.1722	CDS	1605035	1604157	−2	−	879	Mobile element protein	-none-	D23_1c1720	Neut_1720
  fig|6666666.60966.peg.1723	CDS	1605427	1605134	−1	−	294	Mobile element protein	-none-	D23_1c1721	Neut_1719
  fig|6666666.60966.peg.1724	CDS	1606591	1605455	−1	−	1137	8-amino-7-	Biotin biosynthesis;	D23_1c1722	Neut_2137
  							oxononanoate synthase	<br>Biotin biosynthesis
  							(EC 2.3.1.47)	Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.1725	CDS	1608741	1606597	−3	−	2145	hypothetical protein	-none-	D23_1c1723	NA
  fig|6666666.60966.peg.1726	CDS	1610072	1608738	−2	−	1335	hypothetical protein	-none-	D23_1c1724	NA
  fig|6666666.60966.peg.1727	CDS	1610798	1610106	−2	−	693	hypothetical protein	-none-	D23_1c1725	Neut_1626
  fig|6666666.60966.peg.1728	CDS	1611531	1610833	−3	−	699	hypothetical protein	-none-	D23_1c1726	Neut_1626
  fig|6666666.60966.peg.1729	CDS	1611922	1612056	1	+	135	hypothetical protein	-none-	D23_1c1727	NA
  fig|6666666.60966.peg.1731	CDS	1612368	1612991	3	+	624	InterPro IPR000379	-none-	D23_1c1729	Neut_1627
  							COGs COG2945
  fig|6666666.60966.peg.1732	CDS	1614001	1613204	−1	−	798	Carbonic anhydrase (EC	Zinc regulated enzymes	D23_1c1730	Neut_1628
  							4.2.1.1)
  fig|6666666.60966.peg.1734	CDS	1614522	1614355	−3	−	168	hypothetical protein	-none-	D23_1c1731	NA
  fig|6666666.60966.peg.1735	CDS	1614827	1614699	−2	−	129	hypothetical protein	-none-	D23_1c1732	NA
  fig|6666666.60966.peg.1736	CDS	1614794	1616134	2	+	1341	Probable	-none-	D23_1c1733	Neut_1630
  							transmembrane protein
  fig|6666666.60966.peg.1737	CDS	1617043	1616225	−1	−	819	rRNA methylases	-none-	D23_1c1734	Neut_1631
  fig|6666666.60966.peg.1738	CDS	1617516	1617061	−3	−	456	Mobile element protein	-none-	D23_1c1735	Neut_2502
  fig|6666666.60966.peg.1739	CDS	1617913	1617479	−1	−	435	Mobile element protein	-none-	D23_1c1736	Neut_0884
  fig|6666666.60966.peg.1740	CDS	1618427	1618293	−2	−	135	hypothetical protein	-none-	D23_1c1738	NA
  fig|6666666.60966.peg.1741	CDS	1619838	1618420	−3	−	1419	Dihydrolipoamide	5-FCL-like protein;	D23_1c1739	Neut_1632
  							dehydrogenase (EC	<br>Glycine cleavage
  							1.8.1.4)	system;
  								<br>Photorespiration
  								(oxidative C2 cycle);
  								<br>TCA Cycle
  fig|6666666.60966.peg.1742	CDS	1620067	1621053	1	+	987	Malate dehydrogenase	TCA Cycle	D23_1c1740	Neut_1633
  							(EC 1.1.1.37)
  fig|6666666.60966.peg.1743	CDS	1621562	1621107	−2	−	456	Thiol peroxidase, Bcp-	CBSS-	D23_1c1741	Neut_1634
  							type (EC 1.11.1.15)	316057.3.peg.3521;
  								<br>Thioredoxin-
  								disulfide reductase
  fig|6666666.60966.peg.1744	CDS	1622938	1621595	−1	−	1344	Cytochrome c heme	Biogenesis of c-type	D23_1c1742	Neut_1635
  							lyase subunit CcmH	cytochromes;
  								<br>Copper homeostasis
  fig|6666666.60966.peg.1745	CDS	1623399	1622935	−3	−	465	Cytochrome c heme	Biogenesis of c-type	D23_1c1743	Neut_1636
  							lyase subunit CcmL	cytochromes
  fig|6666666.60966.peg.1746	CDS	1623982	1623458	−1	−	525	Cytochrome c-type	Biogenesis of c-type	D23_1c1744	Neut_1637
  							biogenesis protein	cytochromes;
  							CcmG/DsbE,	<br>Periplasmic disulfide
  							thiol:disulfide	interchange
  							oxidoreductase
  fig|6666666.60966.peg.1747	CDS	1626024	1623979	−3	−	2046	Cytochrome c heme	Biogenesis of c-type	D23_1c1745	Neut_1638
  							lyase subunit CcmF	cytochromes;
  								<br>Copper homeostasis
  fig|6666666.60966.peg.1748	CDS	1626514	1626065	−1	−	450	Cytochrome c-type	Biogenesis of c-type	D23_1c1746	Neut_1639
  							biogenesis protein	cytochromes
  							CcmE, heme chaperone
  fig|6666666.60966.peg.1749	CDS	1627373	1626690	−2	−	684	Cytochrome c-type	Biogenesis of c-type	D23_1c1747	Neut_1641
  							biogenesis protein	cytochromes
  							CcmC, putative heme
  							lyase for CcmE
  fig|6666666.60966.peg.1750	CDS	1628195	1627536	−2	−	660	ABC transporter	Biogenesis of c-type	D23_1c1748	Neut_1642
  							involved in cytochrome	cytochromes
  							c biogenesis, CcmB
  							subunit
  fig|6666666.60966.peg.1751	CDS	1628729	1628202	−2	−	528	ABC transporter	Biogenesis of c-type	D23_1c1749	Neut_1643
  							involved in cytochrome	cytochromes
  							c biogenesis, ATPase
  							component CcmA
  fig|6666666.60966.peg.1752	CDS	1629793	1628927	−1	−	867	tRNA pseudouridine	CBSS-	D23_1c1750	Neut_1644
  							synthase B (EC 4.2.1.70)	138119.3.peg.2719;
  								<br>RNA pseudouridine
  								syntheses;
  								<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>tRNA
  								modification Bacteria;
  								<br>tRNA processing
  fig|6666666.60966.peg.1753	CDS	1630354	1630001	−1	−	354	Ribosome-binding	CBSS-	D23_1c1751	Neut_1645
  							factor A	138119.3.peg.2719;
  								<br>NusA-TFII Cluster;
  								<br>Translation
  								initiation factors
  								bacterial
  fig|6666666.60966.peg.1754	CDS	1633073	1630407	−2	−	2667	Translation initiation	CBSS-	D23_1c1752	Neut_1646
  							factor 2	138119.3.peg.2719;
  								<br>NusA-TFII Cluster;
  								<br>Translation
  								initiation factors
  								bacterial; <br>Universal
  								GTPases
  fig|6666666.60966.peg.1756	CDS	1634664	1633192	−3	−	1473	Transcription	NusA-TFII Cluster;	D23_1c1753	Neut_1647
  							termination protein	<br>Transcription
  							NusA	factors bacterial
  fig|6666666.60966.peg.1757	CDS	1635199	1634717	−1	−	483	COG0779: clustered	-none-	D23_1c1754	Neut_1648
  							with transcription
  							termination protein
  							NusA
  fig|6666666.60966.peg.1760	CDS	1636174	1636611	1	+	438	FIG00859331:	-none-	D23_1c1755	Neut_1650
  							hypothetical protein
  fig|6666666.60966.peg.1761	CDS	1637012	1636686	−2	−	327	Cytochrome c4	Soluble cytochromes	D23_1c1756	Neut_1651
  								and functionally related
  								electron carriers
  fig|6666666.60966.peg.1762	CDS	1637371	1637045	−1	−	327	Putative periplasmic	-none-	D23_1c1757	Neut_1652
  							cytochrome type-C
  							oxidoreductase signal
  							peptide protein (EC 1.—.—.—)
  fig|6666666.60966.peg.1763	CDS	1639430	1637484	−2	−	1947	COG0488: ATPase	-none-	D23_1c1758	Neut_1653
  							components of ABC
  							transporters with
  							duplicated ATPase
  							domains
  fig|6666666.60966.peg.1765	CDS	1639660	1640709	1	+	1050	Selenide, water dikinase	Selenocysteine	D23_1c1759	Neut_1654
  							(EC 2.7.9.3)	metabolism; <br>tRNA
  								modification Bacteria
  fig|6666666.60966.peg.1766	CDS	1640702	1641868	2	+	1167	Selenophosphate-	Selenocysteine	D23_1c1760	Neut_1655
  							dependent tRNA 2-	metabolism; <br>tRNA
  							selenouridine synthase	modification Bacteria
  fig|6666666.60966.peg.1767	CDS	1642217	1642050	−2	−	168	hypothetical protein	-none-	D23_1c1761	NA
  fig|6666666.60966.peg.1768	CDS	1643785	1642217	−1	−	1569	4-cresol dehydrogenase	Cresol degradation	D23_1c1762	Neut_1656
  							[hydroxylating]
  							flavoprotein subunit (EC
  							1.17.99.1)
  fig|6666666.60966.peg.1769	CDS	1644507	1643782	−3	−	726	PchX protein	-none-	D23_1c1763	Neut_1657
  fig|6666666.60966.peg.1770	CDS	1644874	1644518	−1	−	357	4-cresol dehydrogenase	Cresol degradation	D23_1c1764	Neut_1658
  							[hydroxylating]
  							cytochrome c subunit
  							precursor
  fig|6666666.60966.peg.1771	CDS	1646175	1645138	−3	−	1038	Dihydroorotase (EC	De Novo Pyrimidine	D23_1c1766	Neut_1659
  							3.5.2.3)	Synthesis; <br>Zinc
  								regulated enzymes
  fig|6666666.60966.peg.1772	CDS	1647130	1646273	−1	−	858	rRNA small subunit	16S rRNA modification	D23_1c1767	Neut_1660
  							methyltransferase I	within P site of
  								ribosome; <br>CBSS-
  								160492.1.peg.550;
  								<br>Heat shock dnaK
  								gene cluster extended
  fig|6666666.60966.peg.1773	CDS	1647311	1649101	2	+	1791	ABC transporter,	-none-	D23_1c1769	Neut_1661
  							multidrug efflux family
  fig|6666666.60966.peg.1774	CDS	1649206	1649556	1	+	351	Predicted endonuclease	CBSS-160492.1.peg.550	D23_1c1770	Neut_1662
  							distantly related to
  							archaeal Holliday
  							junction resolvase
  fig|6666666.60966.peg.1776	CDS	1651143	1649929	−3	−	1215	hypothetical protein	-none-	D23_1c1771	Neut_1663
  fig|6666666.60966.peg.1777	CDS	1651568	1651446	−2	−	123	hypothetical protein	-none-	D23_1c1772	NA
  fig|6666666.60966.peg.1778	CDS	1651714	1652223	1	+	510	Putative lipoprotein	-none-	D23_1c1773	Neut_1664
  fig|6666666.60966.peg.1779	CDS	1652740	1661706	1	+	8967	Cyclic beta-1,2-glucan	Synthesis of	D23_1c1774	Neut_1665
  							synthase (EC 2.4.1.—)	osmoregulated
  								periplasmic glucans
  fig|6666666.60966.peg.1780	CDS	1662138	1661821	−3	−	318	Mobile element protein	-none-	D23_1c1775	Neut_1666
  fig|6666666.60966.peg.1781	CDS	1662168	1662344	3	+	177	hypothetical protein	-none-	D23_1c1776	NA
  fig|6666666.60966.peg.1782	CDS	1662546	1662406	−3	−	141	Mobile element protein	-none-	D23_1c1777	Neut_2190
  fig|6666666.60966.peg.1783	CDS	1663286	1663158	−2	−	129	hypothetical protein	-none-	D23_1c1778	NA
  fig|6666666.60966.peg.1784	CDS	1663556	1664518	2	+	963	Mobile element protein	-none-	D23_1c1779	Neut_1746
  fig|6666666.60966.peg.1785	CDS	1666051	1664585	−1	−	1467	ATP-dependent RNA	ATP-dependent RNA	D23_1c1780	Neut_1668
  							helicase	helicases, bacterial
  							Bcep18194_A5658
  fig|6666666.60966.peg.1786	CDS	1666377	1666147	−3	−	231	Mobile element protein	-none-	D23_1c1781	Neut_2088
  fig|6666666.60966.peg.1787	CDS	1666620	1666441	−3	−	180	Mobile element protein	-none-	D23_1c1782	Neut_0332
  fig|6666666.60966.peg.1788	CDS	1667117	1666644	−2	−	474	Mobile element protein	-none-	D23_1c1783	NA
  fig|6666666.60966.peg.1789	CDS	1668091	1667294	−1	−	798	FIG00861229:	-none-	D23_1c1784	Neut_1669
  							hypothetical protein
  fig|6666666.60966.peg.1790	CDS	1668254	1668093	−2	−	162	hypothetical protein	-none-	D23_1c1785	NA
  fig|6666666.60966.peg.1791	CDS	1669037	1668330	−2	−	708	Cytochrome c family	-none-	D23_1c1786	Neut_2333
  							protein
  fig|6666666.60966.peg.1792	CDS	1670220	1669099	−3	−	1122	FIG00859557:	-none-	D23_1c1787	Neut_1792
  							hypothetical protein
  fig|6666666.60966.peg.1793	CDS	1671929	1670217	−2	−	1713	Hydroxylamine	-none-	D23_1c1788	Neut_2335
  							oxidoreductase
  							precursor (EC 1.7.3.4)
  fig|6666666.60966.peg.1794	CDS	1672280	1672017	−2	−	264	SSU ribosomal protein	-none-	D23_1c1789	NA
  							S20p
  fig|6666666.60966.peg.1795	CDS	1672473	1672634	3	+	162	hypothetical protein	-none-	D23_1c1790	NA
  fig|6666666.60966.peg.1796	CDS	1672870	1672601	−1	−	270	Mobile element protein	-none-	D23_1c1791	Neut_2450
  fig|6666666.60966.peg.1797	CDS	1673187	1672894	−3	−	294	hypothetical protein	-none-	D23_1c1792	Neut_2449
  fig|6666666.60966.peg.1798	CDS	1673875	1673648	−1	−	228	hypothetical protein	-none-	D23_1c1795	Neut_1676
  fig|6666666.60966.peg.1799	CDS	1674438	1674052	−3	−	387	FIG002082: Protein	A Gammaproteobacteria	D23_1c1796	Neut_1677
  							SirB2	Cluster Relating to
  								Translation
  fig|6666666.60966.peg.1800	CDS	1674844	1674500	−1	−	345	FIG00858740:	-none-	D23_1c1797	Neut_1678
  							hypothetical protein
  fig|6666666.60966.peg.1801	CDS	1675595	1674939	−2	−	657	Probable membrane	-none-	D23_1c1798	Neut_1679
  							protein
  fig|6666666.60966.peg.1802	CDS	1675804	1675601	−1	−	204	Probable membrane	-none-	D23_1c1800	Neut_1679
  							protein
  fig|6666666.60966.peg.1803	CDS	1676931	1675825	−3	−	1107	GbcA Glycine betaine	-none-	D23_1c1801	Neut_1680
  							demethylase subunit A
  fig|6666666.60966.peg.1804	CDS	1677301	1678686	1	+	1386	FIG00858667:	-none-	D23_1c1802	Neut_1681
  							hypothetical protein
  fig|6666666.60966.peg.1805	CDS	1678742	1680964	2	+	2223	Helicase PriA essential	-none-	D23_1c1803	Neut_1682
  							for oriC/DnaA-
  							independent DNA
  							replication
  fig|6666666.60966.peg.1806	CDS	1681478	1681032	−2	−	447	Universal stress protein	-none-	D23_1c1804	Neut_1683
  fig|6666666.60966.peg.1807	CDS	1683246	1681597	−3	−	1650	Folate transporter 3	-none-	D23_1c1805	Neut_1684
  fig|6666666.60966.peg.1808	CDS	1684397	1683258	−2	−	1140	Outer membrane stress	Periplasmic Stress	D23_1c1806	Neut_1685
  							sensor protease DegS	Response;
  								<br>Proteolysis in
  								bacteria, ATP-dependent
  fig|6666666.60966.peg.1809	CDS	1684396	1685181	1	+	786	FIG137478:	-none-	D23_1c1807	Neut_1686
  							Hypothetical protein
  							YbgI
  fig|6666666.60966.peg.1810	CDS	1685374	1685249	−1	−	126	hypothetical protein	-none-	D23_1c1808	NA
  fig|6666666.60966.peg.1811	CDS	1685328	1686644	3	+	1317	Membrane-bound lytic	Murein Hydrolases	D23_1c1809	Neut_1687
  							murein transglycosylase
  							A precursor (EC 3.2.1.—)
  fig|6666666.60966.peg.1812	CDS	1687397	1686684	−2	−	714	Thiol:disulfide	Periplasmic disulfide	D23_1c1810	Neut_1688
  							interchange protein	interchange
  							DsbC
  fig|6666666.60966.peg.1813	CDS	1688609	1687443	−2	−	1167	2-octaprenyl-3-methyl-	CBSS-87626.3.peg.3639;	D23_1c1811	Neut_1689
  							6-methoxy-1,4-	<br>Ubiquinone
  							benzoquinol	Biosynthesis;
  							hydroxylase (EC	<br>Ubiquinone
  							1.14.13.—)	Biosynthesis-gjo
  fig|6666666.60966.peg.1814	CDS	1688840	1690807	2	+	1968	Acetyl-coenzyme A	Pyruvate metabolism II:	D23_1c1812	Neut_1690
  							synthetase (EC 6.2.1.1)	acetyl-CoA, acetogenesis
  								from pyruvate
  fig|6666666.60966.peg.1815	CDS	1690825	1691799	1	+	975	Beta-lactamase related	-none-	D23_1c1813	Neut_1691
  							protein
  fig|6666666.60966.peg.1816	CDS	1693183	1691903	−1	−	1281	amidohydrolase	-none-	D23_1c1814	Neut_1692
  fig|6666666.60966.peg.1817	CDS	1693463	1693633	2	+	171	Mobile element protein	-none-	D23_1c1816	Neut_1693
  fig|6666666.60966.peg.1818	CDS	1694024	1695034	2	+	1011	Fatty acid desaturase	-none-	D23_1c1817	Neut_1694
  fig|6666666.60966.peg.1819	CDS	1696649	1695402	−2	−	1248	Mobile element protein	-none-	D23_1c1818	Neut_0357
  fig|6666666.60966.peg.1820	CDS	1697303	1696830	−2	−	474	Mobile element protein	-none-	D23_1c1820	Neut_1256
  fig|6666666.60966.peg.1821	CDS	1697769	1697377	−3	−	393	hypothetical protein	-none-	D23_1c1821	Neut_2449
  fig|6666666.60966.peg.1822	CDS	1698235	1698032	−1	−	204	hypothetical protein	-none-	D23_1c1822	Neut_0363
  fig|6666666.60966.peg.1823	CDS	1698639	1698322	−3	−	318	hypothetical protein	-none-	D23_1c1823	Neut_1695
  fig|6666666.60966.peg.1824	CDS	1698977	1698639	−2	−	339	Mobile element protein	-none-	D23_1c1824	Neut_1696
  fig|6666666.60966.peg.1825	CDS	1699393	1702311	1	+	2919	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1825	Neut_1697
  							subunit A/Na(+) H(+)	antiporter; <br>Multi-
  							antiporter subunit B	subunit cation antiporter
  fig|6666666.60966.peg.1826	CDS	1702311	1702655	3	+	345	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1826	Neut_1698
  							subunit C	antiporter
  fig|6666666.60966.peg.1827	CDS	1702652	1704298	2	+	1647	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1827	Neut_1699
  							subunit D	antiporter
  fig|6666666.60966.peg.1828	CDS	1704295	1704780	1	+	486	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1828	Neut_1700
  							subunit E	antiporter
  fig|6666666.60966.peg.1829	CDS	1704777	1705058	3	+	282	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1829	Neut_1701
  							subunit F	antiporter
  fig|6666666.60966.peg.1830	CDS	1705055	1705480	2	+	426	Na(+) H(+) antiporter	Multi-subunit cation	D23_1c1830	Neut_1702
  							subunit G	antiporter
  fig|6666666.60966.peg.1831	CDS	1708136	1705638	−2	−	2499	FIG00809136:	-none-	D23_1c1831	Neut_1703
  							hypothetical protein
  fig|6666666.60966.peg.1832	CDS	1709066	1708266	−2	−	801	ABC transporter ATP-	-none-	D23_1c1832	Neut_1704
  							binding protein YvcR
  fig|6666666.60966.peg.1833	CDS	1709065	1709676	1	+	612	Arylesterase precursor	-none-	D23_1c1833	Neut_1705
  							(EC 3.1.1.2)
  fig|6666666.60966.peg.1834	CDS	1710780	1709716	−3	−	1065	Ribosomal large subunit	RNA pseudouridine	D23_1c1834	Neut_1706
  							pseudouridine synthase	syntheses;
  							C (EC 4.2.1.70)	<br>Ribosome
  								biogenesis bacterial
  fig|6666666.60966.peg.1835	CDS	1711189	1713738	1	+	2550	Ribonuclease E (EC	RNA processing and	D23_1c1835	Neut_1707
  							3.1.26.12)	degradation, bacterial;
  								<br>Ribosome
  								biogenesis bacterial
  fig|6666666.60966.peg.1836	CDS	1714787	1713870	−2	−	918	Tyrosine recombinase	-none-	D23_1c1836	Neut_1708
  							XerD
  fig|6666666.60966.peg.1837	CDS	1715754	1714909	−3	−	846	CcsA-related protein	-none-	D23_1c1837	Neut_1709
  fig|6666666.60966.peg.1838	CDS	1715897	1717246	2	+	1350	Signal recognition	Bacterial signal	D23_1c1838	Neut_1710
  							particle, subunit Ffh	recognition particle
  							SRP54 (TC 3.A.5.1.1)	(SRP); <br>Universal
  								GTPases
  fig|6666666.60966.peg.1839	CDS	1717562	1718059	2	+	498	Cytosine/adenosine	-none-	D23_1c1840	Neut_1711
  							deaminases
  fig|6666666.60966.peg.1840	CDS	1719089	1718079	−2	−	1011	collagen triple helix	-none-	D23_1c1841	Neut_1712
  							repeat domain protein
  fig|6666666.60966.peg.1841	CDS	1719941	1719435	−2	−	507	Mobile element protein	-none-	D23_1c1843	Neut_1353
  fig|6666666.60966.peg.1843	CDS	1720927	1720256	−1	−	672	Putative TEGT family	CBSS-326442.4.peg.1852	D23_1c1844	Neut_1715
  							carrier/transport
  							protein
  fig|6666666.60966.peg.1844	CDS	1721245	1721081	−1	−	165	hypothetical protein	-none-	D23_1c1845	Neut_1716
  fig|6666666.60966.peg.1845	CDS	1721933	1721268	−2	−	666	Mobile element protein	-none-	D23_1c1846	Neut_1717
  fig|6666666.60966.peg.1846	CDS	1722745	1722137	−1	−	609	Aldehyde	Glycerolipid and	D23_1c1847	Neut_0700
  							dehydrogenase (EC	Glycerophospholipid
  							1.2.1.3)	Metabolism in Bacteria;
  								<br>Methylglyoxal
  								Metabolism;
  								<br>Methylglyoxal
  								Metabolism;
  								<br>Pyruvate
  								metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.1847	CDS	1722896	1723189	2	+	294	Mobile element protein	-none-	D23_1c1848	Neut_1719
  fig|6666666.60966.peg.1848	CDS	1723288	1724166	1	+	879	Mobile element protein	-none-	D23_1c1849	Neut_1720
  fig|6666666.60966.peg.1849	CDS	1724724	1724179	−3	−	546	Aldehyde	Glycerolipid and	D23_1c1850	Neut_0700
  							dehydrogenase (EC	Glycerophospholipid
  							1.2.1.3)	Metabolism in Bacteria;
  								<br>Methylglyoxal
  								Metabolism;
  								<br>Methylglyoxal
  								Metabolism;
  								<br>Pyruvate
  								metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.1850	CDS	1726242	1724995	−3	−	1248	Mobile element protein	-none-	D23_1c1851	Neut_0357
  fig|6666666.60966.peg.1851	CDS	1727368	1727126	−1	−	243	Mobile element protein	-none-	D23_1c1854	Neut_2190
  fig|6666666.60966.peg.1852	CDS	1727480	1727641	2	+	162	hypothetical protein	-none-	D23_1c1855	NA
  fig|6666666.60966.peg.1853	CDS	1727757	1727873	3	+	117	hypothetical protein	-none-	D23_1c1856	NA
  fig|6666666.60966.peg.1854	CDS	1727880	1728818	3	+	939	Major facilitator family	-none-	D23_1c1857	NA
  							transporter
  fig|6666666.60966.peg.1855	CDS	1728936	1730123	3	+	1188	Cytosine deaminase (EC	CBSS-	D23_1c1858	Neut_1722
  							3.5.4.1)	326442.4.peg.1852;
  								<br>Creatine and
  								Creatinine Degradation;
  								<br>pyrimidine
  								conversions
  fig|6666666.60966.peg.1857	CDS	1730427	1730624	3	+	198	Mobile element protein	-none-	D23_1c1859	Neut_1748
  fig|6666666.60966.peg.1858	CDS	1730716	1730937	1	+	222	Mobile element protein	-none-	D23_1c1860	Neut_1747
  fig|6666666.60966.peg.1859	CDS	1731165	1733414	3	+	2250	Lead, cadmium, zinc	Copper Transport	D23_1c1862	Neut_1724
  							and mercury	System; <br>Copper
  							transporting ATPase (EC	homeostasis
  							3.6.3.3) (EC 3.6.3.5);
  							Copper-translocating P-
  							type ATPase (EC 3.6.3.4)
  fig|6666666.60966.peg.1860	CDS	1733755	1733946	1	+	192	hypothetical protein	-none-	D23_1c1863	Neut_1734
  fig|6666666.60966.peg.1861	CDS	1734020	1735762	2	+	1743	Asparagine synthetase	Cyanophycin	D23_1c1864	Neut_1735
  							[glutamine-hydrolyzing]	Metabolism;
  							(EC 6.3.5.4)	<br>Glutamate and
  								Aspartate uptake in
  								Bacteria; <br>Glutamine,
  								Glutamate, Aspartate
  								and Asparagine
  								Biosynthesis
  fig|6666666.60966.peg.1862	CDS	1735929	1737425	3	+	1497	major facilitator	-none-	D23_1c1865	Neut_1736
  							superfamily MFS_1
  fig|6666666.60966.peg.1863	CDS	1737575	1737841	2	+	267	Mobile element protein	-none-	D23_1c1866	NA
  fig|6666666.60966.peg.1864	CDS	1737835	1737975	1	+	141	Mobile element protein	-none-	D23_1c1867	NA
  fig|6666666.60966.peg.1865	CDS	1738803	1738006	−3	−	798	Mobile element protein	-none-	D23_1c1868	Neut_1888
  fig|6666666.60966.peg.1866	CDS	1739186	1738917	−2	−	270	Mobile element protein	-none-	D23_1c1869	Neut_2500
  fig|6666666.60966.peg.1868	CDS	1740582	1739374	−3	−	1209	hypothetical protein	-none-	D23_1c1870	Neut_1740
  fig|6666666.60966.peg.1869	CDS	1742717	1740588	−2	−	2130	Ferrichrome-iron	-none-	D23_1c1871	Neut_1741
  							receptor
  fig|6666666.60966.peg.1870	CDS	1744008	1742806	−3	−	1203	Vibrioferrin	-none-	D23_1c1872	Neut_1742
  							decarboxylase protein
  							PvsE
  fig|6666666.60966.peg.1871	CDS	1745819	1744005	−2	−	1815	Vibrioferrin amide bond	-none-	D23_1c1873	Neut_1743
  							forming protein PvsD @
  							Siderophore synthetase
  							superfamily, group A
  fig|6666666.60966.peg.1872	CDS	1747001	1745829	−2	−	1173	Vibrioferrin membrane-	-none-	D23_1c1874	Neut_1744
  							spanning transport
  							protein PvsC
  fig|6666666.60966.peg.1873	CDS	1748855	1747044	−2	−	1812	Anthrachelin	-none-	D23_1c1875	Neut_1745
  							biosynthesis protein
  							AsbB @ Siderophore
  							synthetase superfamily,
  							group C @ Siderophore
  							synthetase component,
  							ligase
  fig|6666666.60966.peg.1874	CDS	1749327	1749151	−3	−	177	Mobile element protein	-none-	D23_1c1876	Neut_1747
  fig|6666666.60966.peg.1876	CDS	1750647	1749685	−3	−	963	Mobile element protein	-none-	D23_1c1878	Neut_1278
  fig|6666666.60966.peg.1877	CDS	1751012	1752274	2	+	1263	hypothetical protein	-none-	D23_1c1879	Neut_1749
  fig|6666666.60966.peg.1878	CDS	1752303	1753133	3	+	831	Potassium efflux system	Potassium homeostasis	D23_1c1880	NA
  							KefA protein/Small-
  							conductance
  							mechanosensitive
  							channel
  fig|6666666.60966.peg.1879	CDS	1753722	1753153	−3	−	570	hypothetical protein	-none-	D23_1c1881	NA
  fig|6666666.60966.peg.1880	CDS	1753823	1754629	2	+	807	Glutamate racemase	Glutamine, Glutamate,	D23_1c1882	Neut_1752
  							(EC 5.1.1.3)	Aspartate and
  								Asparagine Biosynthesis;
  								<br>Peptidoglycan
  								Biosynthesis
  fig|6666666.60966.peg.1881	CDS	1754733	1755689	3	+	957	Universal stress protein	-none-	D23_1c1883	Neut_1753
  fig|6666666.60966.peg.1882	CDS	1756978	1755725	−1	−	1254	DNA repair protein	DNA repair, bacterial;	D23_1c1884	Neut_1754
  							RadA	<br>Proteolysis in
  								bacteria, ATP-dependent
  fig|6666666.60966.peg.1883	CDS	1757073	1757201	3	+	129	hypothetical protein	-none-	D23_1c1885	NA
  fig|6666666.60966.peg.1884	CDS	1758757	1757372	−1	−	1386	L-serine dehydratase	Glycine and Serine	D23_1c1887	Neut_1760
  							(EC 4.3.1.17)	Utilization; <br>Pyruvate
  								Alanine Serine
  								Interconversions
  fig|6666666.60966.peg.1886	CDS	1759312	1760013	1	+	702	Serine protease	Transcription initiation,	D23_1c1890	Neut_1761
  							precursor MucD/AlgY	bacterial sigma factors
  							associated with sigma
  							factor RpoE
  fig|6666666.60966.peg.1887	CDS	1760622	1761584	3	+	963	Mobile element protein	-none-	D23_1c1892	Neut_1278
  fig|6666666.60966.peg.1888	CDS	1761643	1762524	1	+	882	FIG071646: Sugar	Cell wall related cluster	D23_1c1893	Neut_1762
  							transferase
  fig|6666666.60966.peg.1889	CDS	1762574	1764655	2	+	2082	Sensory transduction	-none-	D23_1c1894	Neut_1763
  							histidine kinases
  fig|6666666.60966.peg.1890	CDS	1764739	1766601	1	+	1863	Lipid A export ATP-	-none-	D23_1c1895	Neut_1764
  							binding/permease
  							protein MsbA
  fig|6666666.60966.peg.1891	CDS	1769731	1766636	−1	−	3096	Cobalt-zinc-cadmium	Cobalt-zinc-cadmium	D23_1c1896	Neut_1765
  							resistance protein CzcA;	resistance; <br>Cobalt-
  							Cation efflux system	zinc-cadmium resistance
  							protein CusA
  fig|6666666.60966.peg.1892	CDS	1770897	1769734	−3	−	1164	Cobalt/zinc/cadmium	Cobalt-zinc-cadmium	D23_1c1897	Neut_1766
  							efflux RND transporter,	resistance
  							membrane fusion
  							protein, CzcB family
  fig|6666666.60966.peg.1893	CDS	1772112	1770907	−3	−	1206	Heavy metal RND efflux	Cobalt-zinc-cadmium	D23_1c1898	Neut_1767
  							outer membrane	resistance
  							protein, CzcC family
  fig|6666666.60966.peg.1894	CDS	1773163	1772504	−1	−	660	FIG00859115:	-none-	D23_1c1899	Neut_1768
  							hypothetical protein
  fig|6666666.60966.peg.1895	CDS	1773250	1773996	1	+	747	Glycerophosphoryl	CBSS-	D23_1c1900	Neut_1769
  							diester	176299.4.peg.1996A;
  							phosphodiesterase (EC	<br>Glycerol and
  							3.1.4.46)	Glycerol-3-phosphate
  								Uptake and Utilization
  fig|6666666.60966.peg.1896	CDS	1774006	1775181	1	+	1176	Aerobic glycerol-3-	Glycerol and Glycerol-3-	D23_1c1901	Neut_1770
  							phosphate	phosphate Uptake and
  							dehydrogenase (EC	Utilization;
  							1.1.5.3)	<br>Glycerolipid and
  								Glycerophospholipid
  								Metabolism in Bacteria;
  								<br>Respiratory
  								dehydrogenases
  1
  fig|6666666.60966.peg.1897	CDS	1775543	1775211	−2	−	333	FIG00859262:	-none-	D23_1c1902	Neut_1771
  							hypothetical protein
  fig|6666666.60966.peg.1898	CDS	1776076	1775636	−1	−	441	FIG00859309:	-none-	D23_1c1903	Neut_1772
  							hypothetical protein
  fig|6666666.60966.peg.1899	CDS	1777538	1776078	−2	−	1461	Dihydrolipoamide	Dehydrogenase	D23_1c1904	Neut_1773
  							dehydrogenase of 2-	complexes; <br>TCA
  							oxoglutarate	Cycle
  							dehydrogenase (EC
  							1.8.1.4)
  fig|6666666.60966.peg.1900	CDS	1778658	1777612	−3	−	1047	Beta N-acetyl-	Murein Hydrolases;	D23_1c1905	Neut_1774
  							glucosaminidase (EC	<br>Recycling of
  							3.2.1.52)	Peptidoglycan Amino
  								Sugars
  fig|6666666.60966.peg.1901	CDS	1779038	1778661	−2	−	378	Holo-[acyl-carrier	Fatty Acid Biosynthesis	D23_1c1906	Neut_1775
  							protein] synthase (EC	FASII
  							2.7.8.7)
  fig|6666666.60966.peg.1902	CDS	1779760	1779035	−1	−	726	Pyridoxine 5&#39;-	Pyridoxin (Vitamin B6)	D23_1c1907	Neut_1776
  							phosphate synthase (EC	Biosynthesis
  							2.6.99.2)
  fig|6666666.60966.peg.1903	CDS	1780768	1779878	−1	−	891	GTP-binding protein Era	Bacterial Cell Division;	D23_1c1908	Neut_1777
  								<br>Glycyl-tRNA
  								synthetase containing
  								cluster; <br>Universal
  								GTPases
  fig|6666666.60966.peg.1904	CDS	1781583	1780846	−3	−	738	Ribonuclease III (EC	RNA processing and	D23_1c1909	Neut_1778
  							3.1.26.3)	degradation, bacterial
  fig|6666666.60966.peg.1905	CDS	1781963	1781580	−2	−	384	possible	-none-	D23_1c1910	Neut_1779
  							transmembrane protein
  fig|6666666.60966.peg.1906	CDS	1782802	1781999	−1	−	804	Signal peptidase I (EC	Signal peptidase	D23_1c1911	Neut_1780
  							3.4.21.89)
  fig|6666666.60966.peg.1907	CDS	1784670	1782874	−3	−	1797	Translation elongation	Heat shock dnaK gene	D23_1c1912	Neut_1781
  							factor LepA	cluster extended;
  								<br>Translation
  								elongation factors
  								bacterial; <br>Universal
  								GTPases
  fig|6666666.60966.peg.1908	CDS	1784806	1784651	−1	−	156	hypothetical protein	-none-	D23_1c1913	NA
  fig|6666666.60966.peg.1909	CDS	1785160	1784972	−1	−	189	COGs COG0526	-none-	D23_1c1914	Neut_1782
  fig|6666666.60966.peg.1910	CDS	1786580	1785222	−2	−	1359	Serine protease	Transcription initiation,	D23_1c1915	Neut_1783
  							precursor MucD/AlgY	bacterial sigma factors
  							associated with sigma
  							factor RpoE
  fig|6666666.60966.peg.1911	CDS	1787446	1786871	−1	−	576	InterPro IPR001687	-none-	D23_1c1916	Neut_1784
  							COGs COG3073
  fig|6666666.60966.peg.1912	CDS	1788062	1787460	−2	−	603	RNA polymerase sigma	Transcription initiation,	D23_1c1917	Neut_1785
  							factor RpoE	bacterial sigma factors
  fig|6666666.60966.peg.1913	CDS	1789111	1788260	−1	−	852	Magnesium and cobalt	CBSS-	D23_1c1919	Neut_1786
  							efflux protein CorC	56780.10.peg.1536;
  								<br>Copper
  								homeostasis: copper
  								tolerance; <br>Glycyl-
  								tRNA synthetase
  								containing cluster;
  								<br>Magnesium
  								transport; <br>tRNA-
  								methylthiotransferase
  								containing cluster
  fig|6666666.60966.peg.1914	CDS	1789590	1789165	−3	−	426	Metal-dependent	CBSS-	D23_1c1920	Neut_1787
  							hydrolase YbeY,	56780.10.peg.1536;
  							involved in rRNA and/or	<br>Glycyl-tRNA
  							ribosome maturation	synthetase containing
  							and assembly	cluster; <br>tRNA-
  								methylthiotransferase
  								containing cluster
  fig|6666666.60966.peg.1915	CDS	1790629	1789619	−1	−	1011	Phosphate starvation-	-none-	D23_1c1921	Neut_1788
  							inducible ATPase PhoH
  							with RNA binding motif
  fig|6666666.60966.peg.1916	CDS	1792022	1790691	−2	−	1332	tRNA-i(6)A37	Methylthiotransferases;	D23_1c1922	Neut_1789
  							methylthiotransferase	<br>tRNA-
  								methylthiotransferase
  								containing cluster;
  								<br>tRNA modification
  								Bacteria; <br>tRNA
  								processing
  fig|6666666.60966.peg.1917	CDS	1793040	1792321	−3	−	720	Cytochrome c-type	-none-	D23_1c1923	Neut_1790
  							protein TorY
  fig|6666666.60966.peg.1918	CDS	1793750	1793043	−2	−	708	Cytochrome c family	-none-	D23_1c1924	Neut_2333
  							protein
  fig|6666666.60966.peg.1919	CDS	1794933	1793812	−3	−	1122	FIG00859557:	-none-	D23_1c1925	Neut_1792
  							hypothetical protein
  fig|6666666.60966.peg.1920	CDS	1796642	1794930	−2	−	1713	Hydroxylamine	-none-	D23_1c1926	Neut_2335
  							oxidoreductase
  							precursor (EC 1.7.3.4)
  fig|6666666.60966.peg.1921	CDS	1801076	1796862	−2	−	4215	DNA-directed RNA	Mycobacterium	D23_1c1927	Neut_1794
  							polymerase beta&#39;	virulence operon
  							subunit (EC 2.7.7.6)	involved in DNA
  								transcription; <br>RNA
  								polymerase bacterial
  fig|6666666.60966.peg.1922	CDS	1805314	1801235	−1	−	4080	DNA-directed RNA	Mycobacterium	D23_1c1928	Neut_1795
  							polymerase beta	virulence operon
  							subunit (EC 2.7.7.6)	involved in DNA
  								transcription; <br>RNA
  								polymerase bacterial
  fig|6666666.60966.peg.1923	CDS	1806051	1805680	−3	−	372	LSU ribosomal protein	LSU ribosomal proteins	D23_1c1929	Neut_1796
  							L7/L12 (P1/P2)	cluster
  fig|6666666.60966.peg.1924	CDS	1806648	1806133	−3	−	516	LSU ribosomal protein	LSU ribosomal proteins	D23_1c1930	Neut_1797
  							L10p (P0)	cluster
  fig|6666666.60966.peg.1925	CDS	1807793	1807098	−2	−	696	LSU ribosomal protein	LSU ribosomal proteins	D23_1c1931	Neut_1798
  							Lip (L10Ae)	cluster
  fig|6666666.60966.peg.1926	CDS	1808121	1807795	−3	−	327	LSU ribosomal protein	LSU ribosomal proteins	D23_1c1932	Neut_1799
  							L11p (L12e)	cluster
  fig|6666666.60966.peg.1927	CDS	1808877	1808344	−3	−	534	Transcription	LSU ribosomal proteins	D23_1c1934	Neut_1800
  							antitermination protein	cluster;
  							NusG	<br>Transcription
  								factors bacterial
  fig|6666666.60966.peg.1928	CDS	1809240	1808896	−3	−	345	Preprotein translocase	LSU ribosomal proteins	D23_1c1935	Neut_1801
  							subunit SecE (TC	cluster
  							3.A.5.1.1)
  fig|6666666.60966.peg.1929	CDS	1810674	1809484	−3	−	1191	Translation elongation	Mycobacterium	D23_1c1937	Neut_1802
  							factor Tu	virulence operon
  								involved in protein
  								synthesis (SSU ribosomal
  								proteins);
  								<br>Translation
  								elongation factors
  								bacterial; <br>Universal
  								GTPases
  fig|6666666.60966.peg.1930	CDS	1813382	1811220	−2	−	2163	Type IV pilus biogenesis	-none-	D23_1c1941	Neut_1803
  fig|6666666.60966.peg.1931	CDS	1813906	1813379	−1	−	528	Type IV pilus biogenesis	-none-	D23_1c1942	Neut_1804
  							protein PilP
  fig|6666666.60966.peg.1932	CDS	1814553	1813903	−3	−	651	Type IV pilus biogenesis	-none-	D23_1c1943	Neut_1805
  							protein PilO
  fig|6666666.60966.peg.1933	CDS	1815161	1814550	−2	−	612	Type IV pilus biogenesis	-none-	D23_1c1944	Neut_1806
  							protein PilN
  fig|6666666.60966.peg.1934	CDS	1816207	1815158	−1	−	1050	Type IV pilus biogenesis	-none-	D23_1c1945	Neut_1807
  							protein PilM
  fig|6666666.60966.peg.1936	CDS	1816441	1818753	1	+	2313	Multimodular	Peptidoglycan	D23_1c1947	Neut_1808
  							transpeptidase-	Biosynthesis
  							transglycosylase (EC
  							2.4.1.129) (EC 3.4.—.—)
  fig|6666666.60966.peg.1937	CDS	1819961	1819041	−2	−	921	Deacetylases, including	-none-	D23_1c1948	Neut_1809
  							yeast histone
  							deacetylase and acetoin
  							utilization protein
  fig|6666666.60966.peg.1939	CDS	1820319	1820170	−3	−	150	hypothetical protein	-none-	D23_1c1949	Neut_1810
  fig|6666666.60966.peg.1941	CDS	1820799	1820638	−3	−	162	Addiction module	-none-	D23_1c1950	Neut_1811
  							antidote protein
  fig|6666666.60966.peg.1942	CDS	1821096	1820914	−3	−	183	hypothetical protein	-none-	D23_1c1951	Neut_1812
  fig|6666666.60966.peg.1943	CDS	1821848	1821985	2	+	138	Prevent host death	Phd-Doc, YdcE-YdcD	D23_1c1953	NA
  							protein, Phd antitoxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.1944	CDS	1821982	1822278	1	+	297	Death on curing	Phd-Doc, YdcE-YdcD	D23_1c1954	NA
  							protein, Doc toxin	toxin-antitoxin
  								(programmed cell death)
  								systems
  fig|6666666.60966.peg.1945	CDS	1822608	1822423	−3	−	186	hypothetical protein	-none-	D23_1c1955	Neut_1816
  fig|6666666.60966.peg.1946	CDS	1822933	1822688	−1	−	246	hypothetical protein	-none-	D23_1c1956	Neut_1817
  fig|6666666.60966.peg.1947	CDS	1823491	1823150	−1	−	342	Predicted	-none-	D23_1c1957	NA
  							transcriptional
  							regulator
  fig|6666666.60966.peg.1948	CDS	1823708	1823484	−2	−	225	Phage-related protein	-none-	D23_1c1958	NA
  fig|6666666.60966.peg.1952	CDS	1824892	1824704	−1	−	189	hypothetical protein	-none-	D23_1c1959	NA
  fig|6666666.60966.peg.1953	CDS	1825371	1825036	−3	−	336	Mobile element protein	-none-	D23_1c1960	Neut_1624
  fig|6666666.60966.peg.1954	CDS	1825828	1825352	−1	−	477	Mobile element protein	-none-	D23_1c1961	Neut_1888
  fig|6666666.60966.peg.1955	CDS	1826127	1825942	−3	−	186	Mobile element protein	-none-	D23_1c1962	Neut_2500
  fig|6666666.60966.peg.1956	CDS	1826660	1826472	−2	−	189	Mobile element protein	-none-	D23_1c1963	Neut_1821
  fig|6666666.60966.peg.1958	CDS	1827279	1826920	−3	−	360	Flagellin protein FlaG	Flagellum	D23_1c1964	Neut_1822
  fig|6666666.60966.peg.1959	CDS	1827931	1827644	−1	−	288	Excinuclease ABC, C	-none-	D23_1c1965	Neut_1823
  							subunit-like
  fig|6666666.60966.peg.1960	CDS	1829557	1828115	−1	−	1443	Flagellin protein FlaB	Flagellum; <br>Flagellum	D23_1c1967	Neut_1824
  								in Campylobacter
  fig|6666666.60966.peg.1961	CDS	1830108	1830230	3	+	123	hypothetical protein	-none-	D23_1c1968	NA
  fig|6666666.60966.peg.1962	CDS	1831067	1830276	−2	−	792	Mobile element protein	-none-	D23_1c1969	Neut_1888
  fig|6666666.60966.peg.1963	CDS	1831366	1831181	−1	−	186	Mobile element protein	-none-	D23_1c1970	Neut_2500
  fig|6666666.60966.peg.1964	CDS	1831759	1831616	−1	−	144	hypothetical protein	-none-	D23_1c1971	NA
  fig|6666666.60966.peg.1965	CDS	1832465	1831749	−2	−	717	hypothetical protein	-none-	D23_1c1972	Neut_1827
  fig|6666666.60966.peg.1967	CDS	1835117	1833291	−2	−	1827	DNA mismatch repair	DNA repair, bacterial	D23_1c1973	Neut_1828
  							protein MutL	MutL-MutS system
  fig|6666666.60966.peg.1968	CDS	1835287	1835946	1	+	660	Ribose 5-phosphate	Calvin-Benson cycle;	D23_1c1974	Neut_1829
  							isomerase A (EC 5.3.1.6)	<br>D-ribose utilization;
  								<br>Pentose phosphate
  								pathway
  fig|6666666.60966.peg.1969	CDS	1836022	1836150	1	+	129	hypothetical protein	-none-	D23_1c1975	NA
  fig|6666666.60966.peg.1970	CDS	1836140	1836859	2	+	720	Phosphate transport	High affinity phosphate	D23_1c1976	Neut_1830
  							system regulatory	transporter and control
  							protein PhoU	of PHO regulon;
  								<br>Phosphate
  								metabolism
  fig|6666666.60966.peg.1971	CDS	1836819	1838420	3	+	1602	Exopolyphosphatase	Phosphate metabolism;	D23_1c1977	Neut_1831
  							(EC 3.6.1.11)	<br>Polyphosphate
  fig|6666666.60966.peg.1972	CDS	1838878	1838429	−1	−	450	Type IV pilus biogenesis	-none-	D23_1c1978	Neut_1832
  							protein PilE
  fig|6666666.60966.peg.1973	CDS	1842290	1838922	−2	−	3369	Type IV fimbrial	-none-	D23_1c1979	Neut_1833
  							biogenesis protein PilY1
  fig|6666666.60966.peg.1974	CDS	1843213	1842362	−1	−	852	Type IV fimbrial	-none-	D23_1c1980	Neut_1834
  							biogenesis protein PilX
  fig|6666666.60966.peg.1975	CDS	1844303	1843239	−2	−	1065	Type IV fimbrial	-none-	D23_1c1981	Neut_1835
  							biogenesis protein PilW
  fig|6666666.60966.peg.1976	CDS	1844806	1844321	−1	−	486	Type IV fimbrial	-none-	D23_1c1982	Neut_1836
  							biogenesis protein PilV
  fig|6666666.60966.peg.1977	CDS	1845339	1844830	−3	−	510	Type IV fimbrial	-none-	D23_1c1983	Neut_1837
  							biogenesis protein FimT
  fig|6666666.60966.peg.1978	CDS	1845616	1845783	1	+	168	hypothetical protein	-none-	D23_1c1984	NA
  fig|6666666.60966.peg.1979	CDS	1846400	1845768	−2	−	633	DNA-binding response	-none-	D23_1c1985	Neut_1839
  							regulator, LuxR family
  fig|6666666.60966.peg.1980	CDS	1847948	1846452	−2	−	1497	Sensory box histidine	-none-	D23_1c1986	Neut_1840
  							kinase/response
  							regulator
  fig|6666666.60966.peg.1981	CDS	1848084	1848206	3	+	123	hypothetical protein	-none-	D23_1c1987	NA
  fig|6666666.60966.peg.1982	CDS	1850161	1848614	−1	−	1548	pilin glycosylation	-none-	D23_1c1988	Neut_1841
  							enzyme, putative
  fig|6666666.60966.peg.1985	CDS	1852587	1850815	−3	−	1773	Gamma-	Glutathione:	D23_1c1989	Neut_1843
  							glutamyltranspeptidase	Biosynthesis and
  							(EC 2.3.2.2)	gamma-glutamyl cycle
  fig|6666666.60966.peg.1986	CDS	1853865	1852903	−3	−	963	Mobile element protein	-none-	D23_1c1990	Neut_1746
  fig|6666666.60966.peg.1987	CDS	1854432	1853923	−3	−	510	putative	-none-	D23_1c1991	Neut_1845
  							transmembrane protein
  fig|6666666.60966.peg.1988	CDS	1855175	1854606	−2	−	570	hypothetical protein	-none-	D23_1c1992	Neut_1849
  fig|6666666.60966.peg.1989	CDS	1855822	1855421	−1	−	402	Glyoxalase family protein	-none-	D23_1c1993	Neut_1850
  fig|6666666.60966.peg.1990	CDS	1855948	1855835	−1	−	114	hypothetical protein	-none-	D23_1c1994	NA
  fig|6666666.60966.peg.1991	CDS	1856595	1856026	−3	−	570	hypothetical protein	-none-	D23_1c1995	Neut_1851
  fig|6666666.60966.peg.1992	CDS	1856572	1856703	1	+	132	hypothetical protein	-none-	D23_1c1996	NA
  fig|6666666.60966.peg.1993	CDS	1858627	1856756	−1	−	1872	hypothetical protein	-none-	D23_1c1997	Neut_1853
  fig|6666666.60966.peg.1994	CDS	1860549	1858642	−3	−	1908	hypothetical protein	-none-	D23_1c1998	Neut_1854
  fig|6666666.60966.peg.1995	CDS	1860536	1860667	2	+	132	hypothetical protein	-none-	D23_1c1999	NA
  fig|6666666.60966.peg.1996	CDS	1861687	1860761	−1	−	927	Expressed protein	-none-	D23_1c2000	Neut_1857
  							precursor
  fig|6666666.60966.peg.1997	CDS	1862145	1861684	−3	−	462	hypothetical protein	-none-	D23_1c2001	Neut_1858
  fig|6666666.60966.peg.1998	CDS	1865471	1862334	−2	−	3138	Proline dehydrogenase	Proline, 4-	D23_1c2002	Neut_1859
  							(EC 1.5.99.8) (Proline	hydroxyproline uptake
  							oxidase)/Delta-1-	and utilization;
  							pyrroline-5-carboxylate	<br>Respiratory
  							dehydrogenase (EC	dehydrogenases	1
  							1.5.1.12)
  fig|6666666.60966.peg.2000	CDS	1865859	1865701	−3	−	159	hypothetical protein	-none-	D23_1c2003	Neut_1860
  fig|6666666.60966.peg.2001	CDS	1866618	1866328	−3	−	291	hypothetical protein	-none-	D23_1c2004	NA
  fig|6666666.60966.peg.2002	CDS	1866574	1866861	1	+	288	Probable	-none-	D23_1c2005	Neut_1861
  							transmembrane protein
  fig|6666666.60966.peg.2004	CDS	1867176	1867955	3	+	780	hypothetical protein	-none-	D23_1c2006	Neut_1863
  fig|6666666.60966.peg.2005	CDS	1870128	1868077	−3	−	2052	Serine peptidase	-none-	D23_1c2007	Neut_1864
  fig|6666666.60966.peg.2006	CDS	1870373	1870546	2	+	174	hypothetical protein	-none-	D23_1c2008	NA
  fig|6666666.60966.peg.2007	CDS	1871555	1870827	−2	−	729	1-acyl-sn-glycerol-3-	Glycerolipid and	D23_1c2009	Neut_1866
  							phosphate	Glycerophospholipid
  							acyltransferase (EC	Metabolism in Bacteria
  							2.3.1.51)
  fig|6666666.60966.peg.2008	CDS	1872097	1871555	−1	−	543	Histidinol-phosphatase	Histidine Biosynthesis	D23_1c2010	Neut_1867
  							(EC 3.1.3.15)
  fig|6666666.60966.peg.2009	CDS	1874271	1872124	−3	−	2148	Glycyl-tRNA synthetase	Glycyl-tRNA synthetase;	D23_1c2011	Neut_1868
  							beta chain (EC 6.1.1.14)	<br>Glycyl-tRNA
  								synthetase containing
  								cluster; <br>tRNA
  								aminoacylation, Gly
  fig|6666666.60966.peg.2010	CDS	1875191	1874268	−2	−	924	Glycyl-tRNA synthetase	Glycyl-tRNA synthetase;	D23_1c2012	Neut_1869
  							alpha chain (EC	<br>Glycyl-tRNA
  							6.1.1.14)	synthetase containing
  								cluster; <br>tRNA
  								aminoacylation, Gly
  fig|6666666.60966.peg.2011	CDS	1876717	1875224	−1	−	1494	Apolipoprotein N-	Copper homeostasis:	D23_1c2013	Neut_1870
  							acyltransferase (EC	copper tolerance;
  							2.3.1.—)/Copper	<br>Lipoprotein
  							homeostasis protein	Biosynthesis; <br>tRNA-
  							CutE	methylthiotransferase
  								containing cluster;
  								<br>tRNA-
  								methylthiotransferase
  								containing cluster
  fig|6666666.60966.peg.2012	CDS	1877111	1876773	−2	−	339	FIG00859587:	-none-	D23_1c2014	Neut_1871
  							hypothetical protein
  fig|6666666.60966.peg.2013	CDS	1877265	1877122	−3	−	144	hypothetical protein	-none-	D23_1c2015	NA
  fig|6666666.60966.peg.2014	CDS	1877596	1879305	1	+	1710	Multicopper oxidase	Copper homeostasis	D23_1c2016	Neut_1872
  fig|6666666.60966.peg.2015	CDS	1879305	1880399	3	+	1095	Zinc ABC transporter,	-none-	D23_1c2017	Neut_1873
  							periplasmic-binding
  							protein ZnuA
  fig|6666666.60966.peg.2016	CDS	1881044	1880847	−2	−	198	hypothetical protein	-none-	D23_1c2018	NA
  fig|6666666.60966.peg.2017	CDS	1881486	1881962	3	+	477	Cytochrome c oxidase	Terminal cytochrome C	D23_1c2020	Neut_1874
  							(B(O/a)3-type) chain II	oxidases
  							(EC 1.9.3.1)
  fig|6666666.60966.peg.2018	CDS	1882000	1883478	1	+	1479	Cytochrome c oxidase	Terminal cytochrome C	D23_1c2021	Neut_1875
  							(B(O/a)3-type) chain I	oxidases
  							(EC 1.9.3.1)
  fig|6666666.60966.peg.2019	CDS	1883574	1884203	3	+	630	Cytochrome oxidase	Biogenesis of	D23_1c2022	Neut_1876
  							biogenesis protein	cytochrome c oxidases
  							Sco1/SenC/PrrC,
  							putative copper
  							metallochaperone
  fig|6666666.60966.peg.2020	CDS	1884187	1884756	1	+	570	hypothetical	-none-	D23_1c2023	Neut_1877
  							cytochrome oxidase
  							associated membrane
  							protein
  fig|6666666.60966.peg.2021	CDS	1885726	1884809	−1	−	918	Nitrite transporter from	-none-	D23_1c2024	Neut_1878
  							formate/nitrite family
  fig|6666666.60966.peg.2022	CDS	1887084	1886077	−3	−	1008	UDP-glucose 4-	CBSS-	D23_1c2026	Neut_1879
  							epimerase (EC 5.1.3.2)	296591.1.peg.2330;
  								<br>N-linked
  								Glycosylation in
  								Bacteria; <br>Rhamnose
  								containing glycans
  fig|6666666.60966.peg.2023	CDS	1888047	1887160	−3	−	888	Glucose-1-phosphate	Rhamnose containing	D23_1c2027	Neut_1880
  							thymidylyltransferase	glycans; <br>dTDP-
  							(EC 2.7.7.24)	rhamnose synthesis
  fig|6666666.60966.peg.2024	CDS	1888279	1888148	−1	−	132	hypothetical protein	-none-	D23_1c2028	NA
  fig|6666666.60966.peg.2025	CDS	1888278	1889198	3	+	921	2-hydroxy-3-	Glycerate metabolism;	D23_1c2029	Neut_1881
  							oxopropionate	<br>Photorespiration
  							reductase (EC 1.1.1.60)	(oxidative C2 cycle)
  fig|6666666.60966.peg.2026	CDS	1889188	1890642	1	+	1455	Glycolate	Glycolate, glyoxylate	D23_1c2030	Neut_1882
  							dehydrogenase (EC	interconversions;
  							1.1.99.14), subunit GlcD	<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.2027	CDS	1890667	1891767	1	+	1101	Glycolate	Glycolate, glyoxylate	D23_1c2031	Neut_1883
  							dehydrogenase (EC	interconversions;
  							1.1.99.14), FAD-binding	<br>Photorespiration
  							subunit GlcE	(oxidative C2 cycle)
  fig|6666666.60966.peg.2028	CDS	1891771	1893039	1	+	1269	Glycolate	Glycolate, glyoxylate	D23_1c2032	Neut_1884
  							dehydrogenase (EC	interconversions;
  							1.1.99.14), iron-sulfur	<br>Photorespiration
  							subunit GlcF	(oxidative C2 cycle)
  fig|6666666.60966.peg.2029	CDS	1893781	1893065	−1	−	717	Putative predicted	Restriction-Modification	D23_1c2033	Neut_1885
  							metal-dependent	System
  							hydrolase
  fig|6666666.60966.peg.2030	CDS	1894582	1893806	−1	−	777	5&#39;-	Adenosyl nucleosidases;	D23_1c2034	Neut_1886
  							methylthioadenosine	<br>Adenosyl
  							nucleosidase (EC	nucleosidases;
  							3.2.2.16)/S-	<br>CBSS-
  							adenosylhomocysteine	320388.3.peg.3759;
  							nucleosidase (EC	<br>CBSS-
  							3.2.2.9)	320388.3.peg.3759;
  								<br>Methionine
  								Biosynthesis;
  								<br>Methionine
  								Degradation;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.2031	CDS	1896116	1894656	−2	−	1461	Exodeoxyribonuclease I	DNA Repair Base	D23_1c2035	Neut_1887
  							(EC 3.1.11.1)	Excision
  fig|6666666.60966.peg.2032	CDS	1896438	1897133	3	+	696	FIG00657740:	-none-	D23_1c2036	Neut_1890
  							hypothetical protein
  fig|6666666.60966.peg.2033	CDS	1898282	1897428	−2	−	855	5,10-	5-FCL-like protein;	D23_1c2038	Neut_1891
  							methylenetetrahydrofolate	<br>Methionine
  							reductase (EC	Biosynthesis; <br>One-
  							1.5.1.20)	carbon metabolism by
  								tetrahydropterines
  fig|6666666.60966.peg.2034	CDS	1898327	1898494	2	+	168	hypothetical protein	-none-	D23_1c2039	NA
  fig|6666666.60966.peg.2035	CDS	1899999	1898563	−3	−	1437	Adenosylhomocysteinase	Methionine	D23_1c2041	Neut_1892
  							(EC 3.3.1.1)	Biosynthesis;
  								<br>Methionine
  								Degradation
  fig|6666666.60966.peg.2036	CDS	1901244	1900135	−3	−	1110	S-adenosylmethionine	Methionine	D23_1c2042	Neut_1893
  							synthetase (EC 2.5.1.6)	Biosynthesis;
  								<br>Methionine
  								Degradation
  fig|6666666.60966.peg.2037	CDS	1901543	1902289	2	+	747	Short chain	-none-	D23_1c2043	Neut_1894
  							dehydrogenase
  fig|6666666.60966.peg.2038	CDS	1902336	1902812	3	+	477	ATPase YjeE, predicted	-none-	D23_1c2044	Neut_1895
  							to have essential role in
  							cell wall biosynthesis
  fig|6666666.60966.peg.2039	CDS	1903046	1904116	2	+	1071	N-acetylmuramoyl-L-	Murein Hydrolases;	D23_1c2045	Neut_1896
  							alanine amidase (EC	<br>Recycling of
  							3.5.1.28)	Peptidoglycan Amino
  								Acids; <br>Zinc
  								regulated enzymes
  fig|6666666.60966.peg.2040	CDS	1904922	1904170	−3	−	753	FIG00859340:	-none-	D23_1c2046	Neut_1897
  							hypothetical protein
  fig|6666666.60966.peg.2041	CDS	1905860	1904919	−2	−	942	Ribosomal protein L11	Heat shock dnaK gene	D23_1c2047	Neut_1898
  							methyltransferase (EC	cluster extended;
  							2.1.1.—)	<br>Ribosome
  								biogenesis bacterial
  fig|6666666.60966.peg.2042	CDS	1907254	1905896	−1	−	1359	Biotin carboxylase of	Fatty Acid Biosynthesis	D23_1c2048	Neut_1899
  							acetyl-CoA carboxylase	FASII
  							(EC 6.3.4.14)
  fig|6666666.60966.peg.2043	CDS	1907784	1907326	−3	−	459	Biotin carboxyl carrier	Fatty Acid Biosynthesis	D23_1c2049	Neut_1900
  							protein of acetyl-CoA	FASII
  							carboxylase
  fig|6666666.60966.peg.2045	CDS	1908294	1907989	−3	−	306	3-dehydroquinate	Chorismate Synthesis;	D23_1c2050	Neut_1901
  							dehydratase II (EC	<br>Common Pathway
  							4.2.1.10)	For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate);
  								<br>Quinate
  								degradation
  fig|6666666.60966.peg.2047	CDS	1908606	1909715	3	+	1110	Glycine oxidase ThiO	Thiamin biosynthesis	D23_1c2051	Neut_1902
  							(EC 1.4.3.19)
  fig|6666666.60966.peg.2048	CDS	1910693	1909722	−2	−	972	4-hydroxy-3-methylbut-	Isoprenoid Biosynthesis;	D23_1c2052	Neut_1903
  							2-enyl diphosphate	<br>Nonmevalonate
  							reductase (EC 1.17.1.2)	Branch of Isoprenoid
  								Biosynthesis
  fig|6666666.60966.peg.2049	CDS	1910983	1911267	1	+	285	FIG00858797:	-none-	D23_1c2053	Neut_1904
  							hypothetical protein
  fig|6666666.60966.peg.2050	CDS	1911307	1912386	1	+	1080	Histidinol-phosphate	Histidine Biosynthesis	D23_1c2054	Neut_1905
  							aminotransferase (EC
  							2.6.1.9)
  fig|6666666.60966.peg.2051	CDS	1912429	1913016	1	+	588	Imidazoleglycerol-	Histidine Biosynthesis	D23_1c2055	Neut_1906
  							phosphate dehydratase
  							(EC 4.2.1.19)
  fig|6666666.60966.peg.2052	CDS	1913079	1913687	3	+	609	Imidazole glycerol	Histidine Biosynthesis	D23_1c2056	Neut_1907
  							phosphate synthase
  							amidotransferase
  							subunit (EC 2.4.2.—)
  fig|6666666.60966.peg.2053	CDS	1913772	1914518	3	+	747	Phosphoribosylformimino-	Chorismate:	D23_1c2057	Neut_1908
  							5-aminoimidazole	Intermediate for
  							carboxamide ribotide	synthesis of Tryptophan,
  							isomerase (EC 5.3.1.16)	PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.; <br>Histidine
  								Biosynthesis
  fig|6666666.60966.peg.2054	CDS	1914604	1915380	1	+	777	Imidazole glycerol	Histidine Biosynthesis	D23_1c2058	Neut_1909
  							phosphate synthase
  							cyclase subunit (EC
  							4.1.3.—)
  fig|6666666.60966.peg.2055	CDS	1915424	1915909	2	+	486	Phosphoribosyl-AMP	Histidine Biosynthesis;	D23_1c2059	Neut_1910
  							cyclohydrolase (EC	<br>Zinc regulated
  							3.5.4.19)	enzymes
  fig|6666666.60966.peg.2056	CDS	1915906	1916259	1	+	354	Phosphoribosyl-ATP	Histidine Biosynthesis;	D23_1c2060	Neut_1911
  							pyrophosphatase (EC	<br>Riboflavin synthesis
  							3.6.1.31)	cluster
  fig|6666666.60966.peg.2057	CDS	1916261	1916611	2	+	351	FIG146285:	-none-	D23_1c2061	Neut_1912
  							Diadenosine
  							tetraphosphate (Ap4A)
  							hydrolase and other HIT
  							family hydrolases
  fig|6666666.60966.peg.2058	CDS	1916631	1916864	3	+	234	Twin-arginine	Cluster-based Subsystem	D23_1c2062	Neut_1913
  							translocation protein	Grouping Hypotheticals-
  							TatA	perhaps Proteosome
  								Related; <br>Twin-
  								arginine translocation
  								system
  fig|6666666.60966.peg.2060	CDS	1916950	1917342	1	+	393	Twin-arginine	Twin-arginine	D23_1c2063	Neut_1914
  							translocation protein	translocation system
  							TatB
  fig|6666666.60966.peg.2061	CDS	1917433	1918209	1	+	777	Twin-arginine	Cluster-based Subsystem	D23_1c2064	Neut_1915
  							translocation protein	Grouping Hypotheticals-
  							TatC	perhaps Proteosome
  								Related; <br>Twin-
  								arginine translocation
  								system
  fig|6666666.60966.peg.2062	CDS	1918395	1920518	3	+	2124	Outer membrane	-none-	D23_1c2065	Neut_1916
  							vitamin B12 receptor
  							BtuB
  fig|6666666.60966.peg.2063	CDS	1920528	1921118	3	+	591	Optional hypothetical	-none-	D23_1c2066	Neut_1917
  							component of the B12
  							transporter BtuM
  fig|6666666.60966.peg.2064	CDS	1921118	1921726	2	+	609	Cob(I)alamin	-none-	D23_1c2067	Neut_1918
  							adenosyltransferase (EC
  							2.5.1.17)
  fig|6666666.60966.peg.2065	CDS	1922713	1922826	1	+	114	hypothetical protein	-none-	D23_1c2069	NA
  fig|6666666.60966.peg.2067	CDS	1923447	1924253	3	+	807	Cytochrome bd-type	-none-	D23_1c2070	Neut_1920
  							quinol oxidase, subunit 1
  fig|6666666.60966.peg.2068	CDS	1926393	1924288	−3	−	2106	Methionyl-tRNA	Scaffold proteins for	D23_1c2071	Neut_1921
  							synthetase (EC 6.1.1.10)	[4Fe—4S] cluster
  								assembly (MRP family);
  								<br>tRNA
  								aminoacylation, Met
  fig|6666666.60966.peg.2069	CDS	1926506	1926390	−2	−	117	hypothetical protein	-none-	D23_1c2072	NA
  fig|6666666.60966.peg.2070	CDS	1926499	1927584	1	+	1086	Scaffold protein for	Scaffold proteins for	D23_1c2073	Neut_1922
  							[4Fe—4S] cluster	[4Fe—4S] cluster
  							assembly ApbC, MRP-	assembly (MRP family)
  							like
  fig|6666666.60966.peg.2071	CDS	1927630	1928163	1	+	534	Deoxycytidine	pyrimidine conversions	D23_1c2074	Neut_1923
  							triphosphate deaminase
  							(EC 3.5.4.13)
  fig|6666666.60966.peg.2072	CDS	1928619	1928251	−3	−	369	COGs COG1917	-none-	D23_1c2075	Neut_1924
  fig|6666666.60966.peg.2073	CDS	1929401	1928631	−2	−	771	Inner membrane	-none-	D23_1c2076	Neut_1925
  							protein
  fig|6666666.60966.peg.2074	CDS	1929596	1929889	2	+	294	Mobile element protein	-none-	D23_1c2077	Neut_1719
  fig|6666666.60966.peg.2075	CDS	1929988	1930866	1	+	879	Mobile element protein	-none-	D23_1c2078	Neut_1720
  fig|6666666.60966.peg.2076	CDS	1930961	1933699	2	+	2739	Ca ion P-type ATPase	-none-	D23_1c2079	Neut_1926
  fig|6666666.60966.peg.2078	CDS	1934003	1934323	2	+	321	hypothetical protein	-none-	D23_1c2080	Neut_1927
  fig|6666666.60966.peg.2079	CDS	1935608	1934517	−2	−	1092	Prophage Lp2 protein 6	-none-	D23_1c2081	Neut_1928
  fig|6666666.60966.peg.2081	CDS	1935893	1936396	2	+	504	ABC transporter ATP-	-none-	D23_1c2083	Neut_1936
  							binding protein YvcR
  fig|6666666.60966.peg.2083	CDS	1936587	1936880	3	+	294	Mobile element protein	-none-	D23_1c2085	Neut_1719
  fig|6666666.60966.peg.2084	CDS	1936979	1937857	2	+	879	Mobile element protein	-none-	D23_1c2086	Neut_1720
  fig|6666666.60966.peg.2085	CDS	1938082	1937936	−1	−	147	hypothetical protein	-none-	D23_1c2087	Neut_1937
  fig|6666666.60966.peg.2086	CDS	1938637	1938188	−1	−	450	Ferric uptake regulation	Bacterial RNA-	D23_1c2088	Neut_1938
  							protein FUR	metabolizing Zn-
  								dependent hydrolases;
  								<br>Oxidative stress
  fig|6666666.60966.peg.2087	CDS	1938848	1939330	2	+	483	Outer membrane	Lipopolysaccharide	D23_1c2089	Neut_1939
  							lipoprotein SmpA, a	assembly
  							component of the
  							essential YaeT outer-
  							membrane protein
  							assembly complex
  fig|6666666.60966.peg.2088	CDS	1939327	1940133	1	+	807	Dihydrodipicolinate	-none-	D23_1c2090	Neut_1940
  							reductase (EC 1.3.1.26)
  fig|6666666.60966.peg.2089	CDS	1941855	1940347	−3	−	1509	ATPase	-none-	D23_1c2091	Neut_1941
  fig|6666666.60966.peg.2090	CDS	1942209	1942087	−3	−	123	hypothetical protein	-none-	D23_1c2092	NA
  fig|6666666.60966.peg.2091	CDS	1942220	1942459	2	+	240	Type I restriction-	Restriction-Modification	D23_1c2093	Neut_1942
  							modification system,	System; <br>Type I
  							DNA-methyltransferase	Restriction-Modification
  							subunit M (EC 2.1.1.72)
  fig|6666666.60966.peg.2092	CDS	1942456	1942860	1	+	405	Cell filamentation	-none-	D23_1c2094	Neut_1943
  							protein fic
  fig|6666666.60966.peg.2093	CDS	1942823	1943278	2	+	456	Mobile element protein	-none-	D23_1c2095	Neut_2502
  fig|6666666.60966.peg.2094	CDS	1943305	1944786	1	+	1482	Outer membrane	-none-	D23_1c2096	Neut_1945
  							component of tripartite
  							multidrug resistance
  							system
  fig|6666666.60966.peg.2095	CDS	1944830	1946014	2	+	1185	Membrane fusion	Multidrug Resistance	D23_1c2097	Neut_1946
  							protein of RND family	Efflux Pumps
  							multidrug efflux pump
  fig|6666666.60966.peg.2096	CDS	1946018	1949131	2	+	3114	RND efflux system,	Multidrug Resistance	D23_1c2098	Neut_1947
  							inner membrane	Efflux Pumps
  							transporter CmeB
  fig|6666666.60966.peg.2097	CDS	1949252	1949386	2	+	135	Type I restriction-	Restriction-Modification	D23_1c2099	NA
  							modification system,	System; <br>Type I
  							restriction subunit R (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.2098	CDS	1949446	1950246	1	+	801	Bis(5&#39;-nucleosyl)-	EC49-61	D23_1c2100	Neut_1949
  							tetraphosphatase,
  							symmetrical (EC
  							3.6.1.41)
  fig|6666666.60966.peg.2099	CDS	1951009	1950200	−1	−	810	1-acyl-sn-glycerol-3-	Glycerolipid and	D23_1c2101	Neut_1950
  							phosphate	Glycerophospholipid
  							acyltransferase (EC	Metabolism in Bacteria
  							2.3.1.51)
  fig|6666666.60966.peg.2100	CDS	1952008	1951073	−1	−	936	InterPro IPR002173	-none-	D23_1c2103	Neut_1951
  							COGs COG0524
  fig|6666666.60966.peg.2101	CDS	1953491	1952040	−2	−	1452	Glycine dehydrogenase	Glycine and Serine	D23_1c2104	Neut_1952
  							[decarboxylating]	Utilization; <br>Glycine
  							(glycine cleavage	cleavage system;
  							system P2 protein) (EC	<br>Photorespiration
  							1.4.4.2)	(oxidative C2 cycle)
  fig|6666666.60966.peg.2102	CDS	1954921	1953566	−1	−	1356	Glycine dehydrogenase	Glycine and Serine	D23_1c2105	Neut_1953
  							[decarboxylating]	Utilization; <br>Glycine
  							(glycine cleavage	cleavage system;
  							system P1 protein) (EC	<br>Photorespiration
  							1.4.4.2)	(oxidative C2 cycle)
  fig|6666666.60966.peg.2103	CDS	1955520	1955131	−3	−	390	Glycine cleavage system	Glycine and Serine	D23_1c2106	Neut_1954
  							H protein	Utilization; <br>Glycine
  								cleavage system;
  								<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.2104	CDS	1956682	1955591	−1	−	1092	Aminomethyltransferase	CBSS-87626.3.peg.3639;	D23_1c2107	Neut_1955
  							(glycine cleavage	<br>Glycine and Serine
  							system T protein) (EC	Utilization; <br>Glycine
  							2.1.2.10)	cleavage system;
  								<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.2106	CDS	1957270	1957133	−1	−	138	hypothetical protein	-none-	D23_1c2108	NA
  fig|6666666.60966.peg.2107	CDS	1958337	1957420	−3	−	918	Coproporphyrinogen III	Heme and Siroheme	D23_1c2109	Neut_1956
  							oxidase, aerobic (EC	Biosynthesis
  							1.3.3.3)
  fig|6666666.60966.peg.2108	CDS	1958499	1959671	3	+	1173	Chorismate synthase	Chorismate Synthesis;	D23_1c2110	Neut_1957
  							(EC 4.2.3.5)	<br>Common Pathway
  								For Synthesis of
  								Aromatic Compounds
  								(DAHP synthase to
  								chorismate)
  fig|6666666.60966.peg.2110	CDS	1960360	1961133	1	+	774	IncF plasmid	-none-	D23_1c2111	Neut_1959
  							conjugative transfer
  							surface exclusion
  							protein TraT
  fig|6666666.60966.peg.2111	CDS	1961191	1961517	1	+	327	hypothetical protein	-none-	D23_1c2112	NA
  fig|6666666.60966.peg.2112	CDS	1961582	1962544	2	+	963	Mobile element protein	-none-	D23_1c2114	Neut_1862
  fig|6666666.60966.peg.2113	CDS	1962848	1962729	−2	−	120	hypothetical protein	-none-	D23_1c2115	NA
  fig|6666666.60966.peg.2115	CDS	1965546	1963441	−3	−	2106	Ferrichrome-iron	-none-	D23_1c2116	Neut_1962
  							receptor
  fig|6666666.60966.peg.2118	CDS	1967221	1966565	−1	−	657	Protein of unknown	-none-	D23_1c2119	Neut_1964
  							function DUF208
  fig|6666666.60966.peg.2119	CDS	1967389	1968672	1	+	1284	FIG00858634:	-none-	D23_1c2120	Neut_1965
  							hypothetical protein
  fig|6666666.60966.peg.2120	CDS	1968691	1969206	1	+	516	FIG00859317:	-none-	D23_1c2121	Neut_1966
  							hypothetical protein
  fig|6666666.60966.peg.2121	CDS	1969209	1969910	3	+	702	InterPro IPR000179	-none-	D23_1c2122	Neut_1967
  							COGs COG1423
  fig|6666666.60966.peg.2122	CDS	1969960	1970334	1	+	375	InterPro IPR003807	-none-	D23_1c2123	Neut_1968
  							COGs COG2149
  fig|6666666.60966.peg.2123	CDS	1971838	1970381	−1	−	1458	Catalase (EC 1.11.1.6)	Oxidative stress;	D23_1c2124	Neut_1969
  								<br>Photorespiration
  								(oxidative C2 cycle);
  								<br>Protection from
  								Reactive Oxygen Species
  fig|6666666.60966.peg.2124	CDS	1973211	1971865	−3	−	1347	FIG00858984:	-none-	D23_1c2125	Neut_1970
  							hypothetical protein
  fig|6666666.60966.peg.2125	CDS	1974046	1973246	−1	−	801	Protein of unknown	-none-	D23_1c2126	Neut_1971
  							function DUF81
  fig|6666666.60966.peg.2126	CDS	1974579	1974124	−3	−	456	Protein of unknown	-none-	D23_1c2127	Neut_1972
  							function DUF55
  fig|6666666.60966.peg.2127	CDS	1976514	1974985	−3	−	1530	Capsular polysaccharide	Capsular Polysaccharides	D23_1c2128	NA
  							biosynthesis protein	Biosynthesis and
  							WcbQ	Assembly
  fig|6666666.60966.peg.2128	CDS	1977322	1976504	−1	−	819	Oxidoreductase, short-	Capsular Polysaccharides	D23_1c2129	Neut_1974
  							chain	Biosynthesis and
  							dehydrogenase/reductase	Assembly
  							family (EC 1.1.1.—)
  fig|6666666.60966.peg.2129	CDS	1978801	1977323	−1	−	1479	Glycosyltransferase	-none-	D23_1c2130	Neut_1975
  fig|6666666.60966.peg.2130	CDS	1979888	1978803	−2	−	1086	possible spore protein	-none-	D23_1c2131	Neut_1976
  							[UI:20467420]
  fig|6666666.60966.peg.2131	CDS	1981090	1979921	−1	−	1170	FIG00858788:	-none-	D23_1c2132	Neut_1977
  							hypothetical protein
  fig|6666666.60966.peg.2132	CDS	1982214	1981231	−3	−	984	hypothetical protein	-none-	D23_1c2133	NA
  fig|6666666.60966.peg.2133	CDS	1982778	1982218	−3	−	561	hypothetical protein	-none-	D23_1c2134	NA
  fig|6666666.60966.peg.2134	CDS	1983862	1982783	−1	−	1080	Glycosyltransferase (EC	-none-	D23_1c2135	Neut_1982
  							2.4.1.—)
  fig|6666666.60966.peg.2135	CDS	1984198	1983896	−1	−	303	hypothetical protein	-none-	D23_1c2136	Neut_1983
  fig|6666666.60966.peg.2136	CDS	1984883	1984704	−2	−	180	Mobile element protein	-none-	D23_1c2137	Neut_1984
  fig|6666666.60966.peg.2137	CDS	1985076	1984852	−3	−	225	hypothetical protein	-none-	D23_1c2138	NA
  fig|6666666.60966.peg.2139	CDS	1985629	1986384	1	+	756	hypothetical protein	-none-	D23_1c2139	Neut_1985
  fig|6666666.60966.peg.2140	CDS	1987287	1988645	3	+	1359	FIG00860556:	-none-	D23_1c2140	Neut_1986
  							hypothetical protein
  fig|6666666.60966.peg.2141	CDS	1988761	1989375	1	+	615	Cytochrome oxidase	Biogenesis of	D23_1c2141	Neut_1987
  							biogenesis protein	cytochrome c oxidases
  							Sco1/SenC/PrrC,
  							putative copper
  							metallochaperone
  fig|6666666.60966.peg.2142	CDS	1989381	1990007	3	+	627	FIG00859788:	-none-	D23_1c2142	Neut_1988
  							hypothetical protein
  fig|6666666.60966.peg.2145	CDS	1990866	1990588	−3	−	279	hypothetical membrane	-none-	D23_1c2144	Neut_1990
  							protein
  fig|6666666.60966.peg.2146	CDS	1991501	1991046	−2	−	456	InterPro IPR000485	-none-	D23_1c2145	Neut_1991
  fig|6666666.60966.peg.2147	CDS	1993914	1991785	−3	−	2130	Phosphate	Fermentations: Lactate;	D23_1c2146	Neut_1995
  							acetyltransferase (EC	<br>Pyruvate
  							2.3.1.8)	metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.2148	CDS	1995278	1994253	−2	−	1026	Fructose-bisphosphate	Calvin-Benson cycle;	D23_1c2147	Neut_1996
  							aldolase class I (EC	<br>Glycolysis and
  							4.1.2.13)	Gluconeogenesis
  fig|6666666.60966.peg.2150	CDS	1995705	1995851	3	+	147	hypothetical protein	-none-	D23_1c2148	NA
  fig|6666666.60966.peg.2152	CDS	1995966	1996298	3	+	333	DNA-binding protein	-none-	D23_1c2150	Neut_1998
  fig|6666666.60966.peg.2154	CDS	1996639	1996932	1	+	294	protein of unknown	-none-	D23_1c2151	Neut_1999
  							function DUF497
  fig|6666666.60966.peg.2155	CDS	1996922	1997203	2	+	282	hypothetical protein	-none-	D23_1c2152	Neut_2000
  fig|6666666.60966.peg.2156	CDS	1997890	1998093	1	+	204	Mobile element protein	-none-	D23_1c2154	NA
  fig|6666666.60966.peg.2157	CDS	1998565	1998266	−1	−	300	VapC toxin protein	Toxin-antitoxin replicon	D23_1c2155	NA
  								stabilization systems
  fig|6666666.60966.peg.2158	CDS	1998899	1998666	−2	−	234	VapB protein (antitoxin	Toxin-antitoxin replicon	D23_1c2156	NA
  							to VapC)	stabilization systems
  fig|6666666.60966.peg.2159	CDS	1999186	1999344	1	+	159	hypothetical protein	-none-	D23_1c2157	NA
  fig|6666666.60966.peg.2160	CDS	1999629	1999339	−3	−	291	transcriptional	-none-	D23_1c2158	NA
  							regulator, XRE family
  fig|6666666.60966.peg.2161	CDS	1999997	1999692	−2	−	306	Phage-related protein	-none-	D23_1c2159	NA
  fig|6666666.60966.peg.2162	CDS	2000147	2000022	−2	−	126	hypothetical protein	-none-	D23_1c2160	NA
  fig|6666666.60966.peg.2163	CDS	2000220	2000486	3	+	267	Mobile element protein	-none-	D23_1c2161	NA
  fig|6666666.60966.peg.2164	CDS	2000507	2000995	2	+	489	Mobile element protein	-none-	D23_1c2162	NA
  fig|6666666.60966.peg.2165	CDS	2001470	2000997	−2	−	474	Mobile element protein	-none-	D23_1c2163	Neut_1256
  fig|6666666.60966.peg.2166	CDS	2001936	2001544	−3	−	393	hypothetical protein	-none-	D23_1c2164	Neut_2449
  fig|6666666.60966.peg.2167	CDS	2002011	2002328	3	+	318	Mobile element protein	-none-	D23_1c2165	NA
  fig|6666666.60966.peg.2168	CDS	2003529	2002369	−3	−	1161	CDP-4-dehydro-6-	-none-	D23_1c2166	NA
  							deoxy-D-glucose 3-
  							dehydratase (EC 4.2.1.—)
  fig|6666666.60966.peg.2169	CDS	2004426	2003539	−3	−	888	NAD-dependent	CBSS-296591.1.peg.2330	D23_1c2167	NA
  							epimerase/dehydratase
  							family protein
  fig|6666666.60966.peg.2170	CDS	2005586	2004468	−2	−	1119	GDP-mannose 4,6-	-none-	D23_1c2168	Neut_0156
  							dehydratase (EC
  							4.2.1.47)
  fig|6666666.60966.peg.2171	CDS	2007467	2005632	−2	−	1836	hypothetical protein	-none-	D23_1c2169	NA
  fig|6666666.60966.peg.2172	CDS	2010568	2007473	−1	−	3096	Minor teichoic acid	-none-	D23_1c2170	NA
  							biosynthesis protein
  							GgaB
  fig|6666666.60966.peg.2173	CDS	2012163	2010694	−3	−	1470	InterPro IPR001173	-none-	D23_1c2171	NA
  							COGs COG0463
  fig|6666666.60966.peg.2174	CDS	2015828	2012172	−2	−	3657	Beta-1,3-	-none-	D23_1c2172	NA
  							glucosyltransferase
  fig|6666666.60966.peg.2175	CDS	2017307	2016147	−2	−	1161	Capsular polysaccharide	Capsular Polysaccharides	D23_1c2173	NA
  							export system inner	Biosynthesis and
  							membrane protein KpsE	Assembly
  fig|6666666.60966.peg.2176	CDS	2017966	2017304	−1	−	663	Capsular polysaccharide	Capsular Polysaccharides	D23_1c2174	Neut_0152
  							ABC transporter, ATP-	Biosynthesis and
  							binding protein KpsT	Assembly
  fig|6666666.60966.peg.2177	CDS	2018757	2017963	−3	−	795	Capsular polysaccharide	Capsular Polysaccharides	D23_1c2175	NA
  							ABC transporter,	Biosynthesis and
  							permease protein KpsM	Assembly;
  								<br>Rhamnose
  								containing glycans
  fig|6666666.60966.peg.2178	CDS	2019947	2018757	−2	−	1191	Capsular polysaccharide	Capsular Polysaccharides	D23_1c2176	Neut_2119
  							biosynthesis/export	Biosynthesis and
  							periplasmic protein	Assembly
  							WcbC
  fig|6666666.60966.peg.2179	CDS	2021279	2019957	−2	−	1323	8-amino-7-	Biotin biosynthesis;	D23_1c2177	Neut_0461
  							oxononanoate synthase	<br>Biotin biosynthesis
  							(EC 2.3.1.47)	Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2180	CDS	2025121	2021276	−1	−	3846	Capsular polysaccharide	-none-	D23_1c2178	NA
  							biosynthesis fatty acid
  							synthase WcbR
  fig|6666666.60966.peg.2181	CDS	2028811	2025266	−1	−	3546	Capsular polysaccharide	-none-	D23_1c2179	Neut_2003
  							biosynthesis fatty acid
  							synthase WcbR
  fig|6666666.60966.peg.2182	CDS	2029053	2029166	3	+	114	hypothetical protein	-none-	D23_1c2180	NA
  fig|6666666.60966.peg.2183	CDS	2029212	2029352	3	+	141	hypothetical protein	-none-	D23_1c2181	NA
  fig|6666666.60966.peg.2184	CDS	2031017	2029434	−2	−	1584	L-aspartate oxidase (EC	Mycobacterium	D23_1c2182	Neut_2004
  							1.4.3.16)	virulence operon
  								possibly involved in
  								quinolinate biosynthesis;
  								<br>NAD and NADP
  								cofactor biosynthesis
  								global
  fig|6666666.60966.peg.2185	CDS	2031267	2032187	3	+	921	Branched-chain amino	Alanine biosynthesis;	D23_1c2184	Neut_2005
  							acid aminotransferase	<br>Branched-Chain
  							(EC 2.6.1.42)	Amino Acid Biosynthesis;
  								<br>Leucine
  								Biosynthesis;
  								<br>Pyruvate Alanine
  								Serine Interconversions
  fig|6666666.60966.peg.2186	CDS	2032212	2032421	3	+	210	FIG00858455:	-none-	D23_1c2185	Neut_2006
  							hypothetical protein
  fig|6666666.60966.peg.2187	CDS	2032485	2033864	3	+	1380	Phosphomannomutase	Mannose Metabolism	D23_1c2186	Neut_2007
  							(EC 5.4.2.8)/
  							Phosphoglucomutase
  							(EC 5.4.2.2)
  fig|6666666.60966.peg.2188	CDS	2033901	2035508	3	+	1608	NAD synthetase (EC	NAD and NADP cofactor	D23_1c2187	Neut_2008
  							6.3.1.5)/Glutamine	biosynthesis global;
  							amidotransferase chain	<br>NAD and NADP
  							of NAD synthetase	cofactor biosynthesis
  								global
  fig|6666666.60966.peg.2189	CDS	2035472	2037178	2	+	1707	Exported zinc	-none-	D23_1c2188	Neut_2009
  							metalloprotease YfgC
  							precursor
  fig|6666666.60966.peg.2190	CDS	2037257	2038402	2	+	1146	Macrolide-specific	Multidrug Resistance	D23_1c2189	Neut_2010
  							efflux protein MacA	Efflux Pumps
  fig|6666666.60966.peg.2191	CDS	2038413	2039180	3	+	768	Macrolide export ATP-	Multidrug Resistance	D23_1c2190	Neut_2011
  							binding/permease	Efflux Pumps
  							protein MacB (EC 3.6.3.—)
  fig|6666666.60966.peg.2192	CDS	2039177	2040400	2	+	1224	Macrolide export ATP-	Multidrug Resistance	D23_1c2191	Neut_2012
  							binding/permease	Efflux Pumps
  							protein MacB (EC 3.6.3.—)
  fig|6666666.60966.peg.2193	CDS	2040442	2040612	1	+	171	hypothetical protein	-none-	D23_1c2192	NA
  fig|6666666.60966.peg.2195	CDS	2040690	2040875	3	+	186	hypothetical protein	-none-	D23_1c2193	NA
  fig|6666666.60966.peg.2196	CDS	2040926	2042374	2	+	1449	ATP synthase beta chain	-none-	D23_1c2194	Neut_2013
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.2197	CDS	2042371	2042781	1	+	411	ATP synthase epsilon	-none-	D23_1c2195	Neut_2014
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.2198	CDS	2042778	2043059	3	+	282	ATP synthase protein I	-none-	D23_1c2196	Neut_2015
  fig|6666666.60966.peg.2199	CDS	2043105	2043398	3	+	294	FIG048548: ATP	-none-	D23_1c2197	Neut_2016
  							synthase protein I2
  fig|6666666.60966.peg.2200	CDS	2043420	2044112	3	+	693	ATP synthase A chain	-none-	D23_1c2198	Neut_2017
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.2201	CDS	2044115	2044393	2	+	279	ATP synthase C chain	-none-	D23_1c2199	Neut_2018
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.2202	CDS	2044400	2045170	2	+	771	ATP synthase B chain	-none-	D23_1c2200	Neut_2019
  							(EC 3.6.3.14)
  fig|6666666.60966.peg.2203	CDS	2045183	2046733	2	+	1551	ATP synthase alpha	-none-	D23_1c2201	Neut_2020
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.2204	CDS	2046810	2047607	3	+	798	ATP synthase gamma	-none-	D23_1c2202	Neut_2021
  							chain (EC 3.6.3.14)
  fig|6666666.60966.peg.2206	CDS	2048344	2050986	1	+	2643	DNA mismatch repair	DNA repair, bacterial	D23_1c2204	Neut_2022
  							protein MutS	MutL-MutS system;
  								<br>DNA repair system
  								including RecA, MutS
  								and a hypothetical
  								protein
  fig|6666666.60966.peg.2207	CDS	2051500	2051021	−1	−	480	FKBP-type peptidyl-	G3E family of P-loop	D23_1c2205	Neut_2023
  							prolyl cis-trans	GTPases (metallocenter
  							isomerase SlyD (EC	biosynthesis);
  							5.2.1.8)	<br>Peptidyl-prolyl cis-
  								trans isomerase;
  								<br>Potassium
  								homeostasis
  fig|6666666.60966.peg.2208	CDS	2052207	2051656	−3	−	552	Ribonuclease HII (EC	Ribonuclease H;	D23_1c2206	Neut_2024
  							3.1.26.4)	<br>Ribonucleases in
  								Bacillus
  fig|6666666.60966.peg.2209	CDS	2052737	2052294	−2	−	444	(3R)-hydroxymyristoyl-	-none-	D23_1c2207	Neut_2025
  							[acyl carrier protein]
  							dehydratase (EC 4.2.1.—)
  fig|6666666.60966.peg.2210	CDS	2053333	2052770	−1	−	564	Outer membrane	Lipopolysaccharide	D23_1c2208	Neut_2026
  							protein H precursor	assembly;
  								<br>Periplasmic Stress
  								Response
  fig|6666666.60966.peg.2211	CDS	2055635	2053359	−2	−	2277	Outer membrane	Lipopolysaccharide	D23_1c2209	Neut_2027
  							protein assembly factor	assembly
  							YaeT precursor
  fig|6666666.60966.peg.2212	CDS	2057020	2055638	−1	−	1383	Membrane-associated	-none-	D23_1c2210	Neut_2028
  							zinc metalloprotease
  fig|6666666.60966.peg.2213	CDS	2058265	2057024	−1	−	1242	1-deoxy-D-xylulose 5-	CBSS-83331.1.peg.3039;	D23_1c2211	Neut_2029
  							phosphate	<br>Isoprenoid
  							reductoisomerase (EC	Biosynthesis;
  							1.1.1.267)	<br>Nonmevalonate
  								Branch of Isoprenoid
  								Biosynthesis
  fig|6666666.60966.peg.2214	CDS	2059089	2058262	−3	−	828	Phosphatidate	Glycerolipid and	D23_1c2212	Neut_2030
  							cytidylyltransferase (EC	Glycerophospholipid
  							2.7.7.41)	Metabolism in Bacteria
  fig|6666666.60966.peg.2215	CDS	2059870	2059124	−1	−	747	Undecaprenyl	CBSS-83331.1.peg.3039;	D23_1c2213	Neut_2031
  							diphosphate synthase	<br>Isoprenoid
  							(EC 2.5.1.31)	Biosynthesis;
  								<br>Isoprenoinds for
  								Quinones;
  								<br>Polyprenyl
  								Diphosphate
  								Biosynthesis
  fig|6666666.60966.peg.2216	CDS	2060476	2059919	−1	−	558	Ribosome recycling	Ribosome recycling	D23_1c2214	Neut_2032
  							factor	related cluster;
  								<br>Translation
  								termination factors
  								bacterial
  fig|6666666.60966.peg.2217	CDS	2061239	2060577	−2	−	663	Uridylate kinase (EC	-none-	D23_1c2215	Neut_2033
  							2.7.4.—)
  fig|6666666.60966.peg.2218	CDS	2061489	2061361	−3	−	129	hypothetical protein	-none-	D23_1c2216	NA
  fig|6666666.60966.peg.2219	CDS	2062729	2061845	−1	−	885	Translation elongation	CBSS-	D23_1c2217	Neut_2034
  							factor Ts	312309.3.peg.1965;
  								<br>Ribosome recycling
  								related cluster;
  								<br>Translation
  								elongation factors
  								bacterial
  fig|6666666.60966.peg.2220	CDS	2063557	2062802	−1	−	756	SSU ribosomal protein	CBSS-	D23_1c2218	Neut_2035
  							S2p (SAe)	312309.3.peg.1965;
  								<br>Ribosome recycling
  								related cluster
  fig|6666666.60966.peg.2221	CDS	2064515	2063772	−2	−	744	transcriptional	Oxidative stress	D23_1c2219	Neut_2036
  							regulator, Crp/Fnr
  							family
  fig|6666666.60966.peg.2222	CDS	2064873	2064562	−3	−	312	Cytochrome c, class I	-none-	D23_1c2220	Neut_2037
  fig|6666666.60966.peg.2223	CDS	2067162	2065111	−3	−	2052	Zinc-regulated outer	-none-	D23_1c2221	Neut_2038
  							membrane receptor
  fig|6666666.60966.peg.2225	CDS	2067907	2068395	1	+	489	Zinc uptake regulation	Glycyl-tRNA synthetase	D23_1c2222	NA
  							protein ZUR	containing cluster;
  								<br>Oxidative stress;
  								<br>Zinc regulated
  								enzymes
  fig|6666666.60966.peg.2226	CDS	2068438	2068560	1	+	123	Mobile element protein	-none-	D23_1c2223	Neut_0884
  fig|6666666.60966.peg.2228	CDS	2068811	2069020	2	+	210	hypothetical protein	-none-	D23_1c2224	NA
  fig|6666666.60966.peg.2231	CDS	2069466	2069332	−3	−	135	hypothetical protein	-none-	D23_1c2225	NA
  fig|6666666.60966.peg.2232	CDS	2069455	2070327	1	+	873	COG0613, Predicted	A cluster relating to	D23_1c2226	Neut_2039
  							metal-dependent	Tryptophanyl-tRNA
  							phosphoesterases (PHP	synthetase; <br>tRNA
  							family)	modification Bacteria
  fig|6666666.60966.peg.2233	CDS	2070450	2071082	3	+	633	YciO family	-none-	D23_1c2227	Neut_2040
  fig|6666666.60966.peg.2234	CDS	2071075	2071740	1	+	666	FIG004556: membrane	A cluster relating to	D23_1c2228	Neut_2041
  							metalloprotease	Tryptophanyl-tRNA
  								synthetase
  fig|6666666.60966.peg.2235	CDS	2071817	2073019	2	+	1203	Tryptophanyl-tRNA	A cluster relating to	D23_1c2229	Neut_2042
  							synthetase (EC 6.1.1.2)	Tryptophanyl-tRNA
  								synthetase; <br>tRNA
  								aminoacylation, Trp
  fig|6666666.60966.peg.2236	CDS	2073064	2073864	1	+	801	Segregation and	-none-	D23_1c2230	Neut_2043
  							condensation protein A
  fig|6666666.60966.peg.2237	CDS	2073830	2074480	2	+	651	Segregation and	-none-	D23_1c2231	Neut_2044
  							condensation protein B
  fig|6666666.60966.peg.2238	CDS	2074504	2075751	1	+	1248	Isocitrate	5-FCL-like protein;	D23_1c2232	Neut_2045
  							dehydrogenase [NADP]	<br>TCA Cycle
  							(EC 1.1.1.42)
  fig|6666666.60966.peg.2239	CDS	2076095	2075892	−2	−	204	Cold shock protein CspD	Cold shock, CspA family	D23_1c2233	Neut_2046
  								of proteins
  fig|6666666.60966.peg.2240	CDS	2076577	2076407	−1	−	171	hypothetical protein	-none-	D23_1c2234	NA
  fig|6666666.60966.peg.2241	CDS	2076576	2076779	3	+	204	ATP-dependent Clp	ClpAS cluster;	D23_1c2235	Neut_2047
  							protease adaptor	<br>Proteolysis in
  							protein ClpS	bacteria, ATP-dependent
  fig|6666666.60966.peg.2242	CDS	2076781	2079051	1	+	2271	ATP-dependent Clp	ClpAS cluster;	D23_1c2236	Neut_2048
  							protease ATP-binding	<br>Proteolysis in
  							subunit ClpA	bacteria, ATP-
  								dependent;
  								<br>Ribosome recycling
  								related cluster
  fig|6666666.60966.peg.2243	CDS	2079170	2080129	2	+	960	TRAP transporter solute	TRAP Transporter	D23_1c2237	Neut_2049
  							receptor, unknown	unknown substrate 6
  							substrate 6
  fig|6666666.60966.peg.2244	CDS	2080157	2080885	2	+	729	Orotate	De Novo Pyrimidine	D23_1c2238	Neut_2050
  							phosphoribosyltransferase	Synthesis
  							(EC 2.4.2.10)
  fig|6666666.60966.peg.2245	CDS	2081203	2082156	1	+	954	COGs COG0715	-none-	D23_1c2239	Neut_2051
  fig|6666666.60966.peg.2246	CDS	2082161	2082997	2	+	837	Alkanesulfonates	Alkanesulfonate	D23_1c2240	Neut_2052
  							transport system	assimilation
  							permease protein
  fig|6666666.60966.peg.2247	CDS	2083232	2083038	−2	−	195	hypothetical protein	-none-	D23_1c2241	NA
  fig|6666666.60966.peg.2248	CDS	2083287	2083823	3	+	537	ABC-type	Alkanesulfonate	D23_1c2242	Neut_2053
  							nitrate/sulfonate/bicarbonate	assimilation
  							transport system,
  							ATPase component
  fig|6666666.60966.peg.2249	CDS	2083938	2086493	3	+	2556	Glycogen	Glycogen metabolism	D23_1c2243	Neut_2054
  							phosphorylase (EC
  							2.4.1.1)
  fig|6666666.60966.peg.2251	CDS	2086807	2086661	−1	−	147	hypothetical protein	-none-	D23_1c2244	NA
  fig|6666666.60966.peg.2252	CDS	2086806	2087288	3	+	483	Flagellar biosynthesis	Flagellum	D23_1c2245	Neut_2055
  							protein FliL
  fig|6666666.60966.peg.2253	CDS	2087301	2088293	3	+	993	Flagellar motor switch	Flagellar motility;	D23_1c2246	Neut_2056
  							protein FliM	<br>Flagellum
  fig|6666666.60966.peg.2254	CDS	2088322	2088795	1	+	474	Flagellar motor switch	Flagellar motility;	D23_1c2247	Neut_2057
  							protein FliN	<br>Flagellum
  fig|6666666.60966.peg.2255	CDS	2088822	2089265	3	+	444	Flagellar biosynthesis	Flagellum	D23_1c2248	Neut_2058
  							protein FliQ
  fig|6666666.60966.peg.2256	CDS	2089255	2090040	1	+	786	Flagellar biosynthesis	Flagellum	D23_1c2249	Neut_2059
  							protein FliP
  fig|6666666.60966.peg.2257	CDS	2090056	2090331	1	+	276	Flagellar biosynthesis	Flagellum	D23_1c2250	Neut_2060
  							protein FliQ
  fig|6666666.60966.peg.2258	CDS	2090429	2091229	2	+	801	Flagellar biosynthesis	Flagellar motility;	D23_1c2251	Neut_2061
  							protein FliR	<br>Flagellum
  fig|6666666.60966.peg.2259	CDS	2091389	2093485	2	+	2097	FIG00858519:	-none-	D23_1c2252	Neut_2062
  							hypothetical protein
  fig|6666666.60966.peg.2260	CDS	2093591	2095027	2	+	1437	FIG00858578:	-none-	D23_1c2253	Neut_2063
  							hypothetical protein
  fig|6666666.60966.peg.2261	CDS	2096049	2095090	−3	−	960	alpha/beta hydrolase	-none-	D23_1c2254	Neut_2064
  							fold
  fig|6666666.60966.peg.2262	CDS	2096035	2096187	1	+	153	hypothetical protein	-none-	D23_1c2255	NA
  fig|6666666.60966.peg.2263	CDS	2097510	2096296	−3	−	1215	Argininosuccinate	Arginine Biosynthesis--	D23_1c2256	Neut_2065
  							synthase (EC 6.3.4.5)	gjo; <br>Arginine
  								Biosynthesis extended
  fig|6666666.60966.peg.2264	CDS	2098473	2097550	−3	−	924	Ornithine	Arginine Biosynthesis--	D23_1c2257	Neut_2066
  							carbamoyltransferase	gjo; <br>Arginine
  							(EC 2.1.3.3)	Biosynthesis extended;
  								<br>Arginine and
  								Ornithine Degradation
  fig|6666666.60966.peg.2266	CDS	2099808	2099680	−3	−	129	hypothetical protein	-none-	D23_1c2259	Neut_2067
  fig|6666666.60966.peg.2265	CDS	2099605	2098649	−1	−	957	Acetylornithine	Arginine Biosynthesis--	D23_1c2259	Neut_2067
  							aminotransferase (EC	gjo; <br>Arginine
  							2.6.1.11)	Biosynthesis extended
  fig|6666666.60966.peg.2267	CDS	2100416	2100066	−2	−	351	FIG00858925:	-none-	D23_1c2260	Neut_2068
  							hypothetical protein
  fig|6666666.60966.peg.2268	CDS	2100762	2100517	−3	−	246	FIG00859242:	-none-	D23_1c2261	Neut_2069
  							hypothetical protein
  fig|6666666.60966.peg.2269	CDS	2102838	2100763	−3	−	2076	FIG00858999:	-none-	D23_1c2262	Neut_2070
  							hypothetical protein
  fig|6666666.60966.peg.2270	CDS	2103683	2102844	−2	−	840	Cysteine synthase B (EC	Cysteine Biosynthesis	D23_1c2263	Neut_2071
  							2.5.1.47)
  fig|6666666.60966.peg.2272	CDS	2106646	2103854	−1	−	2793	FIG00860005:	-none-	D23_1c2264	Neut_2072
  							hypothetical protein
  fig|6666666.60966.peg.2274	CDS	2109519	2108932	−3	−	588	hypothetical protein	-none-	D23_1c2268	Neut_2074
  fig|6666666.60966.peg.2275	CDS	2110331	2109591	−2	−	741	putative (U92432) ORF4	-none-	D23_1c2269	Neut_2316
  							(Nitrosospira sp. NpAV)
  fig|6666666.60966.peg.2276	CDS	2111663	2110398	−2	−	1266	Particulate methane	Particulate methane	D23_1c2270	Neut_2317
  							monooxygenase B-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2277	CDS	2112493	2111663	−1	−	831	Particulate methane	Particulate methane	D23_1c2271	Neut_2318
  							monooxygenase A-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2278	CDS	2113482	2112667	−3	−	816	Particulate methane	Particulate methane	D23_1c2272	Neut_2319
  							monooxygenase C-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2279	CDS	2114624	2114052	−2	−	573	CDP-diacylglycerol--	Glycerolipid and	D23_1c2273	Neut_2079
  							glycerol-3-phosphate 3-	Glycerophospholipid
  							phosphatidyltransferase	Metabolism in Bacteria
  							(EC 2.7.8.5)
  fig|6666666.60966.peg.2280	CDS	2116254	2114755	−3	−	1500	Glycerol kinase (EC	Glycerol and Glycerol-3-	D23_1c2274	Neut_2080
  							2.7.1.30)	phosphate Uptake and
  								Utilization;
  								<br>Glycerolipid and
  								Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.2281	CDS	2116718	2116305	−2	−	414	Regulator of nucleoside	Transcription factors	D23_1c2275	Neut_2081
  							diphosphate kinase	bacterial
  fig|6666666.60966.peg.2282	CDS	2116748	2116897	2	+	150	hypothetical protein	-none-	D23_1c2276	NA
  fig|6666666.60966.peg.2283	CDS	2117727	2117005	−3	−	723	Phosphate regulon	High affinity phosphate	D23_1c2277	Neut_2082
  							transcriptional	transporter and control
  							regulatory protein PhoB	of PHO regulon;
  							(SphR)	<br>PhoR-PhoB two-
  								component regulatory
  								system; <br>Phosphate
  								metabolism
  fig|6666666.60966.peg.2284	CDS	2119187	2118225	−2	−	963	Mobile element protein	-none-	D23_1c2278	Neut_1746
  fig|6666666.60966.peg.2287	CDS	2121603	2120356	−3	−	1248	Aspartokinase (EC	CBSS-216591.1.peg.168;	D23_1c2282	Neut_2084
  							2.7.2.4)	<br>Lysine Biosynthesis
  								DAP Pathway, GJO
  								scratch; <br>Threonine
  								and Homoserine
  								Biosynthesis
  fig|6666666.60966.peg.2288	CDS	2122439	2121855	−2	−	585	Putative peptidoglycan	-none-	D23_1c2283	Neut_2085
  							binding domain 1
  fig|6666666.60966.peg.2289	CDS	2122914	2124089	3	+	1176	Acetate kinase (EC	Fermentations: Lactate;	D23_1c2284	Neut_2086
  							2.7.2.1)	<br>Pyruvate
  								metabolism II: acetyl-
  								CoA, acetogenesis from
  								pyruvate
  fig|6666666.60966.peg.2290	CDS	2124134	2126509	2	+	2376	Xylulose-5-phosphate	Fermentations: Lactate;	D23_1c2285	Neut_2087
  							phosphoketolase (EC	<br>Fermentations:
  							4.1.2.9); Fructose-6-	Lactate; <br>Pentose
  							phosphate	phosphate pathway;
  							phosphoketolase (EC	<br>Pentose phosphate
  							4.1.2.22)	pathway
  fig|6666666.60966.peg.2291	CDS	2126813	2126977	2	+	165	hypothetical protein	-none-	D23_1c2287	NA
  fig|6666666.60966.peg.2292	CDS	2128152	2127058	−3	−	1095	Transaldolase (EC	Pentose phosphate	D23_1c2288	Neut_2089
  							2.2.1.2)	pathway
  fig|6666666.60966.peg.2293	CDS	2128367	2128218	−2	−	150	hypothetical protein	-none-	D23_1c2289	NA
  fig|6666666.60966.peg.2294	CDS	2128351	2128908	1	+	558	FIG006045: Sigma	Iron siderophore sensor	D23_1c2290	Neut_2090
  							factor, ECF subfamily	& receptor system
  fig|6666666.60966.peg.2295	CDS	2128915	2129877	1	+	963	Iron siderophore sensor	Iron siderophore sensor	D23_1c2291	Neut_2091
  							protein	& receptor system
  fig|6666666.60966.peg.2296	CDS	2129956	2132253	1	+	2298	TonB-dependent	Ton and Tol transport	D23_1c2292	Neut_2092
  							receptor	systems
  fig|6666666.60966.peg.2297	CDS	2132801	2132271	−2	−	531	FIG00858714:	-none-	D23_1c2293	Neut_2093
  							hypothetical protein
  fig|6666666.60966.peg.2298	CDS	2133157	2132813	−1	−	345	FIG00858447:	-none-	D23_1c2294	Neut_2094
  							hypothetical protein
  fig|6666666.60966.peg.2299	CDS	2134515	2133133	−3	−	1383	Xaa-Pro	Aminopeptidases (EC	D23_1c2295	Neut_2095
  							aminopeptidase (EC	3.4.11.—); <br>CBSS-
  							3.4.11.9)	87626.3.peg.3639
  fig|6666666.60966.peg.2301	CDS	2134633	2135313	1	+	681	Ribulose-phosphate 3-	Calvin-Benson cycle;	D23_1c2296	Neut_2096
  							epimerase (EC 5.1.3.1)	<br>Pentose phosphate
  								pathway; <br>Riboflavin
  								synthesis cluster
  fig|6666666.60966.peg.2302	CDS	2135328	2136050	3	+	723	Phosphoglycolate	2-phosphoglycolate	D23_1c2297	Neut_2097
  							phosphatase (EC	salvage; <br>Glycolate,
  							3.1.3.18)	glyoxylate
  								interconversions;
  								<br>Photorespiration
  								(oxidative C2 cycle)
  fig|6666666.60966.peg.2303	CDS	2136160	2137647	1	+	1488	Anthranilate synthase,	Chorismate:	D23_1c2298	Neut_2098
  							aminase component (EC	Intermediate for
  							4.1.3.27)	synthesis of Tryptophan,
  								PAPA antibiotics, PABA,
  								3-hydroxyanthranilate
  								and more.;
  								<br>Tryptophan
  								synthesis
  fig|6666666.60966.peg.2304	CDS	2138110	2137682	−1	−	429	Ferredoxin reductase	Anaerobic respiratory	D23_1c2299	Neut_2099
  								reductases
  fig|6666666.60966.peg.2305	CDS	2138482	2138138	−1	−	345	FIG00858997:	-none-	D23_1c2300	Neut_2100
  							hypothetical protein
  fig|6666666.60966.peg.2306	CDS	2138586	2139236	3	+	651	Iron-sulfur cluster	CBSS-196164.1.peg.1690	D23_1c2301	Neut_2101
  							regulator SufR
  fig|6666666.60966.peg.2307	CDS	2139353	2140534	2	+	1182	FIG00859085:	-none-	D23_1c2302	Neut_2102
  							hypothetical protein
  fig|6666666.60966.peg.2308	CDS	2142375	2140606	−3	−	1770	Dihydrolipoamide	Pyruvate metabolism II:	D23_1c2304	Neut_2103
  							dehydrogenase of	acetyl-CoA, acetogenesis
  							pyruvate	from pyruvate; <br>TCA
  							dehydrogenase	Cycle
  							complex (EC 1.8.1.4)
  fig|6666666.60966.peg.2309	CDS	2143648	2142380	−1	−	1269	Gamma-glutamyl	Proline Synthesis	D23_1c2305	Neut_2104
  							phosphate reductase
  							(EC 1.2.1.41)
  fig|6666666.60966.peg.2310	CDS	2144399	2143713	−2	−	687	InterPro IPR001440	-none-	D23_1c2306	Neut_2105
  							COGs COG0457
  fig|6666666.60966.peg.2311	CDS	2145656	2144412	−2	−	1245	TPR/glycosyl	-none-	D23_1c2307	Neut_2106
  							transferase domain
  							protein
  fig|6666666.60966.peg.2312	CDS	2146522	2145650	−1	−	873	Esterase/lipase/thioesterase	-none-	D23_1c2308	Neut_2107
  							family active site
  fig|6666666.60966.peg.2313	CDS	2147373	2146519	−3	−	855	Esterase/lipase/thioesterase	-none-	D23_1c2309	Neut_2108
  							family active site
  fig|6666666.60966.peg.2314	CDS	2147631	2147380	−3	−	252	FIG00858580:	-none-	D23_1c2310	Neut_2109
  							hypothetical protein
  fig|6666666.60966.peg.2315	CDS	2147817	2149007	3	+	1191	Tetraacyldisaccharide	Broadly distributed	D23_1c2311	Neut_2110
  							4&#39;-kinase (EC	proteins not in
  							2.7.1.130)/FIG002473:	subsystems; <br>KDO2-
  							Protein YcaR in KDO2-	Lipid A biosynthesis
  							Lipid A biosynthesis	cluster	2; <br>KDO2-
  							cluster	Lipid A biosynthesis
  								cluster
  2
  fig|6666666.60966.peg.2316	CDS	2149225	2149353	1	+	129	hypothetical protein	-none-	D23_1c2312	NA
  fig|6666666.60966.peg.2318	CDS	2150705	2149527	−2	−	1179	Lipid carrier: UDP-N-	CBSS-	D23_1c2313	Neut_2112
  							acetylgalactosaminyltransferase	296591.1.peg.2330;
  							(EC 2.4.1.—)/	<br>CBSS-
  							Alpha-1,3-N-	296591.1.peg.2330;
  							acetylgalactosamine	<br>CBSS-
  							transferase PglA (EC	296591.1.peg.2330;
  							2.4.1.—); Putative	<br>N-linked
  							glycosyltransferase	Glycosylation in
  								Bacteria; <br>N-linked
  								Glycosylation in Bacteria
  fig|6666666.60966.peg.2319	CDS	2151819	2150689	−3	−	1131	Glycosyl transferase,	-none-	D23_1c2314	Neut_2113
  							group
  1 family protein
  fig|6666666.60966.peg.2320	CDS	2153132	2151816	−2	−	1317	hypothetical protein	-none-	D23_1c2315	NA
  fig|6666666.60966.peg.2321	CDS	2154290	2153199	−2	−	1092	Alpha-1,4-N-	N-linked Glycosylation in	D23_1c2316	Neut_2115
  							acetylgalactosamine	Bacteria
  							transferase PglJ (EC
  							2.4.1.—)
  fig|6666666.60966.peg.2322	CDS	2155270	2154290	−1	−	981	COGs COG0439	-none-	D23_1c2317	Neut_2116
  fig|6666666.60966.peg.2323	CDS	2156578	2155337	−1	−	1242	Membrane protein	-none-	D23_1c2318	Neut_2117
  							involved in the export
  							of O-antigen, teichoic
  							acid lipoteichoic acids
  fig|6666666.60966.peg.2324	CDS	2156818	2157207	1	+	390	Low molecular weight	Capsular Polysaccharides	D23_1c2319	Neut_2118
  							protein-tyrosine-	Biosynthesis and
  							phosphatase Wzb (EC	Assembly
  							3.1.3.48)
  fig|6666666.60966.peg.2325	CDS	2157230	2158477	2	+	1248	Capsule polysaccharide	-none-	D23_1c2320	Neut_2119
  							export protein
  fig|6666666.60966.peg.2326	CDS	2158531	2160774	1	+	2244	Tyrosine-protein kinase	Capsular Polysaccharides	D23_1c2321	Neut_2120
  							Wzc (EC 2.7.10.2)	Biosynthesis and
  								Assembly
  fig|6666666.60966.peg.2327	CDS	2160771	2162330	3	+	1560	Undecaprenyl-	-none-	D23_1c2322	Neut_2121
  							phosphate N-
  							acetylglucosaminyl 1-
  							phosphate transferase
  							(EC 2.7.8.—)
  fig|6666666.60966.peg.2329	CDS	2165972	2162400	−2	−	3573	Chromosome partition	DNA structural proteins,	D23_1c2323	Neut_2122
  							protein smc	bacterial
  fig|6666666.60966.peg.2330	CDS	2166059	2166478	2	+	420	NADPH-dependent 7-	-none-	D23_1c2324	Neut_2123
  							cyano-7-deazaguanine
  							reductase (EC 1.7.1.13)
  fig|6666666.60966.peg.2331	CDS	2166527	2167927	2	+	1401	Fumarate hydratase	TCA Cycle	D23_1c2325	Neut_2124
  							class II (EC 4.2.1.2)
  fig|6666666.60966.peg.2332	CDS	2168192	2168052	−2	−	141	hypothetical protein	-none-	D23_1c2326	NA
  fig|6666666.60966.peg.2333	CDS	2168473	2168640	1	+	168	hypothetical protein	-none-	D23_1c2327	NA
  fig|6666666.60966.peg.2334	CDS	2168888	2169181	2	+	294	Mobile element protein	-none-	D23_1c2328	Neut_1719
  fig|6666666.60966.peg.2335	CDS	2169280	2170158	1	+	879	Mobile element protein	-none-	D23_1c2329	Neut_1720
  fig|6666666.60966.peg.2337	CDS	2171884	2170655	−1	−	1230	diguanylate	-none-	D23_1c2332	Neut_2126
  							phosphodiesterase
  fig|6666666.60966.peg.2338	CDS	2172707	2171898	−2	−	810	Putative diheme	Soluble cytochromes	D23_1c2333	Neut_2127
  							cytochrome c-553	and functionally related
  								electron carriers
  fig|6666666.60966.peg.2339	CDS	2172852	2172977	3	+	126	hypothetical protein	-none-	D23_1c2334	NA
  fig|6666666.60966.peg.2340	CDS	2175331	2172950	−1	−	2382	Type II secretory	-none-	D23_1c2335	Neut_2128
  							pathway, ATPase
  							PulE/Tfp pilus assembly
  							pathway, ATPase PilB
  fig|6666666.60966.peg.2341	CDS	2176108	2175344	−1	−	765	CAMP	cAMP signaling in	D23_1c2336	Neut_2129
  							phosphodiesterases	bacteria
  							class-II:Metallo-beta-
  							lactamase superfamily
  fig|6666666.60966.peg.2342	CDS	2176622	2176197	−2	−	426	Universal stress protein	-none-	D23_1c2337	Neut_2130
  							(Usp)
  fig|6666666.60966.peg.2343	CDS	2177459	2176734	−2	−	726	Membrane protein	-none-	D23_1c2338	Neut_2131
  							TerC, possibly involved
  							in tellurium resistance
  fig|6666666.60966.peg.2344	CDS	2178586	2177462	−1	−	1125	Patatin	-none-	D23_1c2339	Neut_2132
  fig|6666666.60966.peg.2345	CDS	2178900	2179850	3	+	951	Proline iminopeptidase	Proline, 4-	D23_1c2340	Neut_2133
  							(EC 3.4.11.5)	hydroxyproline uptake
  								and utilization
  fig|6666666.60966.peg.2346	CDS	2180553	2179870	−3	−	684	Dethiobiotin synthetase	Biotin biosynthesis;	D23_1c2341	Neut_2134
  							(EC 6.3.3.3)	<br>Biotin biosynthesis
  								Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2347	CDS	2181452	2180556	−2	−	897	Biotin synthesis protein	Biotin biosynthesis;	D23_1c2342	Neut_2135
  							BioC	<br>Biotin biosynthesis
  								Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2348	CDS	2182200	2181442	−3	−	759	Biotin synthesis protein	Biotin biosynthesis;	D23_1c2343	Neut_2136
  							BioH	<br>Biotin biosynthesis
  								Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2349	CDS	2183365	2182202	−1	−	1164	8-amino-7-	Biotin biosynthesis;	D23_1c2344	Neut_2137
  							oxononanoate synthase	<br>Biotin biosynthesis
  							(EC 2.3.1.47)	Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2350	CDS	2184393	2183371	−3	−	1023	Biotin synthase (EC	Biotin biosynthesis;	D23_1c2345	Neut_2138
  							2.8.1.6)	<br>Biotin biosynthesis
  								Experimental; <br>Biotin
  								synthesis cluster
  fig|6666666.60966.peg.2351	CDS	2184641	2184453	−2	−	189	hypothetical protein	-none-	D23_1c2346	NA
  fig|6666666.60966.peg.2352	CDS	2184698	2185168	2	+	471	Competence protein F	Biotin biosynthesis	D23_1c2347	Neut_2139
  							homolog,	Experimental; <br>Biotin
  							phosphoribosyltransferase	synthesis cluster;
  							domain; protein	<br>CBSS-
  							YhgH required for	216591.1.peg.168
  							utilization of DNA as
  							sole source of carbon
  							and energy
  fig|6666666.60966.peg.2353	CDS	2185222	2185686	1	+	465	tRNA (cytidine(34)-	Biotin synthesis cluster;	D23_1c2348	Neut_2140
  							2&#39;-O)-	<br>RNA methylation
  							methyltransferase (EC
  							2.1.1.207) ## TrmL
  fig|6666666.60966.peg.2354	CDS	2185773	2186303	3	+	531	protein of unknown	-none-	D23_1c2349	Neut_2141
  							function DUF1130
  fig|6666666.60966.peg.2355	CDS	2186489	2187325	2	+	837	SAM-dependent	-none-	D23_1c2350	Neut_2142
  							methyltransferase (EC
  							2.1.1.—)
  fig|6666666.60966.peg.2356	CDS	2189013	2187523	−3	−	1491	Glucose-6-phosphate 1-	Pentose phosphate	D23_1c2351	Neut_2143
  							dehydrogenase (EC	pathway
  							1.1.1.49)
  fig|6666666.60966.peg.2357	CDS	2189925	2189017	−3	−	909	6-phosphogluconate	D-gluconate and	D23_1c2352	Neut_2144
  							dehydrogenase,	ketogluconates
  							decarboxylating (EC	metabolism;
  							1.1.1.44)	<br>Pentose phosphate
  								pathway
  fig|6666666.60966.peg.2358	CDS	2191152	2189995	−3	−	1158	COGs COG1397	-none-	D23_1c2353	Neut_2145
  fig|6666666.60966.peg.2359	CDS	2191494	2191195	−3	−	300	UPF0235 protein	CBSS-630.2.peg.3360	D23_1c2354	Neut_2146
  							VC0458
  fig|6666666.60966.peg.2360	CDS	2192054	2191494	−2	−	561	Integral membrane	CBSS-630.2.peg.3360	D23_1c2355	Neut_2147
  							protein YggT, involved
  							in response to
  							extracytoplasmic stress
  							(osmotic shock)
  fig|6666666.60966.peg.2361	CDS	2192939	2192127	−2	−	813	Pyrroline-5-carboxylate	A Hypothetical Protein	D23_1c2356	Neut_2148
  							reductase (EC 1.5.1.2)	Related to Proline
  								Metabolism; <br>CBSS-
  								630.2.peg.3360;
  								<br>Proline Synthesis
  fig|6666666.60966.peg.2362	CDS	2193210	2193019	−3	−	192	FIG00859708:	-none-	D23_1c2357	Neut_2149
  							hypothetical protein
  fig|6666666.60966.peg.2364	CDS	2194302	2194580	3	+	279	Ribonuclease P protein	Cell Division Subsystem	D23_1c2359	Neut_2152
  							component (EC	including YidCD;
  							3.1.26.5)	<br>RNA modification
  								cluster; <br>tRNA
  								processing
  fig|6666666.60966.peg.2365	CDS	2194877	2196745	2	+	1869	Inner membrane	CTP synthase (EC	D23_1c2360	Neut_2154
  							protein translocase	6.3.4.2) cluster; <br>Cell
  							component YidC, long	Division Subsystem
  							form	including YidCD;
  								<br>RNA modification
  								cluster
  fig|6666666.60966.peg.2366	CDS	2196792	2198171	3	+	1380	GTPase and tRNA-U34	Cell Division Subsystem	D23_1c2361	Neut_2155
  							5-formylation enzyme	including YidCD;
  							TrmE	<br>RNA modification
  								and chromosome
  								partitioning cluster;
  								<br>RNA modification
  								cluster; <br>Universal
  								GTPases; <br>mnm5U34
  								biosynthesis bacteria;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.2367	CDS	2198398	2198667	1	+	270	SSU ribosomal protein	-none-	D23_1c2363	Neut_2156
  							S15p (S13e)
  fig|6666666.60966.peg.2368	CDS	2198846	2200963	2	+	2118	Polyribonucleotide	Bacterial RNA-	D23_1c2364	Neut_2157
  							nucleotidyltransferase	metabolizing Zn-
  							(EC 2.7.7.8)	dependent hydrolases;
  								<br>Polyadenylation
  								bacterial
  fig|6666666.60966.peg.2369	CDS	2201167	2201039	−1	−	129	hypothetical protein	-none-	D23_1c2365	NA
  fig|6666666.60966.peg.2371	CDS	2201553	2202926	3	+	1374	RND efflux system,	Multidrug Resistance	D23_1c2367	Neut_2158
  							outer membrane	Efflux Pumps
  							lipoprotein CmeC
  fig|6666666.60966.peg.2372	CDS	2203015	2204220	1	+	1206	Membrane fusion	Multidrug Resistance	D23_1c2368	Neut_2159
  							protein of RND family	Efflux Pumps
  							multidrug efflux pump
  fig|6666666.60966.peg.2373	CDS	2204238	2207432	3	+	3195	RND efflux system,	Multidrug Resistance	D23_1c2369	Neut_2160
  							inner membrane	Efflux Pumps
  							transporter CmeB
  fig|6666666.60966.peg.2375	CDS	2208043	2207702	−1	−	342	hypothetical protein	-none-	D23_1c2370	Neut_2161
  fig|6666666.60966.peg.2376	CDS	2208812	2208072	−2	−	741	conserved hypothetical	-none-	D23_1c2371	Neut_2162
  							protein [Pyrococcus
  							horikoshii]; COG2102:
  							Predicted ATPases of
  							PP-loop superfamily;
  							IPR002761: Domain of
  							unknown function
  							DUF71
  fig|6666666.60966.peg.2377	CDS	2209043	2208924	−2	−	120	FIG00859479:	-none-	D23_1c2372	Neut_2163
  							hypothetical protein
  fig|6666666.60966.peg.2379	CDS	2210878	2209472	−1	−	1407	GTP-binding protein	CBSS-	D23_1c2374	Neut_2164
  							EngA	290633.1.peg.1906;
  								<br>CBSS-
  								498211.3.peg.1415;
  								<br>Universal GTPases
  fig|6666666.60966.peg.2380	CDS	2212159	2210930	−1	−	1230	Outer membrane	CBSS-	D23_1c2375	Neut_2165
  							protein YfgL, lipoprotein	290633.1.peg.1906;
  							component of the	<br>CBSS-
  							protein assembly	498211.3.peg.1415;
  							complex (forms a	<br>Lipopolysaccharide
  							complex with YaeT,	assembly
  							YfiO, and NlpB)
  fig|6666666.60966.peg.2381	CDS	2212800	2212162	−3	−	639	Mlr7403 protein	CBSS-	D23_1c2376	Neut_2166
  								290633.1.peg.1906;
  								<br>CBSS-
  								498211.3.peg.1415
  fig|6666666.60966.peg.2382	CDS	2214088	2212823	−1	−	1266	Histidyl-tRNA	CBSS-	D23_1c2377	Neut_2167
  							synthetase (EC 6.1.1.21)	498211.3.peg.1415;
  								<br>tRNA
  								aminoacylation, His
  fig|6666666.60966.peg.2383	CDS	2215286	2214081	−2	−	1206	1-hydroxy-2-methyl-2-	CBSS-	D23_1c2378	Neut_2168
  							(E)-butenyl 4-	498211.3.peg.1415;
  							diphosphate synthase	<br>CBSS-
  							(EC 1.17.7.1)	83331.1.peg.3039;
  								<br>Isoprenoid
  								Biosynthesis;
  								<br>Nonmevalonate
  								Branch of Isoprenoid
  								Biosynthesis
  fig|6666666.60966.peg.2384	CDS	2216438	2215359	−2	−	1080	FIG021952: putative	CBSS-498211.3.peg.1415	D23_1c2379	Neut_2169
  							membrane protein
  fig|6666666.60966.peg.2385	CDS	2217306	2216428	−3	−	879	Type IV pilus biogenesis	CBSS-498211.3.peg.1415	D23_1c2380	Neut_2170
  							protein PilF
  fig|6666666.60966.peg.2386	CDS	2218414	2217275	−1	−	1140	Ribosomal RNA large	CBSS-	D23_1c2381	Neut_2171
  							subunit	498211.3.peg.1415;
  							methyltransferase N (EC	<br>RNA methylation
  							2.1.1.—)
  fig|6666666.60966.peg.2387	CDS	2218877	2218452	−2	−	426	Nucleoside diphosphate	CBSS-	D23_1c2382	Neut_2172
  							kinase (EC 2.7.4.6)	498211.3.peg.1415;
  								<br>Purine conversions;
  								<br>pyrimidine
  								conversions
  fig|6666666.60966.peg.2389	CDS	2219591	2219175	−2	−	417	Chain A, Red Copper	-none-	D23_1c2383	Neut_2173
  							Protein Nitrosocyanin
  fig|6666666.60966.peg.2390	CDS	2220042	2221430	3	+	1389	Aminotransferase	Hopanes	D23_1c2384	Neut_2174
  							HpnO, required for
  							aminobacteriohopanetriol
  fig|6666666.60966.peg.2391	CDS	2222146	2221442	−1	−	705	DNA polymerase III	CBSS-228410.1.peg.134;	D23_1c2385	Neut_2175
  							epsilon subunit (EC	<br>CBSS-
  							2.7.7.7)	342610.3.peg.1536
  fig|6666666.60966.peg.2392	CDS	2222646	2222158	−3	−	489	Ribonuclease HI (EC	CBSS-228410.1.peg.134;	D23_1c2386	Neut_2176
  							3.1.26.4)	<br>CBSS-
  								342610.3.peg.1536;
  								<br>Ribonuclease H
  fig|6666666.60966.peg.2393	CDS	2223440	2222706	−2	−	735	FIG005121: SAM-	CBSS-228410.1.peg.134;	D23_1c2387	Neut_2177
  							dependent	<br>CBSS-
  							methyltransferase (EC	342610.3.peg.1536;
  							2.1.1.—)	<br>Glutathione: Non-
  								redox reactions
  fig|6666666.60966.peg.2394	CDS	2223500	2224267	2	+	768	Hydroxyacylglutathione	CBSS-228410.1.peg.134;	D23_1c2388	Neut_2178
  							hydrolase (EC 3.1.2.6)	<br>CBSS-
  								342610.3.peg.1536;
  								<br>Glutathione: Non-
  								redox reactions;
  								<br>Methylglyoxal
  								Metabolism
  fig|6666666.60966.peg.2396	CDS	2225143	2224571	−1	−	573	hypothetical protein	-none-	D23_1c2389	Neut_2179
  fig|6666666.60966.peg.2397	CDS	2225287	2225162	−1	−	126	hypothetical protein	-none-	D23_1c2390	NA
  fig|6666666.60966.peg.2398	CDS	2226167	2225250	−2	−	918	hypothetical protein	-none-	D23_1c2391	Neut_2180
  fig|6666666.60966.peg.2399	CDS	2228864	2226171	−2	−	2694	Helicase, SNF2/RAD54	-none-	D23_1c2392	Neut_2181
  							family
  fig|6666666.60966.peg.2401	CDS	2229650	2229480	−2	−	171	hypothetical protein	-none-	D23_1c2393	NA
  fig|6666666.60966.peg.2402	CDS	2229693	2230814	3	+	1122	Oxidoreductase, FMN-	-none-	D23_1c2394	Neut_2182
  							binding
  fig|6666666.60966.peg.2403	CDS	2230925	2231368	2	+	444	Ornithine	Arginine and Ornithine	D23_1c2395	Neut_2183
  							cyclodeaminase (EC	Degradation
  							4.3.1.12)
  fig|6666666.60966.peg.2404	CDS	2231434	2233005	1	+	1572	Phosphoglucomutase	-none-	D23_1c2396	Neut_2184
  							(EC 5.4.2.2)
  fig|6666666.60966.peg.2405	CDS	2233192	2233344	1	+	153	hypothetical protein	-none-	D23_1c2397	NA
  fig|6666666.60966.peg.2406	CDS	2234195	2233347	−2	−	849	Mobile element protein	-none-	D23_1c2398	Neut_1888
  fig|6666666.60966.peg.2407	CDS	2234437	2234252	−1	−	186	Mobile element protein	-none-	D23_1c2399	Neut_2500
  fig|6666666.60966.peg.2408	CDS	2234636	2235049	2	+	414	Cobalt-zinc-cadmium	Cobalt-zinc-cadmium	D23_1c2400	Neut_2185
  							resistance protein	resistance
  fig|6666666.60966.peg.2409	CDS	2235949	2235359	−1	−	591	Hydroxyacylglutathione	CBSS-228410.1.peg.134;	D23_1c2401	Neut_2178
  							hydrolase (EC 3.1.2.6)	<br>CBSS-
  								342610.3.peg.1536;
  								<br>Glutathione: Non-
  								redox reactions;
  								<br>Methylglyoxal
  								Metabolism
  fig|6666666.60966.peg.2410	CDS	2236135	2236287	1	+	153	hypothetical protein	-none-	D23_1c2403	Neut_1255
  fig|6666666.60966.peg.2411	CDS	2236295	2236462	2	+	168	hypothetical protein	-none-	D23_1c2404	Neut_2449
  fig|6666666.60966.peg.2412	CDS	2236616	2236419	−2	−	198	Mobile element protein	-none-	D23_1c2405	Neut_2268
  fig|6666666.60966.peg.2414	CDS	2236758	2237006	3	+	249	Mobile element protein	-none-	D23_1c2406	Neut_1756
  fig|6666666.60966.peg.2417	CDS	2240037	2237515	−3	−	2523	Aconitate hydratase (EC	TCA Cycle	D23_1c2409	Neut_2457
  							4.2.1.3)
  fig|6666666.60966.peg.2418	CDS	2240239	2240093	−1	−	147	Aconitate hydratase (EC	TCA Cycle	D23_1c2410	NA
  							4.2.1.3)
  fig|6666666.60966.peg.2419	CDS	2240661	2241623	3	+	963	Mobile element protein	-none-	D23_1c2411	Neut_1278
  fig|6666666.60966.peg.2421	CDS	2241835	2241987	1	+	153	Mobile element protein	-none-	D23_1c2413	NA
  fig|6666666.60966.peg.2422	CDS	2242232	2242522	2	+	291	hypothetical protein	-none-	D23_1c2414	NA
  fig|6666666.60966.peg.2423	CDS	2242506	2243450	3	+	945	Agmatinase (EC	Arginine and Ornithine	D23_1c2415	Neut_2187
  							3.5.3.11)	Degradation;
  								<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.2424	CDS	2243462	2245420	2	+	1959	Biosynthetic arginine	Arginine and Ornithine	D23_1c2416	Neut_2188
  							decarboxylase (EC	Degradation;
  							4.1.1.19)	<br>Polyamine
  								Metabolism
  fig|6666666.60966.peg.2425	CDS	2246086	2245436	−1	−	651	Mobile element protein	-none-	D23_1c2417	Neut_2189
  fig|6666666.60966.peg.2426	CDS	2247251	2246148	−2	−	1104	hypothetical protein	-none-	D23_1c2418	Neut_2191
  fig|6666666.60966.peg.2427	CDS	2247251	2247436	2	+	186	Mobile element protein	-none-	D23_1c2419	Neut_2500
  fig|6666666.60966.peg.2428	CDS	2247493	2248341	1	+	849	Mobile element protein	-none-	D23_1c2420	Neut_1375
  fig|6666666.60966.peg.2430	CDS	2249188	2249352	1	+	165	Mobile element protein	-none-	D23_1c2422	Neut_2186
  fig|6666666.60966.peg.2431	CDS	2249749	2251734	1	+	1986	Protein-L-isoaspartate	Protein-L-isoaspartate O-	D23_1c2423	Neut_2323
  							O-methyltransferase	methyltransferase;
  							(EC 2.1.1.77)	<br>Stationary phase
  								repair cluster; <br>Ton
  								and Tol transport
  								systems
  fig|6666666.60966.peg.2432	CDS	2252354	2253127	2	+	774	hypothetical protein	-none-	D23_1c2424	Neut_2196
  fig|6666666.60966.peg.2433	CDS	2253955	2253515	−1	−	441	tRNA pseudouridine	Colicin V and Bacteriocin	D23_1c2425	Neut_2203
  							synthase A (EC 4.2.1.70)	Production Cluster;
  								<br>RNA pseudouridine
  								syntheses; <br>tRNA
  								modification Bacteria;
  								<br>tRNA processing
  fig|6666666.60966.peg.2434	CDS	2254408	2254247	−1	−	162	hypothetical protein	-none-	D23_1c2426	NA
  fig|6666666.60966.peg.2435	CDS	2256251	2254536	−2	−	1716	Selenoprotein O and	Selenoprotein O	D23_1c2427	Neut_2204
  							cysteine-containing
  							homologs
  fig|6666666.60966.peg.2436	CDS	2256898	2257503	1	+	606	GCN5-related N-	-none-	D23_1c2429	Neut_2208
  							acetyltransferase
  fig|6666666.60966.peg.2437	CDS	2258004	2257552	−3	−	453	probable multiple	-none-	D23_1c2430	Neut_2211
  							antibiotic resistance
  							protein marC
  fig|6666666.60966.peg.2438	CDS	2258357	2258229	−2	−	129	hypothetical protein	-none-	D23_1c2431	Neut_2212
  fig|6666666.60966.peg.2440	CDS	2259106	2259264	1	+	159	hypothetical protein	-none-	D23_1c2432	NA
  fig|6666666.60966.peg.2441	CDS	2259280	2260221	1	+	942	Ornithine	Arginine and Ornithine	D23_1c2433	Neut_2213
  							cyclodeaminase (EC	Degradation
  							4.3.1.12)
  fig|6666666.60966.peg.2442	CDS	2260562	2261791	2	+	1230	hypothetical protein	-none-	D23_1c2434	Neut_2214
  fig|6666666.60966.peg.2443	CDS	2262110	2262748	2	+	639	hypothetical protein	-none-	D23_1c2435	Neut_2232
  fig|6666666.60966.peg.2444	CDS	2262936	2263406	3	+	471	FIG00858867:	-none-	D23_1c2436	Neut_2233
  							hypothetical protein
  fig|6666666.60966.peg.2446	CDS	2264766	2263630	−3	−	1137	N-succinyl-L,L-	Arginine Biosynthesis--	D23_1c2437	Neut_2234
  							diaminopimelate	gjo; <br>Arginine
  							desuccinylase (EC	Biosynthesis extended;
  							3.5.1.18)	<br>Lysine Biosynthesis
  								DAP Pathway, GJO
  								scratch
  fig|6666666.60966.peg.2447	CDS	2265597	2264815	−3	−	783	Methionine ABC	Methionine	D23_1c2438	Neut_2235
  							transporter ATP-binding	Biosynthesis;
  							protein	<br>Methionine
  								Degradation
  fig|6666666.60966.peg.2448	CDS	2266742	2265597	−2	−	1146	ABC-type transport	-none-	D23_1c2439	Neut_2236
  							system involved in
  							resistance to organic
  							solvents, permease
  							component USSDB6A
  fig|6666666.60966.peg.2449	CDS	2267603	2266767	−2	−	837	Prolipoprotein	Lipoprotein Biosynthesis	D23_1c2440	Neut_2237
  							diacylglyceryl
  							transferase (EC 2.4.99.—)
  fig|6666666.60966.peg.2450	CDS	2267740	2269413	1	+	1674	Dihydroxy-acid	Branched-Chain Amino	D23_1c2441	Neut_2238
  							dehydratase (EC	Acid Biosynthesis
  							4.2.1.9)
  fig|6666666.60966.peg.2451	CDS	2269430	2271499	2	+	2070	Thymidylate kinase (EC	pyrimidine conversions	D23_1c2442	Neut_2241
  							2.7.4.9)
  fig|6666666.60966.peg.2452	CDS	2271523	2271834	1	+	312	Cytochrome c551/c552	Soluble cytochromes	D23_1c2443	Neut_2242
  								and functionally related
  								electron carriers
  fig|6666666.60966.peg.2454	CDS	2272004	2272972	2	+	969	D-3-phosphoglycerate	Glycine and Serine	D23_1c2444	Neut_2243
  							dehydrogenase (EC	Utilization;
  							1.1.1.95)	<br>Pyridoxin (Vitamin
  								B6) Biosynthesis;
  								<br>Serine Biosynthesis
  fig|6666666.60966.peg.2455	CDS	2273050	2273595	1	+	546	dTDP-4-	Rhamnose containing	D23_1c2445	Neut_2244
  							dehydrorhamnose
  3,5-	glycans; <br>dTDP-
  							epimerase (EC 5.1.3.13)	rhamnose synthesis
  fig|6666666.60966.peg.2456	CDS	2273700	2274983	3	+	1284	Permeases of the major	-none-	D23_1c2446	Neut_2245
  							facilitator superfamily
  fig|6666666.60966.peg.2457	CDS	2275758	2274997	−3	−	762	hypothetical protein	-none-	D23_1c2447	NA
  fig|6666666.60966.peg.2458	CDS	2275968	2276633	3	+	666	Chromosomal	Cell Division Subsystem	D23_1c2449	Neut_2247
  							replication initiator	including YidCD;
  							protein DnaA	<br>DNA replication
  								cluster
  1
  fig|6666666.60966.peg.2459	CDS	2276770	2277435	1	+	666	Phosphoserine	Glycine and Serine	D23_1c2450	Neut_2248
  							phosphatase (EC	Utilization; <br>Serine
  							3.1.3.3)	Biosynthesis; <br>Serine
  								Biosynthesis
  fig|6666666.60966.peg.2460	CDS	2277481	2277846	1	+	366	FIG00859424:	-none-	D23_1c2451	Neut_2249
  							hypothetical protein
  fig|6666666.60966.peg.2461	CDS	2277800	2277958	2	+	159	hypothetical protein	-none-	D23_1c2452	NA
  fig|6666666.60966.peg.2462	CDS	2277971	2279434	2	+	1464	Inosine-5&#39;-	Purine conversions;	D23_1c2453	Neut_2250
  							monophosphate	<br>Purine salvage
  							dehydrogenase (EC	cluster
  							1.1.1.205)
  fig|6666666.60966.peg.2463	CDS	2279447	2281006	2	+	1560	GMP synthase	GMP synthase; <br>GMP	D23_1c2454	Neut_2251
  							[glutamine-	synthase; <br>Purine
  							hydrolyzing],	conversions; <br>Purine
  							amidotransferase	conversions; <br>Purine
  							subunit (EC 6.3.5.2)/	salvage cluster;
  							GMP synthase	<br>Purine salvage
  							[glutamine-	cluster
  							hydrolyzing], ATP
  							pyrophosphatase
  							subunit (EC 6.3.5.2)
  fig|6666666.60966.peg.2465	CDS	2282716	2281352	−1	−	1365	hypothetical protein	-none-	D23_1c2455	NA
  fig|6666666.60966.peg.2466	CDS	2282899	2282762	−1	−	138	Mobile element protein	-none-	D23_1c2456	Neut_2501
  fig|6666666.60966.peg.2467	CDS	2283609	2282872	−3	−	738	Mobile element protein	-none-	D23_1c2457	Neut_1888
  fig|6666666.60966.peg.2468	CDS	2283851	2283666	−2	−	186	Mobile element protein	-none-	D23_1c2458	Neut_2500
  fig|6666666.60966.peg.2469	CDS	2285015	2284020	−2	−	996	hypothetical protein	-none-	D23_1c2459	NA
  fig|6666666.60966.peg.2470	CDS	2285305	2285048	−1	−	258	hypothetical protein	-none-	D23_1c2460	NA
  fig|6666666.60966.peg.2471	CDS	2285448	2285573	3	+	126	hypothetical protein	-none-	D23_1c2461	NA
  fig|6666666.60966.peg.2472	CDS	2285631	2286293	3	+	663	Thiopurine S-	-none-	D23_1c2462	Neut_2272
  							methyltransferase (EC
  							2.1.1.67)
  fig|6666666.60966.peg.2473	CDS	2286615	2288795	3	+	2181	hypothetical protein	-none-	D23_1c2463	Neut_2273
  fig|6666666.60966.peg.2474	CDS	2289016	2291046	1	+	2031	oligopeptide	-none-	D23_1c2464	Neut_2274
  							transporter
  fig|6666666.60966.peg.2475	CDS	2291342	2291145	−2	−	198	FIG00859558:	-none-	D23_1c2465	Neut_2275
  							hypothetical protein
  fig|6666666.60966.peg.2476	CDS	2291757	2291362	−3	−	396	FIG00859558:	-none-	D23_1c2466	Neut_2275
  							hypothetical protein
  fig|6666666.60966.peg.2477	CDS	2292959	2291901	−2	−	1059	Putative permease	-none-	D23_1c2467	Neut_2276
  							often clustered with de
  							novo purine synthesis
  fig|6666666.60966.peg.2478	CDS	2293039	2294097	1	+	1059	Phosphoribosylformylglycinamidine	De Novo Purine	D23_1c2468	Neut_2277
  							cyclo-ligase	Biosynthesis
  							(EC 6.3.3.1)
  fig|6666666.60966.peg.2479	CDS	2294109	2294741	3	+	633	Phosphoribosylglycinamide	5-FCL-like protein;	D23_1c2469	Neut_2278
  							formyltransferase	<br>De Novo Purine
  							(EC 2.1.2.2)	Biosynthesis
  fig|6666666.60966.peg.2480	CDS	2294738	2295460	2	+	723	FIG00859545:	-none-	D23_1c2470	Neut_2279
  							hypothetical protein
  fig|6666666.60966.peg.2481	CDS	2295477	2296751	3	+	1275	Fmu (Sun)/eukaryotic	-none-	D23_1c2471	Neut_2280
  							nucleolar NOL1/Nop2p;
  							tRNAand rRNA
  							cytosine-C5-methylases
  fig|6666666.60966.peg.2482	CDS	2297068	2296832	−1	−	237	hypothetical protein	-none-	D23_1c2472	Neut_2281
  							PA0941
  fig|6666666.60966.peg.2483	CDS	2297785	2297237	−1	−	549	InterPro	-none-	D23_1c2473	Neut_2282
  							IPR000694:IPR001734
  fig|6666666.60966.peg.2484	CDS	2297997	2297800	−3	−	198	hypothetical protein	-none-	D23_1c2474	Neut_2283
  fig|6666666.60966.peg.2485	CDS	2298574	2299293	1	+	720	possible	-none-	D23_1c2475	Neut_2284
  							transmembrane protein
  fig|6666666.60966.peg.2486	CDS	2299389	2301113	3	+	1725	Diguanylate	-none-	D23_1c2476	Neut_2285
  							cyclase/phosphodiesterase
  							domain 2 (EAL)
  fig|6666666.60966.peg.2488	CDS	2301326	2301784	2	+	459	FKBP-type peptidyl-	-none-	D23_1c2477	Neut_2286
  							prolyl cis-trans
  							isomerase
  fig|6666666.60966.peg.2489	CDS	2302743	2301856	−3	−	888	Ribosome small	Universal GTPases	D23_1c2478	Neut_2287
  							subunit-stimulated
  							GTPase EngC
  fig|6666666.60966.peg.2490	CDS	2303060	2302782	−2	−	279	Pterin-4-alpha-	Pterin carbinolamine	D23_1c2479	Neut_2288
  							carbinolamine	dehydratase
  							dehydratase (EC
  							4.2.1.96)
  fig|6666666.60966.peg.2491	CDS	2304388	2303120	−1	−	1269	macromolecule	-none-	D23_1c2480	Neut_2289
  							metabolism;
  							macromolecule
  							degradation;
  							degradation of proteins,
  							peptides, glycopeptides
  fig|6666666.60966.peg.2492	CDS	2304540	2305085	3	+	546	3&#39;-to-5&#39;	RNA processing and	D23_1c2481	Neut_2290
  							oligoribonuclease (orn)	degradation, bacterial
  fig|6666666.60966.peg.2493	CDS	2305123	2307678	1	+	2556	Glycogen	Glycogen metabolism	D23_1c2482	Neut_2291
  							phosphorylase (EC
  							2.4.1.1)
  fig|6666666.60966.peg.2494	CDS	2308460	2307702	−2	−	759	Pantoate--beta-alanine	Coenzyme A	D23_1c2483	Neut_2292
  							ligase (EC 6.3.2.1)	Biosynthesis;
  								<br>Coenzyme A
  								Biosynthesis cluster
  fig|6666666.60966.peg.2495	CDS	2309368	2308559	−1	−	810	3-methyl-2-	Coenzyme A	D23_1c2484	Neut_2293
  							oxobutanoate	Biosynthesis;
  							hydroxymethyltransferase	<br>Coenzyme A
  							(EC 2.1.2.11)	Biosynthesis cluster
  fig|6666666.60966.peg.2496	CDS	2310016	2309372	−1	−	645	Deoxyadenosine kinase	Purine conversions;	D23_1c2485	Neut_2294
  							(EC 2.7.1.76)/	<br>Purine conversions
  							Deoxyguanosine kinase
  							(EC 2.7.1.113)
  fig|6666666.60966.peg.2497	CDS	2310525	2310013	−3	−	513	2-amino-4-hydroxy-6-	Folate Biosynthesis	D23_1c2486	Neut_2295
  							hydroxymethyldihydropteridine
  							pyrophosphokinase (EC
  							2.7.6.3)
  fig|6666666.60966.peg.2498	CDS	2311910	2310522	−2	−	1389	Poly(A) polymerase (EC	Polyadenylation	D23_1c2487	Neut_2296
  							2.7.7.19)	bacterial
  fig|6666666.60966.peg.2499	CDS	2313230	2312073	−2	−	1158	Cardiolipin synthetase	Cardiolipin synthesis;	D23_1c2488	Neut_2297
  							(EC 2.7.8.—)	<br>Glycerolipid and
  								Glycerophospholipid
  								Metabolism in Bacteria
  fig|6666666.60966.peg.2500	CDS	2314054	2313227	−1	−	828	Endonuclease/exonuclease/	-none-	D23_1c2489	Neut_2298
  							phosphatase family
  							protein
  fig|6666666.60966.peg.2501	CDS	2315160	2314060	−3	−	1101	Quinolinate synthetase	Mycobacterium	D23_1c2490	Neut_2299
  							(EC 2.5.1.72)	virulence operon
  								possibly involved in
  								quinolinate biosynthesis;
  								<br>NAD and NADP
  								cofactor biosynthesis
  								global
  fig|6666666.60966.peg.2502	CDS	2315495	2316031	2	+	537	FIG00859627:	-none-	D23_1c2491	Neut_2300
  							hypothetical protein
  fig|6666666.60966.peg.2503	CDS	2316137	2316652	2	+	516	LptA, protein essential	Lipopolysaccharide	D23_1c2492	Neut_2301
  							for LPS transport across	assembly
  							the periplasm
  fig|6666666.60966.peg.2504	CDS	2316704	2317426	2	+	723	Lipopolysaccharide ABC	Lipopolysaccharide	D23_1c2493	Neut_2302
  							transporter, ATP-	assembly
  							binding protein LptB
  fig|6666666.60966.peg.2505	CDS	2317432	2318895	1	+	1464	RNA polymerase sigma-	Flagellar motility;	D23_1c2494	Neut_2303
  							54 factor RpoN	<br>Flagellum;
  								<br>Transcription
  								initiation, bacterial
  								sigma factors
  fig|6666666.60966.peg.2506	CDS	2319070	2319405	1	+	336	Ribosome hibernation	Ribosome activity	D23_1c2495	Neut_2304
  							protein YhbH	modulation
  fig|6666666.60966.peg.2507	CDS	2319646	2320116	1	+	471	PTS system nitrogen-	-none-	D23_1c2496	Neut_2305
  							specific IIA component,
  							PtsN
  fig|6666666.60966.peg.2508	CDS	2320103	2321074	2	+	972	HPr	HPr catabolite	D23_1c2497	Neut_2306
  							kinase/phosphorylase	repression system
  							(EC 2.7.1.—) (EC 2.7.4.—)
  fig|6666666.60966.peg.2509	CDS	2321107	2321223	1	+	117	hypothetical protein	-none-	D23_1c2498	NA
  fig|6666666.60966.peg.2510	CDS	2321260	2321874	1	+	615	3-polyprenyl-4-	Ubiquinone	D23_1c2499	Neut_2307
  							hydroxybenzoate	Biosynthesis;
  							carboxy-lyase UbiX (EC	<br>Ubiquinone
  							4.1.1.—)	Biosynthesis-gjo
  fig|6666666.60966.peg.2511	CDS	2322562	2321924	−1	−	639	5-	5-FCL-like protein;	D23_1c2500	Neut_2308
  							formyltetrahydrofolate	<br>Folate Biosynthesis;
  							cyclo-ligase (EC 6.3.3.2)	<br>One-carbon
  								metabolism by
  								tetrahydropterines
  fig|6666666.60966.peg.2512	CDS	2323682	2322555	−2	−	1128	A/G-specific adenine	DNA repair, bacterial	D23_1c2501	Neut_2309
  							glycosylase (EC 3.2.2.—)
  fig|6666666.60966.peg.2513	CDS	2324249	2323704	−2	−	546	Intracellular septation	CBSS-211586.9.peg.2729	D23_1c2503	Neut_2310
  							protein IspA
  fig|6666666.60966.peg.2514	CDS	2326043	2324346	−2	−	1698	Lipid A export ATP-	KDO2-Lipid A	D23_1c2504	Neut_2311
  							binding/permease	biosynthesis cluster	2
  							protein MsbA (EC
  							3.6.3.25)
  fig|6666666.60966.peg.2515	CDS	2327134	2326562	−1	−	573	hypothetical protein	-none-	D23_1c2505	Neut_2312
  fig|6666666.60966.peg.2516	CDS	2329375	2327231	−1	−	2145	Copper resistance	Copper homeostasis	D23_1c2506	Neut_2313
  							protein D
  fig|6666666.60966.peg.2517	CDS	2329755	2329381	−3	−	375	Copper resistance	-none-	D23_1c2507	Neut_2314
  							protein CopC precursor
  fig|6666666.60966.peg.2518	CDS	2330496	2329909	−3	−	588	hypothetical protein	-none-	D23_1c2508	Neut_2074
  fig|6666666.60966.peg.2519	CDS	2331308	2330568	−2	−	741	putative (U92432) ORF4	-none-	D23_1c2509	Neut_2316
  							(Nitrosospira sp. NpAV)
  fig|6666666.60966.peg.2520	CDS	2332640	2331375	−2	−	1266	Particulate methane	Particulate methane	D23_1c2510	Neut_2317
  							monooxygenase B-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2521	CDS	2333470	2332640	−1	−	831	Particulate methane	Particulate methane	D23_1c2511	Neut_2318
  							monooxygenase A-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2522	CDS	2334459	2333644	−3	−	816	Particulate methane	Particulate methane	D23_1c2512	Neut_2319
  							monooxygenase C-	monooxygenase
  							subunit (EC 1.14.13.25)	(pMMO)
  fig|6666666.60966.peg.2523	CDS	2334883	2335908	1	+	1026	TsaC protein (YrdC-Sua5	-none-	D23_1c2513	Neut_2320
  							domains) required for
  							threonylcarbamoyladenosine
  							t(6)A37
  							modification in tRNA
  fig|6666666.60966.peg.2524	CDS	2335923	2336666	3	+	744	Hypothetical protein	-none-	D23_1c2514	Neut_2321
  							CbbY
  fig|6666666.60966.peg.2525	CDS	2337688	2336702	−1	−	987	Lipoprotein NlpD	Stationary phase repair	D23_1c2515	Neut_2322
  								cluster
  fig|6666666.60966.peg.2526	CDS	2338471	2337803	−1	−	669	Protein-L-isoaspartate	Protein-L-isoaspartate O-	D23_1c2516	Neut_2323
  							O-methyltransferase	methyltransferase;
  							(EC 2.1.1.77)	<br>Stationary phase
  								repair cluster; <br>Ton
  								and Tol transport
  								systems
  fig|6666666.60966.peg.2528	CDS	2339405	2338662	−2	−	744	5-nucleotidase SurE (EC	Housecleaning	D23_1c2517	Neut_2324
  							3.1.3.5) @	nucleoside triphosphate
  							Exopolyphosphatase	pyrophosphatases;
  							(EC 3.6.1.11)	<br>Phosphate
  								metabolism;
  								<br>Polyphosphate;
  								<br>Stationary phase
  								repair cluster
  fig|6666666.60966.peg.2529	CDS	2340272	2339964	−2	−	309	Integration host factor	DNA structural proteins,	D23_1c2519	Neut_2325
  							alpha subunit	bacterial
  fig|6666666.60966.peg.2530	CDS	2342785	2340485	−1	−	2301	Phenylalanyl-tRNA	tRNA aminoacylation,	D23_1c2520	Neut_2326
  							synthetase beta chain	Phe
  							(EC 6.1.1.20)
  fig|6666666.60966.peg.2531	CDS	2343901	2342882	−1	−	1020	Phenylalanyl-tRNA	tRNA aminoacylation,	D23_1c2521	Neut_2327
  							synthetase alpha chain	Phe
  							(EC 6.1.1.20)
  fig|6666666.60966.peg.2532	CDS	2344231	2343989	−1	−	243	LSU ribosomal protein	-none-	D23_1c2522	Neut_2328
  							L20p
  fig|6666666.60966.peg.2533	CDS	2345202	2344723	−3	−	480	Translation initiation	Translation initiation	D23_1c2524	Neut_2330
  							factor 3	factors bacterial
  fig|6666666.60966.peg.2534	CDS	2347209	2345302	−3	−	1908	Threonyl-tRNA	tRNA aminoacylation,	D23_1c2525	Neut_2331
  							synthetase (EC 6.1.1.3)	Thr
  fig|6666666.60966.peg.2535	CDS	2348256	2347537	−3	−	720	Cytochrome c-type	-none-	D23_1c2526	Neut_1790
  							protein TorY
  fig|6666666.60966.peg.2536	CDS	2348966	2348259	−2	−	708	Cytochrome c family	-none-	D23_1c2527	Neut_2333
  							protein
  fig|6666666.60966.peg.2537	CDS	2350169	2349048	−2	−	1122	FIG00859557:	-none-	D23_1c2528	Neut_1792
  							hypothetical protein
  fig|6666666.60966.peg.2538	CDS	2351878	2350166	−1	−	1713	Hydroxylamine	-none-	D23_1c2529	Neut_2335
  							oxidoreductase
  							precursor (EC 1.7.3.4)
  fig|6666666.60966.peg.2539	CDS	2352170	2353255	2	+	1086	tRNA-specific 2-	RNA methylation	D23_1c2530	Neut_2336
  							thiouridylase MnmA
  fig|6666666.60966.peg.2540	CDS	2354395	2353256	−1	−	1140	Twitching motility	-none-	D23_1c2531	Neut_2337
  							protein PilT
  fig|6666666.60966.peg.2541	CDS	2355448	2354405	−1	−	1044	Twitching motility	-none-	D23_1c2532	Neut_2338
  							protein PilT
  fig|6666666.60966.peg.2543	CDS	2355643	2356359	1	+	717	Hypothetical protein	A Hypothetical Protein	D23_1c2533	Neut_2339
  							YggS, proline synthase	Related to Proline
  							co-transcribed bacterial	Metabolism; <br>CBSS-
  							homolog PROSC	630.2.peg.3360
  fig|6666666.60966.peg.2544	CDS	2356597	2356328	−1	−	270	4Fe—4S ferredoxin, iron-	Inorganic Sulfur	D23_1c2534	Neut_2340
  							sulfur binding	Assimilation
  fig|6666666.60966.peg.2545	CDS	2357097	2356603	−3	−	495	Phosphopantetheine	CBSS-	D23_1c2535	Neut_2341
  							adenylyltransferase (EC	266117.6.peg.1260;
  							2.7.7.3)	<br>CBSS-269801.1.peg.1715;
  								<br>Coenzyme A
  								Biosynthesis
  fig|6666666.60966.peg.2546	CDS	2357644	2357090	−1	−	555	16S rRNA	CBSS-	D23_1c2536	Neut_2342
  							(guanine(966)-N(2))-	266117.6.peg.1260;
  							methyltransferase (EC	<br>CBSS-
  							2.1.1.171) ## SSU rRNA	269801.1.peg.1715;
  							m(2)G966	<br>Heat shock Cell
  								division Proteases and a
  								Methyltransferase;
  								<br>RNA methylation
  fig|6666666.60966.peg.2547	CDS	2358960	2357659	−3	−	1302	FIG015287: Zinc	Heat shock Cell division	D23_1c2537	Neut_2343
  							protease	Proteases and a
  								Methyltransferase
  fig|6666666.60966.peg.2548	CDS	2359437	2359126	−3	−	312	Transposase	-none-	D23_1c2538	Neut_2344
  fig|6666666.60966.peg.2549	CDS	2360187	2359819	−3	−	369	Mobile element protein	-none-	D23_1c2539	Neut_1814
  fig|6666666.60966.peg.2550	CDS	2360570	2360247	−2	−	324	Putative periplasmic	-none-	D23_1c2540	Neut_2357
  							protein
  fig|6666666.60966.peg.2551	CDS	2361073	2360771	−1	−	303	hypothetical protein	-none-	D23_1c2541	Neut_2349
  fig|6666666.60966.peg.2552	CDS	2361307	2361110	−1	−	198	CsbD family protein	-none-	D23_1c2542	Neut_2359
  fig|6666666.60966.peg.2553	CDS	2361551	2361384	−2	−	168	protein of unknown	-none-	D23_1c2543	NA
  							function DUF1328
  fig|6666666.60966.peg.2554	CDS	2361863	2362066	2	+	204	Mobile element protein	-none-	D23_1c2544	Neut_2365
  fig|6666666.60966.peg.2555	CDS	2362071	2362247	3	+	177	hypothetical protein	-none-	D23_1c2545	NA
  fig|6666666.60966.peg.2556	CDS	2362394	2362957	2	+	564	Alkyl hydroperoxide	Thioredoxin-disulfide	D23_1c2546	Neut_2366
  							reductase protein C (EC	reductase
  							1.6.4.—)
  fig|6666666.60966.peg.2557	CDS	2363052	2363633	3	+	582	putative lipoprotein	-none-	D23_1c2547	Neut_2367
  fig|6666666.60966.peg.2558	CDS	2364440	2363661	−2	−	780	Putative	-none-	D23_1c2548	Neut_2368
  							stomatin/prohibitin-
  							family membrane
  							protease subunit
  							aq_911
  fig|6666666.60966.peg.2559	CDS	2365869	2364442	−3	−	1428	Putative membrane-	-none-	D23_1c2549	Neut_2369
  							bound ClpP-class
  							protease associated
  							with aq_911
  fig|6666666.60966.peg.2560	CDS	2366482	2365880	−1	−	603	ADP-ribose	CBSS-216591.1.peg.168;	D23_1c2550	Neut_2370
  							pyrophosphatase (EC	<br>NADand NADP
  							3.6.1.13)	cofactor biosynthesis
  								global; <br>Nudix
  								proteins (nucleoside
  								triphosphate hydrolases)
  fig|6666666.60966.peg.2561	CDS	2367579	2366665	−3	−	915	putative membrane	-none-	D23_1c2551	Neut_2371
  							protein
  fig|6666666.60966.peg.2562	CDS	2367673	2368539	1	+	867	Protein YicC	CBSS-323097.3.peg.2594	D23_1c2552	Neut_2372
  fig|6666666.60966.peg.2563	CDS	2369652	2368633	−3	−	1020	C4-dicarboxylate	-none-	D23_1c2553	Neut_2373
  							transporter/malic acid
  							transport protein
  fig|6666666.60966.peg.2564	CDS	2371015	2370053	−1	−	963	Mobile element protein	-none-	D23_1c2554	Neut_1746
  fig|6666666.60966.peg.2565	CDS	2371724	2371065	−2	−	660	Glucose-1-phosphate	Rhamnose containing	D23_1c2555	Neut_2374
  							thymidylyltransferase	glycans; <br>dTDP-
  							(EC 2.7.7.24)	rhamnose synthesis
  fig|6666666.60966.peg.2566	CDS	2372737	2371739	−1	−	999	COG3178: Predicted	-none-	D23_1c2556	Neut_2375
  							phosphotransferase
  							related to Ser/Thr
  							protein kinases
  fig|6666666.60966.peg.2567	CDS	2372902	2373210	1	+	309	Putative cytoplasmic	-none-	D23_1c2557	Neut_2376
  							protein
  fig|6666666.60966.peg.2568	CDS	2373276	2374775	3	+	1500	MG(2+) CHELATASE	-none-	D23_1c2559	Neut_2377
  							FAMILY PROTEIN/
  							ComM-related protein
  fig|6666666.60966.peg.2569	CDS	2376191	2374794	−2	−	1398	Replicative DNA	-none-	D23_1c2560	Neut_2378
  							helicase (EC 3.6.1.—)
  fig|6666666.60966.peg.2571	CDS	2376752	2376297	−2	−	456	LSU ribosomal protein	Primosomal replication	D23_1c2561	Neut_2379
  							L9p	protein N clusters with
  								ribosomal proteins
  fig|6666666.60966.peg.2572	CDS	2377049	2376771	−2	−	279	SSU ribosomal protein	Primosomal replication	D23_1c2562	Neut_2380
  							S18p @ SSU ribosomal	protein N clusters with
  							protein S18p, zinc-	ribosomal proteins
  							independent
  fig|6666666.60966.peg.2573	CDS	2377399	2377091	−1	−	309	Primosomal replication	Primosomal replication	D23_1c2563	Neut_2381
  							protein N	protein N clusters with
  								ribosomal proteins
  fig|6666666.60966.peg.2574	CDS	2377721	2377401	−2	−	321	SSU ribosomal protein	Primosomal replication	D23_1c2564	Neut_2382
  							S6p	protein N clusters with
  								ribosomal proteins
  fig|6666666.60966.peg.2576	CDS	2378765	2378340	−2	−	426	hypothetical protein	-none-	D23_1c2565	NA
  fig|6666666.60966.peg.2578	CDS	2379069	2380031	3	+	963	Mobile element protein	-none-	D23_1c2566	Neut_1746
  fig|6666666.60966.peg.2580	CDS	2380409	2380864	2	+	456	Mobile element protein	-none-	D23_1c2567	Neut_0883
  fig|6666666.60966.peg.2581	CDS	2381862	2380975	−3	−	888	Acetylglutamate kinase	Arginine Biosynthesis--	D23_1c2568	Neut_2384
  							(EC 2.7.2.8)	gjo; <br>Arginine
  								Biosynthesis extended
  fig|6666666.60966.peg.2582	CDS	2382398	2381919	−2	−	480	type IV pili signal	-none-	D23_1c2569	Neut_2385
  							transduction protein Pill
  fig|6666666.60966.peg.2583	CDS	2382774	2382427	−3	−	348	twitching motility	-none-	D23_1c2570	Neut_2386
  							protein PilH
  fig|6666666.60966.peg.2584	CDS	2383169	2383639	2	+	471	21 kDa hemolysin	CBSS-160492.1.peg.550	D23_1c2571	Neut_2387
  							precursor
  fig|6666666.60966.peg.2585	CDS	2383676	2385043	2	+	1368	Fe—S protein, homolog	-none-	D23_1c2572	Neut_2388
  							of lactate
  							dehydrogenase SO1521
  fig|6666666.60966.peg.2586	CDS	2386032	2385136	−3	−	897	Heme O synthase,	Biogenesis of	D23_1c2573	Neut_2389
  							protoheme IX	cytochrome c oxidases;
  							farnesyltransferase (EC	<br>CBSS-
  							2.5.1.—) COX10-CtaB	196164.1.peg.1690;
  								<br>CBSS-
  								316057.3.peg.563
  fig|6666666.60966.peg.2587	CDS	2386422	2386123	−3	−	300	Probable	-none-	D23_1c2574	Neut_2390
  							transmembrane protein
  fig|6666666.60966.peg.2588	CDS	2387398	2386679	−1	−	720	Cytochrome oxidase	Biogenesis of	D23_1c2575	Neut_2391
  							biogenesis protein	cytochrome c oxidases;
  							Surf1, facilitates heme	<br>CBSS-
  							A insertion	316057.3.peg.563
  fig|6666666.60966.peg.2589	CDS	2388336	2387491	−3	−	846	Cytochrome c oxidase	CBSS-316057.3.peg.563;	D23_1c2576	Neut_2392
  							polypeptide III (EC	<br>Terminal
  							1.9.3.1)	cytochrome C oxidases
  fig|6666666.60966.peg.2590	CDS	2389047	2388529	−3	−	519	Cytochrome oxidase	Biogenesis of cytochrome c oxidases;	D23_1c2577	Neut_2393
  							biogenesis protein	<br>CBSS-
  							Cox11-CtaG, copper	316057.3.peg.563
  							delivery to Cox1
  fig|6666666.60966.peg.2591	CDS	2390759	2389182	−2	−	1578	Cytochrome c oxidase	Terminal cytochrome C	D23_1c2578	Neut_2394
  							polypeptide I (EC	oxidases
  							1.9.3.1)
  fig|6666666.60966.peg.2592	CDS	2391643	2390819	−1	−	825	Cytochrome c oxidase	CBSS-316057.3.peg.563;	D23_1c2579	Neut_2395
  							polypeptide II (EC	<br>Terminal
  							1.9.3.1)	cytochrome C oxidases
  fig|6666666.60966.peg.2594	CDS	2392145	2392567	2	+	423	Putative TEGT family	CBSS-326442.4.peg.1852	D23_1c2580	NA
  							carrier/transport
  							protein
  fig|6666666.60966.peg.2595	CDS	2392600	2392884	1	+	285	Putative TEGT family	CBSS-326442.4.peg.1852	D23_1c2581	Neut_1715
  							carrier/transport
  							protein
  fig|6666666.60966.peg.2596	CDS	2393084	2393302	2	+	219	Copper chaperone	Copper homeostasis	D23_1c2582	Neut_2397
  fig|6666666.60966.peg.2597	CDS	2393426	2394394	2	+	969	Acetyl-coenzyme A	Fatty Acid Biosynthesis	D23_1c2583	Neut_2398
  							carboxyl transferase	FASII
  							alpha chain (EC 6.4.1.2)
  fig|6666666.60966.peg.2598	CDS	2394357	2395742	3	+	1386	tRNA(Ile)-lysidine	-none-	D23_1c2584	Neut_2399
  							synthetase
  fig|6666666.60966.peg.2599	CDS	2395746	2396807	3	+	1062	dTDP-glucose 4,6-	CBSS-	D23_1c2585	Neut_2400
  							dehydratase (EC	296591.1.peg.2330;
  							4.2.1.46)	<br>Rhamnose
  								containing glycans;
  								<br>dTDP-rhamnose
  								synthesis
  fig|6666666.60966.peg.2600	CDS	2396804	2397700	2	+	897	dTDP-4-	Rhamnose containing	D23_1c2586	Neut_2401
  							dehydrorhamnose	glycans; <br>dTDP-
  							reductase (EC	rhamnose synthesis
  							1.1.1.133)
  fig|6666666.60966.peg.2601	CDS	2398663	2397710	−1	−	954	InterPro IPR002142	-none-	D23_1c2587	Neut_2402
  							COGs COG0616
  fig|6666666.60966.peg.2602	CDS	2399353	2398691	−1	−	663	Outer membrane	Ton and Tol transport	D23_1c2588	Neut_2403
  							lipoprotein omp16	systems
  							precursor
  fig|6666666.60966.peg.2603	CDS	2400398	2399562	−2	−	837	SH3, type 3 domain	-none-	D23_1c2590	Neut_2404
  							protein
  fig|6666666.60966.peg.2604	CDS	2400602	2401477	2	+	876	esterase/lipase/thioesterase	-none-	D23_1c2591	Neut_2408
  							family active site
  fig|6666666.60966.peg.2605	CDS	2402010	2401492	−3	−	519	Mobile element protein	-none-	D23_1c2592	Neut_2502
  fig|6666666.60966.peg.2606	CDS	2402097	2403560	3	+	1464	hypothetical protein	-none-	D23_1c2593	Neut_2493
  fig|6666666.60966.peg.2607	CDS	2403699	2404946	3	+	1248	Lipoprotein releasing	Lipopolysaccharide	D23_1c2594	Neut_2492
  							system transmembrane	assembly;
  							protein LolE	<br>Lipoprotein sorting
  								system
  fig|6666666.60966.peg.2608	CDS	2404939	2405613	1	+	675	Lipoprotein releasing	Lipopolysaccharide	D23_1c2595	Neut_2491
  							system ATP-binding	assembly;
  							protein LolD	<br>Lipoprotein sorting
  								system
  fig|6666666.60966.peg.2609	CDS	2406957	2405641	−3	−	1317	FIG065221: Holliday	CBSS-83333.1.peg.876	D23_1c2596	Neut_2490
  							junction DNA helicase
  fig|6666666.60966.peg.2610	CDS	2407570	2406950	−1	−	621	Outer membrane	CBSS-83333.1.peg.876;	D23_1c2597	Neut_2489
  							lipoprotein carrier	<br>Lipopolysaccharide
  							protein LolA	assembly;
  								<br>Lipoprotein sorting
  								system
  fig|6666666.60966.peg.2611	CDS	2409936	2407630	−3	−	2307	Cell division protein	Bacterial cell Division;	D23_1c2598	Neut_2488
  							FtsK	<br>Bacterial
  								cytoskeleton;
  								<br>Bacterial RNA-
  								metabolizing Zn-
  								dependent hydrolases;
  								<br>CBSS-
  								83333.1.peg.876
  fig|6666666.60966.peg.2612	CDS	2411206	2410151	−1	−	1056	InterPro IPR002110	-none-	D23_1c2600	Neut_2487
  							COGs COG0666
  fig|6666666.60966.peg.2613	CDS	2412939	2411203	−3	−	1737	Succinate	Succinate	D23_1c2601	Neut_2486
  							dehydrogenase	dehydrogenase;
  							flavoprotein subunit (EC	<br>TCA Cycle
  							1.3.99.1)
  fig|6666666.60966.peg.2614	CDS	2413237	2412968	−1	−	270	Succinate	Succinate	D23_1c2602	Neut_2485
  							dehydrogenase	dehydrogenase
  							hydrophobic membrane
  							anchor protein
  fig|6666666.60966.peg.2615	CDS	2413803	2413315	−3	−	489	Succinate	Succinate	D23_1c2603	Neut_2484
  							dehydrogenase	dehydrogenase
  							cytochrome b-556
  							subunit
  fig|6666666.60966.peg.2616	CDS	2413889	2415583	2	+	1695	CTP synthase (EC	CTP synthase (EC	D23_1c2604	Neut_2483
  							6.3.4.2)	6.3.4.2) cluster;
  								<br>pyrimidine
  								conversions
  fig|6666666.60966.peg.2617	CDS	2415872	2417158	2	+	1287	Enolase (EC 4.2.1.11)	Glycolysis and	D23_1c2605	Neut_2482
  								Gluconeogenesis
  fig|6666666.60966.peg.2618	CDS	2417185	2417436	1	+	252	Cell division protein	Bacterial cell Division;	D23_1c2606	Neut_2481
  							DivIC (FtsB), stabilizes	<br>Bacterial
  							FtsL against RasP	cytoskeleton;
  							cleavage	<br>Stationary phase
  								repair cluster
  fig|6666666.60966.peg.2619	CDS	2417726	2417860	2	+	135	hypothetical protein	-none-	D23_1c2607	NA
  fig|6666666.60966.peg.2621	CDS	2419576	2418317	−1	−	1260	Transcription	Transcription factors	D23_1c2609	Neut_2479
  							termination factor Rho	bacterial
  fig|6666666.60966.peg.2622	CDS	2420006	2419791	−2	−	216	Thioredoxin	-none-	D23_1c2610	Neut_2478
  fig|6666666.60966.peg.2624	CDS	2420605	2421762	1	+	1158	Membrane-bound lytic	Murein Hydrolases;	D23_1c2611	Neut_2477
  							murein transglycosylase	<br>Peptidoglycan
  							B precursor (EC 3.2.1.—)	Biosynthesis
  fig|6666666.60966.peg.2625	CDS	2422278	2421835	−3	−	444	Universal stress protein	-none-	D23_1c2612	Neut_2476
  							family COG0589
  fig|6666666.60966.peg.2626	CDS	2424743	2422389	−2	−	2355	Partial urea carboxylase	Urea carboxylase and	D23_1c2613	Neut_2475
  							2 (EC 6.3.4.6)	Allophanate hydrolase
  								cluster; <br>Urea
  								decomposition
  fig|6666666.60966.peg.2627	CDS	2425462	2424797	−1	−	666	Urea carboxylase-	Urea decomposition	D23_1c2614	Neut_2474
  							related
  							aminomethyltransferase
  							(EC 2.1.2.10)
  fig|6666666.60966.peg.2628	CDS	2426187	2425459	−3	−	729	Urea carboxylase-	Urea decomposition	D23_1c2615	Neut_2473
  							related
  							aminomethyltransferase
  							(EC 2.1.2.10)
  fig|6666666.60966.peg.2629	CDS	2427740	2426202	−2	−	1539	Urea carboxylase-	Urea decomposition	D23_1c2616	Neut_2472
  							related amino acid
  							permease
  fig|6666666.60966.peg.2630	CDS	2427773	2427892	2	+	120	hypothetical protein	-none-	D23_1c2617	NA
  fig|6666666.60966.peg.2631	CDS	2428128	2428319	3	+	192	hypothetical protein	-none-	D23_1c2618	NA
  fig|6666666.60966.peg.2632	CDS	2428646	2428518	−2	−	129	hypothetical protein	-none-	D23_1c2620	NA
  fig|6666666.60966.peg.2633	CDS	2428671	2432291	3	+	3621	Urea carboxylase (EC	Urea carboxylase and	D23_1c2621	Neut_2470
  							6.3.4.6)	Allophanate hydrolase
  								cluster; <br>Urea
  								decomposition
  fig|6666666.60966.peg.2634	CDS	2433643	2432279	−1	−	1365	Membrane-bound lytic	CBSS-228410.1.peg.134;	D23_1c2622	Neut_2469
  							murein transglycosylase	<br>CBSS-
  							D precursor (EC 3.2.1.—)	342610.3.peg.1536;
  								<br>Murein Hydrolases
  fig|6666666.60966.peg.2635	CDS	2434924	2433791	−1	−	1134	Ribonucleotide	Ribonucleotide	D23_1c2623	Neut_2468
  							reductase of class Ia	reduction
  							(aerobic), beta subunit
  							(EC 1.17.4.1)
  fig|6666666.60966.peg.2636	CDS	2437918	2434976	−1	−	2943	Ribonucleotide	Ribonucleotide	D23_1c2624	Neut_2467
  							reductase of class Ia	reduction
  							(aerobic), alpha subunit
  							(EC 1.17.4.1)
  fig|6666666.60966.peg.2637	CDS	2438096	2441536	2	+	3441	Long-chain-fatty-acid--	Biotin biosynthesis;	D23_1c2625	Neut_2466
  							CoA ligase (EC 6.2.1.3)	<br>Biotin synthesis
  								cluster; <br>Fatty acid
  								metabolism cluster
  fig|6666666.60966.peg.2638	CDS	2441648	2441788	2	+	141	hypothetical protein	-none-	D23_1c2626	NA
  fig|6666666.60966.peg.2639	CDS	2441958	2441845	−3	−	114	hypothetical protein	-none-	D23_1c2627	NA
  fig|6666666.60966.peg.2640	CDS	2441984	2442337	2	+	354	S-adenosylmethionine	Polyamine Metabolism	D23_1c2628	Neut_2465
  							decarboxylase
  							proenzyme (EC
  							4.1.1.50), prokaryotic
  							class 1B
  fig|6666666.60966.peg.2641	CDS	2442337	2443296	1	+	960	Spermidine synthase	Polyamine Metabolism	D23_1c2629	Neut_2464
  							(EC 2.5.1.16)
  fig|6666666.60966.peg.2642	CDS	2444178	2443342	−3	−	837	Cytochrome c family	-none-	D23_1c2630	Neut_2463
  							protein
  fig|6666666.60966.peg.2643	CDS	2446065	2444275	−3	−	1791	ABC transporter, fused	-none-	D23_1c2631	Neut_2462
  							permease and ATPase
  							domains
  fig|6666666.60966.peg.2644	CDS	2446735	2446268	−1	−	468	Single-stranded DNA-	DNA repair, bacterial	D23_1c2632	Neut_2461
  							binding protein
  fig|6666666.60966.peg.2645	CDS	2448142	2446736	−1	−	1407	Putative transport	-none-	D23_1c2633	Neut_2460
  							protein
  fig|6666666.60966.peg.2646	CDS	2448217	2451054	1	+	2838	Excinuclease ABC	DNA repair, UvrABC	D23_1c2634	Neut_2459
  							subunit A	system
  fig|6666666.60966.peg.2647	CDS	2451051	2452322	3	+	1272	D-glycerate 2-kinase (EC	Glycerate metabolism	D23_1c2635	Neut_2458
  							2.7.1.—)
  fig|6666666.60966.peg.2648	CDS	2455286	2452443	−2	−	2844	Aconitate hydratase (EC	TCA Cycle	D23_1c2637	Neut_2457
  							4.2.1.3)
  fig|6666666.60966.peg.2649	CDS	2455429	2456334	1	+	906	Aldose 1-epimerase	-none-	D23_1c2638	Neut_2456
  fig|6666666.60966.peg.2650	CDS	2456378	2456941	2	+	564	NADPH-dependent	-none-	D23_1c2639	Neut_2455
  							FMN reductase
  fig|6666666.60966.peg.2651	CDS	2457281	2457051	−2	−	231	HrgA protein	-none-	D23_1c2640	Neut_2454
  fig|6666666.60966.peg.2652	CDS	2457998	2457480	−2	−	519	HrgA protein	-none-	D23_1c2641	NA
  fig|6666666.60966.peg.2653	CDS	2459350	2458013	−1	−	1338	hypothetical protein	-none-	D23_1c2642	NA
  fig|6666666.60966.peg.2654	CDS	2460249	2459347	−3	−	903	hypothetical protein	-none-	D23_1c2643	NA
  fig|6666666.60966.peg.2655	CDS	2463305	2460264	−2	−	3042	Type I restriction-	Restriction-Modification	D23_1c2644	NA
  							modification system,	System; <br>Type I
  							restriction subunit R (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.2656	CDS	2463943	2463341	−1	−	603	hypothetical protein	-none-	D23_1c2645	NA
  fig|6666666.60966.peg.2657	CDS	2465348	2463960	−2	−	1389	Type I restriction-	Restriction-Modification	D23_1c2646	NA
  							modification system,	System; <br>Type I
  							specificity subunit S (EC	Restriction-Modification
  							3.1.21.3)
  fig|6666666.60966.peg.2658	CDS	2467567	2465348	−1	−	2220	Type I restriction-	Restriction-Modification	D23_1c2647	Neut_0541
  							modification system,	System; <br>Type I
  							DNA-methyltransferase	Restriction-Modification
  							subunit M (EC 2.1.1.72)
  fig|6666666.60966.peg.2659	CDS	2468029	2467751	−1	−	279	Type I restriction-	Restriction-Modification	D23_1c2648	Neut_2448
  							modification system,	System; <br>Type I
  							DNA-methyltransferase	Restriction-Modification
  							subunit M (EC 2.1.1.72)
  fig|6666666.60966.peg.2660	CDS	2468945	2468235	−2	−	711	RNA polymerase sigma	Flagellar motility;	D23_1c2650	Neut_2447
  							factor for flagellar	<br>Flagellum;
  							operon	<br>Transcription
  								initiation, bacterial
  								sigma factors
  fig|6666666.60966.peg.2661	CDS	2469847	2468954	−1	−	894	Flagellar synthesis	Flagellar motility;	D23_1c2651	Neut_2446
  							regulator FleN	<br>Flagellum
  fig|6666666.60966.peg.2662	CDS	2471090	2469840	−2	−	1251	Flagellar biosynthesis	Flagellar motility;	D23_1c2652	Neut_2445
  							protein FlhF	<br>Flagellum
  fig|6666666.60966.peg.2663	CDS	2473171	2471087	−1	−	2085	Flagellar biosynthesis	Flagellar motility;	D23_1c2653	Neut_2444
  							protein FlhA	<br>Flagellum
  fig|6666666.60966.peg.2664	CDS	2474349	2473219	−3	−	1131	Flagellar biosynthesis	Flagellar motility;	D23_1c2654	Neut_2443
  							protein FlhB	<br>Flagellum
  fig|6666666.60966.peg.2665	CDS	2476208	2474601	−2	−	1608	Peptide chain release	Translation termination	D23_1c2655	Neut_2442
  							factor
  3	factors bacterial
  fig|6666666.60966.peg.2666	CDS	2478262	2476208	−1	−	2055	Dipeptide transport	ABC transporter	D23_1c2656	Neut_2441
  							ATP-binding protein	dipeptide (TC 3.A.1.5.2)
  							DppF (TC 3.A.1.5.2)
  fig|6666666.60966.peg.2667	CDS	2479752	2478259	−3	−	1494	Oligopeptide transport	-none-	D23_1c2657	Neut_2440
  							system permease
  							protein
  fig|6666666.60966.peg.2669	CDS	2480032	2480334	1	+	303	Negative regulator of	Flagellum	D23_1c2658	Neut_2439
  							flagellin synthesis
  fig|6666666.60966.peg.2670	CDS	2480417	2480800	2	+	384	Flagellar biosynthesis	Flagellum	D23_1c2659	Neut_2438
  							protein FlgN
  fig|6666666.60966.peg.2671	CDS	2481184	2483109	1	+	1926	tRNA uridine 5-	Cell Division Subsystem	D23_1c2660	Neut_2437
  							carboxymethylaminomethyl	including YidCD;
  							modification	<br>RNA modification
  							enzyme GidA	and chromosome
  								partitioning cluster;
  								<br>mnm5U34
  								biosynthesis bacteria;
  								<br>tRNA modification
  								Bacteria
  fig|6666666.60966.peg.2672	CDS	2483084	2483728	2	+	645	rRNA small subunit 7-	Cell Division Subsystem	D23_1c2661	Neut_2436
  							methylguanosine (m7G)	including YidCD;
  							methyltransferase GidB	<br>RNA methylation;
  								<br>RNA modification
  								and chromosome
  								partitioning cluster
  fig|6666666.60966.peg.2673	CDS	2483792	2484556	2	+	765	Chromosome (plasmid)	Bacterial Cell Division;	D23_1c2662	Neut_2435
  							partitioning protein	<br>Bacterial
  							ParA/Sporulation	Cytoskeleton;
  							initiation inhibitor	<br>Bacterial
  							protein Soj	Cytoskeleton; <br>Cell
  								Division Subsystem
  								including YidCD;
  								<br>RNA modification
  								and chromosome
  								partitioning cluster
  fig|6666666.60966.peg.2674	CDS	2484637	2485440	1	+	804	Chromosome (plasmid)	Bacterial Cytoskeleton;	D23_1c2663	Neut_2434
  							partitioning protein	<br>Bacterial
  							ParB/Stage 0	Cytoskeleton; <br>Cell
  							sporulation protein J	Division Subsystem
  								including YidCD;
  								<br>RNA modification
  								and chromosome
  								partitioning cluster
  fig|6666666.60966.peg.2675	CDS	2485777	2488083	1	+	2307	Glucose-6-phosphate	Glycolysis and	D23_1c2664	Neut_2433
  							isomerase (EC 5.3.1.9)	Gluconeogenesis
  fig|6666666.60966.peg.2676	CDS	2488076	2489131	2	+	1056	6-phosphogluconate	D-gluconate and	D23_1c2665	Neut_2432
  							dehydrogenase,	ketogluconates
  							decarboxylating (EC	metabolism;
  							1.1.1.44)	<br>Pentose phosphate
  								pathway
  fig|6666666.60966.peg.2677	CDS	2489149	2490591	1	+	1443	Glucose-6-phosphate 1-	Pentose phosphate	D23_1c2666	Neut_2431
  							dehydrogenase (EC	pathway
  							1.1.1.49)
  fig|6666666.60966.peg.2678	CDS	2490598	2490741	1	+	144	hypothetical protein	-none-	D23_1c2667	NA
  fig|6666666.60966.peg.2679	CDS	2491345	2490770	−1	−	576	putative membrane	-none-	D23_1c2668	Neut_2430
  							protein
  fig|6666666.60966.peg.2680	CDS	2491701	2492270	3	+	570	DedA family inner	DedA family of inner	D23_1c2669	Neut_2429
  							membrane protein	membrane proteins
  							YohD
  fig|6666666.60966.peg.2681	CDS	2492664	2492897	3	+	234	Mobile element protein	-none-	D23_1c2671	Neut_2428
  fig|6666666.60966.peg.2682	CDS	2493050	2494789	2	+	1740	ABC-type anion	-none-	D23_1c2672	Neut_2427
  							transport system,
  							duplicated permease
  							component
  fig|6666666.60966.peg.2683	CDS	2494811	2496100	2	+	1290	ABC-type	Alkanesulfonate	D23_1c2673	Neut_2426
  							nitrate/sulfonate/bicarbonate	assimilation
  							transport system,
  							ATPase component
  fig|6666666.60966.peg.2684	CDS	2499268	2496263	−1	−	3006	Exonuclease SbcC	DNA repair, bacterial;	D23_1c2676	Neut_2425
  								<br>Rad50-Mre11 DNA
  								repair cluster
  fig|6666666.60966.peg.2685	CDS	2499230	2499520	2	+	291	hypothetical protein	-none-	D23_1c2677	NA
  fig|6666666.60966.peg.2686	CDS	2500770	2499526	−3	−	1245	Exonuclease SbcD	DNA repair, bacterial;	D23_1c2678	Neut_2424
  								<br>Rad50-Mre11 DNA
  								repair cluster
  fig|6666666.60966.peg.2687	CDS	2501402	2500767	−2	−	636	FIG01057587:	-none-	D23_1c2679	NA
  							hypothetical protein
  fig|6666666.60966.peg.2688	CDS	2501615	2502037	2	+	423	Mobile element protein	-none-	D23_1c2680	Neut_2450
  fig|6666666.60966.peg.2689	CDS	2502217	2502050	−1	−	168	hypothetical protein	-none-	D23_1c2681	NA
  fig|6666666.60966.peg.2691	CDS	2503677	2502628	−3	−	1050	hypothetical protein	-none-	D23_1c2682	Neut_2415
  fig|6666666.60966.peg.2692	CDS	2503893	2504105	3	+	213	hypothetical protein	-none-	D23_1c2683	NA
  fig|6666666.60966.peg.2693	CDS	2505239	2504595	−2	−	645	hypothetical protein	-none-	D23_1c2685	NA
  fig|6666666.60966.peg.2694	CDS	2506092	2505229	−3	−	864	Mobile element protein	-none-	D23_1c2686	Neut_2192
  fig|6666666.60966.peg.2695	CDS	2506385	2506089	−2	−	297	Mobile element protein	-none-	D23_1c2687	Neut_2193
  fig|6666666.60966.peg.2696	CDS	2506924	2506445	−1	−	480	DNA primase/helicase,	Phage replication	D23_1c2688	NA
  							phage-associated
  fig|6666666.60966.peg.2697	CDS	2507166	2506921	−3	−	246	hypothetical protein	-none-	D23_1c2689	NA
  fig|6666666.60966.peg.2698	CDS	2507393	2507166	−2	−	228	hypothetical protein	-none-	D23_1c2690	NA
  fig|6666666.60966.peg.2699	CDS	2507735	2508577	2	+	843	hypothetical protein	-none-	D23_1c2691	NA
  fig|6666666.60966.peg.2700	CDS	2508650	2509111	2	+	462	Putative bacteriophage-	-none-	D23_1c2692	NA
  							related protein
  fig|6666666.60966.peg.2701	CDS	2509108	2510448	1	+	1341	probable DNA invertase	-none-	D23_1c2693	Neut_2563
  fig|6666666.60966.peg.2702	CDS	2510478	2510897	3	+	420	elements of external	-none-	D23_1c2694	NA
  							origin; phage-related
  							functions and
  							prophages
  fig|6666666.60966.peg.2703	CDS	2512240	2511590	−1	−	651	Similar to	2-phosphoglycolate	D23_1c2696	Neut_2506
  							phosphoglycolate	salvage
  							phosphatase, clustered
  							with ubiquinone
  							biosynthesis SAM-
  							dependent O-
  							methyltransferase
  fig|6666666.60966.peg.2704	CDS	2512973	2512269	−2	−	705	3-demethylubiquinol 3-	Ubiquinone	D23_1c2697	Neut_2507
  							O-methyltransferase	Biosynthesis;
  							(EC 2.1.1.64)	<br>Ubiquinone
  								Biosynthesis-gjo
  fig|6666666.60966.peg.2705	CDS	2513079	2512963	−3	−	117	hypothetical protein	-none-	D23_1c2698	NA
  fig|6666666.60966.peg.2706	CDS	2513892	2513197	−3	−	696	Outer membrane	Osmoregulation	D23_1c2699	Neut_2508
  							protein A precursor
  fig|6666666.60966.peg.2708	CDS	2514251	2515009	2	+	759	ABC-type multidrug	CBSS-196164.1.peg.1690	D23_1c2700	Neut_2509
  							transport system,
  							ATPase component
  fig|6666666.60966.peg.2709	CDS	2515006	2515752	1	+	747	gliding motility protein	-none-	D23_1c2701	Neut_2510
  							GldF
  fig|6666666.60966.peg.2710	CDS	2515776	2517128	3	+	1353	Mucin 2 precursor	-none-	D23_1c2702	Neut_2511
  fig|6666666.60966.peg.2711	CDS	2517144	2517959	3	+	816	Formamidopyrimidine-	DNA Repair Base	D23_1c2703	Neut_2512
  							DNA glycosylase (EC	Excision
  							3.2.2.23)
  fig|6666666.60966.peg.2712	CDS	2518479	2517994	−3	−	486	Thioredoxin	-none-	D23_1c2704	Neut_2513
  fig|6666666.60966.peg.2713	CDS	2520458	2518644	−2	−	1815	GTP-binding protein	Universal GTPases	D23_1c2705	Neut_2514
  							TypA/BipA
  fig|6666666.60966.peg.2714	CDS	2520591	2521196	3	+	606	Riboflavin synthase	Riboflavin, FMN and FAD	D23_1c2706	Neut_2515
  							eubacterial/eukaryotic	metabolism;
  							(EC 2.5.1.9)	<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>Riboflavin
  								synthesis cluster;
  								<br>riboflavin to FAD
  fig|6666666.60966.peg.2715	CDS	2521193	2522302	2	+	1110	3,4-dihydroxy-2-	Riboflavin, FMN and FAD	D23_1c2707	Neut_2516
  							butanone 4-phosphate	metabolism;
  							synthase (EC 4.1.99.12)/	<br>Riboflavin, FMN and
  							GTP cyclohydrolase II	FAD metabolism;
  							(EC 3.5.4.25)	<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>Riboflavin,
  								FMN and FAD
  								metabolism in plants;
  								<br>Riboflavin synthesis
  								cluster; <br>Riboflavin
  								synthesis cluster;
  								<br>riboflavin to FAD
  fig|6666666.60966.peg.2716	CDS	2522529	2523026	3	+	498	6,7-dimethyl-8-	Possible RNA	D23_1c2708	Neut_2517
  							ribityllumazine synthase	degradation cluster;
  							(EC 2.5.1.78)	<br>Riboflavin, FMN and
  								FAD metabolism;
  								<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>Riboflavin
  								synthesis cluster
  fig|6666666.60966.peg.2717	CDS	2523023	2523526	2	+	504	Transcription	Riboflavin synthesis	D23_1c2709	Neut_2518
  							termination protein	cluster;
  							NusB	<br>Transcription
  								factors bacterial
  fig|6666666.60966.peg.2719	CDS	2523801	2524787	3	+	987	Thiamine-	5-FCL-like protein;	D23_1c2710	Neut_2519
  							monophosphate kinase	<br>Riboflavin synthesis
  							(EC 2.7.4.16)	cluster; <br>Thiamin
  								biosynthesis
  fig|6666666.60966.peg.2720	CDS	2524864	2525307	1	+	444	Phosphatidylglycerophosphatase	Glycerolipid and	D23_1c2711	Neut_2520
  							A (EC 3.1.3.27)	Glycerophospholipid
  								Metabolism in Bacteria;
  								<br>Riboflavin synthesis
  								cluster
  fig|6666666.60966.peg.2721	CDS	2525304	2525846	3	+	543	C-terminal domain of	DNA repair system	D23_1c2712	Neut_2521
  							CinA type S; Protein	including RecA, MutS
  							Implicated in DNA	and a hypothetical
  							repair function with	protein; <br>NAD and
  							RecA and MutS	NADP cofactor
  								biosynthesis global;
  								<br>NAD and NADP
  								cofactor biosynthesis
  								global; <br>Possible RNA
  								degradation cluster;
  								<br>Riboflavin, FMN and
  								FAD metabolism in
  								plants; <br>Riboflavin
  								synthesis cluster
  fig|6666666.60966.peg.2722	CDS	2527502	2526306	−2	−	1197	FIG00859610:	-none-	D23_1c2713	Neut_2522
  							hypothetical protein
  fig|6666666.60966.peg.2723	CDS	2529448	2527829	−1	−	1620	ATP-dependent DNA	-none-	D23_1c2714	Neut_2523
  							helicase RecQ
  fig|6666666.60966.peg.2724	CDS	2529855	2529445	−3	−	411	Ribosome-associated	DNA replication cluster	D23_1c2715	Neut_2524
  							heat shock protein	1; <br>Heat shock dnaK
  							implicated in the	gene cluster extended
  							recycling of the 50S
  							subunit (S4 paralog)
  fig|6666666.60966.peg.2725	CDS	2530686	2529877	−3	−	810	InterPro IPR002781	-none-	D23_1c2716	Neut_2525
  							COGs COG0730
  fig|6666666.60966.peg.2726	CDS	2532376	2530694	−1	−	1683	FIG003847:	CBSS-269482.4.peg.5018	D23_1c2717	Neut_2526
  							Oxidoreductase
  							(flavoprotein)
  fig|6666666.60966.peg.2727	CDS	2532913	2532488	−1	−	426	Transcriptional	-none-	D23_1c2718	Neut_2527
  							regulator, ArsR family
  fig|6666666.60966.peg.2728	CDS	2533377	2532910	−3	−	468	GENE II AND X	-none-	D23_1c2719	Neut_2528
  							PROTEINS
  fig|6666666.60966.peg.2729	CDS	2533835	2533407	−2	−	429	Probable	-none-	D23_1c2720	Neut_2529
  							transmembrane protein
  fig|6666666.60966.peg.2730	CDS	2533940	2534806	2	+	867	FIG146518: Zn-	CBSS-269482.4.peg.5018	D23_1c2721	Neut_2530
  							dependent hydrolases,
  							including glyoxylases
  fig|6666666.60966.peg.2731	CDS	2535475	2534891	−1	−	585	FIG001587: exported	-none-	D23_1c2722	Neut_2531
  							protein
  fig|6666666.60966.peg.2732	CDS	2537039	2535534	−2	−	1506	FIG00859025:	-none-	D23_1c2723	Neut_2532
  							hypothetical protein
  fig|6666666.60966.peg.2733	CDS	2537388	2537077	−3	−	312	hypothetical protein	-none-	D23_1c2724	NA
  fig|6666666.60966.rna.11	RNA	226254	226324	3	+	71	tRNA-Gly-CCC	tRNAs	NA	NA
  fig|6666666.60966.rna.2	RNA	6795	6868	3	+	74	tRNA-Cys-GCA	tRNAs	NA	NA
  fig|6666666.60966.rna.39	RNA	1810921	1810848	−1	−	74	tRNA-Gly-TCC	-none-	NA	NA
  fig|6666666.60966.rna.23	RNA	969765	969839	3	+	75	tRNA-Gln-TTG	-none-	NA	NA
  fig|6666666.60966.rna.36	RNA	1758968	1759042	2	+	75	tRNA-Val-CAC	tRNAs	NA	NA
  fig|6666666.60966.rna.38	RNA	1810812	1810738	−3	−	75	tRNA-Thr-GGT	-none-	NA	NA
  fig|6666666.60966.rna.1	RNA	6614	6689	2	+	76	tRNA-Gly-GCC	tRNAs	NA	NA
  fig|6666666.60966.rna.7	RNA	120428	120503	2	+	76	tRNA-Ala-TGC	-none-	NA	NA
  fig|6666666.60966.rna.12	RNA	284547	284472	−3	−	76	tRNA-Glu-TTC	-none-	NA	NA
  fig|6666666.60966.rna.13	RNA	284648	284573	−2	−	76	tRNA-Ala-GGC	tRNAs	NA	NA
  fig|6666666.60966.rna.14	RNA	493566	493641	3	+	76	tRNA-Thr-CGT	-none-	NA	NA
  fig|6666666.60966.rna.16	RNA	561828	561903	3	+	76	tRNA-Val-TAC	-none-	NA	NA
  fig|6666666.60966.rna.20	RNA	859357	859282	−1	−	76	tRNA-Lys-TTT	-none-	NA	NA
  fig|6666666.60966.rna.21	RNA	948801	948876	3	+	76	tRNA-Thr-TGT	-none-	NA	NA
  fig|6666666.60966.rna.24	RNA	1157662	1157587	−1	−	76	tRNA-Arg-CCT	-none-	NA	NA
  fig|6666666.60966.rna.25	RNA	1199325	1199250	−3	−	76	tRNA-His-GTG	-none-	NA	NA
  fig|6666666.60966.rna.29	RNA	1470510	1470435	−3	−	76	tRNA-Asn-GTT	-none-	NA	NA
  fig|6666666.60966.rna.33	RNA	1618239	1618314	3	+	76	tRNA-Met-CAT	-none-	NA	NA
  fig|6666666.60966.rna.34	RNA	1673498	1673423	−2	−	76	tRNA-Arg-CCG	tRNAs	NA	NA
  fig|6666666.60966.rna.37	RNA	1809438	1809363	−3	−	76	tRNA-Trp-CCA	tRNAs	NA	NA
  fig|6666666.60966.rna.42	RNA	2107281	2107356	3	+	76	tRNA-Phe-GAA	tRNAs	NA	NA
  fig|6666666.60966.rna.6	RNA	120349	120425	1	+	77	tRNA-Ile-GAT	-none-	NA	NA
  fig|6666666.60966.rna.10	RNA	196762	196838	1	+	77	tRNA-Met-CAT	-none-	NA	NA
  fig|6666666.60966.rna.15	RNA	524553	524629	3	+	77	tRNA-Val-GAC	tRNAs	NA	NA
  fig|6666666.60966.rna.17	RNA	561963	562039	3	+	77	tRNA-Asp-GTC	-none-	NA	NA
  fig|6666666.60966.rna.18	RNA	728392	728316	−1	−	77	tRNA-Pro-CGG	tRNAs	NA	NA
  fig|6666666.60966.rna.26	RNA	1199452	1199376	−1	−	77	tRNA-Arg-TCT	-none-	NA	NA
  fig|6666666.60966.rna.27	RNA	1199573	1199497	−2	−	77	tRNA-Pro-TGG	-none-	NA	NA
  fig|6666666.60966.rna.28	RNA	1427736	1427812	3	+	77	tRNA-Met-CAT	-none-	NA	NA
  fig|6666666.60966.rna.41	RNA	2107137	2107213	3	+	77	tRNA-Arg-ACG	tRNAs	NA	NA
  fig|6666666.60966.rna.44	RNA	2339644	2339568	−1	−	77	tRNA-Pro-GGG	tRNAs	NA	NA
  fig|6666666.60966.rna.19	RNA	835520	835604	2	+	85	tRNA-Leu-GAG	tRNAs	NA	NA
  fig|6666666.60966.rna.32	RNA	1597631	1597715	2	+	85	tRNA-Leu-CAG	tRNAs	NA	NA
  fig|6666666.60966.rna.40	RNA	1811116	1811032	−1	−	85	tRNA-Tyr-GTA	-none-	NA	NA
  fig|6666666.60966.rna.4	RNA	97072	96987	−1	−	86	tRNA-Leu-TAG	-none-	NA	NA
  fig|6666666.60966.rna.31	RNA	1574940	1574854	−3	−	87	tRNA-Leu-CAA	tRNAs	NA	NA
  fig|6666666.60966.rna.30	RNA	1550222	1550135	−2	−	88	tRNA-Ser-TGA	-none-	NA	NA
  fig|6666666.60966.rna.3	RNA	6894	6982	3	+	89	tRNA-Leu-TAA	-none-	NA	NA
  fig|6666666.60966.rna.22	RNA	956464	956374	−1	−	91	tRNA-Ser-GGA	tRNAs	NA	NA
  fig|6666666.60966.rna.35	RNA	1757250	1757342	3	+	93	tRNA-Ser-CGA	tRNAs	NA	NA
  fig|6666666.60966.rna.43	RNA	2120297	2120205	−2	−	93	tRNA-Ser-GCT	-none-	NA	NA
  fig|6666666.60966.peg.111	CDS	108515	108628	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.353	CDS	326760	326647	−3	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.404	CDS	375917	375804	−2	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.432	CDS	397539	397426	−3	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.509	CDS	474482	474369	−2	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.589	CDS	543008	543121	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.838	CDS	770105	770218	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.923	CDS	855159	855046	−3	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.943	CDS	873193	873306	1	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1081	CDS	1010260	1010373	1	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1333	CDS	1235666	1235779	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1414	CDS	1326350	1326463	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1695	CDS	1575540	1575653	3	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1875	CDS	1749599	1749486	−2	−	114	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.2082	CDS	1936491	1936378	−3	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2205	CDS	2047715	2047828	2	+	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2370	CDS	2201390	2201277	−2	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2413	CDS	2236764	2236651	−3	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2577	CDS	2379043	2378930	−1	−	114	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.421	CDS	392634	392518	−3	−	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.431	CDS	397234	397350	1	+	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1104	CDS	1033773	1033889	3	+	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1856	CDS	1730271	1730155	−3	−	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2044	CDS	1907891	1907775	−2	−	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2046	CDS	1908400	1908516	1	+	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2250	CDS	2086632	2086516	−3	−	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2378	CDS	2209362	2209246	−3	−	117	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.28	CDS	31960	31841	−1	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.536	CDS	496598	496717	2	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.866	CDS	794273	794392	2	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1031	CDS	956342	956223	−2	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1238	CDS	1152349	1152230	−1	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1279	CDS	1184453	1184572	2	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1566	CDS	1462529	1462410	−2	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1604	CDS	1492079	1491960	−2	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1610	CDS	1495100	1495219	2	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1938	CDS	1820165	1820046	−2	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1940	CDS	1820392	1820511	1	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2194	CDS	2040715	2040596	−1	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2229	CDS	2069192	2069073	−2	−	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2542	CDS	2355482	2355601	2	+	120	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.477	CDS	444630	444508	−3	−	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.634	CDS	579242	579364	2	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.927	CDS	859107	859229	3	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1015	CDS	941818	941940	1	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1388	CDS	1298114	1298236	2	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1755	CDS	1633195	1633073	−1	−	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2224	CDS	2067753	2067631	−3	−	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2271	CDS	2103666	2103788	3	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2336	CDS	2170340	2170462	2	+	123	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2415	CDS	2237130	2237008	−3	−	123	Hydroxyacylglutathione	CBSS-228410.1.peg.134;	NA	NA
  							hydrolase (EC 3.1.2.6)	<br>CBSS-
  								342610.3.peg.1536;
  								<br>Glutathione: Non-
  								redox reactions;
  								<br>Methylglyoxal
  								Metabolism
  fig|6666666.60966.peg.82	CDS	79801	79676	−1	−	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.585	CDS	541998	542123	3	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1268	CDS	1176741	1176866	3	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1473	CDS	1385674	1385799	1	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1510	CDS	1423155	1423030	−3	−	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1690	CDS	1573599	1573474	−3	−	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1758	CDS	1635456	1635331	−3	−	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1935	CDS	1816227	1816352	3	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1966	CDS	1832788	1832913	1	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2285	CDS	2119314	2119439	3	+	126	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.21	CDS	28650	28522	−3	−	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.27	CDS	31632	31760	3	+	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.247	CDS	231537	231665	3	+	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.300	CDS	272364	272492	3	+	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.864	CDS	792354	792226	−3	−	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1166	CDS	1092637	1092509	−1	−	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1314	CDS	1216530	1216658	3	+	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1730	CDS	1612183	1612311	1	+	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2328	CDS	2162434	2162306	−1	−	129	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.122	CDS	124194	124063	−3	−	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.154	CDS	155514	155645	3	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.874	CDS	801546	801677	3	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.894	CDS	823808	823939	2	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.960	CDS	886681	886550	−1	−	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1188	CDS	1108861	1108730	−1	−	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1578	CDS	1468706	1468837	2	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1950	CDS	1824304	1824435	1	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1983	CDS	1850338	1850469	1	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2066	CDS	1923319	1923450	1	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2445	CDS	2263603	2263472	−1	−	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2570	CDS	2376200	2376331	2	+	132	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.296	CDS	267656	267790	2	+	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1086	CDS	1016149	1016015	−1	−	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1167	CDS	1092703	1092837	1	+	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1560	CDS	1459112	1459246	2	+	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1597	CDS	1486647	1486513	−3	−	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1949	CDS	1824258	1824124	−3	−	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2059	CDS	1916861	1916995	2	+	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2151	CDS	1995848	1995982	2	+	135	FIG00858674:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.2230	CDS	2069201	2069335	2	+	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2363	CDS	2194044	2194178	3	+	135	LSU ribosomal protein	Cell Division Subsystem	NA	NA
  							L34p	including YidCD;
  								<br>RNA modification
  								cluster
  fig|6666666.60966.peg.2527	CDS	2338623	2338489	−3	−	135	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1276	CDS	1182314	1182177	−2	−	138	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1317	CDS	1218021	1218158	3	+	138	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1606	CDS	1493209	1493072	−1	−	138	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1867	CDS	1739233	1739370	1	+	138	Error-prone, lesion	-none-	NA	NA
  							bypass DNA polymerase
  							V(UmuC)
  fig|6666666.60966.peg.2117	CDS	1966387	1966250	−1	−	138	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2227	CDS	2068598	2068735	2	+	138	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.163	CDS	160970	160830	−2	−	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.173	CDS	168825	168965	3	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1286	CDS	1189481	1189621	2	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1416	CDS	1328534	1328674	2	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1422	CDS	1330733	1330873	2	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1759	CDS	1635699	1635839	3	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1775	CDS	1649712	1649572	−3	−	141	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.1984	CDS	1850712	1850572	−3	−	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2003	CDS	1866906	1867046	3	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2080	CDS	1935668	1935808	2	+	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2487	CDS	2301272	2301132	−2	−	141	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.369	CDS	342367	342224	−1	−	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.635	CDS	579509	579652	2	+	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1001	CDS	928837	928980	1	+	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1642	CDS	1524746	1524603	−2	−	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2114	CDS	1962886	1963029	1	+	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2593	CDS	2391861	2392004	3	+	144	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.205	CDS	197036	196890	−2	−	147	Integrase	-none-	NA	NA
  fig|6666666.60966.peg.284	CDS	260995	261141	1	+	147	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1885	CDS	1759287	1759141	−3	−	147	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2453	CDS	2272001	2271855	−2	−	147	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2620	CDS	2417974	2417828	−1	−	147	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2623	CDS	2420545	2420399	−1	−	147	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.108	CDS	106117	106266	1	+	150	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.813	CDS	746234	746085	−2	−	150	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1296	CDS	1205130	1205279	3	+	150	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1334	CDS	1235992	1235843	−1	−	150	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2300	CDS	2134634	2134485	−2	−	150	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.35	CDS	36062	35910	−2	−	153	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1312	CDS	1215961	1216113	1	+	153	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2143	CDS	1990257	1990105	−3	−	153	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.359	CDS	335237	335392	2	+	156	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.546	CDS	506105	505950	−2	−	156	FIG00858972:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.1174	CDS	1095978	1095823	−3	−	156	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.1384	CDS	1296435	1296280	−3	−	156	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2575	CDS	2378324	2378169	−2	−	156	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.89	CDS	85217	85059	−2	−	159	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.556	CDS	516983	516825	−2	−	159	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.562	CDS	523304	523462	2	+	159	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1099	CDS	1029431	1029589	2	+	159	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1571	CDS	1466563	1466405	−1	−	159	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.613	CDS	562226	562065	−2	−	162	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.886	CDS	814562	814401	−2	−	162	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1114	CDS	1043720	1043559	−2	−	162	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.291	CDS	265661	265825	2	+	165	FIG00856904:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.2077	CDS	1934012	1933848	−2	−	165	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.620	CDS	568234	568401	1	+	168	Methyltransferase (EC	-none-	NA	NA
  							2.1.1.—)
  fig|6666666.60966.peg.2317	CDS	2149354	2149521	1	+	168	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.2420	CDS	2241817	2241650	−1	−	168	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.856	CDS	785317	785147	−1	−	171	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1487	CDS	1401876	1401706	−3	−	171	FIG00858878:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.2286	CDS	2119703	2119873	2	+	171	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2707	CDS	2514260	2514090	−2	−	171	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.862	CDS	790885	790712	−1	−	174	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1450	CDS	1360555	1360382	−1	−	174	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.1572	CDS	1466783	1466956	2	+	174	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1608	CDS	1494659	1494835	2	+	177	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2416	CDS	2237303	2237127	−2	−	177	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2668	CDS	2479940	2479764	−2	−	177	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.748	CDS	694556	694377	−2	−	180	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1667	CDS	1550475	1550296	−3	−	180	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2116	CDS	1965779	1965600	−2	−	180	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2144	CDS	1990362	1990541	3	+	180	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.2400	CDS	2229074	2228895	−2	−	180	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.287	CDS	262264	262446	1	+	183	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.422	CDS	392649	392831	3	+	183	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1562	CDS	1459862	1460044	2	+	183	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2388	CDS	2218996	2219178	1	+	183	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.338	CDS	308508	308323	−3	−	186	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1842	CDS	1720173	1719988	−3	−	186	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.286	CDS	262147	261959	−1	−	189	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1202	CDS	1125016	1124828	−1	−	189	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1304	CDS	1209919	1209731	−1	−	189	FIG00858878:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.2395	CDS	2224520	2224332	−2	−	189	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.250	CDS	233011	233202	1	+	192	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.794	CDS	729662	729471	−2	−	192	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1764	CDS	1639415	1639606	2	+	192	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.808	CDS	741018	740824	−3	−	195	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.276	CDS	255673	255870	1	+	198	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.749	CDS	694591	694788	1	+	198	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2718	CDS	2523733	2523536	−1	−	198	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.217	CDS	203959	204159	1	+	201	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.682	CDS	631759	631959	1	+	201	FIG00859622:	-none-	NA	NA
  							hypothetical protein
  fig|6666666.60966.peg.208	CDS	199189	199392	1	+	204	Cold shock protein CspA	Cold shock, CspA family	NA	NA
  								of proteins
  fig|6666666.60966.peg.380	CDS	348880	348677	−1	−	204	SSU ribosomal protein	-none-	NA	NA
  							S16p
  fig|6666666.60966.peg.2149	CDS	1995706	1995503	−1	−	204	dTDP-4-	Rhamnose containing	NA	NA
  							dehydrorhamnose	glycans; <br>dTDP-
  							reductase (EC	rhamnose synthesis
  							1.1.1.133)
  fig|6666666.60966.peg.1148	CDS	1073050	1073259	1	+	210	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2464	CDS	2281343	2281134	−2	−	210	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.522	CDS	484104	484316	3	+	213	LSU ribosomal protein	-none-	NA	NA
  							L29p (L35e)
  fig|6666666.60966.peg.1481	CDS	1395113	1394901	−2	−	213	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.292	CDS	265809	266024	3	+	216	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.511	CDS	475254	475469	3	+	216	SSU ribosomal protein	Mycobacterium	NA	NA
  							S12p (S23e)	virulence operon
  								involved in protein
  								synthesis (SSU ribosomal
  								proteins);
  								<br>Ribosomal protein
  								S12p Asp
  								methylthiotransferase
  fig|6666666.60966.peg.529	CDS	490129	490347	1	+	219	Translation initiation	Translation initiation	NA	NA
  							factor
  1	factors bacterial
  fig|6666666.60966.peg.2374	CDS	2207422	2207640	1	+	219	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2105	CDS	1956719	1956940	2	+	222	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2690	CDS	2502317	2502538	2	+	222	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2153	CDS	1996354	1996578	1	+	225	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2138	CDS	1985283	1985510	3	+	228	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.442	CDS	405529	405299	−1	−	231	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1716	CDS	1598000	1597770	−2	−	231	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2439	CDS	2259000	2258770	−3	−	231	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1111	CDS	1042874	1043110	2	+	237	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.1999	CDS	1865704	1865468	−1	−	237	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1214	CDS	1136308	1136069	−1	−	240	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1733	CDS	1614273	1614031	−3	−	243	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.48	CDS	47253	47498	3	+	246	Alpha-L-Rha alpha-1,3-	Rhamnose containing	NA	NA
  							L-rhamnosyltransferase	glycans
  							(EC 2.4.1.—)
  fig|6666666.60966.peg.423	CDS	393586	393338	−1	−	249	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.429	CDS	396754	396506	−1	−	249	Transglycosylase-	-none-	NA	NA
  							associated protein
  fig|6666666.60966.peg.1147	CDS	1072594	1072842	1	+	249	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1951	CDS	1824656	1824408	−2	−	249	Plasmid stabilization	-none-	NA	NA
  							system protein
  fig|6666666.60966.peg.2579	CDS	2380195	2380446	1	+	252	Mobile element protein	-none-	NA	NA
  fig|6666666.60966.peg.523	CDS	484294	484548	1	+	255	SSU ribosomal protein	-none-	NA	NA
  							S17p (S11e)
  fig|6666666.60966.peg.1022	CDS	948522	948782	3	+	261	Stringent starvation	Carbon Starvation	NA	NA
  							protein B
  fig|6666666.60966.peg.1957	CDS	1826664	1826936	3	+	273	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2273	CDS	2108052	2108336	3	+	285	putative DNA transport	-none-	NA	NA
  							competence protein
  fig|6666666.60966.peg.46	CDS	46807	46481	−1	−	327	Conserved domain	-none-	NA	NA
  							protein
  fig|6666666.60966.peg.2109	CDS	1959886	1960239	1	+	354	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.2429	CDS	2248841	2248488	−2	−	354	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.1579	CDS	1468834	1469334	1	+	501	hypothetical protein	-none-	NA	NA
  fig|6666666.60966.peg.293	CDS	266114	266689	2	+	576	hypothetical protein	-none-	NA	NA

• SUPPLEMENTARY TABLE 2
  Selected D23 sequences

  SEQ ID
  and
  length	Description	Sequence
  SEQ ID	amoC1	MATTLGTSSASSVSSRGYDMSLWYDSKFYKFGLITMLLVAIFWVWYQRYF
  NO: 4	(D23_1c22	AYSHGMDSMEPEFDRVWMGLWRVHMAIMPLFALVTWGWIWKTRDTEEQLN
  (271	72)	NLDPKLEIKRYFYYMMWLGVYIFGVYWGGSFFTEQDASWHQVIIRDTSFT
  aa)	protein	PSHVVVFYGSFPMYIVCGVATYLYAMTRLPLFHRGISFPLVMAIAGPLMI
  		LPNVGLNEWGHAFWFMEELFSAPLHWGFVVLGWAGLFQGGVAAQIITRYS
  		NLTDVVWNNQSKEILNNRVVA
  SEQ ID	amoC1	ATGGCAACTACGTTAGGAACGAGCAGTGCCTCATCAGTCTCATCAAGAGG
  NO: 5	(D23_1c22	CTATGACATGTCACTGTGGTATGACTCCAAATTTTATAAATTTGGTTTAA
  (816	72) DNA	TAACCATGTTGTTGGTAGCGATATTCTGGGTATGGTATCAACGTTACTTT
  nt)		GCCTATTCACACGGAATGGATTCAATGGAACCAGAGTTTGACCGTGTATG
  		GATGGGCCTGTGGCGTGTGCACATGGCCATTATGCCGCTGTTTGCACTGG
  		TAACCTGGGGCTGGATCTGGAAAACACGTGATACAGAAGAGCAATTGAAT
  		AACCTGGATCCGAAACTGGAAATCAAACGCTACTTCTACTACATGATGTG
  		GCTGGGTGTATACATTTTTGGTGTTTACTGGGGTGGTAGCTTCTTTACGG
  		AGCAAGATGCCTCCTGGCACCAGGTGATTATTCGTGACACCAGCTTTACA
  		CCAAGTCACGTAGTCGTGTTTTATGGATCATTTCCGATGTACATCGTCTG
  		CGGAGTTGCAACCTATCTGTATGCAATGACCCGTCTGCCGCTGTTTCATC
  		GTGGAATTTCTTTCCCACTGGTGATGGCGATTGCAGGTCCTCTGATGATT
  		CTGCCAAACGTTGGTCTGAATGAATGGGGTCATGCTTTCTGGTTCATGGA
  		AGAGCTGTTCAGCGCACCGCTGCATTGGGGTTTTGTAGTGCTCGGTTGGG
  		CTGGGTTATTCCAGGGTGGAGTTGCTGCCCAAATCATTACCCGTTATTCC
  		AACCTGACTGACGTGGTCTGGAATAATCAAAGCAAAGAAATTCTGAATAA
  		CCGGGTTGTAGCTTAG
  SEQ ID	amoA1	VSIFRTEEILKAAKMPPEAVHMSRLIDAVYFPILVVLLVGTYHMHFMLLA
  NO: 6	(D23_1c22	GDWDFWMDWKDRQWWPVVTPIVGITYCSAIMYYLWVNYRQPFGATLCVVC
  (276	71)	LLIGEWLTRYWGFYWWSHYPLNFVTPGIMLPGALMLDFTMYLTRNWLVTA
  aa)	protein	LVGGGFFGLLFYPGNWAIFGPTHLPIVVEGTLLSMADYMGHLYVRTGTPE
  		YVRHIEQGSLRTFGGHTTVIAAFFAAFVSMLMFAVWWYLGKVYCTAFFYV
  		KGKRGRIVQRNDVTAFGEEGFPEGIK
  SEQ ID	amoA1	GTGAGTATATTTAGAACAGAAGAGATCCTGAAAGCGGCCAAGATGCCGCC
  NO: 7	(D23_1c22	GGAAGCGGTCCATATGTCACGCCTGATTGATGCGGTTTATTTTCCGATTC
  (831	71) DNA	TGGTTGTTCTGTTGGTAGGTACCTACCATATGCACTTCATGTTGTTGGCA
  nt)		GGTGACTGGGATTTCTGGATGGACTGGAAAGATCGTCAATGGTGGCCTGT
  		AGTAACACCTATTGTAGGCATTACCTATTGCTCGGCAATTATGTATTACC
  		TGTGGGTCAACTACCGTCAACCATTTGGTGCGACTCTGTGCGTAGTGTGT
  		TTGCTGATAGGTGAGTGGCTGACACGTTACTGGGGTTTCTACTGGTGGTC
  		ACACTATCCACTCAATTTTGTAACCCCAGGTATCATGCTCCCGGGTGCAT
  		TGATGTTGGATTTCACAATGTATCTGACACGTAACTGGTTGGTGACTGCA
  		TTGGTTGGGGGTGGATTCTTTGGTCTGCTGTTTTACCCGGGTAACTGGGC
  		AATCTTTGGTCCGACCCATCTGCCAATCGTTGTAGAAGGAACACTGTTGT
  		CGATGGCTGACTATATGGGTCACCTGTATGTTCGTACGGGTACACCTGAG
  		TATGTTCGTCATATTGAACAAGGTTCATTACGTACCTTTGGTGGTCACAC
  		CACAGTTATTGCAGCATTCTTCGCTGCGTTTGTATCCATGCTGATGTTTG
  		CAGTCTGGTGGTATCTTGGAAAAGTTTACTGCACAGCCTTCTTCTACGTT
  		AAAGGTAAAAGAGGACGTATCGTGCAGCGCAATGATGTTACGGCATTTGG
  		TGAAGAAGGGTTTCCAGAGGGGATCAAATAA
  SEQ ID	amoB1	MGIKNLYKRGMMGLCGVAVYAMAALTMTVTLDVSTVAAHGERSQEPFLRM
  NO: 8	(D23_1c22	RTVQWYDVKWGPEVTKVNENAQITGKFHLAEDWPRAAARPDFAFFNVGSP
  (421	70)	SSVYVRLSTKINGHPWFISGPLQIGRDYAFEVQLRARIPGRHHMHAMLNV
  aa)	protein	KDAGPIAGPGAWMNITGSWDDFTNPLKLLTGETIDSETFNLSNGIFWHIL
  		WMSIGIFWIGIFVARPMFLPRSRVLLAYGDDLLLDPMDKKITWVLAILTL
  		AIVWGGYRYTETKHPYTVPIQAGQSKVAPLPVAPNPVAIKITDANYDVPG
  		RALRVSMEVTNNGDTPVTFGEFTTAGIRFVNSTGRKYLDPQYPRELVAVG
  		LNFDDDGAIQPGETKQLRMEAKDALWEIQRLMALLGDPESRFGGLLMSWD
  		SEGNRHINSIAGPVIPVFTKL
  SEQ ID	amoB1	ATGGGTATCAAGAACCTTTATAAACGTGGAATGATGGGACTTTGTGGCGT
  NO: 9	(D23_1c22	TGCTGTTTATGCAATGGCGGCACTGACCATGACAGTGACACTAGATGTCT
  (1266	70) DNA	CAACAGTAGCAGCCCATGGAGAACGATCCCAGGAACCGTTTCTTCGGATG
  nt)		CGTACAGTACAGTGGTACGATGTTAAGTGGGGTCCGGAAGTAACCAAAGT
  		CAATGAGAATGCCCAAATTACCGGCAAATTTCACTTGGCTGAAGACTGGC
  		CGCGTGCGGCAGCAAGACCGGATTTCGCATTCTTTAACGTAGGTAGCCCA
  		AGCTCGGTATACGTGCGTTTGAGTACGAAGATTAATGGCCACCCATGGTT
  		TATTTCAGGTCCGCTGCAAATTGGTCGTGACTATGCGTTCGAAGTTCAGC
  		TGAGAGCACGTATTCCAGGACGCCATCACATGCACGCCATGTTAAACGTT
  		AAAGATGCAGGTCCAATTGCAGGACCGGGTGCATGGATGAACATTACCGG
  		AAGCTGGGATGATTTTACTAATCCACTCAAGCTGCTGACAGGCGAAACAA
  		TTGACTCAGAAACATTCAACCTGTCAAACGGTATTTTCTGGCATATTCTC
  		TGGATGTCAATTGGTATATTTTGGATTGGTATCTTTGTAGCGCGTCCGAT
  		GTTCCTGCCACGTAGCCGGGTATTGCTCGCTTATGGTGATGATCTGTTGC
  		TGGATCCGATGGATAAGAAAATCACCTGGGTACTTGCAATCCTGACCTTG
  		GCTATAGTATGGGGTGGATACCGCTATACAGAAACCAAGCATCCATACAC
  		AGTACCTATCCAGGCTGGTCAATCCAAAGTTGCACCATTACCGGTAGCAC
  		CAAATCCGGTAGCAATCAAAATTACAGATGCTAACTATGACGTACCGGGA
  		CGTGCACTGCGTGTATCGATGGAAGTAACCAACAACGGTGATACACCAGT
  		CACATTTGGTGAATTTACCACAGCAGGTATTCGTTTCGTTAACAGTACCG
  		GCCGCAAGTACCTGGATCCACAGTATCCTCGTGAACTGGTTGCAGTAGGC
  		TTGAATTTTGATGATGATGGTGCAATTCAGCCAGGCGAGACCAAGCAATT
  		GAGGATGGAAGCCAAAGATGCTCTGTGGGAAATCCAACGTCTGATGGCGT
  		TGCTGGGTGACCCGGAAAGCCGTTTTGGTGGACTGTTAATGTCTTGGGAT
  		TCAGAAGGTAATCGCCATATCAACAGTATTGCTGGTCCGGTGATTCCAGT
  		CTTTACCAAGCTCTAA
  SEQ ID	amoC2	MATTLGTSSASSVSSRGYDMSLWYDSKFYKFGLITMLLVAIFWVWYQRYF
  NO: 10	(D23_1c25	AYSHGMDSMEPEFDRVWMGLWRVHMAIMPLFALVTWGWIWKTRDTEEQLN
  (271	12)	NLDPKLEIKRYFYYMMWLGVYIFGVYWGGSFFTEQDASWHQVIIRDTSFT
  aa)	protein	PSHVVVFYGSFPMYIVCGVATYLYAMTRLPLFHRGISFPLVMAIAGPLMI
  		LPNVGLNEWGHAFWFMEELFSAPLHWGFVVLGWAGLFQGGVAAQIITRYS
  		NLTDVVWNNQSKEILNNRVVA
  SEQ ID	amoC2	ATGGCAACTACGTTAGGAACGAGCAGTGCCTCATCAGTCTCATCAAGAGG
  NO: 11	(D23_1c25	CTATGACATGTCACTGTGGTATGACTCCAAATTTTATAAATTTGGTTTAA
  (816	12) DNA	TAACCATGTTGTTGGTAGCGATATTCTGGGTATGGTATCAACGTTACTTT
  nt)		GCCTATTCACACGGAATGGATTCAATGGAACCAGAGTTTGACCGTGTATG
  		GATGGGCCTGTGGCGTGTGCACATGGCCATTATGCCGCTGTTTGCACTGG
  		TAACCTGGGGCTGGATCTGGAAAACACGTGATACAGAAGAGCAATTGAAT
  		AACCTGGATCCGAAACTGGAAATCAAACGCTACTTCTACTACATGATGTG
  		GCTGGGTGTATACATTTTTGGTGTTTACTGGGGTGGTAGCTTCTTTACGG
  		AGCAAGATGCCTCCTGGCACCAGGTGATTATTCGTGACACCAGCTTTACA
  		CCAAGTCACGTAGTCGTGTTTTATGGATCATTTCCGATGTACATCGTCTG
  		CGGAGTTGCAACCTATCTGTATGCAATGACCCGTCTGCCGCTGTTTCATC
  		GTGGAATTTCTTTCCCACTGGTGATGGCGATTGCAGGTCCTCTGATGATT
  		CTGCCAAACGTTGGTCTGAATGAATGGGGTCATGCTTTCTGGTTCATGGA
  		AGAGCTGTTCAGCGCACCGCTGCATTGGGGTTTTGTAGTGCTCGGTTGGG
  		CTGGGTTATTCCAGGGTGGAGTTGCTGCCCAAATCATTACCCGTTATTCC
  		AACCTGACTGACGTGGTCTGGAATAATCAAAGCAAAGAAATTCTGAATAA
  		CCGGGTTGTAGCTTAG
  SEQ ID	amoA2	VSIFRTEEILKAAKMPPEAVHMSRLIDAVYFPILVVLLVGTYHMHFMLLA
  NO: 12	(D23_1c25	GDWDFWMDWKDRQWWPVVTPIVGITYCSAIMYYLWVNYRQPFGATLCVVC
  (276	11)	LLIGEWLTRYWGFYWWSHYPLNFVTPGIMLPGALMLDFTMYLTRNWLVTA
  aa)	protein	LVGGGFFGLLFYPGNWAIFGPTHLPIVVEGTLLSMADYMGHLYVRTGTPE
  		YVRHIEQGSLRTFGGHTTVIAAFFAAFVSMLMFAVWWYLGKVYCTAFFYV
  		KGKRGRIVQRNDVTAFGEEGFPEGIK
  SEQ ID	amoA2	GTGAGTATATTTAGAACAGAAGAGATCCTGAAAGCGGCCAAGATGCCGCC
  NO: 13	(D23_1c25	GGAAGCGGTCCATATGTCACGCCTGATTGATGCGGTTTATTTTCCGATTC
  (831	11) DNA	TGGTTGTTCTGTTGGTAGGTACCTACCATATGCACTTCATGTTGTTGGCA
  nt)		GGTGACTGGGATTTCTGGATGGACTGGAAAGATCGTCAATGGTGGCCTGT
  		AGTAACACCTATTGTAGGCATTACCTATTGCTCGGCAATTATGTATTACC
  		TGTGGGTCAACTACCGTCAACCATTTGGTGCGACTCTGTGCGTAGTGTGT
  		TTGCTGATAGGTGAGTGGCTGACACGTTACTGGGGTTTCTACTGGTGGTC
  		ACACTATCCACTCAATTTTGTAACCCCAGGTATCATGCTCCCGGGTGCAT
  		TGATGTTGGATTTCACAATGTATCTGACACGTAACTGGTTGGTGACTGCA
  		TTGGTTGGGGGTGGATTCTTTGGTCTGCTGTTTTACCCGGGTAACTGGGC
  		AATCTTTGGTCCGACCCATCTGCCAATCGTTGTAGAAGGAACACTGTTGT
  		CGATGGCTGACTATATGGGTCACCTGTATGTTCGTACGGGTACACCTGAG
  		TATGTTCGTCATATTGAACAAGGTTCATTACGTACCTTTGGTGGTCACAC
  		CACAGTTATTGCAGCATTCTTCGCTGCGTTTGTATCCATGCTGATGTTTG
  		CAGTCTGGTGGTATCTTGGAAAAGTTTACTGCACAGCCTTCTTCTACGTT
  		AAAGGTAAAAGAGGACGTATCGTGCAGCGCAATGATGTTACGGCATTTGG
  		TGAAGAAGGGTTTCCAGAGGGGATCAAATAA
  SEQ ID	amoB2	MGIKNLYKRGMMGLCGVAVYAMAALTMTVTLDVSTVAAHGERSQEPFLRM
  NO: 14	(D23_1c25	RTVQWYDVKWGPEVTKVNENAQITGKFHLAEDWPRAAARPDFAFFNVGSP
  (421	10)	SSVYVRLSTKINGHPWFISGPLQIGRDYAFEVQLRARIPGRHHMHAMLNV
  aa)	protein	KDAGPIAGPGAWMNITGSWDDFTNPLKLLTGETIDSETFNLSNGIFWHIL
  		WMSIGIFWIGIFVARPMFLPRSRVLLAYGDDLLLDPMDKKITWVLAILTL
  		AIVWGGYRYTETKHPYTVPIQAGQSKVAPLPVAPNPVAIKITDANYDVPG
  		RALRVSMEVTNNGDTPVTFGEFTTAGIRFVNSTGRKYLDPQYPRELVAVG
  		LNFDDDGAIQPGETKQLRMEAKDALWEIQRLMALLGDPESRFGGLLMSWD
  		SEGNRHINSIAGPVIPVFTKL
  SEQ ID	amoB2	ATGGGTATCAAGAACCTTTATAAACGTGGAATGATGGGACTTTGTGGCGT
  NO: 15	(D23_1c25	TGCTGTTTATGCAATGGCGGCACTGACCATGACAGTGACACTAGATGTCT
  (1266	10) DNA	CAACAGTAGCAGCCCATGGAGAACGATCCCAGGAACCGTTTCTTCGGATG
  nt)		CGTACAGTACAGTGGTACGATGTTAAGTGGGGTCCGGAAGTAACCAAAGT
  		CAATGAGAATGCCCAAATTACCGGCAAATTTCACTTGGCTGAAGACTGGC
  		CGCGTGCGGCAGCAAGACCGGATTTCGCATTCTTTAACGTAGGTAGCCCA
  		AGCTCGGTATACGTGCGTTTGAGTACGAAGATTAATGGCCACCCATGGTT
  		TATTTCAGGTCCGCTGCAAATTGGTCGTGACTATGCGTTCGAAGTTCAGC
  		TGAGAGCACGTATTCCAGGACGCCATCACATGCACGCCATGTTAAACGTT
  		AAAGATGCAGGTCCAATTGCAGGACCGGGTGCATGGATGAACATTACCGG
  		AAGCTGGGATGATTTTACTAATCCACTCAAGCTGCTGACAGGCGAAACAA
  		TTGACTCAGAAACATTCAACCTGTCAAACGGTATTTTCTGGCATATTCTC
  		TGGATGTCAATTGGTATATTTTGGATTGGTATCTTTGTAGCGCGTCCGAT
  		GTTCCTGCCACGTAGCCGGGTATTGCTCGCTTATGGTGATGATCTGTTGC
  		TGGATCCGATGGATAAGAAAATCACCTGGGTACTTGCAATCCTGACCTTG
  		GCTATAGTATGGGGTGGATACCGCTATACAGAAACCAAGCATCCATACAC
  		AGTACCTATCCAGGCTGGTCAATCCAAAGTTGCACCATTACCGGTAGCAC
  		CAAATCCGGTAGCAATCAAAATTACAGATGCTAACTATGACGTACCGGGA
  		CGTGCACTGCGTGTATCGATGGAAGTAACCAACAACGGTGATACACCAGT
  		CACATTTGGTGAATTTACCACAGCAGGTATTCGTTTCGTTAACAGTACCG
  		GCCGCAAGTACCTGGATCCACAGTATCCTCGTGAACTGGTTGCAGTAGGC
  		TTGAATTTTGATGATGATGGTGCAATTCAGCCAGGCGAGACCAAGCAATT
  		GAGGATGGAAGCCAAAGATGCTCTGTGGGAAATCCAACGTCTGATGGCGT
  		TGCTGGGTGACCCGGAAAGCCGTTTTGGTGGACTGTTAATGTCTTGGGAT
  		TCAGAAGGTAATCGCCATATCAACAGTATTGCTGGTCCGGTGATTCCAGT
  		CTTTACCAAGCTCTAA
  SEQ ID	amoC3	MATNILKDKAAQQVADKPTYDKSEWFDAKYYKFGLLPILAVAVMWVYFQR
  NO: 16	(D23_1c16	TYAYSHGMDSMEPEFDRIWMGLWRVQMAALPLIALFTWGWLYKTRNTAEQ
  (274	05)	LANLTPKQEIKRYFYFLMWLGVYIFAVYWGSSFFTEQDASWHQVIIRDTS
  aa)	protein	FTPSHIPLFYGSFPVYIIMGVSMIIYANTRLPLYNKGWSFPLIMTVAGPL
  		MSLPNVGLNEWGHAFWFMEELFSAPLHWGFVILAWAALFQGGLAVQIIAR
  		FSNLLDVEWNKQDRAILDDVVTAP
  SEQ ID	amoC3	ATGGCTACAAATATATTAAAAGACAAAGCTGCACAGCAGGTTGCTGATAA
  NO: 17	(D23_1c16	ACCAACTTATGATAAATCCGAGTGGTTTGATGCTAAATACTATAAATTCG
  (825	05) DNA	GGCTGCTACCTATCTTAGCTGTAGCTGTGATGTGGGTTTATTTCCAGCGC
  nt)		ACATACGCCTATTCTCACGGCATGGATTCAATGGAACCGGAATTTGACCG
  		GATCTGGATGGGCTTGTGGCGTGTTCAAATGGCCGCTCTGCCTCTTATAG
  		CACTTTTTACGTGGGGATGGTTATATAAAACCCGCAATACTGCAGAACAG
  		CTTGCCAATCTGACTCCAAAGCAGGAAATAAAGCGGTATTTCTATTTCCT
  		CATGTGGCTTGGGGTCTATATATTTGCAGTTTACTGGGGATCAAGCTTCT
  		TTACCGAGCAGGACGCTTCATGGCACCAGGTGATTATCAGGGATACAAGT
  		TTTACTCCTAGCCATATTCCTCTGTTTTATGGTTCATTCCCGGTATACAT
  		CATCATGGGAGTATCGATGATTATTTACGCCAACACCCGGTTGCCGCTGT
  		ACAACAAAGGGTGGTCATTCCCTCTGATCATGACCGTAGCAGGACCGTTG
  		ATGAGTCTGCCTAACGTTGGCCTGAACGAGTGGGGACACGCCTTCTGGTT
  		CATGGAAGAACTTTTCAGCGCACCGCTGCACTGGGGCTTCGTGATTCTGG
  		CTTGGGCTGCCCTGTTCCAGGGTGGGCTTGCAGTACAGATCATAGCTCGC
  		TTTTCCAACTTGCTTGACGTGGAGTGGAATAAACAAGACAGAGCCATATT
  		GGACGATGTCGTAACTGCTCCTTAA
  SEQ ID	hao1	MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY
  NO: 18	(D23_1c25	DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER
  (570	29)	KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN
  aa)	protein	NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH
  		LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA
  		EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM
  		SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT
  		RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM
  		DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ
  		LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR
  		AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG
  		MLLAGAIALIGWRKRKQTQA
  SEQ ID	hao1	ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT
  NO: 19	(D23_1c25	GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT
  (1713	29) DNA	ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT
  nt)		GATGCGCTGGTGAAGCGTTACAAGGATCCTGCACATGGTGCTGGCAAGGG
  		CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC
  		CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC
  		AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC
  		ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC
  		CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC
  		AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT
  		AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC
  		ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC
  		CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC
  		GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG
  		CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA
  		GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA
  		TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG
  		CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG
  		TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA
  		TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT
  		GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC
  		CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA
  		CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT
  		GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG
  		GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT
  		TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC
  		GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA
  		CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT
  		GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG
  		TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT
  		GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC
  		TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG
  		ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC
  		ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA
  		AACGCAAGCTTGA
  SEQ ID	hao2	MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY
  NO: 20	(D23_1c19	DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER
  (570	26)	KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN
  aa)	protein	NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH
  		LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA
  		EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM
  		SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT
  		RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM
  		DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ
  		LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR
  		AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG
  		MLLAGAIALIGWRKRKQTQA
  SEQ ID	hao2	ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT
  NO: 21	(D23_1c19	GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT
  (1713	26) DNA	ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT
  nt)		GATGCGCTGGTGAAGCGTTACAAGGATCCTGCACATGGTGCTGGCAAGGG
  		CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC
  		CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC
  		AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC
  		ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC
  		CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC
  		AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT
  		AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC
  		ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC
  		CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC
  		GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG
  		CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA
  		GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA
  		TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG
  		CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG
  		TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA
  		TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT
  		GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC
  		CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA
  		CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT
  		GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG
  		GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT
  		TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC
  		GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA
  		CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT
  		GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG
  		TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT
  		GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC
  		TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG
  		ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC
  		ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA
  		AACGCAAGCTTGA
  SEQ ID	hao3	MRLGEYLKGMLLCAGLLLIGPVQADISTVPDETYEALKLDRSKATPKETY
  NO: 22	(D23_1c17	DALVKRYKDPAHGAGKGTMGDYWEPIALSIYMDPSTFYKPPVSPKEIAER
  (570	88)	KDCVECHSDETPVWVRAWKRSTHANLDKIRNLKPEDPLFYKKGKLEEVEN
  aa)	protein	NLRSMGKLGEKEALKEVGCIDCHVDINAKKKADHTKDVRMPTADVCGTCH
  		LREFAERESERDTMIWPNGQWPDGRPSHALDYTANIETTVWAAMPQREVA
  		EGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNYEAYIM
  		SKHGKLAEMNRENWNWNVRLKDAFSKGGQTAPTCAACHMEYEGEYTHNIT
  		RKTRWANYPFVPGIAENITSDWSEARLDSWVVTCTQCHSERFARSYLDLM
  		DKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPAPEKPGFGIFTQ
  		LFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNR
  		AYVEIQDEYTKMQEMTALQARVNKLEGKKTSLLDLKGAGEKISLGGLGGG
  		MLLAGAIALIGWRKRKQTQA
  SEQ ID	hao3	ATGAGATTAGGGGAGTATTTGAAGGGGATGCTGCTGTGTGCGGGCCTGTT
  NO: 23	(D23_1c17	GTTGATTGGGCCGGTACAGGCGGATATATCGACGGTACCGGATGAGACGT
  (1713	88) DNA	ATGAAGCATTGAAGCTGGATCGCAGCAAAGCCACGCCGAAAGAGACCTAT
  nt)		GATGCGCTGGTGAAGCGTTACAAGGATCCTGCGCATGGTGCTGGCAAGGG
  		CACGATGGGAGACTACTGGGAACCGATAGCGCTTAGTATCTACATGGACC
  		CGAGCACCTTTTACAAACCACCGGTTTCCCCGAAAGAAATTGCTGAGCGC
  		AAAGACTGCGTTGAATGCCACTCTGATGAAACGCCGGTTTGGGTAAGAGC
  		ATGGAAACGCAGCACCCACGCCAACCTGGACAAAATACGCAACCTCAAGC
  		CGGAAGATCCGCTTTTTTACAAAAAAGGCAAGCTGGAAGAAGTTGAGAAC
  		AACCTGCGCTCCATGGGCAAACTTGGAGAGAAGGAAGCGCTCAAGGAAGT
  		AGGCTGTATTGACTGTCACGTTGACATCAACGCCAAAAAGAAAGCAGATC
  		ACACCAAAGACGTACGCATGCCTACAGCTGACGTTTGCGGAACCTGTCAC
  		CTGAGAGAATTTGCCGAGCGTGAATCCGAGCGTGACACCATGATCTGGCC
  		GAATGGCCAGTGGCCTGACGGACGTCCATCCCACGCACTGGACTACACAG
  		CCAACATTGAAACCACCGTTTGGGCAGCCATGCCGCAACGTGAAGTGGCA
  		GAAGGTTGCACCATGTGCCACACCAACCAGAACAAATGCGACAACTGCCA
  		TACCCGCCATGAATTTTCGGCGGCAGAATCCCGCAAACCGGAAGCCTGTG
  		CCACCTGTCACAGCGGCGTGGATCATAATAACTATGAAGCCTACATTATG
  		TCCAAGCACGGCAAACTGGCTGAAATGAACCGGGAGAACTGGAACTGGAA
  		TGTTCGTCTGAAAGACGCCTTCTCCAAAGGAGGTCAGACCGCACCGACCT
  		GTGCAGCCTGCCACATGGAATACGAAGGGGAATATACCCATAACATCACC
  		CGTAAGACCCGCTGGGCAAACTACCCGTTTGTTCCGGGGATTGCAGAAAA
  		CATCACCAGCGACTGGTCAGAAGCTCGTCTGGATTCCTGGGTTGTGACCT
  		GTACCCAATGTCACTCGGAACGGTTTGCCCGCTCCTACCTGGATCTCATG
  		GACAAAGGTACCCTGGAAGGGTTGGCTAAATACCAGGAAGCCAATGCCAT
  		TGTTCACAAAATGTATGAAGACGGCACCCTGACTGGTCAAAAAACCAATC
  		GTCCGAATCCACCGGCGCCAGAGAAACCGGGTTTTGGTATCTTCACCCAA
  		CTGTTCTGGTCCAAGGGTAACAACCCGGCCTCACTTGAACTGAAAGTGCT
  		GGAAATGGCAGAAAACAACCTGGCCAAAATGCACGTAGGACTGGCACACG
  		TTAATCCAGGTGGCTGGACATATACCGAAGGTTGGGGCCCGATGAACCGT
  		GCCTATGTTGAAATCCAGGATGAATACACCAAGATGCAGGAAATGACAGC
  		TCTGCAAGCGCGTGTTAACAAACTGGAAGGTAAAAAAACCAGCCTGCTTG
  		ACCTCAAGGGAGCGGGAGAAAAGATCTCGCTGGGAGGACTGGGAGGTGGC
  		ATGTTGCTGGCGGGAGCGATTGCTCTGATTGGCTGGCGTAAACGTAAGCA
  		AACGCAAGCTTGA
  SEQ ID	c554	MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA
  NO: 24	cycA1	HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI
  (235	(D23_1c25	DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ
  aa)	27)	DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK
  	protein	AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK
  SEQ ID	c554	ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT
  NO: 25	cycA1	GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA
  (708	(D23_1c25	AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC
  nt)	27) DNA	CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA
  		ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT
  		GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA
  		GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG
  		GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCCGGGCAAGCATTTG
  		AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA
  		GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG
  		GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG
  		TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA
  		GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA
  		ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG
  		GAAAATAG
  SEQ ID	cycA2	MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA
  NO: 26	(D23_1c19	HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI
  (235	24)	DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ
  aa)	protein	DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK
  		AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK
  SEQ ID	cycA2	ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT
  NO: 27	(D23_1c19	GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA
  (708	24) DNA	AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC
  nt)		CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA
  		ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT
  		GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA
  		GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG
  		GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCTGGGCAAGCATTTG
  		AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA
  		GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG
  		GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG
  		TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA
  		GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA
  		ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG
  		GAAAATAG
  SEQ ID	cycA3	MKIIIACGLVAAALFTLTSGQSLAADAPFEGRKKCSSCHKPQAQSWKHTA
  NO: 28	(D23_1c17	HAKAMESLKPNVKVEAKQKAKLDPTKDYTQDKDCVGCHVDGFGQKGGYTI
  (235	86)	DSPKPMLTGVGCESCHGPGRKYRGDHRKAGQAFEKSGKKAPRKTLASKGQ
  aa)	protein	DFNFEERCSACHLNYEGSPWKGAKPPYTPYTPEVDPKYTFKFDEMVKDVK
  		AMHEHYKLDGVFDGEPKFKFHDEFQANAKTAKKGK
  SEQ ID	cycA3	ATGAAAATAATAATAGCCTGCGGACTGGTTGCTGCAGCCCTGTTCACCCT
  NO: 29	(D23_1c17	GACAAGTGGGCAGAGTCTGGCAGCGGATGCTCCGTTTGAAGGTCGGAAAA
  (708	86) DNA	AGTGCAGTTCCTGTCACAAACCACAAGCCCAGTCGTGGAAACATACTGCC
  nt)		CACGCCAAGGCGATGGAATCGCTCAAGCCCAATGTCAAAGTGGAAGCCAA
  		ACAAAAAGCCAAACTGGATCCTACCAAGGACTACACCCAGGACAAAGACT
  		GCGTAGGTTGCCACGTGGATGGATTTGGCCAGAAAGGCGGCTACACGATA
  		GACTCCCCCAAACCCATGCTGACTGGCGTAGGCTGTGAATCCTGCCACGG
  		GCCTGGACGTAAATACCGGGGAGATCACCGCAAGGCTGGGCAAGCATTTG
  		AGAAATCGGGCAAAAAAGCGCCGCGCAAGACCCTGGCAAGCAAGGGGCAA
  		GACTTTAATTTTGAAGAACGTTGCAGCGCCTGCCATCTGAACTATGAAGG
  		GTCACCCTGGAAAGGAGCAAAACCTCCCTATACCCCGTATACACCGGAAG
  		TGGATCCGAAATACACCTTCAAGTTTGACGAGATGGTAAAAGACGTCAAA
  		GCCATGCACGAGCATTACAAACTGGATGGCGTATTTGACGGAGAGCCTAA
  		ATTCAAGTTCCATGACGAATTCCAGGCCAACGCTAAAACTGCCAAAAAAG
  		GAAAATAG
  SEQ ID	cM552	MTRLQKGSIGTLLTGALLGIALVAVVFGGEAALSTEEFCTSCHSMSYPQS
  NO: 30	cycB1	ELKESTHYGALGVNPTCKDCHIPQGIENFHLAVATHVVDGARELWLEMVN
  (239	(D23_1c19	DYSTLEKFNERRLEMAHDARMNLKKWDSITCRTCHVKPAPPGESAQAEHK
  aa)	23)	KMETEGATCIDCHQNLVHEEAPMTDLNASLAAGKLVLKPEEGDGDDDDDV
  	protein	DVDDEEEDEEVEVEVEETETADDSDSASSSNHDDDSDDE
  SEQ ID	cM552	ATGACTAGACTGCAAAAAGGATCAATTGGTACTTTACTGACAGGAGCTCT
  NO: 31	cycB1	GCTGGGAATAGCATTGGTGGCTGTGGTTTTTGGTGGGGAAGCTGCGTTAT
  (720	(D23_1c19	CGACCGAAGAGTTTTGTACCAGCTGTCATTCCATGTCATACCCACAGAGT
  nt)	23) DNA	GAATTAAAAGAATCCACCCACTATGGTGCATTGGGGGTTAATCCGACTTG
  		TAAAGACTGTCATATTCCACAAGGGATAGAAAATTTCCACCTGGCAGTAG
  		CAACTCACGTGGTTGATGGTGCCAGAGAACTTTGGTTGGAGATGGTCAAT
  		GACTACTCCACCCTGGAGAAGTTCAACGAAAGAAGATTGGAAATGGCGCA
  		TGATGCCCGGATGAACCTCAAGAAATGGGACAGCATCACCTGCCGTACCT
  		GTCATGTAAAACCAGCTCCTCCGGGAGAAAGCGCCCAGGCGGAACATAAG
  		AAAATGGAAACGGAAGGAGCAACCTGCATAGACTGTCATCAGAATCTGGT
  		GCATGAAGAAGCGCCGATGACAGATTTGAATGCAAGTCTTGCTGCAGGCA
  		AGCTGGTATTAAAGCCAGAAGAGGGTGACGGTGACGATGACGATGACGTT
  		GACGTTGATGACGAGGAGGAGGATGAAGAAGTCGAGGTGGAAGTTGAAGA
  		AACTGAAACAGCTGACGACAGCGACTCCGCTTCCTCCAGCAACCATGATG
  		ACGATAGTGATGATGAGTAA
  SEQ ID	cycB2	MTRLQKGSIGTLLTGALLGIALVAVVFGGEAALSTEEFCTSCHSMSYPQS
  NO: 32	(D23_1c25	ELKESTHYGALGVNPTCKDCHIPQGIENFHLAVATHVVDGARELWLEMVN
  (239	26)	DYSTLEKFNERRLEMAHDARMNLKKWDSITCRTCHVKPAPPGESAQAEHK
  aa)	protein	KMETEGATCIDCHQNLVHEEAPMTDLNASLAAGKLVLKPEEGDDDDDDDV
  		DVDDEEEDEEVEVEVEETETADDSDSASSSNHDDDSDDE
  SEQ ID	cycB2	ATGACTAGACTGCAAAAAGGATCAATTGGCACTTTACTGACAGGAGCTCT
  NO: 33	(D23_1c25	GCTGGGAATAGCATTGGTGGCTGTGGTTTTTGGTGGGGAAGCTGCGTTAT
  (720	26) DNA	CGACCGAAGAGTTTTGTACCAGCTGTCATTCCATGTCATACCCACAGAGT
  nt)		GAATTAAAAGAATCCACCCACTATGGTGCATTGGGGGTTAATCCGACTTG
  		TAAAGACTGTCATATTCCACAAGGGATAGAAAATTTCCACCTGGCAGTAG
  		CAACTCACGTGGTTGATGGTGCCAGAGAACTTTGGTTGGAGATGGTCAAT
  		GACTACTCCACCCTGGAGAAGTTCAACGAAAGAAGATTGGAAATGGCGCA
  		TGATGCCCGGATGAACCTCAAGAAATGGGACAGCATCACCTGCCGTACCT
  		GTCATGTAAAACCAGCTCCTCCGGGAGAAAGCGCCCAGGCGGAACATAAG
  		AAAATGGAAACGGAAGGAGCAACCTGCATAGACTGTCATCAGAATCTGGT
  		GCATGAAGAAGCGCCGATGACAGATTTGAATGCAAGTCTTGCTGCAGGCA
  		AGCTGGTATTAAAGCCAGAAGAGGGTGACGATGACGATGACGATGACGTT
  		GACGTTGATGACGAGGAGGAGGATGAAGAAGTCGAGGTGGAAGTTGAAGA
  		AACTGAAACAGCTGACGACAGCGACTCCGCTTCCTCCAGCAACCATGATG
  		ACGATAGTGATGATGAGTAA

INCORPORATION BY REFERENCE
• All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.
• While specific embodiments of the subject invention have been discussed, the above specification is illustrative and not restrictive. Many variations of the invention will become apparent to those skilled in the art upon review of this specification and the claims below. The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.
• Certain embodiments are within the following claims.

Claims (285)

What is claimed is:

1. A purified preparation of optimized Nitrosomonas eutropha (N. eutropha) bacterium having at least one property selected from:

an optimized growth rate;

an optimized NH₄ ⁺ oxidation rate; and

an optimized resistance to NH₄ ⁺.

2. The preparation of N. eutropha bacterium of claim 1, wherein the optimized growth rate is a rate allowing a continuous culture of N. eutropha at an OD600 (optical density at 600 nm) of about 0.15-0.18 to reach an OD600 of about 0.5-0.6 in about 1-2 days.

3. The preparation of N. eutropha bacterium of claim 1 or 2, wherein the optimized growth rate is a doubling time of about 8 hours when cultured under batch culture conditions.

4. The preparation of N. eutropha bacterium of any of claims 1-3, wherein the optimized NH₄ ⁺ oxidation rate is a rate of at least about 125 micromoles per minute of oxidizing NH₄ ⁺ to NO₂ ⁻.

5. The preparation of N. eutropha bacterium of any of claims 1-4, wherein the optimized resistance to NH₄ ⁺ is an ability to grow in medium comprising about 200 mM NH₄ ⁺ for at least about 48 hours.

6. The preparation of N. eutropha bacterium of any of claims 1-5, which has at least two properties selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

7. The preparation of N. eutropha bacterium of claim 1-6, which has an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

8. The preparation of N. eutropha bacterium of any of claims 1-7, which comprises a chromosome that hybridizes under very high stringency to SEQ ID NO: 1.

9. The preparation of N. eutropha bacterium of any of claim 1-8, which comprises an AmoA protein having an identity to SEQ ID NO: 6 or 12 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an AmoB protein having an identity to SEQ ID NO: 8 or 14 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, an amoC gene having an identity to SEQ ID NO: 4, 10, or 16 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a hydroxylamine oxidoreductase protein having an identity to SEQ ID NO: 18, 20, or 22 selected from at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, a cytochrome c554 protein having an identity to SEQ ID NO: 24, 26, or 28 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical, or a cytochrome c_M552 protein having an identity to SEQ ID NO: 30 or 32 selected from at least about 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, and 100% identical.

10. The preparation of N. eutropha bacterium of any of claims 1-9, which comprises 1-5, 5-10, 10-15, 15-20, 20-25, 25-30, or all of the sequence characteristics of Table 2.

11. The preparation of N. eutropha bacterium of claim 10, which comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 1, e.g., a V at position 1.

12. The preparation of N. eutropha bacterium of any of claims 10-11, which comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 160, e.g., an L at position 160.

13. The preparation of N. eutropha bacterium of any of claims 10-12, which comprises an AmoA1 or AmoA2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 167, e.g., an A at position 167.

14. The preparation of N. eutropha bacterium of any of claims 10-13, which comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 33, e.g., a V at position 33.

15. The preparation of N. eutropha bacterium of any of claims 10-14, which comprises an AmoB1 or AmoB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 165, e.g., an I at position 165.

16. The preparation of N. eutropha bacterium of any of claims 10-15, which comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 79, e.g., an A at position 79.

17. The preparation of N. eutropha bacterium of any of claims 10-16, which comprises an AmoC3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 271, e.g., a V at position 271.

18. The preparation of N. eutropha bacterium of any of claims 10-17, which comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 85, e.g., an S at position 85.

19. The preparation of N. eutropha bacterium of any of claims 10-18, which comprises a Hao1, Hao2, or Hao3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 312, e.g., an E at position 312.

20. The preparation of N. eutropha bacterium of any of claims 10-19, which comprises a Hao1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 163, e.g., an A at position 163.

21. The preparation of N. eutropha bacterium of any of claims 10-20, which comprises a c554 CycA1, c554 CycA2, or c554 CycA3 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 65, e.g., a T at position 65.

22. The preparation of N. eutropha bacterium of any of claims 10-21, which comprises a c554 CycA1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 186, e.g., a T at position 186.

23. The preparation of N. eutropha bacterium of any of claims 10-22, which comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 63, e.g., a V at position 63.

24. The preparation of N. eutropha bacterium of any of claims 10-23, which comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 189, e.g., a P at position 189.

25. The preparation of N. eutropha bacterium of any of claims 10-24, which comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 206, e.g., an insE at position 206.

26. The preparation of N. eutropha bacterium of any of claims 10-25, which comprises a c_M552 CycB1 or c_M552 CycB2 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 207, e.g., an insE at position 207.

27. The preparation of N. eutropha bacterium of any of claims 10-26, which comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 195, e.g., an insD at position 195.

28. The preparation of N. eutropha bacterium of any of claims 10-27, which comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 196, e.g., an insD at position 196.

29. The preparation of N. eutropha bacterium of any of claims 10-28, which comprises a c_M552 CycB1 protein having (or gene encoding) a mutation relative to N. eutropha strain C91 at position 197, e.g., an insD at position 197.

30. The preparation of N. eutropha bacterium of any of the preceding claims, which comprises at least one structural difference, e.g., at least one mutation, relative to a wild-type bacterium such as N. eutropha strain C91.

31. The preparation of N. eutropha bacterium of any of the preceding claims, which comprises a nucleic acid that can be amplified using a pair of primers described herein, e.g., a primer comprising a sequence of SEQ ID NO: 64 and a primer comprising a sequence of SEQ ID NO: 65.

32. The preparation of N. eutropha bacterium of any of the preceding claims, which comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a gene of FIG. 6 or a protein encoded by a gene of FIG. 6.

33. The preparation of N. eutropha bacterium of any of the preceding claims, which comprises a nucleic acid or protein at least 80%, 85%, 90%, 95%, 98%, 99%, 99.5%, or 100% identical to a sequence of any of SEQ ID NOS: 64-66 or a protein encoded by a sequence of any of SEQ ID NOS: 64-66.

34. An N. eutropha bacterium, or a purified preparation thereof, comprising a mutation in an ammonia monooxygenase gene, a hydroxylamine oxidoreductase gene, a cytochrome c554 gene, or a cytochrome c_m552 gene relative to a wild-type bacterium such as N. eutropha strain C91.

35. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the amoA1 gene.

36. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the amoA2 gene.

37. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the amoB1 gene.

38. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the amoB2 gene.

39. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the amoC3 gene.

40. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 34-39, wherein said mutation is at a position described herein, e.g., in Table 2.

41. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 34-39, wherein said mutation is a mutation described herein, e.g., in Table 2.

42. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the hao1 gene.

43. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the hao2 gene.

44. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the hao3 gene.

45. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 42-44, wherein said mutation is at a position described herein, e.g., in Table 2.

46. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 42-44, wherein said mutation is a mutation described herein, e.g., in Table 2.

47. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the c554 cycA1 gene.

48. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the c554 cycA2 gene.

49. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the c554 cycA3 gene.

50. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 47-49, wherein said mutation is at a position described herein, e.g., in Table 2.

51. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 47-49, wherein said mutation is a mutation described herein, e.g., in Table 2.

52. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the c_M552 cycB1 gene.

53. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, wherein said mutation is in the c554 cycB2 gene.

54. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 52-53, wherein said mutation is at a position described herein, e.g., in Table 2.

55. The N. eutropha bacterium, or a purified preparation thereof, of any of claims 52-53, wherein said mutation is a mutation described herein, e.g., in Table 2.

56. The purified preparation of optimized N. eutropha bacterium of claim 1, comprising a mutation in an ammonia monooxygenase gene, a hydroxylamine oxidoreductase gene, a cytochrome c554 gene, or a cytochrome c_m552 gene.

57. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the amoA1 gene.

58. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the amoA2 gene.

59. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the amoB1 gene.

60. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the amoB2 gene.

61. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the amoC3 gene.

62. The purified preparation of optimized N. eutropha bacterium of any of claims 57-61, wherein said mutation is at a position described herein, e.g., in Table 2.

63. The purified preparation of optimized N. eutropha bacterium of any of claims 57-61, wherein said mutation is a mutation described herein, e.g., in Table 2.

64. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the hao1 gene.

65. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the hao2 gene.

66. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the hao3 gene.

67. The purified preparation of optimized N. eutropha bacterium of any of claims 64-66, wherein said mutation is at a position described herein, e.g., in Table 2.

68. The purified preparation of optimized N. eutropha bacterium of any of claims 64-66, wherein said mutation is a mutation described herein, e.g., in Table 2.

69. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the c554 cycA1 gene.

70. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the c554 cycA2 gene.

71. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the c554 cycA3 gene.

72. The purified preparation of optimized N. eutropha bacterium of any of claims 69-71, wherein said mutation is at a position described herein, e.g., in Table 2.

73. The purified preparation of optimized N. eutropha bacterium of any of claims 69-71, wherein said mutation is a mutation described herein, e.g., in Table 2.

74. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the c_M552 cycB1 gene.

75. The purified preparation of optimized N. eutropha bacterium of claim 56, wherein said mutation is in the c_M552 cycB2 gene.

76. The purified preparation of optimized N. eutropha bacterium of any of claims 56, 74, and 75, wherein said mutation is at a position described herein, e.g., in Table 2.

77. The purified preparation of optimized N. eutropha bacterium of any of claims 56, 74, and 75, wherein said mutation is a mutation described herein, e.g., in Table 2.

78. The N. eutropha bacterium, or a purified preparation thereof, of claim 34, which has a mutation in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 positions of one or more of amoA1 gene, amoA2 gene, amoB1 gene, amoB2 gene, amoC3 gene, hao1 gene, hao2 gene, hao3 gene, c554 cycA1 gene, c554 cycA2 gene, c554 cycA3 gene, c_M552 cycB1 gene, and c554 cycB2 gene.

79. The purified preparation of optimized N. eutropha bacterium of claim 56, which has a mutation in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 positions of one or more of amoA1 gene, amoA2 gene, amoB1 gene, amoB2 gene, amoC3 gene, hao1 gene, hao2 gene, hao3 gene, c554 cycA1 gene, c554 cycA2 gene, c554 cycA3 gene, c_M552 cycB1 gene, and c554 cycB2 gene.

80. A N. eutropha bacterium comprising a chromosome that hybridizes at high stringency to SEQ ID NO: 1.

81. The N. eutropha bacterium of claim 80, wherein the chromosome hybridizes at very high stringency to SEQ ID NO: 1.

82. The N. eutropha bacterium of claim 80 or 81, which comprises at least one of the genes of FIGS. 6-8, or a gene with at least 80% identity thereto.

83. The N. eutropha bacterium of claim 80 or 81, which comprises at least one of the genes of FIGS. 6-8.

84. The N. eutropha bacterium of any of claims 80-82, which lacks any plasmid that is at least about 80% identical to SEQ ID NO: 2 or SEQ ID NO: 3.

85. The N. eutropha bacterium of claim any of claims 80-84, which lacks any plasmid.

86. A N. eutropha bacterium comprising one or more of an AmoA1 gene at least about 98.9% identical to SEQ ID NO: 7 and an amoA2 gene at least about 98.8% identical to SEQ ID NO: 13.

87. A N. eutropha bacterium comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.

88. A N. eutropha bacterium comprising one or more of an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9 and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.

89. The N. eutropha bacterium of claim 88, further comprising one or more of an AmoA1 or amoA2 gene at least about 98.9% identical to SEQ ID NO: 7 or 13.

90. An N. eutropha bacterium comprising one or more of an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8 or an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.

91. The N. eutropha bacterium of claim 90, further comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6 and an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12.

92. An N. eutropha bacterium comprising one or more of an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.

93. The N. eutropha bacterium of claim 92, further comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, and an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15.

94. A N. eutropha bacterium comprising an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.

95. The N. eutropha bacterium of claim 94, further comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, and an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14.

96. A N. eutropha bacterium comprising one or more of a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.

97. The N. eutropha bacterium of claim 96, further comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, and an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17.

98. A N. eutropha bacterium comprising one or more of a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.

99. The N. eutropha bacterium of claim 98, further comprising an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, or an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16.

100. An N. eutropha bacterium comprising one or more of a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.

101. The N. eutropha bacterium of claim 100, further comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, and a hao3 gene at least about 99.3% identical to SEQ ID NO: 23.

102. An N. eutropha bacterium comprising one or more of a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.

103. The N. eutropha bacterium of claim 102, further comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, and a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22.

104. A N. eutropha bacterium comprising one or more of a cycB1 gene at least about 96.8% identical to SEQ ID NO: 31 and a cycB2 gene at least about 97.2% identical to SEQ ID NO: 33.

105. The N. eutropha bacterium of claim 104, further comprising one or more of an amoA1 gene at least about 98.9% identical to SEQ ID NO: 7, an amo2 gene at least about 98.9% identical to SEQ ID NO: 13, an amoB1 gene at least about 99.2% identical to SEQ ID NO: 9, an amoB2 gene at least about 99.2% identical to SEQ ID NO: 15, an amoC1 gene at least about 99.9% identical to SEQ ID NO: 5, an amoC2 gene at least about 99.9% identical to SEQ ID NO: 11, an amoC3 gene at least about 99.0% identical to SEQ ID NO: 17, a hao1 gene at least about 99.1% identical to SEQ ID NO: 19, a hao2 gene at least about 99.5% identical to SEQ ID NO: 21, a hao3 gene at least about 99.3% identical to SEQ ID NO: 23, a cycA1 gene at least about 98.1% identical to SEQ ID NO: 25, a cycA2 gene at least about 98.8% identical to SEQ ID NO: 27, and a cycA3 gene at least about 99.4% identical to SEQ ID NO: 28.

106. A N. eutropha bacterium comprising one or more of a CycB1 protein at least about 97.2% identical to SEQ ID NO: 30 or a CycB2 protein at least about 98.8% identical to SEQ ID NO: 32.

107. The N. eutropha bacterium of claim 106, further comprising one or more of an AmoA1 protein at least about 99.0% identical to SEQ ID NO: 6, an AmoA2 protein at least about 99.0% identical to SEQ ID NO: 12, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 8, an AmoB1 protein at least about 99.6% identical to SEQ ID NO: 14, an AmoC3 protein at least about 99.4% identical to SEQ ID NO: 16, a Hao1 protein at least about 99.6% identical to SEQ ID NO: 18, a Hao2 protein at least about 99.7% identical to SEQ ID NO: 20, a Hao3 protein at least about 99.7% identical to SEQ ID NO: 22, a CycA1 protein at least about 99.2% identical to SEQ ID NO: 24, a CycA2 protein at least about 99.7% identical to SEQ ID NO: 26, and a CycA3 protein at least about 99.7% identical to SEQ ID NO: 28.

108. A N. eutropha bacterium comprising one or more genes according to SEQ ID NOS: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, and 33.

109. A N. eutropha bacterium comprising one or more proteins according to SEQ ID NOS: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, and 32.

110. A N. eutropha bacterium comprising a protein that is mutant relative to N. eutropha strain C91 at at least 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, or all of the amino acid positions listed in Table 2.

111. A N. eutropha bacterium comprising proteins that are mutant relative to N. eutropha strain C91 at all of the amino acid positions listed in Table 2.

112. The N. eutropha bacterium of any one of claims 1-111, which is transgenic.

113. The N. eutropha bacterium of any one of claims 80-112, having at least one property selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

114. The N. eutropha bacterium of claim 113, which has at least two properties selected from an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

115. The N. eutropha bacterium of claim 113, which has an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

116. A composition comprising the N. eutropha bacterium of any one of claims 1-115, wherein the composition is substantially free of other organisms.

117. A composition comprising the N. eutropha bacterium of one any of claims 1-115 and further comprising a second organism, wherein the composition is substantially free of other organisms.

118. The composition of claim 117, wherein the second organism is an ammonia oxidizing bacterium.

119. The composition of claim 117, wherein the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus, and Bifidobacter, and combinations thereof.

120. A composition comprising a cell suspension of an actively dividing culture of N. eutropha bacteria having an OD600 of at least about 0.2, wherein the composition is substantially free of other organisms.

121. A composition for topical administration, comprising the N. eutropha bacterium of any one of claims 1-115 and a pharmaceutically or cosmetically acceptable excipient suitable for topical administration.

122. The composition of claim 121, which is substantially free of other organisms.

123. The composition of claim 121, further comprising a second organism.

124. The composition of claim 123, wherein the second organism is an ammonia oxidizing bacterium.

125. The composition of claim 123, wherein the second organism is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, Lactobacillus, Streptococcus, and Bifidobacter, and combinations thereof.

126. The composition of any of claims 121-125, which is provided as or disposed in a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.

127. The composition of any of claims 121-126, which further comprises a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.

128. The composition of any of claims 121-127, wherein the excipient comprises an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener.

129. The composition of any of claims 121-128, wherein the concentration of N. eutropha in the composition is about 10¹¹-10¹² CFU/L.

130. The composition of any of claims 121-129, wherein the concentration of N. eutropha in the composition is about 10⁹ CFU/ml.

131. The composition of any of claims 121-130, wherein the mass ratio of N. eutropha to pharmaceutical excipient is in a range of about 0.1 grams per liter to about 1 gram per liter.

132. A composition comprising at least about 1,000 L at about 10¹² CFUs/L of the N. eutropha bacterium of any one of claims 1-115.

133. A composition comprising at least about 1, 2, 5, 10, 20, 50, 100, 200, or 500 g of the N. eutropha bacterium of any one of claims 1-115, e.g., as a dry formulation such as a powder.

134. An article of clothing comprising the N. eutropha of any one of claims 1-115, e.g., at a concentration that provides one or more of a treatment or prevention of a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth.

135. The article of clothing of claim 134, which is packaged.

136. The article of clothing of claim 134-135, which is packaged in a material that is resistant to gaseous exchange or resistant to water.

137. A cloth comprising the N. eutropha of any one of claims 1-115.

138. A yarn comprising the N. eutropha of any one of claims 1-115.

139. A thread comprising the N. eutropha of any one of claims 1-115.

140. A method of obtaining, e.g., manufacturing, an N. eutropha bacterium having an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, comprising:

(a) culturing the bacterium under conditions that select for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, thereby producing a culture;

(b) testing a sample from the culture for an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺; and

(c) repeating the culturing and testing steps until a bacterium having an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺ is obtained.

141. The method of claim 140, further comprising a step of obtaining an N. eutropha bacterium from a source.

142. The method of claim 141, wherein the source is soil or the skin of an individual.

143. The method of claim 142, wherein culturing the bacterium under conditions that select for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺ comprises culturing the bacterium in N. europae medium that comprises about 200 mM NH₄ ⁺.

144. The method of claim 143, which comprises a step of creating an axenic culture.

145. The method of claim 143 or 144, which comprises a step of co-culturing the N. eutropha together with at least one other type of ammonia oxidizing bacteria.

146. The method of any of claims 140-145, wherein the N. eutropha of step (a) lack an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺.

147. The method of any of claims 140-146, wherein step (c) comprises repeating the culturing and testing steps until a bacterium having at least two of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, and an optimized resistance to NH₄ ⁺ is obtained.

148. An N. eutropha bacterium produced by the method of any of claims 140-147.

149. A method of testing a preparation of N. eutropha, comprising:

assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺; and

if the N. eutropha has one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺, classifying the N. eutropha as accepted.

150. The method of claim 149, further comprising a step of testing the preparation for contaminating organisms.

151. The method of any of claims 149-150, further comprising a step of removing a sample from the preparation and conducting testing on the sample.

152. The method of any of claims 149-151, further comprising testing medium in which the N. eutropha is cultured.

153. The method of any of claims 149-152, further comprising packaging N. eutropha from the preparation into a package.

154. The method of any of claims 149-153, further comprising placing N. eutropha from the preparation into commerce.

155. A method of producing, e.g., manufacturing N. eutropha, comprising contacting N. eutropha with culture medium and culturing the N. eutropha until an OD600 of at least about 0.5 is reached.

156. The method of claim 155, further comprising assaying the N. eutropha and culture medium for contaminating organisms.

157. The method of any of claims 155-156, further comprising assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.

158. The method of any of claims 155-157, which comprises producing at least at least about 1,000 L per day at about 10¹² CFUs/L of N. eutropha.

159. A method of producing, e.g., manufacturing, N. eutropha, comprising contacting N. eutropha with culture medium and culturing the N. eutropha until about at least about 1,000 L at about 10¹² CFUs/L N. eutropha are produced.

160. The method of claim 159, further comprising a step of assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.

161. The method of any of claims 159-160, further comprising a step of testing the N. eutropha or culture medium for contaminating organisms.

162. The method of any of claims 159-161, wherein the N. eutropha brought into contact with the culture medium is an N. eutropha having one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.

163. A method of producing, e.g., manufacturing N. eutropha, comprising:

(a) contacting N. eutropha with a culture medium; and

(b) culturing the N. eutropha for 1-2 days, thereby creating a culture, until the culture reaches an OD600 of about 0.5-0.6.

164. The method of claim 163, further comprising a step of assaying the N. eutropha for one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.

165. The method of any of claims 163-164, further comprising a step of testing the culture for contaminating organisms.

166. The method of any of claims 163-165, wherein the N. eutropha of step (a) is an N. eutropha having one or more of an optimized growth rate, an optimized NH₄ ⁺ oxidation rate, or an optimized resistance to NH₄ ⁺.

167. The method of any of claims 163-166, which comprises producing at least at least about 1,000 L per day at about 10¹² CFUs/L of N. eutropha.

168. An N. eutropha bacterium produced by the method of any of claims 155-167.

169. A preparation of N. eutropha made by the method of any of claims 155-167.

170. The preparation of claim 169, wherein the preparation comprises at least about 0.1 to about 100 milligrams (mg) of N. eutropha.

171. A reaction mixture comprising N. eutropha at an optical density of about 0.5 to about 0.6.

172. A method of producing N. eutropha-bearing clothing, comprising contacting an article of clothing with of the N. eutropha of any one of claims 1-115.

173. The method of claim 172, which comprises producing at least 10, 100, or 1000 articles of clothing.

174. The method of claim 172, which comprises contacting the article of clothing with at least 10¹⁰ CFUs of N. eutropha.

175. The method of claim 172, further comprising packaging the clothing.

176. A method of obtaining a formulation of N. eutropha, combining contacting N. eutropha of any of claims 1-115 with a pharmaceutically or cosmetically acceptable excipient.

177. The method of claim 176, further comprising mixing the N. eutropha and the excipient.

178. The method of claim 176, which is performed under conditions that are substantially free of contaminating organisms.

179. A method of packaging N. eutropha, comprising assembling N. eutropha of any of claim 1-115 into a package.

180. The method of claim 179, wherein the package is resistant to gaseous exchange or resistant to water.

181. The method of claim 179, wherein the package is permeable to gaseous exchange, NH₃, NH₄ ⁺, or NO₂ ⁻.

182. A method of inhibiting microbial growth on a subject's skin, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria of any one of claims 1-115.

183. The method of claim 182, wherein the effective dose is approximately 1.5×10¹⁰ CFU.

184. The method of any of claims 182-183, wherein the administration is performed twice per day.

185. The method of any of claims 182-184, wherein the subject is a human.

186. The method of any of claims 182-185, wherein the microbial growth to be inhibited is growth of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, or Acinetobacter baumannii.

187. A method of supplying nitric oxide to a subject, comprising positioning an effective dose of the N. eutropha bacteria of any one of claims 1-115 in close proximity to the subject.

188. A method of reducing body odor, comprising topically administering to a subject in need thereof an effective dose of the N. eutropha bacteria of any one of claims 1-115.

189. A method of treating a disease associated with low nitrite levels, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria of any of claims 1-115.

190. The method of claim 189, wherein the disease is HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, or cancer.

191. A method of treating a skin disorder, comprising topically administering to a subject in need thereof a therapeutically effective dose of the N. eutropha bacteria of any of claims 1-115.

192. The method of claim 191, wherein the skin disorder is acne, e.g., acne vulgaris, rosacea, eczema, or psoriasis.

193. The method of claim 191, wherein the skin disorder is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer.

194. The method of any one of claims 191-193, wherein topically administering comprises pre-treating the subject with N. eutropha, e.g., an N. eutropha of any of claims 1-115.

195. The method of any one of claims 191-194, wherein topically administering comprises topically administering prior to occurrence of the skin disorder.

196. The method of any one of claims 191-195, wherein topically administering comprises topically administering subsequent to occurrence of the skin disorder.

197. A method of promoting wound healing or closure, comprising administering to a wound an effective dose of the N. eutropha bacteria of any of claims 1-115.

198. The method of claim 197, wherein the wound comprises one or more undesirable bacteria, e.g., pathogenic bacteria.

199. The method of claim 197, wherein the wound comprises Staphylococcus aureus, Pseudomonas aeruginosa, or Acinetobacter baumannii.

200. The method of claim 197, wherein the N. eutropha is administered to the subject prior to occurrence of the wound.

201. The method of claim 197, wherein administering to the wound comprises administering to the subject prior to occurrence of the wound.

202. The method of any one of claims 197-201, further comprising administering N. eutropha to the wound subsequent to occurrence of the wound.

203. A method of killing or inhibiting growth of pathogenic bacteria comprising contacting, e.g., applying, N. eutropha bacteria, e.g., an N. eutropha bacterium of any of claims 1-115, to the skin.

204. The method of claim 203, wherein the pathogenic bacteria contribute to one or more of the following conditions: HIV dermatitis, an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.

205. The method of claim 204, wherein the condition is an ulcer, e.g., venous ulcer, e.g., leg ulcer, e.g., venous leg ulcer, e.g., infection in a diabetic foot ulcer.

206. The method of claim 204, wherein the condition is a venous leg ulcer.

207. The method of claim 204, wherein the condition is acne, e.g., acne vulgaris.

208. The method of claim 204, wherein the condition is acne vulgaris.

209. The method of any one of claims 203-208, wherein the pathogenic bacteria is one or more of Propionibacterium acnes, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, or Acinetobacter baumannii.

210. The method of any one of claims 203-209, further comprising determining whether the subject is in need of killing or inhibiting growth of pathogenic bacteria, e.g., determining that the subject is in need of killing or inhibiting growth of pathogenic bacteria.

211. The method of any one of claims 203-210, further comprising selecting the subject in need of killing or inhibiting growth of pathogenic bacteria.

212. A method of changing a composition of a skin microbiome of a subject comprising:

administering, e.g., applying, a preparation comprising ammonia oxidizing bacteria to a surface of the skin,

wherein the amount and frequency of administration, e.g., application, is sufficient to reduce the proportion of pathogenic bacteria on the surface of the skin.

213. The method of claim 212, further comprising, selecting the subject on the basis of the subject being in need of a reduction in the proportion of pathogenic bacteria on the surface of the skin.

214. The method of any one of claims 212-213, wherein the preparation comprises at least one of ammonia, ammonium salts, and urea.

215. The method of any one of claims 212-214, wherein the preparation comprises a controlled release material, e.g., slow release material.

216. The method of any one of claims 212-215, wherein the preparation of ammonia oxidizing bacteria, further comprises an excipient, e.g., one of a pharmaceutically acceptable excipient or a cosmetically acceptable excipient.

217. The method of claim 216, wherein the excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient, is suitable for one of topical, nasal, pulmonary, and gastrointestinal administration.

218. The method of any one of claims 216-217, wherein the excipient, e.g., one of the pharmaceutically acceptable excipient and the cosmetically acceptable excipient, is a surfactant.

219. The method of claim 218, wherein the surfactant is selected from the group consisting of cocamidopropyl betaine (ColaTeric COAB), polyethylene sorbitol ester (e.g., Tween 80), ethoxylated lauryl alcohol (RhodaSurf 6 NAT), sodium laureth sulfate/lauryl glucoside/cocamidopropyl betaine (Plantapon 611 L UP), sodium laureth sulfate (e.g., RhodaPex ESB 70 NAT), alkyl polyglucoside (e.g., Plantaren 2000 N UP), sodium laureth sulfate (Plantaren 200), Dr. Bronner's Castile soap, Lauramine oxide (ColaLux Lo), sodium dodecyl sulfate (SDS), polysulfonate alkyl polyglucoside (PolySufanate 160 P), sodium lauryl sulfate (Stepanol-WA Extra K), and any combination thereof.

220. The method of any one of claims 212-219, wherein the preparation is substantially free of other organisms.

221. The method of any one of claims 212-220, wherein the preparation is disposed in a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.

222. The method of any one of claims 212-221, wherein the preparation is provided as a powder, cosmetic, cream, stick, aerosol, salve, wipe, or bandage.

223. The method of any one of claims 212-222, wherein the preparation comprises a moisturizing agent, deodorizing agent, scent, colorant, insect repellant, cleansing agent, or UV-blocking agent.

224. The method of any one of claims 216-217, wherein the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient, comprises an anti-adherent, binder, coat, disintegrant, filler, flavor, color, lubricant, glidant, sorbent, preservative, or sweetener.

225. The method of any one of claims 212-224, wherein the preparation comprising ammonia oxidizing bacteria comprises about 10⁸ to about 10¹⁴ CFU/L.

226. The method of claim 225, wherein the preparation comprises between about 1×10⁹ CFU/L to about 10×10⁹ CFU/L.

227. The method of any one of claims 212-226, wherein the preparation comprising ammonia oxidizing bacteria comprises between about 50 milligrams (mg) and about 1000 mg of ammonia oxidizing bacteria.

228. The method of any one of claims 216-227, wherein the mass ratio of ammonia oxidizing bacteria to the excipient, e.g., the pharmaceutically acceptable excipient or the cosmetically acceptable excipient is in a range of about 0.1 grams per liter to about 1 gram per liter.

229. The method of any one of claims 212-228, wherein the preparation of ammonia oxidizing bacteria are useful for treating or preventing a skin disorder, a treatment or prevention of a disease or condition associated with low nitrite levels, a treatment or prevention of body odor, a treatment to supply nitric oxide to a subject, or a treatment to inhibit microbial growth, e.g., pathogenic bacterial growth.

230. The method of any one of claims 212-229, wherein the ammonia oxidizing bacteria is selected from the group consisting of Nitrosomonas, Nitrosococcus, Nitrosospria, Nitrosocystis, Nitrosolobus, Nitrosovibrio, and combinations thereof.

231. The method of any one of claims 212-230, wherein the preparation comprises an organism selected from the group consisting of Lactobacillus, Streptococcus, Bifidobacter, and combinations thereof.

232. The method of any one of claims 212-230, wherein the preparation is substantially free of organisms other than ammonia oxidizing bacteria.

233. The method of any one of claims 212-232, wherein the preparation of ammonia oxidizing bacteria comprises ammonia oxidizing bacteria in a growth state.

234. The method of any one of claims 212-232, wherein the preparation of ammonia oxidizing bacteria comprises ammonia oxidizing bacteria in a storage state.

235. The method of any one of claims 212-234, to deliver a cosmetic product.

236. The method of any one of claims 212-234, to deliver a therapeutic product.

237. The method of any one of claims 212-236, wherein the preparation is useful for treatment of at least one of HIV dermatitis, infection in a diabetic foot ulcer, atopic dermatitis, acne, e.g., acne vulgaris, eczema, contact dermatitis, allergic reaction, psoriasis, uticaria, rosacea, skin infections, vascular disease, vaginal yeast infection, a sexually transmitted disease, heart disease, atherosclerosis, baldness, leg ulcers secondary to diabetes or confinement to bed, angina, particularly chronic, stable angina pectoris, ischemic diseases, congestive heart failure, myocardial infarction, ischemia reperfusion injury, laminitis, hypertension, hypertrophic organ degeneration, Raynaud's phenomenon, fibrosis, fibrotic organ degeneration, allergies, autoimmune sensitization, end stage renal disease, obesity, impotence, pneumonia, primary immunodeficiency, epidermal lysis bulosa, or cancer.

238. The method of claim 237, wherein the preparation is useful for treatment of at least one of acne, e.g., acne vulgaris, eczema, psoriasis, uticaria, rosacea, and skin infections.

239. The method of any one of claims 212-238, wherein the preparation is provided in a container, the preparation and the container having a weight of less than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 grams.

240. The method of any one of claims 212-239, wherein the preparation has less than about 0.1% to about 10% of surfactant.

241. The method of any one of claims 212-240, wherein the preparation is substantially free of surfactant.

242. The method of any one of claims 212-241, wherein the preparation comprises a chelator.

243. The method of any one of claims 212-242, wherein the preparation is applied about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 times per day.

244. The method of any one of claims 212-243, wherein the preparation is applied one time per day.

245. The method of any one of claims 212-243, wherein the preparation is applied two times per day.

246. The method of any one of claims 212-245, wherein the preparation is applied for about 1-3, 3-5, 5-7, 7-9, 5-10, 10-14, 12-18, 12-21, 21-28, 28-35, 35-42, 42-49, 49-56, 46-63, 63-70, 70-77, 77-84, or 84-91 days.

247. The method of any one of claims 212-246, wherein the preparation is applied for about 16 days.

248. The method of any one of claims 212-247 further comprising obtaining a sample from the surface of the skin.

249. The method of claim 248, further comprising isolating DNA of bacteria in the sample.

250. The method of any one of claims 248-249, further comprising sequencing DNA of bacteria in the sample.

251. The method of any one of claims 212-250, wherein administering the ammonia oxidizing bacteria provides for an increase in the proportion of non-pathogenic bacteria on the surface.

252. The method of claim 251, wherein the non-pathogenic bacteria is commensal non-pathogenic bacteria.

253. The method of claim 252, wherein the non-pathogenic bacteria is commensal non-pathogenic bacteria of the genus Staphylococcus.

254. The method of claim 253, wherein the non-pathogenic bacteria is commensal non-pathogenic bacteria Staphylococcus epidermidis.

255. The method of any one of claims 252-254, wherein the non-pathogenic bacteria of the genus Staphylococcus is, or is identified as being, increased after about 2 weeks.

256. The method of claim 255, wherein the non-pathogenic bacteria Staphylococcus epidermidis is, or is identified as being, increased after about 2 weeks.

257. The method of any one of claims 212-256, wherein potentially pathogenic or disease associated Propionibacteria is, or is identified as being, reduced after about 2 weeks.

258. The method of any one of claims 212-257, wherein potentially pathogenic or disease associated Stenotrophomonas is, or is identified as being, reduced after about 2 weeks.

259. The method of any one of claims 212-258, wherein the surface of the skin comprises a wound.

260. A method of treating acne e.g., acne vulgaris, by the method of any one of claims 212-259.

261. A method of treating eczema by the method of any one of claims 212-259.

262. A method of treating psoriasis by the method of any one of claims 212-259.

263. A method of treating uticaria by the method of any one of claims 212-259.

264. A method of treating rosacea by the method of any one of claims 212-259.

265. A method of treating a skin infection by the method of any one of claims 212-259.

266. A method of reducing an amount of undesirable bacteria on a surface of a subject by the method of any one of claims 212-258.

267. A nucleic acid comprising a sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66, or a reverse complement thereof, provided that the nucleic acid has a non-naturally occurring sequence, or another modification, e.g., a label, or both.

268. The nucleic acid of claim 267, wherein the sequence of 15-100 consecutive nucleotides is a sequence not found in N. Eutropha strain C91.

269. The nucleic acid of claim 267 or 268, further comprising a heterologous sequence 5′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66.

270. The nucleic acid of claim 267 or 268, further comprising a heterologous sequence 3′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66.

271. The nucleic acid of claim 267 or 268, further comprising a first heterologous sequence 5′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66 and a second heterologous sequence 3′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66.

272. The nucleic acid of any of claims 267-271, which has a length of 15-20, 20-25, 25-30, 30-24, or 25-40 nucleotides.

273. The nucleic acid of any of claims 267-272, which is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label.

274. A composition comprising:

a first nucleic acid comprising 15-100 consecutive nucleotides from within SEQ ID NO: 66; and

a second nucleic acid comprising 15-100 consecutive nucleotides from within a reverse complement of SEQ ID NO: 66,

provided that the first nucleic acid or the second nucleic acid or both has a non-naturally occurring sequence or a modification such as a label, or both.

275. The composition of claim 274, wherein the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid does not comprise a sequence found in N. Eutropha strain C91.

276. The composition of claim 274 or 275, wherein the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 5′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66.

277. The composition of any of claims 274-276, wherein the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid further comprises a heterologous sequence 3′ to the sequence of 15-100 consecutive nucleotides from within SEQ ID NO: 66.

278. The composition of any of claims 274-277, wherein the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid has a length of 15-20, 20-25, 25-30, 30-24, or 25-40 nucleotides.

279. The composition of any of claims 274-278, wherein the first nucleic acid, the second nucleic acid, or each of the first nucleic acid and second nucleic acid is bound, e.g., covalently bound, to a detectable label, e.g., a fluorescent label.

280. A nucleic acid consisting of the sequence AATCTGTCTCCACAGGCAGC (SEQ ID NO: 64).

281. A nucleic acid consisting of the sequence TATACCCACCACCCACGCTA (SEQ ID NO: 65).

282. A molecule comprising the nucleic acid of claim 280 or 281 and a detectable label, e.g., a fluorescent label.

283. A composition comprising a first nucleic acid consisting of the sequence AATCTGTCTCCACAGGCAGC (SEQ ID NO: 64) and a second nucleic acid consisting of the sequence TATACCCACCACCCACGCTA (SEQ ID NO: 65).

284. A composition comprising:

a first molecule comprising (i) a first nucleic acid consisting of the sequence AATCTGTCTCCACAGGCAGC (SEQ ID NO: 64) and optionally comprising (ii) a detectable label, e.g., a fluorescent label; and

a second molecule comprising (i) a second nucleic acid consisting of the sequence TATACCCACCACCCACGCTA (SEQ ID NO: 65) and optionally comprising (ii) a detectable label, e.g., a fluorescent label.

285. A method of detecting whether a D23 N. eutropha nucleic acid is present in a sample, comprising:

performing a polymerase chain reaction (PCR) on the sample using primers specific to N. eutropha D23, and

determining whether a PCR product is produced, wherein the presence of a PCR product indicates that the D23 N. eutropha nucleic acid was present in the sample.

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