WO1998024475A1 - Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof - Google Patents

Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof Download PDF

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Publication number
WO1998024475A1
WO1998024475A1 PCT/US1997/022104 US9722104W WO9824475A1 WO 1998024475 A1 WO1998024475 A1 WO 1998024475A1 US 9722104 W US9722104 W US 9722104W WO 9824475 A1 WO9824475 A1 WO 9824475A1
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WO
WIPO (PCT)
Prior art keywords
seq
pylori
polypeptide
nucleic acid
fragment
Prior art date
Application number
PCT/US1997/022104
Other languages
French (fr)
Inventor
Douglas Smith
Richard A. Alm
Peter C. Doig
Zita Kabok
Lillian Marie Castriotta
Original Assignee
Astra Aktiebolag
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to SK579-99A priority Critical patent/SK57999A3/en
Application filed by Astra Aktiebolag filed Critical Astra Aktiebolag
Priority to AU58954/98A priority patent/AU739641B2/en
Priority to EEP199900226A priority patent/EE9900226A/en
Priority to EP97954525A priority patent/EP0964699A4/en
Priority to NZ335633A priority patent/NZ335633A/en
Priority to BR9714133-0A priority patent/BR9714133A/en
Priority to CA002273199A priority patent/CA2273199A1/en
Priority to JP52575898A priority patent/JP2001510992A/en
Priority to IL12974697A priority patent/IL129746A0/en
Publication of WO1998024475A1 publication Critical patent/WO1998024475A1/en
Priority to NO992158A priority patent/NO992158L/en
Priority to IS5047A priority patent/IS5047A/en
Priority to US10/335,977 priority patent/US20040052799A1/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/205—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Campylobacter (G)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/02—Bacterial antigens
    • A61K2039/106—Vibrio; Campylobacter; Not used, see subgroups
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • H. pylori is a gram-negative, S-shaped, microaerophilic bacterium that was discovered and cultured from a human gastric biopsy specimen. (Warren, J.R. and B. Marshall, (1983) Lancet ⁇ : 1273-1275; and Marshall et al., (1984) Microbios Lett. 25: 83-88). H. pylori has been strongly linked to chronic gastritis and duodenal ulcer disease. (Rathbone et. al., (1986) Gut 27: 635-641).
  • H. pylori colonizes the human gastric mucosa, establishing an infection that usually persists for decades. Infection by H. pylori is prevalent worldwide. Developed countries have infection rates over 50% of the adult population, while developing countries have infection rates reaching 90% of the adults over the age of 20. (Hopkins R. J. and J. G. Morris (1994) Am. J. Med. 97: 265-277).
  • urease an enzyme that may play a role in neutralizing gastric acid pH
  • Ferrero R.L. and A. Lee (1991) Microb. Ecol. Hlth. Dis. 4: 121-134
  • Labigne et al. (1991) J. Bacteriol. 173: 1920-1931
  • the bacterial flagellar proteins responsible for motility across the mucous layer (Hazell et al., (1986) J. Inf. Dis.
  • This invention relates to novel genes, e.g., genes encoding polypeptides such as bacterial surface proteins, from the organism Helicobacter pylori (H pylori), and other related genes, their products, and uses thereof.
  • the nucleic acids and peptides of the present invention have utility for diagnostic and therapeutics for H. pylori and other Helicobacter species. They can also be used to detect the presence of H. pylori and other Helicobacter species in a sample; and for use in screening compounds for the ability to interfere with the H. pylori life cycle or to inhibit H. pylori infection. More specifically, this invention features compositions of nucleic acids corresponding to entire coding sequences of H.
  • H. pylori proteins including surface or secreted proteins or parts thereof, nucleic acids capable of binding mRNA from H. pylori proteins to block protein translation, and methods for producing H. pylori proteins or parts thereof using peptide synthesis and recombinant DNA techniques.
  • This invention also features antibodies and nucleic acids useful as probes to detect H. pylori infection.
  • vaccine compositions and methods for the protection or treatment of infection by H. pylori are within the scope of this invention. Detailed Description of the Drawings
  • Figure 1 depicts an amino acid sequence alignment of five H. pylori proteins (depicted in the single letter amino acid code and designated by their amino acid Sequence ID Numbers; shown N-terminal to C-terminal, left to right).
  • Figure 2 depicts the N-terminal portion of three H. pylori proteins (depicted in the single letter amino acid code and designated by their amino acid Sequence ID Numbers; shown N-terminal to C-terminal, left to right). Detailed Description of the Invention
  • the invention features a recombinant or substantially pure preparation of H. pylori polypeptide of SEQ ID NO: 98.
  • the invention also includes substantially pure nucleic acid encoding an H. pylori polypeptide of SEQ ID NO: 98, such nucleic acid is contained in SEQ ID NO: 1.
  • the H. pylori polypeptide sequences of the invention described herein are contained in the Sequence Listing, and the nucleic acids encoding H. pylori polypeptides of the invention are contained in the Sequence Listing.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 99, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 2.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 100, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 101, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 4.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 102, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 5.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 103, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 6.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 104, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 7.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 105, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 8.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide havin ⁇ a-i amino acid sequence of SEQ ID NO: 106, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 9.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 107, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 10.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 108, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 11.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 109, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 12.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 110, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 13.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 11 1, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 14.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 112, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 15.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 113, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 16.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 114, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 17.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 115, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 18.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 116, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 19.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 117, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 20.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 118, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 21.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 119, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 22.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 120, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 23.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 121, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 24.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 122, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 25.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 123, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 26.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 124, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 27.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 125, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 28.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 126, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 29.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 127, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 30.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 128, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 31.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 129, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 32.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 130, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 33.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 131, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 34.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 132, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 35.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 133, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 36.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 134, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 37.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 135, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 38.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 136, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 39.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 137, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 40.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 138, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 41.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 139, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 42.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 140, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO:43.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 141, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 44.
  • the invention features a substantially pi re nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 142, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 45.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 143, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 46.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 144, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 47.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 145, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 48.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 146, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 49.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 147, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 50.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 148, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 51.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 149, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 52.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 150, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 53.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 151, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 54.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 152, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 55.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 153, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 56.
  • the irvc >tion features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 154, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 57.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 155, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 58.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 156, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 59.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 157, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 60.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 158, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 61.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 159, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 62.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 160, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 63.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 161, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 64.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 162, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 65.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 163, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 66.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 164, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 67.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 165, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 68.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 166, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 69.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 167, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 70.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 168, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 71.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 169, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 72.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 170, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 73.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 171, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 74.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 172, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 75.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 173, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 76.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 174, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 77.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 175, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 78.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 176, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 79.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 177, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 80.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 178, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 81.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 179, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 82.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 180, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 83.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 181, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 84.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 182, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 85.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 183, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 86.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 184, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 87.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 185, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 88.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 186, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 89.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 187, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 90.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 188, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 91.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 189, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 92.
  • the invention features a substa itially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 190, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 93.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 191, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 94.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 192, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 95.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 193, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 96.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 194, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 97.
  • the invention features an isolated nucleic acid having a nucleotide sequence encoding an H. pylori polypeptide at least about 60% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
  • the isolated nucleic acid includes a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • the invention features an isolated nucleic acid having a nucleotide sequence encoding an H pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
  • the invention features an isolated nucleic acid which encodes an H pylori polypeptide, having a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • the invention features an isolated nucleic acid molecule encoding an H. pylori polypeptide, having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • the invention features an isolated nucleic acid having a nucleotide sequence of at least 8 nucleotides in length, wherein the sequence hybridizes under stringent hybridization conditions to a nucleic acid having a nucleotide sequence selected from the groun c nsisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • an isolated nucleic acid having a nucleotide sequence encoding an H pylori cell envelope polypeptide or a fragment thereof, the nucleic acid selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof encoded by a nucleic acid having a nucleotide sequence of SEQ ID NO: 63, or a complement thereof.
  • the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, and SEQ ID NO: 39, or a complement thereof.
  • the H. pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44, or a complement thereof.
  • the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66, or a complement
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94, or a complement thereof.
  • H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52, or a complement thereof.
  • an isolated nucleic acid having a nucleotide sequence encoding an H. pylori cell envelope polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 160, SEQ
  • the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof having an amino acid sequence of SEQ ID NO: 160.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 1 14, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
  • the H pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NC: 114, SEQ ID NO: 115, SEQ ID NO: 1 16, SEQ ID NO: 140, and SEQ ID NO: 141.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 1 19, SEQ ID NO: 126, SEQ ID NO:
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
  • nucleic acid having a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93, or a complement thereof.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 57 and SEQ ID NO: 58, or a complement thereof.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 86, SEQ ID NO: 87, or a complement thereof.
  • an isolated ruc ' .eic acid having a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184.
  • Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H.
  • nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31 , SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID NO: 95, and SEQ ID NO: 97, or a complement thereof.
  • an isolated nucleic acid having a nucleotide sequence encoding an H pylori secreted polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
  • an isolated nucleic acid having a nucleotide sequence encoding an H pylori cellular polypeptide or a fragment thereof, the nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96, or a complement thereof.
  • an isolated nucleic acid having a nucleotide sequence encoding an H pylori cellular polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 1 18, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEO V) NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
  • the invention features a probe having a nucleotide sequence consisting of at least 8 nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • the invention features an isolated H. pylori polypeptide having an amino acid sequence at least about 60% homologous to an H. pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
  • the invention features an isolated H. pylori polypeptide which is encoded by a nucleic acid having a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97.
  • the isolated H pylori polypeptide is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97.
  • the invention features an isolated H. pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
  • the invention features an isolated H. pylori polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 97-SEQ ID NO: 194.
  • an isolated H. pylori cell envelope polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H pylori flagella-associated polypeptide or a fragment thereof having an amino acid sequence of SEQ ID NO: 160.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 1 16, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
  • the H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 1 16, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
  • the H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146,
  • pylori inner membrane polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 104
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
  • SEQ ID NO: 27 SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 60, and SEQ
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof encoded by a nucleic acid having a nucleotide sequence of SEQ ID NO: 63.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, and SEQ ID NO: 39.
  • the H. pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44.
  • the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 1 1, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51 , SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94.
  • a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID
  • the H pylori outer membrane polypeptide or a fragment thereof is an H pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52.
  • a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52.
  • Particularly preferred is an isolated H.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 57, and SEQ ID NO: 58.
  • the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 86 and SEQ ID NO: 87.
  • an isolated H. pylori cellular polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 118, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
  • J articularly preferred is an isolated H pylori cellular polypeptide or a fragment thereof, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21 , SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96.
  • a nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21 , SEQ ID NO: 33, SEQ ID NO: 37, SEQ
  • an isolated H. pylori secreted polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
  • a nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 32, S
  • the invention features a chimeric H. pylori polypeptide comprising at least two H. pylori polypeptides or fragments thereof, wherein the polypeptides are encoded by nucleic acid sequences selected from the group consisting of SEQ ID NO: 1-SEQ ID NO:97.
  • the invention features a chimeric H. pylori polypeptide comprising at least two H. pylori polypeptides or fragments thereof, wherein the polypeptides are selected from the group consisting of SEQ ID NO:98-SEQ ID NO: 194.
  • the invention features a fusion protein comprising an H. pylori polypeptide which comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194 operatively linked to a non-H. pylori polypeptide.
  • the invention features a vaccine formulation for prophylactic or therapeutic treatment of an H. pylori infection comprising an effective amount of at least one isolated nucleic acid of the invention.
  • the invention features a vaccine formulation for prophylactic or therapeutic treatment of an H. pylori infection comprising an effective amount of at least one H. pylori polypeptide of the invention.
  • the vaccine formulation of the invention further includes a pharmaceutically acceptable carrier.
  • the pharmaceutically acceptable carrier includes an adjuvant.
  • the pharmaceutically acceptable carrier includes a delivery system, e.g., a live vector, e.g., a bacteria or a virus.
  • the pharmaceutically acceptable carrier includes both an adjuvant and a delivery system.
  • the invention features a method of treating or reducing a risk of H. pylori infection in a subject. The method includes administering to a subject a vaccine formulation of the invention, such that treatment or reduction of risk of H. pylori infection occurs.
  • the invention features a method of producing a vaccine formulation of the invention.
  • the method includes combining at least one isolated H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194 with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
  • the invention features a method of producing a vaccine formulation of the invention. The method includes culturing a cell under condition that permit expression of an H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194; isolating the H. pylori polypeptide from the cell; and combining at least one isolated H. pylori polypeptide or a fragment thereof with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
  • the invention pertains to any individual H. pylori polypeptide member or nucleic acid encoding such a member from the above-identified groups of H. pylori polypeptides.
  • the invention features nucleic acids capable of binding mRNA of H. pylori. Such nucleic acid is capable of acting as antisense nucleic acid to control the translation of mRNA of H. pylori.
  • a further aspect features a nucleic acid which is capable of binding specifically to an H. pylori nucleic acid. These nucleic acids are also referred to herein as complements and have utility as probes and as capture reagents.
  • the invention features an expression system comprising an open reading frame corresponding to H. pylori nucleic acid.
  • the nucleic acid further comprises a control sequence compatible with an intended host.
  • the expression system is useful for making polypeptides corresponding to H. pylori nucleic acid.
  • the invention features a cell transformed with the expression system to produce H. pylori polypeptides.
  • the invention features a method of generating antibodies against H pylori polypeptides which are capable of binding specifically to H. pylori polypeptides. Such antibodies have utility as reagents for immunoassays to evaluate the abundance and distribution of H. /?y/ ⁇ r/-specific antigens.
  • the invention features a method of generating vaccines for immunizing an individual against H. pylori.
  • the vaccination method includes: immunizing a subject with at least one H. pylori polypeptide according to the present invention, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmaceutically acceptable carrier. Such vaccines have therapeutic and/or prophylactic utilities.
  • the invention provides a method for generating a vaccine comprising a modified immunogenic H. pylori polypeptide, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmacologically acceptable carrier.
  • a modified immunogenic H. pylori polypeptide e.g., a surface or secreted polypeptide, or active portion thereof
  • a pharmacologically acceptable carrier e.g., a pharmacologically acceptable carrier.
  • the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori polypeptide.
  • the method includes: contacting the candidate compound with an H pylori polypeptide and determining if the compound binds or otherwise interacts with an H. pylori polypeptide.
  • Compounds which bind H. pylori are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.
  • the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori nucleic acid, e.g., DNA or RNA.
  • the method includes: contacting the candidate compound with an H. pylori nucleic acid and determining if the compound binds or otherwise interacts with an H. pylori polypeptide.
  • Compounds which bind H. pylori are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.
  • the invention features H pylori polypeptides, preferably a substantially pure preparation of an H pylori polypeptide, or a recombinant H pylori polypeptide.
  • the polypeptide has biological activity; the polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% identical or homologous to an amino acid sequence of the invention contained in the Sequence
  • the polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide is at least 5, 10, 2 J, 50, 100, or 150 amino acid residues in length; the polypeptide includes at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acid residues of the invention contained in the Sequence Listing.
  • the amino acid sequence which differs in sequence identity by about 7% to about 8% from the H.
  • the H. pylori polypeptide is encoded by a nucleic acid of the invention contained in the Sequence Listing, or by a nucleic acid having at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleic acid of the invention contained in the Sequence Listing.
  • the subject H. pylori polypeptide differs in amino acid sequence at 1, 2, 3, 5, 10 or more residues from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that the H. pylori polypeptide exhibits an H.
  • the H. pylori biological activity e.g., the H. pylori polypeptide retains a biological activity of a naturally occurring H. pylori polypeptide.
  • the polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.
  • the H. pylori polypeptide is a recombinant fusion protein having a first H.
  • pylori polypeptide portion and a second polypeptide portion, e.g., a second polypeptide portion having an amino acid sequence unrelated to H. pylori.
  • the second polypeptide portion can be, e.g., any of glutathione-S-transferase, a DNA binding domain, or a polymerase activating domain.
  • the fusion protein can be used in a two-hybrid assay.
  • Polypeptides of the invention include those which arise as a result of alternative transcription events, alternative RNA splicing events, and alternative translational and postranslational events.
  • the invention also encompasses an immunogenic component which includes at least one H. pylori polypeptide in an immunogenic preparation; the immunogenic component being capable of eliciting an immune response specific for the H. pylori polypeptide, e.g., a humoral response, an antibody response, or a cellular response.
  • the immunogenic component comprises at least one antigenic determinant from a polypeptide of the invention contained in the Sequence Listing.
  • the invention provides a substantially pure nucleic acid having a nucleotide sequence which encodes an H. pylori polypeptide.
  • the encoded polypeptide has biological activity; the encoded polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous to an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length; the encoded polypeptide comprises at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acids of the invention contained in the Sequence Listing.
  • the nucleic acid of the invention is that contained in the Sequence Listing; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or 99%) homologous with a nucleic acid sequence of the invention contained in the Sequence Listing.
  • the encoded H. pylori polypeptide differs (e.g., by amino acid substitution, addition or deletion of at least one amino acid residue) in amino acid sequence at 1, 2, 3, 5, 10 or more residues, from a sequence of the invention contained in the Sequence Listing.
  • the differences are such that: the H. pylori encoded polypeptide exhibits a H. pylori biological activity, e.g., the encoded H pylori enzyme retains a biological activity of a naturally occurring H. pylori.
  • the encoded polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5 ' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.
  • the subject H. pylori nucleic acid will include a transcriptional regulatory sequence, e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence, operably linked to the H. pylori gene sequence, e.g., to render the H pylori gene sequence suitable for expression in a recombinant host cell.
  • a transcriptional regulatory sequence e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence
  • operably linked to the H. pylori gene sequence e.g., to render the H pylori gene sequence suitable for expression in a recombinant host cell.
  • the nucleic acid which encodes an H pylori polypeptide of the invention hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 8 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 12 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 20 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 40 consecutive nucleotides of the invention contained in the Sequence Listing.
  • the nucleic acid encodes a peptide which differs by at least one amino acid residue from the sequences of the invention contained in the Sequence Listing.
  • the nucleic acid differs by at least one nucleotide from a nucleotide sequence of the invention contained in the Sequence Listing which encodes amino acids of the invention contained in the Sequence Listing.
  • the invention encompasses: a vector including a nucleic acid which encodes an H. pylori polypeptide or an H. pylori polypeptide variant as described herein; a host cell transfected with the vector; and a method of producing a recombinant
  • H. pylori polypeptide or H. pylori polypeptide variant including culturing the cell, e.g., in a cell culture medium, and isolating the H. pylori or H. pylori polypeptide variant, e.g., from the cell or from the cell culture medium.
  • the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a sequence of the invention contained in the Sequence Listing.
  • the invention also provides a probe or primer which includes a substantially purified oligonucleotide.
  • the oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 8 consecutive nucleotides of sense or antisense sequence of the invention contained in the Sequence Listing, or naturally occurring mutants thereof.
  • the probe or primer further includes a label group attached thereto.
  • the label group can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor.
  • the oligonucleotide is at least 8 and less than 10, 20, 30, 50, 100, or 150 nucleotides in length.
  • the invention also provides an isolated H. pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid contained in the Sequence Listing.
  • the invention further provides nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.
  • the H. pylori strain from which genomic sequences have been sequenced, has been deposited in the American Type Culture Collection (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) as strain
  • allelic variations include allelic variations; natural mutants; induced mutants; proteins encoded by DNA that hybridizes under high or low stringency conditions to a nucleic acid which encodes a polypeptide of the invention contained in the Sequence Listing (for definitions of high and low stringency see Current Protocols in
  • H. pylori polypeptides specifically bound by antisera to H. pylori polypeptides, especially by antisera to an active site or binding domain of H. pylori polypeptide.
  • the invention also includes fragments, preferably biologically active fragments. These and other polypeptides are also referred to herein as H pylori polypeptide analogs or variants. Putative functions have been determined for several of the H pylori polypeptides of the invention, as shown in Table 1.
  • H pylori polypeptides characterized as shown in Table 1 below, including: H pylori cell envelope proteins, H pylori secreted proteins, H pylori cytoplasmic proteins and H pylori cellular proteins.
  • H pylori cell envelope proteins H pylori secreted proteins
  • H pylori cytoplasmic proteins H pylori cellular proteins.
  • purified polypeptide and “isolated polypeptide” and “a substantially pure preparation of a polypeptide” are used interchangeably herein and, as used herein, mean a polypeptide that has been substantially, and preferably completely, separated from other proteins, lipids, and nucleic acids with which it naturally occurs.
  • the polypeptide is also separated from substances, e.g., antibodies or gel matrix, e.g., polyacrylamide, which are used to purify it.
  • the polypeptide constitutes at least 10, 20, 50 70, 80 or 95% dry weight of the purified preparation.
  • the preparation contains: sufficient polypeptide to allow protein sequencing; at least 1, 10, or 100 ⁇ g of the polypeptide; at least 1, 10, or 100 mg of the polypeptide.
  • purified polypeptide and isolated polypeptide and “a substantially pure preparation of a polypeptide,” as used herein, refer to both a polypeptide obtained from nature or produced by recombinant DNA techniques as described herein.
  • an "isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the H. pylori protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of H. pylori protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language
  • substantially free of cellular material includes preparations of H. pylori protein having less than about 30% (by dry weight) of non-H. pylori protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-H. pylori protein, still more preferably less than about 10% of non-H. pylori protein, and most preferably less than about 5% non-H. pylori protein.
  • the H pylori protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.
  • the language "substantially free of chemical precursors or other chemicals” includes preparations of H. pylori protein i'i which the protein is separated from chemical precusors or other chemicals which are involved in the synthesis of the protein.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of H. pylori protein having less than about 30% (by dry weight) of chemical precursors or non-H. pylori chemicals, more preferably less than about 20%) chemical precursors or non-H. pylori chemicals, still more preferably less than about 10% chemical precursors or non-H. pylori chemicals, and most preferably less than about 5% chemical precursors or non-H. pylori chemicals.
  • a purified preparation of cells refers to, in the case of plant or animal cells, an in vitro preparation of cells and not an entire intact plant or animal. In the case of cultured cells or microbial cells, it consists of a preparation of at least 10% and more preferably 50%) of the subject cells.
  • a purified or isolated or a substantially pure nucleic acid is a nucleic acid which is one or both of the following: not immediately contiguous with both of the coding sequences with which it is immediately contiguous (i.e., one at the 5' end and one at the 3' end) in the naturally-occurring genome of the organism from which the nucleic acid is derived; or which is substantially free of a nucleic acid with which it occurs in the organism from which the nucleic acid is derived.
  • the term includes, for example, a recombinant DNA which is incorporated into a vector, e.g., into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other DNA sequences.
  • Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional H. pylori DNA sequence.
  • a "contig” as used herein is a nucleic acid representing a continuous stretch of genomic sequence of an organism.
  • ORF an "open reading frame”, also referred to herein as ORF, is a region of nucleic acid which encodes a polypeptide. This region may represent a portion of a coding sequence or a total sequence and can be determined from a stop to stop codon or from a start to stop codon.
  • a "coding sequence” is a nucleic acid which is transcribed into messenger RNA and/or translated into a polypeptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a translation start codon at the five prime terminus and a translation stop code at the three prime terminus.
  • a coding sequence can include but is not limited to messenger P A, synthetic DNA, and recombinant nucleic acid sequences.
  • a "complement" of a nucleic acid as used herein referes to an anti-parallel or antisense sequence that participates in Watson-Crick base-pairing with the original sequence.
  • a “gene product” is a protein or structural RNA which is specifically encoded by a gene.
  • probe refers to a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest. Probes are often associated with or capable of associating with a label.
  • a label is a chemical moiety capable of detection. Typical labels comprise dyes, radioisotopes, luminescent and chemiluminescent moieties, fluorophores, enzymes, precipitating agents, amplification sequences, and the like.
  • Capture ligand a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest and immobilizes such molecule is referred herein as a "capture ligand".
  • Capture ligands are typically associated with or capable of associating with a support such as nitro-cellulose, glass, nylon membranes, beads, particles and the like. The specificity of hybridization is dependent on conditions such as the base pair composition of the nucleotides, and the temperature and salt concentration of the reaction. These conditions are readily discernable to one of ordinary skill in the art using routine experimentation.
  • Homologous refers to the sequence similarity or sequence identity between two polypeptides or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position.
  • the percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared x 100. For example, if 6 of 10 of the positions in two sequences are matched or homologous then the two sequences are 60% homologous.
  • the DNA sequences ATTGCC and TATGGC share 50% homology.
  • nucleic acids are hybridizable to each other when at least one strand of a nucleic acid can anneal to the other nucleic acid under defined stringency conditions.
  • Stringency of hybridization is determined by: (a) the temperature at which hybridization and/or washing is performed; and (b) the ionic strength and polarity of the hybridization and washing solutions.
  • Hybridization requires that the two nucleic acids contain complementary sequences; depending on the stringency of hybridization, however, mismatches may be tolerated.
  • hybridization of two sequences at high stingency requires that the sequences be essentially completely homologous.
  • Conditions of intermediate stringency such as, for example, 2X SSC at 65 ° C
  • low stringency such as, for example 2X SSC at 55° C
  • IX SSC is 0.15 M NaCl, 0.015 M Na citrate.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65°C.
  • SSC sodium chloride/sodium citrate
  • peptides, proteins, and polypeptides are used interchangeably herein.
  • surface protein refers to all surface accessible proteins, e.g. inner and outer membrane proteins, proteins adhering to the cell wall, and secreted proteins.
  • a polypeptide has H. pylori biological activity if it has one, two and preferably more of the following properties: (1) if when expressed in the course of an H. pylori infection, it can promote, or mediate the attachment of H pylori to a cell; (2) it has an enzymatic activity, structural or regulatory function characteristic of an H. pylori protein; (3) the gene which encodes it can rescue a lethal mutation in an H. pylori gene; (4) or it is immunogenic in a subject.
  • a polypeptide has biological activity if it is an antagonist, agonist, or super-agonist of a polypeptide having one of the above-listed properties.
  • a biologically active fragment or analog is one having an in vivo or in vitro activity which is characteristic of the H. pylori polypeptides of the invention contained in the Sequence Listing, or of other naturally occurring H. pylori polypeptides, e.g., one or more of the biological activities described herein.
  • fragments which exist in vivo e.g., fragments which arise from post transcriptional processing or which arise from translation of alternatively spliced RNA's. Fragments include those expressed in native or endogenous cells as well as those made in expression systems, e.g., in C ⁇ O cells. Because peptides such as H.
  • H. pylori polypeptides often exhibit a range of physiological properties and because such properties may be attributable to different portions of the molecule, a useful H. pylori fragment or H pylori analog is one which exhibits a biological activity in any biological assay for H. pylori activity. Most preferably the fragment or analog possesses 10%, preferably 40%, more preferably 60%, 70%), 80% or 90% or greater of the activity of H pylori, in any in vivo or in vitro assay. Analogs can differ from naturally occurring H. pylori polypeptides in amino acid sequence or in ways that do not involve sequence, or both.
  • Non-sequence modifications include changes in acetylation, methylation, phosphorylation, carboxylation, or glycosylation.
  • Preferred analogs include H. pylori polypeptides (or biologically ct ' .ve fragments thereof) whose sequences differ from the wild-type sequence by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions which do not substantially diminish the biological activity of the H. pylori polypeptide.
  • Conservative substitutions typically include the substitution of one amino acid for another with similar characteristics, e.g., substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. Other conservative substitutions can be made in view of the table below.
  • analogs within the invention are those with modifications which increase peptide stability; such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the peptide sequence. Also included are: analogs that include residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., ⁇ or ⁇ amino acids; and cyclic analogs.
  • fragment as applied to an H. pylori analog, will ordinarily be at least about 20 residues, more typically at least about 40 residues, preferably at least about 60 residues in length. Fragments of H. pylori polypeptides can be generated by methods known to those skilled in the art. The ability of a candidate fragment to exhibit a biological activity of H pylori polypeptide can be assessed by methods known to those skilled in the art as described herein. Also included are H. pylori polypeptides containing residues that are not required for biological activity of the peptide or that result from alternative mRNA splicing or alternative protein processing events.
  • an “immunogenic component” as used herein is a moiety, such as an H. pylori polypeptide, analog or fragment thereof, that is capable of eliciting a humoral and/or cellular immune response in a host animal alone or in combination with an adjuvant.
  • An “antigenic component” as used herein is a moiety, such as an H. pylori polypeptide, analog or fragment thereof, that is capable of binding to a specific antibody with sufficiently high affinity to form a detectable antigen-antibody complex.
  • transgene means a nucleic acid (encoding, e.g., one or more polypeptides), which is partly or entirely heterologous, i.e., foreign, to the transgenic animal or cell into which it is introduced, or, is homologous to an endogenous gene of the transgenic animal or cell into which it is introduced, but which is designed to be inserted, or is inserted, into the cell's genome in such a way as to alter the genome of the cell into which it is inserted (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout).
  • a transgene can include one or more transcriptional regulatory sequences and any other nucleic acid, such as introns, that may be necessary for optimal expression of the selected nucleic acid, all operably linked to the selected nucleic acid, and may include an enhancer sequence.
  • transgenic cell refers to a cell containing a transgene.
  • a transgenic animal is any animal in which one or more, and preferably essentially all, of the cells of the animal includes a transgene.
  • the transgene can be introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by a process of transformation of competent cells or by microinjection or by infection with a recombinant virus. This molecule may be integrated within a chromosome, or it may be extrachromosomallv replicating DNA.
  • antibody as used herein is intended to include fragments thereof which are specifically reactive with H. pylori polypeptides.
  • cell-specific promoter means a DNA sequence that serves as a promoter, i.e., regulates expression of a selected DNA sequence operably linked to the promoter, and which effects expression of the selected DNA sequence in specific cells of a tissue.
  • the term also covers so-called “leaky” promoters, which regulate expression of a selected DNA primarily in one tissue, but cause expression in other tissues as well.
  • Misexpression refers to a non- wild type pattern of gene expression. It includes: expression at non-wild type levels, i.e., over or under expression; a pattern of expression that differs from wild type in terms of the time or stage at which the gene is expressed, e.g., increased or decreased expression (as compared with wild type) at a predetermined developmental period or stage; a pattern of expression that differs from wild type in terms of decreased expression (as compared with wild type) in a predetermined cell type or tissue type; a pattern of expression that differs from wild type in terms of the splicing size, amino acid sequence, post- transitional modification, or biological activity of the expressed polypeptide; a pattern of expression that differs from wild type in terms of the effect of an environmental stimulus or extracellular stimulus on expression of the gene, e.g., a pattern of increased or decreased expression (as compared with wild type) in the presence of an increase or decrease in the strength of the stimulus.
  • host cells and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refers to cells which can become or have been used as recipients for a recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transfected. It is understood by individuals skilled in the art that the progeny of a single parental cell may not necessarily be completely identical in genomic or total DNA compliment to the original parent, due to accident or deliberate mutation.
  • control sequence refers to a nucleic acid having a base sequence which is recognized by the host organism to effect the expression of encoded sequences to which they are ligated.
  • the nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include a promoter, ribosomal binding site, terminators, and in some cases operators; in eukaryotes, generally such control sequences include promoters, terminators and in some instances, enhancers.
  • the term control sequence is intended to include at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences.
  • the term "operably linked” refers to sequences joined or ligated to function in their intended manner.
  • a control sequence is operably linked to coding sequence by ligation in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequence and host cell.
  • the metabolism of a substance means any aspect of the, expression, function, action, or regulation of the substance.
  • the metabolism of a substance includes modifications, e.g., covalent or non-covalent modifications of the substance.
  • the metabolism of a substance includes modifications, e.g., covalent or non- covalent modification, the substance induces in other substances.
  • the metabolism of a substance also includes changes in the distribution of the substance.
  • the metabolism of a substance includes changes the substance induces in the distribution of other substances.
  • sample refers to a biological sample, such as, for example, tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
  • tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
  • This invention provides nucleotide sequences of the genome of H. pylori which thus comprises a DNA sequence library of H. pylori genomic DNA.
  • the detailed description that follows provides nucleotide sequences of H. pylori, and also describes how the sequences were obtained and how ORFs and protein-coding sequences were identified. Also described are methods of using the disclosed H. pylori sec uences in methods including diagnostic and therapeutic applications.
  • the library can be used as a database for identification and comparison of medically important sequences in this and other strains of H. pylori.
  • H pylori DNA was isolated from a strain of H pylori (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) and mechanically sheared by nebulization to a median size of 2 kb. Following size fractionation by gel electrophoresis, the fragments were blunt-ended, ligated to adapter oligonucleotides, and cloned into each of 20 different pMPX vectors (Rice et al., abstracts of Meeting of Genome Mapping and Sequencing, Cold Spring Harbor, NY, 5/1 1-5/15, 1994, p. 225) to construct a series of "shotgun" subclone libraries.
  • DNA sequencing was achieved using multiplex sequencing procedures essentially as disclosed in Church et al., 1988, Science 240:185; U.S. Patents No. 4,942,124 and 5,149,625).
  • DNA was extracted from pooled cultures and subjected to chemical or enzymatic sequencing. Sequencing reactions were resolved by electrophoresis, and the products were transferred and covalently bound to nylon membranes. Finally, the membranes were sequentially hybridized with a series of labelled oligonucleotides complimentary to "tag" sequences present in the different shotgun cloning vectors. In this manner, a large number of sequences could be obtained from a single set of sequencing reactions. The cloning and sequencing procedures are described in more detail in the Exemplification.
  • oligonucleotides are designed that are complementary to sequences at the end of each contig. These oligonucleotides may be hybridized to libaries of H. pylori genomic DNA in, for example, lambda phage vectors or plasmid vectors to identify clones that contain sequences corresponding to the junctional regions between individual contigs. Such clones are then used to isolate template DNA and the same oligonucleotides are used as primers in polymerase chain reaction (PCR) to amplify junctional fragments, the nucleotide sequence of which is then determined.
  • PCR polymerase chain reaction
  • ORFs comprising at least 180 nucleotides
  • ORFs may not correspond to the ORF of a naturally-occurring H. pylori polypeptide.
  • These ORFs may contain start codons which indicate the initiation of protein synthesis of a naturally- occurring H. pylori polypeptide.
  • Such start codons within the ORFs provided herein can be identified by those of ordinary skill in the relevant art, and the resulting ORF and the encoded H. pylori polypeptide is within the scope of this invention.
  • a codon such as AUG or GUG which is part of the initiation signal for protein synthesis can be identified and the ORF modified to correspond to a naturally-occurring H. pylori polypeptide.
  • the predicted coding regions were defined by evaluating the coding potential of such sequences with the program GENEMARKTM (Borodovsky and Mclninch, 1993, Comp. Chem. 17:123).
  • the nucleic acids of this invention may be obtained directly from the DNA of the above referenced H. pylori strain by using the polymerase chain reaction (PCR). See “PCR, A Practical Approach” (McPherson, Quirke, and Taylor, eds., IRL Press, Oxford, UK, 1991) for details about the PCR. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, the authenticity of amplified products can be checked by conventional sequencing methods.
  • PCR polymerase chain reaction
  • Clones carrying the desired sequences described in this invention may also be obtained by screening the libraries by means of the PCR or by hybridization of synthetic oligonucleotide probes to filter lifts of the library colonies or plaques as known in the art (see, e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual 2nd edition, 1989, Cold Spring Harbor Press, NY).
  • nucleic acids encoding H pylori polypeptides from a cDNA library in accordance with protocols herein described.
  • a cDNA encoding an H. pylori polypeptide can be obtained by isolating total mRNA from an appropriate strain. Double stranded cDNAs can then be prepared from the total mRNA. Subsequently, the cDNAs can be inserted into a suitable plasmid or viral (e.g., bacteriophage) vector using any one of a number of known techniques.
  • Genes encoding H pylori polypeptides can also be cloned using established polymerase chain reaction techniques in accordance with the nucleotide sequence information provided by the invention.
  • the nucleic acids of the invention can be DNA or RNA. Preferred nucleic acids of the invention are contained in the Sequence Listing.
  • the nucleic acids of the invention can also be chemically synthesized using standard techniques.
  • Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et a U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
  • nucleic acids isolated or synthesized in accordance with features of the present invention are useful, by way of example, without limitation, as probes, primers, capture ligands, antisense genes and for developing expression systems for the synthesis of proteins and peptides corresponding to such sequences.
  • the nucleic acid normally consists of all or part (approximately twenty or more nucleotides for specificity as well as the ability to form stable hybridization products) of the nucleic acids of the invention contained in the Sequence Listing. These uses are described in further detail below. Probes
  • a nucleic acid isolated or synthesized in accordance with the sequence of the invention contained in the Sequence Listing can be used as a probe to specifically detect H. pylori.
  • sequences of twenty or more nucleotides are identified which provide the desired inclusivity and exclusivity with respect to H. pylori, and extraneous nucleic acids likely to be encountered during hybridization conditions. More preferably, the sequence will comprise at least twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules.
  • nucleic acids for use as probes, can be provided with a label to facilitate detection of a hybridization product.
  • nucleic acid selected in the manner described above with respect to probes can be readily associated with a support.
  • the manner in which nucleic acid is associated with supports is well known.
  • Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing have utility to separate H. pylori nucleic acid from the nucleic acid of each other and other organisms.
  • Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing can also have utility to separate other Helicobacter species from each other and from other organisms.
  • the sequence will comprise at least twenty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Primers
  • Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility as primers for the amplification of H. pylori nucleic acid. These nucleic acids may also have utility as primers for the amplification of nucleic acids in other Helicobacter species.
  • PCR polymerase chain reaction
  • nucleic acid sequences of > 10-15 nucleotides of the invention contained in the Sequence Listing have utility in conjunction with suitable enzymes and reagents to create copies of H pylori nucleic acid. More preferably, the sequence will comprise twenty or more nucleotides to convey stability to the hybridization product formed between the primer and the intended target molecules. Binding conditions of primers greater than 100 nucleotides are more difficult to control to obtain specificity. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, amplified products can be checked by conventional sequencing methods.
  • the copies can be used in diagnostic assays to detect specific sequences, including genes from H. pylori and/or other Helicobacter species.
  • the copies can also be incorporated into cloning and expression vectors to generate polypeptides corresponding to the nucleic acid synthesized by PCR, as is described in greater detail herein.
  • nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized in accordance with the sequences described herein have utility as antisense agents to prevent the expression of H. pylori genes. These sequences also have utility as antisense agents to prevent expression of genes of other Helicobacter species.
  • nucleic acid or derivatives corresponding to H. pylori nucleic acids is loaded into a suitable carrier such as a liposome or bacteriophage for introduction into bacterial cells.
  • a nucleic acid having twenty or more nucleotides is capable of binding to bacteria nucleic acid or bacteria messenger RNA.
  • the antisense nucleic acid is comprised of 20 or more nucleotides to provide necessary stability of a hybridization product of non-naturally occurring nucleic acid and bacterial nucleic acid and/or bacterial messenger RNA.
  • Nucleic ? ⁇ having a sequence greater than 1000 nucleotides in length is difficult to synthesize but can be generated by recombinant DNA techniques.
  • Methods for loading antisense nucleic acid in liposomes is known in the art as exemplified by U.S. Patent 4,241,046 issued December 23, 1980 to Papahadjopoulos et al. II. Expression of H pylori Nucleic Acids
  • nucleic acid isolated or synthesized in accordance with the sequences described herein have utility to generate polypeptides.
  • the nucleic acid of the invention exemplified in the Sequence Listing or fragments of the nucleic acid encoding active portions of H pylori polypeptides can be cloned into suitable vectors or used to isolate nucleic acid.
  • the isolated nucleic acid is combined with suitable DNA linkers and cloned into a suitable vector.
  • a gene product may be produced in large quantities in an expressing strain for use as an antigen, an industrial reagent, for structural studies, etc. This expression can be accomplished in a mutant strain which lacks the activity of the gene to be tested, or in a strain that does not produce the same gene product(s). This includes, but is not limited to other Helicobacter strains, or other bacterial strains such as E. coli, Norcardia,
  • the expression host will utilize the natural Helicobacter promoter whereas in others, it will be necessary to drive the gene with a promoter sequence derived from the expressing organism (e.g., an E. coli beta-galactosidase promoter for expression in E. coli).
  • a promoter sequence derived from the expressing organism e.g., an E. coli beta-galactosidase promoter for expression in E. coli.
  • a procedure such as the following can be used.
  • a restriction fragment containing the gene of interest, together with its associated natural promoter element and regulatory sequences is cloned into an appropriate recombinant plasmid containing an origin of replication that functions in the host organism and an appropriate selectable marker.
  • the recombinant plasmid is introduced into the host organism by, for example, electroporation and cells containing the recombinant plasmid are identified by selection for the marker on the plasmid.
  • Expression of the desired gene product is detected using an assay specific for that gene product.
  • the body of the gene (coding sequence) is specifically excised and cloned into an appropriate expression plasmid.
  • This subcloning can be done by several methods, but is most easily accomplished by PCR amplification of a specific fragment and ligation into an expression plasmid after treating the PCR product with a restriction enzyme or exonuclease to create suitable ends for cloning.
  • a suitable host cell for expression of a gene can be any procaryotic or eucaryotic cell.
  • an H. pylori polypeptide can be expressed in bacterial cells such as E. coli, insect cells (baculovirus), yeast, or mammalian cells such as Chinese hamster ovary cell (C ⁇ O).
  • Other suitable host cells are known to those skilled in the art.
  • yeast S. cerivisae examples include pYepSecl (Baldari. et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and ⁇ erskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, CA).
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al., (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow, V.A., and Summers, M.D., (1989) Virology 170:31-39).
  • SF 9 cells include the pAc series (Smith et al., (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow, V.A., and Summers, M.D., (1989) Virology 170:31-39).
  • COS cells include the pAc series (Smith et al., (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow, V.A., and Summers, M.D., (1989) Virology 170:31-39).
  • COS cells include the pAc series (Smith et
  • Vector DNA can be introduced into mammalian cells via conventional techniques such as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, or electroporation. Suitable methods for transforming host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.
  • Fusion vectors usually add a number of NH2 terminal amino acids to the expressed target gene. These NH2 terminal amino acids often are referred to as a reporter group. Such reporter groups usually serve two purposes: 1) to increase the solubility of the target recombinant protein; and 2) to aid in the purification of the target recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the reporter group and the target recombinant protein to enable separation of the target recombinant protein from the reporter group subsequent to purification of the fusion protein.
  • Such enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase, maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • a preferred reporter group is poly(His), which may be fused to the amino or carboxy terminus of the protein and which renders the recombinant fusion protein easily purifiable by metal chelate chromatography.
  • Inducible non-fusion expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pETl Id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89). While target gene expression relies on host RNA polymerase transcription from the hybrid trp-lac fusion promoter in pTrc, expression of target genes inserted into pETl Id relies on transcription from the T7 gnlO-lac 0 fusion promoter mediated by coexpressed viral RNA polymerase (T7 gnl).
  • This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident ⁇ prophage harboring a T7 gnl under the transcriptional control of the lacUV 5 promoter.
  • a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding an H. pylori polypeptide can be cultured under appropriate conditions to allow expression of the polypeptide to occur.
  • the polypeptide may be secreted and isolated from a mixture of cells and medium containing the peptide. Alternatively, the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated.
  • a cell culture includes host cells, media and other byproducts.
  • Polypeptides of the invention can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffmity purification with antibodies specific for such polypeptides.
  • polypeptides can be produced by chemical cleavage of a native protein (e.g., tryptic digestion) and the cleavage products can then be purified by standard techniques.
  • membrane bound proteins these can be isolated from a host cell by contacting a membrane-associated protein fraction with a detergent forming a solubilized complex, where the membrane-associated protein is no longer entirely embedded in the membrane fraction and is solubilized at least to an extent which allows it to be chromatographically isolated from the membrane fraction.
  • a detergent suitable for solubilizing these complexes For example, one property considered is the ability of the detergent to solubilize the H. pylori protein within the membrane fraction at minimal denaturation of the membrane- associated protein allowing for the activity or functionality of the membrane-associated protein to return upon reconstitution of the protein.
  • CMC critical micelle concentration
  • a third property considered when selecting a detergent is the hydrophobicity of the detergent.
  • membrane-associated proteins are very hydrophobic and therefore detergents which are also hydrophobic, e.g., the triton series, would be useful for solubilizing the hydrophobic proteins.
  • Another property important to a detergent can be the capability of the detergent to remove the H pylori protein with minimal protein-protein interaction facilitating further purification.
  • a fifth property of the detergent which should be considered is the charge of the detergent.
  • detergent should be an uncharged detergent.
  • Chromatographic techniques which can be used in the final purification step are known in the art and include hydrophobic interaction, lectin affinity, ion exchange, dye affinity and immunoaffinity.
  • One strategy to maximize recombinant H. pylori peptide expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128).
  • Another strategy would be to alter the nucleic acid encoding an H pylori peptide to be inserted into an expression vector so that the individual codons for each amino acid would be those preferentially utilized in highly expressed E. coli proteins (Wada et al., (1992) Nuc. Acids Res. 20:2111-2118). Such alteration of nucleic acids of the invention can be carried out by standard DNA synthesis techniques.
  • the nucleic acids of the invention can also be chemically synthesized using standard techniques.
  • Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See, e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
  • This invention encompasses isolated H pylori polypeptides encoded by the disclosed H pylori genomic sequences, including the polypeptides of the invention contained in the Sequence Listing. Polypeptides of the invention are preferably at least 5 amino acid residues in length. Using the DNA sequence information provided herein, the amino acid sequences of the polypeptides encompassed by the invention can be deduced using methods well-known in the art. It will be understood that the sequence of an entire nucleic acid encoding an H. pylori polypeptide can be isolated and identified based on an ORF that encodes only a fragment of the cognate protein-coding region.
  • polypeptides of the invention can be isolated from wild-type or mutant H pylori cells or from heterologous organisms or cells (including, but not limited to, bacteria, yeast, insect, plant and mammalian cells) into which an H pylori nucleic acid has been introduced and expressed.
  • the polypeptides can be part of recombinant fusion proteins.
  • H pylori polypeptides of the invention can be chemically synthesized using commercially automated procedures such as those referenced herein.
  • H pylori polypeptides of the invention are also intended to include chimeric proteins and truncated proteins as decribed herein.
  • H. pylori chimeric polypeptides comprise one or more H pylori polypeptides fused together. These combined sequences can be made by combining two or more genes, or two or more polypeptide encoding sequences, or at least one gene and at least one polypeptide encoding sequence in tandem, and the subsequent expression of the encoded proteins by conventional molecular biological techniques.
  • the combined nucleotide sequences may be composed of a combination of either full length H. pylori nucleotide sequences or fragments of such sequences, e.g., fragments which contain immunologically relevant portions of the encoded H. pylori protein.
  • These chimeric H pylori proteins then contain the combined or synergistic vaccine potential of each individual H. pylori protein sequence and can be used in vaccine formulations of the invention.
  • Truncated gene expression and protein production H. pylori proteins encoded by a given nucleotide sequence can also be used in a biologically active truncated form. Such truncation can be produced, for example, by the elimination of either 5' and/or 3' regions of the encoding nucleotide sequence. These truncations can affect recombinant expression of the encoded protein and/or subsequent purification of the protein. For example, truncation of a nucleotide sequence encoding a predicted export sequence of a specific protein may alter expression of the protein. Alternatively, C-terminal truncation of an H.
  • nucleic acid coding region by elimination of the 3' end of the nucleic acid coding region may also improve protein expression and subsequent purification and use, as is outlined in Example VIII below. Deletion of nucleic acid regions encoding internal H. pylori protein regions can also result in improved protein expression, purification and/or efficacy as a vaccine candidate.
  • the disclosed H pylori genome sequence includes segments that direct the synthesis of ribonucleic acids and polypeptides, as well as origins of replication, promoters, other types of regulatory sequences, and intergenic nucleic acids.
  • the invention encompasses nucleic acids encoding immunogenic components of vaccines and targets for agents effective against H pylori. Identification of said immunogenic components involved in the determination of the function of the disclosed sequences can be achieved using a variety of approaches. Non-limiting examples of these approaches are described briefly below. Homology to known sequences: Computer-assisted comparison of the disclosed
  • H. pylori sequences with previously reported sequences present in publicly available databases is useful for identifying functional H. pylori nucleic acid and polypeptide sequences.
  • protein-coding sequences may be compared as a whole, and that a high degree of sequence homology between two proteins (such as, for example, >80-90%) at the amino acid level indicates that the two proteins also possess some degree of functional homology, such as, for example, among enzymes involved in metabolism, DNA synthesis, or cell wall synthesis, and proteins involved in transport, cell division, etc.
  • H. pylori proteins identified as containing putative signal sequences and/or transmembrane domains are useful as immunogenic components of vaccines. Identification of essential genes: Nucleic acids that encode proteins essential for growth or viability of H. pylori are preferred drug targets. H. pylori genes can be tested for their biological relevance to the organism by examining the effect of deleting and/or disrupting the genes, i.e., by so-called gene "knockout", using techniques known to those skilled in the relevant art. In this manner, essential genes may be identified.
  • H pylori sequences are useful for identifying, and/or discriminating between, previously known and new H pylori strains. It is believed that other H pylori strains will exhibit at least 70% sequence homology with the presently disclosed sequence. Systematic and routine analyses of DNA sequences derived from samples containing H pylori strains, and comparison with the present sequence allows for the identification of sequences that can be used to discriminate between strains, as well as those that are common to all H. pylori strains.
  • the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that discriminate between different strains of H. pylori.
  • Strain-specific components can also be identified functionally by their ability to elicit or react with antibodies that selectively recognize one or more H. pylori strains.
  • the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that are common to all H. pylori strains but are not found in other bacterial species.
  • the selection of candidate protein antigens for vaccine development can be derived from the nucleic acids encoding H pylori polypeptides.
  • the ORF's can be analyzed for homology to other known exported or membrane proteins and analyzed using the discriminant analysis described by Klein, et al. (Klein, P., Kanehsia, M., and DeLisi, C. (1985) Biochimica et Biophysica Acta 815, 468-476) for predicting exported and membrane proteins.
  • Homology searches can be performed using the BLAST algorithm contained in the Wisconsin Sequence Analysis Package (Genetics Computer Group, Um ' ve.sity Research Park, 575 Science Drive, Madison, WI 53711) to compare each predicted ORF amino acid sequence with all sequences found in the current GenBank, SWISS-PROT and PIR databases.
  • BLAST searches for local alignments between the ORF and the databank sequences and reports a probability score which indicates the probability of finding this sequence by chance in the database.
  • ORF's with significant homology e.g. probabilities lower than lxl 0" 6 that the homology is only due to random chance
  • membrane or exported proteins represent protein antigens for vaccine development. Possible functions can be provided to H. pylori genes based on sequence homology to genes cloned in other organisms.
  • ORF amino acid sequences identified as exported or membrane associated by this algorithm are likely protein antigens for vaccine development.
  • outer membrane proteins are likely to represent the best antigens to provide a protective immune response against H. pylori.
  • algorithms that can be used to aid in prediction of these outer membrane proteins include the presence of an amphipathic beta-sheet region at their C-terminus. This region which has been detected in a large number of outer membrane proteins in Gram negative bacteria is often characterized by hydrophobic residues (Phe or Tyr) approximately at positions 1, 3, 5, 7 and 9 from the C-terminus (e.g., see Figure 1, block F). Importantly, these sequences have not been detected at the C-termini of periplasmic proteins, thus allowing preliminary distinction between these classes of proteins based on primary sequence data. This phenomenon has been reported previously by Struyve et al. (J. Mol. Biol. 218:141-148, 1991).
  • FIG. 1 Also illustrated in Figure 1 are additional amino acid sequence motifs found in many outer membrane proteins of H pylori.
  • the amino acid sequence alignment in Figure 1 depicts portions of the sequence of five H pylori proteins (depicted in the single letter amino acid code) labeled with their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right.
  • Six distinct blocks (labeled A through F) of similar amino acid residues are found including the distinctive hydrophobic residues (Phe or Tyr; F or Y according to the single letter code for amino acid residues) frequently found at positions near the C-terminus of outer membrane proteins.
  • the presence of several shared motifs clearly establishes the similarity between members of this group of proteins.
  • FIG. 2 depicts the N- terminal portion of three H pylori proteins (designated by their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right).
  • H pylori proteins designated by their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right.
  • V Not-T (not-U) ⁇ A or C or G)
  • amino acid translations of this invention account for the ambiguity in the nucleic acid sequence by translating the ambiguous codon as the letter "X". In all cases, the permissible amino acid residues at a position are clear from an examination of the nucleic acid sequence based on the standard genetic code.
  • H. pylori Nucleic Acids and Polypeptides
  • one skilled in the art can alter the disclosed structure (of H. pylori genes), e.g., by producing fragments or analogs, and test the newly produced structures for activity. Examples of techniques known to those skilled in the relevant art which allow the production and testing of fragments and analogs are discussed below.
  • These, or analogous methods can be used to make and screen libraries of polypeptides, e.g., libraries of random peptides or libraries of fragments or analogs of cellular proteins for the ability to bind H pylori polypeptides. Such screens are useful for the identification of inhibitors of H pylori.
  • Fragments of a protein can be produced in several ways, e.g., recombinantly, by proteolytic digestion, or by chemical synthesis.
  • Internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a nucleic acid which encodes the polypeptide.
  • Expression of the mutagenized DNA produces polypeptide fragments. Digestion with "end-nibbling" endonucleases can thus generate DNA's which encode an array of fragments.
  • DNA's which encode fragments of a protein can also be generated by random shearing, restriction digestion or a combination of the above-discussed methods.
  • Fragments can also be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.
  • peptides of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or divided into overlapping fragments of a desired length.
  • Amino acid sequence variants of a protein can be prepared by random mutagenesis of DNA which encodes a protein or a particular domain or region of a protein. Useful methods include PCR mutagenesis and saturation mutagenesis. A library of random amino acid sequence variants can also be generated by the synthesis of a set of degenerate oligonucleotide sequences. (Methods for screening proteins in a library of variants are elsewhere herein).
  • PCR mutagenesis In PCR mutagenesis, reduced Taq polymerase fidelity is used to introduce random mutations into a cloned fragment of DNA (Leung et al., 1989, Technique 1 :11- 15).
  • the DNA region to be mutagenized is amplified using the polymerase chain reaction (PCR) under conditions that reduce the fidelity of DNA synthesis by Taq DNA polymerase, e.g., by using a dGTP/dATP ratio of five and adding Mn ⁇ " to the PCR reaction.
  • the pool of amplified DNA fragments are inserted into appropriate cloning vectors to provide random mutant libraries.
  • B Saturation Mutagenesis
  • Saturation mutagenesis allows for the rapid introduction of a large number of single base substitutions into cloned DNA fragments (Mayers et al., 1985, Science 229:242).
  • This technique includes generation of mutations, e.g., by chemical treatment or irradiation of single-stranded DNA in vitro, and synthesis of a complimentary DNA strand.
  • the mutation frequency can be modulated by modulating the severity of the treatment, and essentially all possible base substitutions can be obtained. Because this procedure does not involve a genetic selection for mutant fragments both neutral substitutions, as well as those that alter function, are obtained. The distribution of point mutations is not biased toward conserved sequence elements.
  • a library of homologs can also be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of a degenerate sequences can be carried out in an automatic DNA synthesizer, and the synthetic genes then ligated into an appropriate expression vector. The synthesis of degenerate oligonucleotides is known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp273-289; Itakura et al. ( ⁇ 9$4) Annu. Rev. Biochem.
  • Non-random or directed, mutagenesis techniques can be used to provide specific sequences or mutations in specific regions. These techniques can be used to create variants which include, e.g., deletions, insertions, or substitutions, of residues of the known amino acid sequence of a protein.
  • the sites for mutation can be modified individually or in series, e.g., by (1) substituting first with conserved .imino acids and then with more radical choices depending upon results achieved, (2) deleting the target residue, or (3) inserting residues of the same or a different class adjacent to the located site, or combinations of options 1-3.
  • Alanine Scanning Mutagenesis A
  • Alanine scanning mutagenesis is a useful method for identification of certain residues or regions of the desired protein that are preferred locations or domains for mutagenesis, Cunningham and Wells (Science 244:1081-1085, 1989).
  • a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine).
  • Replacement of an amino acid can affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell.
  • Those domains demonstrating functional sensitivity to the substitutions are then refined by introducing further or other variants at or for the sites of substitution.
  • the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined.
  • alanine scanning or random mutagenesis may be conducted at the target codon or region and the expressed desired protein subunit variants are screened for the optimal combination of desired activity.
  • Oligonucleotide-mediated mutagenesis is a useful method for preparing substitution, deletion, and insertion variants of DNA, see, e.g., Adelman et al., (DNA 2: 183, 1983). Briefly, the desired DNA is altered by hybridizing an oligonucleotide encoding a mutation to a DNA template, where the template is the single-stranded form of a plasmid or bacteriophage containing the unaltered or native DNA sequence of the desired protein.
  • a DNA polymerase is used to synthesize an entire second complementary strand of the template that will thus incorporate the oligonucleotide primer, and will code for the selected alteration in the desired protein DNA.
  • oligonucleotides of at least 25 nucleotides in length are used.
  • An optimal oligonucleotide will have 12 to 15 nucleotides that are completely complementary to the template on either side of the nucleotide(s) coding for the mutation. This ensures that the oligonucleotide will hybridize properly to the single- stranded DNA template molecule.
  • the oligonucleotides are readily synthesized using techniques known in the art such as th it described by Crea et al. (Proc. Natl. Acad. Sci. USA, 75: 5765[1978]).
  • C Cassette Mutagenesis Another method for preparing variants, cassette mutagenesis, is based on the technique described by Wells et al. (Gene, 34:315[1985]).
  • the starting material is a plasmid (or other vector) which includes the protein subunit DNA to be mutated.
  • the codon(s) in the protein subunit DNA to be mutated are identified. There must be a unique restriction endonuclease site on each side of the identified mutation site(s). If no such restriction sites exist, they may be generated using the above-described oligonucleotide-mediated mutagenesis method to introduce them at appropriate locations in the desired protein subunit DNA.
  • the plasmid is cut at these sites to linearize it.
  • a double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures. The two strands are synthesized separately and then hybridized together using standard techniques.
  • This double-stranded oligonucleotide is referred to as the cassette.
  • This cassette is designed to have 3' and 5' ends that are comparable with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid.
  • This plasmid now contains the mutated desired protein subunit DNA sequence.
  • Combinatorial mutagenesis can also be used to generate mutants (Ladner et al., WO 88/06630).
  • the amino acid sequences for a group of homologs or other related proteins are aligned, preferably to promote the highest homology possible. All of the amino acids which appear at a given position of the aligned sequences can be selected to create a degenerate set of combinatorial sequences.
  • the variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level, and is encoded by a variegated gene library.
  • a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of larger fusion proteins containing the set of degenerate sequences.
  • H. pylori polypeptide it is possible to modify the structure of an H pylori polypeptide for such purposes as increasing solubility, enhancing stability (e.g., shelf life ex vivo and resistar ce to proteolytic degradation in vivo).
  • a modified H. pylori protein or peptide can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition as described herein.
  • H. pylori peptide can also be modified by substitution of cysteine residues preferably with alanine, serine, threonine, leucine or glutamic acid residues to minimize dimerization via disulfide linkages.
  • amino acid side chains of fragments of the protein of the invention can be chemically modified. Another modification is cyclization of the peptide.
  • an H pylori polypeptide can be modified to incorporate one or more polymorphisms in the amino acid sequence of the protein resulting from any natural allelic variation. Additionally, D-amino acids, non- natural amino acids, or non-amino acid analogs can be substituted or added to produce a modified protein within the scope of this invention. Furthermore, an H. pylori polypeptide can be modified using polyethylene glycol (PEG) according to the method of A. Sehon and co-workers (Wie et al., supra) to produce a protein conjugated with PEG. In addition, PEG can be added during chemical synthesis of the protein. Other modifications of H.
  • PEG polyethylene glycol
  • pylori proteins include reduction alkylation (Tarr, Methods of Protein Microcharacterization, J. E. Silver ed., Humana Press, Clifton NJ 155-194 (1986)); acylation (Tarr, supra); chemical coupling to an appropriate carrier (Mishell and Shiigi, eds, Selected Methods in Cellular Immunology, WH Freeman, San Francisco, CA (1980), U.S. Patent 4,939,239; or mild formalin treatment (Marsh, (1971) Int. Arch, of Allergy andAppl. Immunol, 41 . : 199 - 215).
  • H. pylori protein or peptide it is possible to add an amino acid fusion moiety to the peptide backbone.
  • an amino acid fusion moiety for example, hexa-histidine can be added to the protein for purification by immobilized metal ion affinity chromatography (Hochuli, E. et al., (1988)
  • canonical protease sensitive sites can be engineered between regions, each comprising at least one epitope via recombinant or synthetic methods.
  • charged amino acid pairs such as KK or RR
  • the resulting peptide can be rendered sensitive to cleavage by cathepsin and/or other trypsin-like enzymes which would generate portions of the protein containing one or more epitopes.
  • such charged amino acid residues can result in an increase in the solubility of the peptide.
  • Techniques for screening large gene libraries often include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the genes under conditions in which detection of a desired activity, e.g., in this case, binding to H. pylori polypeptide or an interacting protein, facilitates relatively easy isolation of the vector encoding the gene whose product was detected.
  • detection of a desired activity e.g., in this case, binding to H. pylori polypeptide or an interacting protein.
  • Each of the techniques described below is amenable to high through-put analysis for screening large numbers of sequences created, e.g., by random mutagenesis techniques.
  • Two hybrid assays such as the system described above (as with the other screening methods described herein), can be used to identify polypeptides, e.g., fragments or analogs of a naturally-occurring H. pylori polypeptide, e.g., of cellular proteins, or of randomly generated polypeptides which bind to an H. pylori protein.
  • the H. pylori domain is used as the bait protein and the library of variants are expressed as fish fusion proteins.
  • a two hybrid assay (as with the other screening methods described herein), can be used to find polypeptides which bind a H. pylori polypeptide.
  • the candidate peptides are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind an appropriate receptor protein via the displayed product is detected in a "panning assay".
  • the gene library can be cloned into the gene for a surface membrane protein of a bacterial cell, and the resulting fusion protein detected by panning (Ladner et al., WO 88/06630; Fuchs et al. (1991) Bio/Technology 9:1370-1371; and Goward et al. (1992) TIBS 18:136-140).
  • a detectably labeled ligand can be used to score for potentially functional peptide homologs.
  • Fluorescently labeled ligands e.g., receptors
  • fluorescently labeled ligands allows cells to be visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, to be separated by a fluorescence-activated cell sorter.
  • a gene library can be expressed as a fusion prote c n the surface of a viral particle.
  • foreign peptide sequences can be expressed on the surface of infectious phage, thereby conferring two significant benefits.
  • E coli filamentous phages Ml 3, fd., and fl are most often used in phage display libraries.
  • Either of the phage gill or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle.
  • Foreign epitopes can be expressed at the NH2- terminal end of pill and phage bearing such epitopes recovered from a large excess of phage lacking this epitope (Ladner et al. PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267:16007-16010; Griffiths et al.
  • Peptides can be fused to pilin, a protein which polymerizes to form the pilus-a conduit for interbacterial exchange of genetic information (Thiry et al. (1989) Appl. Environ. Microbiol. 55, 984-993).
  • the pilus Because of its role in interacting with other cells, the pilus provides a useful support for the presentation of peptides to the extracellular environment.
  • Another large surface structure used for peptide display is the bacterial motive organ, the flagellum. Fusion of peptides to the subunit protein flagellin offers a dense array of many peptide copies on the host cells (Kuwajima et al. (1988) Bio/Tech. 6, 1080-1083).
  • Surface proteins of other bacterial species have also served as peptide fusion partners. Examples include the Staphylococcus protein A and the outer membrane IgA protease of Neisseria (Hansson et al. (1992) J Bacteriol. 174, 4239-4245 and Klauser et al.
  • the physical link between the ner tide and its encoding DNA occurs by the containment of the DNA within a particle (cell or phage) that carries the peptide on its surface. Capturing the peptide captures the particle and the DNA within.
  • An alternative scheme uses the DNA-binding protein Lad to form a link between peptide and DNA (Cull et al. (1992) PNAS USA 89: 1865-1869). This system uses a plasmid containing the Lad gene with an oligonucleotide cloning site at its 3 '-end.
  • Lacl-peptide fusion protein Under the controlled induction by arabinose, a Lacl-peptide fusion protein is produced. This fusion retains the natural ability of La to bind to a short DNA sequence known as LacO operator (LacO). By installing two copies of LacO on the expression plasmid, the Lacl-peptide fusion binds tightly to the plasmid that encoded it. Because the plasmids in each cell contain only a single oligonucleotide sequence and each cell expresses only a single peptide sequence, the peptides become specifically and stably associated with the DNA sequence that directed its synthesis.
  • LacO operator LacO operator
  • the cells of the library are gently lysed and the peptide-DNA complexes are exposed to a matrix of immobilized receptor to recover the complexes containing active peptides.
  • the associated plasmid DNA is then reintroduced into cells for amplification and DNA sequencing to determine the identity of the peptide ligands.
  • a large random library of dodecapeptides was made and selected on a monoclonal antibody raised against the opioid peptide dynorphin B.
  • a cohort of peptides was recovered, all related by a consensus sequence corresponding to a six-residue portion of dynorphin B. (Cull et al. (1992) Proc. Natl.
  • peptides-on-plasmids differs in two important ways from the phage display methods.
  • the peptides are attached to the C-terminus of the fusion protein, resulting in the display of the library members as peptides having free carboxy termini.
  • Both of the filamentous phage coat proteins, pill and pVIII are anchored to the phage through their C-termini, and the guest peptides are placed into the outward-extending N-terminal domains.
  • the phage- displayed peptides are presented right at the amino terminus of the fusion protein.
  • a second difference is the set of biological biases affecting the population of peptides actually present in the libraries.
  • the La fusion molecules are confined to the cytoplasm of the host cells.
  • the phage coat fusions are exposed briefly to the cytoplasm during translation but are rapidly secreted through the inner membrane into the periplasmic compartment, remaining anchored in the membrane by their C-terminal hydrophobic domains, with the N-termini, containing the peptides, protruding into the periplasm while awaiting assembly into phage particles.
  • the peptides in the Lad and phage libraries may differ significantly as a result of their exposure to different proteolytic activities.
  • phage coat proteins require transport across the inner membrane and signal peptidase processing as a prelude to incorporation into phage. Certain peptides exert a deleterious effect on these processes and are underrepresented in the libraries (Gallop et al. (1994) J. Med. Chem. 37(9): 1233-1251). These particular biases are not a factor in the Lad display system.
  • the polysomes are sufficiently robust to be affinity purified on immobilized receptors in much the same way as the more conventional recombinant peptide display libraries are screened.
  • RNA from the bound complexes is recovered, converted to cDNA, and amplified by PCR to produce a template for the next round of synthesis and screening.
  • the polysome display method can be coupled to the phage display system. Following several rounds of screening, cDNA from the enriched pool of polysomes was cloned into a phagemid vector. This vector serves as both a peptide expression vector, displaying peptides fused to the coat proteins, and as a DNA sequencing vector for peptide identification.
  • polysome-derived peptides on phage By expressing the polysome-derived peptides on phage, one can either continue the affinity selection procedure in this format or assay the peptides on individual clones for binding activity in a phage ⁇ LISA, or for binding specificity in a completion phage ⁇ LISA (Barret, et al. (1992) Anal. Biochem 204,357-364). To identify the sequences of the active peptides one sequences the DNA produced by the phagemid host.
  • the high through-put assays described above can be followed by secondar/ screens in order to identify further biological activities which will, e.g., allow one skilled in the art to differentiate agonists from antagonists.
  • the type of a secondary screen used will depend on the desired activity that needs to be tested.
  • an assay can be developed in which the ability to inhibit an interaction between a protein of interest and its respective ligand can be used to identify antagonists from a group of peptide fragments isolated though one of the primary screens described above. Therefore, methods for generating fragments and analogs and testing them for activity are known in the art. Once the core sequence of interest is identified, it is routine for one skilled in the art to obtain analogs and fragments.
  • the invention also provides for reduction of the protein binding domains of the subject H. pylori polypeptides to generate mimetics, e.g. peptide or non-peptide agents.
  • the peptide mimetics are able to disrupt binding of a polypeptide to its counter ligand, e.g., in the case of an H pylori polypeptide binding to a naturally occurring ligand.
  • the critical residues of a subject H. pylori polypeptide which are involved in molecular recognition of a polypeptide can be determined and used to generate H. peptidomimetics which competitively or noncompetitively inhibit binding of the H.
  • pylori polypeptide with an interacting polypeptide see, for example, European patent applications EP-412,762A and EP-B31.080A.
  • scanning mutagenesis can be used to map the amino acid residues of a particular H. pylori polypeptide involved in binding an interacting polypeptide
  • peptidomimetic compounds e.g. diazepine or isoquinoline derivatives
  • non- hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gama lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G.R.
  • H. pylori Nucleic Acids and Polypeptides This invention also features vaccine compositions or formulations (used interchangeably herein) for protection against infection by H pylori or for treatment of H. pylori infection.
  • treatment of H. pylori infection refers to therapeutic treatment of an existing or established H. pylori infection.
  • protection against H. pylori infection or “prophylactic treatment” refer to the use of H pylori vaccine formulation for reducing the risk of or preventing an infection in a subject at risk for H. pylori infection.
  • the vaccine compositions contain one or more immunogenic components, such as a surface protein, from H pylori, or portion thereof, and a pharmaceutically acceptable carrier.
  • the vaccine formulations of the invention contain at least one or combination of H. pylori polypeptides or fragments thereof, from same or different H pylori antigens.
  • Nucleic acids and H. pylori polypeptides for use in the vaccine formulations of the invention include the nucleic acids and polypeptides set forth in the Sequence Listing, preferably those H. pylori nucleic acids that encode surface proteins and surface proteins or fragments thereof. For example, a preferred nucleic acid and H.
  • pylori polypeptide for use in a vaccine composition of the invention is selected from the group of nucleic acids which encode cell envelope proteins and H pylori cell envelope proteins as set forth in Table 1.
  • nucleic acids which encode cell envelope proteins and H pylori cell envelope proteins as set forth in Table 1.
  • any nucleic acid encoding an immunogenic H. pylori protein and H. pylori polypetide, or portion thereof, can be used in the present invention.
  • These vaccines have therapeutic and/or prophylactic utilities.
  • One aspect of the invention provides a vaccine composition for protection against infection by H. pylori which contains at least one immunogenic fragment of an H pylori protein and a pharmaceutically acceptable carrier.
  • Preferred fragments include peptides of at least about 10 amino acid residues in length, preferably about 10-20 amino acid residues in length, and more preferably about 12-16 amino acid residues in length.
  • Immunogenic components of the invention can be obtained, for example, by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding the full-length H. pylori protein.
  • fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.
  • immunogenic components are identified by the ability of the peptide to stimulate T cells.
  • Peptides which stimulate T cells as determined by, for example, T cell proliferation or cytokine secretion are defined herein as comprising at least one T cell enitrpe.
  • T cell epitopes are believed to be involved in initiation and perpetuation of the immune response to the protein allergen which is responsible for the clinical symptoms of allergy. These T cell epitopes are thought to trigger early events at the level of the T helper cell by binding to an appropriate HLA molecule on the surface of an antigen presenting cell, thereby stimulating the T cell subpopulation with the relevant T cell receptor for the epitope.
  • a T cell epitope is the basic element, or smallest unit of recognition by a T cell receptor, where the epitope comprises amino acids essential to receptor recognition (e.g., approximately 6 or 7 amino acid residues). Amino acid sequences which mimic those of the T cell epitopes are within the scope of this invention.
  • immunogenic components of the invention are identified through genomic vaccination.
  • the basic protocol is based on the idea that expression libraries consisting of all or parts of a pathogen genome, e.g., an H pylori genome, can confer protection when used to genetically immunize a host.
  • This expression library immunization (ELI) is analogous to expression cloning and involves reducing a genomic expression library of a pathogen, e.g., H pylori, into plasmids that can act as genetic vaccines.
  • the plasmids can also be designed to encode genetic adjuvants which can dramatically stimulate the humoral response. These genetic adjuvants can be introduced at remote sites and act as well extracelluraly as intracellularly.
  • An expression library of pathogen DNA is used to immunize a host thereby producing the effects of antigen presentation of a live vaccine without the risk.
  • random fragments from the H pylori genome or from cosmid or plasmid clones, as well as PCR products from genes identified by genomic sequencing can be used to immunize a host.
  • the feasibility of this approach has been demonstrated with Mycoplasma pulmonis (Barry et al., Nature 377:632-635. 1995), where even partial expression libraries of Mycoplasma pulmonis, a natural pathogen in rodents, provided protection against challenge from the pathogen.
  • ELI is a technique that allows for production of a non-infectious multipartite vaccine, even when little is known about pathogen's biology, because ELI uses the immune system to screen candidate genes. Once isolated, these genes can be used as genetic vaccines or for development of recombinant protein vaccines. Thus, ELI allows for production of vaccines in a systematic, largely mechanized fashion.
  • Screening immunogenic components can be accomplished using one or more of several different assays.
  • peptide T cell stimulatory activity is assayed by contacting a peptide known or suspected of being immunogenic with an antigen presenting cell which presents appropriate M ⁇ C molecules in a T cell culture.
  • Presentation of an immunogenic H pylori peptide in association with appropriate M ⁇ C molecules to T cells in conjunction with the necessary costimulation has the effect of transmitting a signal to the T cell that induces the production of increased levels of cytokines, particularly of interleukin-2 and interleukin-4.
  • the culture supernatant can be obtained and assayed for interleukin-2 or other known cytokines.
  • any one of several conventional assays for interleukin-2 can be employed, such as the assay described in Proc. Natl. Acad. Sci USA, 86: 1333 (1989) the pertinent portions of which are incorporated herein by reference.
  • a kit for an assay for the production of interferon is also available from Genzyme Corporation (Cambridge, MA).
  • a common assay for T cell proliferation entails measuring tritiated thymidine incorporation.
  • the proliferation of T cells can be measured in vitro by determining the amount of ⁇ H-labeled thymidine incorporated into the replicating DNA of cultured cells. Therefore, the rate of DNA synthesis and, in turn, the rate of cell division can be quantified.
  • Vaccine compositions or formulations of the invention containing one or more immunogenic components preferably include a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • Suitable pharmaceutically acceptable carriers include, for example, one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof.
  • Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the H. pylori nucleic acid or polypeptide.
  • auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the H. pylori nucleic acid or polypeptide.
  • the polypeptide is preferably coadministered with a suitable adjuvant and/or a delivery system described herein.
  • the therapeutically effective amount of DNA or protein of this invention will depend, inter alia, upon the administration schedule, the unit dose of an H. pylori nucleic acid or polypeptide administered, whether the protein or nucleic acid is administered in combination with other therapeutic agents, the immune status and health of the patient, and the therapeutic activity of the particular protein or nucleic acid.
  • Vaccine formulations are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Methods for intramuscular immunization are described by Wolff et al. (1990) Science 247: 1465-1468 and by Sedegah et al. (1994) Immunology 9J_: 9866-9870. Other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Oral immunization is preferred over parenteral methods for inducing protection against infection by H pylori. Czinn et. al. (1993) Vaccine U_: 637-642.
  • Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like.
  • the vaccine formulation includes, as a pharmaceutically acceptable carrier, an adjuvant.
  • Suitable adjuvants for use in the vaccine formulations of the invention include, but are not limited, to aluminum hydroxide; N-acetyl-muramyl ⁇ L-threonyl-D-isoglutamine (thr-MDP); N-acetyl-nor- muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP); N- acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-( 1 '-2'-dipalmitoyl-sn-glycero-3- hydroxyphos-phoryloxy)-ethylamine (CGP 19835A, referred to a MTP-PE); RIBI, which contains three components from bacteria; monophosphoryl lipid A; trehalose dimycoloate; cell wall skeleton (MPL + TDM + CWS) in a 2% squalene/Tween
  • the vaccine formulation includes, as a pharmaceutically acceptable carrier, a delivery system.
  • Suitable delivery systems for use in the vaccine formulations of the invention include biodegradable microcapsules or immuno- stimulating complexes (ISCOMs), cochleates, or liposomes, genetically engineered attenuated live vectors such as viruses or bacteria, and recombinant (chimeric) virus-like particles, e.g., bluetongue.
  • the vaccine formulation includes both a delivery system and an adjuvant.
  • Delivery systems in humans may include enteric release capsules protecting the antigen from the acidic environment of the stomach, and including H pylori polypeptide in an insoluble form as fusion proteins.
  • Suitable carriers for the vaccines of the invention are enteric coated capsules and polylactide-glycolide microspheres.
  • Suitable diluents are 0.2 N Na ⁇ CO3 and/or saline.
  • Vaccines of the invention can be administered as a primary prophylactic agent in adults or in children, as a secondary prevention, after successful eradication of H pylori in an infected host, or as a therapeutic agent in the aim to induce an immune response in a susceptible host to prevent infection by H. pylori.
  • the vaccines of the invention are administered in amounts readily determined by persons of ordinary skill in the art. Thus, for adults a suitable dosage will be in the range of 10 ⁇ g to 10 g, preferably 10 ⁇ g to 100 mg, for example 50 ⁇ g to 50 mg. A suitable dosage for adults will also be in the range of 5 ⁇ g to 500 mg. Similar dosage ranges will be applicable for children.
  • the amount of adjuvant employed will depend on the type of adjuvant used.
  • the mucosal adjuvant is cholera toxin
  • it is suitably used in an amount of 5 ⁇ g to 50 ⁇ g, for example 10 ⁇ g to 35 ⁇ g.
  • the amount used will depend on the amount employed in the matrix of the microcapsule to achieve the desired dosage. The determination of this amount is within the skill of a person of ordinary skill in the art.
  • the optimal dose may be more or less depending upon the patient's body weight, disease, the route of administration, and other factors.
  • appropriate dosage levels can be obtained based on results with known oral vaccines such as, for example, a vaccine based on an E. coli lysate (6 mg dose daily up to total of 540 mg) and with an enterotoxigenic E. coli purified antigen (4 doses of 1 mg) (Schulman et al., J. Urol. 150:917-921 (1993)); Boedecker et al., American Gastroenterological Assoc. 999:A-222 (1993)).
  • the number of doses will depend upon the disease, the formulation, and efficacy data from clinical trials. Without intending any limitation as to the course of treatment, the treatment can be administered over 3 to 8 doses for a primary immunization schedule over 1 month (Boedeker, American Gastroenterological Assoc. 888: A-222 (1993)).
  • a vaccine composition of the invention can be based on a killed whole E. coli preparation with an immunogenic fragment of an H pylori protein of the invention expressed on its surface or it can be based on an E. coli lysate, wherein the killed E. coli acts as a carrier or an adjuvant.
  • the vaccine composition of the invention provides protection against H pylori infection by stimulating humoral and/or cell-mediated immunity against H.
  • the invention also includes antibodies specifically reactive with the subject H. pylori polypeptide.
  • Anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (See, for example, Antibodies: A Laboratory Manual ed. by ⁇ arlow and Lane (Cold Spring Harbor Press: 1988)).
  • a mammal such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide. Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art.
  • An immunogenic portion of the subject H pylori polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies.
  • the subject antibodies are immunospecific for antigenic determinants of the H. pylori polypeptides of the invention, e.g. antigenic determinants of a polypeptide of the invention contained in the Sequence Listing, or a closely related human or non-human mammalian homolog (e.g., 90% homologous, more preferably at least 95% homologous).
  • the anti-H pylori antibodies do not substantially cross react (i.e., react specifically) with a protein which is for example, less than 80% percent homologous to a sequence of the invention contained in the Sequence Listing.
  • the antibody has a binding affinity for a non-homologous protein which is less than 10 percent, more preferably less than 5 percent, and even more preferably less than 1 percent, of the binding affinity for a protein of the invention contained in the Sequence Listing. In a most preferred embodiment, there is no crossreactivity between bacterial and mammalian antigens.
  • antibody as used herein is intended to include fragments thereof which are also specifically reactive with H. pylori polypeptides.
  • Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab')2 fragments can be generated by treating antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges to produce Fab' fragments.
  • the antibody of the invention is further intended to include bispecific and chimeric molecules having an anti-H. pylori portion.
  • Both monoclonal and polyclonal antibodies (Ab) directed against H pylori polypeptides or H pylori polypeptide variants, and antibody fragments such as Fab' and F(ab')2, can be used to block the action of H. pylori polypeptide and allow the study of the role of a particular H. pylori polypeptide of the invention in aberrant or unwanted intracellular signaling, as well as the normal cellular function of the H pylori and by microinjection of anti-H. pylori polypeptide antibodies of the present invention.
  • Antibodies which specifically bind H pylori epitopes can also be used in immunohistochemical staining of tissue samples in order to evaluate the abundance and pattern of expression of H pylori antigens.
  • Anti H. pylori polypeptide antibodies can be used diagnostically in immuno-precipitation and immuno-blotting to detect and evaluate H pylori levels in tissue or bodily fluid as part of a clinical testing procedure.
  • the ability to monitor H pylori polypeptide levels in an individual can allow determination of the efficacy of a given treatment regimen for an individual afflicted with such a disorder.
  • pylori polypeptide can be measured in cells found in bodily fluid, such as in urine samples or can be measured in tissue, such as produced by gastric biopsy. Diagnostic assays using anti-H pylori antibodies can include, for example, immunoassays designed to aid in early diagnosis of H pylori infections.
  • the present invention can also be used as a method of detecting antibodies contained in samples from individuals infected by this bacterium using specific H pylori antigens.
  • anti-H. pylori polypeptide antibodies of the invention is in the immunological screening of cDNA libraries constructed in expression vectors such as ⁇ gtl 1, ⁇ gtl8-23, ⁇ ZAP, and ⁇ ORF8.
  • Messenger libraries of this type having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins.
  • ⁇ gtl 1 will produce fusion proteins whose amino termini consist of ⁇ -galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide.
  • Antigenic epitopes of a subject H. pylori polypeptide can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from infected plates with anti-H.
  • H. pylori polypeptide antibodies Phage, scored by this assay, can then be isolated from the infected plate. Thus, the presence of H. pylori gene homologs can be detected and cloned from other species, and alternate isoforms (including splicing variants) can be detected and cloned.
  • kits for diagnostic purposes typically comprise the nucleic acid, polypeptides or antibodies in vials or other suitable vessels.
  • Kits typically comprise other reagents for performing hybridization reactions, polymerase chain reactions (PCR), or for reconstitution of lyophilized components, such as aqueous media, salts, buffers, and the like.
  • Kits may also comprise reagents for sample processing such as detergents, chaotropic salts and the like.
  • Kits may also comprise immobilization means such as particles, supports, wells, dipsticks and the like.
  • Kits may also comprise labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like. With the nucleic acid and amino acid sequence information provided herein, individuals skilled in art can readily assemble kits to serve their particular purpose. Kits further can include instructions for use.
  • labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like.
  • the present invention provides assays which can be used to screen for drugs which are either agonists or antagonists of the normal cellular function, in this case, of the subject H pylori polypeptides, or of their role in intracellular signaling.
  • drugs which are either agonists or antagonists of the normal cellular function, in this case, of the subject H pylori polypeptides, or of their role in intracellular signaling.
  • Such inhibitors or potentiators may be useful as new therapeutic agents to combat H. pylori infections in humans.
  • a variety of assay formats will suffice and, in light of the present inventions, will be comprehended by the skilled artisan.
  • the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or change in enzymatic properties of the molecular target. Accordingly, in an exemplary screening assay of the present invention, the compound of interest is contacted with an isolated and purified H pylori polypeptide.
  • Screening assays can be constructed in vitro with a purified H. pylori polypeptide or fragment thereof, such as an H pylori polypeptide having enzymatic activity, such that the activity of .he polypeptide produces a detectable reaction product.
  • the efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound.
  • a control assay can also be performed to provide a baseline for comparison. Suitable products include those with distinctive absorption, fluorescence, or chemi-luminescence properties, for example, because detection may be easily automated.
  • a variety of synthetic or naturally occurring compounds can be tested in the assay to identify those which inhibit or potentiate the activity of the H pylori polypeptide. Some of these active compounds may directly, or with chemical alterations to promote membrane permeability or solubility, also inhibit or potentiate the same activity (e.g., enzymatic activity) in whole, live H. pylori cells.
  • H. pylori chromosomal DNA was isolated according to a basic DNA protocol outlined in Schleif R.F. and Wensink P.C., Practical Methods in Molecular Biology, p.98, Springer- Verlag, NY., 1981, with minor modifications. Briefly, cells were pelleted, resuspended in TE (10 mM Tris, 1 mM EDTA, p ⁇ 7.6) and GES lysis buffer (5.1 M guanidium thiocyanate, 0.1 M EDTA, p ⁇ 8.0, 0.5% N-laurylsarcosine) was added. Suspension was chilled and ammonium acetate (N ⁇ 4 Ac) was added to final concentration of 2.0 M. DNA was extracted, first with chloroform, then with phenol- chloroform, and reextracted with chloroform. DNA was precipitated with isopropanol, washed twice with 70% EtOH, dried and resuspended in TE.
  • the purified DNA fragments were then blunt-ended using T4 DNA polymerase.
  • the healed DNA was then ligated to unique BstXI-linker adapters in 100-1000 fold molar excess.
  • These linkers are complimentary to the BstXI-cut pMPX vectors, while the overhang is not self-complimentary. Therefore, the linkers will not concatemerize nor will the cut-vector religate itself easily.
  • the linker-adopted inserts were separated from the unincorporated linkers on a 1 % agarose gel and purified using GeneClean. The linker-adopted inserts were then ligated to each of the 20 pMPX vectors to construct a series of "shotgun" subclone libraries.
  • the vectors contain an out-of-frame lacZ gene at the cloning site which becomes in-frame in the event that an adapter-dimer is cloned, allowing these to be avoided by their blue-color. All subsequent steps were based on the multiplex DNA sequencing protocols outlined in Church G.M. and Kieffer-Higgins S., Science 240:185-188, 1988. Only major modifications to the protocols are highlighted. Briefly, each of the 20 vectors was then transformed into DH5 ⁇ competent cells (Gibco/BRL, DH5 transformation protocol). The libraries were assessed by plating onto antibiotic plates containing ampicillin, methicillin and IPTG/Xgal. The plates were incubated overnight at 37°C.
  • the DNA was covalently bound to the membranes by exposure to ultraviolet light, and hybridized with labeled oligonucleotides complimentary to tag sequences on the vectors (Church, supra).
  • the membranes were washed to rinse off non-specifically bound probe, and exposed to X-ray film to visualize individual sequence ladders. After autoradiography, the hybridized probe was removed by incubation at 65° C, and the hybridization cycle repeated with another tag sequence until the membrane had been probed 38 times for chemical sequencing membranes and 10 times for the dideoxy sequencing membranes.
  • each gel produced a large number of films, each containing new sequencing information. Whenever a new blot was processed, it was initially probed for an internal standard sequence added to each of the pools.
  • Digital images of the films were generated using a laser-scanning densitomet x (Molecular Dynamics, Sunnyvale, CA).
  • the digitized images were processed on computer workstations (VaxStation 4000's) using the program REPLICATM (Church et al., Automated DNA Sequencing and Analysis (J.C. Venter, ed.), Academic Press, 1994).
  • Image processing included lane straightening, contrast adjustment to smooth out intensity differences, and resolution enhancement by iterative gaussian deconvolution.
  • the sequences were then automatically picked in REPLICATM and displayed for interactive proofreading before being stored in a project database. The proofreading was accomplished by a quick visual scan of the film image followed by mouse clicks on the bands of the displayed image to modify the base calls.
  • sequence errors could be detected and corrected because multiple sequence reads covering the same portion of the genomic DNA provide adequate sequence redundancy for editing.
  • Each sequence automatically received an identification number (corresponding to microtiter plate, probe information, and lane set number). This number serves as a permanent identifier of the sequence so it is always possible to identify the original of any particular sequence without recourse to a specialized database. Routine assembly of H pylori sequences was done using the program FALCON
  • pylori ppiB contains a DNA sequence encoding a ⁇ is-Tag fused to the 5' end of the full length gene, because the protein product of this gene does not contain a signal sequence and is expressed as a cytosolic protein.
  • Sequences chosen (from the list of the DNA sequences of the invention) for cloning from the J99 strain of H pylori were prepared for amplification cloning by polymerase chain reaction (PCR).
  • Synthetic oligonucleotide primers (Table 3) specific for the 5' and 3' ends of open reading frames (ORFs) were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' end of the sequence) were designed to include an Ncol cloning site at the extreme 5' terminus, except for ⁇ pSeq. 4821082 where Ndel was used.
  • H pylori sequence 4821082 where the initiator methionine is immediately followed by the remainder of the native H. pylori DNA sequence.
  • All reverse primers included a EcoRI site at the extreme 5' terminus to permit cloning of each H pylori sequence into the reading frame of the pET-28b.
  • the pET-28b vector provides sequence encoding an additional 20 carboxy-terminal amino acids (only 19 amino acids in ⁇ pSeq.
  • Genomic DNA prepared from the J99 strain of H. pylori was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • genomic DNA 50 nanograms was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers) complementary to and flanking a defined H.
  • pylori ORF 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 2.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 100 microliters.
  • the following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/ GeneAmp PCR System 9600 thermal cycler:
  • each sample of amplified DNA was washed and purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, MD, USA). All amplified DNA samples were subjected to digestion with the restriction endonucleases, Ncol and EcoRI (New England BioLabs, Beverly, MA, USA), or in the case of HpSeq. 4821082 (SEQ ID NO: 1309), with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • DNA samples were then subjected to electrophoresis on 1.0 % NuSeive (FMC BioProducts, Rockland, ME USA) agarose gels. DNA was visualized by exposure to ethidium bromide and long wave uv irradiation. DNA contained in slices isolated from the agarose gel was purified using the Bio 101 GeneClean Kit protocol (Bio 101 Vista, CA, USA).
  • H. pylori DNA sequences into the pET-28b prokaryotic expression vector was prepared for cloning by digestion with Ncol and EcoRI, or in the case of H. pylori protein 4821082 with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • the pET-28a vector which encodes a His-Tag that can be fused to the 5' end of an inserted gene, was used and the cloning site prepared for cloning with the ppiB gene by digestion with BamHI and Xhol restriction endonucleases.
  • DNA inserts were cloned (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) into the previously digested pET-28b expression vector, except for the amplified insert for ppiB, which was cloned into the pET-28a expression vector. Products of the ligation reaction were then used to transform the BL21 strain of E. coli (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et ?1., d ⁇ s., 1994) as described below.
  • Competent bacteria E coli strain BL21 or E. coli strain BL21(DE3), were transformed with recombinant pET expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • ligation reaction 1 microliter was mixed with 50 microliters of electrocompetent cells and subjected to a high voltage pulse, after which, samples were incubated in 0.45 milliliters SOC medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgC12, 10 mM MgSO4 and 20, mM glucose) at 37°C with shaking for 1 hour. Samples were then spread on LB agar plates containing 25 microgram/ml kanamycin sulfate for growth overnight.
  • SOC medium 0.45 milliliters SOC medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgC12, 10 mM MgSO4 and 20, mM glucose
  • the pET vector can be propagated in any E. coli K-12 strain e.g. HMS174,
  • Hosts for expression include E. coli strains containing a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivative that carries the lad gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase is induced by addition of isopropyl-B-D-thiogalactoside (IPTG), and the T7 RN polymerase transcribes any target plasmid, such as pET-28b, carrying a T7 promoter and a gene of interest.
  • IPTG isopropyl-B-D-thiogalactoside
  • BL21(DE3) (Studier, F.W., Rosenberg, A.H., Dunn, J.J., and Dubendorff, J.W. (1990) Meth. Enzymol. 185, 60-89).
  • 50 nanograms of plasmid DNA isolated as described above was used to transform competent BL21 (DE3) bacteria as described above (provided by Novagen as part of the pET expression system kit).
  • the lacZ gene (beta-galactosidase) was expressed in the pET-System as described for the H pylori recombinant constructions.
  • Transformed cells were cultured in SOC medium for 1 hour, and the culture was then plated on LB plates containing 25 micrograms/ml kanamycin sulfate. The following day, bacterial colonies were pooled and grown in LB medium containing kanamycin sulfate (25 micrograms/ml) to an optical density at 600 nM of 0.5 to 1.0 O.D. units, at which point, 1 millimolar IPTG was added to the culture for 3 hours to induce gene expression of the H pylori recombinant DNA constructions.
  • bacteria were pelleted by centrifugation in a Sorvall RC-3B centrifuge at 3500 x g for 15 minutes at 4°C. Pellets were resuspended in 50 milliliters of cold 10 mM Tris- ⁇ Cl, p ⁇ 8.0, 0.1 M NaCl and 0.1 mM EDTA (STE buffer). Cells were then centrifuged at 2000 x g for 20 min at 4°C. Wet pellets were weighed and frozen at -80°C until ready for protein purification.
  • SDS-polyacrylamide gels (12% or 4.0 to 25 % acrylamide gradient gels) were purchased from BioRad (Hercules, CA, USA), and stained with Coomassie blue.
  • Molecular weight markers included rabbit skeletal muscle myosin (200 kDa), E. coli (- galactosidase (116 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anhydrase (31 kDa), soybean trypsin inhibitor (21.5 kDa), egg white lysozyme (14.4 kDa) and bovine aprotinin (6.5 kDa).
  • NTA Ni ⁇ +" nitrilotriacetate-agarose
  • Fractions containing the recombinant proteins from the Ni ⁇ + -NTA-agarose columns were pooled and then concentrated to approximately 5 ml by centrifugal filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 180-ml column (1.6 X 91 cm) of Sephacryl S-100 HR gel filtration medium equilibrated in Buffer A (10 mM Hepes, pH 7.5, 150 mM NaCl, 0.1 mM EGTA) and run in Buffer A at 18 ml/h.
  • Buffer A (10 mM Hepes, pH 7.5, 150 mM NaCl, 0.1 mM EGTA
  • Fractions containing the recombinant protein were identified by absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled and concentrated by centrifugal filtration.
  • Fractions containing the recombinant protein from the Ni ⁇ + -NTA-agarose column were pooled and dialyzed overnight against 1 liter of dialysis buffer (10 mM MOPS, pH 6.5, 50 mM NaCl, 0.1 mM EGTA, 0.02% Brij 35 and 1 mM PMSF).
  • the pellets were washed with lysis buffer containing 10 % glycerol, 10 mM EDTA, 1% Triton X-100, 1 mM PMSF and 0.1% -mercaptoethanol, followed by several washes with lysis buffer containing 1 M urea, 1 mM PMSF and 0.1 % 2- mercaptoethanol.
  • the resulting white pellet was composed primarily of inclusion bodies, free of unbroken cells and membranous materials.
  • the column was washed with 250 ml (50 bed volumes) of lysis buffer containing 8 M urea, 1.0 mM PMSF and 0.1 % 2-mercaptoethanol, and developed with sequential steps of lysis buffer containing 8M urea, 1 mM PMSF, 0.1 % 2- mercaptoethanol and 20, 100, 200, and 500 mM imidazole in succession. Fractions were monitored by absorbance at OD2 O nm ' anc * peak fractions were analyzed by SDS- PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
  • the pellet containing the inclusion bodies was solubilized in buffer B containing 8 M urea, 1 mM PMSF and 0.1 % 2-mercaptoethanol, and incubated for 1 hour at room temperature. Insoluble materials were removed by centrifugation at 20,000 x g for 30 min, and the cleared supernatant was loaded onto a 15 ml ( 1.6 x 7.5 cm ) SP-Sepharose column pre-equilibrated in buffer B, 6 M urea, 1 mM PMSF, 0.1 % 2-mercaptoethanol. After washing the column with 1 b ⁇ d volumes, the column was developed with a linear gradient from 0 to 500 mM NaCl.
  • H. pylori proteins were expressed, characterized immunologically and tested in animal efficacy studies as outlined below. Specifically, the immunomodulatory effects of H. pylori proteins were investigated in a mouse/H. pylori model which mimics the human H pylori infection in humans. In these studies, the effect of oral immunization of selected H pylori polypeptides in H. pylori infected mice was determined.
  • sequences selected for cloning from H. pylori strain J99 were prepared for amplification cloning by the polymerase chain reaction (PCR). All of the selected sequences encode for outer membrane H. pylori proteins, with vac9 (SEQ ID NO:125), vaclO (SEQ ID NO:147), vac22 (SEQ ID NO:121) and vac41 (SEQ ID NO:176) sequences all sharing a terminal phenylalanine residue.
  • vac32 SEQ ID NO: 108
  • vac36 SEQ ID NO: 149
  • vac37 SEQ ID NO: 139
  • Synthetic oligonucleotide primers for each ORF of interest Table 5 specific for the predicted mature 5' end of the ORF and downstream (3') of the predicted translational termination codon were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' terminus of the region of ORF of interest) were designed to include a Bamlll restriction site followed by a Ndel restriction site.
  • primers were designed to permit the initiation of protein translation at a methionine residue encoding within the Ndel restriction site sequence (in the case of producing a non ⁇ is-tagged recombinant protein) or to fuse in frame with the DNA sequence encoding the ⁇ is-tag (for producing ⁇ is-tagged recombinant protein), followed by the coding sequence for the remainder of the native H. pylori DNA.
  • All reverse oligonucleotide primers (specific for downstream (3') of the predicted translational termination codon of the ORF) were designed to include an EcoRI restriction site at the 5' terminus.
  • This combination of primers would enable each ORF of interest to be cloned into p ⁇ T28b (to produce a ⁇ is-tagged recombinant protein) or pET30a (to produce a non ⁇ is-tagged or native recombinant protein).
  • the pET28b vector provides sequence encoding an additional 20 amino- terminal amino acids (plus the methionine in the Ndel restriction site) including a stretch of six histidine residues which makes up the ⁇ is-tag.
  • Genomic DNA prepared from H. pylori strain J99 was used as the source of template DNA for the PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubei et al., eds., 1994).
  • genomic DNA 50 nanograms was introduced into a reaction tube containing 200 nanograms of both the forward and reverse synthetic oligonucleotide primer specific for the ORF of interest, and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies,
  • the PCR SuperMix is supplied in 1.1X concentrations and contains 22mM Tris- ⁇ Cl (p ⁇ 8.4), 55mM KCl, 1.65 mM MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22 units recombinant Taq polymerase/ml and stabilizers.
  • the following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/Gene Amp PCR System thermal cycler.
  • each sample of amplified DNA was subjected to electrophoresis on 1.0% agarose gels.
  • the DNA was visualized by exposure to ethidium bromide and long wave UV irradiation, and cut out in gel slices.
  • DNA was purified using the Wizard PCR Preps Kit (Promega Corp., Madison, WI, USA), and then subjected to digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The digested PCR amplicon was then re-electrophoresed and purified as before. Ligation ofH pylori DNA sequences into cloning vectors
  • the pOK12 vector (J. Vieira and J. Messing, Gene 100:189-194, 1991) was prepared for cloning for digestion with BamHl and EcoRI in the case of Vac9, 10, 22, 31 and 32, whereas the pSU21 vector (B. Bartolome et al, Gene 102:75-78, 1991) was prepared for cloning by digestion with BamHl and EcoRI in the case of Vac 41 (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • the vectors were subjected to electrophoresis on 1.0% agarose gels and purified using the Wizard PCR Preps kit (Promega Corp., Madison, WI, USA). Following ligation of the purified, digested vector and the purified, digested amplified H. pylori ORF, the products of the ligation reaction were transformed into E coli JM109 competent cells according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • Both the p ⁇ T28b and pET30a expression vectors were prepared for cloning by digestion with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • the H pylori DNA sequences were removed from pOK12 (Vac9, 10,23,31 and 32) or pSU21 (Vac41) plasmid backbones by digestion with N ⁇ and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • the p ⁇ T28b, pET30a and ⁇ were prepared for cloning by digestion with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • pylori DNA sequences were all electrophoresed on a 1% agarose gel and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the purified, digested expression vector and the purified, digest H. pylori DNA sequences, the products of the ligation reaction were transformed into E. coli JM109 compe ⁇ e . cells (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • Competent bacterial strains (BL21(DE3), BL21(DE3)pLyS, HMS174(DE3) and HMS174(DE3)pLysS were prepared and transformed with the recombinant pET28b expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). These expression host strains contain a chromosomal copy of the gene for T7 RNA polymerase.
  • T7 RNA polymerase expression is induced by the addition of isopropyl- ⁇ -D thiogalactoside (IPTG), and the T7 RNA polymerase then transcribes any target plasmid, such as pET28b, that carries a T7 promoter sequence and a gene of interest.
  • IPTG isopropyl- ⁇ -D thiogalactoside
  • Transformants were collected from LB agar plates containing 25ug/ml kanamycin sulfate (ensures maintenance of the pET28b-based recombinant plasmids) and used to inoculate LB broth containing 25ug/ml kanamycin sulfate and grown to an optical density at 600nm of 0.5 to 1.0 OD units, at which point ImM IPTG was added to the culture for one to three hours to induce gene expression of the H. pylori recombinant DNA constructions.
  • the host strain that provided the highest level of recombinant protein production was then chosen for use in a large-scale induction in order to purify the recombinant protein. All of the following proteins listed were expressed recombinantly and the strain giving thf highest level of expression listed: BL21(DE3) (vac31, vac26, vac37); BL21(DE3) pLysS (vac 9, 32); HMS174(DE3) (vac 10, 11). Purification of recombinant proteins and generation of specific antiserum
  • the inclusion bodies were dissolved in 20 ml 6M guanidine-HCl in lysis buffer with 1 mM PMSF and 0.1 % ⁇ -mercaptoethanol, and incubated on ice for 1 hour.
  • the column was washed with 20ml (2 bed volumes) of Lysis Buffer containing 6M guanidine-HCl, ImM PMSF and 0.1 % ⁇ -mercaptoethanol, then guanidine-HCl was removed slowly with a 100 ml linear gradient (from 6M to 0 M Guanidine-HCl) of lysis buffer containing 0.5% Brij 35, 1 mM PMSF, 0.1% ⁇ - mercaptochanol. Next, the column was developed with a 25 ml linear gradient of increasing imidazole (5 to 500 mM) in Lysis buffer containing 0.5% Brij 35, 1 mM
  • Fractions containing the recombinant proteins were pooled and then concentrated to approximately 8 ml by centrifugal filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 350-ml column (2.2 X 91 cm) of Sephacyl S-100 HR gel filtration medium equilibrated in Buffer A (50mM Sodium Phosphate, pH 8.0, 500 mM NaCl, 0.1 mM EGTA, 1 mM PMSF, 0.1% ⁇ -mercaptoethanol, 0.5% Brij 35) and ran in Buffer A at 30 ml/h. Fractions containing the recombinant protein were identified by absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled, concentrated to 1.5 to 2 mg/ml and dialysed overnight against 10 mM Potassium
  • a murine model ofH pylori infection was produced by infection of C57BL/6 mice with with H. pylori Sydney strain SSI and was used to assess the efficacy of recombinant H pylori vac36.
  • This mouse-adapted H. pylori strain is cagA+ vacA+, shows colonization levels in C57BL/6 mice equivalent to those observed in humans, forms adhesion pedestals, colonizes for at least 8 months, and elicits a chronic-active gastritis and mucosal atrophy (Lee et al, Gastroenterology, 112:1386-1397, 1997).
  • Dose-response studies have shown 100%) infection rates of inbred C57BL/6 and Balb/C mice at 8 weeks post-challenge with a single inoculation of 10 ⁇ organisms.
  • the presence ofH pylori organisms in gastric tissue was determined by culture of gastric tissue and by a quantitative urease assay. In the latter method, a longitudinal segment of antrum, representing approximately l A of the total antral region was placed in 1 ml of urea broth. After 4 hr, the extent of color change resulting from urea hydrolysis and increased p ⁇ was quantiated by spectrophotometric measurement of A550 (Fox et al, Immunol. 88:400-406, 1996). The assay sensitivity is ⁇ 10 ⁇ H pylori organisms. A positive (H /?v/or/-infected) gastric tissue was defined as that sample showing 2 standard deviations above the mean A550 value derived from a group of unchallenged uninfected age-matched control mice.
  • CT cholera toxin
  • Oral immunization with vac36 antigen interfered with the establishment ofH. pylori infection upon challenge with live H. pylori organisms. Mice immunized with purified recombinant vac36 antigen exhibited a significantly lower level of colonization by H pylori, as assessed by gastric urease activity and bacterial count assays (Table 6). Oral immunization with vac36 antigen also resulted in the generation of a local protective gastric immune response. Greater numbers of CD4 + T cells and of IgACC were recruited in the gastric tissues of vac36-immunized mice when compared with unimmunized H. #y/orz ' -infected mice (Table 7).
  • the level ofH. pylori in gastric tissue was assessed by bacterial counts, and shown as mean colony forming units ⁇ SEM
  • mice generate a local gastric immune response upon challenge with
  • Lysozyme was added to a final concentration of lmg/ml along with, SDS to 1% and RNAse A + Tl to 0.5mg/ml and 5 units/ml respectively, and incubated at 37 C for one hour. Proteinase K was then added to a final concentration of 0.4mg/ml and the sample was incubated at 55 C for more than one hour. NaCl was added to the sample to a concentration of 0.65 M, mixed carefully, and 0.15 ml of 10% CTAB in 0.7M NaCL (final is 1% CTAB/70mM NaCL) was added followed by incubation at 65°C for 20 minutes.
  • Genomic DNA prepared from twelve strains of Helicobacter pylori was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • genomic DNA (10 nanograms) was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers, see Table 8) complementary to and flanking a defined H.
  • pylori ORF 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 0.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 20 microliters in duplicate reactions.
  • Oligonucleotide primers used for PCR amplification ofH pylori DNA sequences.
  • each pair of samples were combined and used directly for cloning into the pCR cloning vector as described below.
  • Competent bacteria E coli strain TOPI OF' or E. coli strain INVaF' were transformed with recombinant pCR expression plasmids carrying the cloned H pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). Briefly, 2 microliters of 0.5 micromolar BME was added to each vial of 50 microliters of competent cells. Subsequently, 2 microliters of ligation reaction was mixed with the competent cells and incubated on ice for 30 minutes.
  • the cells and ligation mixture were then subjected to a "heat shock" at 42°C for 30 seconds, and were subsequently placed on ice for an additional 2 minutes, after which, samples were incubated in 0.45 milliliters SOC medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgC12, 10 mM MgSO4 and 20, mM glucose) at 37°C with shaking for 1 hour. Samples were then spread on LB agar plates containing 25 microgram/ml kanamycin sulfate or 100 micrograms/ml ampicillan for growth overnight. Transformed colonies of TOP10F' or INVaF' were then picked and analyzed to evaluate cloned inserts as described below.
  • Oligonucleotide primers used for sequencing ofH pylori DNA sequences Oligonucleotide primers used for sequencing ofH pylori DNA sequences.
  • Therapeutic targets are chosen from genes wh jse protein products appear to play key roles in essential cell pathways such as cell envelope synthesis, DNA synthesis, transcription, translation, regulation and colonization/virulence.
  • H. pylori Gene Sequences The sequences of the genes or ORFs (open reading frames) selected as knock-out targets are identified from the H. pylori genomic sequence and used to design primers to specifically amplify the genes/ORFs. All synthetic oligonucleotide primers are designed with the aid of the OLIGO program (National Biosciences, Inc., Madison, MN 55447, USA), and can be purchased from Gibco/BRL Life Technologies (Gaithersburg, MD, USA). If the ORF is smaller than 800 to 1000 base pairs, flanking primers are chosen outside of the open reading frame.
  • Genomic DNA prepared from the Helicobacter pylori ⁇ pJ99 strain (ATCC 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) is used as the source of template DNA for amplification of the ORFs by PCR (polymerase chain reaction) (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • PCR polymerase chain reaction
  • the ligation of the PCR product into the vector is accomplished by mixing a 6 fold molar excess of the PCR product, 10 ng of pT7Blue-T vector (Novagen), 1 microliter of T4 DNA Ligase Buffer (New England Biolabs, Beverly, MA, USA), and 200 units of T4 DNA Ligase (New England Biolabs) into a final reaction volume of 10 microliters. Ligation is allowed to proceed for 16 hours at 16°C.
  • Ligation products are electroporated (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994) into electroporation- competent XL-1 Blue or DH5-a E.coli cells (Clontech Lab., Inc. Palo Alto, CA, USA).
  • 1 microliter of ligation reaction is mixed with 40 microliters of electrocompetent cells and subjected to a high voltage pulse (25 microFarads, 2.5 kV, 200 ohms) after which the samples are incubated in 0.45 ml SOC medium (0.5% yeast extract, 2% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl 2 , 10 mM MgSO 4 and 20 mM glucose) at 37°C with shaking for 1 hour.
  • SOC medium 0.5% yeast extract, 2% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl 2 , 10 mM MgSO 4 and 20 mM glucose
  • these pT7Blue plasmid DNAs are used as templates for PCR amplification of the cloned inserts, using the same forward and reverse primers used for the initial amplification of the J99 H.pylori sequence.
  • Recognition of the primers and a PCR product of the correct size as visualized on a 2% TAE, ethidium bromide stained agarose gel are confirmation that the correct inserts had been cloned.
  • Two to six such verified clones are obtained for each knock-out target, and frozen at -70°C for storage. To minimize errors due to PCR, plasmid DNA from these verified clones are pooled, and used in subsequent cloning steps.
  • the sequences of the genes/ORFs are again used to design a second pair of primers which flank the region ofH pylori DNA to be either interrupted or deleted (up to 250 basepairs) within the ORFs but are oriented away from each other.
  • the pool of circular plasmid DNAs of the previously isolated clones are used as templates for this round of PCR. Since the orientation of amplification of this pair of deletion primers is away from each other, the portion of the ORF between the primers is not included in the resultant PCR product.
  • the PCR product is a linear piece of DNA with H. pylori DNA at each end and the pT7Blue vector backbone between them which, in essence, resultes in the deletion of a portion of the ORFs.
  • the PCR product is visualized on a 1% TAE, ethidium bromide stained agarose gel to confirm that only a single product of the correct size has been amplified.
  • a Kanamycin-resistance cassette (Labigne-Roussel et al., 1988 J. Bacteriology 170, 1704-1708) is ligated to this PCR product by the TA cloning method used previously (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • the Kanamycin cassette containing a Campylobacter kanamycin resistance gene is obtained by carrying out an EcoRI digestion of the recombinant plasmid pCTB8:Jt ⁇ « (Cover et al.,1994, J. Biological Chemistry 269, pp. 10566-10573).
  • the proper fragment (1.4 kb) is isolated on a 1% TAE gel, and isolated using the QIAquick gel extraction kit (Qiagen, Gaithersburg, MD, USA).
  • the fragment is end repaired using the Klenow fill-in protocol, which involved mixing 4ug of the DNA fragment, 1 microliter of dATP,dGTP, dCTP, dTTP at 0.5 mM, 2 microliter of Klenow Buffer (New England Biolabs) and 5 units of Klenow DNA Polymerase I Large (Klenow) Fragment (New England Biolabs) into a 20 microliter reaction, incubating at 30°C for 15 min, and inactivating the enzyme by heating to 75°C for 10 minutes.
  • This blunt-ended Kanamycin cassette is then purified through a Qiaquick column (Qiagen, Gaithersburg, MD, USA) to eliminate nucleotides.
  • the "T” overhang is then generated by mixing 5 micrograms of the blunt-ended kanamycin cassette, 10 mM Tris pH 8.3, 50 mM KCl, 2 mM MgCl , 5 units of DNA Polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA), 20 microliters of 5 mM dTTP, in a 100 microliter reaction and incubating the reaction for 2 hours at 37°C.
  • the "Kan-T” cassette is purified using a QIAquick column (Qiagen, Gaithersburg, MD, USA).
  • the PCR product of the deletion primers (F2 and R2) is ligated to the Kan-T cassette by mixing 10 to 25 ng of deletion primer PCR product, 50 - 75 ng Kan-T cassette DNA, 1 microliter lOx T4 DNA Ligase reaction mixture, 0.5 microliter T4 DNA Ligase (New England Biolabs, Beverly, MA, USA) in a 10 microliter reaction and incubating for 16 hours at 16°C.
  • the ligation products are transformed into XL-1 Blue or DH5-a E.coli cells by electroporation as described previously. After recovery in SOC, cells are plated onto LB plates containing 100 microgram/ml Ampicillin and grown overnight at 37°C. These plates are then replica plated onto plates containing 25 microgram/ml Kanamycin and allowed to grow overnight. Resultant colonies have both the Ampicillin resistance gene present in the pT7Blue vector, .a d the newly introduced Kanamycin resistance gene. Colonies are picked into LB containing 25 microgram/ml Kanamycin and plasmid DNA is isolated from the cultured cells using the Qiagen miniprep protocol (Qiagen, Gaithersburg, MD, USA).
  • Several tests by PCR amplification are conducted on these plasmids to verify that the Kanamycin is inserted in the H. pylori gene/ORF, and to determine the orientation of the insertion of the Kanamycin-resistance gene relative to the H. pylori gene/ORF.
  • the plasmid DNAs are used as templates for PCR amplification with the set of primers originally used to clone the H. pylori gene/ORFs.
  • the correct PCR product is the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette.
  • the orientation of the Kanamycin resistance gene with respect to the knock-out gene/ORF is determined and both orientations are eventually used in H. pylori transformations (see below).
  • primers are designed from the ends of the kanamycin resistance gene ("Kan-1" 5'-ATCTTACCTATCACCTCAAAT-3' (SEQ ID NO:255)), and "Kan-2" 5'-AGACAGCAACATCTTTGTGAA-3' (SEQ ID NO:256)).
  • the orientation of the Kanamycin cassette relative to the H.pylori sequence is determined. Positive clones are classified as either in the "A" orientation (the same direction of transcription is present for both the H pylori gene and the Kanamycin resistance gene), or in the "B" orientation (the direction of transcription for the H.pylori gene is opposite to that of the Kanamycin resistance gene). Clones which share the same orientation (A or B) are pooled for subsequent experiments and independently transformed into H. pylori.
  • Two strains ofH. pylori are used for transformation: ATCC 55679. the clinical isolate which provided the DNA from which the H pylori sequence database is obtained, and A ⁇ 244, an isolate which had been passaged in, and has the ability to colonize the mouse stomach.
  • Cells for transformation are grown at 37°C, 10% CO 2 , 100% humidity, either on Sheep-Blood agar plates or in Brucella Broth liquid. Cells are grown to exponential phase, and examined microscopically to determine that the cells are "healthy" (actively moving cells) and not contaminated.
  • cells are harvested by scraping cells from the plate with a sterile loop, suspended in 1 ml of ⁇ 3rucella Broth, spun down (1 minute, top speed in eppendorf microfuge) and resuspended in 200 microliters Brucella Broth. If grown in Brucella Broth liquid, cells are centrifuged (15 minutes at 3000 rpm in a Beckman TJ6 centrifuge) and the cell pellet resuspended in 200 microliters of Brucella broth. An aliquot of cells is taken to determine the optical density at 600 nm, in order to calculate the concentration of cells.
  • Cells are then spread onto that plate using a swab wetted in Brucella broth, and grown for 20 hours at 37°C, 6% CO 2 .
  • Cells are then transferred to a Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin, and allowed to grow for 3 to 5 days at 37°C, 6% CO 2 , 100% humidity. If colonies appear, they are picked and regrown as patches on a fresh Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin.
  • the template for PCR (DNA from the colony) is obtained by a rapid boiling DNA preparation method as follows. An aliquot of the colony (stab of the colony with a toothpick) is introduced into 100 microliters of 1% Triton X-100, 20 mM Tris, pH 8.5, and boiled for 6 minutes. An equal volume of phenol : chloroform (1 :1) is added and vortexed.
  • TEST 1 PCR with cloning primers originally used to amplify the gene/ORF.
  • a positive result of homologous recombination at the correct chromosomal location should show a single PCR product whose size is expected to be the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette.
  • a PCR product of just the size of the gene/ORF is proof that the gene had not been knocked out and that the transformant is not the result of homologous recombination at the correct chromosome location.
  • TEST 2 PCR with F3 (primer designed from sequences upstream of the gene/ORF and not present on the plasmid), and either primer Kan-1 or Kan-2 (primers designed from the ends of the kanamycin resistance gene), depending on whether the plasmid DNA used was of "A" or "B” orientation. Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected s ; ze (i.e., from the location of F3 to the insertion site of kanamycin resistance gene). No PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out. TEST 3.
  • PCR with R3 primer designed from sequences downstream of the gene/ORF and not present on the plasmid
  • primer Kan-1 or Kan-2 depending on whether the plasmid DNA used was of "A" or "B” orientation.
  • Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected size (i.e., from the insertion site of kanamycin resistance gene to the downstream location of R3).
  • no PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out.
  • plasmid DNA is further analyzed by PCR on DNA from transformant populations prior to plating for colony formation. This will verify that the plasmid can enter the cells and undergo homologous recombination at the correct site. Briefly, plasmid DNA is incubated according to the transformation protocol described above.
  • TEST 2 and TEST 3 DNA is extracted from the H pylori cells immediately after incubation with the plasmid DNAs and the DNA is used as template for the above TEST 2 and TEST 3. Positive results in TEST 2 and TEST 3 would verify that the plasmid DNA could enter the cells and undergo homologous recombination at the correct chromosomal location. If TEST 2 and TEST 3 are positive, then failure to obtain viable transformants indicates that the gene is essential, and cells suffering a disruption in that gene are incapable of colony formation.
  • H. pylori target gene and its protein product e.g., an H pylori enzyme
  • the assay is essentially as described by Fisher (Fischer, G., et.al. (1984) Biomed.
  • the assay measures the cis-trans isomerization of the
  • Ala-Pro bond in the test peptide N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (Sigma # S- 7388, lot # 84H5805).
  • the assay is coupled with ⁇ -chymotrypsin, where the ability of the protease to cleave the test peptide occurs only when the Ala-Pro bond is in trans.
  • test peptide The conversion of the test peptide to the trans isomer in the assay is followed at 390 nm on a Beckman Model DU-650 spectophotometer. The data are collected every second with an average scanning of time of 0.5 second. Assays are carried out in 35 mM Hepes, pH 8.0, in a final volume of 400 ul, with 10 ⁇ M ⁇ -chymotrypsin (type 1-5 from bovine Pancreas, Sigma # C-7762, lot 23H7020) and 10 nM PPIase. To initiate the reaction, 10 ⁇ l of the substrate ( 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in DMSO) is added to 390 ⁇ l of reaction mixture at room temperature.
  • substrate 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in DMSO
  • a 50 ml culture of Helicobacter pylori (strain J99) in Brucella broth is harvested at mid-log phase (OD 600 nm ⁇ 1) and resuspended in lysis buffer with the following protease inhibitors: 1 mM PMSF, and 10 ⁇ g/ml of each of aprotinin, leupeptin, pepstatine, TLCK, TPCK, and soybean trypsin inhibitor.
  • the suspension is subjected to 3 cycles of freeze -thaw (15 minutes at -70 C, then 30 minutes at room temperature), followed by sonication (three 20 second bursts).
  • the lysate is centrifuged (12,000 g x 30 minutes) and the supernatant is assayed for enzymatic activity as described above.
  • H. pylori enzymes can be expressed at high levels and in an active form in E coli. Such high yields of purified proteins provide for the design of various high throughput drug screening assays.
  • the p ⁇ T gene expression system Novagen
  • a DNA sequence encoding a peptide tag His-tag
  • the DNA sequence was cloned in frame with the glutathione-S-transferase protein to produce a GST-fusion protein.
  • the vectors used in this case were the pG ⁇ X series from Pharmacia LKB (Uppsala, Sweden).
  • sequences chosen for cloning from H. pylori strain J99 were prepared for amplification cloning by the polymerase chain reaction (PCR).
  • Synthetic oligonucleotide primers for the ORF of interest (Table 11) specific for the predicted mature 5' end of the ORF and either downstream (3') of the predicted translational termination codon or at specific points within the coding region were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' terminus of the region of ORF of interest) were designed to include either a BamHl or a Ndel restriction site.
  • primers within the Ndel restriction site sequence were designed to permit the initiation of protein translation at a methionine residue (encoded within the Ndel restriction site sequence, in the case of producing a non His-tagged recombinant protein) or to fuse in frame with the DNA sequence encoding the His-tag (for producing His tagged recombinant protein), followed by the coding sequence for the remainder of the native H. pylori DNA.
  • the primer with the BamHl restriction site was produced to fuse the H. pylori specific sequence in-frame with the C-terminus of the glutathione-S- transferase gene in the pGEX vectors (Pharmacia LKB, Uppsala, Sweden).
  • This combination of primers would enable the ORF of interest (or parts of the ORF of interest) to be cloned into p ⁇ T28b (to produce a His-tagged recombinant protein), pET30a (to produce a non His tagged or native recombinant protein) or the pGEX-4T or pGEX-5X series (to produce a GST fusion protein).
  • the pET28b vector provides sequence encoding an additional 20 amino-terminal amino acids (plus the methionine in the Ndel restriction site) including a stretch of six histidine residues which makes up the His-tag, whereas the pGEX vectors fuse the H.
  • Genomic DNA prepared from H. pylori strain J99 was used as the source of template DNA for the PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • PCR amplification reactions Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994.
  • genomic DNA 50 nanograms was introduced into a reaction tube containing 200 nanograms of both the forward and reverse synthetic oligonucleotide primer specific for the ORF of interest, and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA) in a total of 50 microliters.
  • the PCR SuperMix is supplied in 1.1X concentrations and contains 22mM Tris-HCl (pH 8.4), 55mM KCl, 1.65mM MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22units recombinant Taq polymerase/ml and stabilizers.
  • the following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/GeneAmp PCR System thermal cycler. Table 11: Oligonucleotide primers
  • DNA was subjected to electrophoresis on 1.0% agarose gels. The DNA was visualized by exposure to ethidium bromide and long wave UV irradiation, and cut out in gel slices. DNA was purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA), and then subjected to digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The digested PCR amplicon was then re-electrophoresed and purified as before.
  • the pOK12 vector (J. Vieira and J. Messing, Gene 100: 189-194, 1991) was prepared for cloning by digestion with BamHl and EcoRI or Ndel and EcoRI in the case of Vac41 (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The vectors were subjected to electrophoresis on 1.0% agarose gels and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA).
  • Both the p ⁇ T28b and pET30a expression vectors were prepared for cloning by digestion with Ndel and EcoRI, and the pG ⁇ X4T-3 vector was prepared for cloning by digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • the H. pylori DNA sequences were removed from pOK12 plasmid backbones by digestion with Ndel and EcoRI or BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • the p ⁇ T28b, pET30a, pGEX4T-3 and H. pylori DNA sequences were all electrophoresed on a 1 % agarose gel and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the purified, digested expression vector and the purified, digested H. pylori DNA sequences, the products of the ligation reaction were transformed into E. coli JM109 competent cells (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
  • Competent bacterial strains BL21(DE3), BL21(DE3) ⁇ LysS, ⁇ MS174(DE3) and HMS174(DE3)pLysS were prepared and transformed with the recombinant pET28b expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). These expression host strains contain a chromosomal copy of the gene for T7 RNA polymerase.
  • T7 RNA polymerase expression is induced by the addition of isopropyl- ⁇ -D-thiogalactoside (IPTG), and the T7 RNA polymerase then transcribes any taget plasmid, such as pET28b, that carries a T7 promoter sequence and a gene of interest.
  • Competent bacterial strains JM109 and DH5 ⁇ were prepared and transformed with the recombinant pGEX4T-3 expression plasmid carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • Transformants were collected from LB agar plates containing 25ug/ml kanamycin sulfate (ensures maintenance of the pET28b-based recombinant plasmids) or 1 OOug/ml ampicillin (ensures maintenance of the pGEX4T-3 -based recombinant plasmids) and used to inoculate LB broth containing 25ug/ml kanamycin sulfate or 1 OOug/ml ampicillin and grown to an optical density at 600nm of 0.5 to 1.0 OD units, at which point ImM IPTG was added to the culture for one to three hours to induce gene expression of the H. pylori recombinant DNA constructions.
  • the host strain that provided the highest level of recombinant protein production was then chosen for use in a large-scale induction in order to purify the recombinant protein.
  • the strains used were HMS174(DE3) (pET28b-based constructs) and DH5 ⁇ (pGEX4T-3 -based constructs).
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI -SENSE NO
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ORGANISM Helicobacter pylori
  • TTAAAAATTT TTGGTTGGCA CTATATCATA GAAACAGGCA GGATTTATAA TTATAATTTT 600
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI -SENSE NO
  • ORGANISM Helicobacter pylori
  • ATGTTAGTTA CTCGTTTTAA AAAAGCCTTC ATTTCTTATT CTTTAGGCGT GCTTGTTGTT 60
  • GGGGAGCAAA CCATAAAGCT TCCTGTTTCC AAAATAGCCT ATATAGGGAG TTATGTAGAA 180 GTGCCTGCCA TGCTTAATGT TTGGGATAGG GTTGTAGGCG TTTCTGATTA TGCCTTTAAG 240
  • CTTTCTTTCC AAGAGACAAC GATTGCAGAG GCCATGCAAG CTATGCAAGC TCAAGCCACG 480 GTCTTAGAAA TTGACGCTTC CAAAAAATTC GCCAAAATGC AAGAAACTTT GGACTTTATT 540
  • AAAATCAGCG GCCATCAAGC CATTAACTCA GACATTTTAC AACAAGGGGG TATTGATAAT 660
  • ATGAAGAAAA AATTTCTGTC ATTAACCTTA GGTTCGCTTT TAGTTTCCGC TTTAAGCGCT 60
  • AAAAACACCA AAGGCATTCA AGATCTTTCA GACAGCTATG AAAGATTGAA CAACCTTTTA 180
  • GGTTATGAAC CAGGACCATA CAGCATTTTA TCCACTGAAA ATTACGCGAA AATCAATAAA 540 GCTTATCAAA TCATCCAAAA GGCTTTTGGG AGCAGCGGAA AAGATATTCC TGCCTTAAGC 600
  • GAGTTCGTAA AAGACTCTTT AGGGGTGTGC CATGAAGTGC AAAACGGCCA TCTCCGTGGC 1140 ACGCCATCCG GCACGGTAAC TGATAACACT TGGGGAGCCG GTTGCGCGTA TGTGGGAGAG 1200
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • FEATURE FEATURE
  • GCGGTCGCTA GCTCTTCTTT TTTGATAGAA AAAAGCCAAC GCTTCCTAAA AGATAAGGGG 420 TATTTTTTAT TCTATAAAGG CGAGCAGTTA AAGAATGAAA TCGCTTATAA AACCACTGAA 480
  • MOLECULE TYPE DNA (genomic)
  • GGGAAATACC TTTATATGGG GGGGTATATG GGTTTAGGCT TGGGGGTTGT GGCGCATGGG 540 GTGAATTATA CGGCGGAATG GGGGATGTCT TTTAACGCAG GATTGGCTCT AACGGTATTA 600
  • GAAAAAAACC GCATTGAATT TGAATTTAAA ATTTTGAATA ATTTCCCTTT TTTGCAATCT 660
  • AATTCTTCAA AAGAGACTTG GTGGGGAGCT ATAGCAAGCA TTGGGTATCA ATATGTGTTC 720
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • CAGCTCACCG AAAAAGGGGT TTCACCCAAA GAGATGGATA AGGATAAGTT TGAAGAAGAA 180
  • CTTAACTTGT CTTATCAAGG GGAGATGTTA GACAGGTATG GCGCAAATGC CCCTAGCGCG 360 TTTAAAAACA ATATCAATAT TAACGCTCCT GTTTCTATGA TTAGCGTTAA ATTTGGGTAT 420
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI-SENSE NO
  • ORIGINAL SOURCE
  • ORGANISM Helicobacter pylori
  • CAGATTGCCC ATGACGCTCT TAAGACATTT TTAAAACATT ATTTTTTGCA CATTCATGAG 1020
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • GCTTTCAATT CGCCAAAGAT GTTTTTGGGG TTGGAGTTTG
  • GCTTAGGCAT CGCTGGGGCG 420
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • TCTAAAACGC CTAACAATAA TCAAGAAATG TTTAATAACT ATACAGCGGT ATGGTTGAGC 360 GATAAAATAG AGTTTTTTGA TTCTAAATTG GTGATAACTC CAGGGCTTAG ATACACTTTT 420
  • CAGCGTCAAA ACGAATGGAG TCCTGCCCTT AATATTGGCT ATAAACCTAT GGAAAATTGG 540
  • ACTAGGACTA ATTACAACCA AATTTTTAAT GAAATTGAAG TGGGGCAGCG CTATAGTTAT 660 AAAAATCTAT TGAGTTTTAA CACCAATTAT TTTGTGATTT TTGCCAAGCG TTACTATGCG 720
  • ACTTCTAACG CTGATGATAT TGCTTATTAT TTTACAGGCA TTGTCAATAA ACCCTTTGAC 900
  • CAAGTAAGCT CAATCTTATG GCAAAGCGGT AGGCATAAAA TCACAGGGAG TTTGCAAATC 1200

Abstract

Recombinant or substantially pure preparations of H. pylori polypeptides are described. The nucleic acids encoding the polypeptides also are described. The H. pylori polypeptides are useful for diagnostics and vaccine compositions, wherein the figure depicts an amino acid sequence alignment of five H. pylori proteins.

Description

NUCLEIC ACID AND AMINO ACID SEQUENCES RELATING TO HELICOBACTER PYLORI ND VACCINE COMPOSITIONS THEREOF
Background of the Invention Helicobacter pylori is a gram-negative, S-shaped, microaerophilic bacterium that was discovered and cultured from a human gastric biopsy specimen. (Warren, J.R. and B. Marshall, (1983) Lancet \ : 1273-1275; and Marshall et al., (1984) Microbios Lett. 25: 83-88). H. pylori has been strongly linked to chronic gastritis and duodenal ulcer disease. (Rathbone et. al., (1986) Gut 27: 635-641). Moreover, evidence is accumulating for an etiologic role of /, pylori in nonulcer dyspepsia, gastric ulcer disease, and gastric adenocarcinoma. (Blaser M. J., (1993) Trends Microbiol. I: 255- 260). Transmission of the bacteria occurs via the oral route, and the risk of infection increases with age. (Taylor, D.N. and M. J. Blaser, (1991) Epidemiol. Rev J_3: 42-50). H. pylori colonizes the human gastric mucosa, establishing an infection that usually persists for decades. Infection by H. pylori is prevalent worldwide. Developed countries have infection rates over 50% of the adult population, while developing countries have infection rates reaching 90% of the adults over the age of 20. (Hopkins R. J. and J. G. Morris (1994) Am. J. Med. 97: 265-277).
The bacterial factors necessary for colonization of the gastric environment, and for virulence of this pathogen, are poorly understood. Examples of the putative virulence factors include the following: urease, an enzyme that may play a role in neutralizing gastric acid pH (Eaton et al., (1991) Infect. Immunol. 59: 2470-2475; Ferrero, R.L. and A. Lee (1991) Microb. Ecol. Hlth. Dis. 4: 121-134; Labigne et al., (1991) J. Bacteriol. 173: 1920-1931); the bacterial flagellar proteins responsible for motility across the mucous layer. (Hazell et al., (1986) J. Inf. Dis. 153: 658-663; Leying et al., (1992) Mol. Microbiol. 6: 2863-2874; and Haas et al., (1993) Mol. Microbiol. 8: 753-760); Vac A, a bacterial toxin that induces the formation of intracellular vacuoles in epithelial cells (Schmitt, W. and R. Haas, (1994) Molecular Microbiol. 12(2): 307-319); and several gastric tissue-specific adhesins. (Boren et al., (1993) Science 262: 1892- 1895; Evans et al., (1993) J Bacteriol. 175: 674-683; and Falk et al., (1993) Proc. Natl. Acad. Sci. USA 90: 2035-203).
Numerous therapeutic agents are currently available that eradicate H. pylori infections in vitro. (Huesca et. al, (1993) Zbl. Bakt. 280: 244-252; Hopkins, R. J. and J. G. Morris, supra). However, many of these treatments are suboptimally effective in vivo because of bacterial resistance, altered drug distribution, patient non-compliance or poor drug availabilty. (Hopkins, R. J. and J. G. Morris, supra). Treatment with antibiotics combined with bismuth are part of the standard regime used to treat H. pylori infection. (Malfertheiner, P. and J. E. Dominguez-Munoz (1993) Clinical Therapeutics j_5 Supp. B: 37-48). Recently, combinations of a proton pump inhibitors and a single antibiotic have been shown to ameliorate duodenal ulcer disease. (Malfertheiner, P. and J. E. Dominguez-Munoz supra). However, methods employing antibiotic agents can have the problem of the emergence of bacterial strains which are resistant to these agents.
(Hopkins, R. J. and J. G. Morris, supra). These limitations demonstrate that new more effective methods are needed to combat H. pylori infections in vivo. In particular, the design of new vaccines that may prevent infection by this bacterium is highly desirable.
Summary of the Invention This invention relates to novel genes, e.g., genes encoding polypeptides such as bacterial surface proteins, from the organism Helicobacter pylori (H pylori), and other related genes, their products, and uses thereof. The nucleic acids and peptides of the present invention have utility for diagnostic and therapeutics for H. pylori and other Helicobacter species. They can also be used to detect the presence of H. pylori and other Helicobacter species in a sample; and for use in screening compounds for the ability to interfere with the H. pylori life cycle or to inhibit H. pylori infection. More specifically, this invention features compositions of nucleic acids corresponding to entire coding sequences of H. pylori proteins, including surface or secreted proteins or parts thereof, nucleic acids capable of binding mRNA from H. pylori proteins to block protein translation, and methods for producing H. pylori proteins or parts thereof using peptide synthesis and recombinant DNA techniques. This invention also features antibodies and nucleic acids useful as probes to detect H. pylori infection. In addition, vaccine compositions and methods for the protection or treatment of infection by H. pylori are within the scope of this invention. Detailed Description of the Drawings
Figure 1 depicts an amino acid sequence alignment of five H. pylori proteins (depicted in the single letter amino acid code and designated by their amino acid Sequence ID Numbers; shown N-terminal to C-terminal, left to right).
Figure 2 depicts the N-terminal portion of three H. pylori proteins (depicted in the single letter amino acid code and designated by their amino acid Sequence ID Numbers; shown N-terminal to C-terminal, left to right). Detailed Description of the Invention
In one aspect, the invention features a recombinant or substantially pure preparation of H. pylori polypeptide of SEQ ID NO: 98. The invention also includes substantially pure nucleic acid encoding an H. pylori polypeptide of SEQ ID NO: 98, such nucleic acid is contained in SEQ ID NO: 1. The H. pylori polypeptide sequences of the invention described herein are contained in the Sequence Listing, and the nucleic acids encoding H. pylori polypeptides of the invention are contained in the Sequence Listing.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 99, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 2.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 100, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 101, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 4.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 102, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 5.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 103, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 6.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 104, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 7.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 105, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 8. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide havin^ a-i amino acid sequence of SEQ ID NO: 106, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 9.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 107, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 10. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 108, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 11.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 109, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 12.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 110, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 13. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 11 1, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 14.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 112, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 15.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 113, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 16.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 114, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 17.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 115, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 18. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 116, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 19.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 117, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 20.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 118, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 21.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 119, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 22. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 120, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 23.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 121, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 24.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 122, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 25. In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 123, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 26.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 124, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 27.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 125, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 28.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 126, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 29.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 127, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 30. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 128, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 31.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 129, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 32.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 130, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 33.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 131, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 34. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 132, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 35.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 133, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 36.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 134, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 37. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 135, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 38.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 136, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 39.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 137, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 40.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 138, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 41.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 139, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 42. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 140, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO:43.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 141, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 44.
In another aspect, the invention features a substantially pi re nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 142, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 45.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 143, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 46. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 144, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 47.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 145, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 48.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 146, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 49. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 147, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 50.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 148, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 51.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 149, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 52.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 150, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 53.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 151, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 54. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 152, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 55.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 153, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 56.
In another aspect, the irvc >tion features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 154, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 57.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 155, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 58. In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 156, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 59.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 157, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 60.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 158, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 61. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 159, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 62.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 160, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 63.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 161, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 64.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 162, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 65.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 163, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 66. In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 164, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 67.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 165, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 68.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 166, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 69.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 167, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 70. In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 168, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 71.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 169, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 72.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 170, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 73. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 171, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 74.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 172, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 75.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 173, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 76.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 174, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 77.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 175, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 78. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 176, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 79.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 177, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 80.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 178, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 81.
In another aspect, the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 179, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 82. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 180, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 83.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 181, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 84.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 182, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 85. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 183, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 86.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 184, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 87.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 185, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 88.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 186, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 89.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 187, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 90. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 188, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 91.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 189, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 92.
In another aspect, the invention features a substa itially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 190, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 93.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 191, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 94. In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 192, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 95.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 193, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 96.
In another aspect, the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 194, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 97. In another aspect, the invention features an isolated nucleic acid having a nucleotide sequence encoding an H. pylori polypeptide at least about 60% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194. In a preferred embodiment, the isolated nucleic acid includes a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
In another aspect, the invention features an isolated nucleic acid having a nucleotide sequence encoding an H pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
In another aspect, the invention features an isolated nucleic acid which encodes an H pylori polypeptide, having a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
In another aspect, the invention features an isolated nucleic acid molecule encoding an H. pylori polypeptide, having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
In another aspect, the invention features an isolated nucleic acid having a nucleotide sequence of at least 8 nucleotides in length, wherein the sequence hybridizes under stringent hybridization conditions to a nucleic acid having a nucleotide sequence selected from the groun c nsisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H pylori cell envelope polypeptide or a fragment thereof, the nucleic acid selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 60, SEQ ID NO: 69, and SEQ ID NO: 83, or a complement thereof.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof encoded by a nucleic acid having a nucleotide sequence of SEQ ID NO: 63, or a complement thereof.
In another embodiment, the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, and SEQ ID NO: 39, or a complement thereof.
In another embodiment, the H. pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44, or a complement thereof.
In another embodiment, the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66, or a complement thereof.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94, or a complement thereof.
In another embodiment, H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H. pylori cell envelope polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 103, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ ID NO: 180.
In another embodiment, the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof having an amino acid sequence of SEQ ID NO: 160.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 1 14, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
In another embodiment, the H pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NC: 114, SEQ ID NO: 115, SEQ ID NO: 1 16, SEQ ID NO: 140, and SEQ ID NO: 141.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 1 19, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, and SEQ ID NO: 163. In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93, or a complement thereof.
In one embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 57 and SEQ ID NO: 58, or a complement thereof.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, wherein the nucleic acid is selected from the group consisting of SEQ ID NO: 86, SEQ ID NO: 87, or a complement thereof.
Particularly preferred is an isolated ruc'.eic acid having a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190. In one embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155. In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184. Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H. pylori secreted polypeptide or a fragment thereof, the nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31 , SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID NO: 95, and SEQ ID NO: 97, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H pylori secreted polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H pylori cellular polypeptide or a fragment thereof, the nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96, or a complement thereof.
Particularly preferred is an isolated nucleic acid having a nucleotide sequence encoding an H pylori cellular polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 1 18, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEO V) NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
In another aspect, the invention features a probe having a nucleotide sequence consisting of at least 8 nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof. In another aspect, the invention features an isolated H. pylori polypeptide having an amino acid sequence at least about 60% homologous to an H. pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
In another aspect, the invention features an isolated H. pylori polypeptide which is encoded by a nucleic acid having a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97. In one embodiment, the isolated H pylori polypeptide is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97. In another aspect, the invention features an isolated H. pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
In another aspect, the invention features an isolated H. pylori polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 97-SEQ ID NO: 194.
Particularly preferred is an isolated H. pylori cell envelope polypeptide or a fragment thereof, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 103, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ ID NO: 180.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H pylori flagella-associated polypeptide or a fragment thereof having an amino acid sequence of SEQ ID NO: 160.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 1 16, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136. In another embodiment, the H. pylori inner membrane polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 1 10, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, and SEQ ID NO: 163. In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
Particularly preferred is an isolated H pylori cell envelope polypeptide or a fragment thereof, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24. SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 60, and SEQ ID NO: 69, SEQ ID NO: 83.
In one embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof encoded by a nucleic acid having a nucleotide sequence of SEQ ID NO: 63.
In another embodiment, the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, and SEQ ID NO: 39.
In another embodiment, the H. pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44.
In another embodiment, the H pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 1 1, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66. In another embodiment, the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51 , SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94.
In another embodiment, the H pylori outer membrane polypeptide or a fragment thereof is an H pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52. Particularly preferred is an isolated H. pylori cytoplasmic polypeptide or a fragment thereof, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190. In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184.
Particularly preferred is an isolated H. pylori cytoplasmic polypeptide or a fragment thereof, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93.
In one embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 57, and SEQ ID NO: 58. In another embodiment, the H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 86 and SEQ ID NO: 87.
Particularly preferred is an isolated H. pylori cellular polypeptide or a fragment thereof, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 118, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
J articularly preferred is an isolated H pylori cellular polypeptide or a fragment thereof, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21 , SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96. Particularly preferred is an isolated H. pylori secreted polypeptide or a fragment thereof, wherein the polypeptide is selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 117, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
Particularly preferred is an isolated H. pylori secreted polypeptide or a fragment thereof, wherein the polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID NO: 95, and SEQ ID NO: 97. In another aspect, the invention features a chimeric H. pylori polypeptide comprising at least two H. pylori polypeptides or fragments thereof, wherein the polypeptides are encoded by nucleic acid sequences selected from the group consisting of SEQ ID NO: 1-SEQ ID NO:97.
In another aspect, the invention features a chimeric H. pylori polypeptide comprising at least two H. pylori polypeptides or fragments thereof, wherein the polypeptides are selected from the group consisting of SEQ ID NO:98-SEQ ID NO: 194. In another aspect, the invention features a fusion protein comprising an H. pylori polypeptide which comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194 operatively linked to a non-H. pylori polypeptide. In another aspect, the invention features a vaccine formulation for prophylactic or therapeutic treatment of an H. pylori infection comprising an effective amount of at least one isolated nucleic acid of the invention.
In another aspect, the invention features a vaccine formulation for prophylactic or therapeutic treatment of an H. pylori infection comprising an effective amount of at least one H. pylori polypeptide of the invention.
Preferably, the vaccine formulation of the invention further includes a pharmaceutically acceptable carrier. In one embodiment, the pharmaceutically acceptable carrier includes an adjuvant. In another embodiment, the pharmaceutically acceptable carrier includes a delivery system, e.g., a live vector, e.g., a bacteria or a virus. In another embodiment, the pharmaceutically acceptable carrier includes both an adjuvant and a delivery system. In another aspect, the invention features a method of treating or reducing a risk of H. pylori infection in a subject. The method includes administering to a subject a vaccine formulation of the invention, such that treatment or reduction of risk of H. pylori infection occurs. In another aspect, the invention features a method of producing a vaccine formulation of the invention. The method includes combining at least one isolated H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194 with a pharmaceutically acceptable carrier to thereby form a vaccine formulation. In another aspect, the invention features a method of producing a vaccine formulation of the invention. The method includes culturing a cell under condition that permit expression of an H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194; isolating the H. pylori polypeptide from the cell; and combining at least one isolated H. pylori polypeptide or a fragment thereof with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
In another aspect, the invention pertains to any individual H. pylori polypeptide member or nucleic acid encoding such a member from the above-identified groups of H. pylori polypeptides. In another aspect, the invention features nucleic acids capable of binding mRNA of H. pylori. Such nucleic acid is capable of acting as antisense nucleic acid to control the translation of mRNA of H. pylori. A further aspect features a nucleic acid which is capable of binding specifically to an H. pylori nucleic acid. These nucleic acids are also referred to herein as complements and have utility as probes and as capture reagents. In another aspect, the invention features an expression system comprising an open reading frame corresponding to H. pylori nucleic acid. The nucleic acid further comprises a control sequence compatible with an intended host. The expression system is useful for making polypeptides corresponding to H. pylori nucleic acid.
In another aspect, the invention features a cell transformed with the expression system to produce H. pylori polypeptides.
In another aspect, the invention features a method of generating antibodies against H pylori polypeptides which are capable of binding specifically to H. pylori polypeptides. Such antibodies have utility as reagents for immunoassays to evaluate the abundance and distribution of H. /?y/ør/-specific antigens. In another aspect, the invention features a method of generating vaccines for immunizing an individual against H. pylori. The vaccination method includes: immunizing a subject with at least one H. pylori polypeptide according to the present invention, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmaceutically acceptable carrier. Such vaccines have therapeutic and/or prophylactic utilities.
In another aspect, the invention provides a method for generating a vaccine comprising a modified immunogenic H. pylori polypeptide, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmacologically acceptable carrier.
In another aspect, the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori polypeptide. The method includes: contacting the candidate compound with an H pylori polypeptide and determining if the compound binds or otherwise interacts with an H. pylori polypeptide. Compounds which bind H. pylori are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.
In another aspect, the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori nucleic acid, e.g., DNA or RNA. The method includes: contacting the candidate compound with an H. pylori nucleic acid and determining if the compound binds or otherwise interacts with an H. pylori polypeptide. Compounds which bind H. pylori are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.
The invention features H pylori polypeptides, preferably a substantially pure preparation of an H pylori polypeptide, or a recombinant H pylori polypeptide. In preferred embodiments: the polypeptide has biological activity; the polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% identical or homologous to an amino acid sequence of the invention contained in the Sequence
Listing, preferably it has about 65% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing, and most preferably it has about 92% to about 99% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide is at least 5, 10, 2 J, 50, 100, or 150 amino acid residues in length; the polypeptide includes at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acid residues of the invention contained in the Sequence Listing. In yet another preferred embodiment, the amino acid sequence which differs in sequence identity by about 7% to about 8% from the H. pylori amino acid sequences of the invention contained in the Sequence Listing is also encompassed by the invention. In preferred embodiments: the H. pylori polypeptide is encoded by a nucleic acid of the invention contained in the Sequence Listing, or by a nucleic acid having at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleic acid of the invention contained in the Sequence Listing. In a preferred embodiment, the subject H. pylori polypeptide differs in amino acid sequence at 1, 2, 3, 5, 10 or more residues from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that the H. pylori polypeptide exhibits an H. pylori biological activity, e.g., the H. pylori polypeptide retains a biological activity of a naturally occurring H. pylori polypeptide. In preferred embodiments, the polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing. In yet other preferred embodiments, the H. pylori polypeptide is a recombinant fusion protein having a first H. pylori polypeptide portion and a second polypeptide portion, e.g., a second polypeptide portion having an amino acid sequence unrelated to H. pylori. The second polypeptide portion can be, e.g., any of glutathione-S-transferase, a DNA binding domain, or a polymerase activating domain. In preferred embodiment the fusion protein can be used in a two-hybrid assay.
Polypeptides of the invention include those which arise as a result of alternative transcription events, alternative RNA splicing events, and alternative translational and postranslational events.
The invention also encompasses an immunogenic component which includes at least one H. pylori polypeptide in an immunogenic preparation; the immunogenic component being capable of eliciting an immune response specific for the H. pylori polypeptide, e.g., a humoral response, an antibody response, or a cellular response. In preferred embodiments, the immunogenic component comprises at least one antigenic determinant from a polypeptide of the invention contained in the Sequence Listing. In another aspect, the invention provides a substantially pure nucleic acid having a nucleotide sequence which encodes an H. pylori polypeptide. In preferred embodiments: the encoded polypeptide has biological activity; the encoded polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous to an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length; the encoded polypeptide comprises at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acids of the invention contained in the Sequence Listing.
In preferred embodiments: the nucleic acid of the invention is that contained in the Sequence Listing; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or 99%) homologous with a nucleic acid sequence of the invention contained in the Sequence Listing.
In a preferred embodiment, the encoded H. pylori polypeptide differs (e.g., by amino acid substitution, addition or deletion of at least one amino acid residue) in amino acid sequence at 1, 2, 3, 5, 10 or more residues, from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that: the H. pylori encoded polypeptide exhibits a H. pylori biological activity, e.g., the encoded H pylori enzyme retains a biological activity of a naturally occurring H. pylori.
In preferred embodiments, the encoded polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5 ' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.
In preferred embodiments, the subject H. pylori nucleic acid will include a transcriptional regulatory sequence, e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence, operably linked to the H. pylori gene sequence, e.g., to render the H pylori gene sequence suitable for expression in a recombinant host cell.
In yet a further preferred embodiment, the nucleic acid which encodes an H pylori polypeptide of the invention, hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 8 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 12 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 20 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 40 consecutive nucleotides of the invention contained in the Sequence Listing. In a preferred embodiment, the nucleic acid encodes a peptide which differs by at least one amino acid residue from the sequences of the invention contained in the Sequence Listing.
In a preferred embodiment, the nucleic acid differs by at least one nucleotide from a nucleotide sequence of the invention contained in the Sequence Listing which encodes amino acids of the invention contained in the Sequence Listing.
In another aspect, the invention encompasses: a vector including a nucleic acid which encodes an H. pylori polypeptide or an H. pylori polypeptide variant as described herein; a host cell transfected with the vector; and a method of producing a recombinant
H. pylori polypeptide or H. pylori polypeptide variant; including culturing the cell, e.g., in a cell culture medium, and isolating the H. pylori or H. pylori polypeptide variant, e.g., from the cell or from the cell culture medium. In another aspect, the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a sequence of the invention contained in the Sequence Listing.
The invention also provides a probe or primer which includes a substantially purified oligonucleotide. The oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 8 consecutive nucleotides of sense or antisense sequence of the invention contained in the Sequence Listing, or naturally occurring mutants thereof. In preferred embodiments, the probe or primer further includes a label group attached thereto. The label group can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor. Preferably the oligonucleotide is at least 8 and less than 10, 20, 30, 50, 100, or 150 nucleotides in length.
The invention also provides an isolated H. pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid contained in the Sequence Listing. The invention further provides nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.
The H. pylori strain, from which genomic sequences have been sequenced, has been deposited in the American Type Culture Collection (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) as strain
ΗP-J99.
Included in the invention are: allelic variations; natural mutants; induced mutants; proteins encoded by DNA that hybridizes under high or low stringency conditions to a nucleic acid which encodes a polypeptide of the invention contained in the Sequence Listing (for definitions of high and low stringency see Current Protocols in
Molecular Biology, John Wiley & Sons, New York. 1989, 6.3.1 - 6.3.6 and 6.4.1-6.4.10, hereby incorporated by reference); and, polypeptides specifically bound by antisera to H. pylori polypeptides, especially by antisera to an active site or binding domain of H. pylori polypeptide. The invention also includes fragments, preferably biologically active fragments. These and other polypeptides are also referred to herein as H pylori polypeptide analogs or variants. Putative functions have been determined for several of the H pylori polypeptides of the invention, as shown in Table 1.
Accordingly, uses of the claimed H pylori polypeptides based on these identified functions, as well as other functions as described herein, are also within the scope of the invention.
In addition, the present invention encompasses H pylori polypeptides characterized as shown in Table 1 below, including: H pylori cell envelope proteins, H pylori secreted proteins, H pylori cytoplasmic proteins and H pylori cellular proteins. Members of these groups were identified by BLAST homology searches and by searches for secretion signal or transmembrane protein motifs. Polypeptides related by significant homology to the polypeptides of Table 1 are also considered to be classified in the manner of the homologs shown in Table 1.
TABLE 1
Figure imgf000028_0001
Figure imgf000029_0001
Figure imgf000030_0001
[In Table 1, "nt" represents nucleotide Seq. ID number and "aa" represents amino acid Seq. ID number] Definitions
The terms "purified polypeptide" and "isolated polypeptide" and "a substantially pure preparation of a polypeptide" are used interchangeably herein and, as used herein, mean a polypeptide that has been substantially, and preferably completely, separated from other proteins, lipids, and nucleic acids with which it naturally occurs. Preferably, the polypeptide is also separated from substances, e.g., antibodies or gel matrix, e.g., polyacrylamide, which are used to purify it. Preferably, the polypeptide constitutes at least 10, 20, 50 70, 80 or 95% dry weight of the purified preparation. Preferably, the preparation contains: sufficient polypeptide to allow protein sequencing; at least 1, 10, or 100 μg of the polypeptide; at least 1, 10, or 100 mg of the polypeptide. Furthermore, the terms "purified polypeptide" and "isolated polypeptide" and "a substantially pure preparation of a polypeptide," as used herein, refer to both a polypeptide obtained from nature or produced by recombinant DNA techniques as described herein.
For example, an "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the H. pylori protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of H. pylori protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language
"substantially free of cellular material" includes preparations of H. pylori protein having less than about 30% (by dry weight) of non-H. pylori protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-H. pylori protein, still more preferably less than about 10% of non-H. pylori protein, and most preferably less than about 5% non-H. pylori protein. When the H pylori protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation. The language "substantially free of chemical precursors or other chemicals" includes preparations of H. pylori protein i'i which the protein is separated from chemical precusors or other chemicals which are involved in the synthesis of the protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals" includes preparations of H. pylori protein having less than about 30% (by dry weight) of chemical precursors or non-H. pylori chemicals, more preferably less than about 20%) chemical precursors or non-H. pylori chemicals, still more preferably less than about 10% chemical precursors or non-H. pylori chemicals, and most preferably less than about 5% chemical precursors or non-H. pylori chemicals.
A purified preparation of cells refers to, in the case of plant or animal cells, an in vitro preparation of cells and not an entire intact plant or animal. In the case of cultured cells or microbial cells, it consists of a preparation of at least 10% and more preferably 50%) of the subject cells.
A purified or isolated or a substantially pure nucleic acid, e.g., a substantially pure DNA, (are terms used interchangeably herein) is a nucleic acid which is one or both of the following: not immediately contiguous with both of the coding sequences with which it is immediately contiguous (i.e., one at the 5' end and one at the 3' end) in the naturally-occurring genome of the organism from which the nucleic acid is derived; or which is substantially free of a nucleic acid with which it occurs in the organism from which the nucleic acid is derived. The term includes, for example, a recombinant DNA which is incorporated into a vector, e.g., into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other DNA sequences. Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional H. pylori DNA sequence. A "contig" as used herein is a nucleic acid representing a continuous stretch of genomic sequence of an organism.
An "open reading frame", also referred to herein as ORF, is a region of nucleic acid which encodes a polypeptide. This region may represent a portion of a coding sequence or a total sequence and can be determined from a stop to stop codon or from a start to stop codon.
As used herein, a "coding sequence" is a nucleic acid which is transcribed into messenger RNA and/or translated into a polypeptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a translation start codon at the five prime terminus and a translation stop code at the three prime terminus. A coding sequence can include but is not limited to messenger P A, synthetic DNA, and recombinant nucleic acid sequences.
A "complement" of a nucleic acid as used herein referes to an anti-parallel or antisense sequence that participates in Watson-Crick base-pairing with the original sequence. A "gene product" is a protein or structural RNA which is specifically encoded by a gene. As used herein, the term "probe" refers to a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest. Probes are often associated with or capable of associating with a label. A label is a chemical moiety capable of detection. Typical labels comprise dyes, radioisotopes, luminescent and chemiluminescent moieties, fluorophores, enzymes, precipitating agents, amplification sequences, and the like. Similarly, a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest and immobilizes such molecule is referred herein as a "capture ligand". Capture ligands are typically associated with or capable of associating with a support such as nitro-cellulose, glass, nylon membranes, beads, particles and the like. The specificity of hybridization is dependent on conditions such as the base pair composition of the nucleotides, and the temperature and salt concentration of the reaction. These conditions are readily discernable to one of ordinary skill in the art using routine experimentation.
Homologous refers to the sequence similarity or sequence identity between two polypeptides or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared x 100. For example, if 6 of 10 of the positions in two sequences are matched or homologous then the two sequences are 60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC share 50% homology. Generally, a comparison is made when two sequences are aligned to give maximum homology. Nucleic acids are hybridizable to each other when at least one strand of a nucleic acid can anneal to the other nucleic acid under defined stringency conditions. Stringency of hybridization is determined by: (a) the temperature at which hybridization and/or washing is performed; and (b) the ionic strength and polarity of the hybridization and washing solutions. Hybridization requires that the two nucleic acids contain complementary sequences; depending on the stringency of hybridization, however, mismatches may be tolerated. Typically, hybridization of two sequences at high stingency (such as, for example, in a solution of 0.5X SSC, at 65° C) requires that the sequences be essentially completely homologous. Conditions of intermediate stringency (such as, for example, 2X SSC at 65 ° C) and low stringency (such as, for example 2X SSC at 55° C), require correspondingly less overall complementarity between the hybridizing sequences. (IX SSC is 0.15 M NaCl, 0.015 M Na citrate). A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65°C.
The terms peptides, proteins, and polypeptides are used interchangeably herein. As used herein, the term "surface protein" refers to all surface accessible proteins, e.g. inner and outer membrane proteins, proteins adhering to the cell wall, and secreted proteins.
A polypeptide has H. pylori biological activity if it has one, two and preferably more of the following properties: (1) if when expressed in the course of an H. pylori infection, it can promote, or mediate the attachment of H pylori to a cell; (2) it has an enzymatic activity, structural or regulatory function characteristic of an H. pylori protein; (3) the gene which encodes it can rescue a lethal mutation in an H. pylori gene; (4) or it is immunogenic in a subject. A polypeptide has biological activity if it is an antagonist, agonist, or super-agonist of a polypeptide having one of the above-listed properties. A biologically active fragment or analog is one having an in vivo or in vitro activity which is characteristic of the H. pylori polypeptides of the invention contained in the Sequence Listing, or of other naturally occurring H. pylori polypeptides, e.g., one or more of the biological activities described herein. Especially preferred are fragments which exist in vivo, e.g., fragments which arise from post transcriptional processing or which arise from translation of alternatively spliced RNA's. Fragments include those expressed in native or endogenous cells as well as those made in expression systems, e.g., in CΗO cells. Because peptides such as H. pylori polypeptides often exhibit a range of physiological properties and because such properties may be attributable to different portions of the molecule, a useful H. pylori fragment or H pylori analog is one which exhibits a biological activity in any biological assay for H. pylori activity. Most preferably the fragment or analog possesses 10%, preferably 40%, more preferably 60%, 70%), 80% or 90% or greater of the activity of H pylori, in any in vivo or in vitro assay. Analogs can differ from naturally occurring H. pylori polypeptides in amino acid sequence or in ways that do not involve sequence, or both. Non-sequence modifications include changes in acetylation, methylation, phosphorylation, carboxylation, or glycosylation. Preferred analogs include H. pylori polypeptides (or biologically ct'.ve fragments thereof) whose sequences differ from the wild-type sequence by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions which do not substantially diminish the biological activity of the H. pylori polypeptide. Conservative substitutions typically include the substitution of one amino acid for another with similar characteristics, e.g., substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. Other conservative substitutions can be made in view of the table below.
TABLE 2
CONSERVATIVE AMINO ACID REPLACEMENTS
Figure imgf000035_0001
Other analogs within the invention are those with modifications which increase peptide stability; such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the peptide sequence. Also included are: analogs that include residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., β or γ amino acids; and cyclic analogs.
As used herein, the term "fragment", as applied to an H. pylori analog, will ordinarily be at least about 20 residues, more typically at least about 40 residues, preferably at least about 60 residues in length. Fragments of H. pylori polypeptides can be generated by methods known to those skilled in the art. The ability of a candidate fragment to exhibit a biological activity of H pylori polypeptide can be assessed by methods known to those skilled in the art as described herein. Also included are H. pylori polypeptides containing residues that are not required for biological activity of the peptide or that result from alternative mRNA splicing or alternative protein processing events.
An "immunogenic component" as used herein is a moiety, such as an H. pylori polypeptide, analog or fragment thereof, that is capable of eliciting a humoral and/or cellular immune response in a host animal alone or in combination with an adjuvant. An "antigenic component" as used herein is a moiety, such as an H. pylori polypeptide, analog or fragment thereof, that is capable of binding to a specific antibody with sufficiently high affinity to form a detectable antigen-antibody complex.
As used herein, the term "transgene" means a nucleic acid (encoding, e.g., one or more polypeptides), which is partly or entirely heterologous, i.e., foreign, to the transgenic animal or cell into which it is introduced, or, is homologous to an endogenous gene of the transgenic animal or cell into which it is introduced, but which is designed to be inserted, or is inserted, into the cell's genome in such a way as to alter the genome of the cell into which it is inserted (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout). A transgene can include one or more transcriptional regulatory sequences and any other nucleic acid, such as introns, that may be necessary for optimal expression of the selected nucleic acid, all operably linked to the selected nucleic acid, and may include an enhancer sequence.
As used herein, the term "transgenic cell" refers to a cell containing a transgene. As used herein, a "transgenic animal" is any animal in which one or more, and preferably essentially all, of the cells of the animal includes a transgene. The transgene can be introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by a process of transformation of competent cells or by microinjection or by infection with a recombinant virus. This molecule may be integrated within a chromosome, or it may be extrachromosomallv replicating DNA.
The term "antibody" as used herein is intended to include fragments thereof which are specifically reactive with H. pylori polypeptides.
As used herein, the term "cell-specific promoter" means a DNA sequence that serves as a promoter, i.e., regulates expression of a selected DNA sequence operably linked to the promoter, and which effects expression of the selected DNA sequence in specific cells of a tissue. The term also covers so-called "leaky" promoters, which regulate expression of a selected DNA primarily in one tissue, but cause expression in other tissues as well.
Misexpression, as used herein, refers to a non- wild type pattern of gene expression. It includes: expression at non-wild type levels, i.e., over or under expression; a pattern of expression that differs from wild type in terms of the time or stage at which the gene is expressed, e.g., increased or decreased expression (as compared with wild type) at a predetermined developmental period or stage; a pattern of expression that differs from wild type in terms of decreased expression (as compared with wild type) in a predetermined cell type or tissue type; a pattern of expression that differs from wild type in terms of the splicing size, amino acid sequence, post- transitional modification, or biological activity of the expressed polypeptide; a pattern of expression that differs from wild type in terms of the effect of an environmental stimulus or extracellular stimulus on expression of the gene, e.g., a pattern of increased or decreased expression (as compared with wild type) in the presence of an increase or decrease in the strength of the stimulus.
As used herein, "host cells" and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refers to cells which can become or have been used as recipients for a recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transfected. It is understood by individuals skilled in the art that the progeny of a single parental cell may not necessarily be completely identical in genomic or total DNA compliment to the original parent, due to accident or deliberate mutation.
As used herein, the term "control sequence" refers to a nucleic acid having a base sequence which is recognized by the host organism to effect the expression of encoded sequences to which they are ligated. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include a promoter, ribosomal binding site, terminators, and in some cases operators; in eukaryotes, generally such control sequences include promoters, terminators and in some instances, enhancers. The term control sequence is intended to include at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences.
As used herein, the term "operably linked" refers to sequences joined or ligated to function in their intended manner. For example, a control sequence is operably linked to coding sequence by ligation in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequence and host cell. The metabolism of a substance, as used herein, means any aspect of the, expression, function, action, or regulation of the substance. The metabolism of a substance includes modifications, e.g., covalent or non-covalent modifications of the substance. The metabolism of a substance includes modifications, e.g., covalent or non- covalent modification, the substance induces in other substances. The metabolism of a substance also includes changes in the distribution of the substance. The metabolism of a substance includes changes the substance induces in the distribution of other substances.
A "sample" as used herein refers to a biological sample, such as, for example, tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
The practice of the invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See e.g., Sambrook, Fritsch, and Maniatis, Molecular Cloning; Laboratory Manual 2nd ed. (1989); DNA Cloning, Volumes I and II (D.N Glover ed. 1985); Oligonucleotide Synthesis (M.J. Gait ed, 1984); Nucleic Acid Hybridization (B.D. Hames & S.J. Higgins eds. 1984); the series, Methods in Enzymoloqy (Academic Press, Inc.), particularly Vol. 154 and Vol. 155 (Wu and
Grossman, eds.) and PCR-A Practical Approach (McPherson, Quirke, and Taylor, eds., 1991).
I. Isolation of Nucleic Acids of H. pylori and Uses Therefor
H pylori Genomic Sequence
This invention provides nucleotide sequences of the genome of H. pylori which thus comprises a DNA sequence library of H. pylori genomic DNA. The detailed description that follows provides nucleotide sequences of H. pylori, and also describes how the sequences were obtained and how ORFs and protein-coding sequences were identified. Also described are methods of using the disclosed H. pylori sec uences in methods including diagnostic and therapeutic applications. Furthermore, the library can be used as a database for identification and comparison of medically important sequences in this and other strains of H. pylori. To determine the genomic sequence of H pylori, DNA was isolated from a strain of H pylori (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) and mechanically sheared by nebulization to a median size of 2 kb. Following size fractionation by gel electrophoresis, the fragments were blunt-ended, ligated to adapter oligonucleotides, and cloned into each of 20 different pMPX vectors (Rice et al., abstracts of Meeting of Genome Mapping and Sequencing, Cold Spring Harbor, NY, 5/1 1-5/15, 1994, p. 225) to construct a series of "shotgun" subclone libraries.
DNA sequencing was achieved using multiplex sequencing procedures essentially as disclosed in Church et al., 1988, Science 240:185; U.S. Patents No. 4,942,124 and 5,149,625). DNA was extracted from pooled cultures and subjected to chemical or enzymatic sequencing. Sequencing reactions were resolved by electrophoresis, and the products were transferred and covalently bound to nylon membranes. Finally, the membranes were sequentially hybridized with a series of labelled oligonucleotides complimentary to "tag" sequences present in the different shotgun cloning vectors. In this manner, a large number of sequences could be obtained from a single set of sequencing reactions. The cloning and sequencing procedures are described in more detail in the Exemplification.
Individual sequence reads obtained in this manner were assembled using the FALCON™ program (Church et al, 1994, Automated DNA Sequencing and Analysis, J.C. Venter, ed., Academic Press) and PHRAP (P. Green, Abstracts of DOE Human Genome Program Contractor-Grantee Workshop V, Jan. 1996, p.157). The average contig length was about 3-4 kb.
A variety of approaches are used to order the contigs so as to obtain a continuous sequence representing the entire H. pylori genome. Synthetic oligonucleotides are designed that are complementary to sequences at the end of each contig. These oligonucleotides may be hybridized to libaries of H. pylori genomic DNA in, for example, lambda phage vectors or plasmid vectors to identify clones that contain sequences corresponding to the junctional regions between individual contigs. Such clones are then used to isolate template DNA and the same oligonucleotides are used as primers in polymerase chain reaction (PCR) to amplify junctional fragments, the nucleotide sequence of which is then determined. The H. pylori sequences were analyzed for the presence of open reading frames
(ORFs) comprising at least 180 nucleotides As a result of the analysis of ORFs based on stop-to-stop codon reads, it should be understood that these ORFs may not correspond to the ORF of a naturally-occurring H. pylori polypeptide. These ORFs may contain start codons which indicate the initiation of protein synthesis of a naturally- occurring H. pylori polypeptide. Such start codons within the ORFs provided herein can be identified by those of ordinary skill in the relevant art, and the resulting ORF and the encoded H. pylori polypeptide is within the scope of this invention. For example, within the ORFs a codon such as AUG or GUG (encoding methionine or valine) which is part of the initiation signal for protein synthesis can be identified and the ORF modified to correspond to a naturally-occurring H. pylori polypeptide. The predicted coding regions were defined by evaluating the coding potential of such sequences with the program GENEMARK™ (Borodovsky and Mclninch, 1993, Comp. Chem. 17:123).
Other H pylori Nucleic Acids
The nucleic acids of this invention may be obtained directly from the DNA of the above referenced H. pylori strain by using the polymerase chain reaction (PCR). See "PCR, A Practical Approach" (McPherson, Quirke, and Taylor, eds., IRL Press, Oxford, UK, 1991) for details about the PCR. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, the authenticity of amplified products can be checked by conventional sequencing methods. Clones carrying the desired sequences described in this invention may also be obtained by screening the libraries by means of the PCR or by hybridization of synthetic oligonucleotide probes to filter lifts of the library colonies or plaques as known in the art (see, e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual 2nd edition, 1989, Cold Spring Harbor Press, NY).
It is also possible to obtain nucleic acids encoding H pylori polypeptides from a cDNA library in accordance with protocols herein described. A cDNA encoding an H. pylori polypeptide can be obtained by isolating total mRNA from an appropriate strain. Double stranded cDNAs can then be prepared from the total mRNA. Subsequently, the cDNAs can be inserted into a suitable plasmid or viral (e.g., bacteriophage) vector using any one of a number of known techniques. Genes encoding H pylori polypeptides can also be cloned using established polymerase chain reaction techniques in accordance with the nucleotide sequence information provided by the invention. The nucleic acids of the invention can be DNA or RNA. Preferred nucleic acids of the invention are contained in the Sequence Listing.
The nucleic acids of the invention can also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et a U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
Nucleic acids isolated or synthesized in accordance with features of the present invention are useful, by way of example, without limitation, as probes, primers, capture ligands, antisense genes and for developing expression systems for the synthesis of proteins and peptides corresponding to such sequences. As probes, primers, capture ligands and antisense agents, the nucleic acid normally consists of all or part (approximately twenty or more nucleotides for specificity as well as the ability to form stable hybridization products) of the nucleic acids of the invention contained in the Sequence Listing. These uses are described in further detail below. Probes
A nucleic acid isolated or synthesized in accordance with the sequence of the invention contained in the Sequence Listing can be used as a probe to specifically detect H. pylori. With the sequence information set forth in the present application, sequences of twenty or more nucleotides are identified which provide the desired inclusivity and exclusivity with respect to H. pylori, and extraneous nucleic acids likely to be encountered during hybridization conditions. More preferably, the sequence will comprise at least twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules.
Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Individuals skilled in the art will readily recognize that the nucleic acids, for use as probes, can be provided with a label to facilitate detection of a hybridization product.
Nucleic acid isolated and synthesized in accordance with the sequence of the invention contained in the Sequence Listing can also be useful as probes to detect homologous regions (especially homologous genes) of other Helicobacter species using appropriate stringency hybridization conditions as described herein. Capture Ligand
For use as a capture ligand, the nucleic acid selected in the manner described above with respect to probes, can be readily associated with a support. The manner in which nucleic acid is associated with supports is well known. Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing have utility to separate H. pylori nucleic acid from the nucleic acid of each other and other organisms. Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing can also have utility to separate other Helicobacter species from each other and from other organisms. Preferably, the sequence will comprise at least twenty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Primers
Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility as primers for the amplification of H. pylori nucleic acid. These nucleic acids may also have utility as primers for the amplification of nucleic acids in other Helicobacter species. With respect to polymerase chain reaction (PCR) techniques, nucleic acid sequences of > 10-15 nucleotides of the invention contained in the Sequence Listing have utility in conjunction with suitable enzymes and reagents to create copies of H pylori nucleic acid. More preferably, the sequence will comprise twenty or more nucleotides to convey stability to the hybridization product formed between the primer and the intended target molecules. Binding conditions of primers greater than 100 nucleotides are more difficult to control to obtain specificity. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, amplified products can be checked by conventional sequencing methods.
The copies can be used in diagnostic assays to detect specific sequences, including genes from H. pylori and/or other Helicobacter species. The copies can also be incorporated into cloning and expression vectors to generate polypeptides corresponding to the nucleic acid synthesized by PCR, as is described in greater detail herein.
Antisense
Nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized in accordance with the sequences described herein have utility as antisense agents to prevent the expression of H. pylori genes. These sequences also have utility as antisense agents to prevent expression of genes of other Helicobacter species. In one embodiment, nucleic acid or derivatives corresponding to H. pylori nucleic acids is loaded into a suitable carrier such as a liposome or bacteriophage for introduction into bacterial cells. For example, a nucleic acid having twenty or more nucleotides is capable of binding to bacteria nucleic acid or bacteria messenger RNA. Preferably, the antisense nucleic acid is comprised of 20 or more nucleotides to provide necessary stability of a hybridization product of non-naturally occurring nucleic acid and bacterial nucleic acid and/or bacterial messenger RNA. Nucleic ? ά having a sequence greater than 1000 nucleotides in length is difficult to synthesize but can be generated by recombinant DNA techniques. Methods for loading antisense nucleic acid in liposomes is known in the art as exemplified by U.S. Patent 4,241,046 issued December 23, 1980 to Papahadjopoulos et al. II. Expression of H pylori Nucleic Acids
Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility to generate polypeptides. The nucleic acid of the invention exemplified in the Sequence Listing or fragments of the nucleic acid encoding active portions of H pylori polypeptides can be cloned into suitable vectors or used to isolate nucleic acid. The isolated nucleic acid is combined with suitable DNA linkers and cloned into a suitable vector.
The function of a specific gene or operon can be ascertained by expression in a bacterial strain under conditions where the activity of the gene product(s) specified by the gene or operon in question can be specifically measured. Alternatively, a gene product may be produced in large quantities in an expressing strain for use as an antigen, an industrial reagent, for structural studies, etc. This expression can be accomplished in a mutant strain which lacks the activity of the gene to be tested, or in a strain that does not produce the same gene product(s). This includes, but is not limited to other Helicobacter strains, or other bacterial strains such as E. coli, Norcardia,
Corynebacterium, Campylobacter, and Streptomyces species. In some cases the expression host will utilize the natural Helicobacter promoter whereas in others, it will be necessary to drive the gene with a promoter sequence derived from the expressing organism (e.g., an E. coli beta-galactosidase promoter for expression in E. coli). To express a gene product using the natural H. pylori promoter, a procedure such as the following can be used. A restriction fragment containing the gene of interest, together with its associated natural promoter element and regulatory sequences (identified using the DNA sequence data) is cloned into an appropriate recombinant plasmid containing an origin of replication that functions in the host organism and an appropriate selectable marker. This can be accomplished by a number of procedures known to those skilled in the art. It is most preferably done by cutting the plasmid and the fragment to be cloned with the same restriction enzyme to produce compatible ends that can be ligated to join the two pieces together. The recombinant plasmid is introduced into the host organism by, for example, electroporation and cells containing the recombinant plasmid are identified by selection for the marker on the plasmid.
Expression of the desired gene product is detected using an assay specific for that gene product.
In the case of a gene that requires a different promoter, the body of the gene (coding sequence) is specifically excised and cloned into an appropriate expression plasmid. This subcloning can be done by several methods, but is most easily accomplished by PCR amplification of a specific fragment and ligation into an expression plasmid after treating the PCR product with a restriction enzyme or exonuclease to create suitable ends for cloning.
A suitable host cell for expression of a gene can be any procaryotic or eucaryotic cell. For example, an H. pylori polypeptide can be expressed in bacterial cells such as E. coli, insect cells (baculovirus), yeast, or mammalian cells such as Chinese hamster ovary cell (CΗO). Other suitable host cells are known to those skilled in the art.
Expression in eucaryotic cells such as mammalian, yeast, or insect cells can lead to partial or complete glycosylation and/or formation of relevant inter- or intra-chain disulfide bonds of a recombinant peptide product. Examples of vectors for expression in yeast S. cerivisae include pYepSecl (Baldari. et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and Ηerskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, CA). Baculovirus vectors available for expression of proteins in cultured insect cells (SF 9 cells) include the pAc series (Smith et al., (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow, V.A., and Summers, M.D., (1989) Virology 170:31-39). Generally, COS cells
(Gluzman, Y., (1981) Cell 23:175-182) are used in conjunction with such vectors as pCDM 8 (Aruffo, A. and Seed, B., (1987) Proc. Natl. Acad. Sci. USA 84:8573-8577) for transient amplification/expression in mammalian cells, while CΗO (dhfr Chinese Hamster Ovary) cells are used with vectors such as pMT2PC (Kaufman et al. (1987), EMBO J. 6: 187-195) for stable amplification/expression in mammalian cells. Vector DNA can be introduced into mammalian cells via conventional techniques such as calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, or electroporation. Suitable methods for transforming host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.
Expression in procaryotes is most often carried out in E. coli with either fusion or non-fusion inducible expression vectors. Fusion vectors usually add a number of NH2 terminal amino acids to the expressed target gene. These NH2 terminal amino acids often are referred to as a reporter group. Such reporter groups usually serve two purposes: 1) to increase the solubility of the target recombinant protein; and 2) to aid in the purification of the target recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the reporter group and the target recombinant protein to enable separation of the target recombinant protein from the reporter group subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase, maltose E binding protein, or protein A, respectively, to the target recombinant protein. A preferred reporter group is poly(His), which may be fused to the amino or carboxy terminus of the protein and which renders the recombinant fusion protein easily purifiable by metal chelate chromatography.
Inducible non-fusion expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pETl Id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89). While target gene expression relies on host RNA polymerase transcription from the hybrid trp-lac fusion promoter in pTrc, expression of target genes inserted into pETl Id relies on transcription from the T7 gnlO-lac 0 fusion promoter mediated by coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident λ prophage harboring a T7 gnl under the transcriptional control of the lacUV 5 promoter. For example, a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding an H. pylori polypeptide can be cultured under appropriate conditions to allow expression of the polypeptide to occur. The polypeptide may be secreted and isolated from a mixture of cells and medium containing the peptide. Alternatively, the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated. A cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. Polypeptides of the invention can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffmity purification with antibodies specific for such polypeptides.
Additionally, in many situations, polypeptides can be produced by chemical cleavage of a native protein (e.g., tryptic digestion) and the cleavage products can then be purified by standard techniques.
In the case of membrane bound proteins, these can be isolated from a host cell by contacting a membrane-associated protein fraction with a detergent forming a solubilized complex, where the membrane-associated protein is no longer entirely embedded in the membrane fraction and is solubilized at least to an extent which allows it to be chromatographically isolated from the membrane fraction. Several different criteria are used for choosing a detergent suitable for solubilizing these complexes. For example, one property considered is the ability of the detergent to solubilize the H. pylori protein within the membrane fraction at minimal denaturation of the membrane- associated protein allowing for the activity or functionality of the membrane-associated protein to return upon reconstitution of the protein. Another property considered when selecting the detergent is the critical micelle concentration (CMC) of the detergent in that the detergent of choice preferably has a high CMC value allowing for ease of removal after reconstitution. A third property considered when selecting a detergent is the hydrophobicity of the detergent. Typically, membrane-associated proteins are very hydrophobic and therefore detergents which are also hydrophobic, e.g., the triton series, would be useful for solubilizing the hydrophobic proteins. Another property important to a detergent can be the capability of the detergent to remove the H pylori protein with minimal protein-protein interaction facilitating further purification. A fifth property of the detergent which should be considered is the charge of the detergent. For example, if it is desired to use ion exchange resins in the purification process then preferably detergent should be an uncharged detergent. Chromatographic techniques which can be used in the final purification step are known in the art and include hydrophobic interaction, lectin affinity, ion exchange, dye affinity and immunoaffinity. One strategy to maximize recombinant H. pylori peptide expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128). Another strategy would be to alter the nucleic acid encoding an H pylori peptide to be inserted into an expression vector so that the individual codons for each amino acid would be those preferentially utilized in highly expressed E. coli proteins (Wada et al., (1992) Nuc. Acids Res. 20:2111-2118). Such alteration of nucleic acids of the invention can be carried out by standard DNA synthesis techniques.
The nucleic acids of the invention can also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See, e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
III. H pylori Polypeptides
This invention encompasses isolated H pylori polypeptides encoded by the disclosed H pylori genomic sequences, including the polypeptides of the invention contained in the Sequence Listing. Polypeptides of the invention are preferably at least 5 amino acid residues in length. Using the DNA sequence information provided herein, the amino acid sequences of the polypeptides encompassed by the invention can be deduced using methods well-known in the art. It will be understood that the sequence of an entire nucleic acid encoding an H. pylori polypeptide can be isolated and identified based on an ORF that encodes only a fragment of the cognate protein-coding region. This can be acheived, for example, by using the isolated nucleic acid encoding the ORF, or fragments thereof, to prime a polymerase chain reaction with genomic H. pylori DNA as template; this is followed by sequencing the amplified product.
The polypeptides of the invention can be isolated from wild-type or mutant H pylori cells or from heterologous organisms or cells (including, but not limited to, bacteria, yeast, insect, plant and mammalian cells) into which an H pylori nucleic acid has been introduced and expressed. In addition, the polypeptides can be part of recombinant fusion proteins.
H pylori polypeptides of the invention can be chemically synthesized using commercially automated procedures such as those referenced herein.
H pylori polypeptides of the invention are also intended to include chimeric proteins and truncated proteins as decribed herein.
Chimeric H. pylori proteins
H. pylori chimeric polypeptides comprise one or more H pylori polypeptides fused together. These combined sequences can be made by combining two or more genes, or two or more polypeptide encoding sequences, or at least one gene and at least one polypeptide encoding sequence in tandem, and the subsequent expression of the encoded proteins by conventional molecular biological techniques. The combined nucleotide sequences may be composed of a combination of either full length H. pylori nucleotide sequences or fragments of such sequences, e.g., fragments which contain immunologically relevant portions of the encoded H. pylori protein. These chimeric H pylori proteins then contain the combined or synergistic vaccine potential of each individual H. pylori protein sequence and can be used in vaccine formulations of the invention.
Truncated gene expression and protein production H. pylori proteins encoded by a given nucleotide sequence can also be used in a biologically active truncated form. Such truncation can be produced, for example, by the elimination of either 5' and/or 3' regions of the encoding nucleotide sequence. These truncations can affect recombinant expression of the encoded protein and/or subsequent purification of the protein. For example, truncation of a nucleotide sequence encoding a predicted export sequence of a specific protein may alter expression of the protein. Alternatively, C-terminal truncation of an H. pylori polypeptide by elimination of the 3' end of the nucleic acid coding region may also improve protein expression and subsequent purification and use, as is outlined in Example VIII below. Deletion of nucleic acid regions encoding internal H. pylori protein regions can also result in improved protein expression, purification and/or efficacy as a vaccine candidate.
IV. Identification of Nucleic Acids Encoding Vaccine Components and Targets for Agents Effective Against H pylori
The disclosed H pylori genome sequence includes segments that direct the synthesis of ribonucleic acids and polypeptides, as well as origins of replication, promoters, other types of regulatory sequences, and intergenic nucleic acids. The invention encompasses nucleic acids encoding immunogenic components of vaccines and targets for agents effective against H pylori. Identification of said immunogenic components involved in the determination of the function of the disclosed sequences can be achieved using a variety of approaches. Non-limiting examples of these approaches are described briefly below. Homology to known sequences: Computer-assisted comparison of the disclosed
H. pylori sequences with previously reported sequences present in publicly available databases is useful for identifying functional H. pylori nucleic acid and polypeptide sequences. It will be understood that protein-coding sequences, for example, may be compared as a whole, and that a high degree of sequence homology between two proteins (such as, for example, >80-90%) at the amino acid level indicates that the two proteins also possess some degree of functional homology, such as, for example, among enzymes involved in metabolism, DNA synthesis, or cell wall synthesis, and proteins involved in transport, cell division, etc. In addition, many structural features of particular protein classes have been identified and correlate with specific consensus sequences, such as, for example, binding domains for nucleotides, DNA, metal ions, and other small molecules; sites for covalent modifications such as phosphorylation, acylation, and the like; sites of proteimprotein interactions, etc. These consensus sequences may be quite short and thus may represent only a fraction of the entire protein-coding sequence. Identification of such a feature in an H. pylori sequence is therefore useful in determining the function of the encoded protein and identifying useful targets of antibacterial drugs.
Of particular relevance to the present invention are structural features that are common to secretory, transmembrane, and surface proteins, including secretion signal peptides and hydrophobic transmembrane domains. H. pylori proteins identified as containing putative signal sequences and/or transmembrane domains are useful as immunogenic components of vaccines. Identification of essential genes: Nucleic acids that encode proteins essential for growth or viability of H. pylori are preferred drug targets. H. pylori genes can be tested for their biological relevance to the organism by examining the effect of deleting and/or disrupting the genes, i.e., by so-called gene "knockout", using techniques known to those skilled in the relevant art. In this manner, essential genes may be identified. Strain-specific sequences: Because of the evolutionary relationship between different H pylori strains, it is believed that the presently disclosed H pylori sequences are useful for identifying, and/or discriminating between, previously known and new H pylori strains. It is believed that other H pylori strains will exhibit at least 70% sequence homology with the presently disclosed sequence. Systematic and routine analyses of DNA sequences derived from samples containing H pylori strains, and comparison with the present sequence allows for the identification of sequences that can be used to discriminate between strains, as well as those that are common to all H. pylori strains. In one embodiment, the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that discriminate between different strains of H. pylori. Strain-specific components can also be identified functionally by their ability to elicit or react with antibodies that selectively recognize one or more H. pylori strains.
In another embodiment, the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that are common to all H. pylori strains but are not found in other bacterial species.
Specific Example: Determination Of Candidate Protein Antigens For Antibody And Vaccine Development
The selection of candidate protein antigens for vaccine development can be derived from the nucleic acids encoding H pylori polypeptides. First, the ORF's can be analyzed for homology to other known exported or membrane proteins and analyzed using the discriminant analysis described by Klein, et al. (Klein, P., Kanehsia, M., and DeLisi, C. (1985) Biochimica et Biophysica Acta 815, 468-476) for predicting exported and membrane proteins. Homology searches can be performed using the BLAST algorithm contained in the Wisconsin Sequence Analysis Package (Genetics Computer Group, Um've.sity Research Park, 575 Science Drive, Madison, WI 53711) to compare each predicted ORF amino acid sequence with all sequences found in the current GenBank, SWISS-PROT and PIR databases. BLAST searches for local alignments between the ORF and the databank sequences and reports a probability score which indicates the probability of finding this sequence by chance in the database. ORF's with significant homology (e.g. probabilities lower than lxl 0"6 that the homology is only due to random chance) to membrane or exported proteins represent protein antigens for vaccine development. Possible functions can be provided to H. pylori genes based on sequence homology to genes cloned in other organisms.
Discriminant analysis (Klein, et al. supra) can be used to examine the ORF amino acid sequences. This algorithm uses the intrinsic information contained in the ORF amino acid sequence and compares it to information derived from the properties of known membrane and exported proteins. This comparison predicts which proteins will be exported, membrane associated or cytoplasmic. ORF amino acid sequences identified as exported or membrane associated by this algorithm are likely protein antigens for vaccine development.
Surface exposed outer membrane proteins are likely to represent the best antigens to provide a protective immune response against H. pylori. Among the algorithms that can be used to aid in prediction of these outer membrane proteins include the presence of an amphipathic beta-sheet region at their C-terminus. This region which has been detected in a large number of outer membrane proteins in Gram negative bacteria is often characterized by hydrophobic residues (Phe or Tyr) approximately at positions 1, 3, 5, 7 and 9 from the C-terminus (e.g., see Figure 1, block F). Importantly, these sequences have not been detected at the C-termini of periplasmic proteins, thus allowing preliminary distinction between these classes of proteins based on primary sequence data. This phenomenon has been reported previously by Struyve et al. (J. Mol. Biol. 218:141-148, 1991).
Also illustrated in Figure 1 are additional amino acid sequence motifs found in many outer membrane proteins of H pylori. The amino acid sequence alignment in Figure 1 depicts portions of the sequence of five H pylori proteins (depicted in the single letter amino acid code) labeled with their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right. Six distinct blocks (labeled A through F) of similar amino acid residues are found including the distinctive hydrophobic residues (Phe or Tyr; F or Y according to the single letter code for amino acid residues) frequently found at positions near the C-terminus of outer membrane proteins. The presence of several shared motifs clearly establishes the similarity between members of this group of proteins.
In addition, outer membrane proteins isolated from H. pylori frequently share a motif near the mature N-terminus (i.e., after processing to remove the secretion signal) as illustrated in the blocked amino acid residues in Figure 2. Figure 2 depicts the N- terminal portion of three H pylori proteins (designated by their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right). One skilled in the art would know that these shared sequence motifs are highly significant and establish a similarity among this group of proteins.
Infrequently it is not possible to distinguish between multiple possible nucleotides at a given position in the nucleic acid sequence. In those cases the ambiguities are denoted by an extended alphabet as follows:
These are the official IUPAC-IUB single-letter base codes
Code Base Description
G Guanine
A Adenine
T Thymine
C Cytosine
R Purine (A or G)
Y Pyrimidine (C or T or U)
M Amino (A or C)
K Ketone [G or T) s Strong interaction (C or G) w Weak interaction (A or T)
H Not-G [A or C or T)
B Not-A C or G or T)
V Not-T (not-U) ^A or C or G)
D Not-C [A or G or T)
N Any ^A or C or G or T)
The amino acid translations of this invention account for the ambiguity in the nucleic acid sequence by translating the ambiguous codon as the letter "X". In all cases, the permissible amino acid residues at a position are clear from an examination of the nucleic acid sequence based on the standard genetic code.
V. Production of Fragments and Analogs of H. pylori Nucleic Acids and Polypeptides Based or the discovery of the H. pylori gene products of the invention provided in the Sequence Lsiting, one skilled in the art can alter the disclosed structure (of H. pylori genes), e.g., by producing fragments or analogs, and test the newly produced structures for activity. Examples of techniques known to those skilled in the relevant art which allow the production and testing of fragments and analogs are discussed below. These, or analogous methods can be used to make and screen libraries of polypeptides, e.g., libraries of random peptides or libraries of fragments or analogs of cellular proteins for the ability to bind H pylori polypeptides. Such screens are useful for the identification of inhibitors of H pylori.
Generation of Fragments
Fragments of a protein can be produced in several ways, e.g., recombinantly, by proteolytic digestion, or by chemical synthesis. Internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a nucleic acid which encodes the polypeptide. Expression of the mutagenized DNA produces polypeptide fragments. Digestion with "end-nibbling" endonucleases can thus generate DNA's which encode an array of fragments. DNA's which encode fragments of a protein can also be generated by random shearing, restriction digestion or a combination of the above-discussed methods. Fragments can also be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, peptides of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or divided into overlapping fragments of a desired length.
Alteration of Nucleic Acids and Polypeptides: Random Methods
Amino acid sequence variants of a protein can be prepared by random mutagenesis of DNA which encodes a protein or a particular domain or region of a protein. Useful methods include PCR mutagenesis and saturation mutagenesis. A library of random amino acid sequence variants can also be generated by the synthesis of a set of degenerate oligonucleotide sequences. (Methods for screening proteins in a library of variants are elsewhere herein).
(A) PCR Mutagenesis In PCR mutagenesis, reduced Taq polymerase fidelity is used to introduce random mutations into a cloned fragment of DNA (Leung et al., 1989, Technique 1 :11- 15). The DNA region to be mutagenized is amplified using the polymerase chain reaction (PCR) under conditions that reduce the fidelity of DNA synthesis by Taq DNA polymerase, e.g., by using a dGTP/dATP ratio of five and adding Mn^ " to the PCR reaction. The pool of amplified DNA fragments are inserted into appropriate cloning vectors to provide random mutant libraries. (B) Saturation Mutagenesis
Saturation mutagenesis allows for the rapid introduction of a large number of single base substitutions into cloned DNA fragments (Mayers et al., 1985, Science 229:242). This technique includes generation of mutations, e.g., by chemical treatment or irradiation of single-stranded DNA in vitro, and synthesis of a complimentary DNA strand. The mutation frequency can be modulated by modulating the severity of the treatment, and essentially all possible base substitutions can be obtained. Because this procedure does not involve a genetic selection for mutant fragments both neutral substitutions, as well as those that alter function, are obtained. The distribution of point mutations is not biased toward conserved sequence elements.
(C) Degenerate Oligonucleotides
A library of homologs can also be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of a degenerate sequences can be carried out in an automatic DNA synthesizer, and the synthetic genes then ligated into an appropriate expression vector. The synthesis of degenerate oligonucleotides is known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp273-289; Itakura et al. (\9$4) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477. Such techniques have been employed in the directed evolution of other proteins (see, for example, Scott et al. (1990) Science 249:386-390; Roberts et al. (1992) PNAS 89:2429- 2433; Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87: 6378- 6382; as well as U.S. Patents Nos. 5,223,409, 5,198,346, and 5,096,815).
Alteration of Nucleic Acids and Polypeptides: Methods for Directed Mutagenesis
Non-random or directed, mutagenesis techniques can be used to provide specific sequences or mutations in specific regions. These techniques can be used to create variants which include, e.g., deletions, insertions, or substitutions, of residues of the known amino acid sequence of a protein. The sites for mutation can be modified individually or in series, e.g., by (1) substituting first with conserved .imino acids and then with more radical choices depending upon results achieved, (2) deleting the target residue, or (3) inserting residues of the same or a different class adjacent to the located site, or combinations of options 1-3. (A) Alanine Scanning Mutagenesis
Alanine scanning mutagenesis is a useful method for identification of certain residues or regions of the desired protein that are preferred locations or domains for mutagenesis, Cunningham and Wells (Science 244:1081-1085, 1989). In alanine scanning, a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine). Replacement of an amino acid can affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell. Those domains demonstrating functional sensitivity to the substitutions are then refined by introducing further or other variants at or for the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined. For example, to optimize the performance of a mutation at a given site, alanine scanning or random mutagenesis may be conducted at the target codon or region and the expressed desired protein subunit variants are screened for the optimal combination of desired activity.
(B) Oligonucleotide-Mediated Mutagenesis Oligonucleotide-mediated mutagenesis is a useful method for preparing substitution, deletion, and insertion variants of DNA, see, e.g., Adelman et al., (DNA 2: 183, 1983). Briefly, the desired DNA is altered by hybridizing an oligonucleotide encoding a mutation to a DNA template, where the template is the single-stranded form of a plasmid or bacteriophage containing the unaltered or native DNA sequence of the desired protein. After hybridization, a DNA polymerase is used to synthesize an entire second complementary strand of the template that will thus incorporate the oligonucleotide primer, and will code for the selected alteration in the desired protein DNA. Generally, oligonucleotides of at least 25 nucleotides in length are used. An optimal oligonucleotide will have 12 to 15 nucleotides that are completely complementary to the template on either side of the nucleotide(s) coding for the mutation. This ensures that the oligonucleotide will hybridize properly to the single- stranded DNA template molecule. The oligonucleotides are readily synthesized using techniques known in the art such as th it described by Crea et al. (Proc. Natl. Acad. Sci. USA, 75: 5765[1978]).
(C Cassette Mutagenesis Another method for preparing variants, cassette mutagenesis, is based on the technique described by Wells et al. (Gene, 34:315[1985]). The starting material is a plasmid (or other vector) which includes the protein subunit DNA to be mutated. The codon(s) in the protein subunit DNA to be mutated are identified. There must be a unique restriction endonuclease site on each side of the identified mutation site(s). If no such restriction sites exist, they may be generated using the above-described oligonucleotide-mediated mutagenesis method to introduce them at appropriate locations in the desired protein subunit DNA. After the restriction sites have been introduced into the plasmid, the plasmid is cut at these sites to linearize it. A double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures. The two strands are synthesized separately and then hybridized together using standard techniques. This double-stranded oligonucleotide is referred to as the cassette. This cassette is designed to have 3' and 5' ends that are comparable with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid. This plasmid now contains the mutated desired protein subunit DNA sequence.
(D Combinatorial Mutagenesis
Combinatorial mutagenesis can also be used to generate mutants (Ladner et al., WO 88/06630). In this method, the amino acid sequences for a group of homologs or other related proteins are aligned, preferably to promote the highest homology possible. All of the amino acids which appear at a given position of the aligned sequences can be selected to create a degenerate set of combinatorial sequences. The variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level, and is encoded by a variegated gene library. For example, a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of larger fusion proteins containing the set of degenerate sequences.
Other Modifications of H yylori Nucleic Acids and Polypeptides
It is possible to modify the structure of an H pylori polypeptide for such purposes as increasing solubility, enhancing stability (e.g., shelf life ex vivo and resistar ce to proteolytic degradation in vivo). A modified H. pylori protein or peptide can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition as described herein.
An H. pylori peptide can also be modified by substitution of cysteine residues preferably with alanine, serine, threonine, leucine or glutamic acid residues to minimize dimerization via disulfide linkages. In addition, amino acid side chains of fragments of the protein of the invention can be chemically modified. Another modification is cyclization of the peptide.
In order to enhance stability and/or reactivity, an H pylori polypeptide can be modified to incorporate one or more polymorphisms in the amino acid sequence of the protein resulting from any natural allelic variation. Additionally, D-amino acids, non- natural amino acids, or non-amino acid analogs can be substituted or added to produce a modified protein within the scope of this invention. Furthermore, an H. pylori polypeptide can be modified using polyethylene glycol (PEG) according to the method of A. Sehon and co-workers (Wie et al., supra) to produce a protein conjugated with PEG. In addition, PEG can be added during chemical synthesis of the protein. Other modifications of H. pylori proteins include reduction alkylation (Tarr, Methods of Protein Microcharacterization, J. E. Silver ed., Humana Press, Clifton NJ 155-194 (1986)); acylation (Tarr, supra); chemical coupling to an appropriate carrier (Mishell and Shiigi, eds, Selected Methods in Cellular Immunology, WH Freeman, San Francisco, CA (1980), U.S. Patent 4,939,239; or mild formalin treatment (Marsh, (1971) Int. Arch, of Allergy andAppl. Immunol, 41. : 199 - 215).
To facilitate purification and potentially increase solubility of an H. pylori protein or peptide, it is possible to add an amino acid fusion moiety to the peptide backbone. For example, hexa-histidine can be added to the protein for purification by immobilized metal ion affinity chromatography (Hochuli, E. et al., (1988)
Bio/Technology, 6: 1321 - 1325). In addition, to facilitate isolation of peptides free of irrelevant sequences, specific endoprotease cleavage sites can be introduced between the sequences of the fusion moiety and the peptide.
To potentially aid proper antigen processing of epitopes within an H. pylori polypeptide, canonical protease sensitive sites can be engineered between regions, each comprising at least one epitope via recombinant or synthetic methods. For example, charged amino acid pairs, such as KK or RR, can be introduced between regions within a protein or fragment during recombinant construction thereof. The resulting peptide can be rendered sensitive to cleavage by cathepsin and/or other trypsin-like enzymes which would generate portions of the protein containing one or more epitopes. In addition, such charged amino acid residues can result in an increase in the solubility of the peptide.
Primary Methods for Screening Polypeptides and Analogs Various techniques are known in the art for screening generated mutant gene products. Techniques for screening large gene libraries often include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the genes under conditions in which detection of a desired activity, e.g., in this case, binding to H. pylori polypeptide or an interacting protein, facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the techniques described below is amenable to high through-put analysis for screening large numbers of sequences created, e.g., by random mutagenesis techniques.
(A) Two Hybrid Systems
Two hybrid assays such as the system described above (as with the other screening methods described herein), can be used to identify polypeptides, e.g., fragments or analogs of a naturally-occurring H. pylori polypeptide, e.g., of cellular proteins, or of randomly generated polypeptides which bind to an H. pylori protein. (The H. pylori domain is used as the bait protein and the library of variants are expressed as fish fusion proteins.) In an analogous fashion, a two hybrid assay (as with the other screening methods described herein), can be used to find polypeptides which bind a H. pylori polypeptide.
(B Display Libraries
In one approach to screening assays, the candidate peptides are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind an appropriate receptor protein via the displayed product is detected in a "panning assay". For example, the gene library can be cloned into the gene for a surface membrane protein of a bacterial cell, and the resulting fusion protein detected by panning (Ladner et al., WO 88/06630; Fuchs et al. (1991) Bio/Technology 9:1370-1371; and Goward et al. (1992) TIBS 18:136-140). In a similar fashion, a detectably labeled ligand can be used to score for potentially functional peptide homologs. Fluorescently labeled ligands, e.g., receptors, can be used to detect homologs which retain ligand- binding activity. The use of fluorescently labeled ligands, allows cells to be visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, to be separated by a fluorescence-activated cell sorter.
A gene library can be expressed as a fusion prote c n the surface of a viral particle. For instance, in the filamentous phage system, foreign peptide sequences can be expressed on the surface of infectious phage, thereby conferring two significant benefits. First, since these phage can be applied to affinity matrices at concentrations well over 10^ phage per milliliter, a large number of phage can be screened at one time. Second, since each infectious phage displays a gene product on its surface, if a particular phage is recovered from an affinity matrix in low yield, the phage can be amplified by another round of infection. The group of almost identical E coli filamentous phages Ml 3, fd., and fl are most often used in phage display libraries. Either of the phage gill or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle. Foreign epitopes can be expressed at the NH2- terminal end of pill and phage bearing such epitopes recovered from a large excess of phage lacking this epitope (Ladner et al. PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267:16007-16010; Griffiths et al. (1993) EMBO J 12:725-734; Clackson et al. (1991) Nature 352:624-628; and Barbas et al. (1992) PNAS 89:4457-4461). A common approach uses the maltose receptor of E. coli (the outer membrane protein, LamB) as a peptide fusion partner (Charbit et al. (1986) EMBO 5, 3029-3037). Oligonucleotides have been inserted into plasmids encoding the LamB gene to produce peptides fused into one of the extracellular loops of the protein. These peptides are available for binding to ligands, e.g., to antibodies, and can elicit an immune response when the cells are administered to animals. Other cell surface proteins, e.g., OmpA
(Schorr et al. (1991) Vaccines 91, pp. 387-392), PhoE (Agterberg, et al. (1990) Gene 88, 37-45), and PAL (Fuchs et al. (1991) Bio/Tech 9, 1369-1372), as well as large bacterial surface structures have served as vehicles for peptide display. Peptides can be fused to pilin, a protein which polymerizes to form the pilus-a conduit for interbacterial exchange of genetic information (Thiry et al. (1989) Appl. Environ. Microbiol. 55, 984-993).
Because of its role in interacting with other cells, the pilus provides a useful support for the presentation of peptides to the extracellular environment. Another large surface structure used for peptide display is the bacterial motive organ, the flagellum. Fusion of peptides to the subunit protein flagellin offers a dense array of many peptide copies on the host cells (Kuwajima et al. (1988) Bio/Tech. 6, 1080-1083). Surface proteins of other bacterial species have also served as peptide fusion partners. Examples include the Staphylococcus protein A and the outer membrane IgA protease of Neisseria (Hansson et al. (1992) J Bacteriol. 174, 4239-4245 and Klauser et al. (1990) EMBO J. 9, 1991- 1999). In the filamentous phage systems and the LamB system described above, the physical link between the ner tide and its encoding DNA occurs by the containment of the DNA within a particle (cell or phage) that carries the peptide on its surface. Capturing the peptide captures the particle and the DNA within. An alternative scheme uses the DNA-binding protein Lad to form a link between peptide and DNA (Cull et al. (1992) PNAS USA 89: 1865-1869). This system uses a plasmid containing the Lad gene with an oligonucleotide cloning site at its 3 '-end. Under the controlled induction by arabinose, a Lacl-peptide fusion protein is produced. This fusion retains the natural ability of La to bind to a short DNA sequence known as LacO operator (LacO). By installing two copies of LacO on the expression plasmid, the Lacl-peptide fusion binds tightly to the plasmid that encoded it. Because the plasmids in each cell contain only a single oligonucleotide sequence and each cell expresses only a single peptide sequence, the peptides become specifically and stably associated with the DNA sequence that directed its synthesis. The cells of the library are gently lysed and the peptide-DNA complexes are exposed to a matrix of immobilized receptor to recover the complexes containing active peptides. The associated plasmid DNA is then reintroduced into cells for amplification and DNA sequencing to determine the identity of the peptide ligands. As a demonstration of the practical utility of the method, a large random library of dodecapeptides was made and selected on a monoclonal antibody raised against the opioid peptide dynorphin B. A cohort of peptides was recovered, all related by a consensus sequence corresponding to a six-residue portion of dynorphin B. (Cull et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89-1869) This scheme, sometimes referred to as peptides-on-plasmids, differs in two important ways from the phage display methods. First, the peptides are attached to the C-terminus of the fusion protein, resulting in the display of the library members as peptides having free carboxy termini. Both of the filamentous phage coat proteins, pill and pVIII, are anchored to the phage through their C-termini, and the guest peptides are placed into the outward-extending N-terminal domains. In some designs, the phage- displayed peptides are presented right at the amino terminus of the fusion protein. (Cwirla, et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6378-6382) A second difference is the set of biological biases affecting the population of peptides actually present in the libraries. The La fusion molecules are confined to the cytoplasm of the host cells. The phage coat fusions are exposed briefly to the cytoplasm during translation but are rapidly secreted through the inner membrane into the periplasmic compartment, remaining anchored in the membrane by their C-terminal hydrophobic domains, with the N-termini, containing the peptides, protruding into the periplasm while awaiting assembly into phage particles. The peptides in the Lad and phage libraries may differ significantly as a result of their exposure to different proteolytic activities. The phage coat proteins require transport across the inner membrane and signal peptidase processing as a prelude to incorporation into phage. Certain peptides exert a deleterious effect on these processes and are underrepresented in the libraries (Gallop et al. (1994) J. Med. Chem. 37(9): 1233-1251). These particular biases are not a factor in the Lad display system.
The number of small peptides available in recombinant random libraries is enormous. Libraries of lO'-lO^ independent clones are routinely prepared. Libraries as large as 10^ recombinants have been created, but this size approaches the practical limit for clone libraries. This limitation in library size occurs at the step of transforming the DNA containing randomized segments into the host bacterial cells. To circumvent this limitation, an in vitro system based on the display of nascent peptides in polysome complexes has recently been developed. This display library method has the potential of producing libraries 3-6 orders of magnitude larger than the currently available phage/phagemid or plasmid libraries. Furthermore, the construction of the libraries, expression of the peptides, and screening, is done in an entirely cell-free format. In one application of this method (Gallop et al. (1994) J. Med. Chem. 37(9):1233-1251), a molecular DNA library encoding 10^2 decapeptides was constructed and the library expressed in an E. coli S30 in vitro coupled transcription/translation system. Conditions were chosen to stall the ribosomes on the mRNA, causing the accumulation of a substantial proportion of the RNA in polysomes and yielding complexes containing nascent peptides still linked to their encoding RNA. The polysomes are sufficiently robust to be affinity purified on immobilized receptors in much the same way as the more conventional recombinant peptide display libraries are screened. RNA from the bound complexes is recovered, converted to cDNA, and amplified by PCR to produce a template for the next round of synthesis and screening. The polysome display method can be coupled to the phage display system. Following several rounds of screening, cDNA from the enriched pool of polysomes was cloned into a phagemid vector. This vector serves as both a peptide expression vector, displaying peptides fused to the coat proteins, and as a DNA sequencing vector for peptide identification. By expressing the polysome-derived peptides on phage, one can either continue the affinity selection procedure in this format or assay the peptides on individual clones for binding activity in a phage ΕLISA, or for binding specificity in a completion phage ΕLISA (Barret, et al. (1992) Anal. Biochem 204,357-364). To identify the sequences of the active peptides one sequences the DNA produced by the phagemid host.
Secondary Screening of Polypeptides and Analogs
The high through-put assays described above can be followed by secondar/ screens in order to identify further biological activities which will, e.g., allow one skilled in the art to differentiate agonists from antagonists. The type of a secondary screen used will depend on the desired activity that needs to be tested. For example, an assay can be developed in which the ability to inhibit an interaction between a protein of interest and its respective ligand can be used to identify antagonists from a group of peptide fragments isolated though one of the primary screens described above. Therefore, methods for generating fragments and analogs and testing them for activity are known in the art. Once the core sequence of interest is identified, it is routine for one skilled in the art to obtain analogs and fragments.
Peptide Mimetics of H pylori Polypeptides
The invention also provides for reduction of the protein binding domains of the subject H. pylori polypeptides to generate mimetics, e.g. peptide or non-peptide agents. The peptide mimetics are able to disrupt binding of a polypeptide to its counter ligand, e.g., in the case of an H pylori polypeptide binding to a naturally occurring ligand. The critical residues of a subject H. pylori polypeptide which are involved in molecular recognition of a polypeptide can be determined and used to generate H.
Figure imgf000061_0001
peptidomimetics which competitively or noncompetitively inhibit binding of the H. pylori polypeptide with an interacting polypeptide (see, for example, European patent applications EP-412,762A and EP-B31.080A). For example, scanning mutagenesis can be used to map the amino acid residues of a particular H. pylori polypeptide involved in binding an interacting polypeptide, peptidomimetic compounds (e.g. diazepine or isoquinoline derivatives) can be generated which mimic those residues in binding to an interacting polypeptide, and which therefore can inhibit binding of an H. pylori polypeptide to an interacting polypeptide and thereby interfere with the function of H pylori polypeptide. For instance, non- hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gama lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto- methylene pseudopeptides (Ewenson et al. (1986) JMed Chem 29:295; and Ewenson et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co. Rockland, IL, 1985), β-turn dipeptide cores (Nagai et al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J Chem Soc Perkin Trans 1:1231), and β-aminoalcohols (Gordon et al. (1°85; Biochem Biophys Res Commun\26:4l9; and Dann et al. (1986) Biochem Biophys Res Commun 134:71).
VI. Vaccine Formulations for H. pylori Nucleic Acids and Polypeptides This invention also features vaccine compositions or formulations (used interchangeably herein) for protection against infection by H pylori or for treatment of H. pylori infection. As used herein, the term "treatment of H. pylori infection" refers to therapeutic treatment of an existing or established H. pylori infection. The terms "protection against H. pylori infection" or "prophylactic treatment" refer to the use of H pylori vaccine formulation for reducing the risk of or preventing an infection in a subject at risk for H. pylori infection. In one embodiment, the vaccine compositions contain one or more immunogenic components, such as a surface protein, from H pylori, or portion thereof, and a pharmaceutically acceptable carrier. For example, in one embodiment, the vaccine formulations of the invention contain at least one or combination of H. pylori polypeptides or fragments thereof, from same or different H pylori antigens. Nucleic acids and H. pylori polypeptides for use in the vaccine formulations of the invention include the nucleic acids and polypeptides set forth in the Sequence Listing, preferably those H. pylori nucleic acids that encode surface proteins and surface proteins or fragments thereof. For example, a preferred nucleic acid and H. pylori polypeptide for use in a vaccine composition of the invention is selected from the group of nucleic acids which encode cell envelope proteins and H pylori cell envelope proteins as set forth in Table 1. However, any nucleic acid encoding an immunogenic H. pylori protein and H. pylori polypetide, or portion thereof, can be used in the present invention. These vaccines have therapeutic and/or prophylactic utilities.
One aspect of the invention provides a vaccine composition for protection against infection by H. pylori which contains at least one immunogenic fragment of an H pylori protein and a pharmaceutically acceptable carrier. Preferred fragments include peptides of at least about 10 amino acid residues in length, preferably about 10-20 amino acid residues in length, and more preferably about 12-16 amino acid residues in length.
Immunogenic components of the invention can be obtained, for example, by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding the full-length H. pylori protein. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.
In one embodiment, immunogenic components are identified by the ability of the peptide to stimulate T cells. Peptides which stimulate T cells, as determined by, for example, T cell proliferation or cytokine secretion are defined herein as comprising at least one T cell enitrpe. T cell epitopes are believed to be involved in initiation and perpetuation of the immune response to the protein allergen which is responsible for the clinical symptoms of allergy. These T cell epitopes are thought to trigger early events at the level of the T helper cell by binding to an appropriate HLA molecule on the surface of an antigen presenting cell, thereby stimulating the T cell subpopulation with the relevant T cell receptor for the epitope. These events lead to T cell proliferation, lymphokine secretion, local inflammatory reactions, recruitment of additional immune cells to the site of antigen/T cell interaction, and activation of the B cell cascade, leading to the production of antibodies. A T cell epitope is the basic element, or smallest unit of recognition by a T cell receptor, where the epitope comprises amino acids essential to receptor recognition (e.g., approximately 6 or 7 amino acid residues). Amino acid sequences which mimic those of the T cell epitopes are within the scope of this invention.
In another embodiment, immunogenic components of the invention are identified through genomic vaccination. The basic protocol is based on the idea that expression libraries consisting of all or parts of a pathogen genome, e.g., an H pylori genome, can confer protection when used to genetically immunize a host. This expression library immunization (ELI) is analogous to expression cloning and involves reducing a genomic expression library of a pathogen, e.g., H pylori, into plasmids that can act as genetic vaccines. The plasmids can also be designed to encode genetic adjuvants which can dramatically stimulate the humoral response. These genetic adjuvants can be introduced at remote sites and act as well extracelluraly as intracellularly.
This is a new approach to vaccine production that has many of the advantages of live/attenuated pathogens but no risk of infection. An expression library of pathogen DNA is used to immunize a host thereby producing the effects of antigen presentation of a live vaccine without the risk. For example, in the present invention, random fragments from the H pylori genome or from cosmid or plasmid clones, as well as PCR products from genes identified by genomic sequencing, can be used to immunize a host. The feasibility of this approach has been demonstrated with Mycoplasma pulmonis (Barry et al., Nature 377:632-635. 1995), where even partial expression libraries of Mycoplasma pulmonis, a natural pathogen in rodents, provided protection against challenge from the pathogen.
ELI is a technique that allows for production of a non-infectious multipartite vaccine, even when little is known about pathogen's biology, because ELI uses the immune system to screen candidate genes. Once isolated, these genes can be used as genetic vaccines or for development of recombinant protein vaccines. Thus, ELI allows for production of vaccines in a systematic, largely mechanized fashion.
Screening immunogenic components can be accomplished using one or more of several different assays. For example, in vitro, peptide T cell stimulatory activity is assayed by contacting a peptide known or suspected of being immunogenic with an antigen presenting cell which presents appropriate MΗC molecules in a T cell culture. Presentation of an immunogenic H pylori peptide in association with appropriate MΗC molecules to T cells in conjunction with the necessary costimulation has the effect of transmitting a signal to the T cell that induces the production of increased levels of cytokines, particularly of interleukin-2 and interleukin-4. The culture supernatant can be obtained and assayed for interleukin-2 or other known cytokines. For example, any one of several conventional assays for interleukin-2 can be employed, such as the assay described in Proc. Natl. Acad. Sci USA, 86: 1333 (1989) the pertinent portions of which are incorporated herein by reference. A kit for an assay for the production of interferon is also available from Genzyme Corporation (Cambridge, MA).
Alternatively, a common assay for T cell proliferation entails measuring tritiated thymidine incorporation. The proliferation of T cells can be measured in vitro by determining the amount of ^H-labeled thymidine incorporated into the replicating DNA of cultured cells. Therefore, the rate of DNA synthesis and, in turn, the rate of cell division can be quantified.
Vaccine compositions or formulations of the invention containing one or more immunogenic components (e.g., H. pylori polypeptide or fragment thereof or nucleic acid encoding an H. pylori polypeptide or fragment thereof) preferably include a pharmaceutically acceptable carrier. The term "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Suitable pharmaceutically acceptable carriers include, for example, one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof. Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the H. pylori nucleic acid or polypeptide. For vaccine formulations of the invention containing H. pylori polypeptides, the polypeptide is preferably coadministered with a suitable adjuvant and/or a delivery system described herein. It will be apparent to those of skill in the art that the therapeutically effective amount of DNA or protein of this invention will depend, inter alia, upon the administration schedule, the unit dose of an H. pylori nucleic acid or polypeptide administered, whether the protein or nucleic acid is administered in combination with other therapeutic agents, the immune status and health of the patient, and the therapeutic activity of the particular protein or nucleic acid.
Vaccine formulations are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Methods for intramuscular immunization are described by Wolff et al. (1990) Science 247: 1465-1468 and by Sedegah et al. (1994) Immunology 9J_: 9866-9870. Other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Oral immunization is preferred over parenteral methods for inducing protection against infection by H pylori. Czinn et. al. (1993) Vaccine U_: 637-642. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like. In one embodiment, the vaccine formulation includes, as a pharmaceutically acceptable carrier, an adjuvant. Examples of the suitable adjuvants for use in the vaccine formulations of the invention include, but are not limited, to aluminum hydroxide; N-acetyl-muramyl~L-threonyl-D-isoglutamine (thr-MDP); N-acetyl-nor- muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP); N- acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-( 1 '-2'-dipalmitoyl-sn-glycero-3- hydroxyphos-phoryloxy)-ethylamine (CGP 19835A, referred to a MTP-PE); RIBI, which contains three components from bacteria; monophosphoryl lipid A; trehalose dimycoloate; cell wall skeleton (MPL + TDM + CWS) in a 2% squalene/Tween 80 emulsion; and cholera toxin. Others which may be used are non-toxic derivatives of cholera toxin, including its B subunit, and/or conjugates or genetically engineered fusions of the H pylori polypeptide with cholera toxin or its B subunit, procholeragenoid, fungal polysaccharides, including schizophyllan, muramyl dipeptide, muramyl dipeptide derivatives, phorbol esters, labile toxin of E. coli, non-H pylori bacterial lysates, block polymers or saponins. In another embodiment, the vaccine formulation includes, as a pharmaceutically acceptable carrier, a delivery system. Suitable delivery systems for use in the vaccine formulations of the invention include biodegradable microcapsules or immuno- stimulating complexes (ISCOMs), cochleates, or liposomes, genetically engineered attenuated live vectors such as viruses or bacteria, and recombinant (chimeric) virus-like particles, e.g., bluetongue. In another embodiment of the invention, the vaccine formulation includes both a delivery system and an adjuvant.
Delivery systems in humans may include enteric release capsules protecting the antigen from the acidic environment of the stomach, and including H pylori polypeptide in an insoluble form as fusion proteins. Suitable carriers for the vaccines of the invention are enteric coated capsules and polylactide-glycolide microspheres. Suitable diluents are 0.2 N NaΗCO3 and/or saline.
Vaccines of the invention can be administered as a primary prophylactic agent in adults or in children, as a secondary prevention, after successful eradication of H pylori in an infected host, or as a therapeutic agent in the aim to induce an immune response in a susceptible host to prevent infection by H. pylori. The vaccines of the invention are administered in amounts readily determined by persons of ordinary skill in the art. Thus, for adults a suitable dosage will be in the range of 10 μg to 10 g, preferably 10 μg to 100 mg, for example 50 μg to 50 mg. A suitable dosage for adults will also be in the range of 5 μg to 500 mg. Similar dosage ranges will be applicable for children.
The amount of adjuvant employed will depend on the type of adjuvant used. For example, when the mucosal adjuvant is cholera toxin, it is suitably used in an amount of 5 μg to 50 μg, for example 10 μg to 35 μg. When used in the form of microcapsules, the amount used will depend on the amount employed in the matrix of the microcapsule to achieve the desired dosage. The determination of this amount is within the skill of a person of ordinary skill in the art.
Those skilled in the art will recognize that the optimal dose may be more or less depending upon the patient's body weight, disease, the route of administration, and other factors. Those skilled in the art will also recognize that appropriate dosage levels can be obtained based on results with known oral vaccines such as, for example, a vaccine based on an E. coli lysate (6 mg dose daily up to total of 540 mg) and with an enterotoxigenic E. coli purified antigen (4 doses of 1 mg) (Schulman et al., J. Urol. 150:917-921 (1993)); Boedecker et al., American Gastroenterological Assoc. 999:A-222 (1993)). The number of doses will depend upon the disease, the formulation, and efficacy data from clinical trials. Without intending any limitation as to the course of treatment, the treatment can be administered over 3 to 8 doses for a primary immunization schedule over 1 month (Boedeker, American Gastroenterological Assoc. 888: A-222 (1993)).
In a preferred embodiment, a vaccine composition of the invention can be based on a killed whole E. coli preparation with an immunogenic fragment of an H pylori protein of the invention expressed on its surface or it can be based on an E. coli lysate, wherein the killed E. coli acts as a carrier or an adjuvant. It will be apparent to those skilled in the art that some of the vaccine compositions of the invention are useful only for preventing H. pylori infection, some are useful only for treating H. pylori infection, and some are useful for both preventing and treating H. pylori infection. In a preferred embodiment, the vaccine composition of the invention provides protection against H pylori infection by stimulating humoral and/or cell-mediated immunity against H. pylori. It should be understood that amelioratio i of any of the symptoms of H. pylori infection is a desirable clinical goal, including a lessening of the dosage of medication used to treat H. />y/or -caused disease, or an increase in the production of antibodies in the serum or mucous of patients. VII. Antibodies Reactive With H pylori Polypeptides
The invention also includes antibodies specifically reactive with the subject H. pylori polypeptide. Anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (See, for example, Antibodies: A Laboratory Manual ed. by Ηarlow and Lane (Cold Spring Harbor Press: 1988)). A mammal such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide. Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. An immunogenic portion of the subject H pylori polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies.
In a preferred embodiment, the subject antibodies are immunospecific for antigenic determinants of the H. pylori polypeptides of the invention, e.g. antigenic determinants of a polypeptide of the invention contained in the Sequence Listing, or a closely related human or non-human mammalian homolog (e.g., 90% homologous, more preferably at least 95% homologous). In yet a further preferred embodiment of the invention, the anti-H pylori antibodies do not substantially cross react (i.e., react specifically) with a protein which is for example, less than 80% percent homologous to a sequence of the invention contained in the Sequence Listing. By "not substantially cross react", it is meant that the antibody has a binding affinity for a non-homologous protein which is less than 10 percent, more preferably less than 5 percent, and even more preferably less than 1 percent, of the binding affinity for a protein of the invention contained in the Sequence Listing. In a most preferred embodiment, there is no crossreactivity between bacterial and mammalian antigens.
The term antibody as used herein is intended to include fragments thereof which are also specifically reactive with H. pylori polypeptides. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab')2 fragments can be generated by treating antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges to produce Fab' fragments. The antibody of the invention is further intended to include bispecific and chimeric molecules having an anti-H. pylori portion.
Both monoclonal and polyclonal antibodies (Ab) directed against H pylori polypeptides or H pylori polypeptide variants, and antibody fragments such as Fab' and F(ab')2, can be used to block the action of H. pylori polypeptide and allow the study of the role of a particular H. pylori polypeptide of the invention in aberrant or unwanted intracellular signaling, as well as the normal cellular function of the H pylori and by microinjection of anti-H. pylori polypeptide antibodies of the present invention. Antibodies which specifically bind H pylori epitopes can also be used in immunohistochemical staining of tissue samples in order to evaluate the abundance and pattern of expression of H pylori antigens. Anti H. pylori polypeptide antibodies can be used diagnostically in immuno-precipitation and immuno-blotting to detect and evaluate H pylori levels in tissue or bodily fluid as part of a clinical testing procedure. Likewise, the ability to monitor H pylori polypeptide levels in an individual can allow determination of the efficacy of a given treatment regimen for an individual afflicted with such a disorder. The level of an H. pylori polypeptide can be measured in cells found in bodily fluid, such as in urine samples or can be measured in tissue, such as produced by gastric biopsy. Diagnostic assays using anti-H pylori antibodies can include, for example, immunoassays designed to aid in early diagnosis of H pylori infections. The present invention can also be used as a method of detecting antibodies contained in samples from individuals infected by this bacterium using specific H pylori antigens.
Another application of anti-H. pylori polypeptide antibodies of the invention is in the immunological screening of cDNA libraries constructed in expression vectors such as λgtl 1, λgtl8-23, λZAP, and λORF8. Messenger libraries of this type, having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins. For instance, λgtl 1 will produce fusion proteins whose amino termini consist of β-galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide. Antigenic epitopes of a subject H. pylori polypeptide can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from infected plates with anti-H. pylori polypeptide antibodies. Phage, scored by this assay, can then be isolated from the infected plate. Thus, the presence of H. pylori gene homologs can be detected and cloned from other species, and alternate isoforms (including splicing variants) can be detected and cloned.
VIII. Kits Containing Nucleic Acids, Polypeptides or Antibodies of the Invention
The nucleic acid, polypeptides and antibodies of the invention can be combined with other reagents and articles to form kits. Kits for diagnostic purposes typically comprise the nucleic acid, polypeptides or antibodies in vials or other suitable vessels. Kits typically comprise other reagents for performing hybridization reactions, polymerase chain reactions (PCR), or for reconstitution of lyophilized components, such as aqueous media, salts, buffers, and the like. Kits may also comprise reagents for sample processing such as detergents, chaotropic salts and the like. Kits may also comprise immobilization means such as particles, supports, wells, dipsticks and the like. Kits may also comprise labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like. With the nucleic acid and amino acid sequence information provided herein, individuals skilled in art can readily assemble kits to serve their particular purpose. Kits further can include instructions for use.
IX. Drug Screening Assays Using H. pylori Polypeptides
By making available purified and recombinant H pylori polypeptides, the present invention provides assays which can be used to screen for drugs which are either agonists or antagonists of the normal cellular function, in this case, of the subject H pylori polypeptides, or of their role in intracellular signaling. Such inhibitors or potentiators may be useful as new therapeutic agents to combat H. pylori infections in humans. A variety of assay formats will suffice and, in light of the present inventions, will be comprehended by the skilled artisan.
In many drug screening programs which test libraries of compounds and natural extracts, high throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays which are performed in cell-free systems, such as may be derived with purified or semi-purified proteins, are often preferred as "primary" screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target which is mediated by a test compound. Moreover, the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or change in enzymatic properties of the molecular target. Accordingly, in an exemplary screening assay of the present invention, the compound of interest is contacted with an isolated and purified H pylori polypeptide.
Screening assays can be constructed in vitro with a purified H. pylori polypeptide or fragment thereof, such as an H pylori polypeptide having enzymatic activity, such that the activity of .he polypeptide produces a detectable reaction product. The efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound. Moreover, a control assay can also be performed to provide a baseline for comparison. Suitable products include those with distinctive absorption, fluorescence, or chemi-luminescence properties, for example, because detection may be easily automated. A variety of synthetic or naturally occurring compounds can be tested in the assay to identify those which inhibit or potentiate the activity of the H pylori polypeptide. Some of these active compounds may directly, or with chemical alterations to promote membrane permeability or solubility, also inhibit or potentiate the same activity (e.g., enzymatic activity) in whole, live H. pylori cells.
This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references and published patent applications cited throughout this application are hereby incorporated by reference.
EXEMPLIFICATION
I. Cloning and Sequencing of H. pylori DNA
H. pylori chromosomal DNA was isolated according to a basic DNA protocol outlined in Schleif R.F. and Wensink P.C., Practical Methods in Molecular Biology, p.98, Springer- Verlag, NY., 1981, with minor modifications. Briefly, cells were pelleted, resuspended in TE (10 mM Tris, 1 mM EDTA, pΗ 7.6) and GES lysis buffer (5.1 M guanidium thiocyanate, 0.1 M EDTA, pΗ 8.0, 0.5% N-laurylsarcosine) was added. Suspension was chilled and ammonium acetate (NΗ4Ac) was added to final concentration of 2.0 M. DNA was extracted, first with chloroform, then with phenol- chloroform, and reextracted with chloroform. DNA was precipitated with isopropanol, washed twice with 70% EtOH, dried and resuspended in TE.
Following isolation whole genomic H. pylori DNA was nebulized (Bodenteich et al., Automated DNA Sequencing and Analysis (J.C. Venter, ed.), Academic Press, 1994) to a median size of 2000 bp. After nebulization, the DNA was concentrated and separated on a standard 1% agarose gel. Several fractions, corresponding to approximate sizes 900-1300 bp, 1300-1700 bp, 1700-2200 bp, 2200-2700 bp, were excised from the gel and purified by the GeneClean procedure (BiolOl, Inc.).
The purified DNA fragments were then blunt-ended using T4 DNA polymerase. The healed DNA was then ligated to unique BstXI-linker adapters in 100-1000 fold molar excess. These linkers are complimentary to the BstXI-cut pMPX vectors, while the overhang is not self-complimentary. Therefore, the linkers will not concatemerize nor will the cut-vector religate itself easily. The linker-adopted inserts were separated from the unincorporated linkers on a 1 % agarose gel and purified using GeneClean. The linker-adopted inserts were then ligated to each of the 20 pMPX vectors to construct a series of "shotgun" subclone libraries. The vectors contain an out-of-frame lacZ gene at the cloning site which becomes in-frame in the event that an adapter-dimer is cloned, allowing these to be avoided by their blue-color. All subsequent steps were based on the multiplex DNA sequencing protocols outlined in Church G.M. and Kieffer-Higgins S., Science 240:185-188, 1988. Only major modifications to the protocols are highlighted. Briefly, each of the 20 vectors was then transformed into DH5α competent cells (Gibco/BRL, DH5 transformation protocol). The libraries were assessed by plating onto antibiotic plates containing ampicillin, methicillin and IPTG/Xgal. The plates were incubated overnight at 37°C. Successful transformants were then used for plating of clones and pooling into the multiplex pools. The clones were picked and pooled into 40 ml growth medium cultures. The cultures were grown overnight at 37°C. DNA was purified using the Qiagen Midi-prep kits and Tip- 100 columns (Qiagen, Inc.). In this manner, 100 μg of DNA was obtained per pool. Fifteen 96-well plates of DNA were generated to obtain a 5-10 fold sequence redundancy assuming 250-300 base average read-lengths.
These purified DNA samples were then sequenced using the multiplex DNA sequencing based on chemical degradation methods (Church G.M. and Kieffer-Higgins S., Science 240:185-188, 1988) or by Sequithrem (Epicenter Technologies) dideoxy sequencing protocols. The sequencing reactions were electrophoresed and transferred onto nylon membranes by direct transfer electrophoresis from 40 cm gels (Richterich P. and Church G.M., Methods in Enzymology 218:187-222, 1993) or by electroblotting (Church, supra). 24 samples were run per gel. 45 successful membranes were produced by chemical sequencing and 8 were produced by dideoxy sequencing. The DNA was covalently bound to the membranes by exposure to ultraviolet light, and hybridized with labeled oligonucleotides complimentary to tag sequences on the vectors (Church, supra). The membranes were washed to rinse off non-specifically bound probe, and exposed to X-ray film to visualize individual sequence ladders. After autoradiography, the hybridized probe was removed by incubation at 65° C, and the hybridization cycle repeated with another tag sequence until the membrane had been probed 38 times for chemical sequencing membranes and 10 times for the dideoxy sequencing membranes. Thus, each gel produced a large number of films, each containing new sequencing information. Whenever a new blot was processed, it was initially probed for an internal standard sequence added to each of the pools.
Digital images of the films were generated using a laser-scanning densitomet x (Molecular Dynamics, Sunnyvale, CA). The digitized images were processed on computer workstations (VaxStation 4000's) using the program REPLICA™ (Church et al., Automated DNA Sequencing and Analysis (J.C. Venter, ed.), Academic Press, 1994). Image processing included lane straightening, contrast adjustment to smooth out intensity differences, and resolution enhancement by iterative gaussian deconvolution. The sequences were then automatically picked in REPLICA™ and displayed for interactive proofreading before being stored in a project database. The proofreading was accomplished by a quick visual scan of the film image followed by mouse clicks on the bands of the displayed image to modify the base calls. Many of the sequence errors could be detected and corrected because multiple sequence reads covering the same portion of the genomic DNA provide adequate sequence redundancy for editing. Each sequence automatically received an identification number (corresponding to microtiter plate, probe information, and lane set number). This number serves as a permanent identifier of the sequence so it is always possible to identify the original of any particular sequence without recourse to a specialized database. Routine assembly of H pylori sequences was done using the program FALCON
(Church, Church et al., Automated DNA Sequenicng and Analysis (J.C. Venter, ed.), Academic Press, 1994). This program has proven to be fast and reliable for most sequences. The assembled contigs were displayed using a modified version of GelAssemble, developed by the Genetics Computer Group (GCG) (Devereux et al., Nucleic Acid Res. 12:387-95, 1984) that interacts with REPLICA™. This provided for an integrated editor that allows multiple sequence gel images to be instantaneously called up from the REPLICA™ database and displayed to allow rapid scanning of contigs and proofreading of gel traces where discrepancies occurred between different sequence reads in the assembly.
II. Identification, cloning and expression of recombinant H pylori DNA sequences
To facilitate the cloning, expression and purification of membrane and secreted proteins from H. pylori a powerful gene expression system, the pET System (Novagen), for cloning and expression of recombinant proteins in E. coli, was selected. Also, a DNA sequence encoding a peptide tag, the Ηis-Tag, was fused to the 3' end of DNA sequences of interest in order to facilitate purification of the recombinant protein products. The 3' end was selected for fusion in order to avoid alteration of any 5' terminal signal sequence. The exception to the above was ppiB, a gene cloned for use as a control in the expression studies. In this study, the sequence for H. pylori ppiB contains a DNA sequence encoding a Ηis-Tag fused to the 5' end of the full length gene, because the protein product of this gene does not contain a signal sequence and is expressed as a cytosolic protein. PCR Amplification and cloning of DNA sequences containing ORF's for membrane and secreted proteins from the J99 Strain of Helicobacter pylori.
Sequences chosen (from the list of the DNA sequences of the invention) for cloning from the J99 strain of H pylori were prepared for amplification cloning by polymerase chain reaction (PCR). Synthetic oligonucleotide primers (Table 3) specific for the 5' and 3' ends of open reading frames (ORFs) were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' end of the sequence) were designed to include an Ncol cloning site at the extreme 5' terminus, except for ΗpSeq. 4821082 where Ndel was used. These primers were designed to permit initiation of protein translation at a methionine residue followed by a valine residue and the coding sequence for the remainder of the native H. pylori DNA sequence. An exception is H pylori sequence 4821082 where the initiator methionine is immediately followed by the remainder of the native H. pylori DNA sequence. All reverse primers (specific for the 3' end of any H. pylori ORF) included a EcoRI site at the extreme 5' terminus to permit cloning of each H pylori sequence into the reading frame of the pET-28b. The pET-28b vector provides sequence encoding an additional 20 carboxy-terminal amino acids (only 19 amino acids in ΗpSeq. 26380318 and ΗpSeq.14640637) including six histidine residues (at the extreme C-terminus), which comprise the Ηis-Tag. An exception to the above, as noted earlier, is the vector construction for the ppiB gene. A synthetic oligonucleotide primer specific for the 5' end of ppiB gene encoded a BamΗI site at its extreme 5' terminus and the primer for the 3' end of the ppiB gene encoded a Xhol site at its extreme 5' terminus.
TABLE 3 Oligonucleotide primers used for PCR amplification of H pylori DNA sequences
Figure imgf000073_0001
Figure imgf000074_0001
Genomic DNA prepared from the J99 strain of H. pylori (ATCC #55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). To amplify a DNA sequence containing an H. pylori ORF, genomic DNA (50 nanograms) was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers) complementary to and flanking a defined H. pylori ORF, 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 2.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 100 microliters. The following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/ GeneAmp PCR System 9600 thermal cycler:
Protein 26054702, Protein 7116626, Protein 29479681, Protein 30100332, and Protein 4821082; Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 15 sec and 72°C for 1.5 min 23 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes.
Protein 16225006;
Denaturation at 94°C for 2 min, 25 cycles at 95°C for 15 sec, 55°C for 15 sec and 72°C for 1.5 min Reaction was concluded at 72°C for 6 minutes.
Protein 4721061;
Denaturation at 94°C for 2 min, 2 cycles at 94°C for 15 sec, 36°C for 15 sec and 72°C for 1.5 min 23 cycles at 94°C for 15 sec, 60°C for 15 sec and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes.
Protein 26380318; Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 38°C for 15 sec and 72°C for 1.5 min 23 cycles at 94°C for 15 sec, 62°C for 15 sec and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes.
Protein 14640637;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 33°C for 15 sec and 72°C for 1.5 min 30 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes. Conditions for amplification of H. pylori ppiB;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 32°C for 15 sec and 72°C for 1.5 min 25 cycles at 94°C for 15 sec, 56°C for 15 sec and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes
Upon completion of thermal cycling reactions, each sample of amplified DNA was washed and purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, MD, USA). All amplified DNA samples were subjected to digestion with the restriction endonucleases, Ncol and EcoRI (New England BioLabs, Beverly, MA, USA), or in the case of HpSeq. 4821082 (SEQ ID NO: 1309), with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). DNA samples were then subjected to electrophoresis on 1.0 % NuSeive (FMC BioProducts, Rockland, ME USA) agarose gels. DNA was visualized by exposure to ethidium bromide and long wave uv irradiation. DNA contained in slices isolated from the agarose gel was purified using the Bio 101 GeneClean Kit protocol (Bio 101 Vista, CA, USA).
Cloning ofH. pylori DNA sequences into the pET-28b prokaryotic expression vector. The pET-28b vector was prepared for cloning by digestion with Ncol and EcoRI, or in the case of H. pylori protein 4821082 with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). In the case of cloning ppiB, the pET-28a vector, which encodes a His-Tag that can be fused to the 5' end of an inserted gene, was used and the cloning site prepared for cloning with the ppiB gene by digestion with BamHI and Xhol restriction endonucleases.
Following digestion, DNA inserts were cloned (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) into the previously digested pET-28b expression vector, except for the amplified insert for ppiB, which was cloned into the pET-28a expression vector. Products of the ligation reaction were then used to transform the BL21 strain of E. coli (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et ?1., dάs., 1994) as described below.
Transformation of competent bacteria with recombinant plasmids
Competent bacteria, E coli strain BL21 or E. coli strain BL21(DE3), were transformed with recombinant pET expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Briefly, 1 microliter of ligation reaction was mixed with 50 microliters of electrocompetent cells and subjected to a high voltage pulse, after which, samples were incubated in 0.45 milliliters SOC medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgC12, 10 mM MgSO4 and 20, mM glucose) at 37°C with shaking for 1 hour. Samples were then spread on LB agar plates containing 25 microgram/ml kanamycin sulfate for growth overnight.
Transformed colonies of BL21 were then picked and analyzed to evaluate cloned inserts as described below.
Identification of recombinant pET expression plasmids carrying H. pylori sequences Individual BL21 clones transformed with recombinant pET-28b-H.pylori ORFs were analyzed by PCR amplification of the cloned inserts using the same forward and reverse primers, specific for each H. pylori sequence, that were used in the original PCR amplification cloning reactions. Successful amplification verified the integration of the H. pylori sequences in the expression vector (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Isolation and Preparation of plasmid DNA from BL21 transformants
Individual clones of recombinant pET-28b vectors carrying properly cloned H. pylori ORFs were picked and incubated in 5 mis of LB broth plus 25 microgram/ml kanamycin sulfate overnight. The following day plasmid DNA was isolated and purified using the Qiagen plasmid purification protocol (Qiagen Inc., Chatsworth, CA, USA).
Expression of recombinant H pylori sequences in E. coli The pET vector can be propagated in any E. coli K-12 strain e.g. HMS174,
HB101, JM109, DH5, etc. for the purpose of cloning or plasmid preparation. Hosts for expression include E. coli strains containing a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivative that carries the lad gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase is induced by addition of isopropyl-B-D-thiogalactoside (IPTG), and the T7 RN polymerase transcribes any target plasmid, such as pET-28b, carrying a T7 promoter and a gene of interest. Strains used include: BL21(DE3) (Studier, F.W., Rosenberg, A.H., Dunn, J.J., and Dubendorff, J.W. (1990) Meth. Enzymol. 185, 60-89). To express recombinant H pylori sequences, 50 nanograms of plasmid DNA isolated as described above was used to transform competent BL21 (DE3) bacteria as described above (provided by Novagen as part of the pET expression system kit). The lacZ gene (beta-galactosidase) was expressed in the pET-System as described for the H pylori recombinant constructions. Transformed cells were cultured in SOC medium for 1 hour, and the culture was then plated on LB plates containing 25 micrograms/ml kanamycin sulfate. The following day, bacterial colonies were pooled and grown in LB medium containing kanamycin sulfate (25 micrograms/ml) to an optical density at 600 nM of 0.5 to 1.0 O.D. units, at which point, 1 millimolar IPTG was added to the culture for 3 hours to induce gene expression of the H pylori recombinant DNA constructions.
After induction of gene expression with IPTG, bacteria were pelleted by centrifugation in a Sorvall RC-3B centrifuge at 3500 x g for 15 minutes at 4°C. Pellets were resuspended in 50 milliliters of cold 10 mM Tris-ΗCl, pΗ 8.0, 0.1 M NaCl and 0.1 mM EDTA (STE buffer). Cells were then centrifuged at 2000 x g for 20 min at 4°C. Wet pellets were weighed and frozen at -80°C until ready for protein purification.
III. Purification of recombinant proteins from E. coli Analytical Methods The concentrations of purified protein preparations were quantified spectrophotometrically using absorbance coefficients calculated from amino acid content (Perkins, S.J. 1986 Eur. J. Biochem. 157, 169-180). Protein concentrations were also measured by the method of Bradford, M.M. (1976) Anal. Biochem. 72, 248-254, and Lowry, O.Η., Rosebrough, N., Fair, A.L. & Randall, R.J. (1951) J. Biol. Chem. 193, pages 265-275, using bovine serum albumin as a standard.
SDS-polyacrylamide gels (12% or 4.0 to 25 % acrylamide gradient gels) were purchased from BioRad (Hercules, CA, USA), and stained with Coomassie blue. Molecular weight markers included rabbit skeletal muscle myosin (200 kDa), E. coli (- galactosidase (116 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anhydrase (31 kDa), soybean trypsin inhibitor (21.5 kDa), egg white lysozyme (14.4 kDa) and bovine aprotinin (6.5 kDa).
/. Purification of soluble proteins All steps were carried out at 4°C. Frozen cells were thawed, resuspended in 5 volumes of lysis buffer (20 mM Tris, pH 7.9, 0.5 M NaCl, 5 mM imidazole with 10% glycerol, 0.1 % 2-mercaptoethanol, 200 μg/ ml lysozyme, 1 mM phenylmethylsulfonyl fluoride (PMSF), and 10 ug/ml each of leupeptin, aprotinin, pepstatin, L-l-chloro-3-[4- tosylamido]-7-amino-2-heptanone (TLCK), L-l -chloro-3-[4-tosylamido]-4-phenyl-2- butanone (TPCK), and soybean trypsin inhibitor, and ruptured by several passages through a small volume microfluidizer (Model M-l 10S, Microfluidics International Co oration, Newton, MA). The resultant homogenate was made 0.1 % Brij 35, and centrifuged at 100,000 x g for 1 hour to yield a clear supernatant (crude extract).
Following filtration through a 0.8 μm Supor filter (Gelman Sciences, FRG) the crude extract was loaded directly onto a Ni^+" nitrilotriacetate-agarose (NTA) with a 5 milliliter bed volume (Hochuli, E., Dbeli, H., and Schacheer, A. (1987) J.
Chromatography 411, 177-184) pre-equilibrated in lysis buffer containing 10 % glycerol, 0.1 % Brij 35 and 1 mM PMSF. The column was washed with 250 ml (50 bed volumes) of lysis buffer containing 10 % glycerol, 0.1 % Brij 35, and was eluted with sequential steps of lysis buffer containing 10 % glycerol, 0.05 % Brij 35, 1 mM PMSF, and 20, 100, 200, and 500 mM imidazole in succession. Fractions were monitored by absorbance at OD28O *1' an& Pea^ fractions were analyzed by SDS-PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
Recombinant protein 14640637 and proteins, beta-galactosidase (lacZ) andpeptidyl- prolyl cis-trans isomerase (ppiB)
Fractions containing the recombinant proteins from the Ni^+-NTA-agarose columns were pooled and then concentrated to approximately 5 ml by centrifugal filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 180-ml column (1.6 X 91 cm) of Sephacryl S-100 HR gel filtration medium equilibrated in Buffer A (10 mM Hepes, pH 7.5, 150 mM NaCl, 0.1 mM EGTA) and run in Buffer A at 18 ml/h.
Fractions containing the recombinant protein were identified by absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled and concentrated by centrifugal filtration.
Recombinant protein 7116626
Fractions containing the recombinant protein from the Ni^+ -NTA-agarose column were pooled and dialyzed overnight against 1 liter of dialysis buffer (10 mM MOPS, pH 6.5, 50 mM NaCl, 0.1 mM EGTA, 0.02% Brij 35 and 1 mM PMSF). In the morning, a fine white precipitate was removed by centrifugation and the resulting supernatant was loaded onto an 8 ml (8 x 75 mm) MonoS high performance liquid chromatography column (Pharmacia Biotechnology, Inc., Piscataway, NJ, USA) equilibrated in buffer B (10 mM MOPS, pH 6.5, 0.1 mM EGTA) containing 50 mM NaCl. The column was washed with 10 bed volumes of buffer B containing 50 mM NaCl, and developed with a 50-ml linear gradient of increasing NaCl (50 to 500 mM). Recombinant protein 7116626 eluted as a sharp peak at 300 mM NaCl. 2. Purification of insoluble proteins from inclusion bodies
The following steps were carried out at 4°C. Cell pellets were resuspended in lysis buffer with 10% glycerol 200 μg/ ml lysozyme, 5 mM EDTA, ImM PMSF and 0.1 % -mercaptoethanol. After passage through the cell disrupter, the resulting homogenate was made 0.2 % deoxycholate, stirred 10 minutes, then centrifuged at 20,000 x g, for 30 min. The pellets were washed with lysis buffer containing 10 % glycerol, 10 mM EDTA, 1% Triton X-100, 1 mM PMSF and 0.1% -mercaptoethanol, followed by several washes with lysis buffer containing 1 M urea, 1 mM PMSF and 0.1 % 2- mercaptoethanol. The resulting white pellet was composed primarily of inclusion bodies, free of unbroken cells and membranous materials.
Recombinant proteins 26054702, 16225006, 30100332, 4721061
The following steps were carried out at room temperature. Purified inclusion bodies were dissolved in 20 ml 8.0 M urea in lysis buffer with 1 mM PMSF and 0.1 % 2-mercaptoethanol, and incubated at room temperature for 1 hour. Materials that did not dissolve were removed by centrifugation. The clear supernatant was filtered, then loaded onto a Ni^+ -NTA agarose column pre-equilibrated in 8.0 M urea in Lysis Buffer. The column was washed with 250 ml (50 bed volumes) of lysis buffer containing 8 M urea, 1.0 mM PMSF and 0.1 % 2-mercaptoethanol, and developed with sequential steps of lysis buffer containing 8M urea, 1 mM PMSF, 0.1 % 2- mercaptoethanol and 20, 100, 200, and 500 mM imidazole in succession. Fractions were monitored by absorbance at OD2 O nm' anc* peak fractions were analyzed by SDS- PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
Recombinant proteins 29479681, 26380318
The pellet containing the inclusion bodies was solubilized in buffer B containing 8 M urea, 1 mM PMSF and 0.1 % 2-mercaptoethanol, and incubated for 1 hour at room temperature. Insoluble materials were removed by centrifugation at 20,000 x g for 30 min, and the cleared supernatant was loaded onto a 15 ml ( 1.6 x 7.5 cm ) SP-Sepharose column pre-equilibrated in buffer B, 6 M urea, 1 mM PMSF, 0.1 % 2-mercaptoethanol. After washing the column with 1 b^d volumes, the column was developed with a linear gradient from 0 to 500 mM NaCl.
Dialysis and concentration of protein samples Urea was removed slowly from the protein samples by dialysis against Tris- buffered saline (TBS; 10 mM Tris pH 8.0, 150 mM NaCl) containing 0.5 % deoxycholate (DOC) with sequential reduction in urea concentration as follows; 6M, 4M, 3M, 2M, IM, 0.5 M and finally TBS without any urea. Each dialysis step was conducted for a minimum of 4 hours at room temperature.
After dialysis, samples were concentrated by pressure filtration using Amicon stirred-cells. Protein concentrations were measured using the methods of Perkins (1986 Eur. J. Biochem. 157, 169-180), Bradford ((1976) Anal. Biochem. 72, 248-254) and Lowry ((1951) J. Biol. Chem. 193, pages 265-275).
The recombinant proteins purified by the methods described above are summarized in Table 4 below.
TABLE 4
Figure imgf000081_0001
Outer Membrane Proteins
Figure imgf000081_0002
Periplasmic/Secreted Protein
Figure imgf000081_0003
Other Surface Proteins
Figure imgf000082_0001
IV. Analysis of H. pylori proteins as Vaccine candidates
To analyze H pylori proteins for use in the vaccine formulations of the invention, several H. pylori proteins were expressed, characterized immunologically and tested in animal efficacy studies as outlined below. Specifically, the immunomodulatory effects of H. pylori proteins were investigated in a mouse/H. pylori model which mimics the human H pylori infection in humans. In these studies, the effect of oral immunization of selected H pylori polypeptides in H. pylori infected mice was determined.
Identification, cloning and expression of recombinant Helicobacter pylori sequences. To facilitate the cloning, expression and purification of membrane and/or secreted proteins from H. pylori, the pET gene expression system (Novagen), for cloning and expression of recombinant proteins in Escherichia coli was selected. Further, for proteins that have a signal sequence at their amino-terminal end, a DNA sequence encoding a peptide tag (Ηis-tag) was fused to the 5' end of the H. pylori DNA sequences of interest in order to facilitate purification of the recombinant protein products. PCR amplification and cloning of DNA sequences containing ORFs for membrane and secreted proteins from the J99 strain of Helicobacter pylori.
The sequences selected (from the list of the DNA sequences of the invention) for cloning from H. pylori strain J99 were prepared for amplification cloning by the polymerase chain reaction (PCR). All of the selected sequences encode for outer membrane H. pylori proteins, with vac9 (SEQ ID NO:125), vaclO (SEQ ID NO:147), vac22 (SEQ ID NO:121) and vac41 (SEQ ID NO:176) sequences all sharing a terminal phenylalanine residue. Likewise, the vac32 (SEQ ID NO: 108), vac36 (SEQ ID NO: 149) and vac37 (SEQ ID NO: 139) sequences all share a terminal phenylalanine residue and a tyrosine cluster at the C-terminus. Synthetic oligonucleotide primers for each ORF of interest (Table 5) specific for the predicted mature 5' end of the ORF and downstream (3') of the predicted translational termination codon were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' terminus of the region of ORF of interest) were designed to include a Bamlll restriction site followed by a Ndel restriction site. These primers were designed to permit the initiation of protein translation at a methionine residue encoding within the Ndel restriction site sequence (in the case of producing a non Ηis-tagged recombinant protein) or to fuse in frame with the DNA sequence encoding the Ηis-tag (for producing Ηis-tagged recombinant protein), followed by the coding sequence for the remainder of the native H. pylori DNA. All reverse oligonucleotide primers (specific for downstream (3') of the predicted translational termination codon of the ORF) were designed to include an EcoRI restriction site at the 5' terminus. This combination of primers would enable each ORF of interest to be cloned into pΕT28b (to produce a Ηis-tagged recombinant protein) or pET30a (to produce a non Ηis-tagged or native recombinant protein). The pET28b vector provides sequence encoding an additional 20 amino- terminal amino acids (plus the methionine in the Ndel restriction site) including a stretch of six histidine residues which makes up the Ηis-tag.
Genomic DNA prepared from H. pylori strain J99 (ATCC 55679) was used as the source of template DNA for the PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubei et al., eds., 1994). To amplify a DNA sequence containing a specific H. pylori ORF, genomic DNA (50 nanograms) was introduced into a reaction tube containing 200 nanograms of both the forward and reverse synthetic oligonucleotide primer specific for the ORF of interest, and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies,
Gaithersburg, MD, USA) in a total of 50 microliters. The PCR SuperMix is supplied in 1.1X concentrations and contains 22mM Tris-ΗCl (pΗ 8.4), 55mM KCl, 1.65 mM MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22 units recombinant Taq polymerase/ml and stabilizers. The following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/Gene Amp PCR System thermal cycler.
Table 5: Oligonucleotide primers
Figure imgf000084_0001
Figure imgf000085_0001
Sequences for Vac32, Vac9 and Vac22
Denaturation at 94°C for 30 sec
35 cycles at. 94°C for 15 sec, 55°C for 15 sec, and 72°C for 1.5 min
Reactions were concluded at 72°C for 8 minutes
Sequences for VaclO and Vac41
Denaturation at 94°C for 30 sec
35 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C for 2.5 min
Reactions were concluded at 72°C for 8 minutes
Sequences for Vac36 and Vac37
Denaturation at
2 cycles at 94°C for 15 sec, 30°C for 15 sec, and 72°C for 1.5 min 23 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C for 1.5 min Reactions were concluded at 72°C for 6 minutes
Upon completion of the thermal cycling reactions, each sample of amplified DNA was subjected to electrophoresis on 1.0% agarose gels. The DNA was visualized by exposure to ethidium bromide and long wave UV irradiation, and cut out in gel slices. DNA was purified using the Wizard PCR Preps Kit (Promega Corp., Madison, WI, USA), and then subjected to digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The digested PCR amplicon was then re-electrophoresed and purified as before. Ligation ofH pylori DNA sequences into cloning vectors
The pOK12 vector (J. Vieira and J. Messing, Gene 100:189-194, 1991) was prepared for cloning for digestion with BamHl and EcoRI in the case of Vac9, 10, 22, 31 and 32, whereas the pSU21 vector (B. Bartolome et al, Gene 102:75-78, 1991) was prepared for cloning by digestion with BamHl and EcoRI in the case of Vac 41 (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). The vectors were subjected to electrophoresis on 1.0% agarose gels and purified using the Wizard PCR Preps kit (Promega Corp., Madison, WI, USA). Following ligation of the purified, digested vector and the purified, digested amplified H. pylori ORF, the products of the ligation reaction were transformed into E coli JM109 competent cells according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). Individual bacterial colonies were screened for those containing the correct recombinant plasmids by incubating in LB broth overnight (plus 25ug/ml kanamycin sulfate for the pOK12 based plasmids or 25ug/ml chloramphenicol for the pSU21 based plasmids) followed by plasmid DNA preparation using the Magic Minipreps system (Promega Corp., Madison, WI, USA), and then analyzed by restriction digestion (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994).
Cloning ofH. pylori DNA sequences into the pET28b and pET30a prokaryotic expression vectors
Both the pΕT28b and pET30a expression vectors were prepared for cloning by digestion with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). The H pylori DNA sequences were removed from pOK12 (Vac9, 10,23,31 and 32) or pSU21 (Vac41) plasmid backbones by digestion with N< and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). The pΕT28b, pET30a and Η. pylori DNA sequences were all electrophoresed on a 1% agarose gel and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the purified, digested expression vector and the purified, digest H. pylori DNA sequences, the products of the ligation reaction were transformed into E. coli JM109 compe^e . cells (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). Individual bacterial colonies were screened for those containing the correct recombinant plasmids by preparing plasmid DNA as described above followed by analysis by restriction digestion profiles and DNA sequencing (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). These recombinant plasmids were then used to transform specific E. coli expression strains. Transformation of competent bacteria with recombinant expression plasmids
Competent bacterial strains (BL21(DE3), BL21(DE3)pLyS, HMS174(DE3) and HMS174(DE3)pLysS were prepared and transformed with the recombinant pET28b expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). These expression host strains contain a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivate that carries the lad gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase expression is induced by the addition of isopropyl-β-D thiogalactoside (IPTG), and the T7 RNA polymerase then transcribes any target plasmid, such as pET28b, that carries a T7 promoter sequence and a gene of interest.
Expression of recombinant H. pylori sequences in E. coli
Transformants were collected from LB agar plates containing 25ug/ml kanamycin sulfate (ensures maintenance of the pET28b-based recombinant plasmids) and used to inoculate LB broth containing 25ug/ml kanamycin sulfate and grown to an optical density at 600nm of 0.5 to 1.0 OD units, at which point ImM IPTG was added to the culture for one to three hours to induce gene expression of the H. pylori recombinant DNA constructions. After induction of gene expression with IPTG, bacteria were pelleted by centrifugation and resuspended in SDS-PAGE solubilization buffer and subjected to SDS-PAGE (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., \994). Proteins were visualized by staining with Coomassie Brilliant Blue or detected by western immunoblotting using the specific anti-His tag monoclonal antibody (Clontech, Palo Alto, CA, USA) using standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The host strain that provided the highest level of recombinant protein production was then chosen for use in a large-scale induction in order to purify the recombinant protein. All of the following proteins listed were expressed recombinantly and the strain giving thf highest level of expression listed: BL21(DE3) (vac31, vac26, vac37); BL21(DE3) pLysS (vac 9, 32); HMS174(DE3) (vac 10, 11). Purification of recombinant proteins and generation of specific antiserum
Large scale cultures were inoculated and grown as above, and induced with ImM IPTG for 3 hours. After induction, bacteria were pelleted by centrifugation in a Sorvall centrifuge at 3500 x g for 15 min at 4°C. All of the expressed recombinant proteins were present in the insoluble inclusion body fraction. Inclusion bodies were purified according to standard protocols (Antibodies, Cold Spring Harbor Laboratory Press, E. Harlow and D. Lane, eds., 1988). The recombinant protein produced by vac32 was solubilized in 8M urea and partially purified by nickel chromatography (REF here). Denatured recombinant proteins were purified by electrophoresis on SDS-PAGE gels, and after visualization with Coomassie Brilliant Blue, the protein was excised from the gel and the gel slices homogenized. This material was used to raise specific polyclonal antibodies in mice or rabbits according to standard protocols (Antibodies, Cold Spring Harbor Laboratory Press, E. Harlow and D. Lane, eds., 1988).
Immunological characterization of recombinant proteins
In all cases where antibody was attempted to be raised, high titre antisera was generated, confirming the immunogenicity of the recombinant proteins. Further, these specific antisera were used to analyze whether the protein encoded by the cloned gene was expressed in H pylori. Western immunoblot analysis using standard protocols (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994) confirmed that the H pylori strain J99 did express proteins of the expected molecular weight that reacted with the vacl 0, vac32, vac31 , vac36 antiserum. The specific antiserum was also used to determine the level of antigenic conservation between a large number ofH. pylori isolates that had been obtained from distinct geographical sites around the world, and from all types of clinical manifestations, including gastritis, duodenal ulcer, gastric ulcer and gastric cancer. It was found that every strain produced a protein that reacted specifically with each antiserum. Further, H. pylori cells from strains J99, 17874, AΗ244 and SSI were fractionated into different cellular compartments (Doig and Trust 1994 Infect. Immun. 62:4526-4533: O oole et al. 1995 J. Bacteriol. 177:6049-6057). The specific antiserum was used to probe Jiese fractions by western immunoblot to identify in which fraction the protein was localized. In all cases, the immunoreactive protein was present in the outer membrane as had been predicted by the sequence features and motif searches described herein. Demonstration of protein efficacy as a vaccine Purification of vac36 for efficacy studies
All the following steps were carried out at 4°C. Cell pellets were resuspended in 5 volumes per gram of cell of lysis buffer (50mM Sodium Phosphate pH 8.0, 0.5 M NaCl, 5mM Imidazole) with lOmM EDTA, 1 mM phenylmethylsulfonyl fluoride
(PMSF) and 0.1 % β-mercaptoethanol, and ruptured by several passages through a small volume microfluidizer (Model M-l 10S, Microfluidics International Corporation, Newton, MA). The resulting homogenate was made 0.2% sodium deoxycholate (DOC), stirred 20 minutes, then centrifuged (10,000 g x 30 min). The pellets were washed twice with Lysis Buffer containing lOmM EDTA, 1% Triton X-100, 1 mM PMSF and 0.1% β -mercaptoethanol, then with lysis buffer containing IM urea, ImM PMSF and 0.1 % β- mercaptoethanol. The resulting white pellet is composed primarily of inclusion bodies, free of unbroken cells and membranous materials.
The inclusion bodies were dissolved in 20 ml 6M guanidine-HCl in lysis buffer with 1 mM PMSF and 0.1 % β-mercaptoethanol, and incubated on ice for 1 hour.
Materials that did not dissolve were removed by centrifugation (100,000 g x 30 min.) The clear supernatant was filtered through a 0.8 μm Supor filter (Gelman Sciences, FRG) and then load directly onto a 10 ml Ni^ " - NTA agarose column (Hochuli et al. 1987) pre-equilibrated in 6M guanidine-HCl in Lysis Buffer containing 1 mM PMSF and 0.1 % β-Mercaptoethanol. The column was washed with 20ml (2 bed volumes) of Lysis Buffer containing 6M guanidine-HCl, ImM PMSF and 0.1 %β-mercaptoethanol, then guanidine-HCl was removed slowly with a 100 ml linear gradient (from 6M to 0 M Guanidine-HCl) of lysis buffer containing 0.5% Brij 35, 1 mM PMSF, 0.1% β- mercaptochanol. Next, the column was developed with a 25 ml linear gradient of increasing imidazole (5 to 500 mM) in Lysis buffer containing 0.5% Brij 35, 1 mM
PMSF and 0.1 % β-mercaptoethanol. The recombinant proteins elute as a peak centered at lOOmM imidazole.
Fractions containing the recombinant proteins were pooled and then concentrated to approximately 8 ml by centrifugal filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 350-ml column (2.2 X 91 cm) of Sephacyl S-100 HR gel filtration medium equilibrated in Buffer A (50mM Sodium Phosphate, pH 8.0, 500 mM NaCl, 0.1 mM EGTA, 1 mM PMSF, 0.1%β-mercaptoethanol, 0.5% Brij 35) and ran in Buffer A at 30 ml/h. Fractions containing the recombinant protein were identified by absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled, concentrated to 1.5 to 2 mg/ml and dialysed overnight against 10 mM Potassium
Phosphate pH 7.5, 150 mM NaCl, 0.1 mM EGTA and 0.5% Brij 35. The concentration of protein in the dialysate was quantified, then aliquoted prior to freezing at - 20°C. Mouse model of Heliocobacter pylori infection
A murine model ofH pylori infection was produced by infection of C57BL/6 mice with with H. pylori Sydney strain SSI and was used to assess the efficacy of recombinant H pylori vac36. This mouse-adapted H. pylori strain is cagA+ vacA+, shows colonization levels in C57BL/6 mice equivalent to those observed in humans, forms adhesion pedestals, colonizes for at least 8 months, and elicits a chronic-active gastritis and mucosal atrophy (Lee et al, Gastroenterology, 112:1386-1397, 1997). Dose-response studies have shown 100%) infection rates of inbred C57BL/6 and Balb/C mice at 8 weeks post-challenge with a single inoculation of 10^ organisms.
Assessment of gastric H pylori infection
The presence ofH pylori organisms in gastric tissue was determined by culture of gastric tissue and by a quantitative urease assay. In the latter method, a longitudinal segment of antrum, representing approximately lA of the total antral region was placed in 1 ml of urea broth. After 4 hr, the extent of color change resulting from urea hydrolysis and increased pΗ was quantiated by spectrophotometric measurement of A550 (Fox et al, Immunol. 88:400-406, 1996). The assay sensitivity is ~ 10^ H pylori organisms. A positive (H /?v/or/-infected) gastric tissue was defined as that sample showing 2 standard deviations above the mean A550 value derived from a group of unchallenged uninfected age-matched control mice.
Assessment of local immune response to immunization in gastric tissue
Longitudinal sections of gastric tissues from the esophageal to the duodenal junction were embedded in OCT embedding compound, frozen in liquid nitrogen, and cryosections immunostained with monoclonal antibodies recognizing CD4+ or CD8+T cells or with antisera against mouse IgA for identification of IgA containing (IgACC) plasma cells (Pappo et al, Infect. Immun. 63:1246-1252, 1995). The degree of local gastric immune response was expressed quantitatively as the number of CD4+' CD8+ or IgACC cells per mm^ of gastric region examined.
Protective activity of purified recombinant H. pylori vac36 antigen
The ability of purified recombinant vac36 antigen derived from H. pylori to interfere with the establishment of an H. pylori infection was examined in mice. Groups (n=10) of 6-8 week-old female C57BL/6 mice were immunized orally 4 times at weekly intervals as follows: 1) 100 μg of recombinant vac36 antigen and 10 μg cholera toxin (CT) adjuvant, 2) 1 mg H. pylori lysate antigens and 10 μg CT, and 3) 0.2 M bicarbonate buffer and 10 wg CT adjuvant. The mice were challenged 2 weeks later on 3 consecutive days by oral administration of 10° H. pylori organisms. The experiment was terminated 2 weeks post-challenge, and the H pylori infection level assessed by bacterial colony counts and by quantitative urease assays.
Oral immunization with vac36 antigen interfered with the establishment ofH. pylori infection upon challenge with live H. pylori organisms. Mice immunized with purified recombinant vac36 antigen exhibited a significantly lower level of colonization by H pylori, as assessed by gastric urease activity and bacterial count assays (Table 6). Oral immunization with vac36 antigen also resulted in the generation of a local protective gastric immune response. Greater numbers of CD4+T cells and of IgACC were recruited in the gastric tissues of vac36-immunized mice when compared with unimmunized H. #y/orz'-infected mice (Table 7).
Table 6
Recombinant vac36 antigen protects mice from challenge with H. pylori
Figure imgf000091_0001
Urease activity is expressed as mean A55Q± SEM of duplicate antral samples from n=10 mice/group. by Wilcoxon Rank Sum Test compared with mice immunized with CT adjuvant alone
The level ofH. pylori in gastric tissue was assessed by bacterial counts, and shown as mean colony forming units±SEM
Table 7 vac36-immunized mice generate a local gastric immune response upon challenge with
H. pylori
Figure imgf000092_0001
a Mean number of cells/mm^ of gastric region + SEM p<0.05 by Wilcoxon Rank Sum Test when compared with unimmunized H pylori infected mice
V. Sequence Variance Analysis of genes in Helicobacter pylori strains Four genes were cloned and sequenced from several strains ofH. pylori to compare the DNA and deduced amino acid sequences. This information was used to determine the sequence variation between the H. pylori strain, J99, and other H. pylori strains isolated from human patients.
Preparation of Chromosomal DNA.
Cultures ofH. pylori strains (as listed in Table 10) were grown in BLBB (1% Tryptone, 1% Peptamin 0.1% Glucose, 0.2% Yeast Extract 0.5% Sodium Chloride, 5% Fetal Bovine Serum) to an OD600 of 0.2. Cells were centrifuged in a Sorvall RC-3B at 3500 x g at 4 C for 15 minutes and the pellet resuspended in 0.95 mis of 10 mM Tris- ΗC1, 0.1 mM EDTA (TE). Lysozyme was added to a final concentration of lmg/ml along with, SDS to 1% and RNAse A + Tl to 0.5mg/ml and 5 units/ml respectively, and incubated at 37 C for one hour. Proteinase K was then added to a final concentration of 0.4mg/ml and the sample was incubated at 55 C for more than one hour. NaCl was added to the sample to a concentration of 0.65 M, mixed carefully, and 0.15 ml of 10% CTAB in 0.7M NaCL (final is 1% CTAB/70mM NaCL) was added followed by incubation at 65°C for 20 minutes. At this point, the samples were extracted with chloroform:isoamyl alcohol, extracted with phenol, and extracted again with chloroform:isoamyl alcohol. DNA was precipitated with either EtOH (1.5 x volumes) or isopropanol (0.6 x volumes) at -70°C for lOminutes, washed in 70% EtOH and resuspended in TE.
PCR Amplification and cloning.
Genomic DNA prepared from twelve strains of Helicobacter pylori was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). To amplify a DNA sequence containing an H. pylori ORF, genomic DNA (10 nanograms) was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers, see Table 8) complementary to and flanking a defined H. pylori ORF, 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 0.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 20 microliters in duplicate reactions.
Table 8
Oligonucleotide primers used for PCR amplification ofH pylori DNA sequences.
Figure imgf000093_0001
The following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/ GeneAmp PCR System 9600 thermal cycler:
Protein 71 16626 and Protein 346;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 15 sec and 72°C for 1.5 min
23 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C for 1.5 min
Reactions were concluded at 72°C for 6 minutes.
Protein 26054702 for strains AH5, 5155, 7958, AH24,and J99;
Denaturation at 94°C for 2 min,
2 cycles at 94°C for 15 sec, 30°C for 15 sec and 72°C for 1.5 min
25 cycles at 94°C for 15 sec, 55°C for 15 sec and 72°C for 1.5 min Reaction was concluded at 72°C for 6 minutes.
Protein 26054702 and Protein 294796813 for strains AH4, AH15, AH61, 5294, 5640, AH18, and Hp244 ; Denaturation at 94°C for 2 min, 2 cycles at 94°C for 15 sec, 30°C for 20 sec and 72°C for 2 min 25 cycles at 94°C for 15 sec, 55°C for 20 sec and 72°C for 2 min Reactions were concluded at 72°C for 8 minutes.
Upon completion of thermal cycling reactions, each pair of samples were combined and used directly for cloning into the pCR cloning vector as described below.
Cloning ofH pylori DNA sequences into the pCR TA cloning vector.
All amplified inserts were cloned into the pCR 2.1 vector by the method described in the Original TA cloning kit (Invitrogen, San Diego, CA). Products of the ligation reaction were then used to transform the TOPI OF' (INVaF' in the case ofH pylori sequence 350) strain of E. coli as described below.
Transformation of competent bacteria with recombinant plasmids
Competent bacteria, E coli strain TOPI OF' or E. coli strain INVaF' were transformed with recombinant pCR expression plasmids carrying the cloned H pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). Briefly, 2 microliters of 0.5 micromolar BME was added to each vial of 50 microliters of competent cells. Subsequently, 2 microliters of ligation reaction was mixed with the competent cells and incubated on ice for 30 minutes. The cells and ligation mixture were then subjected to a "heat shock" at 42°C for 30 seconds, and were subsequently placed on ice for an additional 2 minutes, after which, samples were incubated in 0.45 milliliters SOC medium (0.5% yeast extract, 2.0 % tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgC12, 10 mM MgSO4 and 20, mM glucose) at 37°C with shaking for 1 hour. Samples were then spread on LB agar plates containing 25 microgram/ml kanamycin sulfate or 100 micrograms/ml ampicillan for growth overnight. Transformed colonies of TOP10F' or INVaF' were then picked and analyzed to evaluate cloned inserts as described below.
Identification of recombinant PCR plasmids carrying H. pylori sequences
Individual TOPI OF' or INVaF' clones transformed with recombinant pCR- Hpylori ORFs were analyzed by PCR amplification of the cloned inserts using the same forward and reverse primers, specific for each H. pylori sequence, that were used in the original PCR amplification cloning reactions. Successful amplification verified the integration of the H. pylori sequences in the cloning vector (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
Individual clones of recombinant pCR vectors carrying properly cloned H pylori ORFs were picked for sequence analysis. Sequence analysis was performed on ABI Sequencers using standard protocols (Perkin Elmer) using vector-specific primers (as found in PCRII or pCR2.1, Invitrogen, San Diego, CA) and sequencing primers specific to the ORF as listed in Table 9 below.
Table 9
Oligonucleotide primers used for sequencing ofH pylori DNA sequences.
Figure imgf000096_0001
Results
To establish the PCR error rate in these experiments, five individual clones of Protein 26054702, prepared from five separate PCR reaction mixtures from H pylori strain J99, were sequenced over a total length of 897 nucleotides for a cumulative total of 4485 bases of DNA sequence. DNA sequence for the five clones was compared to a DNA sequence obtained previously by a different method, i.e., random shotgun cloning and sequencing. The PCR error rate for the experiments described herein was determined to be 2 base changes out of 4485 bases, which is equivalent to an estimated error rate of less than or equal to 0.04%. DNA sequence analysis was performed on four different open reading frames identified as genes and amplified by PCR methods from a dozen different strains of the bacterium Helicobacter pylori . The deduced amino acid sequences of three of the four open reading frames that were selected for this study showed statistically significant BLAST homology to defined proteins present in other bacterial species. Those ORFs included: Protein 26054702, homologous to the val A & B genes encoding an ABC transporter in F. novicida; Protein 7116626, homologous to lipoprotein e (P4) present in the outer membrane of Η. influenzae; Protein 29479681, homologous to fecA, an outer membrane receptor in iron (III) dicitrate transport in E. coli. Protein 346 was identified as an unknown open reading frame, because it showed low homology with sequences in the public databases.
To assess the extent of conservation or variance in the ORFs across various strains ofH. pylori, changes in DNA sequence and the deduced protein sequence were compared to the DNA and deduced protein sequences found in the J99 strain ofH pylori (see Table 10 below). Results are presented as percent identity to the J99 strain of H. pylori sequenced by random shotgun cloning. To control for any variations in the J99 sequence each of the four open reading frames were cloned and sequenced again from the J99 bacterial strain and that sequence information was compared to the sequence information that had been collected from inserts cloned by random shotgun sequencing of the J99 strain. The data demonstrate that there is variation in the DNA sequence ranging from as little as 0.12 % difference (Protein 346, J99 strain) to approximately 7% change (Protein 26054702, strain AΗ5). The deduced protein sequences show either no variation ( Protein 346, strains AH 18 and AH24) or up to as much as 7.66% amino acid changes (Protein 26054702, Strain AH5). Table 10
Multiple Strain DNA Sequence analysis of H. pylori Vaccine Candidates J99 Protein #: 26054702 26054702 71 16626 71 16626 29479681 29479681 346 346
Length of Region
Sequenced: 248 a.a. 746 nt. 232 a.a. 96 nt. 182 a.a. 548 nt. 273 a.a. 819 nt.
Strain Tested
AA Nuc. AA Nuc. AA Nuc. AA Nuc. identity identity identity identity identity identity identity identity
J99 100.00% 100.00% 100.00% 100.00% 100.00% 100.00% 99.63% 99.88%
AH244 95.16% 95.04% n.d. n.d. 99.09% 96.71% 98.90% 96.45%
AH4 95.97% 95.98% 97.84% 95.83% n.d. n.d. 97.80% 95.73%
AH5 92.34% 93.03% 98.28% 96.12% 98.91% 96.90% 98.53% 95.73%
AH15 95.16% 94.91% 97.41% 95.98% 99.82% 97.99% 99.63% 96.09%
AH61 n.d. n.d. 97.84% 95.98% 99.27% 97.44% n.d. n.d.
5155 n.d. n.d. n.d. n.d. 99.45% 97.08% 98.53% 95.60%
5294 94.35% 94.37% 98.28% 95.40% 99.64% 97.26% 97.07% 95.48%
7958 94.35% 94.10% 97.84% 95.40% n.d. n.d. 99.63% 96.46%
5640 95.16% 94.37% 97.41% 95.69% 99.09% 97.63% 98.53% 95.48%
AH18 n.d. n.d. 98.71% 95.69% 99.64% 97.44% 100.00% 95.97%
AH24 94.75% 95.04% 97.84% 95.40% 99.27% 96.71% 100.00% 96.46%
n.d.= not done.
VI. Experimental Knock-Out Protocol for the Determination of Essential H. pylori Genes as Potential Therapeutic Targets
Therapeutic targets are chosen from genes wh jse protein products appear to play key roles in essential cell pathways such as cell envelope synthesis, DNA synthesis, transcription, translation, regulation and colonization/virulence.
The protocol for the deletion of portions ofH. pylori genes/ORFs and the insertional mutagenesis of a kanamycin-resistance cassette in order to identify genes which are essential to the cell is modified from previously published methods (Labigne- Roussel et al., 1988, J. Bacteriology 170, pp. 1704-1708; Cover et al.,1994, J. Biological Chemistry 269, pp. 10566-10573; Reyrat et al., 1995, Proc. Natl. Acad. Sci. 92, pp 8768-8772). The result is a gene "knock-out."
Identification and Cloning ofH. pylori Gene Sequences The sequences of the genes or ORFs (open reading frames) selected as knock-out targets are identified from the H. pylori genomic sequence and used to design primers to specifically amplify the genes/ORFs. All synthetic oligonucleotide primers are designed with the aid of the OLIGO program (National Biosciences, Inc., Plymouth, MN 55447, USA), and can be purchased from Gibco/BRL Life Technologies (Gaithersburg, MD, USA). If the ORF is smaller than 800 to 1000 base pairs, flanking primers are chosen outside of the open reading frame.
Genomic DNA prepared from the Helicobacter pylori ΗpJ99 strain (ATCC 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) is used as the source of template DNA for amplification of the ORFs by PCR (polymerase chain reaction) (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). For the preparation of genomic DNA from H. pylori, see Example I. PCR amplification is carried out by introducing 10 nanograms of genomic HpJ99 DNA into a reaction vial containing 10 mM Tris pH 8.3, 50 mM KCl, 2 mM MgCl2, 2 microMolar synthetic oligonucleotide primers (forward=F 1 and reverse=Rl), 0.2 mM of each deoxynucleotide triphosphate
(dATP,dGTP, dCTP, dTTP), and 1.25 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 40 microliters. The PCR is carried out with Perkin Elmer Cetus/GeneAmp PCR System 9600 thermal cyclers. Upon completion of thermal cycling reactions, each sample of amplified DNA is visualized on a 2% TAE agarose gel stained with Ethidium Bromide (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994) to determine that a single product of the expected size had resulted from the reaction. Amplified DNA is then washed and purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, MD, USA).
PCR products a. e cloned into the pT7Blue T- Vector (catalog#69820-l, Novagen, Inc., Madison, WI, USA) using the TA cloning strategy (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). The ligation of the PCR product into the vector is accomplished by mixing a 6 fold molar excess of the PCR product, 10 ng of pT7Blue-T vector (Novagen), 1 microliter of T4 DNA Ligase Buffer (New England Biolabs, Beverly, MA, USA), and 200 units of T4 DNA Ligase (New England Biolabs) into a final reaction volume of 10 microliters. Ligation is allowed to proceed for 16 hours at 16°C.
Ligation products are electroporated (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994) into electroporation- competent XL-1 Blue or DH5-a E.coli cells (Clontech Lab., Inc. Palo Alto, CA, USA). Briefly, 1 microliter of ligation reaction is mixed with 40 microliters of electrocompetent cells and subjected to a high voltage pulse (25 microFarads, 2.5 kV, 200 ohms) after which the samples are incubated in 0.45 ml SOC medium (0.5% yeast extract, 2% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl2, 10 mM MgSO4 and 20 mM glucose) at 37°C with shaking for 1 hour. Samples are then spread onto LB (10 g/1 bacto tryptone, 5 g/1 bacto yeast extract, 10 g/1 sodium chloride) plates containing 100 microgram/ml of Ampicillin, 0.3% X-gal, and 100 microgram/ml IPTG. These plates are incubated overnight at 37°C. Ampicillin-resistant colonies with white color are selected, grown in 5 ml of liquid LB containing 100 microgram/ml of Ampicillin, and plasmid DNA is isolated using the Qiagen miniprep protocol (Qiagen, Gaithersburg, MD, USA).
To verify that the correct H.pylori DNA inserts had been cloned, these pT7Blue plasmid DNAs are used as templates for PCR amplification of the cloned inserts, using the same forward and reverse primers used for the initial amplification of the J99 H.pylori sequence. Recognition of the primers and a PCR product of the correct size as visualized on a 2% TAE, ethidium bromide stained agarose gel are confirmation that the correct inserts had been cloned. Two to six such verified clones are obtained for each knock-out target, and frozen at -70°C for storage. To minimize errors due to PCR, plasmid DNA from these verified clones are pooled, and used in subsequent cloning steps.
The sequences of the genes/ORFs are again used to design a second pair of primers which flank the region ofH pylori DNA to be either interrupted or deleted (up to 250 basepairs) within the ORFs but are oriented away from each other. The pool of circular plasmid DNAs of the previously isolated clones are used as templates for this round of PCR. Since the orientation of amplification of this pair of deletion primers is away from each other, the portion of the ORF between the primers is not included in the resultant PCR product. The PCR product is a linear piece of DNA with H. pylori DNA at each end and the pT7Blue vector backbone between them which, in essence, resultes in the deletion of a portion of the ORFs. The PCR product is visualized on a 1% TAE, ethidium bromide stained agarose gel to confirm that only a single product of the correct size has been amplified. A Kanamycin-resistance cassette (Labigne-Roussel et al., 1988 J. Bacteriology 170, 1704-1708) is ligated to this PCR product by the TA cloning method used previously (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). The Kanamycin cassette containing a Campylobacter kanamycin resistance gene is obtained by carrying out an EcoRI digestion of the recombinant plasmid pCTB8:Jtα« (Cover et al.,1994, J. Biological Chemistry 269, pp. 10566-10573). The proper fragment (1.4 kb) is isolated on a 1% TAE gel, and isolated using the QIAquick gel extraction kit (Qiagen, Gaithersburg, MD, USA). The fragment is end repaired using the Klenow fill-in protocol, which involved mixing 4ug of the DNA fragment, 1 microliter of dATP,dGTP, dCTP, dTTP at 0.5 mM, 2 microliter of Klenow Buffer (New England Biolabs) and 5 units of Klenow DNA Polymerase I Large (Klenow) Fragment (New England Biolabs) into a 20 microliter reaction, incubating at 30°C for 15 min, and inactivating the enzyme by heating to 75°C for 10 minutes. This blunt-ended Kanamycin cassette is then purified through a Qiaquick column (Qiagen, Gaithersburg, MD, USA) to eliminate nucleotides. The "T" overhang is then generated by mixing 5 micrograms of the blunt-ended kanamycin cassette, 10 mM Tris pH 8.3, 50 mM KCl, 2 mM MgCl , 5 units of DNA Polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA), 20 microliters of 5 mM dTTP, in a 100 microliter reaction and incubating the reaction for 2 hours at 37°C. The "Kan-T" cassette is purified using a QIAquick column (Qiagen, Gaithersburg, MD, USA). The PCR product of the deletion primers (F2 and R2) is ligated to the Kan-T cassette by mixing 10 to 25 ng of deletion primer PCR product, 50 - 75 ng Kan-T cassette DNA, 1 microliter lOx T4 DNA Ligase reaction mixture, 0.5 microliter T4 DNA Ligase (New England Biolabs, Beverly, MA, USA) in a 10 microliter reaction and incubating for 16 hours at 16°C.
The ligation products are transformed into XL-1 Blue or DH5-a E.coli cells by electroporation as described previously. After recovery in SOC, cells are plated onto LB plates containing 100 microgram/ml Ampicillin and grown overnight at 37°C. These plates are then replica plated onto plates containing 25 microgram/ml Kanamycin and allowed to grow overnight. Resultant colonies have both the Ampicillin resistance gene present in the pT7Blue vector, .a d the newly introduced Kanamycin resistance gene. Colonies are picked into LB containing 25 microgram/ml Kanamycin and plasmid DNA is isolated from the cultured cells using the Qiagen miniprep protocol (Qiagen, Gaithersburg, MD, USA). Several tests by PCR amplification are conducted on these plasmids to verify that the Kanamycin is inserted in the H. pylori gene/ORF, and to determine the orientation of the insertion of the Kanamycin-resistance gene relative to the H. pylori gene/ORF. To verify that the Kanamycin cassette is inserted into the H. pylori sequence, the plasmid DNAs are used as templates for PCR amplification with the set of primers originally used to clone the H. pylori gene/ORFs. The correct PCR product is the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette. To avoid potential polar effects of the kanamycin resistance cassette on H. pylori gene expression, the orientation of the Kanamycin resistance gene with respect to the knock-out gene/ORF is determined and both orientations are eventually used in H. pylori transformations (see below). To determine the orientation of insertion of the kanamycin resistance gene, primers are designed from the ends of the kanamycin resistance gene ("Kan-1" 5'-ATCTTACCTATCACCTCAAAT-3' (SEQ ID NO:255)), and "Kan-2" 5'-AGACAGCAACATCTTTGTGAA-3' (SEQ ID NO:256)). By using each of the cloning primers in conjunction with each of the Kan primers (4 combinations of primers), the orientation of the Kanamycin cassette relative to the H.pylori sequence is determined. Positive clones are classified as either in the "A" orientation (the same direction of transcription is present for both the H pylori gene and the Kanamycin resistance gene), or in the "B" orientation (the direction of transcription for the H.pylori gene is opposite to that of the Kanamycin resistance gene). Clones which share the same orientation (A or B) are pooled for subsequent experiments and independently transformed into H. pylori.
Transformation of Plasmid DNA into H pylori cells
Two strains ofH. pylori are used for transformation: ATCC 55679. the clinical isolate which provided the DNA from which the H pylori sequence database is obtained, and AΗ244, an isolate which had been passaged in, and has the ability to colonize the mouse stomach. Cells for transformation are grown at 37°C, 10% CO2, 100% humidity, either on Sheep-Blood agar plates or in Brucella Broth liquid. Cells are grown to exponential phase, and examined microscopically to determine that the cells are "healthy" (actively moving cells) and not contaminated. If grown on plates, cells are harvested by scraping cells from the plate with a sterile loop, suspended in 1 ml of τ3rucella Broth, spun down (1 minute, top speed in eppendorf microfuge) and resuspended in 200 microliters Brucella Broth. If grown in Brucella Broth liquid, cells are centrifuged (15 minutes at 3000 rpm in a Beckman TJ6 centrifuge) and the cell pellet resuspended in 200 microliters of Brucella broth. An aliquot of cells is taken to determine the optical density at 600 nm, in order to calculate the concentration of cells. An aliquot (1 to 5 OD600 units/25 microliter) of the resuspended cells is placed onto a prewarmed Sheep-Blood agar plate, and the plate is further incubated at 37°C, 6% CO2, 100% humidity for 4 hours. After this incubation, 10 microliters of plasmid DNA (100 micrograms per microliter) is spotted onto these cells. A positive control (plasmid DNA with the ribonuclease H gene disrupted by kanamycin resistance gene) and a negative control (no plasmid DNA) are done in parallel. The plates are returned to 37°C, 6% CO for an additional 4 hours of incubation. Cells are then spread onto that plate using a swab wetted in Brucella broth, and grown for 20 hours at 37°C, 6% CO2. Cells are then transferred to a Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin, and allowed to grow for 3 to 5 days at 37°C, 6% CO2, 100% humidity. If colonies appear, they are picked and regrown as patches on a fresh Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin.
Three sets of PCR tests are done to verify that the colonies of transformants have arisen from homologous recombination at the proper chromosomal location. The template for PCR (DNA from the colony) is obtained by a rapid boiling DNA preparation method as follows. An aliquot of the colony (stab of the colony with a toothpick) is introduced into 100 microliters of 1% Triton X-100, 20 mM Tris, pH 8.5, and boiled for 6 minutes. An equal volume of phenol : chloroform (1 :1) is added and vortexed. The mixture is microfuged for 5 minutes and the supernatant is used as DNA template for PCR with combinations of the following primers to verify homologous recombination at the proper chromosomal location. TEST 1. PCR with cloning primers originally used to amplify the gene/ORF. A positive result of homologous recombination at the correct chromosomal location should show a single PCR product whose size is expected to be the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette. A PCR product of just the size of the gene/ORF is proof that the gene had not been knocked out and that the transformant is not the result of homologous recombination at the correct chromosome location.
TEST 2. PCR with F3 (primer designed from sequences upstream of the gene/ORF and not present on the plasmid), and either primer Kan-1 or Kan-2 (primers designed from the ends of the kanamycin resistance gene), depending on whether the plasmid DNA used was of "A" or "B" orientation. Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected s;ze (i.e., from the location of F3 to the insertion site of kanamycin resistance gene). No PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out. TEST 3. PCR with R3 (primer designed from sequences downstream of the gene/ORF and not present on the plasmid) and either primer Kan-1 or Kan-2, depending on whether the plasmid DNA used was of "A" or "B" orientation. Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected size (i.e., from the insertion site of kanamycin resistance gene to the downstream location of R3). Again, no PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out.
Transformants showing positive results for all three tests above indicate that the gene is not essential for survival in vitro.
A negative result in any of the three above tests for each transformant indicates that the gene had not been disrupted, and that the gene is essential for survival in vitro. In the event that no colonies result from two independent transformations while the positive control with the disrupted ribonuclease H plasmid DNA produces transformants, the plasmid DNA is further analyzed by PCR on DNA from transformant populations prior to plating for colony formation. This will verify that the plasmid can enter the cells and undergo homologous recombination at the correct site. Briefly, plasmid DNA is incubated according to the transformation protocol described above. DNA is extracted from the H pylori cells immediately after incubation with the plasmid DNAs and the DNA is used as template for the above TEST 2 and TEST 3. Positive results in TEST 2 and TEST 3 would verify that the plasmid DNA could enter the cells and undergo homologous recombination at the correct chromosomal location. If TEST 2 and TEST 3 are positive, then failure to obtain viable transformants indicates that the gene is essential, and cells suffering a disruption in that gene are incapable of colony formation.
VII. High-throughput drug screen assay Cloning, expression and protein purification
Cloning, transformation, expression and purification of the H. pylori target gene and its protein product,e.g., an H pylori enzyme, to be used in a high-throughput drug screen assay, is carried out essentially as described in Examples II and III above.
Development and application of a screening assay for a particular H. pylori gene product, peptidyl-propyl cis-trans isomerase, is described below as a specific example.
Enzymatic Assay
The assay is essentially as described by Fisher (Fischer, G., et.al. (1984) Biomed.
Biochim. Acta 43:1101-1111). The assay measures the cis-trans isomerization of the
Ala-Pro bond in the test peptide N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (Sigma # S- 7388, lot # 84H5805). The assay is coupled with α-chymotrypsin, where the ability of the protease to cleave the test peptide occurs only when the Ala-Pro bond is in trans.
The conversion of the test peptide to the trans isomer in the assay is followed at 390 nm on a Beckman Model DU-650 spectophotometer. The data are collected every second with an average scanning of time of 0.5 second. Assays are carried out in 35 mM Hepes, pH 8.0, in a final volume of 400 ul, with 10 μM α-chymotrypsin (type 1-5 from bovine Pancreas, Sigma # C-7762, lot 23H7020) and 10 nM PPIase. To initiate the reaction, 10 μl of the substrate ( 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in DMSO) is added to 390 μl of reaction mixture at room temperature.
Enzymatic assay in crude bacterial extract.
A 50 ml culture of Helicobacter pylori (strain J99) in Brucella broth is harvested at mid-log phase (OD 600 nm ~ 1) and resuspended in lysis buffer with the following protease inhibitors: 1 mM PMSF, and 10 μg/ml of each of aprotinin, leupeptin, pepstatine, TLCK, TPCK, and soybean trypsin inhibitor. The suspension is subjected to 3 cycles of freeze -thaw (15 minutes at -70 C, then 30 minutes at room temperature), followed by sonication (three 20 second bursts). The lysate is centrifuged (12,000 g x 30 minutes) and the supernatant is assayed for enzymatic activity as described above.
Many H. pylori enzymes can be expressed at high levels and in an active form in E coli. Such high yields of purified proteins provide for the design of various high throughput drug screening assays.
VIII. Truncated gene expression and protein production
Identification, cloning and expression of recombinant Helicobacter pylori sequences.
To facilitate the cloning, expression and purification of membrane proteins from H. pylori, the pΕT gene expression system (Novagen), for cloning and expression of recombinant proteins in Escherichia coli was selected. Further, for proteins that have a signal sequence at their amino-terminal end, a DNA sequence encoding a peptide tag (His-tag) was fused to the 5' end of the H. pylori DNA sequences of interest in order to facilitate purification of the recombinant protein products. In some cases, the DNA sequence was cloned in frame with the glutathione-S-transferase protein to produce a GST-fusion protein. The vectors used in this case were the pGΕX series from Pharmacia LKB (Uppsala, Sweden).
PCR amplification and cloning of DNA sequences containing ORFs for membrane and secreted proteins from the J99 strain of Helicobacter pylori.
The sequences chosen (from the list of the DNA sequences of the invention) for cloning from H. pylori strain J99 were prepared for amplification cloning by the polymerase chain reaction (PCR). Synthetic oligonucleotide primers for the ORF of interest (Table 11) specific for the predicted mature 5' end of the ORF and either downstream (3') of the predicted translational termination codon or at specific points within the coding region were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' terminus of the region of ORF of interest) were designed to include either a BamHl or a Ndel restriction site. These primers within the Ndel restriction site sequence were designed to permit the initiation of protein translation at a methionine residue (encoded within the Ndel restriction site sequence, in the case of producing a non His-tagged recombinant protein) or to fuse in frame with the DNA sequence encoding the His-tag (for producing His tagged recombinant protein), followed by the coding sequence for the remainder of the native H. pylori DNA. The primer with the BamHl restriction site was produced to fuse the H. pylori specific sequence in-frame with the C-terminus of the glutathione-S- transferase gene in the pGEX vectors (Pharmacia LKB, Uppsala, Sweden). All reverse oligonucleotide primers designed to include an EcoRI restriction site at the 5' terminus. Several reverse oligonucleotide primers were selected that would cause a truncation of the polypeptide to remove certain portions of the C-terminus, and in these cases the EcoRI restriction site at the 5' end was followed by a translational termination codon. This combination of primers would enable the ORF of interest (or parts of the ORF of interest) to be cloned into pΕT28b (to produce a His-tagged recombinant protein), pET30a (to produce a non His tagged or native recombinant protein) or the pGEX-4T or pGEX-5X series (to produce a GST fusion protein). The pET28b vector provides sequence encoding an additional 20 amino-terminal amino acids (plus the methionine in the Ndel restriction site) including a stretch of six histidine residues which makes up the His-tag, whereas the pGEX vectors fuse the H. pylori protein to a 26,000Da glutathione- S-transferase protein. Genomic DNA prepared from H. pylori strain J99 (ATCC 55679) was used as the source of template DNA for the PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). To amplify a DNA sequence containing a specific H. pylori ORF, genomic DNA (50 nanograms) was introduced into a reaction tube containing 200 nanograms of both the forward and reverse synthetic oligonucleotide primer specific for the ORF of interest, and 45 microliters of PCR SuperMix purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA) in a total of 50 microliters. The PCR SuperMix is supplied in 1.1X concentrations and contains 22mM Tris-HCl (pH 8.4), 55mM KCl, 1.65mM MgCl2, 220 micromolar of each dATP, dCTP, dGTP and dTTP, 22units recombinant Taq polymerase/ml and stabilizers. The following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/GeneAmp PCR System thermal cycler. Table 11: Oligonucleotide primers
Figure imgf000107_0001
Sequences for Vac38 (full length or truncated)
Denaturation at 94°C for 30 sec
35 cycles at 94°C for 15 sec, 55°C for 15 sec, and 72°C for 1.5 min
Reactions were concluded at 72 C for 8 minutes
Upon completion of the thermal cycling reactions, each sample of amplified
DNA was subjected to electrophoresis on 1.0% agarose gels. The DNA was visualized by exposure to ethidium bromide and long wave UV irradiation, and cut out in gel slices. DNA was purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA), and then subjected to digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The digested PCR amplicon was then re-electrophoresed and purified as before.
Ligation ofH. pylori DNA sequences into cloning vectors
The pOK12 vector (J. Vieira and J. Messing, Gene 100: 189-194, 1991) was prepared for cloning by digestion with BamHl and EcoRI or Ndel and EcoRI in the case of Vac41 (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The vectors were subjected to electrophoresis on 1.0% agarose gels and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the purified, digested vector and the purified, digested amplified H pylori ORF, the products of the ligation reaction were transformed into E coli JM109 competent cells according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Individual bacterial colonies were screened for those containing the correct recombinant plasmids by incubating in LB broth overnight (plus 25ug/ml kanamycin sulfate) followed by plasmid DNA preparation using the Magic Minipreps system (Promega Corp., Madison WI, USA), and then analyzed by restriction digestion (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Cloning ofH. pylori DNA sequences into the pET28b, pET30a and pGEX4T-3 prokaryotic expression vectors
Both the pΕT28b and pET30a expression vectors were prepared for cloning by digestion with Ndel and EcoRI, and the pGΕX4T-3 vector was prepared for cloning by digestion with BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The H. pylori DNA sequences were removed from pOK12 plasmid backbones by digestion with Ndel and EcoRI or BamHl and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). The pΕT28b, pET30a, pGEX4T-3 and H. pylori DNA sequences were all electrophoresed on a 1 % agarose gel and purified using the Wizard PCR Preps kit (Promega Corp., Madison WI, USA). Following ligation of the purified, digested expression vector and the purified, digested H. pylori DNA sequences, the products of the ligation reaction were transformed into E. coli JM109 competent cells (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al, eds., 1994). Individual bacterial colonies were screened for those containing the correct recombinant plasmids by preparing plasmid DNA as described above followed by analysis by restriction digestion profiles and DNA sequencing (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds.. 1994). These recombinant plasmids were then used to transform specific E. coli expression strains.
Transformation of competent bacteria with recombinant expression plasmids
Competent bacterial strains BL21(DE3), BL21(DE3)ρLysS, ΗMS174(DE3) and HMS174(DE3)pLysS were prepared and transformed with the recombinant pET28b expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). These expression host strains contain a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivative that carries the /αc/gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase expression is induced by the addition of isopropyl-β-D-thiogalactoside (IPTG), and the T7 RNA polymerase then transcribes any taget plasmid, such as pET28b, that carries a T7 promoter sequence and a gene of interest. Competent bacterial strains JM109 and DH5α were prepared and transformed with the recombinant pGEX4T-3 expression plasmid carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
Expression of recombinant H. pylori sequences in E. coli
Transformants were collected from LB agar plates containing 25ug/ml kanamycin sulfate (ensures maintenance of the pET28b-based recombinant plasmids) or 1 OOug/ml ampicillin (ensures maintenance of the pGEX4T-3 -based recombinant plasmids) and used to inoculate LB broth containing 25ug/ml kanamycin sulfate or 1 OOug/ml ampicillin and grown to an optical density at 600nm of 0.5 to 1.0 OD units, at which point ImM IPTG was added to the culture for one to three hours to induce gene expression of the H. pylori recombinant DNA constructions. After induction of gene expression with IPTG, bacteria were pelleted by centrifugation and resuspended in SDS- PAGE solubilization buffer and subjected to SDS-PAGE (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Proteins were visualized by staining with Coomassie Brilliant Blue or detected by western immunoblotting using the specific anti-His tag monoclonal antibody (Clontech, Palo Alto, CA, USA) or the anti-GST tag antibody (Pharmacia LKB) using standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The host strain that provided the highest level of recombinant protein production was then chosen for use in a large-scale induction in order to purify the recombinant protein. The strains used were HMS174(DE3) (pET28b-based constructs) and DH5α (pGEX4T-3 -based constructs).
Removal of the C-terminal regions appeared in both systems to improve the level of expression, although this increase was far more prominent in the GST-fusion system. All recombi ant proteins produced were of the predicted molecular weight based on the DNA sequence plus, if necessary, the size of the fusion tag. The truncated portion of the H. pylori protein contains some extremely hydrophobic stretches, and removal of these may be the reason for the increased expression. EOUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments and methods described herein. Such equivalents are intended to be encompassed by the scope of the following claims.
SEQUENCE LISTING 1) GENERAL INFORMATION: (i) APPLICANT:
(A) NAME: Astra A tiebolag
(B) STREET: S-151 85
(C) CITY: Sodertalje
(D) STATE: (E) COUNTRY: Sweden
(F) POSTAL CODE (ZIP)
(ii) TITLE OF INVENTION: NUCLEIC ACID AND AMINO ACID SEQUENCES
RELATING TO HELICOBACTER PYLORI AND VACCINE COMPOSITIONS THEREOF
(iii) NUMBER OF SEQUENCES: 275
(iv) COMPUTER READABLE FORM: (A) MEDIUM TYPE: CD/ROM ISO9660
(B) COMPUTER:
(C) OPERATING SYSTEM:
(D) SOFTWARE: (v) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER
(B) FILING DATE:
(vi) PRIOR APPLICATION DATA: (A) APPLICATION NUMBER:US 08/759,625
(B) FILING DATE: 05-DEC-1996
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 08/823,745 (B) FILING DATE: 25-MAR-1997
(viii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 08/891,928
(B) FILING DATE: 14- ULY-1997
(ix) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: LAHIVE & COCKFIELD
(B) STREET: 28 State Street
(C) CITY: Boston (D) STATE: Massachusetts
(E) COUNTRY: USA
(F) ZIP: 02109-1875
(x) ATTORNEY/AGENT INFORMATION: (A) NAME: Mandragouras , Amy E.
(B) REGISTRATION NUMBER: 36,207
(C) REFERENCE/DOCKET NUMBER: GTN-011CP2PC
(xi) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: (617)227-7400
(B) TELEFAX: (617)227-5941
(2) INFORMATION FOR SEQ ID NO : 1 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 687 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...687 (xi) SEQUENCE DESCRIPTION: SEQ ID NO : 1 :
ATGAGATTTA AGGGTTCAAG AGTGGAAGCG TTTTTAGGAG CGTTAGAATT TCAAGAGAAT 60
GAATATGAAG AGTTTAAAGA GCTTTATGAG AGCTTAAAAA CCAAGCAAAA GCCCCACACT 120
TTGTTCATTT CTTGCGTGGA TTCACGAGTC GTGCCTAATT TAATCACAGG CACCCAACCG 180 GGCGAATTGT ATGTGATCCG CAACATGGGC AATGTGATCC CCCCTAAAAC AAGCTATAAA 240
GAATCCCTTT CTACCATTGC GAGCGTTGAA TACGCTATCG CGCATGTGGG CGTTCAAAAC 300
TTAATCATTT GCGGGCATAG CGATTGTGGG GCTTGCGGGA GCATTCATTT AATCCATGAT 360
GAAACCACCA AAGCTAAAAC CCCTTACATT GCAAACTGGA TACAATTTTT AGAGCCTATT 420
AAAGAAGAAT TAAAAAACCA CCCGCAATTC AGCAACCATT TCGCCAAGCG TTCATGGCTT 480 ACAGAGCGTT TGAATGCGCG CTTGCAACTC AACAACCTCT TAAGCTATGA TTTCATTCAA 540
GAAAGAGTAA TAAATAACGA ATTAAAAATT TTTGGTTGGC ACTATATCAT AGAAACAGGC 600
AGGATTTATA ATTATAATTT TGAAAGCCAT TTTTTTGAGC CGATTGAAGA AACCATTAAA 660
CAAAGGATAA GTCATGAAAA CTTCTAA 687 (2) INFORMATION FOR SEQ ID NO : 2 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 666 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: ~i -cular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: - I l l -
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...666
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:
GTGGAAGCGT TTTTAGGAGC GTTAGAATTT CAAGAGAATG AATATGAAGA GTTTAAAGAG 60 CTTTATGAGA GCTTAAAAAC CAAGCAAAAG CCCCACACTT TGTTCATTTC TTGCGTGGAT 120
TCACGAGTCG TGCCTAATTT AATCACAGGC ACCCAACCGG GCGAATTGTA TGTGATCCGC 180
AACATGGGCA ATGTGATCCC CCCTAAAACA AGCTATAAAG AATCCCTTTC TACCATTGCG 240
AGCGTTGAAT ACGCTATCGC GCATGTGGGC GTTCAAAACT TAATCATTTG CGGGCATAGC 300
GATTGTGGGG CTTGCGGGAG CATTCATTTA ATCCATGATG AAACCACCAA AGCTAAAACC 360 CCTTACATTG CAAACTGGAT ACAATTTTTA GAGCCTATTA AAGAAGAATT AAAAAACCAC 420
CCGCAATTCA GCAACCATTT CGCCAAGCGT TCATGGCTTA CAGAGCGTTT GAATGCGCGC 480
TTGCAACTCA ACAACCTCTT AAGCTATGAT TTCATTCAAG AAAGAGTAAT AAATAACGAA 540
TTAAAAATTT TTGGTTGGCA CTATATCATA GAAACAGGCA GGATTTATAA TTATAATTTT 600
GAAAGCCATT TTTTTGAGCC GATTGAAGAA ACCATTAAAC AAAGGATAAG TCATGAAAAC 660 TTCTAA 666
(2) INFORMATION FOR SEQ ID NO: 3:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1008 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1008
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 3 : ATGTTAGTTA CTCGTTTTAA AAAAGCCTTC ATTTCTTATT CTTTAGGCGT GCTTGTTGTT 60 rr ATTATTAT TGAATGTGTG CAACGCTTCA GCACAAGAAG TCAAAGTCAA GGATTATTTT 120
GGGGAGCAAA CCATAAAGCT TCCTGTTTCC AAAATAGCCT ATATAGGGAG TTATGTAGAA 180
GTGCCTGCCA TGCTTAATGT TTGGGATAGG GTTGTAGGCG TTTCTGATTA TGCCTTTAAG 240
GATGACATTG TCAAAGCCAC TCTCAAAGGC GAGGATCTTA AACGAGTCAA ACACATGAGC 300 ACCGATCATA CAGCCGCGTT GAATGTGGAA TTATTAAAAA AGCTTAGCCC TGATCTTGTG 360
GTAACCTTTG TGGGTAACCC TAAAGCGGTA GAGCATGCGA AAAAATTTGG GATTTCATTC 420
CTTTCTTTCC AAGAGACAAC GATTGCAGAG GCCATGCAAG CTATGCAAGC TCAAGCCACG 480
GTCTTAGAAA TTGACGCTTC CAAAAAATTC GCCAAAATGC AAGAAACTTT GGACTTTATT 540
GCTGAGCGTT TGAAGGGCGT TAAAAAGAAA AAGGGGGTGG AGCTTTTCCA TAAAGCCAAT 600 AAAATCAGCG GCCATCAAGC CATTAGCTCA GACATTTTAG AAAAAGGGGG TATAGATAAT 660
TTTGGCTTGA AATACGTTAA GTTTGGACGC GCTGACATTA GTGTGGAAAA AATCGTTAAA 720
GAAAACCCTG AAATCATTTT CATTTGGTGG GTAAGCCCAC TCACTCCTGA AGACGTGTTG 780
AACAACCCTA AATTTTCCAC TATCAAAGCC ATTAAAAATA AGCAAGTCTA TAAGCTCCCC 840
ACGATGGATA TTGGCGGTCC TAGAGCCCCA CTCATTAGTC TTTTTATCGC TTTAAAAGCC 900
CACCCTGAAG CCTTTAAAGG CGTGGATATT AATGCGATAG TCAAAGATTA TTATAAAGTG 960
GTCTTTGATT TGAATGATGC GGAAATTGAG CCATTCTTAT GGCACTGA 1008
(2) INFORMATION FOR SEQ ID NO: 4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 825 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...825 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4:
ATGTTAGTTA CTCGTTTTAA AAAAGCCTTC ATTTCTTATT CTTTAGGCGT GCTTGTTGTT 60
TCATTATTAT TGAATGTGTG CAACGCTTCA GCACAAGAAG TCAAAGTCAA GGATTATTTT 120
GGGGAGCAAA CCATAAAGCT TCCTGTTTCC AAAATAGCCT ATATAGGGAG TTATGTAGAA 180 GTGCCTGCCA TGCTTAATGT TTGGGATAGG GTTGTAGGCG TTTCTGATTA TGCCTTTAAG 240
GATGACATTG TCAAAGCCAC TCTCAAAGGC GAGGATCTTA AACGAGTCAA ACACATGAGC 300
ACCGATCATA CAGCCGCGTT GAATGTGGAA TTATTAAAAA AGCTTAGCCC TGATCTTGTG 360
GTAACCTTTG TGGGTAACCC TAAAGCGGTA GAGCATGCGA AAAAATTTGG GATTTCATTC 420
CTTTCTTTCC AAGAGACAAC GATTGCAGAG GCCATGCAAG CTATGCAAGC TCAAGCCACG 480 GTCTTAGAAA TTGACGCTTC CAAAAAATTC GCCAAAATGC AAGAAACTTT GGACTTTATT 540
GCTGATCGTT TGAAGGGCGT TAAAAAGAAA AAGGGGGTGG AGCTTTTCCA TAAAGCCAAT 600
AAAATCAGCG GCCATCAAGC CATTAACTCA GACATTTTAC AACAAGGGGG TATTGATAAT 660
TTTGGCTTGA AATACGTCAA GTTTGGACGC GCTGACATTA GTGTGGAAAA AATCGTTAAA 720
GAAAACCCTG AAATCATTTT CATTAGGTGG GTAACCCCAC TCACTCCTGA TTACGTGTTG 780 AACAACCCAA AATTTTCTAC TATCAATGCC ATTAAAAACA TATAA P25
(2) INFORMATION FOR SEQ ID NO: 5:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1287 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1287
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 5:
ATGAAGAAAA AATTTCTGTC ATTAACCTTA GGTTCGCTTT TAGTTTCCGC TTTAAGCGCT 60
GAAGACAACG GCTTTTTTGT GAGCGCCGGC TATCAAATCG GTGAATCCGC TCAAATGGTG 120
AAAAACACCA AAGGCATTCA AGATCTTTCA GACAGCTATG AAAGATTGAA CAACCTTTTA 180
ACGAATTATA GCGTCCTAAA CGCTCTCATC AGGCAGTCCG CCGACCCCAA CGCCATCAAT 240 AACGCAAGGG GCAATTTGAA CGCGAGCGCG AAGAATTTGA TCAATGATAA AAAGAATTCC 300
CCGGCGTATC AAGCCGTGCT TTTAGCCTTG AATGCGGCAG CGGGGTTGTG GCAAGTCATG 360
AGCTATGCGA TCAGCCCTTG TGGTCCCGGT AAAGACACAA GCAAAAATGG GGGCGTTCAA 420
ACTTTCCACA ACACGCCTTC AAATCAATGG GGAGGCACTA CCATTACTTG TGGCACTACT 480
GGTTATGAAC CAGGACCATA CAGCATTTTA TCCACTGAAA ATTACGCGAA AATCAATAAA 540 GCTTATCAAA TCATCCAAAA GGCTTTTGGG AGCAGCGGAA AAGATATTCC TGCCTTAAGC 600
GACACCAACA CAGAACTCAA ATTCACAATC AATAAAAATA ATGGAAACAC GAATACGAAT 660
AATAATGGAG AAGAAATTGT TACAAAAAAT AACGCTCAAG TTCTTTTAGA ACAGGCTAGC 720
ACCATTATAA CTACCCTTAA TAGCGCATGC CCATGGATCA ACAATGGTGG TGCAGGTGGT 780
GCGAGTAGTG GTAGTTTATG GGAAGGAATA TATTTGAAAG GCGATGGGAG CGCTTGCGGG 840 ATTTTTAAAA ATGAAATCAG CGCGATTCAA GACATGATCA AAAACGCTGC AATAGCCGTA 900
GAGCAATCCA AGATCGTTGC TGCAAACGCG CAAAACCAGC GCAACCTAGA CACCGGGAAG 960
ACATTCAACC CCTATAAAGA CGCCAACTTC GCCCAAAGCA TGTTCGCTAA CGCCAAAGCG 1020
CAAGCGGAGA TTTTAAACCG CGCCCAAGCA GTGGTGAAAG ACTTTGAAAG AATCCCTGCA 1080
GAGTTCGTAA AAGACTCTTT AGGGGTGTGC CATGAAGTGC AAAACGGCCA TCTCCGTGGC 1140 ACGCCATCCG GCACGGTAAC TGATAACACT TGGGGAGCCG GTTGCGCGTA TGTGGGAGAG 1200
ACCGTAACGA ATCTAAAAGA CAGCATCGCT CATTTTGGCG ACCAAGCCGA GCGAATCCAT 1260
AACGCGCGCA ACCTCGCTAC ACTTTAG 1287
(2) INFORMATION FOR SEQ ID NO: 6:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 537 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...537
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 6 :
ATGAACCCCT TATTGCAAGA TTATGCGCGC ATCCTTTTAG AATGGAATCA AACGCACAAC 60
TTGAGCGGCG CGAGAAATTT AAGCGAATTA GAACCCCAGA TCACAGACGC TCTAAAGCCC 120 TTAGAATTTG TCAAAGATTT TAAAAGCTGC TTGGATATTG GGAGCGGGGC GGGACTTCCT 180
GCTATCCCTT TAGCCCTTGA AAAACCTGAA GCGCAATTCA TTCTTTTAGA GCCAAGGGTA 240
AAAAGAGCGG CTTTTTTAAA CTACCTTAAA AGCGTTTTGC CTTTAAACAA CATTGAAATC 300
ATTAAAAAGC GTTTAGAAGA TTATCAAAAT CTTTTACAAG TGGATTTAAT CACTTCTAGA 360
GCGGTCGCTA GCTCTTCTTT TTTGATAGAA AAAAGCCAAC GCTTCCTAAA AGATAAGGGG 420 TATTTTTTAT TCTATAAAGG CGAGCAGTTA AAGAATGAAA TCGCTTATAA AACCACTGAA 480
TGCTTTATGC ATCAAAAGCG CGTTTATTTT TACAAATCAA AGGAAAGTTT ATGTTAA 537
(2) INFORMATION FOR SEQ ID NO : 7 : (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 723 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...723
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7:
TTGGGTCTTA AAAAACGAGC TATTTTATGG TCTTTAATGG GATTTTGTGC AGGATTGAGC 60
GCGCTTGATT ATGACACCCT AGACCCAAAA TATTACAAAT ATATCAAGTA TTATAAGGCT 120
TATGAAGATA AAGAAGTTGA AGAATTGATC AGAGACTTGA AAAGGGCGAA CGCTAAAAGC 180
GGGCTTATTT TAGGGATCAA TACCGGTTTT TTTTATAACC ATGAAATCAT GGTCAAAACC 240 AATAGCTCCA GTATCACC3G GAATATTTTA AATTATTTGT TCGCCTATGG CTTGCGTTTT 300
GGCTATCAAA CTTTC-3.CC GTCGTTTTTT GCGCGCTTGG TTAAGCCCAA TATCATTGGC 360
AGGCGCATCT ATATTCAATA TTATGGAGGA GCTCCTAAGA AAGCGGGCTT TGGGAGCGTG 420
GGGTTTCAAT CGGTCATGTT GAATGGGGAT TTTTTATTAG ACTTTCCTTT GCCCTTTGTG 480
GGGAAATACC TTTATATGGG GGGGTATATG GGTTTAGGCT TGGGGGTTGT GGCGCATGGG 540 GTGAATTATA CGGCGGAATG GGGGATGTCT TTTAACGCAG GATTGGCTCT AACGGTATTA 600
GAAAAAAACC GCATTGAATT TGAATTTAAA ATTTTGAATA ATTTCCCTTT TTTGCAATCT 660
AATTCTTCAA AAGAGACTTG GTGGGGAGCT ATAGCAAGCA TTGGGTATCA ATATGTGTTC 720
TAA 723 (2) INFORMATION FOR SEQ ID NO: 8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 942 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...942
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8:
TTGAAACTCA AATACTGGTT AGTTTATCTG GCGTTCATTA TAGGACTTCA AGCGACAGAT 60 TATGACAATT TAGAAGAAGA AAACCAACAA TTAGACGAAA AAATAAACAA TTTAAAGCGA 120
CAGCTCACCG AAAAAGGGGT TTCACCCAAA GAGATGGATA AGGATAAGTT TGAAGAAGAA 180
TATTTAGAGC GAACTTACCC AAAGATTTCT TCAAAGAAAA GAAAAAAATT GCTCAAATCT 240
TTTTCCATAG CCGATGATAA GAGTGGGGTG TTTTTAGGGG GCGGGTATGC TTATGGGGAA 300
CTTAACTTGT CTTATCAAGG GGAGATGTTA GACAGGTATG GCGCAAATGC CCCTAGCGCG 360 TTTAAAAACA ATATCAATAT TAACGCTCCT GTTTCTATGA TTAGCGTTAA ATTTGGGTAT 420
CAAAAATACT TCGTGCCTTA TTTTGGGACA CGATTTTATG GGGATTTGTT GCTTGGGGGA 480
GGGGCGTTAA AAGAGAACGC GCTCAAGCAG CCTGTAGGCT CGTTTTTTTA TGTTTTAGGG 540
GCTATGAATA CCGATTTATT GTTTGACATG CCTTTAGATT TTAAGACTAA AAAGCATTTT 600
TTAGGCGTTT ATGCGGGTTT TGGGATAGGG CTTATGCTTT ATCAAGACAA GCCTAATCAA 660 AACGGGAGGA ATTTGATAGT AGGGGGTTAT TCAAGCCCTA ATTTTTTATG GAAATCTTTG 720
ATTGAAGTGG ATTACACTTT TAATGTGGGC GTGAGTTTAA CGCTTTATAG GAAACACCGC 780
TTAGAGATTG GCACAAAATT ACCGATTAGC TATTTGAGGA TGGGAGTAGA AGAGGGAGCG 840
ATTTATCACA ATAAAGAAAA TGATGAACGA TTGTTGATTT CGGCTAACAA CCAGTTCAAA 900
CGATCCAGTT TTTTATTAGT GAATTATGCG TTCATTTTTT GA 942
(2) INFORMATION FOR SEQ ID NO : 9 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1182 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1182
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 9: ATGACTTCAG CTTCAAGCCA TTCTTTTAAA GAACAAGATT TTCATATTCC TATCGCTTTC 60
GCTTTTGATA AGAATTATCT CATTCCTGCG GGCGCATGCA TTTATTCCTT GCTAGAAAGC 120
ATCGCTAAAG CCAATAAAAA AATCCGTTAC ACCTTACACG CTTTAGTGGT AGGCTTGAAT 180
GAAGAAGATA AAACAAAACT TAACCAAATC ACAGAGCCTT TTAAAGAATT TGCTGTTTTA 240
GAAGTAAAAG ATATTGAACC TTTTTTAGAC ACTATCCCTA ACCCTTTTGA TGAGGATTTC 300 ACCAAGCGTT TTTCTAAAAT GGTGTTAGTG AAGTATTTTC TAGCGGATTT ATTCCCCAAA 360
TATTCTAAAA TGGTGTGGAG CGATGTGGAT GTTATCTTTT GTAATGAATT TAGCGCTGAT 420
TTCTTAAACA TTAAAGAAGA TGATGAGAAT TATTTTTATG GGGTTTATGA CAAAATATAC 480
CCGTATGAAG GCTTTTTTTA TTGCAACTTA ACTTACCAGC GAAAAAATCA ATTTTGTAAA 540
AAAATATTAG AAATCATACG CGCACAAAAA ATAGATAAAG AACCGCAATT GACAGAATTT 600 TGTCGTTCAA AGATCGCGCC ATTAAAAATA GAGTATTGTA TTTTCCCACA CTATTATAGC 660
CTTTCTGAAG AGCATTTAAA GGGCGTGGCC AATGCAATTT ATCATAACAC CATTAAACAA 720
GCCCTAAGAG AACCTATCGT TATACAATAT GACTCTCATC CTTATTTTCA AATCAAGCCT 780
TGGACATATC CTTTTGGTTT GAAAGCGGAT TTATGGCTGA ACGCTTTGGC TAAAACCCCA 840
TTTATGAGCG ATTGGTCTTA TTTGATCACA GGGGGTGGGG GGATAGGTGG AGAAAAATGG 900 CATTACTACC ATGGCATTGC CGCTTATCAT TACTACTTTC CTTTATGGAA AGCAGAAGAA 960
CAGATTGCCC ATGACGCTCT TAAGACATTT TTAAAACATT ATTTTTTGCA CATTCATGAG 1020
ATTCCCCAAA ACGCAAGGCG AAGACTATTC AAATACTGCA TTTCAATACC GCTTAAGAGC 1080
TTTATTAGTA AAACCCTTAA ATTTCTAAAA CTCCATGCAT TGGTGAAAAA AATCCTAATC 1140
CAACTCAAGC TCTTAAAAAA GAACCAGAGC CAAAACTTTT AA 1182
(2) INFORMATION FOR SEQ ID NO: 10:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1308 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...1308
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 10:
TTGATTTTCT TAAAAAAATC TCTTTGCGCG TTGTTAATTT CAGGTTTTTT CATACCACCC 60 TTAATGAAAG CGGCTAGTTT TGTCTATGAC TTGAAGTTTA TGAGCTTTAA TTTCAATCTG 120
GCTTCCCCTC CAAATAACCC CTATTGGAAT AGCCTAACCA AAATGCAAGG TCGTCTCATG 180
CCTCAAATTG GCGTCCAATT AGACAAAAGA CAGGCCTTGA TGTTTGGGGC GTGGTTCATT 240
CAAAATTTGC ACACGCATTA TAGCTATTTC CCTTATTCGT GGGGGGTTAC CATGTATTAC 300 CAATACATAG GGAAAAATTT GAGATTTTTT TTAGGCATTG TGCCACGAAG CTATCAAATA 360
GGGCATTACC CTTTAAGCGC TTTTAAAAAA CTTTTCTGGT TTATAGACCC TACTTTTAGG 420
GGAGGAGCGT TCCAATTCAA ACCGGCTTAT GATCCCAATC GTTGGTGGAA TGGGTGGTTT 480
GAGGGCGTTG TGGATTGGTA TGGGGGGCGT AATTGGAACA ACCAGCCCAA AAAGAAAAAT 540
TACGATTTTG ATCAATTCTT GTATTTTGTT TCTTCAGAAT TTCAGTTTCT TAAAGGGTAT 600 TTAGGTTTGG GGGGACAGCT TGTCATTTTT CATAACGCCA ACTCTCATAG TATGGGGGAT 660
AACTACCCTT ATGGCGGGAA TTCCTACTTA AAACCAGGCG ATGCAACCCC ACAATGGCCT 720
AATGGCTACC CTTATTTCAG CCAAAAAGAT AACCCACAAG GCGGAGAAAT AGGGAAATAC 780
TCTAACCCTA CCATTTTAGA CAGGGTTTAT TACCATGCTT ATTTAAAAGC AGATTTTAAA 840
AATCTCATGC CTTATATGGA CAATATTTTC ATGACCTTTG GCACGCAGTC GTCTCAAACC 900 CATTATTGCG TGCGTTATGC TAGCGAGTGT AAAAACGCCC GATTTTATAA CAGCTTTGGG 960
GGGGAATTTT ACGCTCAAGC GCAATACAAA GGCTTTGGGA TCTTTAACAG ATACTATTTT 1020
TCCAACAAAC CCCAAATGCA TTTTTATGCC ACTTATGGCC AATCCCTTTA TACCGGATTG 1080
CCATGGTATA GAGCCCCTAA TTTTGACATG ATAGGGCTTT ATTATCTTTA TAAAAACAAA 1140
TGGTTAAGCG TGCGAGCGGA TGCGTTTTTT AGCTTTGTGG GTGGGGGCGA TGGGTACCAT 1200 TTGTATGGCA AGGGGGGTAA GTGGTTTGTG ATGTATCAGC AATTTTTAAC CCTAACCATA 1260
GACACAAGAG AGTTGATTGA TTTTGTCAAA TCTAAAATCC CTAAATAA 1308
(2) INFORMATION FOR SEQ ID NO: 11: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 663 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...663
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 11:
ATGAATAAAA CAACAATTAA AATATTAATG G ,C iTGGCGT TATTATCATC GCTTCAAGCC 60
GCAGAGGCAG AGCTTGATGA AAAATCAAAA AAACCTAAAT TTGCGGATAG GAATACGTTT 120
TATTTAGGGG TTGGGTATCA GCTTAGCGCG ATCAACACGT CTTTTAGCAC CAGTTCTATA 180
GATAAATCGT ATTTCATGAC CGGCAATGGT TTTGGCGTGG TGTTGGGGGG GAAATTTGTG 240 GCTAAAACGC AAGCTGTAGA GCATGTGGGT TTTCGTTACG GGTTGTTTTA TGATCAGACC 300
TTTTCTTCTC ACAAATCCTA TATTTCTACC TATGGTTTAG AATTTAGCGG TTTGTGGGAC 360
GCTTTCAATT CGCCAAAGAT GTTTTTGGGG TTGGAGTTTG GCTTAGGCAT CGCTGGGGCG 420
ACTTACATGC CAGGAGGGGC CATGCATGGG ATTATCGCTC AATATTTAGG CAAAGAAAAT 480
TCGCTTTTCC AATTGCTTGT GAAAGTGGGT TTTCGTTTTG GCTTTTTCCA CAATGAAATC 540 ACCTTTGGGT TGAAATTCCC TGTCATTCCT AACAAAAAAA CGGAAATCGT TGATGGCTTG 600 AGCGCGACCA CTTTATGGCA ACGCTTGCCG GTAGCCTATT TCAATTATAT CTATAATTTT 660 TAG 663 (2) INFORMATION FOR SEQ ID NO : 12 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...351
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12:
TTGAATCTCC ATTTTATGAA AGGATTTGTT ATGAGTGGAT TAAGAACATT TAGTTGTGTA 60
GTGGTTTTAT GCGGTGCAAT GGTTAATGTA GCTGTAGCTG GTCCTAAAAT AGAGGCAAGG 120 GGTGAATTAG GCAAATTTGT AGGGGGAGCT GTTGGAAATT TTGTTGGTGA TAAAATGGGC 180
GGATTTGTTG GTGGTGCAAT AGGAGGATAT ATTGGGTCTG AAGTAGGCGA TAGGGTAGAA 240
GATTATATCC GTGGCGTTGA TAGAGAGCCA CAAAACAAAG AACCACAAAC CCCAAGAGAA 300
CCTATCCGTG ATTTTTATGA TTACGGCTAT AGTTTTGGGC ATGCTTGGTG A 351 (2) INFORMATION FOR SEQ ID NO:13:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1311 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1311 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:
ATGTCAAGGG ATTTTAAATT TGATTCTAAC TATTTAAATG TCAATACCAA TCCTAAATTA 60 GGCCCCGTTT ATACCAATCA AAATTATCCA GGATTTTTTA TCTTTGATCA TTTAAGGCGT 120
TATGTGATGA ACGCTTTTGA GCCTAATTTG AACTTAGTTG TCAATACCAA TAAAGTTAAG 180
CAAACTTTTA ATGTGGGCAT GCGTTTTATG ACAATGGATA TGTTCATTAG ATCCGATCAA 240
AGCACATGCG AAAAAACAGA TATTATCAAT GGGGTGTGCC ACATGCCTCC TTATGTCCTT 300
TCTAAAACGC CTAACAATAA TCAAGAAATG TTTAATAACT ATACAGCGGT ATGGTTGAGC 360 GATAAAATAG AGTTTTTTGA TTCTAAATTG GTGATAACTC CAGGGCTTAG ATACACTTTT 420
TTGAACTATA ACAACAAAGA GCCAGAAAAG CATGATTTTT CCGTATGGAC CAGTAAAAAA 480
CAGCGTCAAA ACGAATGGAG TCCTGCCCTT AATATTGGCT ATAAACCTAT GGAAAATTGG 540
ATATGGTATG CGAACTACCG CCGCAGTTTT ATCCCCCCAC AACACACAAT GGTAGGCATT 600
ACTAGGACTA ATTACAACCA AATTTTTAAT GAAATTGAAG TGGGGCAGCG CTATAGTTAT 660 AAAAATCTAT TGAGTTTTAA CACCAATTAT TTTGTGATTT TTGCCAAGCG TTACTATGCG 720
GGAGGCTATA GCCCACAGCC TGTGGATGCC AGAAGTCAAG GGGTGGAATT GGAATTGTAT 780
TACGCGCCGA TTAGGGGTTT GCAATTCCAT GTGGCTTACA CTTATATTGA TGCGCGCATC 840
ACTTCTAACG CTGATGATAT TGCTTATTAT TTTACAGGCA TTGTCAATAA ACCCTTTGAC 900
ATTAAAGGGA AGCGCTTGCC CTATGTGAGT CCTAACCAAT TCATATTTGA CATGATGTAT 960 ACTTACAAGC ACACGACTTT TGGTATCAGC AGCTATTTTT ATAGCCGCGC TTATAGTTCC 1020
ATGCTCAATC AAGCCAAAGA TCAAACCGTA TGCCTGCCCT TAAACCCAGA ATACACAGGG 1080
GGGTTAAAGT ATGGTTGTAA TTCAGTGGGG TTATTGCCCT TGTATTTTGT GTTGAATGTC 1140
CAAGTAAGCT CAATCTTATG GCAAAGCGGT AGGCATAAAA TCACAGGGAG TTTGCAAATC 1200
AATAACCTTT TTAACATGAA GTATTATTTT AGGGGGATTG GCACAAGCCC TACAGGGAGA 1260 GAACCCGCGC CAGGGAGATC CATTACAGCG TATTTGAATT ATGAGTTTTA A 1311
(2) INFORMATION FOR SEQ ID NO: 14:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2304 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS : double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...2304
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: ATGAAAAGAA TTTTAGTTTC TTTGGCTGTT TTGAGTCATA GCGCGCATGC TGTCAAAACT 60
CATAATTTGG AAAGGGTGGA AGCTTCAGGG GTGGCTAACG ATAAAGAAGC GCCTTTAAGC 120
TGGAGGAGCA AGGAAGTTAG AAATTATATG GGTTCTCGCA CGGTGATTTC TAACAAGCAA 180
CTCACTAAAA GCGCCAATCA AAGCATTGAA GAAGCTTTGC AAAATGTGCC AGGCGTGCAT 240
ATTAGAAACT CTACCGGTAT TGGAGCTGTG CCTAGCATTT CCATTAGGGG GTTTGGTGCT 300 GGAGGCCCAG GGCATTCTAA TACGGGAATG ATTCTAGTCA ATGGGATTCC TATTTATGTC 360
GCGCCCTATG TTGAAATTGG CACGGTTATT TTTCCTGTAA CCTTTCAGTC TGTGGATAGA 420
ATCAGCGTAA CTAAGGGTGG GGAGAGCGTG CGTTATGGCC CTAACGCTTT TGGCGGTGTG 480
ATCAACATCA TCACCAAAGG CATTCCTACC AATTGGGAAA GTCAGGTGAG CGAGAGGACC 540 ACTTTTTGGG GCAAGTCTGA AAACGGGGGC TTTTTCAATC AAAATTCTAA AAACATTGAT 600
AAAAGCTTAG TTAATAACAT GCTTTTTAAC ACCTATTTAA GAACGGGGGG TATGATGAAT 660
AAGCATTTTG GAATCCAAGC TCAAGTCAAT TGGCTCAAAG GGCAAGGGTT TAGATACAAC 720
AGCCCTACGG ATATTCAAAA TTACATGTTA GATTCATTGT ATCAAATCAA TGATAGCAAT 780
AAAATCACCG CTTTTTTTCA ATATTATAGT TATTTCTTGA CAGACCCTGG ATCTTTAGGC 840 ATAGCCGCTT ACAATCAAAA TCGTTTTCAA AACAACCGCC CCAATAACGA TAAAAGCGGG 900
AGAGCGAAGC GATGGGGAGC TGTGTATCAA AACTTTTTTG GGGACACGGA TAGGGTAGGG 960
GGGGATTTCA CTTTTAGCTA CTATGGGCAT GACATGTCAA GGGATTTTAA ATTTGATTCT 1020
AACTATTTAA ATGTCAATAC CAATCCTAAA TTAGGCCCCG TTTATACCAA TCAAAATTAT 1080
CCAGGATTTT TTATCTTTGA TCATTTAAGG CGTTATGTGA TGAACGCTTT TGAGCCTAAT 1140 TTGAACTTAG TTGTCAATAC CAATAAAGTT AAGCAAACTT TTAATGTGGG CATGCGTTTT 1200
ATGACAATGG ATATGTTCAT TAGATCCGAT CAAAGCACAT GCGAAAAAAC AGATATTATC 1260
AATGGGGTGT GCCACATGCC TCCTTATGTC CTTTCTAAAA CGCCTAACAA TAATCAAGAA 1320
ATGTTTAATA ACTATACAGC GGTATGGTTG AGCGATAAAA TAGAGTTTTT TGATTCTAAA 1380
TTGGTGATAA CTCCAGGGCT TAGATACACT TTTTTGAACT ATAACAACAA AGAGCCAGAA 1440 AAGCATGATT TTTCCGTATG GACCAGTAAA AAACAGCGTC AAAACGAATG GAGTCCTGCC 1500
CTTAATATTG GCTATAAACC TATGGAAAAT TGGATATGGT ATGCGAACTA CCGCCGCAGT 1560
TTTATCCCCC CACAACACAC AATGGTAGGC ATTACTAGGA CTAATTACAA CCAAATTTTT 1620
AATGAAATTG AAGTGGGGCA GCGCTATAGT TATAAAAATC TATTGAGTTT TAACACCAAT 1680
TATTTTGTGA TTTTTGCCAA GCGTTACTAT GCGGGAGGCT ATAGCCCACA GCCTGTGGAT 1740 GCCAGAAGTC AAGGGGTGGA ATTGGAATTG TATTACGCGC CGATTAGGGG TTTGCAATTC 1800
CATGTGGCTT ACACTTATAT TGATGCGCGC ATCACTTCTA ACGCTGATGA TATTGCTTAT 1860
TATTTTACAG GCATTGTCAA TAAACCCTTT GACATTAAAG GGAAGCGCTT GCCCTATGTG 1920
AGTCCTAACC AATTCATATT TGACATGATG TATACTTACA AGCACACGAC TTTTGGTATC 1980
AGCAGCTATT TTTATAGCCG CGCTTATAGT TCCATGCTCA ATCAAGCCAA AGATCAAACC 2040 GTATGCCTGC CCTTAAACCC AGAATACACA GGGGGGTTAA AGTATGGTTG TAATTCAGTG 2100
GGGTTATTGC CCTTGTATTT TGTGTTGAAT GTCCAAGTAA GCTCAATCTT ATGGCAAAGC 2160
GGTAGGCATA AAATCACAGG GAGTTTGCAA ATCAATAACC TTTTTAACAT GAAGTATTAT 2220
TTTAGGGGGA TTGGCACAAG CCCTACAGGG AGAGAACCCG CGCCAGGGAG ATCCATTACA 2280
GCGTATTTGA ATTATGAGTT TTAA 2304
(2) INFORMATION FOR SEQ ID NO: 15:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 348 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc feature (B) LOCATION 1 . . . 348
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 15: TTGCACCCTC TATGCGCACA CGGCCAATGT GGAAGCGAAG CGATTGCGTG TTTAGAAGCC 60
ATTAGCGTGG GGATTGTGCC TGTTATCGCT AATAGCCCTT TAAGCGCGAC CAGGCAATTC 120
GCGCTAGATG AACGATCGTT ATTTGAGCCT AATAACGCTA AAGATTTGAG CGCTAAAATA 180
GACTGGTGGT TAGAAAACAA ACTTGAAAGA GAAAGAATGC AAAACGAATA CGCTAAAAGC 240
GCTTTAAACT ACACTTTAGA AAATTCAGTC ATTCAAATTG AAAAAGTTTA TGAAGAAGCG 300 ATCAAAGATT TTAAAAACAA CCCCAACCTC TTTAAAACCT TATCGTAA 348
(2) INFORMATION FOR SEQ ID NO: 16:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1170 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1170
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: ATGGTTATTG TTTTAGTCGT GGATAGCTTT AAAGACACCA GTAATGGCAC TTCTATGACA 60
GCGTTTCGTT TTTTTGAAGC GCTGAAAAAA AGAGGGCATG CGATGAGAGT GGTCGCCCCT 120
CATGTGGATA ATTTAGGGAG TGAAGAAGAG GGGTATTACA ACCTTAAAGA GCGCTATATC 180
CCCCTAGTTA CAGAAATTTC ACACAAGCAA CACATTCTTT TTGCCAAACC GGATGAAAAA 240
ATTCTACGAA AGGCTTTTAA GGGAGCGGAT ATGATCCATA CTTACTTGCC TTTTTTGCTA 300 GAAAAAACAG CCGTAAAAAT CGCGCGAGAA ATGCGAGTGC CTTATATTGG CTCTTTCCAT 360
TTACAGCCAG AGCATATTTC TTATAACATG AAATTGGGGC AATTTTCTTG GCTAAATACC 420
ATGCTTTTTT CATGGTTTAA ATCTTCGCAT TACCGCTATA TCCACCATAT CCATTGCCCA 480
TCAAAATTCA TTGTAGAAGA ATTGGAAAAA TACAACTATG GAGGAAAAAA ATACGCTATC 540
TCTAACGGCT TTGATCCCAT GTTTAAGTTT GAGCACCCGC AAAAAAGCCT TTTTGACACC 600 ACGCCCTTTA AAATCGCTAT GGTAGGC GC TATTCTAATG AAAAAAATCA AAGCGTTCTC 660
ATTAAAGCGG TTGCTTTAAG CCGA-.A_AAA CAAGACATTG TATTATTACT CAAAGGCAAG 720
GGGCCTGATG AGAAAAAAAT CAAACTTCTA GCCCAAAAAC TAGGCGTAAA AACGGAGTTT 780
GGGTTTGTCA ATTCCCATGA ATTGTTAGAG ATTTTAAAAA CTTGCACCCT CTATGCGCAC 840
ACGGCCAATG TGGAAAGCGA AGCGATTGCG TGTTTAGAAG CCATTAGCGT GGGGATTGTG 900 CCTGTTATCG CTAATAGCCC TTTAAGCGCG ACCAGGCAAT TCGCGCTAGA TGAACGATCG 960
TTATTTGAGC CTAATAACGC TAAAGATTTG AGCGCTAAAA TAGACTGGTG GTTAGAAAAC 1020
AAACTTGAAA GAGAAAGAAT GCAAAACGAA TACGCTAAAA GCGCTTTAAA CTACACTTTA 1080
GAAAATTCAG TCATTCAAAT TGAAAAAGTT TATGAAGAAG CGATCAAAGA TTTTAAAAAC 1140
AACCCCAACC TCTTTAAAAC CTTATCGTAA 1170 (2) INFORMATION FOR SEQ ID NO: 17:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 939 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS : double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...939
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 17: TTGGCTTCTT ACGGGTTTTT TTTAGGAGCG TTGTTTATTT TAGCGAGCGG GATCGTGTGC 60
TTACAGACTG CCGGTAATCC CTTTGTAACC TTGCTTTCTA AAGGTAAAGA AGCCAGAAAC 120
TTGGTTTTAG TCCAGGCGTT CAATTCGCTT GGCACGACTT TAGGGCCTAT TTTTGGGAGC 180
TTGTTGATTT TTAGCGCGAC CAAAACGAGC GATAATTTAA GCCTGATAGA CAAGTTAGCG 240
GACGCTAAAA GCGTTCAAAT GCCTTATTTG GGTTTAGCGG TGTTTTCGCT TCTTTTAGCG 300 CTTGTGATGT ATCTTTTAAA ATTGCCTGAT GTGGAAAAAG AAATGCCCAA AGAAACGACG 360
CAAAAAAGCC TGTTTTCGCA CAAACACTTT GTTTTTGGGG CTTTAGGGAT CTTTTTCTAT 420
GTGGGGGGAG AAGTGGCGAT TGGATCATTC TTGGTGCTAA GCTTTGAAAA GCTTTTGAAT 480
TTAGACGCTC AATCAAGCGC GCATTACTTG GTGTATTATT GGGGCGGCGC GATGGTAGGG 540
CGTTTCTTAG GCAGCGCTTT GATGAATAAA ATCGCTCCTA ATAAATACCT GGCTTTCAAC 600 GCCTTAAGCT CTATCATTCT TATCGCTTTG GCTATTCTTA TTGGAGGCAA GATCGCTTTA 660
TTCGCTCTGA CTTTTGTGGG CTTTTTCAAC TCTATCATGT TCCCTACAAT CTTTTCTTTG 720
GCTACGCTCA ATTTAGGGCA TCTCACTTCT AAGGCTTCTG GAGTGATTAG CATGGCGATT 780
GTGGGAGGGG CGTTAATCCC CCCCATTCAA GGCGTGGTTA CAGACATGCT CACAGCAACC 840
GAATCGAATC TGCTCTACGC TTATAGCGTG CCGTTGTTGT GCTATTTTTA TATCCTCTTC 900 TTTGCACTTA AGGGGTATAA ACAAGAAGAA AACTCCTAA 939
(2) INFORMATION FOR SEQ ID NO:18:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1224 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1224
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 18:
ATGCAAAAAA CTTCTAACAC TTTAGCGCTG GGGAGTTTGA CGGCGCTATT CTTTCTAATG 60
GGTTTTATCA CGGTTTTAAA CGACATTTTG ATCCCGCATT TAAAGCCCAT TTTTGACTTG 120
ACCTATTTTG AAGCTTCGCT CATTCAATTT TGCTTTTTTG GGGCGTATTT CATCATGGGG 180
GGAGTCTTTG GGAACGTGAT CAGTAAAATC GGCTACCCTT TTGGCGTGGT GCTTGGTTTT 240 GTGATCACAG CGAGCGGGTG CGCGTTGTTT TATCCGGCGG CGCATTTTGG CTCTTACGGG 300
TTTTTTTTAG GAGCGTTGTT TATTTTAGCG AGCGGGATCG TGTGCTTACA GACTGCCGGT 360
AATCCCTTTG TAACCTTGCT TTCTAAAGGT AAAGAAGCCA GAAACTTGGT TTTAGTCCAG 420
GCGTTCAATT CGCTTGGCAC GACTTTAGGG CCTATTTTTG GGAGCTTGTT GATTTTTAGC 480
GCGACCAAAA CGAGCGATAA TTTAAGCCTG ATAGACAAGT TAGCGGACGC TAAAAGCGTT 540 CAAATGCCTT ATTTGGGTTT AGCGGTGTTT TCGCTTCTTT TAGCGCTTGT GATGTATCTT 600
TTAAAATTGC CTGATGTGGA AAAAGAAATG CCCAAAGAAA CGACGCAAAA AAGCCTGTTT 660
TCGCACAAAC ACTTTGTTTT TGGGGCTTTA GGGATCTTTT TCTATGTGGG GGGAGAAGTG 720
GCGATTGGAT CATTCTTGGT GCTAAGCTTT GAAAAGCTTT TGAATTTAGA CGCTCAATCA 780
AGCGCGCATT ACTTGGTGTA TTATTGGGGC GGCGCGATGG TAGGGCGTTT CTTAGGCAGC 840 GCTTTGATGA ATAAAATCGC TCCTAATAAA TACCTGGCTT TCAACGCCTT AAGCTCTATC 900
ATTCTTATCG CTTTGGCTAT TCTTATTGGA GGCAAGATCG CTTTATTCGC TCTGACTTTT 960
GTGGGCTTTT TCAACTCTAT CATGTTCCCT ACAATCTTTT CTTTGGCTAC GCTCAATTTA 1020
GGGCATCTCA CTTCTAAGGC TTCTGGAGTG ATTAGCATGG CGATTGTGGG AGGGGCGTTA 1080
ATCCCCCCCA TTCAAGGCGT GGTTACAGAC ATGCTCACAG CAACCGAATC GAATCTGCTC 1140 TACGCTTATA GCGTGCCGTT GTTGTGCTAT TTTTATATCC TCTTCTTTGC ACTTAAGGGG 1200
TATAAACAAG AAGAAAACTC CTAA 1224
(2) INFORMATION FOR SEQ ID NO: 19: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 378 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...378
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 19: ATGAATAAAA TCGCTCCTAA TAAATACCTG GCTTTCGGCG CCTTAAGCTC TATCATTCTT 60
ATCGCTTTGG CTATTCTTAT TGGAGGCAAG ATCGCTTTAT TCGCTCTGAC TTTTGTGGGC 120
TTTTTCAACT CTATCATGTT CCCTACAATC TTTTCTTTGG CTACGCTCAA TTTAGGCATC 180 TCACTTCTAA TGGCTTCTGG AGTGATTAGC ATGGCGATTG TGGGAGGGGC GTTAATCCCC 240
CCCATTCAAG GCGTGGTTAC AGACATGCTC ACAGCAACCG AATCGAATCT GCTCTACGCT 300
TATAGCGTGC CGTTGTTGTG CTATTTTTAT ATCCTCTTCT TTGCACTTAA GGGGTATAAA 360
CAAGAAGAAA ACTCCTAA 378 (2) INFORMATION FOR SEQ ID NO:20:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 993 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...993
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 20:
TTGAAAAAAA TATTACCGGC TTTGTTAATG GGGTTTGTGG GATTGAATGC TAGTGATCGT 60
TTGTTAGAAA TCATGCGCCT TTATCAAAAA CAAGGCTTGG AAGTGGTGGG TCAAAAATTG 120 GATTCTTATT TAGCGGATAA GTCTTTTTGG GCAGAAGAGC TTCAAAACAA GGACACGGAT 180
TTTGGCTATT ATCAAAACAA GCAGTTTTTA TTTGTGGCGG ATAAATCCAA GCCCAGTTTG 240
GAGTTTTATG AAATAGAAAA TAACATGCTT AAAAAAATCA ACAGCTCTAA AGCCCTTGTA 300
GGCTCTAAAA AGGGCGATAA AACTTTAGAG GGCGATTTGG CCACGCCTAT TGGAGTGTAT 360
CGTATCACGC AGAAATTAGA GCGTTTGGAT CAATATTATG GCGTTTTGGC TTTTGTAACG 420 AATTACCCTA ATTTGTATGA CACTTTGAAA AAACGCACCG GGCATGGCAT TTGGGTGCAT 480
GGAATGCCTT TAAATGGCGA TAGGAATGAA TTGAACACTA AGGGTTGCAT TGCGATTGAA 540
AACCCTATTC TAAGCTCTTA TGACAAAGTG TTAAAAGGCG AAAAAGCGTT CCTTATCACT 600
TATGAAGACA AGTTTTCCCC TAGCACTAAA GAAGAATTGA GCATGATTTT AAGCTCCCTT 660
TTCCAATGGA AAGAAGCTTG GGCTAGGGGC GATTTTGAAC GCTACATGCG TTTTTATAAC 720 CCCAATTTCA CTCGCTATGA CGGCATGAGT TTTAACGCTT TT^iAAGAGTA TAAAAAAAGG 780
GTGTTTGCAA AAAATGAAAA AAAGAATATC GCTTTTTCCT C .ATCAATGT GATCCCTTAC 840
CCCAACTCTC AAAACAAACG CTTGTTTTAT GTGGTATTTG ACCAAGATTA CAAAGCCTAC 900
CAGCAAAACA AGCTCTCTTA TAGCTCCAAT TCTCAAAAAG AACTCTATGT AGAGATTGAA 960
AACAATCAAG CGTCTATTAT AATGGAAAAA TAA 993
INFORMATION FOR SEQ ID NO: 21:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 510 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...510
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: TTGTTTGAGA AATGGATTGG TCTGACCTTA CTCCTTAGTT CCTTAGGCTA TCCATGCCAA 60
AAGGTAAGTA TTAGTTTCAA GCAATACGAA AATCTTATCC ATATCCATCA AAAAGGTTGC 120
AACAATGAAG TGGTGTGCAG AACGCTCATC TCTATCGCTl TACTAGAAAG CTCTCTAGGG 180
TTGAACAACA AGCGAGAAAA ATCCCTTAAA GACACTTCTT ACTCCATGTT CCATATCACC 240
TTAAACACCG CTAAAAAGTT CTACCCTACC TATTCTAAAA CGCTCCTCAA AACCAAATTG 300 TTAAATGATG TGGGTTTTGC GATCCAATTA GCCAAACAAA TTTTAAAAGA AAATTTTGAT 360
TATTACCACC AAAAACACCC CAACAAAAGC GTGTATCAAT TAGTACAAAT GGCCATAGGC 420
GCTTACAATG GGGGAATGAA ACACAACCCT AATGGCGCTT ACATGAAGAA GTTTCGTTGC 480
ATTTATTCTC AAGTGCGATA CAACGAATAA 510 (2) INFORMATION FOR SEQ ID NO: 22:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 648 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...648
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:22:
ATGAAAAAAC CCTACAGAAA GATTTCTGAT TATGCGATCG TGGGTGGTTT GAGCGCGTTA 60 GTGATGGTAA GCATTGTGGG GTGTAAGAGC AATGCCGATG ACAAACCAAA AGAGCAAAGC 120 TCTTTAAGTC AAAGCGTTCA AAAAGGCGCG TTTGTGATTT TAGAAGAGCA AAAGGATAAA 180
TCTTACAAGG TTGTTGAAGA ATACCCCAGC TCAAGAACCC ACATTGTAGT GCGCGATTTG 240
CAAGGCAATG AACGCGTGTT GAGCAATGAA GAGATTCAAA AGCTCATCAA AGAAGAAGAA 300
GCCAAAATTG ATAACGGCAC GAGCAAGCTT GTCCAGCCTA ATAATGGAGG GAGTAATGAA 360
GGATCAGGCT TTGGCTTGGG AAGCGCGATT TTAGGGAGCG CGGCGGGGGC GATTTTAGGG 420
AGTTATATTG GCAATAAGCT TTTTAATAAC CCTAATTATC AGCAAAACGC CCAACGGACC 480
TACAAATCCC CACAAGCTTA CCAACGCTCT CAAAATTCTT TTTCTAAAAG CGCACCCAGC 540
GCTTCAAGCA TGGGCACAGC GAGTAAGGGA CAGAGCGGGT TTTTTGGCTC TAGTAGGCCT 600
ACTAGTTCGC CTGCAATAAG CTCTGGGACA AGGGGCTTTA ACGCATAA 648
(2) INFORMATION FOR SEQ ID NO: 23:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...762
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 23:
TTGAAAACTC TATTTAGTGT TTATCTCTTT TTGTCGTTGA ATCCACTCTT TTTAGAAGCT 60 AAAGAAATCA CTTGGTCTCA ATTCTTGGAA AATTTTAAAA ACAAGAATGA AGACGACAAA 120
CCTAAACCCC TAACCATTGA CAAAAACAAT GAAAAACAGC AAATCCTAGA CAAAAACCAG 180
CAAATCTTAA AAAGGGCTTT AGAAAAAAGC CTTAAATTTT TCTTTATTTT TGGATACAAC 240
TATTCGCAAG CCGCTTATTC AACCACTAAT CAAAACTTGA CTCTTACGGC GAATAGCATA 300
GGGTTTAACA CCGCTACAGG CTTGGAGCAT TTTTTAAGAA ACCACCCTAA AGTCGGTTTT 360 AGAATCTTTA GCGTCTATAA CTATTTCCAT TCCGTTTCGC TCTCCCAGCC TCAAATCCTA 420
ATGGTGCAAA ATTACGGAGG CGCGTTAGAT TTTTCTTGGA TTTTTGTGGA TAAAAAAACC 480
TATCGCTTTA GGAGTTATTT AGGAATCGCT TTAGAGCAAG GGGTGTTGTT AGTGGATACG 540
ATTAAAACCG GCTCTTTCAC AACCATCATC CCAAGAACCA AGAAAACCTT TTTTCAAGCC 600
CCTTTGCGTT TTGGTTTTAT CGTGGATTTT ATCGGCTATT TGTCTTTGCA ATTAGGGATT 660 GAAATGCCCT TAGTGAGGAA TGTTTTTTAC ACCTACAATA ACCATCAAGA AAGATTCAAA 720
CCACGATTTA ACGCTAAI 2" TTCTTTAATC GTTTCGTTTT AG 762
(2) INFORMATION FOR SEQ ID NO:24: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1011 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1011 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24:
TTGTTTTTCA AATTTATTTT ATGTTTATCA TTAGGAATAT TTGCATGGGC AAAAGAGGTC 60
ATTCCCACCC CTTCAACCCC ATTAACGCCC TCTAAACGCT ATTCTATCAA TTTGATGACT 120
GAAAATGATG GTTATATCAA TCCTTACATT GATGAGTATT ACACGGCAGG CAATCAAATA 180 GGCTTTTCTA CTAAAGAGTT TGATTTTTCT AAAAATAAAG CGATGAAATG GTCTTCGTAT 240
TTAGGGTTTT TCAATAAAAG CCCTAGGGTT ACTCGTTTTG GCATTTCTCT CGCCCAAGAC 300
ATGTATACCC CCTCACTTGC AAACAGAAAA CTGGTGCATT TGCATGACAA CCACCCTTAT 360
GGGGGGTATT TGAGGGTGAA TTTGAACGTG TATAACCGCC ATCAAACTTT CATGGAGTTA 420
TTCACGATTT CTTTAGGCAC GACAGGGCAA GATTCTTTGG CCGCTCAAAC GCAGCGTCTC 480 ATTCATAAAT GGGGTCATGA TCCCCAATTT TATGGCTGGA ACACGCAGCT CAAAAACGAA 540
TTTATCTTTG AACTGCACTA CCAATTGCTT AAAAAAGTCC CCCTTTTAAA GACTCGTTTT 600
TTTTCTATGG AGTTGATGCC TGGGTTTAAT GTGGAACTGG GTAATGCGAG GGATTATTTC 660
CAACTCGGCT CGCTCTTTAG GGCTGGGTAT AACTTGGACG CTGATTATGG GGTCAATAAG 720
GTCAATACCG CTTTTGATGG GGGCATGCCT TATAGCGATA AGTTTTCCAT CTATTTTTTT 780 GCAGGGGCTT TTGGGCGCTT CCAACCCCTT AACATCTTCA TTCAAGGCAA TAGCCCTGAA 840
ACTAGGGGCA TTGCCAATTT GGAATACTTT GTTTATGCCA GTGAAATAGG AGCGGCTATG 900
ATGTGGCGTA GCCTCAGGGT GGCTTTTACA ATCACTGATA TTAGTAAAAC CTTTCAGTCC 960
CAGCCTAAGC ACCATCAGAT CGGCACCTTA GAATTGAATT TCGCCTTTTG A 1011 (2) INFORMATION FOR SEQ ID NO: 25:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 327 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...327 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 25:
ATGAAACCAA TCTTTAGCCT CTTTTTCCTC CTTATTGTTT TAAAAGCGCA CCCCATAAAC 60
CCCTTATTAG AGCCGTTATA TTTCCCCAGT TACACGCAAT TTTTAGATTT AGAACCTCAT 120
TTTGTCATTA AAAAAAAGCG CGCTTACAGG CCTTTTCAAT GGGGGAACAC TATTATTATC 180
AAACGCCATG ATTTAGAAGA GCGCCAGAGC AACCAACCAA GCGATATTTT CCGCCAGAAC 240
GCTGAAATCA ATGTGTCTTC TCAAACTTTT TTAAGAGGAA TCAGCAGCGC TTCTTCACGC 300
ATAGTGATCG ATTCGGTCGC TCAGTAA 327
(2) INFORMATION FOR SEQ ID NO:26:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 588 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...588
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 26:
ATGAGCAATA ACCCCTTTAA AAAAGTGGGC ATGATCAGCT CTCAAAACAA TAACGGCGCT 60 TTGAACGGGC TTGGCGTGCA AGTGGGTTAT AAACAATTCT TTGGCGAAAG CAAAAGATGG 120
GGGTTAAGGT ATTATGGTTT CTTTGATTAC AACCACGGCT ATATCAAATC CAGCTTTTTT 180
AATTCTTCTT CTGATATATG GACTTATGGC GGTGGGAGCG ATTTGTTAGT GAATTTTATC 240
AACGATAGCA TCACAAGAAA GAACAACAAG CTTTCTGTGG GTCTTTTTGG TGGTATCCAA 300
CTAGCAGGGA CTACATGGCT TAATTCTCAA TACATGAATT TAACAGCGTT CAATAACCCT 360 TACAGCGCGA AAGTCAATGC TTCCAATTTC CAATTTTTGT TCAATCTCGG CTTGAGGACG 420
AATCTCGCTA CAGCTAAGAA AAAAGACAGC GAACGTTCCG CGCAACATGG CGTTGAACTG 480
GGCATTAAAA TCCCTACCAT TAACACCAAT TATTATTCTT TTCTAGGCAC TAAGCTAGAA 540
TACAGAAGGC TTTATAGCGT GTATCTCAAT TATGTGTTTG CTTATTAA 588 (2) INFORMATION FOR SEQ ID NO: 27:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 684 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...684
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:27:
GTGCGTTTTG GTAAAATTGA TTATTTGAAC ATGCTCCCTT TTGATGTGTT TATCAAATCC 60 TACCCCACCC CTTGTTATTT CAAACAATTC TTACGGCTTA AAAAAACCTA CCCCTCCAAA 120
CTCAATGAGA GTTTTTTATT CAGGCGCATT GATGCGGGGT TTATTTCTTC TATCGCTGGC 180
TATCCATTCG CTCTTTGTTC TTATTCTCTA GGCATTGTCG CTTATAAGGA AGTTTTAAGC 240
GTGTTGGTTG TAAATAGAGA AAACGCTTTT GACAAAGAAA GCGCTTCTTC AAACGCCCTC 300
TCTAAAGTGT TAGGGTTAAA AGGCGAGGTC TTAATCGGCA ATAAAGCGCT GCAATTTTAT 360 TATTCCAACC CTAAAAAAGA TTTTATAGAT TTAGCCGCTC TGTGGTATGA AAAAAAACGC 420
TTGCCGTTTG TTTTTGGGCG TCTGTGCTAT TATCAAAACA AGGATTTTTA CAAACGCTTG 480
TCTTTAGCCT TCAAACATCA AAAAACAAAA ATCCCTCACT ACATCCTTAA AGAAGCCGCT 540
TTGAAAACCA ACTTGAAACG CCAAGATATT CTAAACTACT TGCAAAAAAT TTACTACACT 600
TTAGGCAAAA AGGAACAATC AGGCCTTAAA GCGTTCTATC GTGAATTGTT GTTCAAACGC 660 ATCCAAAAAC CCAAGCGGTT TTAG 684
(2) INFORMATION FOR SEQ ID NO: 28:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 918 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...918
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 28: ATGGGTAGAA TTGAATCAAA AAAGCGTTTG AAAGCACTCA TTTTTTTAGC GAGTTTGGGG 60
GTGTTGTGGG GCAATGCGGC TGAAAAAACG CCTTTTTTTA AAACTAAAAA CCACATTTAT 120
TTGGGTTTTA GGCTAGGCAC AGGGGCTACT ACGCGCACAA GCATGTGGCA ACAAGCCTAT 180
AAAGACAACC CCACTTGCCC TAGCAGCGTG TGTTATGGCG AGAAATTAGA AGCCCATTAT 240
AAGGGGGGTA AAAACTTATC TTATACCGGG CAAATAGGCG ATGAAATAGC TTTTGATAAA 300 TACCATATTT TAGGCTTAAG GGTGTGGGGG GATGTAGAAT ACGCTAAGGC TCAATTAGGT 360
CAAAAAGTGG GGGGTAACAC CCTTTTATCC CAAGCGAATT ATAACCCAAG CGCGATTAAA 420
ACCTACGATC CTACTTCAAA CGCTCAAGGC TCTTTAGTTT TGCAAAAAAC CCCAAGCCCC 480
CAAGATTTCC TTTTCAATAA CGGGCATTTC ATGGCGTTTG GTTTGAACGT GAACATGTTT 540 GTCAATCTCC CTATAGACAC CCTTTTAAAA CTCGCTTTAA AAACGGAAAA AATGCTGTTT 600
TTTAAAATAG GCGTGTTTGG TGGGGGTGGG GTGGAATACG CAATCTTGTG GAGTCCTCAA 660
TATAAAAATC AAAATACCCA TCAAGACGAT AAATTTTTTG CCGCAGGTGG GGGGTTTTTT 720
GTGAATTTTG GAGGCTCTTT GTATATAGGC AAGCGCAACC GCTTCAATGT GGGGCTAAAA 780
ATCCCTTATT ATAGCTTGAG CGCGCAAAGT TGGAAAAATT TTGGCTCTAG CAATGTGTGG 840 CAGCAACAAA CGATCCGACA AAACTTCAGC GTTTTTAGGA ATAAAGAAGT TTTTGTCAGC 900
TACGCGTTCT TGTTTTAG 918
(2) INFORMATION FOR SEQ ID NO: 29: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 777 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...777
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 29:
ATGTTTTTAA GATCATACCC AAAGCTTAGA TACGCTTTAT GTTTACCCCT ACTCACTGAG 60
ACTTGCTATA GCGAGGAGCG CACTTTAAAT AAGGTTACCA CCCAAGCTAA AAGGATTTTC 120
ACTTACAATA ATGAGTTTAA GGTTACTTCT AAAGAATTGG ATCAACGCCA AAGCAATGAA 180
GTCAAAGACC TGTTTAGGAC TAACCCTGAT GTGAATGTGG GCGGAGGGAG CGTGATGGGG 240 CAGAAAATCT ACGTGAGAGG CATTGAAGAC AGGCTTTTAA GGGTTACGGT GGATGGGGCT 300
GCGCAAAATG GCAACATCTA CCACCACCAA GGCAACACCG TGATTGACCC TGGCATGCTC 360
AAAAGCGTGG AAGTTACTAA AGGCGCGGCG AATGCGAGCG CGGGGCCAGG AGCGATCGCG 420
GGAGTGATTA AAATGGAGAC TAAAGGAGCG GCTGATTTTA TCCCTAGGGG GAAAAATTAT 480
GCAGCGAGTG GGGCGGTGAG TTTTTATACC AATTTTGGGG ACAGAGAGAC TTTTAGATCG 540 GCCTATCAAA GCOCGCATTT TGATATTATC GCTTACTACA CGCACCAAAA TATTTTCTAT 600
TATAGGAGCG JC CCACAGT GATGAAAAAC CTTTTCAAAC CCACACAAGC CGATAAAGAG 660
CCAGGAACTC CCAGCGAGCA AAACAACGCT TTGATTAAAA TGAATGGCTA TTTGAGCGAC 720
AGAGACACGC TCACTTTCAG CTGGAACATG ACACGAGATA ACGCCACACG CCTTTAA 777 (2) INFORMATION FOR SEQ ID NO: 30:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 579 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...579
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:30:
ATGTTTTTAA GATCATACCC AAAGCTTAGA TACGCTTTAT GTTTACCCCT ACTCACTGAG 60 ACTTGCTATA GCGAGGAGCG CACTTTAAAT AAGGTTACCA CCCAAGCTAA AAGGATTTTC 120
ACTTACAATA ATGAGTTTAA GGTTACTTCT AAAGAATTGG ATCAACGCCA AAGCAATGAA 180
GTCAAAGACC TGTTTAGGAC TAACCCTGAT GTGAATGTGG GCGGAGGGAG CGTGATGGGG 240
CAGAAAATCT ACGTGAGAGG CATTGAAGAC AGGCTTTTAA GGGTTACGGT GGATGGGGCT 300
GCGCAAAATG GCAACATTTA CCACCACCAA GGCAACACCG TGATTGACCC TGGCATGCTC 360 AAAAGCGTGG AAGTTACTAA AGGCGCGGCG AATGCGAGCG CGGGGCCAGG AGCGATCGCG 420
GGAGTGATTA AAATGGAGAC TAAAGGAGCG GCTGATTTTA TCCCTAGGGG GAAAAATTAT 480
GCAGCGAGTG GGGCGGTGAG TTTTTATACC AATTTTGGGG ACAGAGAGAC TTTTAGATCG 540
GCCTATCAAA GCGCGCATTT TGATATTATC GCTTACTAG 579 (2) INFORMATION FOR SEQ ID NO:31:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 381 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...381
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:31:
GTGCCCTTGA GTTTGGGAGG CAACCTCTTA AACCCTAACA ACAGTAGCGT GCTGAATTTA 60 AAAAACAGCC AGCTTGTTTT TAGCGATCAA GGGAGCTTGA ATATCGCTAA CATTGATTTA 120 CTAAGCGATC TGAATGGTAA TAAAAATCGT GTGTATAACA TCATTCAAGC GGACATGAAT 180
GGTAATTGGT ATGAGCGTAT CAACTTCTTT GGCATGCGCA TTAATGATGG GATTTATGAC 240
GCTAAAAACC AAACTTATAG TTTCACTAAC CCTCTCAATA ACGCCGTAAA ATTCACCGAG 300
AGCTTTTTCA TACACCGCCT GTGCGGTTCG CTCTCTCAAA TACAAAAAAA AAAAAACACA 360 ATAGTCTCAC CTCGGCTCTG A 381
(2) INFORMATION FOR SEQ ID NO:32:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1698 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1698
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:32: GTGTATTCTT ATAGCGATGA CGCACAAGGC GTGTTTTATC TCACGAGCAG CGTGAAAGGC 60
TATTACAACC CCAACCAATC CTATCAAGCC AGCGGCAGCA ATAACACCAC GAAAAATAAC 120
AATCTAACCT CTGAATCTTC TGTCATTTCG CAAACCTATA ACGCGCAAGG CAACCCTATC 180
AGCGCGTTAC ACGTCTATAA CAAGGGCTAT AATTTCAGTA ATATCAAAGC GTTAGGGCAA 240
ATGGCGCTCA AACTCTACCC TGAAATCAAA AAGATATTAG GGAATGATTT TTCGCTTTCA 300 AGTTTGAGCA ATTTAAAAGG CGATGCGCTA AACCAGCTTA CCAAGCTCAT CACGCCTAGC 360
GATTGGAAAA ACATTAACGA GTTGATTGAT AACGCAAACA ATTCGGTCGT GCAAAATTTC 420
AATAACGGCA CTTTGATTAT AGGAGCGACT AAAATAGGGC AAACAGACAC CAATAGTGCG 480
GTGGTTTTTG GGGGCTTGGG CTATCAAAAG CCTTGCGATT ACACTGATAT TGTGTGCCAA 540
AAATTTAGAG GCACTTATTT GGGGCAGCTT TTGGAGTCCA ACTCCGCTGA TTTGGGCTAT 600 ATTGACACGA CTTTTAACGC TAAAGAAATT TATCTTACCG GCACTTTAGG GAGCGGGAAC 660
GCATGGGGGA CTGGGGGGAG TGCGAGCGTA ACTTTTAACA GCCAAACTTC GCTCATTCTC 720
AACCAAGCGA ATATCGTAAG CTCGCAAACC GATGGGATTT TTAGCATGCT GGGTCAAGAG 780
GGCATCAATA AGGTTTTCAA TCAAGCCGGG CTCGCTAATA TTTTGGGCGA AGTGGCAATG 840
CAATCCATTA ACAAAGCCGG GGGATTAGGG AATTTGATAG TAAATACGCT AGGGAGTGAT 900 AGCGTGATTG GGGGGTATTT AACGCCTGAG CAAAAAAATC AAACCCTAAG CAGCTTTTG 960
GGGCAGAATA ATTTTGATAA CCTCATGAAC GATAGCGGTT TGAACACG^ GATTAAGGAT 1020
TTGATCAGAC AAAAATTAGG CTTTTGGACC GGGCTAGTGG GGGGATTAGC CGGACTGGGG 1080
GGCATTGATT TGCAAAACCC TGAAAAGCTT ATAGGCAGCA TGTCCATCAA TGATTTATTG 1140
AGTAAAAAGG GGTTGTTCAA TCAGATCACC GGCTTTATTT CCGCTAACGA TATAGGGCAA 1200 GTCATAAGCG TGATGCTGCA AGATATTGTC AAGCCGAGCG ACGCTTTAAA AAACGATGTA 1260
GCCGCTTTGG GCAAGCAAAT GATTGGCGAA TTTTTAGGCC AAGACACGCT CAATTCTTTA 1320
GAAAGCTTGC TGCAAAACCA GCAGATTAAA AGCGTTTTAG ACAAAGTCTT AGCGGCTAAA 1380
GGATTAGGGT CTATTTATGA ACAAGGTTTG GGGGATTTGA TCCCTAATCT TGGTAAAAAG 1440
GGGATTTTCG CTCCCTATGG CTTGAGTCAA GTGTGGCAAA AAGGGGATTT TAGTTTCAAC 1500 GCGCAAGGCA ATGTTTTTGT GCAAAATTCC ACTTTCTCTA ACGCTAATGG AGGCACGCTC 1560
AGTTTTAACG CAGGAAATTC GCTCATTTTT GCCGGAAACA ACCACATCGC TTTCACTAAC 1620
CATTCTGGAA CGCTCAATTT GTTGTCTAAT CAAGTTTCTA ACATTAACGT CACCATGCTT 1680
AACGCAGCAA CGGCCTAA 1698
(2) INFORMATION FOR SEQ ID NO: 33:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 519 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...519
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:33:
GTGTTTGGAT TGAGTTTGGC GGATATGATT TTAGAGCGTT TTAAAGATTT TATGAGAGAA 60 TACCCTGAGC CTTACAAGTT TTTACAGGTT TTTTACGCGC AAGAAAAAGA ACGCTTCTTA 120
AATCATAAAA TGAACGATTA TATCAAGCAA AATAAGAGCA AGGAAGAGGC TAGTATTTTG 180
GCCAGACAAG GCTTTGTCAG CGTAATTGGA AGAGCGTTAG AAAAAATCAT AGAACTTTTA 240
TTAAAAGATT TTTGTATTAA AAACAATGTA AAAATGACGA ACGATAAAAC CTTAAGGGCT 300
AAGCGCATTA ATGGCGAATT AGATAAGGTC AAACGGGCTT TATTGGTGCA TTTTGGAGGA 360 TATAGCGTTT TACCCGATAT TATTCTTTAT CAAACCAACA AAGATAATAT CAAAATCCTA 420
GCGATTTTAT CGGTAAAAAA TTCGTTTAGA GAGCGTTTCA CAAAAGACGC CTTATTGGAA 480
ATTAAAACTT TTGCAATCGC CTGTAACTTC TCACATTAA 519
(2) INFORMATION FOR SEQ ID NO: 34:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 996 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circulrr
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...996
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:34:
ATGAAAAGAT TTGTTTTATT CTTGTTATTC ATATGTGTTT GCGTTTGCGT TCAAGCTTAC 60
GCTGAGCAAG ATTACTTTTT TAGGGATTTT AAATCTATAG ATTTGCCCCA AAAACTCCAC 120 CTTGATAAAA AGCTCTCCCA AACAATACAG CCATGCGCGC AACTTAACGC ATCAAAACAC 180
TACACTGCTA CTGGGGTTAG AGAGCCTGAT GCCTGCACCA AGAGTTTTAA AAAATCCGCT 240
ATGGTTTCCT ATGATTTAGC GCTAGGCTAT TTAGTGAGCC AAAACAAACC ATACGGCTTA 300
AAAGCTATAG AGATTTTAAA CGCTTGGGCT AATGAGCTTC AAAGCGTGGA TACTTATCAA 360
AGCGAGGACA ATATCAATTT TTACATGCCT TATATGAACA TGGCTTATTG GTTTGTCAAA 420 AAAGAATTTC CTAGCCCAGA ATATGAAGAT TTCATTAGGC GGATGCGTCA GTATTCTCAA 480
TCAGCTCTTA ACACTAACCA TGGGGCGTGG GGGATTCTCT TTGATGTGAG CTCTGCACTA 540
GCGCTAGATG ATCATGCCCT TTTGCAAAGT AGCGCTAATC GGTGGCAGGA GTGGGTGTTT 600
AAAGCCATAG ATGAGAACGG GGTTATTGCT AGCGCGATCA CTAGGAGCGA TACGAGCGAT 660
TATCATGGCG GCCCTACAAA GGGCATTAAG GGGATAGCTT ATACCAATTT TGCGCTTCTT 720 GCGATAACTA TATCAGGCGA ATTGCTTTTT GAGAACGGGT ATGATTTGTG GGGTAGTGGA 780
GCCGGGCAAA GGCTCTCTGT GGCGTATAAC AAAGCCGCAA CATGGATTCT AAACCCTGAA 840
ACTTTCCCCT ATTTTCAGCC TAACCTCATT GGGGTGCATA ACAACGCCTA TT CATTATT 900
TTAGCCAAAC ATTATTCTAG CCCTAGCGCG GATGAGCTTT TAGAGCAAGG CGATTTGCAT 960
GAAGATGGCT TCAGGCTGAA ACTCCGATCG CCATGA 996
(2) INFORMATION FOR SEQ ID NO: 35:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 384 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...384
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 35:
ATGCGTCAGT ATTCTCAATC AGCTCTTAAC ACTAACCATG GGGCGTGGGG GATTCTCTTT 60 GATGTGAGCT CTGCACTAGC GCTAGATGAT CATGCCCTTT TGCAAAGTAG CGCTAATCGG 120
TGGCAGGAGT GGGTGTTTAA AGCCATAGAT GAGAACGGGG TTATTGCTAG CGCGATCACT 180
AGGAGCGATA CGAGCGATTA TCATGGCGGC CCTACAAAGG GCATTAAGGG GATAGCTTAT 240
ACCAATTTTG CGCTTCTTGC GATAACTATA TCAGGCGAAT TGCTTTTTGA GAACGGGTAT 300
GATTTGTGGG GTAGTGGAGC CGGGCAAAGG CTCTCTGTGG CGTATAACAA AGCCGCAACA 360 TGGATTCTAA ACCCTGAAAC TTTC 384
(2) INFORMATION FOR SEQ ID NO: 36: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 738 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...738
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 36:
TTGAGAACCT TGTTAAAAAT GTTGGTTGGT GTGAGCTTAC TAACACACGC TTTAATGGCT 60
ACAGAAGAAA GCGCTGCCCC TTCTTGGACA AAAAATTTGT ATATGGGATT CAATTACCAA 120
ACAGGTTCTA TCAATTTAAT GACTAATATT CATGAAGTTA GAGAAGTTAC TAGCTATCAA 180
ACCGGTTACA CCAATGTAAT GACTAGCATT AATAGCGTTA AAAAACTCAC TAACATGGGT 240 TCTAATGGGA TTGGCTTAGT CATGGGCTAT AACCACTTTT TCCATCCGGA TAAAGTCTTG 300
GGTTTGCGCT ATTTTGCTTT TTTAGATTGG CAAGGCTATG GCATGAGATA CCCTAAAGGC 360
TATTATGGGG GCAATAACAT GATCACTTAT GGCGTGGGCG TGGATGCGAT ATGGAATTTC 420
TTCCAAGGGA GTTTTTATCA AGATGATATT GGCGTGGATA TTGGCGTTTT TGGGGGGATT 480
GCGATTGCTG GGAATAGCTG GTATATTGGC AATAAAGGGC AGGAATTATT AGGCATCACC 540 AATAGTAGTG CGGTTGATAA CACCTCTTTT CAATTCCTCT TTAACTTTGG TTTCAAAGCT 600
TTATTTGTAG ATGAACATGA ATTTGAAATT GGGTTTAAAT TCCCCACTCT TAACAACAAA 660
TACTACACCA CCGACGCGCT CAAGGTTCAA ATGCGTAGGG TCTTTGCCTT TTATGTGGGG 720
TATAATTACC ACTTCTAA 738 (2) INFORMATION FOR SEQ ID NO: 37:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 873 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...873
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 37:
ATGTTTGAAG AAATTACCCT AGCGCATAAG GACTTGTTTT CAAGGTTTTT ACAAACTCAA 60 AAAATCGTTT TATCGGATGT GAGTTTTACC AATTGCTTTT TATGGCAGCA CGCAAGGCTC 120
ATTCAAGTGG CTGTGATTAG GGATTGTTTG GTGATTCAAA CCACTTATGA AAACCAAAAA 180
CCCTTTTATT TCTATCCTAT CGGTAAGAGG CCGCATGAAT GCGTGAAAGA GCTTTTGGAA 240
TTAGAAAAAA ATTTAAGATT CCACTCCCTG ACTTTAGAGC AAAAAGACGA TTTGAAAGAC 300
AATTTTGTAG GGGTGTTTGA TTTCACTTAC AACCGAGACA GGAGCGATTA TGTTTATTCT 360 ATTGAAGAAC TAATCGCGCT CAAAGGGAAA AAATACCATA AGAAAAAAAA CCACTTAAAC 420
CAGTTTTTAA CCAATCATGC GAATTTTGTT TATGAAAAAA TTTCTCCTCA AAACAGAAAG 480
GAAGTTTTAG AAGCCTCTAA AGCGTGGTTT TTAGAAAGCC AGACCGATGA TATAGGGTTA 540
ATCAACGAAA ATAAGGGCAT TCAAAGCGTT TTAGAAAATT ATGAAAGCTT GGATTTAAAG 600
GGGGGGCTTA TTAGGGTTAA TGGGGAAATA GTCTCGTTTA GTTTTGGGGA AGTTTTAAAC 660 GAAGAGAGCG CGCTCATCCA CATTGAAAAA GCCCGCACAG ATATTGCAGG CGCGTATCAA 720
ATCATCAACC AACAATTGCT TTTGAATGAA TTTAGCCATT TAACTTACGC TAACAGAGAA 780
GAAGATCTAG GATTAGAGGG CTTAAGAAGG TCTAAAATGA GCTATAACCC GGTGTTTTTG 840
ATAGACAAAT ACGAAGCGGT TGCTAGAAAT TAA 873 (2) INFORMATION FOR SEQ ID NO: 38:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 333 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...333
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 38:
ATGATGTTCA TTGTAGCGGT TTTGATGCTG GCGTTTTTGA TCTTTGTCCA TGAGTTAGGG 60
CATTTCATTA TCGCTAGGAT TTGTGGGGTG AAAGTGGAAG TGTTTAGCAT TGGTTTTGGT 120 AAAAAACTCT GGTTTTTCAA GCTTTTTGGC ACGCAATTCG CTCTGTCTTT GATCCCGCTT 180
GGGGGCTATG TGAAATTAAA GGGCATGGAT AAAGAAGAAA ATGAAGAAAA TAAAATTAAT 240
CAAGCGAATG ATAGCTACGC CAAAAAAGCC CTTTCCAAAA GCTATGGATA TTGTTTGGTG 300
GGGCGTTTTT TAATTTTCTT TTTGCGGTTT TAG 333 (2) INFORMATION FOR SEQ ID NO: 39:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1056 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...1056
(xi) SEQUENCE DESCRIPTION: SEQ ID HO: 39:
ATGATGTTCA TTGTAGCGGT TTTGATGCTG GCGTTTTTGA TCTTTGTCCA TGAGTTAGGG 60 CATTTCATTA TCGCTAGGAT TTGTGGGGTG AAAGTGGAAG TGTTTAGCAT TGGTTTTGGT 120
AAAAAACTCT GGTTTTTCAA GCTTTTTGGC ACGCAATTCG CTCTGTCTTT GATCCCGCTT 180
GGGGGCTATG TGAAATTAAA GGGCATGGAT AAAGAAGAAA ATGAAGAAAA TAAAATTAAT 240
CAAGCGAATG ATAGCTACGC GCAAAAAAGC CCTTTCCAAA AGCTATGGAT ATTGTTTGGT 300
GGGGCGTTTT TTAATTTTCT TTTTGCGGTT TTAGTGTATT TTTTTCTGGC ATTGAGCGGG 360 GAAAAAGTCT TACTGCCCGT CATTGGCGGT TTAGAAAAAA ACGCGCTAGA AGCCGGGCTG 420
TTAAAGGGGG ATAGAATCCT TTCTATCAAC CATCAAAAAA TAGCGAGTTT TAGAGAGATT 480
AGAGAGATAG TGGCGCGTTC TCAAGGCGAG TTAATTTTAG AAATAGAGCG AAACAATCAG 540
ATTTTAGAAA AACGACTGAC CCCCAAAATC GTGGCGGTGA TAAGCGAGTC TAATGATCCT 600
AATGAAATCA TCAAGTATAA AATAATAGGC ATTAAACCGG ACATGCAAAA AATGGGCGTT 660 GTCTCTTATT CCGTGTTTCA AGCGTTTGAA AAGGCTTTGA GTCGGTTTAA AGAGGGCGTT 720
GTTTTGATTG TGGATTCTTT AAGGCGTTTG ATTATGGGGA GCGCTTCAGT TAAAGAATTG 780
AGTGGGGTAA TAGGCATTGT GGGGGCGTTA AGCCATGCCA ATAGCGTGAG CATGCTTTTG 840
TTGTTTGGGG CGTTTTTATC TATCAATCTA GGGATTTTAA ATTTATTACC CATTCCAGCC 900
TTAGATGGGG CGCAAATGCT AGGGGTCGTT TTTAAAAATA TTTTTCATAT CGCTTTGCCA 960 ACGCCCATAC AAAATGCGTT GTGGCTAGTG GGGGTGGGGT TTTTGGTTTT TGTCATGTTT 1020
TTAGGGCTTT TTAATGACAT TACTCGTTTG CTATAA 1056
(2) INFORMATION FOR SEQ ID NO: 40: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH. '03 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO ( iv) ANTI - SENSE : NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...303 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 40:
ATGCAAAAGA ATTTGGATAG TCTTTTAGAA AATTTAAGGG CTGAAATTGA TGCGTTGGAT 60
AATGAATTGA GCGATCTTTT AGACAAACGC TTAGGAATCG CTTTAAAAAT CGCTCTCATC 120
AAACAAGAAA GCCCCCAAGA AAACCCCATT TATTGCCCTA AAAGAGAGCA AGAGATTTTA 180 AAACGACTCA GCCAAAGGGG TTTCAAGCAT TTGAATGGAG AAATCCTTGC AAGTTTTTAT 240
GCAGAGGTTT TTAAGATTTC TAGAAATTTT CAAGAAAACG CCCTAAAAGA GTTAAAAAAA 300
TAA 303
(2) INFORMATION FOR SEQ ID NO: 41:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 525 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...525 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 41:
GTGAAAATGC GTTTTTTTAG TGGTTTTGGG TTTGTTAATG AAAGCGTTTT GTTTGAAGAG 60
TGGCTTTTAA AAGGGGCTTA TGATGTGTCA GGCTTTTCTA TGGGGGCGAT TAAGGCGATA 120
GAATACGCCT ATAATGAAGT CTTGCAACAA CGGCGCATCC ATTCCTTATT GTTGTTTTCG 180 CCTTGCATGC TAGCGCATAA GAGTTTGGCG TTCAAACGCT TGCAACTTTT CTTGTTTCAA 240
AAAGATCCGC AAAGCTACAT GGATAACTTT TATAAGGAAG TGGGATTGGA CGCTCAATTG 300
GAGCGTTTTA AAAAAGAGGG TTCTTTAGAA GAATTGGAAT TTTTATTGGA TTACAAGTAT 360
AGTGATTCTA TAATTAGATT TTTATTGGAA AAGGGCGTGA AGATTGAAGT GTTTATCGGT 420
TTAAAAGATA GAATCACTGA CATTCAAGCC CTTTTAGAAT TTTTTATGCC CTTAGTTCAA 480 GTGTGGCAGT TTAAGGATTG TAACCATTTG TTGCAAAAAT CTTAA 525
(2) INFORMATION FOR SEQ ID NO: 42: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1416 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1416
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:42:
ATGAAAAATA CCAATACAAA AGAGATAAAG AATACAAGGA TGAAAAAAGG TTATAGTCAA 60
TACCACACGC TCAAAAAAGG GCTTTTAAAA ACCGCTCTGC TTTTTAGCCT TCCTTTAAGC 120
GTGGCGTTAG CTGAAGACGA TGGCTTTTAT ATGGGAGTGG GCTATCAAAT CGGCGGCGCG 180
CAACAAAACA TCAACAACAA AGGCAGCACC CTAAGGAATA ATGTCATTGA TGATTTCCGC 240 CAAGTGGGCG TGGGTATGGC AGGGGGTAAT GGGCTTTTAG CTTTAGCGAC AAACACGACC 300
ATGGACGCTC TTTTAGGGAT AGGCAACCAA ATTGTCAATA CTAATACAAC TGTTGGCAAC 360
AACAACGCAG AGTTAACCCA GTTTAAAAAA ATACTCCCCC AAATTGAACA ACGCTTTGAG 420
ACGAATAAAA ACGCTTATAG CGTTCAAGCC TTGCAAGTGT ATTTGAGTAA TGTGCTTTAT 480
AACTTGGTTA ATAATAGTAA TAATGGTAGC AATAATGGAG TCGTTCCTGA ATATGTAGGG 540 ATTATAAAAG TTCTCTATGG TTCTCAAAAT GAATTCAGTC TCTTAGCCAC GGAGAGTGTG 600
GCGCTTTTAA ACGCGCTCAC GAGAGTGAAT CTGGATAGTA ATTCGGTGTT TTTAAAAGGG 660
CTATTAGCCC AAATGCAGCT TTTTAATGAC ACTTCTTCAG CAAAGCTAGG TCAGATCGCA 720
GAAAACTTGA AGAACGGTGG TGCAGGGGCC ATGCTTCAAA AGGATGTGAA AACCATCTCG 780
GATCGAATCG CTACTTACCA AGAGAATCTA AAACAGCTAG GAGGGATGTT AAAGAATTAC 840 GATGAGCCAT ACCTACCCCA ATTTGGGCCA GGCACAAGCT CTCAGCATGG GGTTATTAAT 900
GGCTTTGGCA TTCAAGTGGG CTATAAGCAA TTTTTTGGGA GCAAGAAGAA TATAGGCTTA 960
CGATATTACG CTTTCTTTGA TTATGGCTTT ACGCAATTGG GCAGTCTTAA CAGTGCTGTT 1020
AAAGCGAACA TCTTTACTTA TGGTGCTGGC ACGGACTTTT TATGGAATAT CTTTAGAAGG 1080
GTTTTTAGCG ATCAGTCCTT GAATGTGGGG GTGTTTGGGG GCATTCAAAT AGCGGGTAAC 1140 ACTTGGGATA GCTCTTTAAG AGGTCAAATT GAAAACTCGT TTAAAGAATA CCCCACTCCC 1200
ACGAATTTCC AATTTTTGTT TAATTTGGGC TTAAGGGCTC ATTTTGCCAG CACCATGCAC 1260
CGCCGGTTTT TGAGCGCGTC TCAAAGCATT CAGCATGGTA TGGAATTTGG CGTGAAAATC 1320
CCAGCTATCA ATCAAAGGTA TTTGAAAGCG AATGGGGCTG ATGTGGATTA CAGGCGTTTG 1380
TATGCGTTCT ATATCAATTA CACGATAGGT TTTTAA 1416
(2) INFORMATION FOR SEQ ID NO: 43
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 390 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...390
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:43: ATGAAAAGCA TCAGAAGAGG CGATGGGCTG AATGTTGTCC CTTTCATTGA TATTATGCTC 60
GTCTTACTAG CGATTGTGTT GAGTATTTCT ACTTTTATCG CGCAAGGTAA GATTAAAGTC 120
AGTCTCCCTA ACGCTAAAAA TGCGGAAAAA TCCCAGCCAA ACGATCAAAA AGTGGTGGTC 180
ATCTCTGTGG ATGAGCATGA CAATATTTTC GTAGATGACA AACCGACGAA TTTAGAAGCT 240
TTGAGCGCTG TAGTCAAGCA AACAGACCCT AAAACCCTTA TAGATTTAAA AAGCGACAAG 300 AGCTCTCGTT TTGAAACTTT TATCAGCATT ATGGATATTT TAAAAGAGCA TAATCATGAA 360
AATTTCTCCA TCTCCACGCA AGCTCAGTAA 390
(2) INFORMATION FOR SEQ ID NO: 44: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 225 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...225
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:44:
ATGCTCGTCT TACTAGCGAT TGTGTTGAGT ATTT T .CTT TTATCGCGCA AGGTAAGATT 60
AAAGTCAGTC TCCCTAACGC TAAAAATGCG GAAAAATCCC GACCAAACGA TCAAAAAGTG 120
GTGGTCATCT CTGTGGATGA GCATGACAAT ATTTTCGTAG ATGACAAACC GACGAATTTA 180
GAAGCTTTGA GCGCTGTAGT CAAGCAAACA GACCCTAAAA CCCTT 225
(2) INFORMATION FOR SEQ ID NO: 45:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 672 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...672
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 5: ATGTTTTCAC TTTCTTATGT TTCCAAGAAA TTTTTAAGCG TGTTGCTATT GATTTCGCTG 60
TTTTTAAGCG CTTGCAAATC CAACAATAAA GACAAATTGG ATGAAAATCT TTTAAGCTCC 120
GGCACTCAAA GCTCCAAAGA ATTAAACGAC AAGCGAGACA ATATAGACAA AAAGAGCTAC 180
GCTGGTTTAG AAGATGTTTT TTTAGACAAC AAGTCCATTA GCCCTAATGA TAAATACATG 240
CTTTTAGTTT TTGGCCGTAA TGGTTGCTCC TATTGTGAAA GGCTTAAAAA AGATCTCAAA 300 AATGTCAAAG AATTGCGCAA CTATATTAAA GAGCATTTTA GTGCTTACTA TGTCAATATC 360
AGCTATTCTA AAGAGCATAA TTTTAAAGTC GGCGATAAGG ATAAAAATGA TGAAAAAGAA 420
ATCAAAATGT CCACAGAAGA ATTAGCGCAA ATTTATGCCG TCCAATCCAC CCCTACGATT 480
GTTTTATCCG ATAAAACCGG CAAAACCATC TATGAATTGC CGGGCTATAT GCCTTCTGTG 540
CAATTTTTAG CCGTGTTAGA ATTTATCGGC GATGGGAAGT ATCAAGACAC GAAAAACGAT 600 GAGGATCTCA CTAAAAAATT AAAGGCTTAC ATCAAGTATA AAACCAACCT TTCTAAGAGC 660
AAGTCCAGCT AG 672
(2) INFORMATION FOR SEQ ID NO:46: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...351
(xi) SEQUENCE DESCRIPTION: SEQ ID NO.-46: TTGATGAAAT CTAAAATCAC TCATTTTATC GTTATCTCTT TTGTTTTAAG CGTGTTGAGC 60
GCCTGCAAAG ATGAGCCTAA AAAATCGTCC CAATCGCACC AAAACAACAC TAAAACCACT 120
CAAAACAATC AAATCAATCA ACCTAATAAG GATATAAAAA AGATTGAGCA TGAAGAAGAA 180
GATGAAAAAG TCACCAAAGA AGTGAATGAT CTGATCAATA ACGAAAATAA AATTGATGAA 240
ATCAATAATG AAGAAAACGC TGATCCTTCG CAAAAAAGAA CGAACAATGT TTTGCAACGA 300
GCCACTAACC ACCAAGACAA TCTCAGTTCC CCACTCAACA GGAAGTATTA A 351
(2) INFORMATION FOR SEQ ID NO: 47:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 240 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...240 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:47:
ATGTTTGAAA AAATACGCAA GATTTTAGCG GATATTGAAG ATTCGCAAAA TGAAATTGAA 60
ATGCTTTTAA AATTAGCGAA TTTGAGTTTG GGGGATTTTA TTGAGATTAA AAGAGGGAGC 120
ATGGACATGC CAAAGGGCGT GAATGAAGCG TTTTTTACGC AATTAAGCGA AGAAGTGGAG 180 CGCCTAAAGG AGCTTATCAA CGCTTTGAAT AAAATCAAAA AAGGGTTATT GGTGTTTTAA 240
(2) INFORMATION FOR SEQ ID NO: 48:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 156 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...156
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 48:
ATGTCTATGT TCATTTCTAA TCTGGCTTTC ACGAGCGAAC ATAAGGACGC TATGGAAGTG 60 GCAAAAATTG CGATTTTACT CGGATCTTTG ATTTCTGGGA TCATAGGGGC TTTATATTTA 120 TTCGCACTAG ATAAAAGAGC GGCTTTAAAG AAATAG 156 (2) INFORMATION FOR SEQ ID NO: 49:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1350 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1350
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 49:
ATGGGTTTGA AAATAAAAAT TTTAAGGTTG TCTATGAATC TCAAAAAAAC AGAAAACGCG 60
CTCAGTTTGA CGCTTAAAAA CTTCATTAAA AGCGAGTCTT TTGGAGGGAT TTTCCTCTTT 120 TTGAACGCCG TTTTAGCGAT GGTGGTGGCT AATTCGTTTT TAAAAGAAAG TTATTTTGCG 180
CTATGGCACA CCCCTTTTGG GTTTCAAGTA GGGGATTTTT TTATCGGCTT TAGTTTGCAC 240
AACTGGATTG ATGATGTCTT AATGGCGTTA TTCTTTTTAA TGATAGGCTT AGAGATCAAG 300
CGAGAATTGT TGTTTGGGGA ATTATCCAGT TTTAAAAAAG CTTCTTTCCC TGTGATCGCA 360
GCCATAGGGG GCATGATAGC TCCAGGATTG ATTTATTTTT TTCTTAACGC CAACACGCCC 420 TCTCAGCATG GTTTTGGGAT CCCTATGGCA ACGGATATTG CGTTCGCTTT AGGCGTGATC 480
ATGCTTTTAG GCAAGAGGGT GCCAACCGCC TTAAAGGTTT TTTTAATCAC TCTAGCGGTG 540
GCTGATGACT TAGGGGCTAT TGTGGTGATC GCGCTCTTTT ATACCACGAA TTTAAAATTC 600
GCATGGCTTT TAGGGGCTTT AGGGGTGGTT CTTGTTTTAG CCATATTGAA CCGCCTGAAT 660
ATCCGATCGC TCATCCCTTA CTTGCTTTTA GGGGTGTTGC TTTGGTTTTG CGTGCATCAA 720 AGCGGTATCC ATGCGACGAT CGCTGCGGTG GTTCTAGCTT TTATGATACC GGr:GAAAATC 780
CCTAAAGATT CTAAAAATGT AGAGCTTTTG GAATTAGGCA AACGATACGC Af.AGACGAGT 840
TCAGGAGTGC TTTTAACCAA AGAGCAGCAA GAAATCTTGC ATTCTATTGA AGAAAAAGCG 900
AGTGCTTTAC AAAGCCCCTT AGAAAGATTG GAGCATTTTC TAGCCCCCAT CAGCGGGTAT 960
TTCATCATGC CCTTATTCGC GTTTGCAAAC GCTGGGGTGA GCGTTGATTC TAGCATCAAT 1020 TTAGAAGTGG ATAAGGTGCT TTTAGGGGTT ATTTTAGGGC TTTGTTTGGG CAAGCCTTTA 1080
GGGATTTTCT TAATCACTTT CATAAGCGAA AAGCTTAAAA TCACTGCGCG CCCTAAAGGC 1140
ATCGGCTGGT GGCATATTTT AGGGGCTGGG CTTTTAGCAG GGATTGGCTT TACCATGTCT 1200
ATGTTCATTT CTAATCTGGC TTTCACGAGC GAACATAAGG ACGCTATGGA AGTGGCAAAA 1260
ATTGCGATTT TACTCGGATC TTTGATTTCT GGGATCATAG GGGCTTTATA TTTATTCGCA 1320 CTAGATAAAA GAGCGGCTTT AAAGAAATAG 1350
(2) INFORMATION FOR SEQ ID NO: 50: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2448 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...2448
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 50:
ATGAATGACA AGCGTTTTAG AAAATATTGT AGTTTTTCTA TTTTTTTGTC CTTATTAGGA 60
ACGTTTGAAT TAGAGGCTAA AGAAGAAGAA AAAGAAGAAA AAAAGACAGA AAGGAACAAA 120
GATAAAGAAA AGAACGCCCA ACACACTTTG GGTAAAGTTA CCACTCAAGC GGCTAAAATC 180
TTTAATTACA ACAACCAGAC AACCATTTCA AGTAAAGAAT TAGAAAGAAG GCAAGCCAAC 240 CAAATCAGCG ACATGTTTAG AAGAAACCCC AATATCAATG TGGGCGGTGG TGCGGTGATA 300
GCGCAAAAAA TTTACGTGCG CGGTATTGAA GACAGATTGG CTAGGGTTAC GGTGGATGGC 360
GTGGCGCAAA TGGGCGCAAG CTATGGGCAT CAAGGCAATA CAATCATTGA CCCTGGAATG 420
CTCAAAAGCG TGGTGGTTAC CAAGGGGGCG GCTCAAGCGA GCGCGGGGCC TATGGCTTTA 480
ATTGGCGCGA TCAAAATGGA GACTAGGAGC GCGAGCGATT TTATCCCTAA AGGCAAAGAC 540 TACGCCATAA GTGGGGCTGC CACTTTTTTA ACCAACTTTG GGGATAGGGA AACCATTATG 600
GGCGCTTATC GTAACCATCA TTTTGATGCG CTTTTGTATT ACACGCACCA AAATATTTTT 660
TATTATCGTG ATGGGGATAA CGCGATGAAA AATCTTTTTG ACCCTAAAGC GGATAATAAA 720
GTTACAGCAA GCCCTAGCGA ACAAAACAAT GTGATGGCTA AGATCAATGG TTATTTGAGC 780
GAAAGGGATA CCTTAACGCT CAGTTATAAC ATGACTAGAG ATAACGCCAA TCGCCCTTTA 840 AGAGCGAATT TTACCGGCAC TTTTTTACCC TATTCTTGTG GTGATTTCAA CGCTTTCCCT 900
AACGAGAAAA ACCCTAGCGA TTGTTTGTTT GAAAATGACG CCAGTTTGTT TAAAACTTAT 960
AGCGTCAATT TAGTGCATAA CGTGAGCTTG AATTATGAAA GGGAAGGGGG GAGTCGCTTT 1020
GGCGATCCTA AATTAAAAAT CAATGGCTAC ACGAGCATTA GGAATGTCCA AATTGATCCG 1080
CTTTTCAGAC CTAGCGATAT AGCGACTACC ATTCCTTTCA CCCCAAACCC GCAGCTCTCT 1140 CAAGGCGAAG AAAATCAATG CGTGGCGCAA GGGGGCATTT ATGACGCTCT TAAACAAACT 1200
TGCTCCATCA CTTTTAAAAG CCTTGGAG^C GGTTCTGTTG TCGCTAATAA AAATTTATTC 1260
ATCATCAATT CTGGGTTTAA TGCGAACGTG ATCCACACCA TAGACCACAA GAATGACAAT 1320
CTTTTGGAAT ACGGGTTGAA TTACCAGAAT TTAACCACTT TTGATAAAGC GATCCCTGAT 1380
AGCGAATTAG TCAAGCCCGG CGATGCCCCT GATGCGTGCT TAAGAGTTAC AGGACCTGAT 1440 GATCCTAACA TGAACGGGCG CTGCCAACGG AATGGCGCTA CGGCGAATGT GGTTGGGGTG 1500
TATGCGCAAG CGAATTACAC CTTGCACCCT ATGGTAACTT TAGGGGCAGG GACTCGTTAT 1560
GACGTTTATA CTTTAGTGGA TAAAGACTGG CAATTGCACG TAACTCAAGG GTTTAGCCCT 1620
AGCGCGGCTT TAAACGTCTC GCCTTTAGAA AATTTGAATT TCAGGCTTTC TTACGCGTAT 1680
GTAACTAGAG GCCCTATGCC TGGAGGTTTG GTGTGGATGC GTCAAGACAA TTTGCGCTAT 1740 AACCGCAATT TAAAGCCAGA AATTGGGCAA AATGCGGAAT TTAACACCGA ATACAGCAGT 1800
CAGTATTTTG ATTTCAGAGC CGCCGGTTTT GTCCAATTGA TTTCTAATTA CATCAATCAA 1860
TTTTCTTCAA CGCTTTTTGT CACCAACTTG CCCGCACAAG ATATTATTTA TGTGCCTGGC 1920
TATGAAGTTT CAGGGACGGC TAAATACAAG GGTTTTTCTT TAGGCTTGAG CGTGGCGCGA 1980 TCATGGCCTT CTTTAAAAGG GCGTTTGATC GCTGACGTGT ATGAATTGGC GGCTACGACA 2040
GGCAATGTGT TTATTTTAAC GGCAAGCTAT ACAATCCCAC GCACCGGCCT TAGCATCACT 2100
TGGCTTTCAC GCTTTGTTAC TAATTTGAGT TATTGCTCTT ATAGCCCTTA TCGTAACGGC 2160
CCTACGGATA TTGACAGAAG GCCTAGTAAT TGCCCTAAAA CGCCCGGGAT TTTTCATGTG 2220
CATAAACCCG GCTATGGGGT GAGCAGTTTC TTTATCACTT ACAAGCCTAC TTATAAGAAA 2280 CTCAAAGGGT TGAGCCTGAA CGCGGTGTTT AATAATGTTT TTAACCAACA ATATATTGAT 2340
CAAGCAAGCC CGGTGATGAG CCCTGATGAA CCCAATCAAG ACAAATACGC AAGGGGCATG 2400
GCAGAGCCTG GCTTTAACGC TAGGTTTGAA ATTTCTTATA AGTTTTAA 2448
(2) INFORMATION FOR SEQ ID NO: 51:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2445 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...2445 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 51:
ATGACAAGCG TTTTAGAAAA ATATTGTAGT TTTTCTATTT TTTTGTCCTT ATTAGGAACG 60
TTTGAATTAG AGGCTAAAGA AGAAGAAAAA GAAGAAAAAA AGACAGAAAG GAACAAAGAT 120
AAAGAAAAGA ACGCCCAACA CACTTTGGGT AAAGTTACCA CTCAAGCGGC TAAAATCTTT 180 AATTACAACA ACCAGACAAC CATTTCAAGT AAAGAATTAG AAAGAAGGCA AGCCAACCAA 240
ATCAGCGACA TGTTTAGAAG AAACCCCAAT ATCAATGTGG GCGGTGGTGC GGTGATAGCG 300
CAAAAAATTT ACGTGCGCGG TATTGAAGAC AGATTGGCTA GGGTTACGGT GGATGGCGTG 360
GCGCAAATGG GCGCAAGCTA TGGGCATCAA GGCAATACAA TCATTGACCC TGGAATGCTC 420
AAAAGCGTGG TGGTTACCAA GGGGGCGGCT CAAGCGAGCG CGGGGCCTAT GGCTTTAATT 480 GGCGCGAT A AAATGGAGAC TAGGAGCGCG AGCGATTTTA TCCCTAAAGG CAAAGACTAC 540 TG GGGCTGCCAC TTTTTTAACC AACTTTGGGG ATAGGGAAAC CATTATGGGC 600
GCTTATCGTA ACCATCATTT TGATGCGCTT TTGTATTACA CGCACCAAAA TATTTTTTAT 660
TATCGTGATG GGGATAACGC GATGAAAAAT CTTTTTGACC CTAAAGCGGA TAATAAAGTT 720
ACAGCAAGCC CTAGCGAACA AAACAATGTG ATGGCTAAGA TCAATGGTTA TTTGAGCGAA 780 AGGGATACCT TAACGCTCAG TTATAACATG ACTAGAGATA ACGCCAATCG CCCTTTAAGA 840
GCGAATTTTA CCGGCACTTT TTTACCCTAT TCTTGTGGTG ATTTCAACGC TTTCCCTAAC 900
GAGAAAAACC CTAGCGATTG TTTGTTTGAA AATGACGCCA GTTTGTTTAA AACTTATAGC 960
GTCAATTTAG TGCATAACGT GAGCTTGAAT TATGAAAGGG AAGGGGGGAG TCGCTTTGGC 1020
GATCCTAAAT TAAAAATCAA TGGCTACACG AGCATTAGGA ATGTCCAAAT TGATCCGCTT 1080 TTCAGACCTA GCGATATAGC GACTACCATT CCTTTCACCC CAAACCCGCA GCTCTCTCAA 1140
GGCGAAGAAA ATCAATGCGT GGCGCAAGGG GGCATTTATG ACGCTCTTAA ACAAACTTGC 1200
TCCATCACTT TTAAAAGCCT TGGAGGGGGT TCTGTTGTCG CTAATAAAAA TTTATTCATC 1260
ATCAATTCTG GGTTTAATGC GAACGTGATC CACACCATAG ACCACAAGAA TGACAATCTT 1320 TTGGAATACG GGTTGAATTA CCAGAATTTA ACCACTTTTG ATAAAGCGAT CCCTGATAGC 1380
GAATTAGTCA AGCCCGGCGA TGCCCCTGAT GCGTGCTTAA GAGTTACAGG ACCTGATGAT 1440
CCTAACATGA ACGGGCGCTG CCAACGGAAT GGCGCTACGG CGAATGTGGT TGGGGTGTAT 1500
GCGCAAGCGA ATTACACCTT GCACCCTATG GTAACTTTAG GGGCAGGGAC TCGTTATGAC 1560
GTTTATACTT TAGTGGATAA AGACTGGCAA TTGCACGTAA CTCAAGGGTT TAGCCCTAGC 1620 GCGGCTTTAA ACGTCTCGCC TTTAGAAAAT TTGAATTTCA GGCTTTCTTA CGCGTATGTA 1680
ACTAGAGGCC CTATGCCTGG AGGTTTGGTG TGGATGCGTC AAGACAATTT GCGCTATAAC 1740
CGCAATTTAA AGCCAGAAAT TGGGCAAAAT GCGGAATTTA ACACCGAATA CAGCAGTCAG 1800
TATTTTGATT TCAGAGCCGC CGGTTTTGTC CAATTGATTT CTAATTACAT CAATCAATTT 1860
TCTTCAACGC TTTTTGTCAC CAACTTGCCC GCACAAGATA TTATTTATGT GCCTGGCTAT 1920 GAAGTTTCAG GGACGGCTAA ATACAAGGGT TTTTCTTTAG GCTTGAGCGT GGCGCGATCA 1980
TGGCCTTCTT TAAAAGGGCG TTTGATCGCT GACGTGTATG AATTGGCGGC TACGACAGGC 2040
AATGTGTTTA TTTTAACGGC AAGCTATACA ATCCCACGCA CCGGCCTTAG CATCACTTGG 2100
CTTTCACGCT TTGTTACTAA TTTGAGTTAT TGCTCTTATA GCCCTTATCG TAACGGCCCT 2160
ACGGATATTG ACAGAAGGCC TAGTAATTGC CCTAAAACGC CCGGGATTTT TCATGTGCAT 2220 AAACCCGGCT ATGGGGTGAG CAGTTTCTTT ATCACTTACA AGCCTACTTA TAAGAAACTC 2280
AAAGGGTTGA GCCTGAACGC GGTGTTTAAT AATGTTTTTA ACCAACAATA TATTGATCAA 2340
GCAAGCCCGG TGATGAGCCC TGATGAACCC AATCAAGACA AATACGCAAG GGGCATGGCA 2400
GAGCCTGGCT TTAACGCTAG GTTTGAAATT TCTTATAAGT TTTAA 2445 (2) INFORMATION FOR SEQ ID NO: 52:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1584 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1584
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 52:
ATGAAACAAA ATTTAAAGCC ATTCAAAATG ATTAAGGAAA ATTTAATGAC ACAATCTCAA 60
AAAGTAAGAT TCTTAGCCCC TTTGAGCCTA GCGTTAAGCT TGAGCTTCAA TCCAGTGGGC 120 GCTGAAGAAG ATGGGGGCTT TATGACCTTT GGGTATGAAT TAGGTCAGGT GGTCCAGCAA 180
GTGAAAAACC CGGGTAAAAT CAAAGCCGAA GAATTAGCGG GCCTGTTAAA CTCTACCACG 240
ACAAACAACA CCAATATCAA TATTGCAGGC ACAGGAGGGA ATGTCGCCGG GACTTTGGGC 300
AACCTTTTTA TGAACCAATT GGGCAATTTG ATTGATTTGT ATCCTACTTT GAAAACTAAT 360
AATCTTCACC AATGCGGTAG CACTAATAGC GGTAATGGCG CTACTGCTGC CGCTGCTACT 420 AACAATAGCC CTTGTTTCCA AGGTAACCTG GCTCTTTATA ACGAAATGGT TGACTCTATC 480
AAAACTTTGA GTCAAAACAT CAGCAAGAAC ATCTTTCAAG GCGACAACAA CACCACGAGC 540
GCTAATCTCT CCAACCAGCT CAGTGAGTTG AACACCGCTA GCGTTTATTT GACTTACATG 600
AACTCGTTCT TAAACGCCAA CAACCAAGCG GGTGGGATTT TTCAAAACAA CACCAATCAA 660 GCTTACGAGA ATGGTGTTAC CGCTCAACAA ATCGCTTATG TCCTAAAGCA AGCTTCAATC 720
ACTATGGGGC CAAGCGGTGA TAGTGGGGCT GCGGGAGCGT TTTTAGACGC CGCTTTAGCC 780
CAACATGTTT TCAACTCGGC TAACGCTGGG AACGATTTGA GCGCTAAGGA ATTCACTAGC 840
TTGGTGCAAA ACATCGTCAA TAATTCTCAA AACGCTTTAA CGCTAGCCAA CAACGCTAAC 900
ATCAGCAATT CAACAGGCTA TCAAGTGAGC TATGGTGGGA ATATTGATCA AGCGCGCTCT 960 ACCCAACTGT TAAACAACAC CACAAACACT TTGGCTAAAG TTACCGCTCT AAACAACGAG 1020
CTTAAAGCTA ACCCATGGCT TGGGAATTTC GCTGCTGGTA ACAGCTCTCA AGTGAATGCG 1080
TTTAACGGGT TTATCACTAA AATCGGTTAT AAGCAATTCT TCGGGGAAAA CAAGAATGTG 1140
GGCTTACGCT ACTACGGGTT CTTCAGCTAT AACGGCGCGG GCGTGGGTAA TGGCCCCACT 1200
TACAATCAAG TCAATCTGCT CACTTATGGG GTGGGGACTG ATGTGCTTTA CAATGTGTTT 1260 AGCCGCTCTT TTGGCAGTAG GAGTCTTAAT GCGGGCTTCT TTGGGGGGAT CCAACTCGCA 1320
GGGGACACTT ACATCAGCAC GCTAAGAAAC AGCCCTCAGC TTGCGAGCAG ACCTACAGCG 1380
ACAAAATTCC AATTCTTGTT TGATGTGGGC TTACGCATGA ACTTTGGTAT CTTGAAAAAA 1440
GACCTAAAAA GCCATAACCA GCATTCTATA GAAATCGGTG TGCAAATCCC TACGATTTAC 1500
AACACTTACT ATAAAGCTGG TGGCGCTGAA GTGAAATACT TCCGCCCTTA TAGCGTGTAT 1560 TGGGTCTATG GCTACGCCTT CTAA 1584
(2) INFORMATION FOR SEQ ID NO: 53:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1380 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1380
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 53: GTGGTGTTAT TAACAATGAC AAAACGACTT TTTAAAGGGT TGTTAG GAT TTCTCTTGCG 60
GTGAGTTTGC ATGGTGGTGA AGTTAAGGAA AAAAAGCCGG TCA^G' GGT CAAAGAAGAT 120
CCGCAAGAAT TAGCGGCTAA AAGGGTGGAA GCGTTCAGTC GTTTCTCTAA TGTGGTTACA 180
GAAATTGAAA AAAAGTATGT GGATAAGATC AGTATTTCTG AGATCATGAC TAAAGCGATT 240
GAAGGCTTAC TCTCTAATTT GGACGCGCAT TCAGCGTATT TGAATGAAAA GAAGTTTAAG 300 GAATTTCAGG CCCAAACCGA GGGCGAATTT GGGGGGCTTG GGATCACGGT GGGCATGCGC 360
GATGGCGTTT TGACCGTTAT TGCACCTTTA GAGGGCACTC CAGCTTACAA GGCTGGGGTT 420
AAATCAGGCG ATAGCATTTT AAAAATCAAT AACGAAAGCA CGCTGAGCAT GAGCATTGAT 480
GATGCGGTTA ATCTCATGCG CGGCAAGCCA AAAACCTCTA TTCAGATCAC TGTTGTTAGG 540
AAAAATGAGC CAAAACCCTT GGTATTTAAT ATCGTTAGGG ATATTATCAA GATCCCCTCT 600 GTCTATGTGA AAAAGATTAA AGACACACCT TATTTGTACG TGAGAGTCAA TTCTTTTGAT 660
AAAAATGTTA CCAAATCGGT TTTAGACGGC TTGAAGGCTA ACCCTAACAT TAAGGGCGTT 720
GTGTTGGATT TGAGGGGGAA TCCTGGAGGG CTATTAAACC AGGCGGTAGG CTTGTCTAAC 780
CTTTTCATTA AAGAGGGGGT TTTAGTCTCT CAAAGAGGCA AAAATAAGGA GGAAAACTTA 840 GAATACAAGG CTAATGGCAG AGCCCCTTAT ACCAATTTAC CTGTTGTGGT GTTAGTCAAT 900
GGCGGTTCAG CGAGCGCGAG CGAGATCGTC GCAGGGGCAC TGCAAGATCA CAAGCGAGCC 960
ATCATTATCG GTGAAAAAAC CTTTGGTAAG GGAAGCGTGC AAGTGTTGCT CCCTGTCAAT 1020
AAAGACGAAG CCATTAAAAT CACGACCGCG CGCTATTATT TGCCGAGCGG GCGCACCATT 1080
CAAGCTAAGG GGATCACGCC TGATATTGTG ATTTATCCGG GTAAAGTGCC AGAAAATGAA 1140 AATAAATTCA GTTTGAAAGA AGCGGATTTA AAACACCATT TAGAGCAAGA GCTTAAAAAA 1200
CTTGATGATA AAACCCCTAT TTCCAAAGAG GCGGATAAAG ACAAGAAAAG CGAAGAGGAA 1260
AAAGAGGTTA CTCCTAAAAT GATCAATGAT GATATTCAGC TAAAAACCGC TATTGACAGC 1320
TTGAAAACCT GGTCTATCGT AGATGAGAAA ATGGATGAAA AAGTGCCTAA GAAGAAATAA 1380 (2) INFORMATION FOR SEQ ID NO: 54:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 315 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...315
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:54:
TTGCTTTTGC ACCCCTTGCA TGCTCATGCA CAAGTGCTTG GCTTCACAAA CCACGATCAC 60
GCCCCTTGGC TCTATGATTT CATCAAAAGT TTCTGCAATT TGAGTGGTCA GCCTTTCTTG 120 GATTTGCAGG CGTTTGCTAT AAATTTCAAT GAGTTTAGCG ATCGCGCTAA TGCCTACAAT 180
CTTTTCCTTA GGGATATATC CCACGCTAAT ATTCCCAAAA AAAGGGAGCA AATGGTGCTC 240
GCAAGTGGAG TAAAATTCAA TGTTTTGAGC CACTATCATT TCATCGCAAA CGCCTTGAAA 300
ATACGCGCTT TTTAA 315 (2) INFORMATION FOR SEQ Ir> NO: 55:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 498 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...498
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 55:
ATGATTGAAC TAATCTTACA CAATAAGTCC ATACAAATTG ATGAAACATT GCTGAATGTA 60 AAAGAGCATT TAGAAAAGTT TTATTCAAAC AAAGAACAAG AGACAATCGC AAAAACCTTA 120
GAGAGCCAAA CAGAGCTTAC TTGCAGTTAT TTATTGGATA AAGATTTTTC ATTGCTAGAA 180
AAGCATTTAG AAAATAGCTT AGGGCATTTT ACTTTTGAGA GTGAGTTTGC CCTACTAAAA 240
GACAAAGAGC CTTTGAATTT AGCTCAAATC AAACAAATCG GTGTTTTAAA GGTTATTACC 300
TATGAAATGA CACAAGCCTT AAAAAATCAA ATCATTCATT TAACGCAAAT TGTCAATGAA 360 GAAAATTTAG AGTTTGATGA AGAACTTGTT ATTTATCACT TAAATTTTAA GCTCAATCAA 420
AATACTTACA AAGTGTTAGC GAAATTTTGC GTATTAAAAA AGAAAGGAAC ATTGCATGAA 480
AAATTTAAGG CATTTTAG 498
(2) INFORMATION FOR SEQ ID NO: 56:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 642 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...642 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 56:
ATGGATACCG AAACACAAGA AAAGTTTTTA GCGTATTTGT TTGAAAAAGC TTTACAAAAA 60
AATCTACAAG CTTATTGGAT AACAACAACT GAAACTAAGA ATGAATTAAC AAGAGAAGAG 120
TTTTCAAATT TAATAAGAAA AACAATGATT GAACTAATCT TACACAATAA GTCCATACAA 180 ATTGATGAAA CATTGCTGAA TGTAAAAGAG CATTTAGAAA AGTTTTATTC AAACAAAGAA 240
CAAGAGACAA TCGCAAAAAC CTTAGAGAGC CAAACAGAGC TTACTTGCAG TTATTTATTG 300
GATAAAGATT TTTCATTGCT AGAAAAGCAT TTAGAAAATA GCTTAGGGCA TTTTACTTTT 360
GAGAGTGAGT TTGCCCTACT AAAAGACAAA GAGCCTTTGA ATTTAGCTCA AATCAAACAA 420
ATCGGTGTTT TAAAGGTTAT TACCTATGAA ATGACACAAG CCTTAAAAAA TCAAATCATT 480 CATTTAACGC AAATTGTCAA TGAAGAAAAT TTAGAGTTTG ATGAAGAACT TGTTATTTAT 540 CACTTAAATT TTAAGCTCAA TCAAAATACT TACAAAGTGT TAGCGAAATT TTGCGTATTA 600 AAAAAGAAAG GAACATTGCA TGAAAAATTT AAGGCATTTT AG 642 (2) INFORMATION FOR SEQ ID NO: 57:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...762
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:57:
ATGGCGATCT CTATTAAAAG CCCAAAAGAA ATCAAAGCCC TAAGAAAAGC CGGGGAATTA 60
ACCGCTCAAG CGTTAGCCCT TTTAGAGCGA GAAGTAAGGC CTGGGGTTTC ACTTTTAGAG 120 CTGGATAAAA TGGCTGAAGA TTTTATCAAA TCCTCGCATG CTAGGCCTGC TTTTAAGGGG 180
CTCTATGGTT TCCCTAACTC TGTGTGCATG TCCTTAAATG AGGTGGTTAT TCATGGTATT 240
CCTACGGATT ATGTTTTACA AGAAGGGGAT ATTATAGGCT TGGATTTGGG GGTGGAGGTG 300
GATGGCTATT ATGGCGATTC AGCCCTCACG CTTCCCATAG GCGCGATAAG CCCGCAAGAT 360
GAAAAATTGC TCGCTTGCTC TAAAGAGAGC TTGATGCATG CCATTAGCTC AATTAGAGTG 420 GGCATGCATT TTAAAGAGTT GAGTCAGATT TTAGAGGGCG CTATTACAGA AAGGGGCTTT 480
GTGCCTTTGA AGGGATTTTG CGGGCATGGC ATTGGTAAAA AGCCCCATGA AGAGCCAGAA 540
ATCCCCAACT ACCTAGAAAA AGGCGTCAAA GCTAATAGCG GCCCTAAAAT CAAAGAGGGC 600
ATGGTGTTTT GTTTAGAGCC TATGGTGTGT CAAAAACAAG GCGAGCCTAA AATACTAGCG 660
GATAAGTGGA GCGTGGTTTC AGTGGATGGA CTTAACACAA GCCACCATGA GCATACTATC 720 GCCATAGTTG GCAATAAAGC AGTGATTCTT ACGGAGCGTT AA 762
(2) INFORMATION FOR SEQ ID NO: 58:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 744 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...744
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 58:
AAGCCCAAAA GAAATCAAAG CCCTAAGAAA AGCCGGGAAT TAACCGCTCA AGCGTTAGCC 60
CTTTTAGAGC GAGAAGTAAG GCCTGGGGTT TCACTTTTAG AGCTGGATAA AATGGCTGAA 120
GATTTTATCA AATCCTCGCA TGCTAGGCCT GCTTTTAAGG GGCTCTATGG TTTCCCTAAC 180
TCTGTGTGCA TGTCCTTAAA TGAGGTGGTT ATTCATGGTA TTCCTACGGA TTATGTTTTA 240 CAAGAAGGGG ATATTATAGG CTTGGATTTG GGGGTGGAGG TGGATGGCTA TTATGGCGAT 300
TCAGCCCTCA CGCTTCCCAT AGGCGCGATA AGCCCGCAAG ATGAAAAATT GCTCGCTTGC 360
TCTAAAGAGA GCTTGATGCA TGCCATTAGC TCAATTAGAG TGGGCATGCA TTTTAAAGAG 420
TTGAGTCAGA TTTTAGAGGG CGCTATTACA GAAAGGGGCT TTGTGCCTTT GAAGGGATTT 480
TGCGGGCATG GCATTGGTAA AAAGCCCCAT GAAGAGCCAG AAATCCCCAA CTACCTAGAA 540 AAAGGCGTCA AAGCTAATAG CGGCCCTAAA ATCAAAGAGG GCATGGTGTT TTGTTTAGAG 600
CCTATGGTGT GTCAAAAACA AGGCGAGCCT AAAATACTAG CGGATAAGTG GAGCGTGGTT 660
TCAGTGGATG GACTTAACAC AAGCCACCAT GAGCATACTA TCGCCATAGT TGGCAATAAA 720
GCAGTGATTC TTACGGAGCG TTAA 744 (2) INFORMATION FOR SEQ ID NO: 59:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1023 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1023
(xi) SEQUENCE DESCRIPTION: SEQ ID N 59
ATGTATCGTA AAGATTTGGA TAATTACTTA AAACAGCGCC TCCCTAAAGC GGTGTTTTTG 60
TATGGGGAGT TTGATTTTTT CATCCATTAT TATATTCAAA CGATTAGCGC GCTTTTTAAA 120 GGCAATAACC CTGACACAGA AACTTCGCTT TTTTATGCGA GCGATTATGA AAAAAGCCAG 180
ATTGCGACCC TTTTAGAGCA GGATTCTTTA TTTGGAGGGA GCAGTTTAGT TATTTTAAAA 240
CTGGATTTTG CATTGCATAA GAAATTTAAG GAAAATGATA TCAATCCTTT TTTAAAAGCT 300
TTAGAGCGGC CTAGCCATAA TAGGCTTATC ATAGGGCTTT ATAATGCTAA AAGCGACACC 360
ACAAAATACA AATACACTAG CGAAATTATC GTTAAATTTT TCCAAAAAAG CCCCTTGAAA 420 GATGAAGCCA TTTGCGTGCG CTTTTTTACC CCTAAAGCGT GGGAGAGTTT GAAATTCTTG 480
CAAGAAAGGG CTAATTTTTT GCATTTAGAC ATCAGCGGCC ATCTTTTAAA CGCTCTTTTT 540
GAAATTAATA ACGAAGATTT AAGCGTTTCG TTTAACGATT TAGACAAGCT AGCGGTTTTA 600
AACGCGCCCA TCACTTTAGA AGACATTCAA GAATTAAGCT CCAATGCGGG GGATATGGAT 660 TTGCAAAAGC TCATTTTAGG GCTTTTTTTG AAAAAAAGCG TCCTTGATAT TTATGATTAT 720
TTGTTAAAAG AGGGCAAAAA GGATGCGGAT ATTTTAAGGG GGTTAGAGCG CTATTTTTAC 780
CAGCTTTTTT TATTTTTCGC CCACATTAAA ACGACCGGTT TAATGGACGC TAAAGAGGTC 840
TTAGGCTACG CTCCTCCTAA AGAGATTGTA GAAAATTACG CTAAAAACGC CCTGCGTTTG 900
AAAGAAGCCG GCTATAAGAG GGTTTTTGAA ATTTTTAGGT TATGGCACCT TCAAAGCATG 960 CAAGGGCAAA AGGAATTGGG CTTTTTGTAT TTGACCCCCA TTCAAAAAAT CATTAACCCT 1020
TGA 1023
(2) INFORMATION FOR SEQ ID NO: 60: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 603 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...603
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 60:
GTGTTTATGA CAAGCGCTCT GTTAGGCTTA CAAATTGTTT TAGCGGTATT GATTGTGGTG 60
GTGGTTTTGT TGCAAAAAAG TTCTAGCATC GGCTTAGGGG CTTATAGCGG AAGCAACGAT 120
TCTTTATTTG GCGCTAAAGG GCCCGCAAGC TTTATGGCGA AATTGACCAT GTTTTTAGGT 180
TTATTGTTTG TCATCAACAC CATCGCTTTG GGCTATTTTT ACAACAAAGA ATACGGCAAG 240 AGCGTTTTAG ATGAAACTAA AACCAATAAA GAGCTTTCGC CCTTAGTCCC TGCCACCGGC 300
ACGCTCAACC CTACGCTTAA TCCCACATTA AACCCAACGC TCAACCCTTT AGAGCAAGCC 360
CCCACTAATC CTTTAATGCC TACACAAACG CCTAAAGAGC TTCCTAAAGA GCCAGCCAAA 420
ACGCCTTTTG TTGAAAGCCC CAAACAGAAT GAAAAGAATG AAAAGAATGA TGCCAAAGAA 480
AATGGTATAA AGGGTGTTGA AAAAAACAAA GAGAACGCCA AAACGCCCCC AACCACCCAC 540 CAAAAGCCTA AAACGCArGC GACAACCAAC GCCCATACCA ACCAAAAAAA GGATGAAAAA 600
TAA 603
(2) INFORMATION FOR SEQ ID NO: 61: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 480 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...480 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 61:
ATGCGTTCTC CAAATTTAGA AAAAGAAGAA ACTGAAATCA TAGAAACGCT TCTTGTGCGT 60
GAAAAAATGC GTTTATGCCC CTTGTATTGG CGCATCTTAG CGTTTTTAAT CGATAGTTTA 120
TTGGTGGCGT TTTTATTGAG CGATCTTTTA AGGGCATGCG CTTTTTTACA TTCTTTATAT 180 TGGCTGACTA ACCCCATTTA TTACAGCGCG TTTGTTGTGA TGGGTTTTAT CATCTTGTAT 240
GGCGTTTATG AAATCTTTTT TGTGTGTTTG TGCAAGATGA GTTTGGCTAA ACTGGTTTTT 300
AGGATTAAGA TCATTGATAT TTATTTAGCG GATTGCCCCA GTAGGGCTAT TTTATTGAAG 360
CGTTTAGGGT TAAAAATCGT GGTTTTTCTA TGCCCCTTTT TATGGTTTGT GGTGTTTAAA 420
AACCCCTATC ATAGGGCATG GCATGAAGAA AAAAGCAAAA GTCTTTTGGT GTTGTTTTAA 480
(2) INFORMATION FOR SEQ ID NO: 62:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 705 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...705
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 62:
TTGAATACGG ACTTTAGCCA TATCACCGAT ATTGAGGGCA TGCGTTTTGT TAATGAAGAA 60 GACGCTTTAA ACAAATTGAT TAATGAAATC CACACGCGCC ACATTGATTT AAAAGATTCC 120
ATCATGCTCG CTTTGAGTTT TAACGCCTTG TATTTAGCTA ACGCTTTAGC GCAAAAATTT 180
GGGGCGACTT ATGATATACT TTTTTTAGAA CCTATCTTAG CCCCTTTAAA CTCAAAGTGT 240
GAAATCGCTT TAGTGAGTGA AAGCATGGAT ATAGTGATGA ATGAAAGTTT AATCAATTCC 300
TTTGACATCG CTTTAGACTA TGTTTATGGG GAAGCCAAGC GGGCTTATGA AGAAGACATT 360 CTGTCTCACA TCTATCAGTA TCGCAAAGGC AATGCGATCA AAAGCCTAAA AGATAAAAAT 420
ATTTTTATCG TAGATAGGGG GATTGAGACC GGGTTTAGAG CAGGGTTAGG CGTGCAAACT 480
TGTTTGAAAA AAGAATGCCA AGACATTTAT ATTTTAACCC CCATTCTCGC GCAAAATGTC 540
GCTCAAGGCT TAGAAAGCTT GTGCGATGGG GTGATTAGCG TGTATCGCCC TGAATGTTTT 600 GTCTCTGTGG AACACCATTA TAAAGAACTC AAGCGATTAA GCAATGAAGA AATTGAAAAA 660
TACTTGGGCG CTAACAACGC GCCCAATCTC AAAAAGGAAC ATTAA 705
(2) INFORMATION FOR SEQ ID NO: 63: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 864 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...864
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:63:
TTGAAACAAA GCGAAATGGC CATGGAATTT AATGATCCTA GGATGCGTTT TTTTATTGGC 60
GATGTCAGGG ATTTAGAACG CTTGAATTAC GCTTTAGAGG GCGTGGATAT TTGTATCCAT 120
GCGGCCGCGC TCAAGCATGT GCCTATCGCT GAATACAACC CCCTAGAATG CATTAAAACT 180
AACATCATGG GAGCGAGCAA TGTGATTAAC GCATGCTTAA AAAATGAAAT CAGCCAGGTT 240 ATTGCCCTAA GCACCGATAA AGCCGCTAAC CCCATTAACC TCTACGGCGC AACCAAATTG 300
TGCAGCGACA AGCTCTTTGT GAGCGCGAAC AACTTTAAAG GCCCTTCTCA AACGCAATTT 360
GGCGTGGTGC GTTATGGTAA TGTGGTGGGG AGTCGTGGGA GCGTGGTGCC GTTTTTTAAA 420
AAATTAGTCC AAAACAAAGC GAGTGAAATC CCCATTACCG ATATTCGCAT GACACGATTT 480
TGGATCACCT TAGATGAGGG GGTTTCTTTT GTGCTTAAAA GCTTGAAAAG AATGCATGGG 540 GGGGAAATTT TTGTGCCTAA AATCCCCAGC ATGAAAATGA TTGATCTCGC CAAAGCCCTA 600
GCCCCCAATA TCCCTACTAA AATCATAGGG ATTCGCCCGG GCGAAAAACT CCATGAAGTG 660
ATGATCCCTA AAGATGAAAG CCATTTAGCC CTAGAATTTG AAGACTTTTT TATTATTCAG 720
CCCACTATAA GCTTCCAAAC GCCTAAAGAT TACACGCTCA CCAAACTCCA TGAAAAAGGC 780
CAAAAAGTCG CCCCTGATTT TGAATACAGC AGCCATACTA ATAACCAATG GCTAGAGCCT 840 GATGATTTGT TAAAATTATT ATGA 864
(2) INFORMATION FOR SEQ ID NO:64:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 606 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...606
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 64:
ATGCGTTTGC ACACTGCCTT TTTTGGTATT AATTCGTTGC TTGTCGCCAC TCTTTTGATA 60
AGCGGTTGCA GTCTCTTTAA AAAGCGTAAC ACTAACGCTC AGCTAATCCC CCCTTCAGCT 120
AACGGGTTGC AAGCCCCCAT TTATCCCCCA ACCAATTTCA CCCCCAGAAA GAGCATTCAG 180
CCTCTCCCAA GCCCTCGCCT TGAGAATAAC GATCAGCCCA TCATTAGCTC TAATCCCACT 240 AACGCTATCC CTAACACCCC CATTCTCACG CCCAATAATG TCATTGAGTT GAATGCGGTG 300
GGCATGGGTG TGGCTCCAGA ATCCACCATT TCGCCCTCTC AAGCTCTAGC TTTAGCTAAG 360
CGAGCGGCTA TTGTTGATGG CTACCGCCAG TTGGGTGAAA AAATGTATGG CATCAGAGTG 420
AACGCTCAAG ACACCGTCAA AGACATGGTT TTACAAAATT CCGTGATTAA AACGAGAGTG 480
AATGCCCTCA TTCGTAACGC TGAAATCACT GAGACTATCT ATAAAGACGG CTTGTGCCAG 540 GTAAGCATGG AGCTTAAATT AGACGGCAGG ATTTGGTATC GTATTTTGAG CGGATCGAGA 600
GGATAA 606
(2) INFORMATION FOR SEQ ID NO: 65: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1068 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: mis _ .eature
(B) LOCATION 1...1068
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:65:
ATGAGTTATA CTATTAATAA ACGCTTTTCT GTGGGTGTGG GTTTAAGGGG GCTTTATGCG 60
ACCGGGAGCT TTAATAACAC CGTTTATGTG CCTTTAGAGG GCGCTTCAGT TTTGAGCGCG 120
GAGCAAATCT TAAACTTACC CAACAATGTT TTTGCCGATC AAGTGCCAAG TAACATGATG 180
ACTTTATTAG GCAATATTGG CTACCAACCA GCGCTTAATT GCCAAAAAGC CGGTGGGGAC 240 ATGAGTGATC AGAGCTGTCA AGAGTTTTAC AACGGCTTGA AAAAAATCAT GGGTTATAGC 300
GGTTTAATCA AAGCGAGCGC GAATCTTTAT GGCACGACTC AAGTCGTGCA AAAATCTAAC 360
GGACAAGGCG TATCGGGGGG GTATAGAGTG GGTTCGAGTT TGCGTGTGTT TGATCATGGC 420
ATGTTTTCTG TGGTGTATAA TTCTTCAGTT ACCTTTAACA TGAAAGGCGG TTTGGTGGCT 480 ATCACAGAGC TTGGCCCTTC TTTAGGGAGC GTTTTGACTA AAGGCAGCTT GAATATCAAT 540
GTTTCACTCC CCCAAACTTT AAGCTTAGCC TACGCCCACC AATTTTTTAA AGATCGCCTA 600
AGGGTTGAAG GGGTGTTTGA GCGCACTTTT TGGAGTCAAG GGAATAAATT TTTAGTCACC 660
CCTGATTTTG CGAACGCCAC TTACAAGGGC TTGAGCGGGA CGGTGGCTTC CTTGGACTCT 720
GAAACGCTTA AAAAAATGGT AGGCCTAGCG AATTTTAAAA GCGTGATGAA CATGGGGGCT 780 GGCTGGAGGG ACACCAACAC CTTTAGATTA GGGGTAACTT ACATGGGTAA AAGCTTGCGT 840
TTAATGGGCG CTATTGATTA TGATCAAGCC CCAAGCCCCC AAGACGCGAT AGGCATTCCG 900
GACTCTAATG GCTATACCGT GGCTTTTGGG ACTAAATACA ATTTTAGGGG CTTTGATTTG 960
GGCGTAGCGG GGAGTTTCAC TTTTAAGAGC AACCGCTCCA GTTTGTATCA ATCCCCAACT 1020
ATTGGGCAAT TGAGAATCTT TAGCGCCTCT TTAGGCTATC GCTGGTAA 1068
(2) INFORMATION FOR SEQ ID NO: 66:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1764 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...1764
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 66:
ATGAAAAACT TTTCCCCACT CTATTGTCTT AAAAAGCTCA AAAAACGCCA TTTAATCGCT 60 CTGAGTCTGC CCTTGCTTTC TTATGCGAAT GGCTTTAAAA TCCAAGAGCA AAGCTTGAAT 120
GGCACGGCTT TAGGCTCGGC GTATGTCGCT GGGGCTAGGG GTGCTGACGC TTCTTTTTAC 180
AACCCGGCTA ACATGGGCTT TACTAACGAT TGGGGCGAAA ACAGAAGCGA ATTTGAAATG 240
ACCACCACCG TGATCAATAT CCCGGCCTTT AGCTTTAAAG TCCCTACGAC CAATCAAGGC 300
TTATATTCGG TAACAAGTTT AGAAATTGAT AAAAGCCAAC AAAATATTTT AGGCATCATC 360 AACACTATAG GGTTAGGCAA TATCCTTAAA GCGCTTGGCA ATACGGCCGC TACCAATGGC 420
TTA..C .CAAG CTATCAATCG TGTTCAAGGG CTTATGAACT TAACCAATCA AAAAGTCGTA 480
ACCCTCGCTT CAAAACCTGA CACTCAAATC GTGAATGGCT GGACAGGCAC GACTAATTTT 540
GTTTTACCTA AATTCTTTTA TAAAACGCGC ACGCATAACG GCTTCACTTT TGGGGGGAGT 600
TTTACCGCTC CTAGTGGGTT GGGTATGAAA TGGAATGGTA AGGGGGGGGA ATTTTTGCAT 660 GACGTGTTTA TCATGATGGT AGAGCTTGCC CCTAGCATGA GTTATACTAT TAATAAACGC 720
TTTTCTGTGG GTGTGGGTTT AAGGGGGCTT TATGCGACCG GGAGCTTTAA TAACACCGTT 780
TATGTGCCTT TAGAGGGCGC TTCAGTTTTG AGCGCGGAGC AAATCTTAAA CTTACCCAAC 840
AATGTTTTTG CCGATCAAGT GCCAAGTAAC ATGATGACTT TATTAGGCAA TATTGGCTAC 900
CAACCAGCGC TTAATTGCCA AAAAGCCGGT GGGGACATGA GTGATCAGAG CTGTCAAGAG 960 TTTTACAACG GCTTGAAAAA AATCATGGGT TATAGCGGTT TAATCAAAGC GAGCGCGAAT 1020
CTTTATGGCA CGACTCAAGT CGTGCAAAAA TCTAACGGAC AAGGCGTATC GGGGGGGTAT 1080
AGAGTGGGTT CGAGTTTGCG TGTGTTTGAT CATGGCATGT TTTCTGTGGT GTATAATTCT 1140
TCAGTTACCT TTAACATGAA AGGCGGTTTG GTGGCTATCA CAGAGCTTGG CCCTTCTTTA 1200 GGGAGCGTTT TGACTAAAGG CAGCTTGAAT ATCAATGTTT CACTCCCCCA AACTTTAAGC 1260
TTAGCCTACG CCCACCAATT TTTTAAAGAT CGCCTAAGGG TTGAAGGGGT GTTTGAGCGC 1320
ACTTTTTGGA GTCAAGGGAA TAAATTTTTA GTCACCCCTG ATTTTGCGAA CGCCACTTAC 1380
AAGGGCTTGA GCGGGACGGT GGCTTCCTTG GACTCTGAAA CGCTTAAAAA AATGGTAGGC 1440
CTAGCGAATT TTAAAAGCGT GATGAACATG GGGGCTGGCT GGAGGGACAC CAACACCTTT 1500 AGATTAGGGG TAACTTACAT GGGTAAAAGC TTGCGTTTAA TGGGCGCTAT TGATTATGAT 1560
CAAGCCCCAA GCCCCCAAGA CGCGATAGGC ATTCCGGACT CTAATGGCTA TACCGTGGCT 1620
TTTGGGACTA AATACAATTT TAGGGGCTTT GATTTGGGCG TAGCGGGGAG TTTCACTTTT 1680
AAGAGCAACC GCTCCAGTTT GTATCAATCC CCAACTATTG GGCAATTGAG AATCTTTAGC 1740
GCCTCTTTAG GCTATCGCTG GTAA 1764
(2) INFORMATION FOR SEQ ID NO: 67:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 618 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...618
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 67:
TTGATTTTTA GATTTTTCTT AATCTTAAGC CTTTTAAAAG GGGTTTTACT GGCCAAAAAG 60 GATTGGAATT TTTTCAAACC TTTAGAGCCT ACTAAAAAAT ATTTTGGCTC TTTTAAAATC 120
GGCTATCTTT ACCAACATGC AGAAACGACT AAAAGATTCC CCATCCGCCC TAAAAACCGC 180
CCGCCTATTT TAATGGATAA AATTTACCAT GACGCTTCTT TGGGTTTTGA CGCAGGGTAT 240
GTTTTGAAAA AGAAAGCTTT ATTGGGGGGG TATTTGGATG CAGGAATGGG CGATTCGTAT 300
TTCATGAGCG CTGGGCTAGT CGCTGGGGTG AGGCTTTTTA AGGGGTGGGT TATCCCTAAA 360 ATCGCCTTAG GCTATCAGCT TCAAATTTTA GGGGCTAAGA TTGATAAGTA TCAATTCAAT 420
ATCCAATCAG CGGTGGGGAG TGTGGGCTTG TTTTTCAATG CGGCTAAAAA TTTTGGCTTG -_jr
AGTATAGAAG CAAGGGGCGG TATCCCTTTT TATTTCATTC AGAGCAGGTT TTCTAAGGCT 540
TTCGGCACGC CACGATTGAA TATCTATTCT GTTGGTATCA CATTCACTTT TTATGACTTT 600
ACGAGATTTT TAGGGTAA 618
(2) INFORMATION FOR SEQ ID NO:68:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 762 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...762
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 68: TTGTGGCATG CTGCCTTTAG CGTTGGCGAG TGGGGATGGA ACGGCGATGA AATCCCCTAT 60
AGGGATTGCG ATGAGTGGGG GCTTGATGAT TTCTATGGTG TTAAGCCTAC TGATTGTGCC 120
GGTGTTTTAT CGTTTGCTCG CTCCCATAGA CGACAAAATC AAGCGGTTTT ATCAAAACCA 180
AAAAGCTTTA GAATGAAAAA AATTGCTTTC ATTTTGGCTT TATGGGTGGG CTTGTTAGGG 240
GCGTTTGAGC CTAAAAAAAG TCATATTTAT TTTGGGGCTA TGGTGGGTTT AGCCCCTGTT 300 AAAATAACCC CAAAACCGGC TAGTGATTCT TCTTATACGG CTTTTTTATG GGGGGCTAAA 360
GGGGGGTATC AATTCGCTTT TTTTAAAGCT CTAGCGTTAA GGGGTGAATT TTCCTACCTT 420
ATGGCGATCA AACCCACCGC ACTGCACACG ATTAACACTT CTTTATTGAG TTTAAATATG 480
GATGTGTTGA GCGATTTTTA CACTTATAAA AAATACAGCT TTGGGGTGTA TGGGGGGCTT 540
GGGATAGGGT ATTTTTATCA AAGCAACCAT TTAGGCATGA AAAATAGTTC GTTTATGGGT 600 TATAACGGCT TGTTTAATGT GGGGCTTGGC AGCACGATCG ATCGCCACCA CCGCGTAGAG 660
CTTGGGGCTA AGATCCCTTT TTCAAAGACT AGAAATTCTT TTAAAAATTC TTATTTTTTA 720
GAGAGCGTTT TTATCCATGC GGCTTATAGT TATATGTTTT AA 762
(2) INFORMATION FOR SEQ ID NO: 69:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1239 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1239 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 69:
ATGGAATCAG TAAAAACAGT AAAAACAAAT AAAGTTGGCA AAAACACAGA GACAGCTAAC 60
ACAGAGGCAA GTAAAGAGAC TCATTTTAAA CAAGCGAGTG CCATTACAAA TACGCTCCGA 120 TCAATTGGTG GGATTTTTAC AAAAATTGCA AAGAAAGTTA GAGAACTTGT GAAAAAACAT 180
CCCAAGAAAA GCAGTGTGGC ATTAGTAGTA TTGACCCATA TTGCGTGCAA GAGGGCAAAA 240
GAATTGGACG ATAAAGTCCA AGATAAATCC AAACAAGCTG AAAAAGAAAA TCAAATCAAT 300
TGGTGGAAAT ATTCAGGATT AACAATAGCG GCAAGTTTAT TATTAGCCGC TTGTAGCACT 360
GGTGATATTG ATAAACAAAT AGAACTAGAA CAAGAAAAAA AGGAAGCAAA TAAGAGTGGG 420 ATAAAGTTAG AACAAGAAAG ACAGAAAACA GAACAAGAAA GACAGAAGAC AAATAAGAGT 480
GAGATAGAGT TAGAACAAGA AAGACAAAAA ACAAACAAGA GTGGGATAGA ACTCGCTAAT 540
AGTCAAATAA AAGCAGAACA AGAAAGACAA AAGACAGAAC AAGAAAAACA AAAAGCAAAT 600
AAGAGTGAGA TAGAGTTAGA ACAGCAAAAA CAAAAGACAA TTAATACACA AAGAGATTTG 660
ATTAAAGAAC AGAAAGATTT CATTAAAGAA ACAGAACAAA ATTGCCAAGA AAAACATGGC 720 CAATTGTTTA TTAAAAAAGC AAGAATTAAG ACCGGTATTA CTACTGGTAT TGCCATAGAA 780
ATAGAAGCTG AATGCAAAAC CCCTAAACCT GCAAAAACCA ATCAAACCCC TATCCAGCCA 840
AAACACCTCC CAAACTCTAA ACAACCCCGC TCTCAAAGAG GATCAAAAGC GCAAGAGCTT 900
ATCGCTTATT TGCAAAAAGA GCTAGAATCT CTGCCCTATT CGCAAAAAGC TATCGCTAAA 960
CAAGTGGATT TTTATAAACC AAGTTCTATC GCTTATTTAG AACTAGACCC TAGAGATTTT 1020 AAGGTTACAG AAGAATGGCA AAAAGAAAAT TTAAAAATAC GCTCTAAAGC TCAAGCTAAA 1080
ATGCTTGAAA TGAGAAACCC ACAAGCCCAC CTTCCAACCT CTCAAAGCCT TTTGTTCGTT 1140
CAAAAAATAT TTGCTGATAT TAATAAAGAA ATAGAAGCAG TTGCTAATAC TGAAAAGAAA 1200
ACAGAAAAAG CGGGTTATGG TTATAGTAAA AGGATGTAG 1239 (2) INFORMATION FOR SEQ ID NO: 70:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 450 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...450
(xi) SEQUENCE DEJC ilPTION: SEQ ID NO:70:
TTGAATTGGG AGCATTTGAT GAAAAAATTA GCGTTTTCTT TATTATTTAC AGGGACTTTT 60
TTGGGGCTTT TTTTGAATGC GAGTGATTTT AAGAGCATGG ATAACAAGCA ACTATTAGAG 120 CAAGCAGGGA AAGTCGCTCC TAGCGAAGTT CCAGAGTTTC GCACAGAAGT CAATAAACGA 180
TTAGAAGCGA TGAAAGAAGA AGAGCGTCAA AAATATAAAG CGGATTTTAA GAAAGCGATG 240
GATAAGAATT TGGCTTCTTT AAGCCAAGAA GATCGCAACA AGCGTAAAAA AGAAATCCTT 300
GAAGTCATTG CTAACAAAAA GAAAACAATG ACCATGAAAG AGTATCGTGA AGAGGGGTTG 360
GATTTGCATG ATTGCGCATG CGAAGGCCCT TTTCATGATC ATGAAAAAAA GGGGCAAAAA 420 GGGAAAAAAC CAAGCCATCA TAAGCATTAG 450
(2) INFORMATION FOR SEQ ID NO: 71: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...615
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 71:
ATGCAAGCAG TGATTTTAGC GAATGGGGAG TTTCCTAAAT CTAAAAAATG CTTAGACATT 60
TTACAAAACG CTCCCTTTTT AATCGCATGC GATGGGGCTG TTATATCATT GCATGCGCTT 120
CAATTCAAAC CCAGCGTTGT TATAGGCGAT TTGGATAGCA TTGATTCGCA TTTGAAAGCC 180
TTGTATAACC CTATACGCGT GAGCGAACAA GACAGCAACG ATTTGTCCAA AGCCTTTTTT 240 TATGCTTTGA ATAGGGGTTG TGATGATTTT ATTTTTTTAG GGTTGAATGG CAAGCGAGAA 300
GACCACGCTT TAGCGAACAC TTTTTTATTG TTGGAGTATT TTAAATTTTG CAAAAAAATC 360
CAATCCGTAA GCGATTATGG CCTTTTTAGG GTGTTAGAAA CCCCTTTTAC TTTGCCCAGT 420
TTTAAGGGGG AGCAAATCTC GCTTTTTAGC TTGGATCTTA AAGCCCGATT CACTTCTAAA 480
AACCTCAAAT ACCCCTTAAA AGACTTGCGT CTAAAAACGC TCTTTTCCGG CTCGCTCAAT 540 GAAGCCACTA ATCATTGTTT TAGCCTTAGC TCTGAACCTA AATCGGTGGT GCTAGTGTAT 600
CAAAAATTCT CATGA 615
(2) INFORMATION FOR SEQ ID NO: 72: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 843 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...843 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 72:
GTGTTTGACT CATTGGGCGG ATTTTTGGGG TATAAAACTT TTAAGCCGAT AGTGGATAAG 60
GTTAAAAATA TAAACGCTTG GATAAAAAAT TACGATAATA AAAAAGCTCA AGAGATTATG 120
GGTTTTATAG AAAATCCTAC GCCTGATTTC CAAAATAATA AGTTTTTGTG TGTTTTAAAC 180 CGACAAGGAA CAAGGCACAA CAATTATCTT GGTTTAACCT CTACAAACCT TCTAATCGGC 240
GCGATCTATT TCTCCATCCG CCATTGCATC AAAGCCACAT GGCAAAACGA TAGGGATCAA 300
TTCTACGCCC CTTATGATGA CGCTTTCCAA GACGACAGCG AGTTTAAAAA CAATTGTTTG 360
GCGTTCATGC TTTTTCACAC CCAAAACCGC ATCACTGCCA CTCAAGGGAC TAACCATTTT 420
ATCCCCTTTA GCGAAGATGA AGTTGATTCT AAAGAAAGGT ATTTGAGCCA TGCTTTATTA 480 GACTTTTTAA AAGGCGAAAT CAAAGAACCT AAAAAGAGCG ATAGCCTCTT TTTAAACGCC 540
AAAAAAGAAA ACAAGCCCCT AAAATTCAGC TCGAGCGCTT CAAAGGTGTT TGACGCTGGC 600
AGAGAGATTT ATCGCTATTA CCACACACAA GATTTCATCC ACACCCCCTA TAACGCTAAC 660
GCAAGCCTTT ATGACATCAA AGAATTTTTT CAAGGCCGTA ACAAGCAAGG CAGATTAAAC 720
TCACCCACCA AAGCCAAAGA TGAATATTAC AAACAGCTTT ACGCTAACTT GCAATACGCC 780 CTAAAAGATC TCGCCAAAGA AATACAGCCT AAAGTCTATG AATACGGATT TTTAAGGGAG 840
TAG 843
(2) INFORMATION FOR SEQ ID NO: 73: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 930 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...930
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 73:
TGTGACAGGG CAATTCCCCA TTGGCTTTTT AGTCTGGGAT ACCGCTACCC CCCCCC^T'.A 60
AAACCAACCA ACGCGTTCAA TTTAGAAGTG TTTGACTCAT TGGGCGGATT TTTGGGGTAT 120
AAAACTTTTA AGCCGATAGT GGATAAGGTT AAAAATATAA ACGCTTGGAT AAAAAATTAC 180
GATAATAAAA AAGCTCAAGA GATTATGGGT TTTATAGAAA ATCCTACGCC TGATTTCCAA 240 AATAATAAGT TTTTGTGTGT TTTAAACCGA CAAGGAACAA GGCACAACAA TTATCTTGGT 300
TTAACCTCTA CAAACCTTCT AATCGGCGCG ATCTATTTCT CCATCCGCCA TTGCATCAAA 360
GCCACATGGC AAAACGATAG GGATCAATTC TACGCCCCTT ATGATGACGC TTTCCAAGAC 420
GACAGCGAGT TTAAAAACAA TTGTTTGGCG TTCATGCTTT TTCACACCCA AAACCGCATC 480
ACTGCCACTC AAGGGACTAA CCATTTTATC CCCTTTAGCG AAGATGAAGT TGATTCTAAA 540 GAAAGGTATT TGAGCCATGC TTTATTAGAC TTTTTAAAAG GCGAAATCAA AGAACCTAAA 600
AAGAGCGATA GCCTCTTTTT AAACGCCAAA AAAGAAAACA AGCCCCTAAA ATTCAGCTCG 660
AGCGCTTCAA AGGTGTTTGA CGCTGGCAGA GAGATTTATC GCTATTACCA CACACAAGAT 720
TTCATCCACA CCCCCTATAA CGCTAACGCA AGCCTTTATG ACATCAAAGA ATTTTTTCAA 780
GGCCGTAACA AGCAAGGCAG ATTAAACTCA CCCACCAAAG CCAAAGATGA ATATTACAAA 840
CAGCTTTACG CTAACTTGCA ATACGCCCTA AAAGATCTCG CCAAAGAAAT ACAGCCTAAA 900
GTCTATGAAT ACGGATTTTT AAGGGAGTAG 930
(2) INFORMATION FOR SEQ ID NO: 74:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 564 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...564 (xi) SEQUENCE DESCRIPTION: SEQ ID NO : 74 :
TTGGAAACTT ATATCATTGA TGCAGATAAT ATAGATGGGG ATTTATTTTT CTATAATCTT 60
ACTAGAAACA GCAATGATTT TTCCATGTTG CCCGTTTTTG AACTCGATCG CATTGCCCAA 120
AAAATTAGAA ATATTCTTAA AAAACATGGC AGTAGAAAAG ACATTATTTT AAAACACAAT 180 GAAATTAAAG AAGCCTTTTT TAGCCCGTTC AAACCGCAGC TAAAAACCGT TCAAGTGTTC 240
CTCTCGCACT CGCATGCGGA TAAAAATAAG GCTTTAGGGG TTAAGGACTA TTTGGAAAGC 300
AAAACAAAAC GCAAAGTGTT TATCGATTCG CTTTTTTGGG ATTATAAAGA CGATGTTTTA 360
AACAAATTGG CAAAACACGA TGATATAAGC AAGATTGAAG ACGCTTTCAC GCTCATTCTC 420
AGAAAATCTT TACAAGATAT GATTGAAAAA TGCCCTTATT TTGTGTTTTT ACAAAGCAAG 480 AACAGCGTTT CTAATCAAGG GCTATCACGC ATCACTTATT CCGCATGGAT TTATGAAGAA 540
TTAAAAATCG CTTCATTCTA TTAG 564
(2) INFORMATION FOR SEQ ID NO: 75: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 597 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO ( iv) ANTI - SENSE : NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...597 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 75:
TTGGAAACTT ATATCATTGA TGCAGATAAT ATAGATGGGG ATTTATTTTT CTATAATCTT 60
ACTAGAAACA GCAATGATTT TTCCATGTTG CCCGTTTTTG AACTCGATCG CATTGCCCAA 120
AAAATTAGAA ATATTCTTAA AAAACATGGC AGTAGAAAAG ACATTATTTT AAAACACAAT 180 GAAATTAAAG AAGCCTTTTT TAGCCCGTTC AAACCGCAGC TAAAAACCGT TCAAGTGTTC 240
CTCTCGCACT CGCATGCGGA TAAAAATAAG GCTTTAGGGG TTAAGGACTA TTTGGAAAGC 300
AAAACAAAAC GCAAAGTGTT TATCGATTCG CTTTTTTGGG ATTATAAAGA CGATGTTTTA 360
AACAAATTGG CAAAACACGA TGATATAAGC AAGATTGAAG ACGCTTTCAC GCTCATTCTC 420
AGAAAATCTT TACAAGATAT GATTGAAAAA TGCCCTTATT TTGTGTTTTT ACAAAGCAAG 480 AACAGCGTTT CTAATCAAGG GCTATCACGC ATCACTTATT CCGCATGGAT TTATGAAGAA 540
TTAAAAATCG CTTCATTTCT ATTAGCGCTA TTAACGAGAG TCGCCCAATT CCAATGA 597
(2) INFORMATION FOR SEQ ID NO: 76: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 570 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...570
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:76:
ATGATGACTA h^,P ..CGCTTA TGCGTTTGTC GTGATTGAAA AAAGTATTAT GGTGTTTAAA 60
TGCGCCAAAG ACAAGGGGCT AATCCCTATC ACTGAAGGCT TTGTGCCGTT AAAAGAGGGC 120
TTTTTGAGAA GTTTTAAAGA GCGTTGCAAT CTGGATTTTT TAGAAAATTT AGACCTTTTG 180
TTTTTGTATG ACTACCAATT TCCAAGCGAG GTTTTTTCAT TGTGTAAGGA TTTGAAAAAT 240 TCCATTTGGG ACAGAAAGCT TGTGGTAGTG CTAGTGGAGG CTTTGGAGGG TTTTAAGGGT 300
TTGAATTTGT CTCTTAAGAT AGAAGATAGG CATTCTAATA GCTTGGGTAA TGGCGTTCAA 360
AAATTGCTCA CCAACGCTGA TTTGGGGAGC AACCACAAAC CAATCGTAAT AGACAGCATG 420
AAAACATACC ACCAAAGCCA GCAAGAAAAA TACAAAAGAG AAAGAGGCGA AACGCTAGAG 480
GTTCGCCCCA CAACACCCCC TAGCTATGGG GGTGGGAGCA TTAGAATCAG CGGCGATAAA 540 AAGCCTGATT CCAATGAAGA AAATTTTTAA 570
(2) INFORMATION FOR SEQ ID NO: 77: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1773 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...1773
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 77:
ATGAAAGCGA TAAAAATACT TCTTATAATG ACACTCAGTT TAAACGCTAT CAGCGTGAAT 60
AGGGCGTTGT TTGATTTAAA AGATTCGCAA TTAAAAGGGG AATTAACGCC AAAAATAGTG 120
GATTTTGGGG GTTATAAAAG CAACACCACA GAGTGGGGAG CTACGGCTTT AAACTATATC 180
AATGCGGCTA ATGGCGATGC GAAAAAATTC AGCGCGTTAG TGGAAAAAAT GCGTTTTAAC 240 TCTGGTATCT TGGGGAATTT TAGAGCGCAT GCACATTTGA GGCAAGCCCT AAAATTGCAA 300
AAGAATTTGA AATATTGCCT TAAAATCATC GCTAGGGATT CTTTTTATAG TTACCGCACC 360
GGTATTTATA TCCCCTTAGG CATTTCTTTA AAAGATCAAA AAACGGCTCA AAAAATGCTC 420
GCTGATTTGA GCGTGGTAGG GGCGTATCTT AAAAAGCAAC AGGAGAATGA AAAGGCTCAA 480
AGCCCTTATT ACAGGAGCAA CAACTATTAC AACTCCTACT ATAGCCCTTA TTATGGCATG 540 TATGGCATGT ATGGAATGGG CATGTATGGA ATGTATGGCA TGGGCATGTA TGATTTTTAT 600
GACTTTTATG ATGGCATGTA TGGGTTCTAC CCTAACATGT TTTTCATGAT GCAAGTTCAA 660
GACTACTTGA TGTTAGAAAA TTACATGTAT GCACTCGATC AAGAAGAGAT TTTAGACCAT 720
GACGCTTCCA TCAACCAACT TGATACGCCT ACTGATGATG ACAGAGACGA TAAAGACGAT 780
AAATCTTCGC AACCAGCGAA TCTCATGAGC TTTTATCGTG ATCCCAAATT CAGCAAAGAC 840 ATTCAAACCA ACCGCTTGAA TAGCGCCTTA GTCAATTTAG ACAACAGCCA CATGCTCAAA 900
GACAATTCGC TCTTCCACAC TAAAGCCATG CCCACTAAAA GCGTGGATGC GATCACTTCT 960
CAAGCTAAAG AGCTTAACCA TTTGGTGGGG CAAATCAAAG AGATGAAGCA AGACGGGGCG 1020
AGTCCTAATA AGATTGATTC AGTGGTCAAT AAAGCTATGG AGGTTAGGGA CAAATTAGAC 1080
AACAACCTCA ACCAACTAGA CAATGACTTA AAAGATCAAA AAGGGCTTTC AAGCGAGCAG 1140 CAAGCCCAAG TGGATAAAGC CTTAGACAGC GTGCAACAAT TAAGCCATAG CAGCGATGTG 1200
GTAGGGAATT ATTTAGACGG GAGTTTGAAA ATTGATGGCG ATGACAGAGA CGATTTGAAT 1260
GATGCGATCA ATAACCCTAT GCAACAACCT GCGCAACAAA CGCCTATTAA CAACATGGAC 1320
AACACCCATG CAAATGACAG CAAAGATCAA GGGGGTAACG CGCTCATAAA CCCTAACAAC 1380
GCCACCAACG ATGATCACAA CGATGATCAC ATGGACACTA ACACCACTGA CACTAGCAAC 1440 GCAAACGACA CCCCCACTGA TGATAAAGAT GCTAGCGGCA ACAATACCGG CGATATGAAT 1500
AACACCGACA CCGGCAATAC GGACACTGGC AACACCGACA CCGGTAACAC TGATGATATG 1560
AGCAACATGA ACAACGGCAA CGATGATACG GGTAACACTA ACGACGACAT GGGTAATAGC 1620
AACGACATGG GCGATGACAT GAATAACGCG AACGACATGA ACGACGACAT GGGTAACAGC 1680
AACGATGACA TGGGCGATAT GGGGGACATG AACGATGACA TGGGTGGCGA TATGGGAGAC 1740 ATGGGGGATA TGGGTGGCGA TATGGGGAAT TGA 1773
(2) INFORMATION FOR SEQ ID NO: 78: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 588 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...588
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 78:
TTGAATTTAC GATTGGCTGG AGCAAGCGTT TTAACGGCTT GTGTCTTTTC GGGGTGTTTT 60
TTTTTAAAAA TGTTTGACAA AAAACTTTCT AGCAACGATT GGCATATCCA AAAAGTAGAA 120
ATGAACCATC AAGTGTATGA CATTGAAACC ATGCTCGCTG ATAGCGCTTT TAGAGAGCAT 180
GAAGAAGAGC AAGACTCCTC TTTAAATACC GCTTTGCCTG AAGATAAAAC AGCGATTGAA 240 GCCAAAGAGC AAGAGCAAAA AGAAAAAAGG AAACACTGGT ATGAGCTTTT TAAAAAGAAG 300
CCAAAGCCCA AAAGCTCTAT GGGAGAGTTT GTGTTTGATC AAAAAGAAAA TCGTATTTAT 360
GGGAAAGGCT ATTGCAACCG GTATTTTGCT AGCTACACAT GGCAGGGCGA TAGGCACATC 420
GCAATTGAAG ATAGCGGGAT TTCAAGAAAA GTGTGTAGAG ATGAGCATTT GATGGCGTTT 480
GAATTGGAAT TTATGGAGAA TTTTAAGGGT AATTTTGCGG TAACTAAGGG CAAGGACACG 540 CTCATTTTAG ACAACCAAAA AATGAAAATT TATTTGAAAA CGCCATGA 588
(2) INFORMATION FOR SEQ ID NO: 79:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2235 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...2235
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 79:
ATGTTAAAAC TCGCCAGTAA AACGATTTGT TTGTCCCTAA TCAGCTCATT CACGGCTGTA 60
GAAGCCTTTC AAAAACACCA AAAAGACGGC TTTTTCATAG AAGCCGGCTT TGAAACCGGG 120
CTATTACAAG GCACACAAAC CCAAGAACAA ACCATAGCCA CCACTCAAGA AAAACCCAAA 180
CCCAAACCCA AACCAAAACC CATTACCCCT CAAAGCACCT ATGGGAAATA CTACATCTCC 240 CAAAGCACCA TTTTAAAGAA TGCGACTGAG TTGTTTGCAG AGGATAATAT CACCAACTTA 300
ACCTTTTACT CTCAAAACCC TGTGTATGTA ACCGCTTATA ACCAAGAAAG CGCTGAAGAA 360
GCTGGCTATG GTAATAACAG CTTGATTATG ATACAAAACT TCTTGCCTTA TAACTTGAAC 420
AACATTGAGC TGAGTTACAC GGACGATCAA GGCAATGTGG TCAGTTTGGG CGTGATAGAG 480
ACTATCCCTA AACAATCTCA AATCATTCTG CCCGCAAGCT TGTTTAACGA CCCACAGCTT 540 AACGCCGATG GCTTCCAACA ACTCCAAACC AACACCACAC GATTTTCTGA TGCCAGCACG 600
CAGAATCTGT TTAACAAGCT CAGCAAGGTT ACAACCAATC TTCAAATGAC TTATATCAAT 660
TACAACCAAT TTTCTAGCGG TAACGGCAGT GGCTCTAAAC CCCCATGCCC CCCATACGAA 720
AACCAAGCAA ATTGTGTGGC TAAAGTGCCG CCTTTCACCT CTCAAGACGC TAAAAATTTG 780
ACCAATTTAA TGCTGAACAT GATGGCGGTG TTTGATTCTA AATCTTGGGA AGACGCCGTC 840 TTAAACGCTC CTTTCCAATT CAGCGACAAC AACCTGTCAG CGCCATGTTA TTCTGATTAC 900
CTTACATGCG TGAATCCTTA CAACGATGGG CTTGTTGATC CTAAATTGAT CGCCAAAAAT 960
AAAGGAGATG AATACAATAT AGAAAACGGG CAAACAGGCT CAGTGATATT AACGCCGCAA 1020
GATGTTATCT ATAGCTATAG AGTCGCTAAT AATATTTATG TGAATCTCTT GCCCACAAGA 1080
GGAGGGGATT TAGGGTTAGG GTCTCAATAT GGTGGCCCGA ATGGCCCAGG CGATGATGGC 1140 ACCAATTTTG GCGCTTTAGG GATATTGTCC CCTTTCTTAG ACCCTGAAAT ATTGTTTGGC 1200
AAAGAATTGA ATAAAGTCGC CATCATGCAA TTAAGAGACA TCATCCATGA ATACGGCCAT 1260
ACTTTAGGCT ATACGCATAA CGGGAACATG ACTTATCAAA GAGTGCGCAT GTGCGAAGAA 1320
AACAATGGGC CAGAAGAGCG CTGTCAGGGC GGAAGGATAG AGCAAGTGGA TGGGAAAGAA 1380
GTGCAAGTGT TTGACAACGG GCATGAAGTG CGAGACACCG ATGGCTCTAC CTATGATGTG 1440 TGTTCTCGTT TTAAAGATAA GCCCTATACA GCGGGCAGCT ATCCTAATTC CATCTATACC 1500
GATTGCTCTC AAGTCCCCGC TGGGCTTATA GGCGTTACCA GCGCTGTTTG GCAACAACTC 1560
ATTGATCAAA ACGCCCTACC GGTGGATTTT ACTAATTTGA GCAGCCAAAC CAACTATTTG 1620
AACGCCAGCT TGAACACGCA AGACTTTGCG ACCACCATGC TTAGCGCGAT CAGTCAAAGC 1680
CTTTCATCTT CTAAATCTAG CGCCACTACT TATCGCACTT CAAAAACCTC ACGGCCCTTT 1740 GGAGCCCCCC TATTAGGCGT TAATCTTAAA ATGGGCTATC AAAAATATTT TAATGATTAT 1800
CTAGGGTTGT CTTCTTATGG CATTATCAAA TACAACTACG CTCAAGCCAA CAACGAAAAA 1860
ATCCAGCAAT TAAGCTATGG CGTGGGAATG GATGTGCTGT TTGATTTCAT CACCAATTAC 1920
ACTAACGAAA AGAACCCCAA AAGCAATCTA ACCAAGAAAG TTTTCACTTC CTCTCTTGGG 1980
GTGTTTGGGG GGTTAAGGGG CTTATACAAC AGCTATTATT TGTTGAACCA ATACAAAGGG 2040 AGCGGTAATT TAAATGTGAC CGGTGGGTTG AATTACCGCT ACAAGCATTC CAAATATTCT 2100
ATAGGCATTA GCGTTCCTTT GGTCCAGTTG AAATCTAGGA TCGTTTCTAG CGATGGTGCT 2160
TATACCAATT CTATCACCCT CAATGAAGGG GGCAGTCATT TTAAAGTGTT TTTTAATTAC 2220
GGGTGGATTT TCTAA 2235 (2) INFORMATION FOR SEQ ID NO: 80:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1590 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...1590
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 80:
ATGACTTATA TCAATTACAA CCAATTTTCT AGCGGTAACG GCAGTGGCTC TAAACCCCCA 60 TGCCCCCCAT ACGAAAACCA AGCAAATTGT GTGGCTAAAG TGCCGCCTTT CACCTCTCAA 120
GACGCTAAAA ATTTGACCAA TTTAATGCTG AACATGATGG CGGTGTTTGA TTCTAAATCT 180
TGGGAAGACG CCGTCTTAAA CGCTCCTTTC CAATTCAGCG ACAACAACCT GTCAGCGCCA 240
TGTTATTCTG ATTACCTTAC ATGCGTGAAT CCTTACAACG ATGGGCTTGT TGATCCTAAA 300
TTGATCGCCA AAAATAAAGG AGATGAATAC AATATAGAAA ACGGGCAAAC AGGCTCAGTG 360 ATATTAACGC CGCAAGATGT TATCTATAGC TATAGAGTCG CTAATAATAT TTATGTGAAT 420
CTCTTGCCCA CAAGAGGAGG GGATTTAGGG TTAGGGTCTC AATATGGTGG CCCGAATGGC 480
CCAGGCGATG ATGGCACCAA TTTTGGCGCT TTAGGGATAT ΪGTCCCCTTT CTTAGACCCT 540
GAAATATTGT TTGGCAAAGA ATTGAATAAA GTCGCCATCA TGCAATTAAG AGACATCATC 600
CATGAATACG GCCATACTTT AGGCTATACG CATAACGGGA ACATGACTTA TCAAAGAGTG 660 CGCATGTGCG AAGAAAACAA TGGGCCAGAA GAGCGCTGTC AGGGCGGAAG GATAGAGCAA 720
GTGGATGGGA AAGAAGTGCA AGTGTTTGAC AACGGGCATG AAGTGCGAGA CACCGATGGC 780
TCTACCTATG ATGTGTGTTC TCGTTTTAAA GATAAGCCCT ATACAGCGGG CAGCTATCCT 840
AATTCCATCT ATACCGATTG CTCTCAAGTC CCCGCTGGGC TTATAGGCGT TACCAGCGCT 900
GTTTGGCAAC AACTCATTGA TCAAAACGCC CTACCGGTGG ATTTTACTAA TTTGAGCAGC 960 CAAACCAACT ATTTGAACGC CAGCTTGAAC ACGCAAGACT TTGCGACCAC CATGCTTAGC 1020
GCGATCAGTC AAAGCCTTTC ATCTTCTAAA TCTAGCGCCA CTACTTATCG CACTTCAAAA 1080
ACCTCACGGC CCTTTGGAGC CCCCCTATTA GGCGTTAATC TTAAAATGGG CTATCAAAAA 1140
TATTTTAATG ATTATCTAGG GTTGTCTTCT TATGGCATTA TCAAATACAA CTACGCTCAA 1200
GCCAACAACG AAAAAATCCA GCAATTAAGC TATGGCGTGG GAATGGATGT GCTGTTTGAT 1260 TTCATCACCA ATTACACTAA CGAAAAGAAC CCCAAAAGCA ATCTAACCAA GAAAGTTTTC 1320
ACTTCCTCTC TTGGGGTGTT TGGGGGGTTA AGGGGCTTAT ACAACAGCTA TTATTTGTTG 1380
AACCAATACA AAGGGAGCGG TAATTTAAAT GTGACCGGTG GGTTGAATTA CCGCTACAAG 1440
CATTCCAAAT ATTCTATAGG CATTAGCGTT CCTTTGGTCC AGTTGAAATC TAGGATCGTT 1500
TCTAGCGATG GTGCTTATAC CAATTCTATC ACCCTCAATG AAGGGGGCAG TCATTTTAAA 1560 GTGTTTTTTA ATTACGGGTG GATTTTCTAA 1590
(2) INFORMATION FOR SEQ ID NO: 81:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 564 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...564
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 81:
TTGGGTTGCG TATCAATGAC TCTAGGTATT GATGAAGCGG GGAGGGGGTG TTTGGCCGGT 60
TCGCTTTTTG TGGCGGGGGT GGTGTGTAAT GAAAAAATAG CCTTAGAATT TCTAAAAATG 120
GGTCTTAAGG ATAGCAAGAA GCTCAGCCCC AAAAAGCGCT TTTTCTTAGA AGATAAAATC 180
AAAACGCATG GTGAGGTGGG GTTTTTCGTG GTTAAAAAAA GCGCGAATGA AATTGATCAT 240 TTGGGCTTAG GGGCGTGTTT GAAACTCGCT ATTGAAGAAA TTGTAGAAAA TGGTTGCTCT 300
TTAGCCAATG AAATAAAAAT AGATGGCAAC ACGGCGTTTG GCTTGAACAA ACGCTACCCC 360
AACATACAAA CCATCATCAA GGGCGATGAA ACAATCGCTC AAATCGCTAT GGCGTCTGTT 420
TTGGCGAAAG CTTCTAAGGA TAGGGAAATG TTAGAACTGC ACGCTTTGTT TAAGGAATAC 480
GGCTGGGATA AGAATTGCGG GTATGGGACT AAACAACATA TAGAAGCGAT CAATAAGCTA 540 GGGGCTACGC TTTCATCGGC ATAG 564
(2) INFORMATION FOR SEQ ID NO: 82:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...615
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 82: ATGACTCTAG GTATTGATGA AGCGGGGAGG GGGTGTTTGG CCGGTTCGCT TTTTGTGGCG 60
GGGGTGGTGT GTAATGAAAA AATAGCCTTA GAATTTCTAA AAATGGGTCT TAAGGATAGC 12
AAGAAGCTCA GCCCCAAAAA GCGCTTTTTC TTAGAAGATA AAATCAAAAC GCATGGTGAG 180
GTGGGGTTTT TCGTGGTTAA AAAAAGCGCG AATGAAATTG ATCATTTGGG CTTAGGGGCG 240
TGTTTGAAAC TCGCTATTGA AGAAATTGTA GAAAATGGTT GCTCTTTAGC CAATGAAATA 300 AAAATAGATG GCAACACGGC GTTTGGCTTG AACAAACGCT ACCCCAACAT ACAAACCATC 360
ATCAAGGGCG ATGAAACAAT CGCTCAAATC GCTATGGCGT CTGTTTTGGC GAAAGCTTCT 420
AAGGATAGGG AAATGTTAGA ACTGCACGCT TTGTTTAAGG AATACGGCTG GGATAAGAAT 480
TGCGGGTATG GGACTAAACA ACATATAGAA GCGATCAATA AGCTAGGGGC TACGCCTTTT 540
CATCGGCATA GCTTCACGCT TAAAAACCGC ATCTTAAATC CCAAACTCTT AGAGGTGGAA 600 CAACGCCTTG TTTAA 615
(2) INFORMATION FOR SEQ ID NO: 83: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 579 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...579
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 83:
ATGAATGCAT TGAAAAAATT AAGTTTTTGC GCCTTGTTAT CCCTAGGCCT CTTCGCTCAA 60
ACAGTGCATG CTCAGCATTT AAAGGACACG ATTAACTATC CTGATTGGCT TAAAATCAAT 120
CTTTTTGATA AAAAGAACCC GCCCAATCAA TATGTCGGAT CGGCTTCAAT TTCTGGTAAA 180
AGGAACGATT TTTATTCCAA TTACATCCCC TATGATGACA AATTGCCCCC TGAAAAGAAC 240 GCTGAAGAAA TCGCTCTTTT AAGGGCCAGA ATGAACGCTT ACAGCACTTT AGAAAGCGCT 300
TTACTCACTA AAATGTGCAA TCGCATTGTT AAAGCGCTTC AAGTTAAAAA TAATGTTATC 360
AGCCATTTAT TCGGGTTTGT TGATTTTTTA ACGTCTAAAT CCATTTTGGC TAAAAGGTTC 420
GTGGATACCA CCAACCATCG TGTGTATGTC ATGGTGCAAT TCCCTTTCAT TCAGCCTGAA 480
GACTTAATCG CTTACTTTAA AGCCAAACGC ATCGACCTTT CTTTAGCGAG CGCTACCAAT 540 CTCAGCGCCA TTTTAAACAA GGCGTTGTTC CACCTCTAA 579
(2) INFORMATION FOR SEQ ID NO: 84:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 261 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...261
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 84:
ATGAATGCAT TGAAAAAATT AAGTTTTTGC GCCTTGTTAT CCCTAGGCCT CTTCGCTCAA 60
ACAGTGCATG CTCAGCATTT AAAGGACACG ATTAACTATC CTGATTGGCT TAAAATCAAT 120
CTTTTTGATA AAAAGAACCC GCCCAATCAA TATGTCGGAT CGGCTTCAAT TTCTGGTAAA 180
AGGAACGATT TTTATTCCAA TTACATCCCC TATGATGACA AATTGCCCCC TGAAAGAACG 240 CTGAAGAAAT CGCTCTTTTA A 261
(2) INFORMATION FOR SEQ ID NO: 85:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 228 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...228
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 85: TTGAAAATTT TAACCCTTTT TTTGATAGGT TTAAACGCAT TGTTCGCCCT AGATTTGAAC 60
GCGCTTAAAA CAGAAATCAA AGAAACCTAT CTCAAAGAAT ACAAAGACTT AAAATTGGAA 120
ATTGAAACAA TTAATTTAGA AATCCCAGAG CGTTTTTCTC ACGCTTCCAT TTTAAGCTAT 180
GAATTGAACG CTTCTAACAA GCTTAAAAAA GATGGGTCGT GTTTTTAA 228 (2) INFORMATION FOR SEQ ID NO: 86:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 636 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOG- : circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...636
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 86:
ATGTTTTCAA TAATTCTGGG GGGGGGGGGG GGTAATACCC CATGCGGCTT GACATGGCAA 60 CACTTCAAAT TAGGGGATTT GTTTGAAATT GAAAAAACCT TAAGCTTTAA TAAAGACGCT 120
TTAACGCAAG GACAAGATTA CGATTATATT ACAAGAACTT CGCAAAATCA AGGCGTTTTG 180
CAAACTACAG GATTTGTCAA TGCAGAAAAT TTAAACCCAC CATTTACTTG GAGTTTAGGG 240
CTTTTGCAAA TGGATTTTTT CTATCGTAAA AAGTCATGGT ATGCGGGACA ATTCATGCGA 300
AAAATCACAC CAAAAACTGA AATTAAAAAT AAAATTAATT CACGCATAGC CCACTATTTC 360 ACAACGCTTT TAAACGCCTT AAAACGCCCT TTATTGAGTG TATTAGTTAG GGATATTGAT 420
AAAACTTTTA GGGAGCAAAA AATCCAACTA CCCCTAAAAC CCACCGCTAA AACTCAAAGC 480
CTTGATGGTA TTGATTTTGA TTTCATGCAC ACCCTAATCA ACGCCCTGAT GAAGCAAACC 540
ATTCAAGGCG TGGTTCAATA CTGCGACGCT AAAATACAGG CTACAAAAGA AGTTATCAGC 600
CAAGAAACGC CTATTCAAAA AGACTCGTTA TTTTGA 636
(2) INFORMATION FOR SEQ ID NO:87:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 1221 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...1221
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 87:
GTGATTGGCC CCCTTAGCAG CCAACTCAAC GCTATTAAGT GGGGCGAGTT CAAATTAGGG 60 GATTTGTTTG AAGCGAGTAA CGGCGATTTT GACATTCAAA AACGCCACAT CAATCATAAG 120
GGCGAATTTG TCATCACCGC AGGGCTTAGC AATAATGGCG TTTTAGGGCA AAGCGATATA 180
AAAGCAAAAG TTTTTGAAAG CCATACCATT ACTATTGACA TGTTTGGTTG CGCGTTTTAT 240
CGCAGTTTTG CTTATAAAAT GGTAACACAT GCTAGGGTAT TTTCTCTCAA ACCTAAATTT 300
GAAATCAACC ATAAAATCGG CTTGTTTTTA TCCACGCTAT TTTTTGGTTA CCATAAAAAA 360 TTCGGCTATG AAAACATGTG TTCATGGGCA AAAATTAAAA ACGATAAAGT CATTCTACCC 420
CTAAAACCCA CCGCTAACAC TCAAACCCTT GAGGGTATTG ATTTTGATTT CATGGAAAAA 480
TTCATAGCCG AACTTGAGCA GTGTCGGCTC GCCGAACTTC AGGCTTATTT AAAAGCTACA 540
GGGCTAGAAA ACACCACCCT TTCTAACGAT GAAGAAAATG CCCTTAATGT TTTCAATAAT 600
TCTGGGGGGG GGGGGGGTAA TACCCCATGC GGCTTGACAT GGCAACACTT CAAATTAGGG 660 GATTTGTTTG AAATTGAAAA AACCTTAAGC TTTAATAAAG ACGCTTTAAC GCAAGGACAA 720
GATTACGATT ATATTACAAG AACTTCGCAA AATCAAGGCG TTTTGCAAAC TACAGGATTT 780
GTCAATGCAG AAAATTTAAA CCCACCATTT ACTTGGAGTT TAGGGCTTTT GCAAATGGAT 840
TTTTTCTATC GTAAAAAGTC ATGGTATGCG GGACAATTCA TGCGAAAAAT CACACCAAAA 900 ACTGAAATTA AAAATAAAAT TAATTCACGC ATAGCCCACT ATTTCACAAC GCTTTTAAAC 960
GCCTTAAAAC GCCCTTTATT GAGTGTATTA GTTAGGGATA TTGATAAAAC TTTTAGGGAG 1020
CAAAAAATCC AACTACCCCT AAAACCCACC GCTAAAACTC AAAGCCTTGA TGGTATTGAT 1080
TTTGATTTCA TGCACACCCT AATCAACGCC CTGATGAAGC AAACCATTCA AGGCGTGGTT 1140
CAATACTGCG ACGCTAAAAT ACAGGCTACA AAAGAAGTTA TCAGCCAAGA AACGCCTATT 1200 CAAAAAGACT CGTTATTTTG A 1221
(2) INFORMATION FOR SEQ ID NO: 88:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 828 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...828
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:88: ATGAGTAAGA GTTTATACCA AACTTTAAAC GTGAGCGAAA ACGCCAGCCA AGATGAAATC 60
AAAAAATCCT ACCGCCGTTT AGCCAGGCAA TACCACCCGG ATTTGAATAA AACCAAAGAA 120
GCCGAAGAGA AATTCAAAGA AATCAACGCC GCTTATGAAA TTTTGAGCGA TGAAGAAAAA 180
CGCCGCCAAT ACGATCAATT TGGCGACAAC ATGTTTGGCG GGCAGAATTT CAGCGATTTT 240
GCCAGAAGCC GTGGTCCTAG TGAAGATTTA GATGATATTT TAAGCTCTAT TTTTGGGAAA 300 GGAGGCTTTT CGCAAAGATT TTCTCAAAAT TCGCAAGGCT TTTCTGGCTT TAATTTTTCC 360
AATTTCGCCC CTGAAAATTT AGATGTAACC GCTATTTTAA ATGTCTCTGT TTTAGACACC 420
CTTTTAGGCA ATAAAAAACA AGTGAGCGTC AATAATGAGA CTTTTAGCCT TAAAATCCCT 480
ATCGGCGTGG AAGAGGGCGA AAAGATTAGG GTTCGCAACA AAGGGAAAAT GGGGCGAACG 540
GGTAGGGGCG ATTTGCTCTT ACAGATCCAT ATTGAAGAAG ATGAAATGTA TAGGCGCGAA 600 AAAGACGATA TTATCCAAAT CTTTGATTTA CCCTTAAAAA CGGCTCTTTT TGGAGGGAAA 660
ATTGAAATCG CTACTTGGCA TAAAACCTTA ACCCTAACCA TTCCCCCTAA CACCAAACJC 720
ATGCAAAAAT TCCGCATCAA AGACAAAGGG ATCAAAAGCA GAAAAACTTC GCATGTGGGG 780
GATTGTATTG CAAGCTCGTT TGATCTGCTA AAATTGAAAC GCTTCTAA 828 (2) INFORMATION FOR SEQ ID NO: 89:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 837 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...837
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 89:
ATGAGTAAGA GTTTATACCA AACTTTAAAC GTGAGCGAAA ACGCCAGCCA AGATGAAATC 60 AAAAAATCCT ACCGCCGTTT AGCCAGGCAA TACCACCCGG ATTTGAATAA AACCAAAGAA 120
GCCGAAGAGA AATTCAAAGA AATCAACGCC GCTTATGAAA TTTTGAGCGA TGAAGAAAAA 180
CGCCGCCAAT ACGATCAATT TGGCGACAAC ATGTTTGGCG GGCAGAATTT CAGCGATTTT 240
GCCAGAAGCC GTGGTCCTAG TGAAGATTTA GATGATATTT TAAGCTCTAT TTTTGGGAAA 300
GGAGGCTTTT CGCAAAGATT TTCTCAAAAT TCGCAAGGCT TTTCTGGCTT TAATTTTTCC 360 AATTTCGCCC CTGAAAATTT AGATGTAACC GCTATTTTAA ATGTCTCTGT TTTAGACACC 420
CTTTTAGGCA ATAAAAAACA AGTGAGCGTC AATAATGAGA CTTTTAGCCT TAAAATCCCT 480
ATCGGCGTGG AAGAGGGCGA AAAGATTAGG GTTCGCAACA AAGGGAAAAT GGGGCGAACG 540
GGTAGGGGCG ATTTGCTCTT ACAGATCCAT ATTGAAGAAG ATGAAATGTA TAGGCGCGAA 600
AAAGACGATA TTATCCAAAT CTTTGATTTA CCCTTAAAAA CGGCTCTTTT TGGAGGGAAA 660 ATTGAAATCG CTACTTGGCA TAAAACCTTA ACCCTAACCA TTCCCCCTAA CACCAAAGCC 720
ATGCAAAAAT TCCGCATCAA AGACAAAGGG ATCAAAAGCA GAAAAACTTC GCATGTGGGG 780
GATTGTATTG CAAGCTCGTT TGATCTGCCT AAAATTGAAA CGCTTCTAAT GAGTTGA 837
(2) INFORMATION FOR SEQ ID NO: 90:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 699 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...699 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 90:
GTGGTTCAAA AATTTAATTT TTATAAGACA GGTGGCATGC GTTTAAAACA TTTTAAGACA 60
TTCCTTTTTA TCACAATGGC GGTGATTGTG ATAGGCACTG GTTGTGCGAA TAAAAAGAAA 120 AAAAAAGATG AATACAACAA ACCGGCGATC TTTTGGTATC AAGGGATTTT GAGAGAAATT 180
CTTTTTGCTA ATTTAGAAAC AGCGGACAAT TACTATTCTT CCTTACAGAG CGAACACATC 240
AATTCCCCCC TTGTCCCAGA AGCTATGCTA GCTTTAGGGC AAGCGCACAT GAAAAAGAAA 300
GAGTATGTTT TAGCGTCTTT TTACTTTGAT GAATACATCA AGCGCTTTGG GACGAAGGAC 360
AATGTGGATT ATTTGACCTT TTTGAAACTG CAATCGCATT ATTACGCTTT CAAAAACCAT 420 TCTAAAGACC AGGAATTTAT CTCTAATTCT ATTGTGAGTT TAGGCGAATT TATAGAAAAA 480
TACCCTAACA GCCGTTACCG CCCCTATGTA GAATACATGC AAATCAAATT CATTTTAGGG 540
CAAAATGAGC TCAATCGCGC GATCGCGAAT GTCTATAAAA AACGCCACAA GCCCGAGGGC 600
GTGAAACGCT ATTTAGAAAG GATAGATGAG ACTTTAGAAA AAGAGACTAA ACCCAAACCA 660
TCGCACATGC CTTGGTATGT GTTAATTTTT GATTGGTAG 699
(2) INFORMATION FOR SEQ ID NO: 91:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 345 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...345
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 91:
ATGCGTTTTT TGAATAACAA ACATAGAGAA AAGGGCTTAA AGGCTGAAGA AGAAGCTTGC 60 GGGTTTTTAA AAACGCTGGG TTTTGAAATG ATAGAGAGGA ACTTTTTTTC ACAATTTGGT 120
GAAATTGATA TTATCGCTTT GAAAAAAGGG GTTTTGCATT TCATTGAAGT CAAAAGCGGG 180
GAAAATTTTG ATCCCATTTA TGCGATCACG CCGAGCAAAT TAAAAAAGAT GATTAAAACG 240
ATCCGCTGTT ATTTGTCTCA AAAAGATCCC AATAGCGATT TTTGCATTGA CGCTCTTATT 300
GTGAAAAATG GTAAATTTGA GCTTTTAGAA AATATCACTT TTTAG 345
(2) INFORMATICS 'OR SEQ ID NO : 92 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 306 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...306
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 92 : ATGGGCAGCA TTGGGGCTAT GACTAAAGGG AGCTCTGATA GGTATTTTCA AGAGGGCGTG 60
GCGAGTGAAA AATTAGTCCC AGAAGGCATT GAGGGGCGTG TGCCTTATCG TGGTAAGGTT 120
TCGGATATGA TTTTCCAATT AGTAGGGGGC GTGCGTTCTT CTATGGGGTA TCAGGGGGCG 180
AAGAATATTT TGGAATTGTA TCAAAACGCT GAATTTGTAG AAATCACTAG CGCGGGGTTA 240
AAAAAAAGCC ATGTGCATGG CGTGGATATT ACTAAAGAAG CCCCTAATAT TATGGGTGAA 300 TTTTAA 306
(2) INFORMATION FOR SEQ ID NO: 93:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1446 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...1446
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 93: ATGAGAATTT TACAAAGGGC TTTGACTTTT GAAGACGTGT TGATGGTGCC TAGAAAATCC 60
AGCGTTTTAC CTAAAGATGT GAGCTTAAAG TCTCGCCTAA CCAAAAACAT TGGTTTGAAT 120
ATCCCTTTTA TTAGTGCGGC TATGGATACG GTTACAGAGC ATAAAACCGC TATCGCTATG 180
GCGCGCCTTG GGGGTATTGG CATCGTGCAT AAAAACATGG ATATTCAAAC GCAAGTCAAA 240
GAAATCACTA AAGTTAAAAA AAGCGAGAGC GGGGTGATTA ATGATCCTAT TTTTATCCAT 300 GCGCACAGGA CGCTAGCGGA CGCTAAAGTC ATAACGGATA ATTATAAGAT TTCAGGCGTG 360
CCTGTGGTAG ATGATAAGGG GTTGTTGATT GGGATTTTAA CCAACAGAGA CGTGCGTTTT 420
GAAACCGATT TGAGTAAAAA AGTGGGCGAT GTGATGACTA AAATGCCTTT AGTTACCGCT 480
CATGTGGGCA TTAGCTTAGA TGAAGCGAGC GATTTGATGC ACAAGCATAA GATTGAAAAA 540
TTGCCCATTG TGGATAAAGA TAATGTTTTA AAAGGCTTGA TCACGATCAA AGACATTCAA 600 AAACGCATTG AATACCCTGA GGCCAATAAA GATGATTTTG GGAGGTTGAG AGTGGGGGCG 660
GCTATTGGAG TGGGGCAGTT GGATAGGGCT GAAATGTTAG TTAAAGCGGG GGTGGATGCG 720
TTGGTGTTAG ACAGCGCGCA TGGGCATTCA GCCAATATTT TACACACTTT AGAAGAGATT 780
AAAAAAAGCT TGGTAGTGGA TGTGATTGTG GGGAATGTGG TTACTAAAGA AGCCACAAGC 840 GATTTGATTA GCGCGGGAGC GGACGCTGTT AAAGTGGGTA TTGGGCCAGG AAGCATTTGC 900
ACCACTAGGA TTGTGGCCGG GGTGGGAATG CCCCAAGTGA GCGCAATTGA TAATTGCGTG 960
GAAGTGGCGT CTAAATTTGA TATTCCTGTG ATTGCCGATG GAGGGATCCG CTATTCAGGC 1020
GATGTGGCTA AGGCTCTAGC TTTAGGAGCA TCAAGCGTGA TGATAGGCTC TTTACTCGCT 1080
GGCACAGAAG AATCTCCAGG GGATTTTATG ATTTACCAAG GGAGGCAATA TAAAAGCTAT 1140 AGGGGCATGG GCAGCATTGG GGCTATGACT AAAGGGAGCT CTGATAGGTA TTTTCAAGAG 1200
GGCGTGGCGA GTGAAAAATT AGTCCCAGAA GGCATTGAGG GGCGTGTGCC TTATCGTGGT 1260
AAGGTTTCGG ATATGATTTT CCAATTAGTA GGGGGCGTGC GTTCTTCTAT GGGGTATCAG 1320
GGGGCGAAGA ATATTTTGGA ATTGTATCAA AACGCTGAAT TTGTAGAAAT CACTAGCGCG 1380
GGGTTAAAAG AAAGCCATGT GCATGGCGTG GATATTACTA AAGAAGCCCC TAATTATTAT 1440 GGGTGA 1446
(2) INFORMATION FOR SEQ ID NO: 94:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 615 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...615
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 94: ATGCAAGGGT TTCTTTTACA AACACAAAGC ATAAGAGATG AAGATTTGAT CGTGCACGTT 60
TTAACCAAAA ACCAGCTCAA AACCCTCTAT CGTTTCTATG GCAAACGCCA CAGCGTGCTG 120
AATGTGGGTC GTAAAATTGA TTTTGAAGAA GAAAACGATG ATAAATTTTT ACCCAAGTTA 180
AGGAATATTT TGCATTTAGG CTATATTTGG GAAAGAGAAA TGGAGCGCTT GTTTTTTTGG 240
CAACGCTTTT GCGCTCTTTT GTTCAAGCAT TTAGAGGGCG TGCATTCTTT AGATAGCATC 300 TATTTTGACA CTTTAGATGA TGGGGCTAGC AAACTCTCCA AACAGCACCC CTT^AGAGTG 360
ATTTTAGAAA TGTATGCAGT CCTTTTGAAT TTTGAAGGGC GCTTGCAAAG -T .CAATTCT 420
TGTTTTTTAT GCGATGCAAA ATTAGAGCGT TCTGTCGCTT TAGCGCAAGG GTTTATTTTA 480
GCGCACCCCT CTTGCTTGAA AGCTAAAAGC TTGGATTTAG AAAAAATCCA AGCTTTTTTC 540
CGCACTCAAA GCACGATTGA TCTAGAAACA GAAGAAGTGG AAGAATTATG GCGCACGCTG 600 AATTTAGGGT TTTGA 615
(2) INFORMATION FOR SEQ ID NO: 95: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 249 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...249
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 95:
ATGGGCGTCG GACGGGTCGG CAATATGGCA CTGTTGGCGT GTGCAGGTCC GATGGGCATC 60
GGCGCTATTG CTATCGCCAT TAACGGCGGC AGACAACGGT CGCGGATGTT GGTGGTCGAT 120
ATAGACGACA AACGTCTGGA GCAGGTACAG AAGATGCTGC CGGGGAATTG GCGGCCAGTA 180
ACGGCATTGA GCTGGTGTCT GTGCATACCA AAGCGAGGAG CGATCCGTGC CAGATGCTGC 240 GAGCGCTGA 249
(2) INFORMATION FOR SEQ ID NO: 96:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 204 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_featυ re
(B) LOCATION 1...204
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 96: TTGTCCGGTA CAGCCGTGAG TTGCCGGTGC ACATGCCGCA TACAGTTGGT ATTGGTGCGC 60
ACCAGCATCC CGGTTGTTAT CGGGTGCTCA TGCCCATTCC TTTCCAGTAT TGGGTTCACA 120
ACGGGAACCC ACCAATCACC CGTTAAACGC TGCGGGGTTA ACGCCGGAAA AACACCGTCA 180
AAAAAACATT TGCATTTAAA CTAA 204 (2) INFORMATION FOR SEQ ID NO: 97:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 345 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...345
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 97:
GTGTGGCTGG CGGCGCTGGG CTTCCTGATC ACCGCGGTGG GGCTGCCGGT GATCACCGTG 60 ATCGCCCTGG CCAAGGTCGG CGGTTCGTCG ACGCCCTCAG CCATCCGATC GGCAGGTATG 120
CCGGCGGCCT GCTGGCGGCG GTCTGCTACC TGGCGGTCGG CCCGCTGTTC GCCATTCCGC 180
GCACCGCCAC GGTGTCCTTC GAAGGTCAGC GTGGTGCCGC TGCTCGGCGA AGAAGCGGCA 240
CGGCGCTGTT CGTCTACAGC CTGGCGTACT TCCTCCTCGC CCTGGCCATC TCCCTCTACC 300
CCGGTCGCCT GCTGGACACC GTCGGACGCT TCCTCGCCCC GCTGA 345
(2) INFORMATION FOR SEQ ID NO:98:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 228 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...228
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 98:
Met Arg Phe Lys Gly Ser Arg Val Glu Ala Phe Leu Gly Ala Leu Glu 1 5 10 15
Phe Gin Glu Asn Glu Tyr Glu Glu Phe Lys Glu Leu Tyr Glu Ser Leu 20 25 30 Lys Thr Lys Gin Lys Pro His Thr Leu Phe lie Ser Cys Val Asp Ser
35 40 45
Arg Val Val Pro Asn Leu lie Thr Gly Thr Gin Pro Gly Glu Leu Tyr 50 55 60 Val lie Arg Asn Met Gly Asn Val lie Pro Pro Lys Thr Ser Tyr Lys 65 70 75 80
Glu Ser Leu Ser Thr lie Ala Ser Val Glu Tyr Ala He Ala His Val
85 90 95
Gly Val Gin Asn Leu He He Cys Gly His Ser Asp Cys Gly Ala Cys 100 105 110
Gly Ser He His Leu He His Asp Glu Thr Thr Lys Ala Lys Thr Pro
115 120 125
Tyr He Ala Asn Trp He Gin Phe Leu Glu Pro He Lys Glu Glu Leu
130 135 140 Lys Asn His Pro Gin Phe Ser Asn His Phe Ala Lys Arg Ser Trp Leu
145 150 155 160
Thr Glu Arg Leu Asn Ala Arg Leu Gin Leu Asn Asn Leu Leu Ser Tyr
165 170 175
Asp Phe He Gin Glu Arg Val He Asn Asn Glu Leu Lys He Phe Gly 180 185 190
Trp His Tyr He He Glu Thr Gly Arg He Tyr Asn Tyr Asn Phe Glu
195 200 205
Ser His Phe Phe Glu Pro He Glu Glu Thr He Lys Gin Arg He Ser 210 215 220 His Glu Asn Phe 225
(2) INFORMATION FOR SEQ ID NO: 99: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 221 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...221
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 99:
Val Glu Ala Phe Leu Gly Ala Leu Glu Phe Gin Glu Asn Glu Tyr Glu 1 5 10 15 Glu Phe Lys Glu Leu Tyr Glu Ser Leu Lys Thr Lys Gin Lys Pro His 20 25 30
Thr Leu Phe He Ser Cys Val Asp Ser Arg Val Val Pro Asn Leu He
35 40 45
Thr Gly Thr Gin Pro Gly Glu Leu Tyr Val He Arg Asn Met Gly Asn 50 55 60
Val He Pro Pro Lys Thr Ser Tyr Lys Glu Ser Leu Ser Thr He Ala 65 70 75 80
Ser Val Glu Tyr Ala He Ala His Val Gly Val Gin Asn Leu He He 85 90 95
Cys Gly His Ser Asp Cys Gly Ala Cys Gly Ser He His Leu He His
100 105 110
Asp Glu Thr Thr Lys Ala Lys Thr Pro Tyr He Ala Asn Trp He Gin 115 120 125 Phe Leu Glu Pro He Lys Glu Glu Leu Lys Asn His Pro Gin Phe Ser 130 135 140
Asn His Phe Ala Lys Arg Ser Trp Leu Thr Glu Arg Leu Asn Ala Arg 145 150 155 160
Leu Gin Leu Asn Asn Leu Leu Ser Tyr Asp Phe He Gin Glu Arg Val 165 170 175
He Asn Asn Glu Leu Lys He Phe Gly Trp His Tyr He He Glu Thr
180 185 190
Gly Arg He Tyr Asn Tyr Asn Phe Glu Ser His Phe Phe Glu Pro He 195 200 205 Glu Glu Thr He Lys Gin Arg He Ser His Glu Asn Phe 210 215 220
(2) INFORMATION FOR SEQ ID NO: 100: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 335 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...335
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 100:
Met Leu Val Thr Arg Phe Lys Lys Ala Phe He Ser Tyr Ser Leu Gly 1 5 10 15 Val Leu Val Val Ser Leu Leu Leu Asn Val Cys Asn Ala Ser Ala Gin 20 25 30
Glu Val Lys Val Lys Asp Tyr Phe Gly Glu Gin Thr He Lys Leu Pro
35 40 45
Val Ser Lys He Ala Tyr He Gly Ser Tyr Val Glu Val Pro Ala Met 50 55 60
Leu Asn Val Trp Asp Arg Val Val Gly Val Ser Asp Tyr Ala Phe Lys 65 70 75 80
Asp Asp He Val Lys Ala Thr Leu Lys Gly Glu Asp Leu Lys Arg Val 85 90 95 Lys His Met Ser Thr Asp His Thr Ala Ala Leu Asn Val Glu Leu Leu
100 105 110
Lys Lys Leu Ser Pro Asp Leu Val Val Thr Phe Val Gly Asn Pro Lys 115 120 125 Ala Val Glu His Ala Lys Lys Phe Gly He Ser Phe Leu Ser Phe Gin 130 135 140
Glu Thr Thr He Ala Glu Ala Met Gin Ala Met Gin Ala Gin Ala Thr 145 150 155 160
Val Leu Glu He Asp Ala Ser Lys Lys Phe Ala Lys Met Gin Glu Thr 165 170 175
Leu Asp Phe He Ala Glu Arg Leu Lys Gly Val Lys Lys Lys Lys Gly
180 185 190
Val Glu Leu Phe His Lys Ala Asn Lys He Ser Gly His Gin Ala He 195 200 205 Ser Ser Asp He Leu Glu Lys Gly Gly He Asp Asn Phe Gly Leu Lys 210 215 220
Tyr Val Lys Phe Gly Arg Ala Asp He Ser Val Glu Lys He Val Lys 225 230 235 240
Glu Asn Pro Glu He He Phe He Trp Trp Val Ser Pro Leu Thr Pro 245 250 255
Glu Asp Val Leu Asn Asn Pro Lys Phe Ser Thr He Lys Ala He Lys
260 265 270
Asn Lys Gin Val Tyr Lys Leu Pro Thr Met Asp He Gly Gly Pro Arg 275 280 285 Ala Pro Leu He Ser Leu Phe He Ala Leu Lys Ala His Pro Glu Ala 290 295 300
Phe Lys Gly Val Asp He Asn Ala He Val Lys Asp Tyr Tyr Lys Val 305 310 315 320
Val Phe Asp Leu Asn Asp Ala Glu He Glu Pro Phe Leu Trp His 325 330 335
(2) INFORMATION FOR SEQ ID NO: 101:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 274 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...274 (xi) SEQUENCE DESCRIPTION : SEQ ID NO : 101 :
Met Leu Val Thr Arg Phe Lys Lys Ala Phe He Ser Tyr Ser Leu Gly
1 5 10 15
Val Leu Val Val Ser Leu Leu Leu Asn Val Cys Asn Ala Ser Ala Gin 20 25 30
Glu Val Lys Val Lys Asp Tyr Phe Gly Glu Gin Thr He Lys Leu Pro
35 40 45
Val Ser Lys He Ala Tyr He Gly Ser Tyr Val Glu Val Pro Ala Met 50 55 60
Leu Asn Val Trp Asp Arg Val Val Gly Val Ser Asp Tyr Ala Phe Lys 65 70 75 80
Asp Asp He Val Lys Ala Thr Leu Lys Gly Glu Asp Leu Lys Arg Val 85 90 95 Lys His Met Ser Thr Asp His Thr Ala Ala Leu Asn Val Glu Leu Leu 100 105 110
Lys Lys Leu Ser Pro Asp Leu Val Val Thr Phe Val Gly Asn Pro Lys
115 120 125
Ala Val Glu His Ala Lys Lys Phe Gly He Ser Phe Leu Ser Phe Gin 130 135 140
Glu Thr Thr He Ala Glu Ala Met Gin Ala Met Gin Ala Gin Ala Thr
145 150 155 160
Val Leu Glu He Asp Ala Ser Lys Lys Phe Ala Lys Met Gin Glu Thr
165 170 175 Leu Asp Phe He Ala Asp Arg Leu Lys Gly Val Lys Lys Lys Lys Gly
180 185 190
Val Glu Leu Phe His Lys Ala Asn Lys He Ser Gly His Gin Ala He
195 200 205
Asn Ser Asp He Leu Gin Gin Gly Gly He Asp Asn Phe Gly Leu Lys 210 215 220
Tyr Val Lys Phe Gly Arg Ala Asp He Ser Val Glu Lys He Val Lys 225 230 235 240
Glu Asn Pro Glu He He Phe He Arg Trp Val Thr Pro Leu Thr Pro 245 250 255 Asp Tyr Val Leu Asn Asn Pro Lys Phe Ser Thr He Asn Ala He Lys 260 265 270
Asn He
(2) INFORMATION FOR SEQ ID NO:102:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 428 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...428
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:102: Met Lys Lys Lys Phe Leu Ser Leu Thr Leu Gly Ser Leu Leu Val Ser 1 5 10 15
Ala Leu Ser Ala Glu Asp Asn Gly Phe Phe Val Ser Ala Gly Tyr Gin 20 25 30 He Gly Glu Ser Ala Gin Met Val Lys Asn Thr Lys Gly He Gin Asp 35 40 45
Leu Ser Asp Ser Tyr Glu Arg Leu Asn Asn Leu Leu Thr Asn Tyr Ser
50 55 60
Val Leu Asn Ala Leu He Arg Gin Ser Ala Asp Pro Asn Ala He Asn 65 70 75 80
Asn Ala Arg Gly Asn Leu Asn Ala Ser Ala Lys Asn Leu He Asn Asp
85 90 95
Lys Lys Asn Ser Pro Ala Tyr Gin Ala Val Leu Leu Ala Leu Asn Ala 100 105 110 Ala Ala Gly Leu Trp Gin Val Met Ser Tyr Ala He Ser Pro Cys Gly 115 120 125
Pro Gly Lys Asp Thr Ser Lys Asn Gly Gly Val Gin Thr Phe His Asn
130 135 140
Thr Pro Ser Asn Gin Trp Gly Gly Thr Thr He Thr Cys Gly Thr Thr 145 150 155 160
Gly Tyr Glu Pro Gly Pro Tyr Ser He Leu Ser Thr Glu Asn Tyr Ala
165 170 175
Lys He Asn Lys Ala Tyr Gin He He Gin Lys Ala Phe Gly Ser Ser 180 185 190 Gly Lys Asp He Pro Ala Leu Ser Asp Thr Asn Thr Glu Leu Lys Phe 195 200 205
Thr He Asn Lys Asn Asn Gly Asn Thr Asn Thr Asn Asn Asn Gly Glu
210 215 220
Glu He Val Thr Lys Asn Asn Ala Gin Val Leu Leu Glu Gin Ala Ser 225 230 235 240
Thr He He Thr Thr Leu Asn Ser Ala Cys Pro Trp He Asn Asn Gly
245 250 255
Gly Ala Gly Gly Ala Ser Ser Gly Ser Leu Trp Glu Gly He Tyr Leu 260 265 270 Lys Gly Asp Gly Ser Ala Cys Gly He Phe Lys Asn Glu He Ser Ala 275 280 285
He Gin Asp Met He Lys Asn Ala Ala He Ala Val Glu Gin Ser Lys
290 295 300
He Val Ala Ala Asn Ala Gin Asn Gin Arg Asn Leu Asp Thr Gly Lys 305 310 315 320
Thr Phe Asn Pro Tyr Lys Asp Ala Asn Phe Ala Gin Ser Met Phe Ala
325 330 335
Asn Ala Lys Ala Gin Ala Glu He Leu Asn Arg Ala Gin Ala Val Val 340 345 350 Lys Asp Phe Glu Arg He Pro Ala Glu Phe Val Lys Asp Ser Leu Gly 355 360 365
Val Cys His Glu Val Gin Asn Gly His Leu Arg Gly Thr Pro Ser Gly
370 375 380
Thr Val Thr Asp Asn Thr Trp Gly Ala Gly Cys Ala Tyr Val Gly Glu 385 390 395 400
Thr Val Thr Asn Leu Lys Asp Ser He Ala His Phe Gly Asp Gin Ala
405 410 415
Glu Arg He His Asn Ala Arg Asn Leu Ala Thr Leu 420 425 (2) INFORMATION FOR SEQ ID NO:103:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 178 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...178 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:103:
Met Asn Pro Leu Lea Gin Asp Tyr Ala Arg He Leu Leu Glu Trp Asn 1 5 10 15
Gin Thr His Asn Leu Ser Gly Ala Arg Asn Leu Ser Glu Leu Glu Pro 20 25 30
Gin He Thr Asp Ala Leu Lys Pro Leu Glu Phe Val Lys Asp Phe Lys
35 40 45
Ser Cys Leu Asp He Gly Ser Gly Ala Gly Leu Pro Ala He Pro Leu 50 55 60 Ala Leu Glu Lys Pro Glu Ala Gin Phe He Leu Leu Glu Pro Arg Val 65 70 75 80
Lys Arg Ala Ala Phe Leu Asn Tyr Leu Lys Ser Val Leu Pro Leu Asn
85 90 95
Asn He Glu He He Lys Lys Arg Leu Glu Asp Tyr Gin Asn Leu Leu 100 105 110
Gin Val Asp Leu He Thr Ser Arg Ala Val Ala Ser Ser Ser Phe Leu
115 120 125
He Glu Lys Ser Gin Arg Phe Leu Lys Asp Lys Gly Tyr Phe Leu Phe
130 135 140 Tyr Lys Gly Glu Gin Leu Lys Asn Glu He Ala Tyr Lys Thr Thr Glu
145 150 155 160
Cys Phe Met His Gin Lys Arg Val Tyr Phe Tyr Lys Ser Lys Glu Ser
165 170 175
Leu Cys
(2) INFORMATION FOR SEQ ID NO: 104:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 240 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...240
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 104:
Leu Gly Leu Lys Lys Arg Ala He Leu Trp Ser Leu Met Gly Phe Cys 1 5 10 15 Ala Gly Leu Ser Ala Leu Asp Tyr Asp Thr Leu Asp Pro Lys Tyr Tyr 20 25 30
Lys Tyr He Lys Tyr Tyr Lys Ala Tyr Glu Asp Lys Glu Val Glu Glu
35 40 45
Leu He Arg Asp Leu Lys Arg Ala Asn Ala Lys Ser Gly Leu He Leu 50 55 60
Gly He Asn Thr Gly Phe Phe Tyr Asn His Glu He Met Val Lys Thr 65 70 75 80
Asn Ser Ser Ser He Thr Gly Asn He Leu Asn Tyr Leu Phe Ala Tyr 85 90 95 Gly Leu Arg Phe Gly Tyr Gin Thr Phe Arg Pro Ser Phe Phe Ala Arg 100 105 110
Leu Val Lys Pro Asn He He Gly Arg Arg He Tyr He Gin Tyr Tyr
115 120 125
Gly Gly Ala Pro Lys Lys Ala Gly Phe Gly Ser Val Gly Phe Gin Ser 130 135 140
Val Met Leu Asn Gly Asp Phe Leu Leu Asp Phe Pro Leu Pro Phe Val
145 150 155 160
Gly Lys Tyr Leu Tyr Met Gly Gly Tyr Met Gly Leu Gly Leu Gly Val
165 170 175 Val Ala His Gly Val Asn Tyr Thr Ala Glu Trp Gly Met Ser Phe Asn
180 185 190
Ala Gly Leu Ala Leu Thr Val Leu Glu Lys Asn Arg He Glu Phe Glu
195 200 205
Phe Lys He Leu Asn Asn Phe Pro Phe Leu Gin Ser Asn Ser Ser Lys 210 215 220
Glu Thr Trp Trp Gly Ala He Ala Ser He Gly Tyr Gin Tyr Val Phe 225 230 235 240
(2) INFORMATION FOR SEQ ID NO: 105:
(i) SEQUENCE HARACTERISTICS:
(A) LENGTH: 313 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...313
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 105: Leu Lys Leu Lys Tyr Trp Leu Val Tyr Leu Ala Phe He He Gly Leu 1 5 10 15
Gin Ala Thr Asp Tyr Asp Asn Leu Glu Glu Glu Asn Gin Gin Leu Asp
20 25 30
Glu Lys He Asn Asn Leu Lys Arg Gin Leu Thr Glu Lys Gly Val Ser 35 40 45
Pro Lys Glu Met Asp Lys Asp Lys Phe Glu Glu Glu Tyr Leu Glu Arg
50 55 60
Thr Tyr Pro Lys He Ser Ser Lys Lys Arg Lys Lys Leu Leu Lys Ser 65 70 75 80 Phe Ser He Ala Asp Asp Lys Ser Gly Val Phe Leu Gly Gly Gly Tyr
85 90 95
Ala Tyr Gly Glu Leu Asn Leu Ser Tyr Gin Gly Glu Met Leu Asp Arg
100 105 110
Tyr Gly Ala Asn Ala Pro Ser Ala Phe Lys Asn Asn He Asn He Asn 115 120 125
Ala Pro Val Ser Met He Ser Val Lys Phe Gly Tyr Gin Lys Tyr Phe
130 135 140
Val Pro Tyr Phe Gly Thr Arg Phe Tyr Gly Asp Leu Leu Leu Gly Gly 145 150 155 160 Gly Ala Leu Lys Glu Asn Ala Leu Lys Gin Pro Val Gly Ser Phe Phe
165 170 175
Tyr Val Leu Gly Ala Met Asn Thr Asp Leu Leu Phe Asp Met Pro Leu
180 185 190
Asp Phe Lys Thr Lys Lys His Phe Leu Gly Val Tyr Ala Gly Phe Gly 195 200 205
He Gly Leu Met Leu Tyr Gin Asp Lys Pro Asn Gin Asn Gly Arg Asn
210 215 220
Leu He Val Gly Gly Tyr Ser Ser Pro Asn Phe Leu Trp Lys Ser Leu 225 230 235 240 He Glu Val Asp Tyr Thr Phe Asn Val Gly Val Ser Leu Thr Leu Tyr
245 250 255
Arg Lys His Arg Leu Glu He Gly Thr Lys Leu Pro He Ser Tyr Leu
260 265 270
Arg Met Gly Val Glu Glu Gly Ala He Tyr His Asn Lys Glu Asn Asp 275 280 285
Glu Arg Leu Leu He Ser Ala Asn Asn Gin Phe Lys Arg Ser Ser Phe
290 295 300
Leu Leu Val Asn Tyr Ala Phe He Phe 305 310
(2) INFORMATION FOR SEQ ID NO: 106:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 393 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...393 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:106:
Met Thr Ser Ala Ser Ser His Ser Phe Lys Glu Gin Asp Phe His He 1 5 10 15
Pro He Ala Phe Ala Phe Asp Lys Asn Tyr Leu He Pro Ala Gly Ala 20 25 30
Cys He Tyr Ser Leu Leu Glu Ser He Ala Lys Ala Asn Lys Lys He
35 40 45
Arg Tyr Thr Leu His Ala Leu Val Val Gly Leu Asn Glu Glu Asp Lys 50 55 60 Thr Lys Leu Asn Gin He Thr Glu Pro Phe Lys Glu Phe Ala Val Leu 65 70 75 80
Glu Val Lys Asp He Glu Pro Phe Leu Asp Thr He Pro Asn Pro Phe
85 90 95
Asp Glu Asp Phe Thr Lys Arg Phe Ser Lys Met Val Leu Val Lys Tyr 100 105 110
Phe Leu Ala Asp Leu Phe Pro Lys Tyr Ser Lys Met Val Trp Ser Asp
115 120 125
Val Asp Val He Phe Cys Asn Glu Phe Ser Ala Asp Phe Leu Asn He
130 135 140 Lys Glu Asp Asp Glu Asn Tyr Phe Tyr Gly Val Tyr Asp Lys He Tyr
145 150 155 160
Pro Tyr Glu Gly Phe Phe Tyr Cys Asn Leu Thr Tyr Gin Arg Lys Asn
165 170 175
Gin Phe Cys Lys Lys He Leu Glu He He Arg Ala Gin Lys He Asp 180 185 190
Lys Glu Pro Gin Leu Thr Glu Phe Cys Arg Ser Lys He Ala Pro Leu
195 200 205
Lys He Glu Tyr Cys He Phe Pro His Tyr Tyr Ser Leu Ser Glu Glu
210 215 220 His Leu Lys Gly Val Ala Asn Ala He Tyr His Asn Thr He Lys '3In
225 230 235 240
Ala Leu Arg Glu Pro He Val He Gin Tyr Asp Ser His Pro Tyr Phe
245 250 255
Gin He Lys Pro Trp Thr Tyr Pro Phe Gly Leu Lys Ala Asp Leu Trp 260 265 270
Leu Asn Ala Leu Ala Lys Thr Pro Phe Met Ser Asp Trp Ser Tyr Leu
275 280 285
He Thr Gly Gly Gly Gly He Gly Gly Glu Lys Trp His Tyr Tyr His 290 295 300 Gly He Ala Ala Tyr His Tyr Tyr Phe Pro Leu Trp Lys Ala Glu Glu
305 310 315 320
Gin He Ala His Asp Ala Leu Lys Thr Phe Leu Lys His Tyr Phe Leu
325 330 335 His He His Glu He Pro Gin Asn Ala Arg Arg Arg Leu Phe Lys Tyr
340 345 350
Cys He Ser He Pro Leu Lys Ser Phe He Ser Lys Thr Leu Lys Phe
355 360 365
Leu Lys Leu His Ala Leu Val Lys Lys He Leu He Gin Leu Lys Leu 370 375 380
Leu Lys Lys Asn Gin Ser Gin Asn Phe 385 390
(2) INFORMATION FOR SEQ ID NO: 107:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 435 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...435
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 107:
Leu He Phe Leu Lys Lys Ser Leu Cys Ala Leu Leu He Ser Gly Phe 1 5 10 15
Phe He Pro Pro Leu Met Lys Ala Ala Ser Phe Val Tyr Asp Leu Lys
20 25 30
Phe Met Ser Phe Asn Phe Asn Leu Ala Ser Pro Pro Asn Asn Pro Tyr 35 40 45 Trp Asn Ser Leu Thr Lys Met Gin Gly Arg Leu Met Pro Gin He Gly 50 55 60
Val Gin Leu Asp Lys Arg Gin Ala Leu Met Phe Gly Ala Trp Phe He 65 70 75 80
Gin Asn Leu His Thr His Tyr Ser Tyr Phe Pro Tyr Ser Trp Gly Val 85 90 95
Thr Met Tyr Tyr Gin Tyr He Gly L/f Asn Leu Arg Phe Phe Leu Gly
100 105 110
He Val Pro Arg Ser Tyr Gin He Gly His Tyr Pro Leu Ser Ala Phe 115 120 125 Lys Lys Leu Phe Trp Phe He Asp Pro Thr Phe Arg Gly Gly Ala Phe 130 135 140
Gin Phe Lys Pro Ala Tyr Asp Pro Asn Arg Trp Trp Asn Gly Trp Phe 145 150 155 160
Glu Gly Val Val Asp Trp Tyr Gly Gly Arg Asn Trp Asn Asn Gin Pro 165 170 175
Lys Lys Lys Asn Tyr Asp Phe Asp Gin Phe Leu Tyr Phe Val Ser Ser
180 185 190
Glu Phe Gin Phe Leu Lys Gly Tyr Leu Gly Leu Gly Gly Gin Leu Val 195 200 205
He Phe His Asn Ala Asn Ser His Ser Met Gly Asp Asn Tyr Pro Tyr
210 215 220
Gly Gly Asn Ser Tyr Leu Lys Pro Gly Asp Ala Thr Pro Gin Trp Pro 225 230 235 240 Asn Gly Tyr Pro Tyr Phe Ser Gin Lys Asp Asn Pro Gin Gly Gly Glu
245 250 255
He Gly Lys Tyr Ser Asn Pro Thr He Leu Asp Arg Val Tyr Tyr His
260 265 270
Ala Tyr Leu Lys Ala Asp Phe Lys Asn Leu Met Pro Tyr Met Asp Asn 275 280 285
He Phe Met Thr Phe Gly Thr Gin Ser Ser Gin Thr His Tyr Cys Val
290 295 300
Arg Tyr Ala Ser Glu Cys Lys Asn Ala Arg Phe Tyr Asn Ser Phe Gly 305 310 315 320 Gly Glu Phe Tyr Ala Gin Ala Gin Tyr Lys Gly Phe Gly He Phe Asn
325 330 335
Arg Tyr Tyr Phe Ser Asn Lys Pro Gin Met His Phe Tyr Ala Thr Tyr
340 345 350
Gly Gin Ser Leu Tyr Thr Gly Leu Pro Trp Tyr Arg Ala Pro Asn Phe 355 360 365
Asp Met He Gly Leu Tyr Tyr Leu Tyr Lys Asn Lys Trp Leu Ser Val
370 375 380
Arg Ala Asp Ala Phe Phe Ser Phe Val Gly Gly Gly Asp Gly Tyr His 385 390 395 400 Leu Tyr Gly Lys Gly Gly Lys Trp Phe Val Met Tyr Gin Gin Phe Leu
405 410 415
Thr Leu Thr He Asp Thr Arg Glu Leu He Asp Phe Val Lys Ser Lys
420 425 430
He Pro Lys 435
(2) INFORMATION FOR SEQ ID NO: 108:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 220 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) .irPOTHΞTICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...220 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:108:
Met Asn Lys Thr Thr He Lys He Leu Met Gly Met Ala Leu Leu Ser 1 5 10 15 Ser Leu Gin Ala Ala Glu Ala Glu Leu Asp Glu Lys Ser Lys Lys Pro 20 25 30
Lys Phe Ala Asp Arg Asn Thr Phe Tyr Leu Gly Val Gly Tyr Gin Leu
35 40 45
Ser Ala He Asn Thr Ser Phe Ser Thr Ser Ser He Asp Lys Ser Tyr 50 55 60
Phe Met Thr Gly Asn Gly Phe Gly Val Val Leu Gly Gly Lys Phe Val 65 70 75 80
Ala Lys Thr Gin Ala Val Glu His Val Gly Phe Arg Tyr Gly Leu Phe 85 90 95 Tyr Asp Gin Thr Phe Ser Ser His Lys Ser Tyr He Ser Thr Tyr Gly 100 105 110
Leu Glu Phe Ser Gly Leu Trp Asp Ala Phe Asn Ser Pro Lys Met Phe
115 120 125
Leu Gly Leu Glu Phe Gly Leu Gly He Ala Gly Ala Thr Tyr Met Pro 130 135 140
Gly Gly Ala Met His Gly He He Ala Gin Tyr Leu Gly Lys Glu Asn
145 150 155 160
Ser Leu Phe Gin Leu Leu Val Lys Val Gly Phe Arg Phe Gly Phe Phe
165 170 175 His Asn Glu He Thr Phe Gly Leu Lys Phe Pro Val He Pro Asn Lys
180 185 190
Lys Thr Glu He Val Asp Gly Leu Ser Ala Thr Thr Leu Trp Gin Arg
195 200 205
Leu Pro Val Ala Tyr Phe Asn Tyr He Tyr Asn Phe 210 215 220
(2) INFORMATION FOR SEQ ID NO: 109:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 116 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...116 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 109:
Leu Asn Leu His Phe Met Lys Gly Phe Val Met Ser Gly Leu Arg Thr
1 5 10 15
Phe Ser Cys Val Val Val Leu Cys Gly Ala Met Val Asn Val Ala Val 20 25 30
Ala Gly Pro Lys He Glu Ala Arg Gly Glu Leu Gly Lys Phe Val Gly
35 40 45
Gly Ala Val Gly Asn Phe Val Gly Asp Lys Met Gly Gly Phe Val Gly 50 55 60
Gly Ala He Gly Gly Tyr He Gly Ser Glu Val Gly Asp Arg Val Glu 65 70 75 80
Asp Tyr He Arg Gly Val Asp Arg Glu Pro Gin Asn Lys Glu Pro Gin 85 90 95 Thr Pro Arg Glu Pro He Arg Asp Phe Tyr Asp Tyr Gly Tyr Ser Phe 100 105 110
Gly His Ala Trp 115 (2) INFORMATION FOR SEQ ID NO: 110:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 436 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...436
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:110: Met Ser Arg Asp Phe Lys Phe Asp Ser Asn Tyr Leu Asn Val Asn Thr 1 5 10 15
Asn Pro Lys Leu Gly Pro Val Tyr Thr Asn Gin Asn Tyr Pro Gly Phe
20 25 30
Phe He Phe Asp His Leu Arg Arg Tyr Val Met Asn Ala Phe Glu Pro 35 40 45
Asn Leu Asn Leu Val Val Asn Thr Asn Lys Val Lys Gin Thr Phe Asn
50 55 60
Val Gly Met Arg Phe Met Thr Met Asp Met Phe He Arg Ser Asp Gin 65 70 75 80 Ser Thr Cys Glu Lys Thr Asp He He Asn Gly Val Cys Fis Met Pro
85 90 95
Pro Tyr Val Leu Ser Lys Thr Pro Asn Asn Asn Gin Glu Met Phe Asn
100 105 110
Asn Tyr Thr Ala Val Trp Leu Ser Asp Lys He Glu Phe Phe Asp Ser 115 120 125
Lys Leu Val He Thr Pro Gly Leu Arg Tyr Thr Phe Leu Asn Tyr Asn
130 135 140
Asn Lys Glu Pro Glu Lys His Asp Phe Ser Val Trp Thr Ser Lys Lys 145 150 155 160 Gln Arg Gin Asn Glu Trp Ser Pro Ala Leu Asn He Gly Tyr Lys Pro
165 170 175
Met Glu Asn Trp He Trp Tyr Ala Asn Tyr Arg Arg Ser Phe He Pro 180 185 190 Pro Gin His Thr Met Val Gly He Thr Arg Thr Asn Tyr Asn Gin He 195 200 205
Phe Asn Glu He Glu Val Gly Gin Arg Tyr Ser Tyr Lys Asn Leu Leu
210 215 220
Ser Phe Asn Thr Asn Tyr Phe Val He Phe Ala Lys Arg Tyr Tyr Ala 225 230 235 240
Gly Gly Tyr Ser Pro Gin Pro Val Asp Ala Arg Ser Gin Gly Val Glu
245 250 255
Leu Glu Leu Tyr Tyr Ala Pro He Arg Gly Leu Gin Phe His Val Ala 260 265 270 Tyr Thr Tyr He Asp Ala Arg He Thr Ser Asn Ala Asp Asp He Ala 275 280 285
Tyr Tyr Phe Thr Gly He Val Asn Lys Pro Phe Asp He Lys Gly Lys
290 295 300
Arg Leu Pro Tyr Val Ser Pro Asn Gin Phe He Phe Asp Met Met Tyr 305 310 315 320
Thr Tyr Lys His Thr Thr Phe Gly He Ser Ser Tyr Phe Tyr Ser Arg
325 330 335
Ala Tyr Ser Ser Met Leu Asn Gin Ala Lys Asp Gin Thr Val Cys Leu 340 345 350 Pro Leu Asn Pro Glu Tyr Thr Gly Gly Leu Lys Tyr Gly Cys Asn Ser 355 360 365
Val Gly Leu Leu Pro Leu Tyr Phe Val Leu Asn Val Gin Val Ser Ser
370 375 380
He Leu Trp Gin Ser Gly Arg His Lys He Thr Gly Ser Leu Gin He 385 390 395 400
Asn Asn Leu Phe Asn Met Lys Tyr Tyr Phe Arg Gly He Gly Thr Ser
405 410 415
Pro Thr Gly Arg Glu Pro Ala Pro Gly Arg Ser He Thr Ala Tyr Leu 420 425 430 Asn Tyr Glu Phe 435
(2) INFORMATION FOR SEQ ID NO: 111: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 767 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...767 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 111:
Met Lys Arg He Leu Val Ser Leu Ala Val Leu Ser His Ser Ala His 1 5 10 15
Ala Val Lys Thr His Asn Leu Glu Arg Val Glu Ala Ser Gly Val Ala
20 25 30
Asn Asp Lys Glu Ala Pro Leu Ser Trp Arg Ser Lys Glu Val Arg Asn 35 40 45 Tyr Met Gly Ser Arg Thr Val He Ser Asn Lys Gin Leu Thr Lys Ser 50 55 60
Ala Asn Gin Ser He Glu Glu Ala Leu Gin Asn Val Pro Gly Val His 65 70 75 80
He Arg Asn Ser Thr Gly He Gly Ala Val Pro Ser He Ser He Arg 85 90 95
Gly Phe Gly Ala Gly Gly Pro Gly His Ser Asn Thr Gly Met He Leu
100 105 110
Val Asn Gly He Pro He Tyr Val Ala Pro Tyr Val Glu He Gly Thr 115 120 125 Val He Phe Pro Val Thr Phe Gin Ser Val Asp Arg He Ser Val Thr 130 135 140
Lys Gly Gly Glu Ser Val Aig Tyr Gly Pro Asn Ala Phe Gly Gly Val 145 150 155 160
He Asn He He Thr Lys Gly He Pro Thr Asn Trp Glu Ser Gin Val 165 170 175
Ser Glu Arg Thr Thr Phe Trp Gly Lys Ser Glu Asn Gly Gly Phe Phe
180 185 190
Asn Gin Asn Ser Lys Asn He Asp Lys Ser Leu Val Asn Asn Met Leu 195 200 205 Phe Asn Thr Tyr Leu Arg Thr Gly Gly Met Met Asn Lys His Phe Gly 210 215 220
He Gin Ala Gin Val Asn Trp Leu Lys Gly Gin Gly Phe Arg Tyr Asn 225 230 235 240
Ser Pro Thr Asp He Gin Asn Tyr Met Leu Asp Ser Leu Tyr Gin He 245 250 255
Asn Asp Ser Asn Lys He Thr Ala Phe Phe Gin Tyr Tyr Ser Tyr Phe
260 265 270
Leu Thr Asp Pro Gly Ser Leu Gly He Ala Ala Tyr Asn Gin Asn Arg 275 280 285 Phe Gin Asn Asn Arg Pro Asn Asn Asp Lys Ser Gly Arg Ala Lys Arg 290 295 300
Trp Gly Ala Val Tyr Gin Asn Phe Phe Gly Asp Thr Asp Arg Val Gly 305 310 315 320
Gly Asp Phe Thr Phe Ser Tyr Tyr Gly His Asp Met Ser Arg Asp Phe 325 330 335
L_,f Phe Asp Ser Asn Tyr Leu Asn Val Asn Thr Asn Pro Lys Leu Gly
340 345 350
Pro Val Tyr Thr Asn Gin Asn Tyr Pro Gly Phe Phe He Phe Asp His 355 360 365 Leu Arg Arg Tyr Val Met Asn Ala Phe Glu Pro Asn Leu Asn Leu Val 370 375 380
Val Asn Thr Asn Lys Val Lys Gin Thr Phe Asn Val Gly Met Arg Phe 385 390 395 400
Met Thr Met Asp Met Phe He Arg Ser Asp Gin Ser Thr Cys Glu Lys 405 410 415
Thr Asp He He Asn Gly Val Cys His Met Pro Pro Tyr Val Leu Ser
420 425 430
Lys Thr Pro Asn Asn Asn Gin Glu Met Phe Asn Asn Tyr Thr Ala Val 435 440 445
Trp Leu Ser Asp Lys He Glu Phe Phe Asp Ser Lys Leu Val He Thr
450 455 460
Pro Gly Leu Arg Tyr Thr Phe Leu Asn Tyr Asn Asn Lys Glu Pro Glu 465 470 475 480 Lys His Asp Phe Ser Val Trp Thr Ser Lys Lys Gin Arg Gin Asn Glu
485 490 495
Trp Ser Pro Ala Leu Asn He Gly Tyr Lys Pro Met Glu Asn Trp He
500 505 510
Trp Tyr Ala Asn Tyr Arg Arg Ser Phe He Pro Pro Gin His Thr Met 515 520 525
Val Gly He Thr Arg Thr Asn Tyr Asn Gin He Phe Asn Glu He Glu
530 535 540
Val Gly Gin Arg Tyr Ser Tyr Lys Asn Leu Leu Ser Phe Asn Thr Asn 545 550 555 560 Tyr Phe Val He Phe Ala Lys Arg Tyr Tyr Ala Gly Gly Tyr Ser Pro
565 570 575
Gin Pro Val Asp Ala Arg Ser Gin Gly Val Glu Leu Glu Leu Tyr Tyr
580 585 590
Ala Pro He Arg Gly Leu Gin Phe His Val Ala Tyr Thr Tyr He Asp 595 600 605
Ala Arg He Thr Ser Asn Ala Asp Asp He Ala Tyr Tyr Phe Thr Gly
610 615 620
He Val Asn Lys Pro Phe Asp He Lys Gly Lys Arg Leu Pro Tyr Val 625 630 635 640 Ser Pro Asn Gin Phe He Phe Asp Met Met Tyr Thr Tyr Lys His Thr
645 650 655
Thr Phe Gly He Ser Ser Tyr Phe Tyr Ser Arg Ala Tyr Ser Ser Met
660 665 670
Leu Asn Gin Ala Lys Asp Gin Thr Val Cys Leu Pro Leu Asn Pro Glu 675 680 685
Tyr Thr Gly Gly Leu Lys Tyr Gly Cys Asn Ser Val Gly Leu Leu Pro
690 695 700
Leu Tyr Phe Val Leu Asn Val Gin Val Ser Ser He Leu Trp Gin Ser 705 710 715 720 Gly Arg His Lys He Thr Gly Ser Leu Gin He Asn Asn Leu Phe Asn
725 730 735
Met Lys Tyr Tyr Phe Arg Gly He Gly Thr Ser Pro Thr Gly Arg Glu
740 745 750
Pro Ala Pro Gly Arg Ser He Thr Ala Tyr Leu Asn Tyr Glu Phe 755 760 765
(2) INFORMATION FOR SEQ ID NO : 112 :
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 115 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...115
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 112:
Leu His Pro Leu Cys Ala His Gly Gin Cys Gly Ser Glu Ala He Ala 1 5 10 15 Cys Leu Glu Ala He Ser Val Gly He Val Pro Val He Ala Asn Ser 20 25 30
Pro Leu Ser Ala Thr Arg Gin Phe Ala Leu Asp Glu Arg Ser Leu Phe
35 40 45
Glu Pro Asn Asn Ala Lys Asp Leu Ser Ala Lys He Asp Trp Trp Leu 50 55 60
Glu Asn Lys Leu Glu Arg Glu Arg Met Gin Asn Glu Tyr Ala Lys Ser 65 70 75 80
Ala Leu Asn Tyr Thr Leu Glu Asn Ser Val He Gin He Glu Lys Val 85 90 95 Tyr Glu Glu Ala He Lys Asp Phe Lys Asn Asn Pro Asn Leu Phe Lys 100 105 110
Thr Leu Ser 115 (2) INFORMATION FOR SEQ ID NO: 113:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 389 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...389
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:113: Met Val He Val Leu Val Val Asp Ser Phe Lys Asp Thr Ser Asn Gly 1 5 10 15
Thr Ser Met Thr Ala Phe Arg Phe Phe Glu Ala Leu Lys Lys Arg Gly
20 25 30
His Ala Met Arg Val Val Ala Pro His Val Asp Asn Leu Gly Ser Glu 35 40 45
Glu Glu Gly Tyr Tyr Asn Leu Lys Glu Arg Tyr He Pro Leu Val Thr
50 . 55 60
Glu He Ser His Lys Gin His He Leu Phe Ala Lys Pro Asp Glu Lys 65 70 75 80
He Leu Arg Lys Ala Phe Lys Gly Ala Asp Met He His Thr Tyr Leu
85 90 95
Pro Phe Leu Leu Glu Lys Thr Ala Val Lys He Ala Arg Glu Met Arg 100 105 110 Val Pro Tyr He Gly Ser Phe His Leu Gin Pro Glu His He Ser Tyr 115 120 125
Asn Met Lys Leu Gly Gin Phe Ser Trp Leu Asn Thr Met Leu Phe Ser
130 135 140
Trp Phe Lys Ser Ser His Tyr Arg Tyr He His His He His Cys Pro 145 150 155 160
Ser Lys Phe He Val Glu Glu Leu Glu Lys Tyr Asn Tyr Gly Gly Lys
165 170 175
Lys Tyr Ala He Ser Asn Gly Phe Asp Pro Met Phe Lys Phe Glu His 180 185 190 Pro Gin Lys Ser Leu Phe Asp Thr Thr Pro Phe Lys He Ala Met Val 195 200 205
Gly Arg T r Ser Asn Glu Lys Asn Gin Ser Val Leu He Lys Ala Val
210 215 220
Ala Leu Ser Arg Tyr Lys Gin Asp He Val Leu Leu Leu Lys Gly Lys 225 230 235 240
Gly Pro Asp Glu Lys Lys He Lys Leu Leu Ala Gin Lys Leu Gly Val
245 250 255
Lys Thr Glu Phe Gly Phe Val Asn Ser His Glu Leu Leu Glu He Leu 260 265 270 Lys Thr Cys Thr Leu Tyr Ala His Thr Ala Asn Val Glu Ser Glu Ala 275 280 285
He Ala Cys Leu Glu Ala He Ser Val Gly He Val Pro Val He Ala
290 295 300
Asn Ser Pro Leu Ser Ala Thr Arg Gin Phe Ala Leu Asp Glu Arg Ser 305 310 315 320
Leu Phe Glu Pro Asn Asn Ala Lys Asp Leu Ser Ala Lys He Asp Trp
325 330 335
Trp Leu Glu Asn Lys Leu Glu Arg Glu Arg Met Gin Asn Glu Tyr Ala 340 345 350 Lys Ser Ala Leu Asn Tyr Thr Leu Glu Asn Ser Val He Gin He Glu 355 360 365
Lys Val Tyr Glu Glu Ala He Lys Asp Phe Lys Asn Asn Pro Asn Leu
370 375 380
Phe Lys Thr Leu Ser 385
(2) INFORMATION FOR SEQ ID NO : 114 :
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 312 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...312
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 114:
Leu Ala Ser Tyr Gly Phe Phe Leu Gly Ala Leu Phe He Leu Ala Ser 1 5 10 15 Gly He Val Cys Leu Gin Thr Ala Gly Asn Pro Phe Val Thr Leu Leu 20 25 30
Ser Lys Gly Lys Glu Ala Arg Asn Leu Val Leu Val Gin Ala Phe Asn
35 40 45
Ser Leu Gly Thr Thr Leu Gly Pro He Phe Gly Ser Leu Leu He Phe 50 55 60
Ser Ala Thr Lys Thr Ser Asp Asn Leu Ser Leu He Asp Lys Leu Ala 65 70 75 80
Asp Ala Lys Ser Val Gin Met Pro Tyr Leu Gly Leu Ala Val Phe Ser 85 90 95 Leu Leu Leu Ala Leu Val Met Tyr Leu Leu Lys Leu Pro Asp Val Glu 100 105 110
Lys Glu Met Pro Lys Glu Thr Thr Gin Lys Ser Leu Phe Ser His Lys
115 120 125
His Phe Val Phe Gly Ala Leu Gly He Phe Phe Tyr Val Gly Gly Glu 130 135 140
Val Ala He Gly Ser Phe Leu Val Leu Ser Phe Glu Lys Leu Leu Asn
145 150 155 160
Leu Asp Ala Gin Ser Ser Ala His Tyr Leu Val Tyr Tyr Trp Gly Gly
165 170 175 Ala Met Val Gly Arg Phe Leu Gly Ser Ala Leu Met Asn Lys He Ala
180 185 190
Pro Asn Lys Tyr Leu Ala Phe Asn Ala Leu Ser Ser He He Leu He
195 200 205
Ala Leu Ala He Leu He Gly Gly Lys He Ala Leu Phe Ala Leu Thr 210 215 220
Phe Val Gly Phe Phe Asn Ser He Met Phe Pro Thr He Phe Ser Leu
225 230 235 240
Ala Thr Leu Asn Leu Gly His Leu Thr Ser Lys Ala Ser Gly Val He
245 250 255 Ser Met Ala He Val Gly Gly Ala Leu He Pro Pro He Gin Gly Val
260 265 270
Val Thr Asp Met Leu Thr Ala Thr Glu Ser Asn Leu Leu Tyr Ala Tyr
275 280 285
Ser Val Pro Leu Leu Cys Tyr Phe Tyr He Leu Phe Phe Ala Leu Lys 290 295 300
Gly Tyr Lys Gin Glu Glu Asn Ser 305 310
(2) INFORMATION FOR SEQ ID NO: 115: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 407 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...407
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 115: Met Gin Lys Thr Ser Asn Thr Leu Ala Leu Gly Ser Leu Thr Ala Leu 1 5 10 15
Phe Phe Leu Met Gly Phe He Thr Val Leu Asn Asp He Leu He Pro
20 25 30
His Leu Lys Pro He Phe Asp Leu Thr Tyr Phe Glu Ala Ser Leu He 35 40 45
Gin Phe Cys Phe Phe Gly Ala Tyr Phe He Met Gly Gly Val Phe Gly
50 55 60
Asn Val He Ser Lys He Gly Tyr Pro Phe Gly Val Val Leu Gly Phe 65 70 75 80 Val He Thr Ala Ser Gly Cys Ala Leu Phe Tyr Pro Ala Ala His Phe
85 90 95
Gly Ser Tyr Gly Phe Phe Leu Gly Ala Leu Phe He Leu Ala Ser Gly
100 105 110
He Val Cys Leu Gin Thr Ala Gly Asn Pro Phe Val Thr Leu Leu Ser 115 120 125
Lys Gly Lys Glu Ala Arg Asn Leu Val Leu Val Gin Ala Phe Asn Ser
130 135 140
Leu Gly Thr Thr Leu Gly Pro He Phe Gly Ser Leu Leu He Phe Ser 145 150 155 160 Ala Thr Lys Thr Ser Asp Asn Leu Ser Leu He Asp Lys Leu Ala Asp
165 170 175
Ala Lys Ser Val Gin Met Pro Tyr Leu Gly Leu Ala Val Phe Ser Leu
180 185 190
Leu Leu Ala Leu Val Met Tyr Leu Leu Lys Leu Pro Asp Val Glu Lys 195 200 205
Glu Met Pro Lys Glu Thr Thr Gin Lys Ser Leu Phe Ser His Lys _I: J
210 215 220
Phe Val Phe Gly Ala Leu Gly He Phe Phe Tyr Val Gly Gly Glu Val 225 230 235 240 Ala He Gly Ser Phe Leu Val Leu Ser Phe Glu Lys Leu Leu Asn Leu
245 250 255
Asp Ala Gin Ser Ser Ala His Tyr Leu Val Tyr Tyr Trp Gly Gly Ala
260 265 270
Met Val Gly Arg Phe Leu Gly Ser Ala Leu Met Asn Lys He Ala Pro 275 280 285
Asn Lys Tyr Leu Ala Phe Asn Ala Leu Ser Ser He He Leu He Ala
290 295 300
Leu Ala He Leu He Gly Gly Lys He Ala Leu Phe Ala Leu Thr Phe 305 310 315 320
Val Gly Phe Phe Asn Ser He Met Phe Pro Thr He Phe Ser Leu Ala
325 330 335
Thr Leu Asn Leu Gly His Leu Thr Ser Lys Ala Ser Gly Val He Ser 340 345 350 Met Ala He Val Gly Gly Ala Leu He Pro Pro He Gin Gly Val Val 355 360 365
Thr Asp Met Leu Thr Ala Thr Glu Ser Asn Leu Leu Tyr Ala Tyr Ser
370 375 380
Val Pro Leu Leu Cys Tyr Phe Tyr He Leu Phe Phe Ala Leu Lys Gly 385 390 395 400
Tyr Lys Gin Glu Glu Asn Ser 405
(2) INFORMATION FOR SEQ ID NO: 116:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 125 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...125
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 116:
Met Asn Lys He Ala Pro Asn Lys Tyr Leu Ala Phe Gly Ala Leu Ser 1 5 10 15
Ser He He Leu He Ala Leu Ala He Leu He Gly Gly Lys He Ala
20 25 30
Leu Phe Ala Leu Thr Phe Val Gly Phe Phe Asn Ser He Met Phe Pro 35 40 45 Thr He Phe Ser Leu Ala Thr Leu Asn Leu Gly He Ser Leu Leu Met 50 55 60
Ala Ser Gly Val He Ser Met Ala He Val Gly Gly Ala Leu He Pro 65 70 75 80
Pro He Gin Gly Val Val Thr Asp Met Leu Thr Ala Thr Glu Ser Asn 85 90 95
Leu Leu Tyr Ala Tyr Ser Val Pro Leu Leu Cys Tyr Phe Tyr He Leu
100 105 110
Phe Phe Ala Leu Lys Gly Tyr Lys Gin Glu Glu Asn Ser 115 120 125 (2) INFORMATION FOR SEQ ID NO: 117:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 330 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...330 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 117:
Leu Lys Lys He Leu Pro Ala Leu Leu Met Gl Phe Val Gly Leu Asn 1 5 10 15
Ala Ser Asp Arg Leu Leu Glu He Met Arg Leu Tyr Gin Lys Gin Gly 20 25 30
Leu Glu Val Val Gly Gin Lys Leu Asp Ser Tyr Leu Ala Asp Lys Ser
35 40 45
Phe Trp Ala Glu Glu Leu Gin Asn Lys Asp Thr Asp Phe Gly Tyr Tyr 50 55 60 Gin Asn Lys Gin Phe Leu Phe Val Ala Asp Lys Ser Lys Pro Ser Leu 65 70 75 80
Glu Phe Tyr Glu He Glu Asn Asn Met Leu Lys Lys He Asn Ser Ser
85 90 95
Lys Ala Leu Val Gly Ser Lys Lys Gly Asp Lys Thr Leu Glu Gly Asp 100 105 110
Leu Ala Thr Pro He Gly Val Tyr Arg He Thr Gin Lys Leu Glu Arg
115 120 125
Leu Asp Gin Tyr Tyr Gly Val Leu Ala Phe Val Thr Asn Tyr Pro Asn
130 135 140 Leu Tyr Asp Thr Leu Lys Lys Arg Thr Gly His Gly He Trp Val His
145 150 155 160
Gly Met Pro Leu Asn Gly Asp Arg Asn Glu Leu Asn Thr Lys Gly Cys
165 170 175
He Ala He Glu Asn Pro He Leu Ser Ser Tyr Asp Lys Val Leu Lys mo 185 190
Gly Glu Lyt, ; la Phe Leu He Thr Tyr Glu Asp Lys Phe Ser Pro Ser
195 200 205
Thr Lys Glu Glu Leu Ser Met He Leu Ser Ser Leu Phe Gin Trp Lys
210 215 220 Glu Ala Trp Ala Arg Gly Asp Phe Glu Arg Tyr Met Arg Phe Tyr Asn
225 230 235 240
Pro Asn Phe Thr Arg Tyr Asp Gly Met Ser Phe Asn Ala Phe Lys Glu
245 250 255
Tyr Lys Lys Arg Val Phe Ala Lys Asn Glu Lys Lys Asn He Ala Phe 260 265 270
Ser Ser He Asn Val He Pro Tyr Pro Asn Ser Gin Asn Lys Arg Leu
275 280 285
Phe Tyr Val Val Phe Asp Gin Asp Tyr Lys Ala Tyr Gin Gin Asn Lys
290 295 300
Leu Ser Tyr Ser Ser Asn Ser Gin Lys Glu Leu Tyr Val Glu He Glu 305 310 315 320
Asn Asn Gin Ala Ser He He Met Glu Lys 325 330
(2) INFORMATION FOR SEQ ID NO: 118:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 169 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...169
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:118:
Leu Phe Glu Lys Trp He Gly Leu Thr Leu Leu Leu Ser Ser Leu Gly 1 5 10 15
Tyr Pro Cys Gin Lys Val Ser He Ser Phe Lys Gin Tyr Glu Asn Leu 20 25 30 He His He His Gin Lys Gly Cys Asn Asn Glu Val Val Cys Arg Thr 35 40 45
Leu He Ser He Ala Leu Leu Glu Ser Ser Leu Gly Leu Asn Asn Lys
50 55 60
Arg Glu Lys Ser Leu Lys Asp Thr Ser Tyr Ser Met Phe His He Thr 65 70 75 80
Leu Asn Thr Ala Lys Lys Phe Tyr Pro Thr Tyr Ser Lys Thr Leu Leu
85 90 95
Lys Thr Lys Leu Leu Asn Asp Val Gly Phe Ala He Gin Leu Ala Lys 100 105 110 Gin He Leu Lys Glu Asn Phe Asp Tyr Tyr His Gin Lys His Pro Asn 115 120 125
Lys Ser Val Tyr Gin Leu Val Gin Met Ala He Gly Ala Tyr Asn Gly
130 135 140
Gly Met Lys His Asn Pro Asn Gly Ala Tyr Met Lys Lys Phe Arg Cys 145 150 155 160
He Tyr Ser Gin Val Arg Tyr Asn Glu 165
(2) INFORMATION FOR SEQ ID NO: 119: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 215 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...215
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 119: Met Lys Lys Pro Tyr Arg Lys He Ser Asp Tyr Ala He Val Gly Gly 1 5 10 15
Leu Ser Ala Leu Val Met Val Ser He Val Gly Cys Lys Ser Asn Ala
20 25 30
Asp Asp Lys Pro Lys Glu Gin Ser Ser Leu Ser Gin Ser Val Gin Lys 35 40 45
Gly Ala Phe Val He Leu Glu Glu Gin Lys Asp Lys Ser Tyr Lys Val
50 55 60
Val Glu Glu Tyr Pro Ser Ser Arg Thr His He Val Val Arg Asp Leu 65 70 75 80 Gin Gly Asn Glu Arg Val Leu Ser Asn Glu Glu He Gin Lys Leu He
85 90 95
Lys Glu Glu Glu Ala Lys He Asp Asn Gly Thr Ser Lys Leu Val Gin
100 105 110
Pro Asn Asn Gly Gly Ser Asn Glu Gly Ser Gly Phe Gly Leu Gly Ser 115 120 125
Ala He Leu Gly Ser Ala Ala Gly Ala He Leu Gly Ser Tyr He Gly
130 135 140
Asn Lys Leu Phe Asn Asn Pro Asn Tyr Gin Gin Asn Ala Gin Arg Thr 145 150 155 160 Tyr Lys Ser Pro Gin Ala Tyr Gin Arg Ser Gin Asn Ser Phe Ser Lys
165 170 175
Ser Ala Pro Ser Ala Ser Ser Met Gly Thr Ala Ser Lys Gly Gin Ser
180 185 190
Gly Phe Phe Gly Ser Ser Arg Pro Thr Ser Ser Pro Ala He Ser Ser 195 200 205
Gly Thr Arg Gly Phe Asn Ala 210 215
(2) INFORMATION FOR SEQ ID NO: 120:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 253 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...253
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 120: Leu Lys Thr Leu Phe Ser Val Tyr Leu Phe Leu Ser Leu Asn Pro Leu 1 5 10 15
Phe Leu Glu Ala Lys Glu He Thr Trp Ser Gin Phe Leu Glu Asn Phe
20 25 30
Lys Asn Lys Asn Glu Asp Asp Lys Pro Lys Pro Leu Thr He Asp Lys 35 40 45
Asn Asn Glu Lys Gin Gin He Leu Asp Lys Asn Gin Gin He Leu Lys
50 55 60
Arg Ala Leu Glu Lys Ser Leu Lys Phe Phe Phe He Phe Gly Tyr Asn 65 70 75 80 Tyr Ser Gin Ala Ala Tyr Ser Thr Thr Asn Gin Asn Leu Thr Leu Thr
85 90 95
Ala Asn Ser He Gly Phe Asn Thr Ala Thr Gly Leu Glu His Phe Leu
100 105 110
Arg Asn His Pro Lys Val Gly Phe Arg He Phe Ser Val Tyr Asn Tyr 115 120 125
Phe His Ser Val Ser Leu Ser Gin Pro Gin He Leu Met Val Gin Asn
130 135 140
Tyr Gly Gly Ala Leu Asp Phe Ser Trp He Phe Val Asp Lys Lys Thr 145 150 155 160 Tyr Arg Phe Arg Ser Tyr Leu Gly He Ala Leu Glu Gin Gly Val Leu
165 170 175
Leu Val Asp Thr He Lys Thr Gly Ser Phe Thr Thr He He Pro Arg
180 185 190
Thr Lys Lys Thr Phe Phe Gin Ala Pro Leu Arg Phe Gly Phe He Val 195 200 205
Asp Phe He Gly Tyr Leu Ser Leu Gin Leu Gly He Glu Met Pro Leu
210 215 220
Val Arg Asn Val Phe Tyr Thr Tyr Asn Asn His Gin Glu Arg Phe Lys 225 230 235 240 Pro Arg Phe Asn Ala Asn Leu Se-: Leu He Val Ser Phe
245 250
(2) INFORMATION FOR SEQ ID NO: 121: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 336 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...336
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 121:
Leu Phe Phe Lys Phe He Leu Cys Leu Ser Leu Gly He Phe Ala Trp 1 5 10 15
Ala Lys Glu Val He Pro Thr Pro Ser Thr Pro Leu Thr Pro Ser Lys
20 25 30
Arg Tyr Ser He Asn Leu Met Thr Glu Asn Asp Gly Tyr He Asn Pro 35 40 45 Tyr He Asp Glu Tyr Tyr Thr Ala Gly Asn Gin He Gly Phe Ser Thr 50 55 60
Lys Glu Phe Asp Phe Ser Lys Asn Lys Ala Met Lys Trp Ser Ser Tyr 65 70 75 80
Leu Gly Phe Phe Asn Lys Ser Pro Arg Val Thr Arg Phe Gly He Ser 85 90 95
Leu Ala Gin Asp Met Tyr Thr Pro Ser Leu Ala Asn Arg Lys Leu Val
100 105 110
His Leu His Asp Asn His Pro Tyr Gly Gly Tyr Leu Arg Val Asn Leu 115 120 125 Asn Val Tyr Asn Arg His Gin Thr Phe Met Glu Leu Phe Thr He Ser 130 135 140
Leu Gly Thr Thr Gly Gin Asp Ser Leu Ala Ala Gin Thr Gin Arg Leu 145 150 155 160
He His Lys Trp Gly His Asp Pro Gin Phe Tyr Gly Trp Asn Thr Gin 165 170 175
Leu Lys Asn Glu Phe He Phe Glu Leu His Tyr Gin Leu Leu Lys Lys
180 185 190
Val Pro Leu Leu Lys Thr Arg Phe Phe Ser Met Glu Leu Met Pro Gly 195 200 205 Phe Asn Val Glu Leu Gly Asn Ala Arg Asp Tyr Phe Gin Leu Gly Ser 210 215 220
Leu Phe Arg Ala Gly Tyr Asn Leu Asp Ala Asp Tyr Gly Val Asn Lys 225 230 235 240
Val Asn Thr Ala Phe Asp Gly Gly Met Pro Tyr Ser Asp Lys Phe Ser 245 250 255
He I" r Phe Phe Ala Gly Ala Phe Gly Arg Phe Gin Pro Leu Asn He
260 265 270
Phe He Gin Gly Asn Ser Pro Glu Thr Arg Gly He Ala Asn Leu Glu 275 280 285 Tyr Phe Val Tyr Ala Ser Glu He Gly Ala Ala Met Met Trp Arg Ser 290 295 300
Leu Arg Val Ala Phe Thr He Thr Asp He Ser Lys Thr Phe Gin Ser 305 310 315 320
Gin Pro Lys His His Gin He Gly Thr Leu Glu Leu Asn Phe Ala Phe 325 330 335
(2) INFORMATION FOR SEQ ID NO: 122: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 108 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...108
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:122;
Met Lys Pro He Phe Ser Leu Phe Phe Leu Leu He Val Leu Lys Ala 1 5 10 15 His Pro He Asn Pro Leu Leu Glu Pro Leu Tyr Phe Pro Ser Tyr Thr 20 25 30
Gin Phe Leu Asp Leu Glu Pro His Phe Val He Lys Lys Lys Arg Ala
35 40 45
Tyr Arg Pro Phe Gin Trp Gly Asn Thr He He He Lys Arg His Asp 50 55 60
Leu Glu Glu Arg Gin Ser Asn Gin Pro Ser Asp He Phe Arg Gin Asn 65 70 75 80
Ala Glu He Asn Val Ser Ser Gin Thr Phe Leu Arg Gly He Ser Ser 85 90 95 Ala Ser Ser Arg He Val He Asp Ser Val Ala Gin 100 105
(2) INFORMATION FOR SEQ ID NO:123: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 195 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...195 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 123:
Met Ser Asn Asn Pro Phe Lys Lys Val Gly Met He Ser Ser Gin Asn 1 5 10 15
Asn Asn Gly Ala Leu Asn Gly Leu Gly Val Gin Val Gly Tyr Lys Gin
20 25 30
Phe Phe Gly Glu Ser Lys Arg Trp Gly Leu Arg Tyr Tyr Gly Phe Phe 35 40 45 Asp Tyr Asn His Gly Tyr He Lys Ser Ser Phe Phe Asn Ser Ser Ser 50 55 60
Asp He Trp Thr Tyr Gly Gly Gly Ser Asp Leu Leu Val Asn Phe He 65 70 75 80
Asn Asp Ser He Thr Arg Lys Asn Asn Lys Leu Ser Val Gly Leu Phe 85 90 95
Gly Gly He Gin Leu Ala Gly Thr Thr Trp Leu Asn Ser Gin Tyr Met
100 105 110
Asn Leu Thr Ala Phe Asn Asn Pro Tyr Ser Ala Lys Val Asn Ala Ser 115 120 125 Asn Phe Gin Phe Leu Phe Asn Leu Gly Leu Arg Thr Asn Leu Ala Thr 130 135 140
Ala Lys Lys Lys Asp Ser Glu Arg Ser Ala Gin His Gly Val Glu Leu 145 150 155 160
Gly He Lys He Pro Thr He Asn Thr Asn Tyr Tyr Ser Phe Leu Gly 165 170 175
Thr Lys Leu Glu Tyr Arg Arg Leu Tyr Ser Val Tyr Leu Asn Tyr Val
180 185 190
Phe Ala Tyr 195
(2) INFORMATION FOR SEQ ID NO: 124:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 227 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...227
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 124:
Val Arg Phe Gly Lys He Asp Tyr Leu Asn Met Leu Pro Phe Asp Val 1 5 10 15
Phe He Lys Ser Tyr Pro Thr Pro Cys Tyr Phe Lys Gin Phe Leu Arg 20 25 30 Leu Lys Lys Thr Tyr Pro Ser Lys Leu Asn Glu Ser Phe Leu Phe Arg
35 40 45
Arg He Asp Ala Gly Phe He Ser Ser He Ala Gly Tyr Pro Phe Ala 50 55 60 Leu Cys Ser Tyr Ser Leu Gly He Val Ala Tyr Lys Glu Val Leu Ser 65 70 75 80
Val Leu Val Val Asn Arg Glu Asn Ala Phe Asp Lys Glu Ser Ala Ser
85 90 95
Ser Asn Ala Leu Ser Lys Val Leu Gly Leu Lys Gly Glu Val Leu He 100 105 110
Gly Asn Lys Ala Leu Gin Phe Tyr Tyr Ser Asn Pro Lys Lys Asp Phe
115 120 125
He Asp Leu Ala Ala Leu Trp Tyr Glu Lys Lys Arg Leu Pro Phe Val
130 135 140 Phe Gly Arg Leu Cys Tyr Tyr Gin Asn Lys Asp Phe Tyr Lys Arg Leu
145 150 155 160
Ser Leu Ala Phe Lys His Gin Lys Thr Lys He Pro His Tyr He Leu
165 170 175
Lys Glu Ala Ala Leu Lys Thr Asn Leu Lys Arg Gin Asp He Leu Asn 180 185 190
Tyr Leu Gin Lys He Tyr Tyr Thr Leu Gly Lys Lys Glu Gin Ser Gly
195 200 205
Leu Lys Ala Phe Tyr Arg Glu Leu Leu Phe Lys Arg He Gin Lys Pro 210 215 220 Lys Arg Phe 225
(2) INFORMATION FOR SEQ ID NO: 125: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 305 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...305
(xi) SEQUENCE DE_ \IPTION: SEQ ID NO: 125:
Met Gly Arg He Glu Ser Lys Lys Arg Leu Lys Ala Leu He Phe Leu 1 5 10 15 Ala Ser Leu Gly Val Leu Trp Gly Asn Ala Ala Glu Lys Thr Pro Phe 20 25 30
Phe Lys Thr Lys Asn His He Tyr Leu Gly Phe Arg Leu Gly Thr Gly
35 40 45
Ala Thr Thr Arg Thr Ser Met Trp Gin Gin Ala Tyr Lys Asp Asn Pro 50 55 60
Thr Cys Pro Ser Ser Val Cys Tyr Gly Glu Lys Leu Glu Ala His Tyr 65 70 75 80
Lys Gly Gly Lys Asn Leu Ser Tyr Thr Gly Gin He Gly Asp Glu He 85 90 95
Ala Phe Asp Lys Tyr His He Leu Gly Leu Arg Val Trp Gly Asp Val
100 105 110
Glu Tyr Ala Lys Ala Gin Leu Gly Gin Lys Val Gly Gly Asn Thr Leu 115 120 125 Leu Ser Gin Ala Asn Tyr Asn Pro Ser Ala He Lys Thr Tyr Asp Pro 130 135 140
Thr Ser Asn Ala Gin Gly Ser Leu Val Leu Gin Lys Thr Pro Ser Pro 145 150 155 160
Gin Asp Phe Leu Phe Asn Asn Gly His Phe Met Ala Phe Gly Leu Asn 165 170 175
Val Asn Met Phe Val Asn Leu Pro He Asp Thr Leu Leu Lys Leu Ala
180 185 190
Leu Lys Thr Glu Lys Met Leu Phe Phe Lys He Gly Val Phe Gly Gly 195 200 205 Gly Gly Val Glu Tyr Ala He Leu Trp Ser Pro Gin Tyr Lys Asn Gin 210 215 220
Asn Thr His Gin Asp Asp Lys Phe Phe Ala Ala Gly Gly Gly Phe Phe 225 230 235 240
Val Asn Phe Gly Gly Ser Leu Tyr He Gly Lys Arg Asn Arg Phe Asn 245 250 255
Val Gly Leu Lys He Pro Tyr Tyr Ser Leu Ser Ala Gin Ser Trp Lys
260 265 270
Asn Phe Gly Ser Ser Asn Val Trp Gin Gin Gin Thr He Arg Gin Asn 275 280 285 Phe Ser Val Phe Arg Asn Lys Glu Val Phe Val Ser Tyr Ala Phe Leu 290 295 300
Phe 305 (2) INFORMATION FOR SEQ ID NO:126:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 258 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...258
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 126: Met Phe Leu Arg Ser Tyr Pro Lys Leu Arg Tyr Ala Leu Cys Leu Pro 1 5 10 15
Leu Leu Thr Glu Thr Cys Tyr Ser Glu Glu Arg Thr Leu Asn Lys Val 20 25 30 Thr Thr Gin Ala Lys Arg He Phe Thr Tyr Asn Asn Glu Phe Lys Val 35 40 45
Thr Ser Lys Glu Leu Asp Gin Arg Gin Ser Asn Glu Val Lys Asp Leu
50 55 60
Phe Arg Thr Asn Pro Asp Val Asn Val Gly Gly Gly Ser Val Met Gly 65 70 75 80
Gin Lys He Tyr Val Arg Gly He Glu Asp Arg Leu Leu Arg Val Thr
85 90 95
Val Asp Gly Ala Ala Gin Asn Gly Asn He Tyr His His Gin Gly Asn 100 105 110 Thr Val He Asp Pro Gly Met Leu Lys Ser Val Glu Val Thr Lys Gly 115 120 125
Ala Ala Asn Ala Ser Ala Gly Pro Gly Ala He Ala Gly Val He Lys
130 135 140
Met Glu Thr Lys Gly Ala Ala Asp Phe He Pro Arg Gly Lys Asn Tyr 145 150 155 160
Ala Ala Ser Gly Ala Val Ser Phe Tyr Thr Asn Phe Gly Asp Arg Glu
165 170 175
Thr Phe Arg Ser Ala Tyr Gin Ser Ala His Phe Asp He He Ala Tyr 180 185 190 Tyr Thr His Gin Asn He Phe Tyr Tyr Arg Ser Gly Ala Thr Val Met 195 200 205
Lys Asn Leu Phe Lys Pro Thr Gin Ala Asp Lys Glu Pro Gly Thr Pro
210 215 220
Ser Glu Gin Asn Asn Ala Leu He Lys Met Asn Gly Tyr Leu Ser Asp 225 230 235 240
Arg Asp Thr Leu Thr Phe Ser Trp Asn Met Thr Arg Asp Asn Ala Thr
245 250 255
Arg Leu
(2) INFORMATION FOR SEQ ID NO: 127:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 192 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...192
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 127: Met Phe Leu Arg Ser Tyr Pro Lys Leu Arg Tyr Ala Leu Cys Leu Pro 1 5 10 15
Leu Leu Thr Glu Thr Cys Tyr Ser Glu Glu Arg Thr Leu Asn Lys Val 20 25 30
Thr Thr Gin Ala Lys Arg He Phe Thr Tyr Asn Asn Glu Phe Lys Val
35 40 45
Thr Ser Lys Glu Leu Asp Gin Arg Gin Ser Asn Glu Val Lys Asp Leu 50 55 60 Phe Arg Thr Asn Pro Asp Val Asn Val Gly Gly Gly Ser Val Met Gly 65 70 75 80
Gin Lys He Tyr Val Arg Gly He Glu Asp Arg Leu Leu Arg Val Thr
85 90 95
Val Asp Gly Ala Ala Gin Asn Gly Asn He Tyr His His Gin Gly Asn 100 105 110
Thr Val He Asp Pro Gly Met Leu Lys Ser Val Glu Val Thr Lys Gly
115 120 125
Ala Ala Asn Ala Ser Ala Gly Pro Gly Ala He Ala Gly Val He Lys
130 135 140 Met Glu Thr Lys Gly Ala Ala Asp Phe He Pro Arg Gly Lys Asn Tyr
145 150 155 160
Ala Ala Ser Giy Ala Val Ser Phe Tyr Thr Asn Phe Gly Asp Arg Glu
165 170 175
Thr Phe Arg Ser Ala Tyr Gin Ser Ala His Phe Asp He He Ala Tyr 180 185 190
(2) INFORMATION FOR SEQ ID NO: 128:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 126 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...126 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 128:
Val Pro Leu Ser Leu Gly Gly Asn Leu Leu Asn Pro Asn Asn Ser Ser 1 5 10 15
Val Leu Asn Leu Lys Asn Ser Gin Leu Val Phe Ser Asp Gin Gly Ser 20 25 30
Leu Asn He Ala Asn He Asp Leu Leu Ser Asp Leu Asn Gly Asn Lys
35 40 45
Asn Arg Val Tyr Asn He He Gin Ala Asp Met Asn Gly Asn Trp Tyr 50 55 60 Glu Arg He Asn Phe Phe Gly Met Arg He Asn Asp Gly He Tyr Asp 65 70 75 80
Ala Lys Asn Gin Thr Tyr Ser Phe Thr Asn Pro Leu Asn Asn Ala Val 85 90 95 Lys Phe Thr Glu Ser Phe Phe He His Arg Leu Cys Gly Ser Leu Ser 100 105 110
Gin He Gin Lys Lys Lys Asn Thr He Val Ser Pro Arg Leu 115 120 125 (2) INFORMATION FOR SEQ ID NO: 129:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 565 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...565
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 129: Val Tyr Ser Tyr Ser Asp Asp Ala Gin Gly Val Phe Tyr Leu Thr Ser 1 5 10 15
Ser Val Lys Gly Tyr Tyr Asn Pro Asn Gin Ser Tyr Gin Ala Ser Gly
20 25 30
Ser Asn Asn Thr Thr Lys Asn Asn Asn Leu Thr Ser Glu Ser Ser Val 35 40 45
He Ser Gin Thr Tyr Asn Ala Gin Gly Asn Pro He Ser Ala Leu His
50 55 60
Val Tyr Asn Lys Gly Tyr Asn Phe Ser Asn He Lys Ala Leu Gly Gin 65 70 75 80 Met Ala Leu Lys Leu Tyr Pro Glu He Lys Lys He Leu Gly Asn Asp
85 90 95
Phe Ser Leu Ser Ser Leu Ser Asn Leu Lys Gly Asp Ala Leu Asn Gin
100 105 110
Leu Thr Lys Leu He Thr Pro Ser Asp Trp Lys Asn He Asn Glu Leu 115 320 125
He Asp Asn Ala Asn Asn Sei Val Val Gin Asn Phe Asn Asn Gly Thr
130 135 140
Leu He He Gly Ala Thr Lys He Gly Gin Thr Asp Thr Asn Ser Ala 145 150 155 160 Val Val Phe Gly Gly Leu Gly Tyr Gin Lys Pro Cys Asp Tyr Thr Asp
165 170 175
He Val Cys Gin Lys Phe Arg Gly Thr Tyr Leu Gly Gin Leu Leu Glu
180 185 190
Ser Asn Ser Ala Asp Leu Gly Tyr He Asp Thr Thr Phe Asn Ala Lys 195 200 205
Glu He Tyr Leu Thr Gly Thr Leu Gly Ser Gly Asn Ala Trp Gly Thr
210 215 220
Gly Gly Ser Ala Ser Val Thr Phe Asn Ser Gin Thr Ser Leu He Leu 225 230 235 240
Asn Gin Ala Asn He Val Ser Ser Gin Thr Asp Gly He Phe Ser Met
245 250 255
Leu Gly Gin Glu Gly He Asn Lys Val Phe Asn Gin Ala Gly Leu Ala 260 265 270 Asn He Leu Gly Glu Val Ala Met Gin Ser He Asn Lys Ala Gly Gly 275 280 285
Leu Gly Asn Leu He Val Asn Thr Leu Gly Ser Asp Ser Val He Gly
290 295 300
Gly Tyr Leu Thr Pro Glu Gin Lys Asn Gin Thr Leu Ser Gin Leu Leu 305 310 315 320
Gly Gin Asn Asn Phe Asp Asn Leu Met Asn Asp Ser Gly Leu Asn Thr
325 330 335
Ala He Lys Asp Leu He Arg Gin Lys Leu Gly Phe Trp Thr Gly Leu 340 345 350 Val Gly Gly Leu Ala Gly Leu Gly Gly He Asp Leu Gin Asn Pro Glu 355 360 365
Lys Leu He Gly Ser Met Ser He Asn Asp Leu Leu Ser Lys Lys Gly
370 375 380
Leu Phe Asn Gin He Thr Gly Phe He Ser Ala Asn Asp He Gly Gin 385 390 395 400
Val He Ser Val Met Leu Gin Asp He Val Lys Pro Ser Asp Ala Leu
405 410 415
Lys Asn Asp Val Ala Ala Leu Gly Lys Gin Met He Gly Glu Phe Leu 420 425 430 Gly Gin Asp Thr Leu Asn Ser Leu Glu Ser Leu Leu Gin Asn Gin Gin 435 440 445
He Lys Ser Val Leu Asp Lys Val Leu Ala Ala Lys Gly Leu Gly Ser
450 455 460
He Tyr Glu Gin Gly Leu Gly Asp Leu He Pro Asn Leu Gly Lys Lys 465 470 475 480
Gly He Phe Ala Pro Tyr Gly Leu Ser Gin Val Trp Gin Lys Gly Asp
485 490 495
Phe Ser Phe Asn Ala Gin Gly Asn Val Phe Val Gin Asn Ser Thr Phe 500 505 510 Ser Asn Ala Asn Gly Gly Thr Leu Ser Phe Asn Ala Gly Asn Ser Leu 515 520 525
He Phe Ala Gly Asn Asn His He Ala Phe Thr Asn His Ser Gly Thr
530 535 540
Leu Asn Leu Leu Ser Asn Gin Val Ser Asn He Asn Val Thr Met Leu 545 550 555 560
At,.. Ala Ala Thr Ala 565
(2) INFORMATION FOR SEQ ID NO: 130:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 172 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...172
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 130: Val Phe Gly Leu Ser Leu Ala Asp Met He Leu Glu Arg Phe Lys Asp 1 5 10 15
Phe Met Arg Glu Tyr Pro Glu Pro Tyr Lys Phe Leu Gin Val Phe Tyr
20 25 30
Ala Gin Glu Lys Glu Arg Phe Leu Asn His Lys Met Asn Asp Tyr He 35 40 45
Lys Gin Asn Lys Ser Lys Glu Glu Ala Ser He Leu Ala Arg Gin Gly
50 55 60
Phe Val Ser Val He Gly Arg Ala Leu Glu Lys He He Glu Leu Leu 65 70 75 80 Leu Lys Asp Phe Cys He Lys Asn Asn Val Lys Met Thr Asn Asp Lys
85 90 95
Thr Leu Arg Ala Lys Arg He Asn Gly Glu Leu Asp Lys Val Lys Arg
100 105 110
Ala Leu Leu Val His Phe Gly Gly Tyr Ser Val Leu Pro Asp He He 115 120 125
Leu Tyr Gin Thr Asn Lys Asp Asn He Lys He Leu Ala He Leu Ser
130 135 140
Val Lys Asn Ser Phe Arg Glu Arg Phe Thr Lys Asp Ala Leu Leu Glu 145 150 155 160 He Lys Thr Phe Ala He Ala Cys Asn Phe Ser His
165 170
(2) INFORMATION FOR SEQ ID NO: 131: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 331 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...331 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 131:
Met Lys Arg Phe Val Leu Phe Leu Leu Phe He Cys Val Cys Val Cys 1 5 10 15
Val Gin Ala Tyr Ala Glu Gin Asp Tyr Phe Phe Arg Asp Phe Lys Ser
20 25 30
He Asp Leu Pro Gin Lys Leu His Leu Asp Lys Lys Leu Ser Gin Thr 35 40 45 He Gin Pro Cys Ala Gin Leu Asn Ala Ser Lys His Tyr Thr Ala Thr 50 55 60
Gly Val Arg Glu Pro Asp Ala Cys Thr Lys Ser Phe Lys Lys Ser Ala 65 70 75 80
Met Val Ser Tyr Asp Leu Ala Leu Gly Tyr Leu Val Ser Gin Asn Lys 85 90 95
Pro Tyr Gly Leu Lys Ala He Glu He Leu Asn Ala Trp Ala Asn Glu
100 105 110
Leu Gin Ser Val Asp Thr Tyr Gin Ser Glu Asp Asn He Asn Phe Tyr 115 120 125 Met Pro Tyr Met Asn Met Ala Tyr Trp Phe Val Lys Lys Glu Phe Pro 130 135 140
Ser Pro Glu Tyr Glu Asp Phe He Arg Arg Met Arg Gin Tyr Ser Gin 145 150 155 160
Ser Ala Leu Asn Thr Asn His Gly Ala Trp Gly He Leu Phe Asp Val 165 170 175
Ser Ser Ala Leu Ala Leu Asp Asp His Ala Leu Leu Gin Ser Ser Ala
180 185 190
Asn Arg Trp Gin Glu Trp Val Phe Lys Ala He Asp Glu Asn Gly Val 195 200 205 He Ala Ser Ala He Thr Arg Ser Asp Thr Ser Asp Tyr His Gly Gly 210 215 220
Pro Thr Lys Gly He Lys Gly He Ala Tyr Thr Asn Phe Ala Leu Leu 225 230 235 240
Ala He Thr He Ser Gly Glu Leu Leu Phe Glu Asn Gly Tyr Asp Leu 245 250 255
Trp Gly Ser Gly Ala Gly Gin Arg Leu Ser Val Ala Tyr Asn Lys Ala
260 265 270
Ala Thr Trp He Leu Asn Pro Glu Thr Phe Pro Tyr Phe Gin Pro Asn 275 280 285 Leu He Gly Val His Asn Asn Ala Tyr Phe He He Leu Ala Lys His 290 295 300
Tyr Ser Ser Pro Ser Ala Asp Glu Leu Leu Glu Gin Gly Asp Leu His 305 310 315 320
Glu Asp Gly Phe Arg Leu Lys Leu Arg Ser Pro 325 330
(2) INFORMATION FOR SEQ ID NO: 132:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 128 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...128
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 132:
Met: Arg Gin Tyr Ser Gin Ser Ala Leu Asn Thr Asn His Gly Ala Trp 1 5 10 15 Gly He Leu Phe Asp Val Ser Ser Ala Leu Ala Leu Asp Asp His Ala 20 25 30
Leu Leu Gin Ser Ser Ala Asn Arg Trp Gin Glu Trp Val Phe Lys Ala
35 40 45
He Asp Glu Asn Gly Val He Ala Ser Ala He Thr Arg Ser Asp Thr 50 55 60
Ser Asp Tyr His Gly Gly Pro Thr Lys Gly He Lys Gly He Ala Tyr 65 70 75 80
Thr Asn Phe Ala Leu Leu Ala He Thr He Ser Gly Glu Leu Leu Phe 85 90 95 Glu Asn Gly Tyr Asp Leu Trp Gly Ser Gly Ala Gly Gin Arg Leu Ser 100 105 110
Val Ala Tyr Asn Lys Ala Ala Thr Trp He Leu Asn Pro Glu Thr Phe 115 120 125 (2) INFORMATION FOR SEQ ID NO: 133:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 245 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCA-I^N 1...245
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:133: Leu Arg Thr Leu Leu Lys Met Leu Val Gly Val Ser Leu Leu Thr His 1 5 10 15
Ala Leu Met Ala Thr Glu Glu Ser Ala Ala Pro Ser Trp Thr Lys Asn
20 25 30
Leu Tyr Met Gly Phe Asn Tyr Gin Thr Gly Ser He Asn Leu Met Thr 35 40 45
Asn He His Glu Val Arg Glu Val Thr Ser Tyr Gin Thr Gly Tyr Thr
50 55 60
Asn Val Met Thr Ser He Asn Ser Val Lys Lys Leu Thr Asn Met Gly 65 70 75 80
Ser Asn Gly He Gly Leu Val Met Gly Tyr Asn His Phe Phe His Pro
85 90 95
Asp Lys Val Leu Gly Leu Arg Tyr Phe Ala Phe Leu Asp Trp Gin Gly 100 105 110 Tyr Gly Met Arg Tyr Pro Lys Gly Tyr Tyr Gly Gly Asn Asn Met He 115 120 125
Thr Tyr Gly Val Gly Val Asp Ala He Trp Asn Phe Phe Gin Gly Ser
130 135 140
Phe Tyr Gin Asp Asp He Gly Val Asp He Gly Val Phe Gly Gly He 145 150 155 160
Ala He Ala Gly Asn Ser Trp Tyr He Gly Asn Lys Gly Gin Glu Leu
165 170 175
Leu Gly He Thr Asn Ser Ser Ala Val Asp Asn Thr Ser Phe Gin Phe 180 185 190 Leu Phe Asn Phe Gly Phe Lys Ala Leu Phe Val Asp Glu His Glu Phe 195 200 205
Glu He Gly Phe Lys Phe Pro Thr Leu Asn Asn Lys Tyr Tyr Thr Thr
210 215 220
Asp Ala Leu Lys Val Gin Met Arg Arg Val Phe Ala Phe Tyr Val Gly 225 230 235 240
Tyr Asn Tyr His Phe 245
(2) INFORMATION FOR SEQ ID NO:134:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 290 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...290
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 134:
Met Phe Glu Glu He Thr Leu Ala His Lys Asp Leu Phe Ser Arg Phe 1 5 10 15
Leu Gin Thr Gin Lys He Val Leu Ser Asp Val Ser Phe Thr Asn Cys
20 25 30
Phe Leu Trp Gin His Ala Arg Leu He Gin Val Ala Val He Arg Asp 35 40 45 Cys Leu Val He Gin Thr Thr Tyr Glu Asn Gin Lys Pro Phe Tyr Phe
50 55 60
Tyr Pro He Gly Lys Arg Pro His Glu Cys Val Lys Glu Leu Leu Glu 65 70 75 80 Leu Glu Lys Asn Leu Arg Phe His Ser Leu Thr Leu Glu Gin Lys Asp
85 90 95
Asp Leu Lys Asp Asn Phe Val Gly Val Phe Asp Phe Thr Tyr Asn Arg
100 105 110
Asp Arg Ser Asp Tyr Val Tyr Ser He Glu Glu Leu He Ala Leu Lys 115 120 125
Gly Lys Lys Tyr His Lys Lys Lys Asn His Leu Asn Gin Phe Leu Thr
130 135 140
Asn His Ala Asn Phe Val Tyr Glu Lys He Ser Pro Gin Asn Arg Lys 145 150 155 160 Glu Val Leu Glu Ala Ser Lys Ala Trp Phe Leu Glu Ser Gin Thr Asp
165 170 175
Asp He Gly Leu He Asn Glu Asn Lys Gly He Gin Ser Val Leu Glu
180 185 190
Asn Tyr Glu Ser Leu Asp Leu Lys Gly Gly Leu He Arg Val Asn Gly 195 200 205
Glu He Val Ser Phe Ser Phe Gly Glu Val Leu Asn Glu Glu Ser Ala
210 215 220
Leu He His He Glu Lys Ala Arg Thr Asp He Ala Gly Ala Tyr Gin 225 230 235 240 He He Asn Gin Gin Leu Leu Leu Asn Glu Phe Ser His Leu Thr Tyr
245 250 255
Ala Asn Arg Glu Glu Asp Leu Gly Leu Glu Gly Leu Arg Arg Ser Lys
260 265 270
Met Ser Tyr Asn Pro Val Phe Leu He Asp Lys Tyr Glu Ala Val Ala 275 280 285
Arg Asn 290
(2) INFORMATION FOR SEQ ID NO: 135:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 110 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...110
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 135:
Met Met Phe He Val Ala Val Leu Met Leu Ala Phe Leu He Phe Val 1 5 10 15
His Glu Leu Gly His Phe He He Ala Arg He Cys Gly Val Lys Val
20 25 30
Glu Val Phe Ser He Gly Phe Gly Lys Lys Leu Trp Phe Phe Lys Leu 35 40 45
Phe Gly Thr Gin Phe Ala Leu Ser Leu He Pro Leu Gly Gly Tyr Val
50 55 60
Lys Leu Lys Gly Met Asp Lys Glu Glu Asn Glu Glu Asn Lys He Asn 65 70 75 80 Gin Ala Asn Asp Ser Tyr Ala Lys Lys Ala Leu Ser Lys Ser Tyr Gly
85 90 95
Tyr Cys Leu Val Gly Arg Phe Leu He Phe Phe Leu Arg Phe 100 105 110 (2) INFORMATION FOR SEQ ID NO: 136:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 351 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...351
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:136: Met Met Phe He Val Ala Val Leu Met Leu Ala Phe Leu He Phe Val 1 5 10 15
His Glu Leu Gly His Phe He He Ala Arg He Cys Gly Val Lys Val
20 25 30
Glu Val Phe Ser He Gly Phe Gly Lys Lys Leu Trp Phe Phe Lys Leu 35 40 45
Phe Gly Thr Gin Phe Ala Leu Ser Leu He Pro Leu Gly Gly Tyr Val
50 55 60
Lys Leu Lys Gly Met Asp Lys Glu Glu Asn Glu Glu Asn Lys He Asn 65 70 75 80 Gin Ala Asn Asp Ser Tyr Ala Gin Lys Ser Pro Phe Gin Lys Leu Trp
85 9 95
He Leu Phe Gly Gly Ala Phe Phe Asn Phe Leu Phe Ala Val Leu Val
100 105 110
Tyr Phe Phe Leu Ala Leu Ser Gly Glu Lys Val Leu Leu Pro Val He 115 120 125
Gly Gly Leu Glu Lys Asn Ala Leu Glu Ala Gly Leu Leu Lys Gly Asp
130 135 140
Arg He Leu Ser He Asn His Gin Lys He Ala Ser Phe Arg Glu He 145 150 155 160 Arg Glu He Val Ala Arg Ser Gin Gly Glu Leu He Leu Glu He Glu
165 170 175
Arg Asn Asn Gin He Leu Glu Lys Arg Leu Thr Pro Lys He Val Ala 180 185 190 Val He Ser Glu Ser Asn Asp Pro Asn Glu He He Lys Tyr Lys He 195 200 205
He Gly He Lys Pro Asp Met Gin Lys Met Gly Val Val Ser Tyr Ser
210 215 220
Val Phe Gin Ala Phe Glu Lys Ala Leu Ser Arg Phe Lys Glu Gly Val 225 230 235 240
Val Leu He Val Asp Ser Leu Arg Arg Leu He Met Gly Ser Ala Ser
245 250 255
Val Lys Glu Leu Ser Gly Val He Gly He Val Gly Ala Leu Ser His 260 265 270 Ala Asn Ser Val Ser Met Leu Leu Leu Phe Gly Ala Phe Leu Ser He 275 280 285
Asn Leu Gly He Leu Asn Leu Leu Pro He Pro Ala Leu Asp Gly Ala
290 295 300
Gin Met Leu Gly Val Val Phe Lys Asn He Phe His He Ala Leu Pro 305 310 315 320
Thr Pro He Gin Asn Ala Leu Trp Leu Val Gly Val Gly Phe Leu Val
325 330 335
Phe Val Met Phe Leu Gly Leu Phe Asn Asp He Thr Arg Leu Leu 340 345 350
(2) INFORMATION FOR SEQ ID NO: 137:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 100 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...100
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 137:
Met Gin Ly_, ;.sn Leu Asp Ser Leu Leu Glu Asn Leu Arg Ala Glu He
1 5 10 15
Asp Ala Leu Asp Asn Glu Leu Ser Asp Leu Leu Asp Lys Arg Leu Gly 20 25 30 He Ala Leu Lys He Ala Leu He Lys Gin Glu Ser Pro Gin Glu Asn
35 40 45
Pro He Tyr Cys Pro Lys Arg Glu Gin Glu He Leu Lys Arg Leu Ser
50 55 60
Gin Arg Gly Phe Lys His Leu Asn Gly Glu He Leu Ala Ser Phe Tyr 65 70 75 80
Ala Glu Val Phe Lys He Ser Arg Asn Phe Gin Glu Asn Ala Leu Lys
85 90 95
Glu Leu Lys Lys 100
(2) INFORMATION FOR SEQ ID NO: 138:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 174 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...174 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 138:
Val Lys Met Arg Phe Phe Ser Gly Phe Gly Phe Val Asn Glu Ser Val 1 5 10 15
Leu Phe Glu Glu Trp Leu Leu Lys Gly Ala Tyr Asp Val Ser Gly Phe 20 25 30
Ser Met Gly Ala He Lys Ala He Glu Tyr Ala Tyr Asn Glu Val Leu
35 40 45
Gin Gin Arg Arg He His Ser Leu Leu Leu Phe Ser Pro Cys Met Leu 50 55 60 Ala His Lys Ser Leu Ala Phe Lys Arg Leu Gin Leu Phe Leu Phe Gin 65 70 75 80
Lys Asp Pro Gin Ser Tyr Met Asp Asn Phe Tyr Lys Glu Val Gly Leu
85 90 95
Asp Ala Gin Leu Glu Arg Phe Lys Lys Glu Gly Ser Leu Glu Glu Leu 100 105 110
Glu Phe Leu Leu Asp Tyr Lys Tyr Ser Asp Ser He He Arg Phe Leu
115 120 125
Leu Glu Lys Gly Val Lys He Glu Val Phe He Gly Leu Lys Asp Arg 130 135 140 He Thr Asp He Gin Ala Leu Leu Glu Phe Phe Met Pro Leu Val Gin 145 150 155 160
Val Trp Gin Phe Lys Asp Cys Asn His Leu Leu Gin Lys Ser 165 170 (2) INFORMATION FOR SEQ ID NO: 139:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 471 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...471
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 139:
Met Lys Asn Thr Asn Thr Lys Glu He Lys Asn Thr Arg Met Lys Lys 1 5 10 15
Gly Tyr Ser Gin Tyr His Thr Leu Lys Lys Gly Leu Leu Lys Thr Ala 20 25 30 Leu Leu Phe Ser Leu Pro Leu Ser Val Ala Leu Ala Glu Asp Asp Gly 35 40 45
Phe Tyr Met Gly Val Gly Tyr Gin He Gly Gly Ala Gin Gin Asn He
50 55 60
Asn Asn Lys Gly Ser Thr Leu Arg Asn Asn Val He Asp Asp Phe Arg 65 70 75 80
Gin Val Gly Val Gly Met Ala Gly Gly Asn Gly Leu Leu Ala Leu Ala
85 90 95
Thr Asn Thr Thr Met Asp Ala Leu Leu Gly He Gly Asn Gin He Val 100 105 110 Asn Thr Asn Thr Thr Val Gly Asn Asn Asn Ala Glu Leu Thr Gin Phe 115 120 125
Lys Lys He Leu Pro Gin He Glu Gin Arg Phe Glu Thr Asn Lys Asn
130 135 140
Ala Tyr Ser Val Gin Ala Leu Gin Val Tyr Leu Ser Asn Val Leu Tyr 145 150 155 160
Asn Leu Val Asn Asn Ser Asn Asn Gly Ser Asn Asn Gly Val Val Pro
165 170 175
Glu Tyr Val Gly He He Lys Val Leu Tyr Gly Ser Gin Asn Glu Phe 180 185 190 Ser Leu Leu Ala Thr Glu Ser Val Ala Leu Leu Asn Ala Leu Thr Arg 195 200 205
Val Asn Leu Asp Ser Asn Ser Val Phe Leu Lys Gly Leu Leu Ala Gin
210 215 220
Met Gin Leu Phe Asn Asp Thr Ser Ser Ala Lys Leu Gly Gin He Ala 225 230 235 240
Glu Asn Leu Lys Asn Gly Gly Ala Gly Ala Met Leu Gin -_ Asp Val
245 250 255
Lys Thr He Ser Asp Arg He Ala Thr Tyr Gin Glu Asn Leu Lys Gin 260 265 270 Leu Gly Gly Met Leu Lys Asn Tyr Asp Glu Pro Tyr Leu Pro Gin Phe 275 280 285
Gly Pro Gly Thr Ser Ser Gin His Gly Val He Asn Gly Phe Gly He
290 295 300
Gin Val Gly Tyr Lys Gin Phe Phe Gly Ser Lys Lys Asn He Gly Leu 305 310 315 320
Arg Tyr Tyr Ala Phe Phe Asp Tyr Gly Phe Thr Gin Leu Gly Ser Leu
325 330 335
Asn Ser Ala Val Lys Ala Asn He Phe Thr Tyr Gly Ala Gly Thr Asp 340 345 350
Phe Leu Trp Asn He Phe Arg Arg Val Phe Ser Asp Gin Ser Leu Asn
355 360 365
Val Gly Val Phe Gly Gly He Gin He Ala Gly Asn Thr Trp Asp Ser
370 375 380 Ser Leu Arg Gly Gin He Glu Asn Ser Phe Lys Glu Tyr Pro Thr Pro
385 390 395 400
Thr Asn Phe Gin Phe Leu Phe Asn Leu Gly Leu Arg Ala His Phe Ala
405 410 415
Ser Thr Met His Arg Arg Phe Leu Ser Ala Ser Gin Ser He Gin His 420 425 430
Gly Met Glu Phe Gly Val Lys He Pro Ala He Asn Gin Arg Tyr Leu
435 440 445
Lys Ala Asn Gly Ala Asp Val Asp Tyr Arg Arg Leu Tyr Ala Phe Tyr 450 455 460 He Asn Tyr Thr He Gly Phe 465 470
(2) INFORMATION FOR SEQ ID NO: 140: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 129 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...129
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:140:
Met Lys Ser He Arg Arg Gly Asp Gly Leu Asn Val Val Pro Phe He 1 5 10 15 Asp He Met Leu Val Leu Leu Al i He Val Leu Ser He Ser Thr Phe 20 25 30
He Ala Gin Gly Lys He Lys Val Ser Leu Pro Asn Ala Lys Asn Ala
35 40 45
Glu Lys Ser Gin Pro Asn Asp Gin Lys Val Val Val He Ser Val Asp 50 55 60
Glu His Asp Asn He Phe Val Asp Asp Lys Pro Thr Asn Leu Glu Ala 65 70 75 80
Leu Ser Ala Val Val Lys Gin Thr Asp Pro Lys Thr Leu He Asp Leu 85 90 95 Lys Ser Asp Lys Ser Ser Arg Phe Glu Thr Phe He Ser He Met Asp
100 105 110
He Leu Lys Glu His Asn His Glu Asn Phe Ser He Ser Thr Gin Ala 115 120 125 Gin
(2) INFORMATION FOR SEQ ID NO: 141: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 75 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...75
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 141:
Met Leu Val Leu Leu Ala He Val Leu Ser He Ser Thr Phe He Ala
1 5 10 15 Gin Gly Lys He Lys Val Ser Leu Pro Asn Ala Lys Asn Ala Glu Lys 20 25 30
Ser Arg Pro Asn Asp Gin Lys Val Val Val He Ser Val Asp Glu His 35 40 45
Asp Asn He Phe Val Asp Asp Lys Pro Thr Asn Leu Glu Ala Leu Ser 50 55 60
Ala Val Val Lys Gin Thr Asp Pro Lys Thr Leu
65 70 75
(2) INFORMATION FOR SEQ ID NO:142:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 223 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
'ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B ) LOCATION 1 . . . 223
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 142: Met Phe Ser Leu Ser Tyr Val Ser Lys Lys Phe Leu Ser Val Leu Leu 1 5 10 15
Leu He Ser Leu Phe Leu Ser Ala Cys Lys Ser Asn Asn Lys Asp Lys
20 25 30
Leu Asp Glu Asn Leu Leu Ser Ser Gly Thr Gin Ser Ser Lys Glu Leu 35 40 45
Asn Asp Lys Arg Asp Asn He Asp Lys Lys Ser Tyr Ala Gly Leu Glu
50 55 60
Asp Val Phe Leu Asp Asn Lys Ser He Ser Pro Asn Asp Lys Tyr Met 65 70 75 80 Leu Leu Val Phe Gly Arg Asn Gly Cys Ser Tyr Cys Glu Arg Leu Lys
85 90 95
Lys Asp Leu Lys Asn Val Lys Glu Leu Arg Asn Tyr He Lys Glu His
100 105 110
Phe Ser Ala Tyr Tyr Val Asn He Ser Tyr Ser Lys Glu His Asn Phe 115 120 125
Lys Val Gly Asp Lys Asp Lys Asn Asp Glu Lys Glu He Lys Met Ser
130 135 140
Thr Glu Glu Leu Ala Gin He Tyr Ala Val Gin Ser Thr Pro Thr He 145 150 155 160 Val Leu Ser Asp Lys Thr Gly Lys Thr He Tyr Glu Leu Pro Gly Tyr
165 170 175
Met Pro Ser Val Gin Phe Leu Ala Val Leu Glu Phe He Gly Asp Gly
180 185 190
Lys Tyr Gin Asp Thr Lys Asn Asp Glu Asp Leu Thr Lys Lys Leu Lys 195 200 205
Ala Tyr He Lys Tyr Lys Thr Asn Leu Ser Lys Ser Lys Ser Ser 210 215 220
(2) INFORMATION FOR SEQ ID NO: 143:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 116 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...116
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 143:
Leu Met Lys Ser Lys He Thr His Phe He Val He Ser Phe Val Leu 1 5 10 15
Ser Val Leu Ser Ala Cys Lys Asp Glu Pro Lys Lys Ser Ser Gin Ser
20 25 30
His Gin Asn Asn Thr Lys Thr Thr Gin Asn Asn Gin He Asn Gin Pro 35 40 45
Asn Lys Asp He Lys Lys He Glu His Glu Glu Glu Asp Glu Lys Val
50 55 60
Thr Lys Glu Val Asn Asp Leu He Asn Asn Glu Asn Lys He Asp Glu 65 70 75 80 He Asn Asn Glu Glu Asn Ala Asp Pro Ser Gin Lys Arg Thr Asn Asn
85 90 95
Val Leu Gin Arg Ala Thr Asn His Gin Asp Asn Leu Ser Ser Pro Leu
100 105 110
Asn Arg Lys Tyr 115
(2) INFORMATION FOR SEQ ID NO:144:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 79 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...79 (xi) SEQUENCE DESCRIPTION : SEQ ID NO : 144 :
Met Phe Glu Lys He Arg Lys He Leu Ala Asp He Glu Asp Ser Gin
1 5 10 15
Asn Glu He Glu Met Leu Leu Lys Leu Ala Asn Leu Ser Leu Gly Asp 20 25 30
Phe He Glu He Lys Arg Gly Ser Met Asp Met Pro Lys Gly Val Asn
35 40 45
Glu Ala Phe Phe Thr Gin Leu Ser Glu Glu Val Glu Arg Leu Lys Glu 50 55 60 Leu He Asn Ala Leu Asn Lys He Lys Lys Gly Leu Leu Val Phe 65 70 75
(2) INFORMATION FOR SEQ ID NO: 145: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 51 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...51
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:145:
Met Ser Met Phe He Ser Asn Leu Ala Phe Thr Ser Glu His Lys Asp 1 5 10 15
Ala Met Glu Val Ala Lys He Ala He Leu Leu Gly Ser Leu He Ser
20 25 30
Gly He He Gly Ala Leu Tyr Leu Phe Ala Leu Asp Lys Arg Ala Ala 35 40 45 Leu Lys Lys 50
(2) INFORMATION FOR SEQ ID NO: 146: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 449 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...449
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:146
Met Gly Leu Lys He Lys He Leu Arg Leu Ser Met Asn Leu Lys Lys 1 5 10 15 Thr Glu Asn Ala Leu Ser Leu Thr Leu Lys Asn Phe He Lys Ser Glu 20 25 30
Ser Phe Gly Gly He Phe Leu Phe Leu Asn Ala Val Leu Ala Met Val
35 40 45
Val Ala Asn Ser Phe Leu Lys Glu Ser Tyr Phe Ala Leu Trp His Thr 50 55 60
Pro Phe Gly Phe Gin Val Gly Asp Phe Phe He Gly Phe Ser Leu His 65 70 75 80
Asn Trp He Asp Asp Val Leu Met Ala Leu Phe Phe Leu Met He Gly 85 90 95 Leu Glu He Lys Arg Glu Leu Leu Phe Gly Glu Leu Ser Ser Phe Lys
100 105 110
Lys Ala Ser Phe Pro Val He Ala Ala He Gly Gly Met He Ala Pro 115 120 125 Gly Leu He Tyr Phe Phe Leu Asn Ala Asn Thr Pro Ser Gin His Gly 130 135 140
Phe Gly He Pro Met Ala Thr Asp He Ala Phe Ala Leu Gly Val He 145 150 155 160
Met Leu Leu Gly Lys Arg Val Pro Thr Ala Leu Lys Val Phe Leu He 165 170 175
Thr Leu Ala Val Ala Asp Asp Leu Gly Ala He Val Val He Ala Leu
180 185 190
Phe Tyr Thr Thr Asn Leu Lys Phe Ala Trp Leu Leu Gly Ala Leu Gly 195 200 205 Val Val Leu Val Leu Ala He Leu Asn Arg Leu Asn He Arg Ser Leu 210 215 220
He Pro Tyr Leu Leu Leu Gly Val Leu Leu Trp Phe Cys Val His Gin 225 230 235 240
Ser Gly He His Ala Thr He Ala Ala Val Val Leu Ala Phe Met He 245 250 255
Pro Val Lys He Pro Lys Asp Ser Lys Asn Val Glu Leu Leu Glu Leu
260 265 270
Gly Lys Arg Tyr Ala Glu Thr Ser Ser Gly Val Leu Leu Thr Lys Glu 275 280 285 Gin Gin Glu He Leu His Ser He Glu Glu Lys Ala Ser Ala Leu Gin 290 295 300
Ser Pro Leu Glu Arg Leu Glu His Phe Leu Ala Pro He Ser Gly Tyr 305 310 315 320
Phe He Met Pro Leu Phe Ala Phe Ala Asn Ala Gly Val Ser Val Asp 325 330 335
Ser Ser He Asn Leu Glu Val Asp Lys Val Leu Leu Gly Val He Leu
340 345 350
Gly Leu Cys Leu Gly Lys Pro Leu Gly He Phe Leu He Thr Phe He 355 360 365 Ser Glu Lys Leu Lys He Thr Ala Arg Pro Lys Gly He Gly Trp Trp 370 375 380
His He Leu Gly Ala Gly Leu Leu Ala Gly He Gly Phe Thr Met Ser 385 390 395 400
Met Phe He Ser Asn Leu Ala Phe Thr Ser Glu His Lys Asp Ala Met 405 410 415
Glu Val Ala Lys He Ala He Leu Leu Gly Ser Leu He Ser Gly He
420 425 430
He Gly Ala Leu Tyr Leu Phe Ala Leu Asp Lys Arg Ala Ala Leu Lys 435 440 445 Lys
(2) INFORMATION FOR SEQ ID NO: 147: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 815 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...815
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 147:
Met Asn Asp Lys Arg Phe Arg Lys Tyr Cys Ser Phe Ser He Phe Leu 1 5 10 15
Ser Leu Leu Gly Thr Phe Glu Leu Glu Ala Lys Glu Glu Glu Lys Glu
20 25 30
Glu Lys Lys Thr Glu Arg Asn Lys Asp Lys Glu Lys Asn Ala Gin His 35 40 45 Thr Leu Gly Lys Val Thr Thr Gin Ala Ala Lys He Phe Asn Tyr Asn 50 55 60
Asn Gin Thr Thr He Ser Ser Lys Glu Leu Glu Arg Arg Gin Ala Asn 65 70 75 80
Gin He Ser Asp Met Phe Arg Arg Asn Pro Asn He Asn Val Gly Gly 85 90 95
Gly Ala Val He Ala Gin Lys He Tyr Val Arg Gly He Glu Asp Arg
100 105 110
Leu Ala Arg Val Thr Val Asp Gly Val Ala Gin Met Gly Ala Ser Tyr 115 120 125 Gly His Gin Gly Asn Thr He He Asp Pro Gly Met Leu Lys Ser Val 130 135 140
Val Val Thr Lys Gly Ala Ala Gin Ala Ser Ala Gly Pro Met Ala Leu 145 150 155 160
He Gly Ala He Lys Met Glu Thr Arg Ser Ala Ser Asp Phe He Pro 165 170 175
Lys Gly Lys Asp Tyr Ala He Ser Gly Ala Ala Thr Phe Leu Thr Asn
180 185 190
Phe Gly Asp Arg Glu Thr He Met Gly Ala Tyr Arg Asn His His Phe 195 200 205 Asp Ala Leu Leu Tyr Tyr Thr His Gin Asn He Phe Tyr Tyr Arg Asp 210 215 220
Gly Asp Asn Ala Met Lys Asn Leu Phe Asp Pro Lys Ala Asp Asn Lys 225 230 235 240
Val Thr Ala Ser Pro Ser Glu Gin Asn Asn Val Met Ala Lys He Asn 245 250 255
Gly Tyr Leu Ser Glu Arg Asp Thr Leu Thr Leu Ser Tyr Asn Met l.ii
260 265 270
Arg Asp Asn Ala Asn Arg Pro Leu Arg Ala Asn Phe Thr Gly Thr Phe 275 280 285 Leu Pro Tyr Ser Cys Gly Asp Phe Asn Ala Phe Pro Asn Glu Lys Asn 290 295 300
Pro Ser Asp Cys Leu Phe Glu Asn Asp Ala Ser Leu Phe Lys Thr Tyr 305 310 315 320
Ser Val Asn Leu Val His Asn Val Ser Leu Asn Tyr Glu Arg Glu Gly 325 330 335
Gly Ser Arg Phe Gly Asp Pro Lys Leu Lys He Asn Gly Tyr Thr Ser
340 345 350
He Arg Asn Val Gin He Asp Pro Leu Phe Arg Pro Ser Asp He Ala 355 360 365
Thr Thr He Pro Phe Thr Pro Asn Pro Gin Leu Ser Gin Gly Glu Glu
370 375 380
Asn Gin Cys Val Ala Gin Gly Gly He Tyr Asp Ala Leu Lys Gin Thr 385 390 395 400 Cys Ser He Thr Phe Lys Ser Leu Gly Gly Gly Ser Val Val Ala Asn
405 410 415
Lys Asn Leu Phe He He Asn Ser Gly Phe Asn Ala Asn Val He His
420 425 430
Thr He Asp His Lys Asn Asp Asn Leu Leu Glu Tyr Gly Leu Asn Tyr 435 440 445
Gin Asn Leu Thr Thr Phe Asp Lys Ala He Pro Asp Ser Glu Leu Val
450 455 460
Lys Pro Gly Asp Ala Pro Asp Ala Cys Leu Arg Val Thr Gly Pro Asp 465 470 475 480 Asp Pro Asn Met Asn Gly Arg Cys Gin Arg Asn Gly Ala Thr Ala Asn
485 490 495
Val Val Gly Val Tyr Ala Gin Ala Asn Tyr Thr Leu His Pro Met Val
500 505 510
Thr Leu Gly Ala Gly Thr Arg Tyr Asp Val Tyr Thr Leu Val Asp Lys 515 520 525
Asp Trp Gin Leu His Val Thr Gin Gly Phe Ser Pro Ser Ala Ala Leu
530 535 540
Asn Val Ser Pro Leu Glu Asn Leu Asn Phe Arg Leu Ser Tyr Ala Tyr 545 550 555 560 Val Thr Arg Gly Pro Met Pro Gly Gly Leu Val Trp Met Arg Gin Asp
565 570 575
Asn Leu Arg Tyr Asn Arg Asn Leu Lys Pro Glu He Gly Gin Asn Ala
580 585 590
Glu Phe Asn Thr Glu Tyr Ser Ser Gin Tyr Phe Asp Phe Arg Ala Ala 595 600 605
Gly Phe Val Gin Leu He Ser Asn Tyr He Asn Gin Phe Ser Ser Thr
610 615 620
Leu Phe Val Thr Asn Leu Pro Ala Gin Asp He He Tyr Val Pro Gly 625 630 635 640 Tyr Glu Val Ser Gly Thr Ala Lys Tyr Lys Gly Phe Ser Leu Gly Leu
645 650 655
Ser Val Ala Arg Ser Trp Pro Ser Leu Lys Gly Arg Leu He Ala Asp
660 665 670
Val Tyr Glu Leu Ala Ala Thr Thr Gly Asn Val Phe He Leu Thr Ala 675 680 685
Ser Tyr Thr He Pro Arg Thr Gly Leu _e-- He Thr Trp Leu Ser Arg
690 695 700
Phe Val Thr Asn Leu Ser Tyr Cys Ser Tyr Ser Pro Tyr Arg Asn Gly 705 710 715 720 Pro Thr Asp He Asp Arg Arg Pro Ser Asn Cys Pro Lys Thr Pro Gly
725 730 735
He Phe His Val His Lys Pro Gly Tyr Gly Val Ser Ser Phe Phe He
740 745 750
Thr Tyr Lys Pro Thr Tyr Lys Lys Leu Lys Gly Leu Ser Leu Asn Ala 755 760 765
Val Phe Asn Asn Val Phe Asn Gin Gin Tyr He Asp Gin Ala Ser Pro
770 775 780
Val Met Ser Pro Asp Glu Pro Asn Gin Asp Lys Tyr Ala Arg Gly Met 785 790 795 800
Ala Glu Pro Gly Phe Asn Ala Arg Phe Glu He Ser Tyr Lys Phe 805 810 815
(2) INFORMATION FOR SEQ ID NO: 148:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 814 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...814
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 148:
Met Thr Ser Val Leu Glu Lys Tyr Cys Ser Phe Ser He Phe Leu Ser 1 5 10 15
Leu Leu Gly Thr Phe Glu Leu Glu Ala Lys Glu Glu Glu Lys Glu Glu
20 25 30
Lys Lys Thr Glu Arg Asn Lys Asp Lys Glu Lys Asn Ala Gin His Thr 35 40 45 Leu Gly Lys Val Thr Thr Gin Ala Ala Lys He Phe Asn Tyr Asn Asn 50 55 60
Gin Thr Thr He Ser Ser Lys Glu Leu Glu Arg Arg Gin Ala Asn Gin 65 70 75 80
He Ser Asp Met Phe Arg Arg Asn Pro Asn He Asn Val Gly Gly Gly 85 90 95
Ala Val He Ala Gin Lys He Tyr Val Arg Gly He Glu Asp Arg Leu
100 105 110
Ala Arg Val Thr Val Asp Gly Val Ala Gin Met Gly Ala Ser Tyr Gly 115 120 125 His Gin Gly Asn Thr He He Asp Pro Gly Met Leu Lys Ser Val Val 130 135 140
Val Thr Lys Gly Ala Ala Gin Ala Ser Ala Gly Pro Met Ala Leu He 145 150 155 160
Gly Ala He Lys Met Glu Thr Arg Ser Ala Ser Asp Phe He Pro Lys 165 170 175
Gly Lys Asp Tyr Ala He Ser Gly Ala Ala Thr Phe Leu Thr Asn Phe
180 185 190
Gly Asp Arg Glu Thr He Met Gly Ala Tyr Arg Asn His His Phe Asp 195 200 205 Ala Leu Leu Tyr Tyr Thr His Gin Asn He Phe Tyr Tyr Arg Asp Gly
210 215 220
Asp Asn Ala Met Lys Asn Leu Phe Asp Pro Lys Ala Asp Asn Lys Val 225 230 235 240 Thr Ala Ser Pro Ser Glu Gin Asn Asn Val Met Ala Lys He Asn Gly
245 250 255
Tyr Leu Ser Glu Arg Asp Thr Leu Thr Leu Ser Tyr Asn Met Thr Arg
260 265 270
Asp Asn Ala Asn Arg Pro Leu Arg Ala Asn Phe Thr Gly Thr Phe Leu 275 280 285
Pro Tyr Ser Cys Gly Asp Phe Asn Ala Phe Pro Asn Glu Lys Asn Pro
290 295 300
Ser Asp Cys Leu Phe Glu Asn Asp Ala Ser Leu Phe Lys Thr Tyr Ser 305 310 315 320 Val Asn Leu Val His Asn Val Ser Leu Asn Tyr Glu Arg Glu Gly Gly
325 330 335
Ser Arg Phe Gly Asp Pro Lys Leu Lys He Asn Gly Tyr Thr Ser He
340 345 350
Arg Asn Val Gin He Asp Pro Leu Phe Arg Pro Ser Asp He Ala Thr 355 360 365
Thr He Pro Phe Thr Pro Asn Pro Gin Leu Ser Gin Gly Glu Glu Asn
370 375 380
Gin Cys Val Ala Gin Gly Gly He Tyr Asp Ala Leu Lys Gin Thr Cys 385 390 395 400 Ser He Thr Phe Lys Ser Leu Gly Gly Gly Ser Val Val Ala Asn Lys
405 410 415
Asn Leu Phe He He Asn Ser Gly Phe Asn Ala Asn Val He His Thr
420 425 430
He Asp His Lys Asn Asp Asn Leu Leu Glu Tyr Gly Leu Asn Tyr Gin 435 440 445
Asn Leu Thr Thr Phe Asp Lys Ala He Pro Asp Ser Glu Leu Val Lys
450 455 460
Pro Gly Asp Ala Pro Asp Ala Cys Leu Arg Val Thr Gly Pro Asp Asp 465 470 475 480 Pro Asn Met Asn Gly Arg Cys Gin Arg Asn Gly Ala Thr Ala Asn Val
485 490 495
Val Gly Val Tyr Ala Gin Ala Asn Tyr Thr Leu His Pro Met Val Thr
500 505 510
Leu Gly Ala Gly Thr Arg Tyr Asp Val Tyr Thr Leu Val Asp Lys Asp 515 520 525
Trp Gin Leu His Val Thr Gin Gly Phe Ser Pro Ser Ala Ala Leu Asn
530 535 540
Val Ser Pro Leu Glu Asn Leu Asn Phe Arg Leu Ser Tyr Ala Tyr Val 545 550 555 560 Thr Arg Gly Pro Met Pro Gly Gly Leu Val Trp Met Arg Gin Asp Asn
565 570 575
Leu Arg Tyr Asn Arg Asn Leu Lys Pro Glu He Gly Gin Asn Ala Glu
580 585 590
Phe Asn Thr Glu Tyr Ser Ser Gin Tyr Phe Asp Phe Arg Ala Ala Gly 595 600 605
Phe Val Gin Leu He Ser Asn Tyr He Asn Gin Phe Ser Ser Thr Leu
610 615 620
Phe Val Thr Asn Leu Pro Ala Gin Asp He He Tyr Val Pro Gly Tyr 625 630 635 640 Glu Val Ser Gly Thr Ala Lys Tyr Lys Gly Phe Ser Leu Gly Leu Ser
645 650 655
Val Ala Arg Ser Trp Pro Ser Leu Lys Gly Arg Leu He Ala Asp Val 660 665 670 Tyr Glu Leu Ala Ala Thr Thr Gly Asn Val Phe He Leu Thr Ala Ser 675 680 685
Tyr Thr He Pro Arg Thr Gly Leu Ser He Thr Trp Leu Ser Arg Phe
690 695 700
Val Thr Asn Leu Ser Tyr Cys Ser Tyr Ser Pro Tyr Arg Asn Gly Pro 705 710 715 720
Thr Asp He Asp Arg Arg Pro Ser Asn Cys Pro Lys Thr Pro Gly He
725 730 735
Phe His Val His Lys Pro Gly Tyr Gly Val Ser Ser Phe Phe He Thr 740 745 750 Tyr Lys Pro Thr Tyr Lys Lys Leu Lys Gly Leu Ser Leu Asn Ala Val 755 760 765
Phe Asn Asn Val Phe Asn Gin Gin Tyr He Asp Gin Ala Ser Pro Val
770 775 780
Met Ser Pro Asp Glu Pro Asn Gin Asp Lys Tyr Ala Arg Gly Met Ala 785 790 795 800
Glu Pro Gly Phe Asn Ala Arg Phe Glu He Ser Tyr Lys Phe 805 810
(2) INFORMATION FOR SEQ ID NO: 149:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 527 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...527
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 149:
Met Lys Gin Asn Leu Lys Pro Phe Lys Met He Lys Glu Asn Leu Met 1 5 10 15
Thr Gin Ser Gin Lys Val Arg Phe Leu Ala Pro Leu Ser ^t Ala Leu
20 25 30
Ser Leu Ser Phe Asn Pro Val Gly Ala Glu Glu Asp Gly Gly Phe Met 35 40 45 Thr Phe Gly Tyr Glu Leu Gly Gin Val Val Gin Gin Val Lys Asn Pro 50 55 60
Gly Lys He Lys Ala Glu Glu Leu Ala Gly Leu Leu Asn Ser Thr Thr 65 70 75 80
Thr Asn Asn Thr Asn He Asn He Ala Gly Thr Gly Gly Asn Val Ala 85 90 95
Gly Thr Leu Gly Asn Leu Phe Met Asn Gin Leu Gly Asn Leu He Asp
100 105 110
Leu Tyr Pro Thr Leu Lys Thr Asn Asn Leu His Gin Cys Gly Ser Thr 115 120 125
Asn Ser Gly Asn Gly Ala Thr Ala Ala Ala Ala Thr Asn Asn Ser Pro
130 135 140
Cys Phe Gin Gly Asn Leu Ala Leu Tyr Asn Glu Met Val Asp Ser He 145 150 155 160 Lys Thr Leu Ser Gin Asn He Ser Lys Asn He Phe Gin Gly Asp Asn
165 170 175
Asn Thr Thr Ser Ala Asn Leu Ser Asn Gin Leu Ser Glu Leu Asn Thr
180 185 190
Ala Ser Val Tyr Leu Thr Tyr Met Asn Ser Phe Leu Asn Ala Asn Asn 195 200 205
Gin Ala Gly Gly He Phe Gin Asn Asn Thr Asn Gin Ala Tyr Glu Asn
210 215 220
Gly Val Thr Ala Gin Gin He Ala Tyr Val Leu Lys Gin Ala Ser He 225 230 235 240 Thr Met Gly Pro Ser Gly Asp Ser Gly Ala Ala Gly Ala Phe Leu Asp
245 250 255
Ala Ala Leu Ala Gin His Val Phe Asn Ser Ala Asn Ala Gly Asn Asp
260 265 270
Leu Ser Ala Lys Glu Phe Thr Ser Leu Val Gin Asn He Val Asn Asn 275 280 285
Ser Gin Asn Ala Leu Thr Leu Ala Asn Asn Ala Asn He Ser Asn Ser
290 295 300
Thr Gly Tyr Gin Val Ser Tyr Gly Gly Asn He Asp Gin Ala Arg Ser 305 310 315 320 Thr Gin Leu Leu Asn Asn Thr Thr Asn Thr Leu Ala Lys Val Thr Ala
325 330 335
Leu Asn Asn Glu Leu Lys Ala Asn Pro Trp Leu Gly Asn Phe Ala Ala
340 345 350
Gly Asn Ser Ser Gin Val Asn Ala Phe Asn Gly Phe He Thr Lys He 355 360 365
Gly Tyr Lys Gin Phe Phe Gly Glu Asn Lys Asn Val Gly Leu Arg Tyr
370 375 380
Tyr Gly Phe Phe Ser Tyr Asn Gly Ala Gly Val Gly Asn Gly Pro Thr 385 390 395 400 Tyr Asn Gin Val Asn Leu Leu Thr Tyr Gly Val Gly Thr Asp Val Leu
405 410 415
Tyr Asn Val Phe Ser Arg Ser Phe Gly Ser Arg Ser Leu Asn Ala Gly
420 425 430
Phe Phe Gly Gly He Gin Leu Ala Gly Asp Thr Tyr He Ser Thr Leu 435 440 445
Arg Asn Ser Pro Gin Leu Ala _.i: Arg Pro Thr Ala Thr Lys Phe Gin
450 455 460
Phe Leu Phe Asp Val Gly Leu Arg Met Asn Phe Gly He Leu Lys Lys 465 470 475 480 Asp Leu Lys Ser His Asn Gin His Ser He Glu He Gly Val Gin He
485 490 495
Pro Thr He Tyr Asn Thr Tyr Tyr Lys Ala Gly Gly Ala Glu Val Lys
500 505 510
Tyr Phe Arg Pro Tyr Ser Val Tyr Trp Val Tyr Gly Tyr Ala Phe 515 520 525
(2) INFORMATION FOR SEQ ID NO: 150: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 459 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...459
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 150:
Val Val Leu Leu Thr Met Thr Lys Arg Leu Phe Lys Gly Leu Leu Ala 1 5 10 15 He Ser Leu Ala Val Ser Leu His Gly Gly Glu Val Lys Glu Lys Lys 20 25 30
Pro Val Lys Pro Val Lys Glu Asp Pro Gin Glu Leu Ala Ala Lys Arg
35 40 45
Val Glu Ala Phe Ser Arg Phe Ser Asn Val Val Thr Glu He Glu Lys 50 55 60
Lys Tyr Val Asp Lys He Ser He Ser Glu He Met Thr Lys Ala He 65 70 75 80
Glu Gly Leu Leu Ser Asn Leu Asp Ala His Ser Ala Tyr Leu Asn Glu 85 90 95 Lys Lys Phe Lys Glu Phe Gin Ala Gin Thr Glu Gly Glu Phe Gly Gly 100 105 110
Leu Gly He Thr Val Gly Met Arg Asp Gly Val Leu Thr Val He Ala
115 120 125
Pro Leu Glu Gly Thr Pro Ala Tyr Lys Ala Gly Val Lys Ser Gly Asp 130 135 140
Ser He Leu Lys He Asn Asn Glu Ser Thr Leu Ser Met Ser He Asp
145 150 155 160
Asp Ala Val Asn Leu Met Arg Gly Lys Pro Lys Thr Ser He Gin He
165 170 175 Thr VaT Val Arg Lys Asn Glu Pro Lys Pro Leu Val Phe Asn He Val
180 185 190
Arg Asp He He Lys He Pro Ser Val Tyr Val Lys Lys He Lys Asp
195 200 205
Thr Pro Tyr Leu Tyr Val Arg Val Asn Ser Phe Asp Lys Asn Val Thr 210 215 220
Lys Ser Val Leu Asp Gly Leu Lys Ala Asn Pro Asn He Lys Gly Val 225 230 235 240
Val Leu Asp Leu Arg Gly Asn Pro Gly Gly Leu Leu Asn Gin Ala Val 245 250 255 Gly Leu Ser Asn Leu Phe He Lys Glu Gly Val Leu Val Ser Gin Arg
260 265 270
Gly Lys Asn Lys Glu Glu Asn Leu Glu Tyr Lys Ala Asn Gly Arg Ala 275 280 285 Pro Tyr Thr Asn Leu Pro Val Val Val Leu Val Asn Gly Gly Ser Ala 290 295 300
Ser Ala Ser Glu He Val Ala Gly Ala Leu Gin Asp His Lys Arg Ala 305 310 315 320
He He He Gly Glu Lys Thr Phe Gly Lys Gly Ser Val Gin Val Leu 325 330 335
Leu Pro Val Asn Lys Asp Glu Ala He Lys He Thr Thr Ala Arg Tyr
340 345 350
Tyr Leu Pro Ser Gly Arg Thr He Gin Ala Lys Gly He Thr Pro Asp 355 360 365 He Val He Tyr Pro Gly Lys Val Pro Glu Asn Glu Asn Lys Phe Ser 370 375 380
Leu Lys Glu Ala Asp Leu Lys His His Leu Glu Gin Glu Leu Lys Lys 385 390 395 400
Leu Asp Asp Lys Thr Pro He Ser Lys Glu Ala Asp Lys Asp Lys Lys 405 410 415
Ser Glu Glu Glu Lys Glu Val Thr Pro Lys Met He Asn Asp Asp He
420 425 430
Gin Leu Lys Thr Ala He Asp Ser Leu Lys Thr Trp Ser He Val Asp 435 440 445 Glu Lys Met Asp Glu Lys Val Pro Lys Lys Lys 450 455
(2) INFORMATION FOR SEQ ID NO: 151: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 104 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...104
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 151:
Leu Leu Leu His Pro Leu His Ala His Ala Gin Val Leu Gly Phe Thr 1 5 10 15 Asn His Asp His Ala Pro Trp Leu Tyr Asp Phe He Lys Ser Phe Cys 20 25 30
Asn Leu Ser Gly Gin Pro Phe Leu Asp Leu Gin Ala Phe Ala He Asn
35 40 45
Phe Asn Glu Phe Ser Asp Arg Ala Asn Ala Tyr Asn Leu Phe Leu Arg 50 55 60
Asp He Ser His Ala Asn He Pro Lys Lys Arg Glu Gin Met Val Leu 65 70 75 80
Ala Ser Gly Val Lys Phe Asn Val Leu Ser His Tyr His Phe He Ala
85 90 95
Asn Ala Leu Lys He Arg Ala Phe 100
(2) INFORMATION FOR SEQ ID NO: 152:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 165 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...165
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:152:
Met He Glu Leu He Leu His Asn Lys Ser He Gin He Asp Glu Thr 1 5 10 15
Leu Leu Asn Val Lys Glu His Leu Glu Lys Phe Tyr Ser Asn Lys Glu
20 25 30
Gin Glu Thr He Ala Lys Thr Leu Glu Ser Gin Thr Glu Leu Thr Cys 35 40 45 Ser Tyr Leu Leu Asp Lys Asp Phe Ser Leu Leu Glu Lys His Leu Glu 50 55 60
Asn Ser Leu Gly His Phe Thr Phe Glu Ser Glu Phe Ala Leu Leu Lys 65 70 75 80
Asp Lys Glu Pro Leu Asn Leu Ala Gin He Lys Gin He Gly Val Leu 85 90 95
Lys Val He Thr Tyr Glu Met Thr Gin Ala Leu Lys Asn Gin He He
100 105 110
His Leu Thr Gin He Val Asn Glu Glu Asn Leu Glu Phe Asp Glu Glu 115 120 125 Leu Val He Tyr His Leu Asn Phe Lys Leu Asn Gin Asn Thr Tyr Lys 130 135 HO
Val Leu Ala Lys Phe Cys Val Leu Lys Lys Lys Gly Thr Leu His Glu 145 150 155 / 160
Lys Phe Lys Ala Phe 165
(2) INFORMATION FOR SEQ ID NO: 153:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 213 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...213
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 153:
Met Asp Thr Glu Thr Gin Glu Lys Phe Leu Ala Tyr Leu Phe Glu Lys 1 5 10 15 Ala Leu Gin Lys Asn Leu Gin Ala Tyr Trp He Thr Thr Thr Glu Thr 20 25 30
Lys Asn Glu Leu Thr Arg Glu Glu Phe Ser Asn Leu He Arg Lys Thr
35 40 45
Met He Glu Leu He Leu His Asn Lys Ser He Gin He Asp Glu Thr 50 55 60
Leu Leu Asn Val Lys Glu His Leu Glu Lys Phe Tyr Ser Asn Lys Glu 65 70 75 80
Gin Glu Thr He Ala Lys Thr Leu Glu Ser Gin Thr Glu Leu Thr Cys 85 90 95 Ser Tyr Leu Leu Asp Lys Asp Phe Ser Leu Leu Glu Lys His Leu Glu 100 105 110
Asn Ser Leu Gly His Phe Thr Phe Glu Ser Glu Phe Ala Leu Leu Lys
115 120 125
Asp Lys Glu Pro Leu Asn Leu Ala Gin He Lys Gin He Gly Val Leu 130 135 140
Lys Val He Thr Tyr Glu Met Thr Gin Ala Leu Lys Asn Gin He He
145 150 155 160
His Leu Thr Gin He Val Asn Glu Glu Asn Leu Glu Phe Asp Glu Glu
165 170 175 Leu Val He Tyr His Leu Asn Phe Lys Leu Asn Gin Asn Thr Tyr Lys
180 185 190
Val Leu Ala Lys Phe Cys Val Leu Lys Lys Lys Gly Thr Leu His Glu
195 200 205
Lys Phe Lys Ala Phe 210
(2) INFORMATION FOR SEQ ID NO: 154:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 253 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc__feature
(B) LOCATION 1...253
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 154:
Met Ala He Ser He Lys Ser Pro Lys Glu He Lys Ala Leu Arg Lys 1 5 10 15 Ala Gly Glu Leu Thr Ala Gin Ala Leu Ala Leu Leu Glu Arg Glu Val 20 25 30
Arg Pro Gly Val Ser Leu Leu Glu Leu Asp Lys Met Ala Glu Asp Phe
35 40 45
He Lys Ser Ser His Ala Arg Pro Ala Phe Lys Gly Leu Tyr Gly Phe 50 55 60
Pro Asn Ser Val Cys Met Ser Leu Asn Glu Val Val He His Gly He 65 70 75 80
Pro Thr Asp Tyr Val Leu Gin Glu Gly Asp He He Gly Leu Asp Leu 85 90 95 Gly Val Glu Val Asp Gly Tyr Tyr Gly Asp Ser Ala Leu Thr Leu Pro 100 105 110
He Gly Ala He Ser Pro Gin Asp Glu Lys Leu Leu Ala Cys Ser Lys
115 120 125
Glu Ser Leu Met His Ala He Ser Ser He Arg Val Gly Met His Phe 130 135 140
Lys Glu Leu Ser Gin He Leu Glu Gly Ala He Thr Glu Arg Gly Phe
145 150 155 160
Val Pro Leu Lys Gly Phe Cys Gly His Gly He Gly Lys Lys Pro His
165 170 175 Glu Glu Pro Glu He Pro Asn Tyr Leu Glu Lys Gly Val Lys Ala Asn
180 185 190
Ser Gly Pro Lys He Lys Glu Gly Met Val Phe Cys Leu Glu Pro Met
195 200 205
Val Cys Gin Lys Gin Gly Glu Pro Lys He Leu Ala Asp Lys Trp Ser 210 215 220
Val Val Ser Val Asp Gly Leu Asn Thr Ser His His Glu His Thr He 225 230 235 240
Ala He Val Gly Asn Lys Ala Val He Leu Thr Glu Arg 245 250
(2) INFORMATION FOR SEQ ID NO: 155:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 247 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...247 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 155:
Lys Pro Lys Arg Asn Gin Ser Pro Lys Lys Ser Arg Glu Leu Thr Ala 1 5 10 15
Gin Ala Leu Ala Leu Leu Glu Arg Glu Val Arg Pro Gly Val Ser Leu 20 25 30
Leu Glu Leu Asp Lys Met Ala Glu Asp Phe He Lys Ser Ser His Ala
35 40 45
Arg Pro Ala Phe Lys Gly Leu Tyr Gly Phe Pro Asn Ser Val Cys Met 50 55 60 Ser Leu Asn Glu Val Val He His Gly He Pro Thr Asp Tyr Val Leu 65 70 75 80
Gin Glu Gly Asp He He Gly Leu Asp Leu Gly Val Glu Val Asp Gly
85 90 95
Tyr Tyr Gly Asp Ser Ala Leu Thr Leu Pro He Gly Ala He Ser Pro 100 105 110
Gin Asp Glu Lys Leu Leu Ala Cys Ser Lys Glu Ser Leu Met His Ala
115 120 125
He Ser Ser He Arg Val Gly Met His Phe Lys Glu Leu Ser Gin He
130 135 140 Leu Glu Gly Ala He Thr Glu Arg Gly Phe Val Pro Leu Lys Gly Phe
145 150 155 160
Cys Gly His Gly He Gly Lys Lys Pro His Glu Glu Pro Glu He Pro
165 170 175
Asn Tyr Leu Glu Lys Gly Val Lys Ala Asn Ser Gly Pro Lys He Lys 180 185 190
Glu Gly Met Val Phe Cys Leu Glu Pro Met Val Cys Gin Lys Gin Gly
195 200 205
Glu Pro Lys He Leu Ala Asp Lys Trp Ser Val Val Ser Val Asp Gly 210 215 220 Leu Asn Thr Ser His His Glu His Thr He Ala He Val Gly Asn Lys 225 230 235 240
Ala Val He Leu Thr Glu Arg 245 (2) INFORMATION FOR SEQ ID NO:156:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 340 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...340
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:156:
Met Tyr Arg Lys Asp Leu Asp Asn Tyr Leu Lys Gin Arg Leu Pro Lys 1 5 10 15
Ala Val Phe Leu Tyr Gly Glu Phe Asp Phe Phe He His Tyr Tyr He 20 25 30 Gin Thr He Ser Ala Leu Phe Lys Gly Asn Asn Pro Asp Thr Glu Thr 35 40 45
Ser Leu Phe Tyr Ala Ser Asp Tyr Glu Lys Ser Gin He Ala Thr Leu
50 55 60
Leu Glu Gin Asp Ser Leu Phe Gly Gly Ser Ser Leu Val He Leu Lys 65 70 75 80
Leu Asp Phe Ala Leu His Lys Lys Phe Lys Glu Asn Asp He Asn Pro
85 90 95
Phe Leu Lys Ala Leu Glu Arg Pro Ser His Asn Arg Leu He He Gly 100 105 110 Leu Tyr Asn Ala Lys Ser Asp Thr Thr Lys Tyr Lys Tyr Thr Ser Glu 115 120 125
He He Val Lys Phe Phe Gin Lys Ser Pro Leu Lys Asp Glu Ala He
130 135 140
Cys Val Arg Phe Phe Thr Pro Lys Ala Trp Glu Ser Leu Lys Phe Leu 145 150 155 160
Gin Glu Arg Ala Asn Phe Leu His Leu Asp He Ser Gly His Leu Leu
165 170 175
Asn Ala Leu Phe Glu He Asn Asn Glu Asp Leu Ser Val Ser Phe Asn 180 185 190 Asp Leu Asp Lys Leu Ala Val Leu Asn Ala Pro He Thr Leu Glu Asp 195 200 205
He Gin Glu Leu Ser Ser Asn Ala Gly Asp Met Asp Leu Gin Lys Leu
210 215 220
He Leu Gly Leu Phe Leu Lys Lys Ser Val Leu Asp He Tyr Asp Tyr 225 230 235 240
Leu Leu Lys Glu Gly Lys Lys Asp Ala Asp He Leu Arg Gly Leu Glu
245 250 255
Arg Tyr Phe Tyr Gin Leu Phe Leu Phe Phe Ala His He Lys Thr Thr 260 265 270 Gly Leu Met Asp Ala Lys Glu Val Leu Gly myr Ala Pro Pro Lys Glu 275 280 285
He Val Glu Asn Tyr Ala Lys Asn Ala Leu Arg Leu Lys Glu Ala Gly
290 295 300
Tyr Lys Arg Val Phe Glu He Phe Arg Leu Trp His Leu Gin Ser Met 305 310 315 320
Gin Gly Gin Lys Glu Leu Gly Phe Leu Tyr Leu Thr Pro He Gin Lys
325 330 335
He He Asn Pro 340 (2) INFORMATION FOR SEQ ID NO: 157:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 200 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...200 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 157:
Val Phe Met Thr Ser Ala Leu Leu Gly Leu Gin He Val Leu Ala Val 1 5 10 15
Leu He Val Val Val Val Leu Leu Gin Lys Ser Ser Ser He Gly Leu 20 25 30
Gly Ala Tyr Ser Gly Ser Asn Asp Ser Leu Phe Gly Ala Lys Gly Pro
35 40 45
Ala Ser Phe Met Ala Lys Leu Thr Met Phe Leu Gly Leu Leu Phe Val 50 55 60 He Asn Thr He Ala Leu Gly Tyr Phe Tyr Asn Lys Glu Tyr Gly Lys 65 70 75 80
Ser Val Leu Asp Glu Thr Lys Thr Asn Lys Glu Leu Ser Pro Leu Val
85 90 95
Pro Ala Thr Gly Thr Leu Asn Pro Thr Leu Asn Pro Thr Leu Asn Pro 100 105 110
Thr Leu Asn Pro Leu Glu Gin Ala Pro Thr Asn Pro Leu Met Pro Thr
115 120 125
Gin Thr Pro Lys Glu Leu Pro Lys Glu Pro Ala Lys Thr Pro Phe Val
130 135 140 Glu Ser Pro Lys Gin Asn Glu Lys Asn Glu Lys Asn Asp Ala Lys Glu
145 150 155 160
Asn Gly He Lys Gly Val Glu Lys Asn Lys Glu Asn Ala Lys Thr Pro
165 170 175
Pro Thr Thr His Gin Lys Pro Lys Thr His Ala Thr Thr Asn Ala His 180 185 190
Thr Asn Gin Lys Lys Asp Glu Lys 195 200
(2) INFORMATION FOR SEQ ID NO: 158:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 159 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...159
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:158: Met Arg Ser Pro Asn Leu Glu Lys Glu Glu Thr Glu He He Glu Thr 1 5 10 15
Leu Leu Val Arg Glu Lys Met Arg Leu Cys Pro Leu Tyr Trp Arg He
20 25 30
Leu Ala Phe Leu He Asp Ser Leu Leu Val Ala Phe Leu Leu Ser Asp 35 40 45
Leu Leu Arg Ala Cys Ala Phe Leu His Ser Leu Tyr Trp Leu Thr Asn
50 55 60
Pro He Tyr Tyr Ser Ala Phe Val Val Met Gly Phe He He Leu Tyr 65 70 75 80 Gly Val Tyr Glu He Phe Phe Val Cys Leu Cys Lys Met Ser Leu Ala
85 90 95
Lys Leu Val Phe Arg He Lys He He Asp He Tyr Leu Ala Asp Cys
100 105 110
Pro Ser Arg Ala He Leu Leu Lys Arg Leu Gly Leu Lys He Val Val 115 120 125
Phe Leu Cys Pro Phe Leu Trp Phe Val Val Phe Lys Asn Pro Tyr His
130 135 140
Arg Ala Trp His Glu Glu Lys Ser Lys Ser Leu Leu Val Leu Phe 145 150 155
(2) INFORMATION FOR SEQ ID NO: 159:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 234 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...234
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 159: Leu Asn Thr Asp Phe Ser His He Thr Asp He Glu Gly Met Arg Phe 1 5 10 15
Val Asn Glu Glu Asp Ala Leu Asn Lys Leu He Asn Glu He His Thr 20 25 30
Arg His He Asp Leu Lys Asp Ser He Met Leu Ala Leu Ser Phe Asn
35 40 45
Ala Leu Tyr Leu Ala Asn Ala Leu Ala Gin Lys Phe Gly Ala Thr Tyr 50 55 60 Asp He Leu Phe Leu Glu Pro He Leu Ala Pro Leu Asn Ser Lys Cys 65 70 75 80
Glu He Ala Leu Val Ser Glu Ser Met Asp He Val Met Asn Glu Ser
85 90 95
Leu He Asn Ser Phe Asp He Ala Leu Asp Tyr Val Tyr Gly Glu Ala 100 105 110
Lys Arg Ala Tyr Glu Glu Asp He Leu Ser His He Tyr Gin Tyr Arg
115 120 125
Lys Gly Asn Ala He Lys Ser Leu Lys Asp Lys Asn He Phe He Val
130 135 140 Asp Arg Gly He Glu Thr Gly Phe Arg Ala Gly Leu Gly Val Gin Thr
145 150 155 160
Cys Leu Lys Lys Glu Cys Gin Asp He Tyr He Leu Thr Pro He Leu
165 170 175
Ala Gin Asn Val Ala Gin Gly Leu Glu Ser Leu Cys Asp Gly Val He 180 185 190
Ser Val Tyr Arg Pro Glu Cys Phe Val Ser Val Glu His His Tyr Lys
195 200 205
Glu Leu Lys Arg Leu Ser Asn Glu Glu He Glu Lys Tyr Leu Gly Ala 210 215 220 Asn Asn Ala Pro Asn Leu Lys Lys Glu His 225 230
(2) INFORMATION FOR SEQ ID NO: 160: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 287 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...287
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 160:
Leu Lys Gin Ser Glu Met Ala Met Glu Phe Asn Asp Pro Arg Met Arg 1 5 10 15 Phe Phe He Gly Asp Val Arg Asp Leu Glu Arg Leu Asn Tyr Ala Leu
20 25 30
Glu Gly Val Asp He Cys He His Ala Ala Ala Leu Lys His Val Pro 35 40 45 He Ala Glu Tyr Asn Pro Leu Glu Cys He Lys Thr Asn He Met Gly 50 55 60
Ala Ser Asn Val He Asn Ala Cys Leu Lys Asn Glu He Ser Gin Val 65 70 75 80
He Ala Leu Ser Thr Asp Lys Ala Ala Asn Pro He Asn Leu Tyr Gly 85 90 95
Ala Thr Lys Leu Cys Ser Asp Lys Leu Phe Val Ser Ala Asn Asn Phe
100 105 110
Lys Gly Pro Ser Gin Thr Gin Phe Gly Val Val Arg Tyr Gly Asn Val 115 120 125 Val Gly Ser Arg Gly Ser Val Val Pro Phe Phe Lys Lys Leu Val Gin 130 135 140
Asn Lys Ala Ser Glu He Pro He Thr Asp He Arg Met Thr Arg Phe 145 150 155 160
Trp He Thr Leu Asp Glu Gly Val Ser Phe Val Leu Lys Ser Leu Lys 165 170 175
Arg Met His Gly Gly Glu He Phe Val Pro Lys He Pro Ser Met Lys
180 185 190
Met He Asp Leu Ala Lys Ala Leu Ala Pro Asn He Pro Thr Lys He 195 200 205 He Gly He Arg Pro Gly Glu Lys Leu His Glu Val Met He Pro Lys 210 215 220
Asp Glu Ser His Leu Ala Leu Glu Phe Glu Asp Phe Phe He He Gin 225 230 235 240
Pro Thr He Ser Phe Gin Thr Pro Lys Asp Tyr Thr Leu Thr Lys Leu 245 250 255
His Glu Lys Gly Gin Lys Val Ala Pro Asp Phe Glu Tyr Ser Ser His
260 265 270
Thr Asn Asn Gin Trp Leu Glu Pro Asp Asp Leu Leu Lys Leu Leu 275 280 285
(2) INFORMATION FOR SEQ ID NO: 161:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 201 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...201
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 161: Met Arg Leu His Thr Ala Phe Phe Gly He Asn Ser Leu Leu Val Ala 1 5 10 15
Thr Leu Leu He Ser Gly Cys Ser Leu Phe Lys Lys Arg Asn Thr Asn 20 25 30
Ala Gin Leu He Pro Pro Ser Ala Asn Gly Leu Gin Ala Pro He Tyr
35 40 45
Pro Pro Thr Asn Phe Thr Pro Arg Lys Ser He Gin Pro Leu Pro Ser 50 55 60 Pro Arg Leu Glu Asn Asn Asp Gin Pro He He Ser Ser Asn Pro Thr 65 70 75 80
Asn Ala He Pro Asn Thr Pro He Leu Thr Pro Asn Asn Val He Glu
85 90 95
Leu Asn Ala Val Gly Met Gly Val Ala Pro Glu Ser Thr He Ser Pro 100 105 110
Ser Gin Ala Leu Ala Leu Ala Lys Arg Ala Ala He Val Asp Gly Tyr
115 120 125
Arg Gin Leu Gly Glu Lys Met Tyr Gly He Arg Val Asn Ala Gin Asp
130 135 140 Thr Val Lys Asp Met Val Leu Gin Asn Ser Val He Lys Thr Arg Val
145 150 155 160
Asn Ala Leu He Arg Asn Ala Glu He Thr Glu Thr He Tyr Lys Asp
165 170 175
Gly Leu Cys Gin Val Ser Met Glu Leu Lys Leu Asp Gly Arg He Trp 180 185 190
Tyr Arg He Leu Ser Gly Ser Arg Gly 195 200
(2) INFORMATION FOR SEQ ID NO:162:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 355 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...355
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 162:
Met Ser Tyr Thr He Asn Lys Arg Phe Ser Val Gly Val Gly Leu Arg 1 5 10 15
Gly Leu Tyr Ala Thr Gly Ser Phe Asn Asn Thr Val Tyr Val Pro Leu
20 25 30
Glu Gly Ala Ser Val Leu Ser Ala Glu Gin He Leu Asn Leu Pro Asn 35 40 45 Asn Val Phe Ala Asp Gin Val Pro Ser Asn Met Met Thr Leu Leu Gly
50 55 60
Asn He Gly Tyr Gin Pro Ala Leu Asn Cys Gin Lys Ala Gly Gly Asp 65 70 75 80 Met Ser Asp Gin Ser Cys Gin Glu Phe Tyr Asn Gly Leu Lys Lys He
85 90 95
Met Gly Tyr Ser Gly Leu He Lys Ala Ser Ala Asn Leu Tyr Gly Thr
100 105 110
Thr Gin Val Val Gin Lys Ser Asn Gly Gin Gly Val Ser Gly Gly Tyr 115 120 125
Arg Val Gly Ser Ser Leu Arg Val Phe Asp His Gly Met Phe Ser Val
130 135 140
Val Tyr Asn Ser Ser Val Thr Phe Asn Met Lys Gly Gly Leu Val Ala 145 150 155 160 He Thr Glu Leu Gly Pro Ser Leu Gly Ser Val Leu Thr Lys Gly Ser
165 170 175
Leu Asn He Asn Val Ser Leu Pro Gin Thr Leu Ser Leu Ala Tyr Ala
180 185 190
His Gin Phe Phe Lys Asp Arg Leu Arg Val Glu Gly Val Phe Glu Arg 195 200 205
Thr Phe Trp Ser Gin Gly Asn Lys Phe Leu Val Thr Pro Asp Phe Ala
210 215 220
Asn Ala Thr Tyr Lys Gly Leu Ser Gly Thr Val Ala Ser Leu Asp Ser 225 230 235 240 Glu Thr Leu Lys Lys Met Val Gly Leu Ala Asn Phe Lys Ser Val Met
245 250 255
Asn Met Gly Ala Gly Trp Arg Asp Thr Asn Thr Phe Arg Leu Gly Val
260 265 270
Thr Tyr Met Gly Lys Ser Leu Arg Leu Met Gly Ala He Asp Tyr Asp 275 280 285
Gin Ala Pro Ser Pro Gin Asp Ala He Gly He Pro Asp Ser Asn Gly
290 295 300
Tyr Thr Val Ala Phe Gly Thr Lys Tyr Asn Phe Arg Gly Phe Asp Leu 305 310 315 320 Gly Val Ala Gly Ser Phe Thr Phe Lys Ser Asn Arg Ser Ser Leu Tyr
325 330 335
Gin Ser Pro Thr He Gly Gin Leu Arg He Phe Ser Ala Ser Leu Gly
340 345 350
Tyr Arg Trp 355
(2) INFORMATION FOR SEQ ID NO:163:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 587 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...587
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:163:
Met Lys Asn Phe Ser Pro Leu Tyr Cys Leu Lys Lys Leu Lys Lys Arg 1 5 10 15 His Leu He Ala Leu Ser Leu Pro Leu Leu Ser Tyr Ala Asn Gly Phe 20 25 30
Lys He Gin Glu Gin Ser Leu Asn Gly Thr Ala Leu Gly Ser Ala Tyr
35 40 45
Val Ala Gly Ala Arg Gly Ala Asp Ala Ser Phe Tyr Asn Pro Ala Asn 50 55 60
Met Gly Phe Thr Asn Asp Trp Gly Glu Asn Arg Ser Glu Phe Glu Met 65 70 75 80
Thr Thr Thr Val He Asn He Pro Ala Phe Ser Phe Lys Val Pro Thr 85 90 95 Thr Asn Gin Gly Leu Tyr Ser Val Thr Ser Leu Glu He Asp Lys Ser 100 105 110
Gin Gin Asn He Leu Gly He He Asn Thr He Gly Leu Gly Asn He
115 120 125
Leu Lys Ala Leu Gly Asn Thr Ala Ala Thr Asn Gly Leu Ser Gin Ala 130 135 140
He Asn Arg Val Gin Gly Leu Met Asn Leu Thr Asn Gin Lys Val Val
145 150 155 160
Thr Leu Ala Ser Lys Pro Asp Thr Gin He Val Asn Gly Trp Thr Gly
165 170 175 Thr Thr Asn Phe Val Leu Pro Lys Phe Phe Tyr Lys Thr Arg Thr His
180 185 190
Asn Gly Phe Thr Phe Gly Gly Ser Phe Thr Ala Pro Ser Gly Leu Gly
195 200 205
Met Lys Trp Asn Gly Lys Gly Gly Glu Phe Leu His Asp Val Phe He 210 215 220
Met Met Val Glu Leu Ala Pro Ser Met Ser Tyr Thr He Asn Lys Arg
225 230 235 240
Phe Ser Val Gly Val Gly Leu Arg Gly Leu Tyr Ala Thr Gly Ser Phe
245 250 255 Asn Asn Thr Val Tyr Val Pro Leu Glu Gly Ala Ser Val Leu Ser Ala
260 265 270
Glu Gin He Leu Asn Leu Pro Asn Asn Val Phe Ala Asp Gin Val Pro
275 280 285
Ser Asn Met Met Thr Leu Leu Gly Asn He Gly Tyr Gin Pro Ala Leu 290 295 300
Asn Cys Gin Lys Ala Gly Gly Asp Met Ser Asp Gin Ser Cys Gin Glu
305 310 315 320
Phe Tyr Asn Gly Leu Lys Lys He Met Gly Tyr Ser Gly Leu He Lys
325 330 335 Ala Ser Ala Asn Leu Tyr Gly Thr Thr Gin Val Val Gin Lys Ser Asn
340 345 350
Gly Gin Gly Val Ser Gly Gly Tyr Arg Val Gly Ser Ser Leu Arg Val
355 360 365
Phe Asp His Gly Met Phe Ser Val Val Tyr Asn Ser Ser Val Thr Phe 370 375 380
Asn Met Lys Gly Gly Leu Val Ala He Thr Glu Leu Gly Pro Ser Leu 385 390 395 400
Gly Ser Val Leu Thr Lys Gly Ser Leu Asn He Asn Val Ser Leu Pro 405 410 415
Gin Thr Leu Ser Leu Ala Tyr Ala His Gin Phe Phe Lys Asp Arg Leu
420 425 430
Arg Val Glu Gly Val Phe Glu Arg Thr Phe Trp Ser Gin Gly Asn Lys 435 440 445 Phe Leu Val Thr Pro Asp Phe Ala Asn Ala Thr Tyr Lys Gly Leu Ser 450 455 460
Gly Thr Val Ala Ser Leu Asp Ser Glu Thr Leu Lys Lys Met Val Gly 465 470 475 480
Leu Ala Asn Phe Lys Ser Val Met Asn Met Gly Ala Gly Trp Arg Asp 485 490 495
Thr Asn Thr Phe Arg Leu Gly Val Thr Tyr Met Gly Lys Ser Leu Arg
500 505 510
Leu Met Gly Ala He Asp Tyr Asp Gin Ala Pro Ser Pro Gin Asp Ala 515 520 525 He Gly He Pro Asp Ser Asn Gly Tyr Thr Val Ala Phe Gly Thr Lys 530 535 540
Tyr Asn Phe Arg Gly Phe Asp Leu Gly Val Ala Gly Ser Phe Thr Phe 545 550 555 560
Lys Ser Asn Arg Ser Ser Leu Tyr Gin Ser Pro Thr He Gly Gin Leu 565 570 575
Arg He Phe Ser Ala Ser Leu Gly Tyr Arg Trp 580 585
(2) INFORMATION FOR SEQ ID NO:164:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 205 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...205
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:164:
Leu He Phe Arg Phe Phe Leu He Leu Ser Leu Leu Lys Gly Val Leu 1 5 10 15
Leu Ala Lys Lys Asp Trp Asn Phe Phe Lys Pro Leu Glu Pro Thr Lys
20 25 30
Lys Tyr Phe Gly Ser Phe Lys He Gly Tyr Leu Tyr Gin His Ala Glu 35 40 45 Thr Thr Lys Arg Phe Pro He Arg Pro Lys Asn Arg Pro Pro He Leu
50 55 60
Met Asp Lys He Tyr His Asp Ala Ser Leu Gly Phe Asp Ala Gly Tyr 65 70 75 80 Val Leu Lys Lys Lys Ala Leu Leu Gly Gly Tyr Leu Asp Ala Gly Met
85 90 95
Gly Asp Ser Tyr Phe Met Ser Ala Gly Leu Val Ala Gly Val Arg Leu
100 105 110
Phe Lys Gly Trp Val He Pro Lys He Ala Leu Gly Tyr Gin Leu Gin 115 120 125
He Leu Gly Ala Lys He Asp Lys Tyr Gin Phe Asn He Gin Ser Ala
130 135 140
Val Gly Ser Val Gly Leu Phe Phe Asn Ala Ala Lys Asn Phe Gly Leu 145 150 155 160 Ser He Glu Ala Arg Gly Gly He Pro Phe Tyr Phe He Gin Ser Arg
165 170 175
Phe Ser Lys Ala Phe Gly Thr Pro Arg Leu Asn He Tyr Ser Val Gly
180 185 190
He Thr Phe Thr Phe Tyr Asp Phe Thr Arg Phe Leu Gly 195 200 205
(2) INFORMATION FOR SEQ ID NO: 165:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 253 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...253 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 165:
Leu Trp His Ala Ala Phe Ser Val Gly Glu Trp Gly Trp Asn Gly Asp 1 5 10 15
Glu He Pro Tyr Arg Asp Cys Asp Glu Trp Gly Leu Asp Asp Phe Tyr 20 25 30
Gly Val Lys Pro Thr As^ ys Ala Gly Val Leu Ser Phe Ala Arg Ser
35 40 45
His Arg Arg Gin Asn Gin Ala Val Leu Ser Lys Pro Lys Ser Phe Arg 50 55 60 Met Lys Lys He Ala Phe He Leu Ala Leu Trp Val Gly Leu Leu Gly 65 70 75 80
Ala Phe Glu Pro Lys Lys Ser His He Tyr Phe Gly Ala Met Val Gly
85 90 95
Leu Ala Pro Val Lys He Thr Pro Lys Pro Ala Ser Asp Ser Ser Tyr 100 105 110
Thr Ala Phe Leu Trp Gly Ala Lys Gly Gly Tyr Gin Phe Ala Phe Phe
115 120 125
Lys Ala Leu Ala Leu Arg Gly Glu Phe Ser Tyr Leu Met Ala He Lys 130 135 140
Pro Thr Ala Leu His Thr He Asn Thr Ser Leu Leu Ser Leu Asn Met
145 150 155 160
Asp Val Leu Ser Asp Phe Tyr Thr Tyr Lys Lys Tyr Ser Phe Gly Val
165 170 175 Tyr Gly Gly Leu Gly He Gly Tyr Phe Tyr Gin Ser Asn His Leu Gly
180 185 190
Met Lys Asn Ser Ser Phe Met Gly Tyr Asn Gly Leu Phe Asn Val Gly
195 200 205
Leu Gly Ser Thr He Asp Arg His His Arg Val Glu Leu Gly Ala Lys 210 215 220
He Pro Phe Ser Lys Thr Arg Asn Ser Phe Lys Asn Ser Tyr Phe Leu 225 230 235 240
Glu Ser Val Phe He His Ala Ala Tyr Ser Tyr Met Phe 245 250
(2) INFORMATION FOR SEQ ID NO: 166:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 412 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...412
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 166:
Met Glu Ser Val Lys Thr Val Lys Thr Asn Lys Val Gly Lys Asn Thr 1 5 10 15
Glu Thr Ala Asn Thr Glu Ala Ser Lys Glu Thr His Phe Lys Gin Ala 20 25 30 r;er Ala He Thr Asn Thr Leu Arg Ser He Gly Gly He Phe Thr Lys 35 40 45
He Ala Lys Lys Val Arg Glu Leu Val Lys Lys His Pro Lys Lys Ser
50 55 60
Ser Val Ala Leu Val Val Leu Thr His He Ala Cys Lys Arg Ala Lys 65 70 75 80
Glu Leu Asp Asp Lys Val Gin Asp Lys Ser Lys Gin Ala Glu Lys Glu
85 90 95
Asn Gin He Asn Trp Trp Lys Tyr Ser Gly Leu Thr He Ala Ala Ser 100 105 110 Leu Leu Leu Ala Ala Cys Ser Thr Gly Asp He Asp Lys Gin He Glu
115 120 125
Leu Glu Gin Glu Lys Lys Glu Ala Asn Lys Ser Gly He Lys Leu Glu
130 135 140 Gin Glu Arg Gin Lys Thr Glu Gin Glu Arg Gin Lys Thr Asn Lys Ser
145 150 155 160
Glu He Glu Leu Glu Gin Glu Arg Gin Lys Thr Asn Lys Ser Gly He
165 170 175
Glu Leu Ala Asn Ser Gin He Lys Ala Glu Gin Glu Arg Gin Lys Thr 180 185 190
Glu Gin Glu Lys Gin Lys Ala Asn Lys Ser Glu He Glu Leu Glu Gin
195 200 205
Gin Lys Gin Lys Thr He Asn Thr Gin Arg Asp Leu He Lys Glu Gin
210 215 220 Lys Asp Phe He Lys Glu Thr Glu Gin Asn Cys Gin Glu Lys His Gly
225 230 235 240
Gin Leu Phe He Lys Lys Ala Arg He Lys Thr Gly He Thr Thr Gly
245 250 255
He Ala He Glu He Glu Ala Glu Cys Lys Thr Pro Lys Pro Ala Lys 260 265 270
Thr Asn Gin Thr Pro He Gin Pro Lys His Leu Pro Asn Ser Lys Gin
275 280 285
Pro Arg Ser Gin Arg Gly Ser Lys Ala Gin Glu Leu He Ala Tyr Leu
290 295 300 Gin Lys Glu Leu Glu Ser Leu Pro Tyr Ser Gin Lys Ala He Ala Lys
305 310 315 320
Gin Val Asp Phe Tyr Lys Pro Ser Ser He Ala Tyr Leu Glu Leu Asp
325 330 335
Pro Arg Asp Phe Lys Val Thr Glu Glu Trp Gin Lys Glu Asn Leu Lys 340 345 350
He Arg Ser Lys Ala Gin Ala Lys Met Leu Glu Met Arg Asn Pro Gin
355 360 365
Ala His Leu Pro Thr Ser Gin Ser Leu Leu Phe Val Gin Lys He Phe 370 375 380 Ala Asp He Asn Lys Glu He Glu Ala Val Ala Asn Thr Glu Lys Lys 385 390 395 400
Thr Glu Lys Ala Gly Tyr Gly Tyr Ser Lys Arg Met 405 410 (2) INFORMATION FOR SEQ ID NO: 167:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 149 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...149
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 167:
Leu Asn Trp Glu His Leu Met Lys Lys Leu Ala Phe Ser Leu Leu Phe 1 5 10 15
Thr Gly Thr Phe Leu Gly Leu Phe Leu Asn Ala Ser Asp Phe Lys Ser 20 25 30 Met Asp Asn Lys Gin Leu Leu Glu Gin Ala Gly Lys Val Ala Pro Ser 35 40 45
Glu Val Pro Glu Phe Arg Thr Glu Val Asn Lys Arg Leu Glu Ala Met
50 55 60
Lys Glu Glu Glu Arg Gin Lys Tyr Lys Ala Asp Phe Lys Lys Ala Met 65 70 75 80
Asp Lys Asn Leu Ala Ser Leu Ser Gin Glu Asp Arg Asn Lys Arg Lys
85 90 95
Lys Glu He Leu Glu Val He Ala Asn Lys Lys Lys Thr Met Thr Met 100 105 110 Lys Glu Tyr Arg Glu Glu Gly Leu Asp Leu His Asp Cys Ala Cys Glu 115 120 125
Gly Pro Phe His Asp His Glu Lys Lys Gly Gin Lys Gly Lys Lys Pro
130 135 140
Ser His His Lys His 145
(2) INFORMATION FOR SEQ ID NO: 168:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 204 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: .68:
Met Gin Ala Val He Leu Ala Asn Gly Glu Phe Pro Lys Ser Lys Lys 1 5 10 15
Cys Leu Asp He Leu Gin Asn Ala Pro Phe Leu He Ala Cys Asp Gly 20 25 30
Ala Val He Ser Leu His Ala Leu Gin Phe Lys Pro Ser Val Val He
35 40 45
Gly Asp Leu Asp Ser He Asp Ser His Leu Lys Ala Leu Tyr Asn Pro 50 55 60 Ile Arg Val Ser Glu Gin Asp Ser Asn Asp Leu Ser Lys Ala Phe Phe 65 70 75 80
Tyr Ala Leu Asn Arg Gly Cys Asp Asp Phe He Phe Leu Gly Leu Asn 85 90 95 Gly Lys Arg Glu Asp His Ala Leu Ala Asn Thr Phe Leu Leu Leu Glu 100 105 110
Tyr Phe Lys Phe Cys Lys Lys He Gin Ser Val Ser Asp Tyr Gly Leu
115 120 125
Phe Arg Val Leu Glu Thr Pro Phe Thr Leu Pro Ser Phe Lys Gly Glu 130 135 140
Gin He Ser Leu Phe Ser Leu Asp Leu Lys Ala Arg Phe Thr Ser Lys 145 150 155 160
Asn Leu Lys Tyr Pro Leu Lys Asp Leu Arg Leu Lys Thr Leu Phe Ser 165 170 175 Gly Ser Leu Asn Glu Ala Thr Asn His Cys Phe Ser Leu Ser Ser Glu 180 185 190
Pro Lys Ser Val Val Leu Val Tyr Gin Lys Phe Ser 195 200 (2) INFORMATION FOR SEQ ID NO: 169:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 280 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...280
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 169: Val Phe Asp Ser Leu Gly Gly Phe Leu Gly Tyr Lys Thr Phe Lys Pro
1 5 10 15
He Val Asp Lys Val Lys Asn He Asn Ala Trp He Lys Asn Tyr Asp
20 25 30
Asn Lys Lys Ala Gin Glu He Met Gly Phe He Glu Asn Pro Thr Pro 35 40 45
Asp Phe Gin As.. :.sn Lys Phe Leu Cys Val Leu Asn Arg Gin Gly Thr
50 55 60
Arg His Asn Asn Tyr Leu Gly Leu Thr Ser Thr Asn Leu Leu He Gly 65 70 75 80 Ala He Tyr Phe Ser He Arg His Cys He Lys Ala Thr Trp Gin Asn
85 90 95
Asp Arg Asp Gin Phe Tyr Ala Pro Tyr Asp Asp Ala Phe Gin Asp Asp
100 105 110
Ser Glu Phe Lys Asn Asn Cys Leu Ala Phe Met Leu Phe His Thr Gin 115 120 125
Asn Arg He Thr Ala Thr Gin Gly Thr Asn His Phe He Pro Phe Ser
130 135 140
Glu Asp Glu Val Asp Ser Lys Glu Arg Tyr Leu Ser His Ala Leu Leu 145 150 155 160
Asp Phe Leu Lys Gly Glu He Lys Glu Pro Lys Lys Ser Asp Ser Leu
165 170 175
Phe Leu Asn Ala Lys Lys Glu Asn Lys Pro Leu Lys Phe Ser Ser Ser 180 185 190 Ala Ser Lys Val Phe Asp Ala Gly Arg Glu He Tyr Arg Tyr Tyr His 195 200 205
Thr Gin Asp Phe He His Thr Pro Tyr Asn Ala Asn Ala Ser Leu Tyr
210 215 220
Asp He Lys Glu Phe Phe Gin Gly Arg Asn Lys Gin Gly Arg Leu Asn 225 230 235 240
Ser Pro Thr Lys Ala Lys Asp Glu Tyr Tyr Lys Gin Leu Tyr Ala Asn
245 250 255
Leu Gin Tyr Ala Leu Lys Asp Leu Ala Lys Glu He Gin Pro Lys Val 260 265 270 Tyr Glu Tyr Gly Phe Leu Arg Glu 275 280
(2) INFORMATION FOR SEQ ID NO: 170: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 309 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...309
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 170:
Cys Asp Arg Ala He Pro His Trp Leu Phe Ser Leu Gly Tyr Arg Tyr 1 5 10 15 Pro Pro Pro Leu Lys Pro Thr Asn Ala Phe Asn Leu Glu Val Phe Asp 20 25 30
Ser Leu Gly Gly Phe Leu Gly Tyr Lys Thr Phe Lys Pro He Val Asp
35 40 45
Lys Val Lys Asn He Asn Ala Trp He Lys Asn Tyr Asp Asn Lys Lys 50 55 60
Ala Gin Glu He Met Gly Phe He Glu Asn Pro Thr Pro Asp Phe Gin 65 70 75 80
Asn Asn Lys Phe Leu Cys Val Leu Asn Arg Gin Gly Thr Arg His Asn 85 90 95 Asn Tyr Leu Gly Leu Thr Ser Thr Asn Leu Leu He Gly Ala He Tyr
100 105 110
Phe Ser He Arg His Cys He Lys Ala Thr Trp Gin Asn Asp Arg Asp 115 120 125 Gin Phe Tyr Ala Pro Tyr Asp Asp Ala Phe Gin Asp Asp Ser Glu Phe 130 135 140
Lys Asn Asn Cys Leu Ala Phe Met Leu Phe His Thr Gin Asn Arg He 145 150 155 160
Thr Ala Thr Gin Gly Thr Asn His Phe He Pro Phe Ser Glu Asp Glu 165 170 175
Val Asp Ser Lys Glu Arg Tyr Leu Ser His Ala Leu Leu Asp Phe Leu
180 185 190
Lys Gly Glu He Lys Glu Pro Lys Lys Ser Asp Ser Leu Phe Leu Asn 195 200 205 Ala Lys Lys Glu Asn Lys Pro Leu Lys Phe Ser Ser Ser Ala Ser Lys 210 215 220
Val Phe Asp Ala Gly Arg Glu He Tyr Arg Tyr Tyr His Thr Gin Asp 225 230 235 240
Phe He His Thr Pro Tyr Asn Ala Asn Ala Ser Leu Tyr Asp He Lys 245 250 255
Glu Phe Phe Gin Gly Arg Asn Lys Gin Gly Arg Leu Asn Ser Pro Thr
260 265 270
Lys Ala Lys Asp Glu Tyr Tyr Lys Gin Leu Tyr Ala Asn Leu Gin Tyr 275 280 285 Ala Leu Lys Asp Leu Ala Lys Glu He Gin Pro Lys Val Tyr Glu Tyr 290 295 300
Gly Phe Leu Arg Glu 305 (2) INFORMATION FOR SEQ ID NO: 171:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 187 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...187
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 171: Leu Glu Thr Tyr He He Asp Ala Asp Asn He Asp Gly Asp Leu Phe 1 5 10 15
Phe Tyr Asn Leu Thr Arg Asn Ser Asn Asp Phe Ser Met Leu Pro Val
20 25 30
Phe Glu Leu Asp Arg He Ala Gin Lys He Arg Asn He Leu Lys Lys 35 40 45
His Gly Ser Arg Lys Asp He He Leu Lys His Asn Glu He Lys Glu
50 55 60
Ala Phe Phe Ser Pro Phe Lys Pro Gin Leu Lys Thr Val Gin Val Phe 65 70 75 80
Leu Ser His Ser His Ala Asp Lys Asn Lys Ala Leu Gly Val Lys Asp
85 90 95
Tyr Leu Glu Ser Lys Thr Lys Arg Lys Val Phe He Asp Ser Leu Phe 100 105 110 Trp Asp Tyr Lys Asp Asp Val Leu Asn Lys Leu Ala Lys His Asp Asp 115 120 125
He Ser Lys He Glu Asp Ala Phe Thr Leu He Leu Arg Lys Ser Leu
130 135 140
Gin Asp Met He Glu Lys Cys Pro Tyr Phe Val Phe Leu Gin Ser Lys 145 150 155 160
Asn Ser Val Ser Asn Gin Gly Leu Ser Arg He Thr Tyr Ser Ala Trp
165 170 175
He Tyr Glu Glu Leu Lys He Ala Ser Phe Tyr 180 185
(2) INFORMATION FOR SEQ ID NO: 172:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 198 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...198
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 172:
Leu Glu Thr Tyr He He Asp Ala Asp Asn He Asp Gly Asp Leu Phe 1 5 10 15
Phe Tyr Asn Leu Thr Arg Asn Ser Asn Asp Phe Ser Met Leu Pro Val 20 25 30 Phe Glu Leu Asp Arg He Ala Gin Lyπ He Arg Asn He Leu Lys Lys 35 40 45
His Gly Ser Arg Lys Asp He He Leu Lys His Asn Glu He Lys Glu
50 55 60
Ala Phe Phe Ser Pro Phe Lys Pro Gin Leu Lys Thr Val Gin Val Phe 65 70 75 80
Leu Ser His Ser His Ala Asp Lys Asn Lys Ala Leu Gly Val Lys Asp
85 90 95
Tyr Leu Glu Ser Lys Thr Lys Arg Lys Val Phe He Asp Ser Leu Phe 100 105 110 Trp Asp Tyr Lys Asp Asp Val Leu Asn Lys Leu Ala Lys His Asp Asp
115 120 125
He Ser Lys He Glu Asp Ala Phe Thr Leu He Leu Arg Lys Ser Leu
130 135 140 Gin Asp Met He Glu Lys Cys Pro Tyr Phe Val Phe Leu Gin Ser Lys
145 150 155 160
Asn Ser Val Ser Asn Gin Gly Leu Ser Arg He Thr Tyr Ser Ala Trp
165 170 175
He Tyr Glu Glu Leu Lys He Ala Ser Phe Leu Leu Ala Leu Leu Thr 180 185 190
Arg Val Ala Gin Phe Gin 195
(2) INFORMATION FOR SEQ ID NO:173:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 189 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...189
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:173:
Met Met Thr Lys Asn Ala Tyr Ala Phe Val Val He Glu Lys Ser He 1 5 10 15
Met Val Phe Lys Cys Ala Lys Asp Lys Gly Leu He Pro He Thr Glu
20 25 30
Gly Phe Val Pro Leu Lys Glu Gly Phe Leu Arg Ser Phe Lys Glu Arg 35 40 45 Cys Asn Leu Asp Phe Leu Glu Asn Leu Asp Leu Leu Phe Leu Tyr Asp 50 55 60
Tyr Gin Phe Pro Ser Glu Val Phe Ser Leu Cys Lys Asp Leu Lys Asn 65 70 75 80
Ser He Trp Asp Arg Lys Leu Val Val Val Leu Val Glu Ala Leu Glu 85 90 95
Gly Phe I /s Gly Leu Asn Leu Ser Leu Lys He Glu Asp Arg His Ser
100 105 110
Asn Ser Leu Gly Asn Gly Val Gin Lys Leu Leu Thr Asn Ala Asp Leu 115 120 125 Gly Ser Asn His Lys Pro He Val He Asp Ser Met Lys Thr Tyr His 130 135 140
Gin Ser Gin Gin Glu Lys Tyr Lys Arg Glu Arg Gly Glu Thr Leu Glu 145 150 155 160
Val Arg Pro Thr Thr Pro Pro Ser Tyr Gly Gly Gly Ser He Arg He 165 170 175
Ser Gly Asp Lys Lys Pro Asp Ser Asn Glu Glu Asn Phe 180 185 (2) INFORMATION FOR SEQ ID NO: 174:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 590 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...590
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 174: Met Lys Ala He Lys He Leu Leu He Met Thr Leu Ser Leu Asn Ala 1 5 10 15
He Ser Val Asn Arg Ala Leu Phe Asp Leu Lys Asp Ser Gin Leu Lys
20 25 30
Gly Glu Leu Thr Pro Lys He Val Asp Phe Gly Gly Tyr Lys Ser Asn 35 40 45
Thr Thr Glu Trp Gly Ala Thr Ala Leu Asn Tyr He Asn Ala Ala Asn
50 55 60
Gly Asp Ala Lys Lys Phe Ser Ala Leu Val Glu Lys Met Arg Phe Asn 65 70 75 80 Ser Gly He Leu Gly Asn Phe Arg Ala His Ala His Leu Arg Gin Ala
85 90 95
Leu Lys Leu Gin Lys Asn Leu Lys Tyr Cys Leu Lys He He Ala Arg
100 105 110
Asp Ser Phe Tyr Ser Tyr Arg Thr Gly He Tyr He Pro Leu Gly He 115 120 125
Ser Leu Lys Asp Gin Lys Thr Ala Gin Lys Met Leu Ala Asp Leu Ser
130 135 140
Val Val Gly Ala Tyr Leu Lys Lys Gin Gin Glu Asn Glu Lys Ala Gin 145 150 155 160 Ser Pro Tyr Tyr Arg Ser Asn Asn Tyr Tyr Asn Ser Tyr Tyr Ser Pro
165 170 175
Tyr Tyr Gly Met Tyr Gly Met Tyr Gly Met Gly Met Tyr Gly Met Tyr
180 185 190
Gly Met Gly Met Tyr Asp Phe Tyr Asp Phe Tyr Asp Gly Met Tyr Gly 195 200 205
Phe Tyr Pro Asn Met Phe Phe Met Met Gin Val Gin Asp Tyr Leu Met
210 215 220
Leu Glu Asn Tyr Met Tyr Ala Leu Asp Gin Glu Glu He Leu Asp His 225 230 235 240 Asp Ala Ser He Asn Gin Leu Asp Thr Pro Thr Asp Asp Asp Arg Asp
245 250 255
Asp Lys Asp Asp Lys Ser Ser Gin Pro Ala Asn Leu Met Ser Phe Tyr 260 265 270 Arg Asp Pro Lys Phe Ser Lys Asp He Gin Thr Asn Arg Leu Asn Ser 275 280 285
Ala Leu Val Asn Leu Asp Asn Ser His Met Leu Lys Asp Asn Ser Leu
290 295 300
Phe His Thr Lys Ala Met Pro Thr Lys Ser Val Asp Ala He Thr Ser 305 310 315 320
Gin Ala Lys Glu Leu Asn His Leu Val Gly Gin He Lys Glu Met Lys
325 330 335
Gin Asp Gly Ala Ser Pro Asn Lys He Asp Ser Val Val Asn Lys Ala 340 345 350 Met Glu Val Arg Asp Lys Leu Asp Asn Asn Leu Asn Gin Leu Asp Asn 355 360 365
Asp Leu Lys Asp Gin Lys Gly Leu Ser Ser Glu Gin Gin Ala Gin Val
370 375 380
Asp Lys Ala Leu Asp Ser Val Gin Gin Leu Ser His Ser Ser Asp Val 385 390 395 400
Val Gly Asn Tyr Leu Asp Gly Ser Leu Lys He Asp Gly Asp Asp Arg
405 410 415
Asp Asp Leu Asn Asp Ala He Asn Asn Pro Met Gin Gin Pro Ala Gin 420 425 430 Gin Thr Pro He Asn Asn Met Asp Asn Thr His Ala Asn Asp Ser Lys 435 440 445
Asp Gin Gly Gly Asn Ala Leu He Asn Pro Asn Asn Ala Thr Asn Asp
450 455 460
Asp His Asn Asp Asp His Met Asp Thr Asn Thr Thr Asp Thr Ser Asn 465 470 475 480
Ala Asn Asp Thr Pro Thr Asp Asp Lys Asp Ala Ser Gly Asn Asn Thr
485 490 495
Gly Asp Met Asn Asn Thr Asp Thr Gly Asn Thr Asp Thr Gly Asn Thr 500 505 510 Asp Thr Gly Asn Thr Asp Asp Met Ser Asn Met Asn Asn Gly Asn Asp 515 520 525
Asp Thr Gly Asn Thr Asn Asp Asp Met Gly Asn Ser Asn Asp Met Gly
530 535 540
Asp Asp Met Asn Asn Ala Asn Asp Met Asn Asp Asp Met Gly Asn Ser 545 550 555 560
Asn Asp Asp Met Gly Asp Met Gly Asp Met Asn Asp Asp Met Gly Gly
565 570 575
Asp Met Gly Asp Met Gly Asp Met Gly Gly Asp Met Gly Asn 580 585 590
(2) INFORMATION FOR SEQ ID NO: 175:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 195 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...195 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:175:
Leu Asn Leu Arg Leu Ala Gly Ala Ser Val Leu Thr Ala Cys Val Phe 1 5 10 15
Ser Gly Cys Phe Phe Leu Lys Met Phe Asp Lys Lys Leu Ser Ser Asn 20 25 30
Asp Trp His He Gin Lys Val Glu Met Asn His Gin Val Tyr Asp He
35 40 45
Glu Thr Met Leu Ala Asp Ser Ala Phe Arg Glu His Glu Glu Glu Gin 50 55 60 Asp Ser Ser Leu Asn Thr Ala Leu Pro Glu Asp Lys Thr Ala He Glu 65 70 75 80
Ala Lys Glu Gin Glu Gin Lys Glu Lys Arg Lys His Trp Tyr Glu Leu
85 90 95
Phe Lys Lys Lys Pro Lys Pro Lys Ser Ser Met Gly Glu Phe Val Phe 100 105 110
Asp Gin Lys Glu Asn Arg He Tyr Gly Lys Gly Tyr Cys Asn Arg Tyr
115 120 125
Phe Ala Ser Tyr Thr Trp Gin Gly Asp Arg His He Ala He Glu Asp
130 135 140 Ser Gly He Ser Arg Lys Val Cys Arg Asp Glu His Leu Met Ala Phe
145 150 155 160
Glu Leu Glu Phe Met Glu Asn Phe Lys Gly Asn Phe Ala Val Thr Lys
165 170 175
Gly Lys Asp Thr Leu He Leu Asp Asn Gin Lys Met Lys He Tyr Leu 180 185 190
Lys Thr Pro 195
(2) INFORMATION FOR SEQ ID NO: 176:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 744 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: - otein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...744
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 176: Met Leu Lys Leu Ala Ser Lys Thr He Cys Leu Ser Leu He Ser Ser 1 5 10 15
Phe Thr Ala Val Glu Ala Phe Gin Lys His Gin Lys Asp Gly Phe Phe
20 25 30
He Glu Ala Gly Phe Glu Thr Gly Leu Leu Gin Gly Thr Gin Thr Gin 35 40 45
Glu Gin Thr He Ala Thr Thr Gin Glu Lys Pro Lys Pro Lys Pro Lys
50 55 60
Pro Lys Pro He Thr Pro Gin Ser Thr Tyr Gly Lys Tyr Tyr He Ser 65 70 75 80 Gin Ser Thr He Leu Lys Asn Ala Thr Glu Leu Phe Ala Glu Asp Asn
85 90 95
He Thr Asn Leu Thr Phe Tyr Ser Gin Asn Pro Val Tyr Val Thr Ala
100 105 110
Tyr Asn Gin Glu Ser Ala Glu Glu Ala Gly Tyr Gly Asn Asn Ser Leu 115 120 125
He Met He Gin Asn Phe Leu Pro Tyr Asn Leu Asn Asn He Glu Leu
130 135 140
Ser Tyr Thr Asp Asp Gin Gly Asn Val Val Ser Leu Gly Val He Glu 145 150 155 160 Thr He Pro Lys Gin Ser Gin He He Leu Pro Ala Ser Leu Phe Asn
165 170 175
Asp Pro Gin Leu Asn Ala Asp Gly Phe Gin Gin Leu Gin Thr Asn Thr
180 185 190
Thr Arg Phe Ser Asp Ala Ser Thr Gin Asn Leu Phe Asn Lys Leu Ser 195 200 205
Lys Val Thr Thr Asn Leu Gin Met Thr Tyr He Asn Tyr Asn Gin Phe
210 215 220
Ser Ser Gly Asn Gly Ser Gly Ser Lys Pro Pro Cys Pro Pro Tyr Glu 225 230 235 240 Asn Gin Ala Asn Cys Val Ala Lys Val Pro Pro Phe Thr Ser Gin Asp
245 250 255
Ala Lys Asn Leu Thr Asn Leu Met Leu Asn Met Met Ala Val Phe Asp
260 265 270
Ser Lys Ser Trp Glu Asp Ala Val Leu Asn Ala Pro Phe Gin Phe Ser 275 280 285
Asp Asn Asn Leu Ser Ala Pro Cys Tyr Ser Asp Tyr Leu Thr Cys Val
290 295 300
Asn Pro Tyr Asn Asp Gly Leu Val Asp Pro Lys Leu He Ala Lys Asn 305 310 315 320 L-"s Gly Asp Glu Tyr Asn He Glu Asn Gly Gin Thr Gly Ser Val He
325 330 335
Leu Thr Pro Gin Asp Val He Tyr Ser Tyr Arg Val Ala Asn Asn He
340 345 350
Tyr Val Asn Leu Leu Pro Thr Arg Gly Gly Asp Leu Gly Leu Gly Ser 355 360 365
Gin Tyr Gly Gly Pro Asn Gly Pro Gly Asp Asp Gly Thr Asn Phe Gly
370 375 380
Ala Leu Gly He Leu Ser Pro Phe Leu Asp Pro Glu He Leu Phe Gly 385 390 395 400 Lys Glu Leu Asn Lys Val Ala He Met Gin Leu Arg Asp He He His
405 410 415
Glu Tyr Gly His Thr Leu Gly Tyr Thr His Asn Gly Asn Met Thr Tyr 420 425 430 Gin Arg Val Arg Met Cys Glu Glu Asn Asn Gly Pro Glu Glu Arg Cys 435 440 445
Gin Gly Gly Arg He Glu Gin Val Asp Gly Lys Glu Val Gin Val Phe
450 455 460
Asp Asn Gly His Glu Val Arg Asp Thr Asp Gly Ser Thr Tyr Asp Val 465 470 475 480
Cys Ser Arg Phe Lys Asp Lys Pro Tyr Thr Ala Gly Ser Tyr Pro Asn
485 490 495
Ser He Tyr Thr Asp Cys Ser Gin Val Pro Ala Gly Leu He Gly Val 500 505 510 Thr Ser Ala Val Trp Gin Gin Leu He Asp Gin Asn Ala Leu Pro Val 515 520 525
Asp Phe Thr Asn Leu Ser Ser Gin Thr Asn Tyr Leu Asn Ala Ser Leu
530 535 540
Asn Thr Gin Asp Phe Ala Thr Thr Met Leu Ser Ala He Ser Gin Ser 545 550 555 560
Leu Ser Ser Ser Lys Ser Ser Ala Thr Thr Tyr Arg Thr Ser Lys Thr
565 570 575
Ser Arg Pro Phe Gly Ala Pro Leu Leu Gly Val Asn Leu Lys Met Gly 580 585 590 Tyr Gin Lys Tyr Phe Asn Asp Tyr Leu Gly Leu Ser Ser Tyr Gly He 595 600 605
He Lys Tyr Asn Tyr Ala Gin Ala Asn Asn Glu Lys He Gin Gin Leu
610 615 620
Ser Tyr Gly Val Gly Met Asp Val Leu Phe Asp Phe He Thr Asn Tyr 625 630 635 640
Thr Asn Glu Lys Asn Pro Lys Ser Asn Leu Thr Lys Lys Val Phe Thr
645 650 655
Ser Ser Leu Gly Val Phe Gly Gly Leu Arg Gly Leu Tyr Asn Ser Tyr 660 665 670 Tyr Leu Leu Asn Gin Tyr Lys Gly Ser Gly Asn Leu Asn Val Thr Gly 675 680 685
Gly Leu Asn Tyr Arg Tyr Lys His Ser Lys Tyr Ser He Gly He Ser
690 695 700
Val Pro Leu Val Gin Leu Lys Ser Arg He Val Ser Ser Asp Gly Ala 705 710 715 720
Tyr Thr Asn Ser He Thr Leu Asn Glu Gly Gly Ser His Phe Lys Val
725 730 735
Phe Phe Asn Tyr Gly Trp He Phe 740
(2) INFORMATION FOR SEQ ID NO: 177:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 529 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...529 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:177:
Met Thr Tyr He Asn Tyr Asn Gin Phe Ser Ser Gly Asn Gly Ser Gly 1 5 10 15
Ser Lys Pro Pro Cys Pro Pro Tyr Glu Asn Gin Ala Asn Cys Val Ala 20 25 30
Lys Val Pro Pro Phe Thr Ser Gin Asp Ala Lys Asn Leu Thr Asn Leu
35 40 45
Met Leu Asn Met Met Ala Val Phe Asp Ser Lys Ser Trp Glu Asp Ala 50 55 60 Val Leu Asn Ala Pro Phe Gin Phe Ser Asp Asn Asn Leu Ser Ala Pro 65 70 75 80
Cys Tyr Ser Asp Tyr Leu Thr Cys Val Asn Pro Tyr Asn Asp Gly Leu
85 90 95
Val Asp Pro Lys Leu He Ala Lys Asn Lys Gly Asp Glu Tyr Asn He 100 105 110
Glu Asn Gly Gin Thr Gly Ser Val He Leu Thr Pro Gin Asp Val He
115 120 125
Tyr Ser Tyr Arg Val Ala Asn Asn He Tyr Val Asn Leu Leu Pro Thr
130 135 140 Arg Gly Gly Asp Leu Gly Leu Gly Ser Gin Tyr Gly Gly Pro Asn Gly
145 150 155 160
Pro Gly Asp Asp Gly Thr Asn Phe Gly Ala Leu Gly He Leu Ser Pro
165 170 175
Phe Leu Asp Pro Glu He Leu Phe Gly Lys Glu Leu Asn Lys Val Ala 180 185 190
He Met Gin Leu Arg Asp He He His Glu Tyr Gly His Thr Leu Gly
195 200 205
Tyr Thr His Asn Gly Asn Met Thr Tyr Gin Arg Val Arg Met Cys Glu
210 215 220 Glu Asn Asn Gly Pro Glu Glu Arg Cys Gin Gly Gly Arg He Glu Gin
225 230 235 240
Val Asp Gly Lys Glu Val Gin Val Phe Asp Asn Gly His Glu Val Arg
245 250 255
Asp Thr Asp Gly Ser Thr Tyr Asp Val Cys Ser Arg Phe Lys Asp Lys 260 265 270
Pro Tyr Thr Ala Gly Ser Tyr Pro Asn Ser iif Tyr Thr Asp Cys Ser
275 280 285
Gin Val Pro Ala Gly Leu He Gly Val Thr Ser Ala Val Trp Gin Gin
290 295 300 Leu He Asp Gin Asn Ala Leu Pro Val Asp Phe Thr Asn Leu Ser Ser
305 310 315 320
Gin Thr Asn Tyr Leu Asn Ala Ser Leu Asn Thr Gin Asp Phe Ala Thr
325 330 335
Thr Met Leu Ser Ala He Ser Gin Ser Leu Ser Ser Ser Lys Ser Ser 340 345 350
Ala Thr Thr Tyr Arg Thr Ser Lys Thr Ser Arg Pro Phe Gly Ala Pro
355 360 365
Leu Leu Gly Val Asn Leu Lys Met Gly Tyr Gin Lys Tyr Phe Asn Asp 370 375 380
Tyr Leu Gly Leu Ser Ser Tyr Gly He He Lys Tyr Asn Tyr Ala Gin
385 390 395 400
Ala Asn Asn Glu Lys He Gin Gin Leu Ser Tyr Gly Val Gly Met Asp
405 410 415 Val Leu Phe Asp Phe He Thr Asn Tyr Thr Asn Glu Lys Asn Pro Lys
420 425 430
Ser Asn Leu Thr Lys Lys Val Phe Thr Ser Ser Leu Gly Val Phe Gly
435 440 445
Gly Leu Arg Gly Leu Tyr Asn Ser Tyr Tyr Leu Leu Asn Gin Tyr Lys 450 455 460
Gly Ser Gly Asn Leu Asn Val Thr Gly Gly Leu Asn Tyr Arg Tyr Lys
465 470 475 480
His Ser Lys Tyr Ser He Gly He Ser Val Pro Leu Val Gin Leu Lys
485 490 495 Ser Arg He Val Ser Ser Asp Gly Ala Tyr Thr Asn Ser He Thr Leu
500 505 510
Asn Glu Gly Gly Ser His Phe Lys Val Phe Phe Asn Tyr Gly Trp He
515 520 525
Phe
(2) INFORMATION FOR SEQ ID NO: 178:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 187 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...187 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 178:
Leu Gly Cys Val Ser Met Thr Leu Gly He Asp Glu Ala Gly Arg Gly 1 5 10 15
Cys Leu Ala Gly Ser Leu Phe Val Ala Gly Val Val Cys Asn Glu Lys 20 25 30
He Ala Leu Glu Phe Leu Lys Met Gly Leu Lys Asp Ser Lys Lys Leu
35 40 45
Ser Pro Lys Lys Arg Phe Phe Leu Glu Asp Lys He Lys Thr His Gly 50 55 60 Glu Val Gly Phe Phe Val Val Lys Lys Ser Ala Asn Glu He Asp His 65 70 75 80
Leu Gly Leu Gly Ala Cys Leu Lys Leu Ala He Glu Glu He Val Glu 85 90 95 Asn Gly Cys Ser Leu Ala Asn Glu He Lys He Asp Gly Asn Thr Ala 100 105 110
Phe Gly Leu Asn Lys Arg Tyr Pro Asn He Gin Thr He He Lys Gly
115 120 125
Asp Glu Thr He Ala Gin He Ala Met Ala Ser Val Leu Ala Lys Ala 130 135 140
Ser Lys Asp Arg Glu Met Leu Glu Leu His Ala Leu Phe Lys Glu Tyr 145 150 155 160
Gly Trp Asp Lys Asn Cys Gly Tyr Gly Thr Lys Gin His He Glu Ala 165 170 175 He Asn Lys Leu Gly Ala Thr Leu Ser Ser Ala 180 185
(2) INFORMATION FOR SEQ ID NO: 179: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 204 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 179:
Met Thr Leu Gly He Asp Glu Ala Gly Arg Gly Cys Leu Ala Gly Ser 1 5 10 15 Leu Phe Val Ala Gly Val Val Cys Asn Glu Lys He Ala Leu Glu Phe 20 25 30
Leu Lys Met Gly Leu Lys Asp Ser Lys Lys Leu Ser Pro Lys Lys Arg
35 40 45
Phe Phe Leu Glu Asp Lys He Lys Thr His Gly Glu Val Gly Phe Phe 50 55 60
Val Val Lys Lys Ser Ala Asn Glu He Asp His Leu Gly Leu Gly Ala 65 70 75 80
Cys Leu Lys Leu Ala He Glu Glu He Val Glu Asn Gly Cys Ser Leu 85 90 95 Ala Asn Glu He Lys He Asp Gly Asn Thr Ala Phe Gly Leu Asn Lys 100 105 110
Arg Tyr Pro Asn He Gin Thr He He Lys Gly Asp Glu Thr He Ala
115 120 125
Gin He Ala Met Ala Ser Val Leu Ala Lys Ala Ser Lys Asp Arg Glu 130 135 140
Met Leu Glu Leu His Ala Leu Phe Lys Glu Tyr Gly Trp Asp Lys Asn 145 150 155 160
Cys Gly Tyr Gly Thr Lys Gin His He Glu Ala He Asn Lys Leu Gly
165 170 175
Ala Thr Pro Phe His Arg His Ser Phe Thr Leu Lys Asn Arg He Leu
180 185 190
Asn Pro Lys Leu Leu Glu Val Glu Gin Arg Leu Val 195 200
(2) INFORMATION FOR SEQ ID NO: 180:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 192 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...192
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 180:
Met Asn Ala Leu Lys Lys Leu Ser Phe Cys Ala Leu Leu Ser Leu Gly 1 5 10 15
Leu Phe Ala Gin Thr Val His Ala Gin His Leu Lys Asp Thr He Asn 20 25 30 Tyr Pro Asp Trp Leu Lys He Asn Leu Phe Asp Lys Lys Asn Pro Pro 35 40 45
Asn Gin Tyr Val Gly Ser Ala Ser He Ser Gly Lys Arg Asn Asp Phe
50 55 60
Tyr Ser Asn Tyr He Pro Tyr Asp Asp Lys Leu Pro Pro Glu Lys Asn 65 70 75 80
Ala Glu Glu He Ala Leu Leu Arg Ala Arg Met Asn Ala Tyr Ser Thr
85 90 95
Leu Glu Ser Ala Leu Leu Thr Lys Met Cys Asn Arg He Val Lys Ala 100 105 110 Leu Gin Val Lys Asn Asn Val He Ser His Leu Phe Gly Phe Val sp 115 120 125
Phe Leu Thr Ser Lys Ser He Leu Ala Lys Arg Phe Val Asp Thr Thr
130 135 140
Asn His Arg Val Tyr Val Met Val Gin Phe Pro Phe He Gin Pro Glu 145 150 155 160
Asp Leu He Ala Tyr Phe Lys Ala Lys Arg He Asp Leu Ser Leu Ala
165 170 175
Ser Ala Thr Asn Leu Ser Ala He Leu Asn Lys Ala Leu Phe His Leu 180 185 190 (2) INFORMATION FOR SEQ ID NO: 181:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 86 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...86 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 181:
Met Asn Ala Leu Lys Lys Leu Ser Phe Cys Ala Leu Leu Ser Leu Gly 1 5 10 15
Leu Phe Ala Gin Thr Val His Ala Gin His Leu Lys Asp Thr He Asn 20 25 30
Tyr Pro Asp Trp Leu Lys He Asn Leu Phe Asp Lys Lys Asn Pro Pro
35 40 45
Asn Gin Tyr Val Gly Ser Ala Ser He Ser Gly Lys Arg Asn Asp Phe 50 55 60 Tyr Ser Asn Tyr He Pro Tyr Asp Asp Lys Leu Pro Pro Glu Arg Thr 65 70 75 80
Leu Lys Lys Ser Leu Phe 85 (2) INFORMATION FOR SEQ ID NO: 182:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 75 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...75
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 182: Leu Lys He Leu Thr Leu Phe Leu He Gly Leu Asn Ala Leu Phe Ala 1 5 10 15
Leu Asp Leu Asn Ala Leu Lys Thr Glu He Lys Glu Thr Tyr Leu Lys 20 25 30 Glu Tyr Lys Asp Leu Lys Leu Glu He Glu Thr He Asn Leu Glu He 35 40 45
Pro Glu Arg Phe Ser His Ala Ser He Leu Ser Tyr Glu Leu Asn Ala
50 55 60
Ser Asn Lys Leu Lys Lys Asp Gly Ser Cys Phe 65 70 75
(2) INFORMATION FOR SEQ ID NO:183:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 211 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...211 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 183:
Met Phe Ser He He Leu Gly Gly Gly Gly Gly Asn Thr Pro Cys Gly 1 5 10 15
Leu Thr Trp Gin His Phe Lys Leu Gly Asp Leu Phe Glu He Glu Lys 20 25 30
Thr Leu Ser Phe Asn Lys Asp Ala Leu Thr Gin Gly Gin Asp Tyr Asp
35 40 45
Tyr He Thr Arg Thr Ser Gin Asn Gin Gly Val Leu Gin Thr Thr Gly 50 55 60 Phe Val Asn Ala Glu Asn Leu Asn Pro Pro Phe Thr Trp Ser Leu Gly 65 70 75 80
Leu Leu Gin Met Asp Phe Phe Tyr Arg Lys Lys Ser Trp Tyr Ala Gly
85 90 95
Gin Phe Met Arg Lys He Thr Pro Lys Thr Glu He Lys Asn Lys He 100 105 110
Asn Ser ..r_. He Ala His Tyr Phe Thr Thr Leu Leu Asn Ala Leu Lys
115 120 125
Arg Pro Leu Leu Ser Val Leu Val Arg Asp He Asp Lys Thr Phe Arg
130 135 140 Glu Gin Lys He Gin Leu Pro Leu Lys Pro Thr Ala Lys Thr Gin Ser
145 150 155 160
Leu Asp Gly He Asp Phe Asp Phe Met His Thr Leu He Asn Ala Leu
165 170 175
Met Lys Gin Thr He Gin Gly Val Val Gin Tyr Cys Asp Ala Lys He 180 185 190
Gin Ala Thr Lys Glu Val He Ser Gin Glu Thr Pro He Gin Lys Asp
195 200 205
Ser Leu Phe 210
(2) INFORMATION FOR SEQ ID NO: 184:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 406 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...406 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:184:
Val He Gly Pro Leu Ser Ser Gin Leu Asn Ala He Lys Trp Gly Glu 1 5 10 15
Phe Lys Leu Gly Asp Leu Phe Glu Ala Ser Asn Gly Asp Phe Asp He 20 25 30
Gin Lys Arg His He Asn His Lys Gly Glu Phe Val He Thr Ala Gly
35 40 45
Leu Ser Asn Asn Gly Val Leu Gly Gin Ser Asp He Lys Ala Lys Val 50 55 60 Phe Glu Ser His Thr He Thr He Asp Met Phe Gly Cys Ala Phe Tyr 65 70 75 80
Arg Ser Phe Ala Tyr Lys Met Val Thr His Ala Arg Val Phe Ser Leu
85 90 95
Lys Pro Lys Phe Glu He Asn His Lys He Gly Leu Phe Leu Ser Thr 100 105 110
Leu Phe Phe Gly Tyr His Lys Lys Phe Gly Tyr Glu Asn Met Cys Ser
115 120 125
Trp Ala Lys He Lys Asn Asp Lys Val He Leu Pro Leu Lys Pro Thr
130 135 140 Ala Asn Thr Gin Thr Leu Glu Gly He Asp Phe Asp Phe Met Glu Lys
145 150 155 160
Phe He Ala Glu Leu Glu Gin Cys Arg Leu Ala Glu Leu Gin Ala Tyr
165 170 175
Leu Lys Ala Thr Gly Leu Glu Asn Thr Thr Leu Ser Asn Asp Glu Glu 180 185 190
Asn Ala Leu Asn Val Phe Asn Asn Ser Gly Gly Gly Gly Gly Asn Thr
195 200 205
Pro Cys Gly Leu Thr Trp Gin His Phe Lys Leu Gly Asp Leu Phe Glu 210 215 220 Ile Glu Lys Thr Leu Ser Phe Asn Lys Asp Ala Leu Thr Gin Gly Gin
225 230 235 240
Asp Tyr Asp Tyr He Thr Arg Thr Ser Gin Asn Gin Gly Val Leu Gin
245 250 255 Thr Thr Gly Phe Val Asn Ala Glu Asn Leu Asn Pro Pro Phe Thr Trp
260 265 270
Ser Leu Gly Leu Leu Gin Met Asp Phe Phe Tyr Arg Lys Lys Ser Trp
275 280 285
Tyr Ala Gly Gin Phe Met Arg Lys He Thr Pro Lys Thr Glu He Lys 290 295 300
Asn Lys He Asn Ser Arg He Ala His Tyr Phe Thr Thr Leu Leu Asn
305 310 315 320
Ala Leu Lys Arg Pro Leu Leu Ser Val Leu Val Arg Asp He Asp Lys
325 330 335 Thr Phe Arg Glu Gin Lys He Gin Leu Pro Leu Lys Pro Thr Ala Lys
340 345 350
Thr Gin Ser Leu Asp Gly He Asp Phe Asp Phe Met His Thr Leu He
355 360 365
Asn Ala Leu Met Lys Gin Thr He Gin Gly Val Val Gin Tyr Cys Asp 370 375 380
Ala Lys He Gin Ala Thr Lys Glu Val He Ser Gin Glu Thr Pro He 385 390 395 400
Gin Lys Asp Ser Leu Phe 405
(2) INFORMATION FOR SEQ ID NO: 185:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 275 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...275
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 185:
Met Ser Lys Ser Leu Tyr Gin Thr Leu Asn Val Ser G_.d Asn Ala Ser 1 5 10 15
Gin Asp Glu He Lys Lys Ser Tyr Arg Arg Leu Ala Arg Gin Tyr His 20 25 30 Pro Asp Leu Asn Lys Thr Lys Glu Ala Glu Glu Lys Phe Lys Glu He
35 40 45
Asn Ala Ala Tyr Glu He Leu Ser Asp Glu Glu Lys Arg Arg Gin Tyr
50 55 60
Asp Gin Phe Gly Asp Asn Met Phe Gly Gly Gin Asn Phe Ser Asp Phe 65 70 75 80
Ala Arg Ser Arg Gly Pro Ser Glu Asp Leu Asp Asp He Leu Ser Ser
85 90 95
He Phe Gly Lys Gly Gly Phe Ser Gin Arg Phe Ser Gin Asn Ser Gin 100 105 110
Gly Phe Ser Gly Phe Asn Phe Ser Asn Phe Ala Pro Glu Asn Leu Asp
115 120 125
Val Thr Ala He Leu Asn Val Ser Val Leu Asp Thr Leu Leu Gly Asn
130 135 140 Lys Lys Gin Val Ser Val Asn Asn Glu Thr Phe Ser Leu Lys He Pro
145 150 155 160
He Gly Val Glu Glu Gly Glu Lys He Arg Val Arg Asn Lys Gly Lys
165 170 175
Met Gly Arg Thr Gly Arg Gly Asp Leu Leu Leu Gin He His He Glu 180 185 190
Glu Asp Glu Met Tyr Arg Arg Glu Lys Asp Asp He He Gin He Phe
195 200 205
Asp Leu Pro Leu Lys Thr Ala Leu Phe Gly Gly Lys He Glu He Ala
210 215 220 Thr Trp His Lys Thr Leu Thr Leu Thr He Pro Pro Asn Thr Lys Ala
225 230 235 240
Met Gin Lys Phe Arg He Lys Asp Lys Gly He Lys Ser Arg Lys Thr
245 250 255
Ser His Val Gly Asp Cys He Ala Ser Ser Phe Asp Leu Leu Lys Leu 260 265 270
Lys Arg Phe 275
(2) INFORMATION FOR SEQ ID NO:186:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 278 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...T78
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:186:
Met Ser Lys Ser Leu Tyr Gin Thr Leu Asn Val Ser Glu Asn Ala Ser 1 5 10 15
Gin Asp Glu He Lys Lys Ser Tyr Arg Arg Leu Ala Arg Gin Tyr His
20 25 30
Pro Asp Leu Asn Lys Thr Lys Glu Ala Glu Glu Lys Phe Lys Glu He 35 40 45 Asn Ala Ala Tyr Glu He Leu Ser Asp Glu Glu Lys Arg Arg Gin Tyr
50 55 60
Asp Gin Phe Gly Asp Asn Met Phe Gly Gly Gin Asn Phe Ser Asp Phe 65 70 75 80 Ala Arg Ser Arg Gly Pro Ser Glu Asp Leu Asp Asp He Leu Ser Ser
85 90 95
He Phe Gly Lys Gly Gly Phe Ser Gin Arg Phe Ser Gin Asn Ser Gin
100 105 110
Gly Phe Ser Gly Phe Asn Phe Ser Asn Phe Ala Pro Glu Asn Leu Asp 115 120 125
Val Thr Ala He Leu Asn Val Ser Val Leu Asp Thr Leu Leu Gly Asn
130 135 140
Lys Lys Gin Val Ser Val Asn Asn Glu Thr Phe Ser Leu Lys He Pro 145 150 155 160 He Gly Val Glu Glu Gly Glu Lys He Arg Val Arg Asn Lys Gly Lys
165 170 175
Met Gly Arg Thr Gly Arg Gly Asp Leu Leu Leu Gin He His He Glu
180 185 190
Glu Asp Glu Met Tyr Arg Arg Glu Lys Asp Asp He He Gin He Phe 195 200 205
Asp Leu Pro Leu Lys Thr Ala Leu Phe Gly Gly Lys He Glu He Ala
210 215 220
Thr Trp His Lys Thr Leu Thr Leu Thr He Pro Pro Asn Thr Lys Ala 225 230 235 240 Met Gin Lys Phe Arg He Lys Asp Lys Gly He Lys Ser Arg Lys Thr
245 250 255
Ser His Val Gly Asp Cys He Ala Ser Ser Phe Asp Leu Pro Lys He
260 265 270
Glu Thr Leu Leu Met Ser 275
(2) INFORMATION FOR SEQ ID NO: 187:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 232 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...232 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 187:
Val Val Gin Lys Phe Asn Phe Tyr Lys Thr Gly Gly Met Arg Leu Lys
1 5 10 15
His Phe Lys Thr Phe Leu Phe He Thr Met Ala Val He Val He Gly 20 25 30
Thr Gly Cys Ala Asn Lys Lys Lys Lys Lys Asp Glu Tyr Asn Lys Pro
35 40 45
Ala He Phe Trp Tyr Gin Gly He Leu Arg Glu He Leu Phe Ala Asn 50 55 60
Leu Glu Thr Ala Asp Asn Tyr Tyr Ser Ser Leu Gin Ser Glu His He 65 70 75 80
Asn Ser Pro Leu Val Pro Glu Ala Met Leu Ala Leu Gly Gin Ala His 85 90 95 Met Lys Lys Lys Glu Tyr Val Leu Ala Ser Phe Tyr Phe Asp Glu Tyr 100 105 110
He Lys Arg Phe Gly Thr Lys Asp Asn Val Asp Tyr Leu Thr Phe Leu
115 120 125
Lys Leu Gin Ser His Tyr Tyr Ala Phe Lys Asn His Ser Lys Asp Gin 130 135 140
Glu Phe He Ser Asn Ser He Val Ser Leu Gly Glu Phe He Glu Lys
145 150 155 160
Tyr Pro Asn Ser Arg Tyr Arg Pro Tyr Val Glu Tyr Met Gin He Lys
165 170 175 Phe He Leu Gly Gin Asn Glu Leu Asn Arg Ala He Ala Asn Val Tyr
180 185 190
Lys Lys Arg His Lys Pro Glu Gly Val Lys Arg Tyr Leu Glu Arg He
195 200 205
Asp Glu Thr Leu Glu Lys Glu Thr Lys Pro Lys Pro Ser His Met Pro 210 215 220
Trp Tyr Val Leu He Phe Asp Trp 225 230
(2) INFORMATION FOR SEQ ID NO: 188:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 114 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...114
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 188:
Met Arg Phe Leu Asn Asn Lys His Arg Glu Lys Gly Leu Lys Ala Glu 1 5 10 15
Glu Glu Ala Cys Gly Phe Leu Lys Thr Leu Gly Phe Glu Met He Glu
20 25 30
Arg Asn Phe Phe Ser Gin Phe Gly Glu He Asp He He Ala Leu Lys 35 40 45 Lys Gly Val Leu His Phe He Glu Val Lys Ser Gly Glu Asn Phe Asp
50 55 60
Pro He Tyr Ala He Thr Pro Ser Lys Leu Lys Lys Met He Lys Thr 65 70 75 80
He Arg Cys Tyr Leu Ser Gin Lys Asp Pro Asn Ser Asp Phe Cys He
85 90 95
Asp Ala Leu He Val Lys Asn Gly Lys Phe Glu Leu Leu Glu Asn He
100 105 110
Thr Phe
(2) INFORMATION FOR SEQ ID NO: 189:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 101 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...101 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 189:
Met Gly Ser He Gly Ala Met Thr Lys Gly Ser Ser Asp Arg Tyr Phe 1 5 10 15
Gin Glu Gly Val Ala Ser Glu Lys Leu Val Pro Glu Gly He Glu Gly 20 25 30
Arg Val Pro Tyr Arg Gly Lys Val Ser Asp Met He Phe Gin Leu Val
35 40 45
Gly Gly Val Arg Ser Ser Met Gly Tyr Gin Gly Ala Lys Asn He Leu 50 55 60 Glu Leu Tyr Gin Asn Ala Glu Phe Val Glu He Thr Ser Ala Gly Leu 65 70 75 80
Lys Lys Ser His Val His Gly Val Asp He Thr Lys Glu Ala Pro Asn
85 90 95
He Met Gly Glu Phe
Figure imgf000276_0001
(2) INFORMATION FOR SEQ ID NO: 190:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 481 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...481
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:190:
Met Arg He Leu Gin Arg Ala Leu Thr Phe Glu Asp Val Leu Met Val 1 5 10 15 Pro Arg Lys Ser Ser Val Leu Pro Lys Asp Val Ser Leu Lys Ser Arg 20 25 30
Leu Thr Lys Asn He Gly Leu Asn He Pro Phe He Ser Ala Ala Met
35 40 45
Asp Thr Val Thr Glu His Lys Thr Ala He Ala Met Ala Arg Leu Gly 50 55 60
Gly He Gly He Val His Lys Asn Met Asp He Gin Thr Gin Val Lys 65 70 75 80
Glu He Thr Lys Val Lys Lys Ser Glu Ser Gly Val He Asn Asp Pro 85 90 95 He Phe He His Ala His Arg Thr Leu Ala Asp Ala Lys Val He Thr 100 105 110
Asp Asn Tyr Lys He Ser Gly Val Pro Val Val Asp Asp Lys Gly Leu
115 120 125
Leu He Gly He Leu Thr Asn Arg Asp Val Arg Phe Glu Thr Asp Leu 130 135 140
Ser Lys Lys Val Gly Asp Val Met Thr Lys Met Pro Leu Val Thr Ala
145 150 155 160
His Val Gly He Ser Leu Asp Glu Ala Ser Asp Leu Met His Lys His
165 170 175 Lys He Glu Lys Leu Pro He Val Asp Lys Asp Asn Val Leu Lys Gly
180 185 190
Leu He Thr He Lys Asp He Gin Lys Arg He Glu Tyr Pro Glu Ala
195 200 205
Asn Lys Asp Asp Phe Gly Arg Leu Arg Val Gly Ala Ala He Gly Val 210 215 220
Gly Gin Leu Asp Arg Ala Glu Met Leu Val Lys Ala Gly Val Asp Ala
225 230 235 240
Leu Val Leu Asp Ser Ala His Gly His Ser Ala Asn He Leu His Thr
245 250 255 Leu Glu Glu He Lys Lys Ser Leu Val Val Asp Val He Val Gly Asn
260 265 270
Val Val Thr Lys Glu Ala Thr Ser Asp Leu He Ser Ala Gly Ala Asp
275 280 285
Ala Val Lys Val Gly He Gly Pro Gly Ser He Cys Thr Thr Arg He 290 295 300
Val Ala Gly Val Gly Met Pro Gin Val Ser Ala He Asp Asn Cys Val 305 310 315 320
Glu Val Ala Ser Lys Phe Asp He Pro Val He Ala Asp Gly Gly He 325 330 335 Arg Tyr Ser Gly Asp Val Ala Lys Ala Leu Ala Leu Gly Ala Ser Ser
340 345 350
Val Met He Gly Ser Leu Leu Ala Gly Thr Glu Glu Ser Pro Gly Asp 355 360 365 Phe Met He Tyr Gin Gly Arg Gin Tyr Lys Ser Tyr Arg Gly Met Gly 370 375 380
Ser He Gly Ala Met Thr Lys Gly Ser Ser Asp Arg Tyr Phe Gin Glu 385 390 395 400
Gly Val Ala Ser Glu Lys Leu Val Pro Glu Gly He Glu Gly Arg Val 405 410 415
Pro Tyr Arg Gly Lys Val Ser Asp Met He Phe Gin Leu Val Gly Gly
420 425 430
Val Arg Ser Ser Met Gly Tyr Gin Gly Ala Lys Asn He Leu Glu Leu 435 440 445 Tyr Gin Asn Ala Glu Phe Val Glu He Thr Ser Ala Gly Leu Lys Glu 450 455 460
Ser His Val His Gly Val Asp He Thr Lys Glu Ala Pro Asn Tyr Tyr 465 470 475 480
Gly
(2) INFORMATION FOR SEQ ID NO: 191:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 204 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...204 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 191:
Met Gin Gly Phe Leu Leu Gin Thr Gin Ser He Arg Asp Glu Asp Leu 1 5 10 15
He Val His Val Leu Thr Lys Asn Gin Leu Lys Thr Leu Tyr Arg Phe 20 25 30
Tyr Gly Lys Arg His Ser Val Leu Asn Val Gly Arg Lys He Asp Phe
35 40 45
Glu Glu Glu Asn Asp Asp Lys Phe Leu Pro Lys Leu Arg Asn He Leu 50 55 60 His Leu Gly Tyr He Trp Glu Arg Glu Met Glu Arg Leu Phe Phe Trp 65 70 75 80
Gin Arg Phe Cys Ala Leu Leu Phe Lys His Leu Glu Gly Val His Ser
85 90 95
Leu Asp Ser He Tyr Phe Asp Thr Leu Asp Asp Gly Ala Ser Lys Leu 100 105 110
Ser Lys Gin His Pro Leu Arg Val He Leu Glu Met Tyr Ala Val Leu
115 120 125
Leu Asn Phe Glu Gly Arg Leu Gin Ser Tyr Asn Ser Cys Phe Leu Cys 130 135 140
Asp Ala Lys Leu Glu Arg Ser Val Ala Leu Ala Gin Gly Phe He Leu 145 150 155 160
Ala His Pro Ser Cys Leu Lys Ala Lys Ser Leu Asp Leu Glu Lys He 165 170 175 Gin Ala Phe Phe Arg Thr Gin Ser Thr He Asp Leu Glu Thr Glu Glu 180 185 190
Val Glu Glu Leu Trp Arg Thr Leu Asn Leu Gly Phe 195 200 (2) INFORMATION FOR SEQ ID NO: 192:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 82 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...82
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 192: Met Gly Val Gly Arg Val Gly Asn Met Ala Leu Leu Ala Cys Ala Gly 1 5 10 15
Pro Met Gly He Gly Ala He Ala He Ala He Asn Gly Gly Arg Gin
20 25 30
Arg Ser Arg Met Leu Val Val Asp He Asp Asp Lys Arg Leu Glu Gin 35 40 45
Val Gin Lys Met Leu Pro Gly Asn Trp Arg Pro Val Thr Ala Leu Ser
50 55 60
Trp Cys Leu Cys He Pro Lys Arg Gly Ala He Arg Ala Arg Cys Cys 65 70 75 80 Glu Arg
(2) INFORMATION FOR SEQ ID NO:193: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 67 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...67
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 193:
Leu Ser Gly Thr Ala Val Ser Cys Arg Cys Thr Cys Arg He Gin Leu 1 5 10 15
Val Leu Val Arg Thr Ser He Pro Val Val He Gly Cys Ser Cys Pro
20 25 30
Phe Leu Ser Ser He Gly Phe Thr Thr Gly Thr His Gin Ser Pro Val 35 40 45 Lys Arg Cys Gly Val Asn Ala Gly Lys Thr Pro Ser Lys Lys His Leu 50 55 60
His Leu Asn 65 (2) INFORMATION FOR SEQ ID NO: 194:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 114 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(iii) HYPOTHETICAL: YES
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...114
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 194: Val Trp Leu Ala Ala Leu Gly Phe Leu He Thr Ala Val Gly Leu Pro 1 5 .0 15
Val He Thr Val He Ala Leu Ala Lys Val Gly Gly Ser Ser Thr Pro
20 25 30
Ser Ala He Arg Ser Ala Gly Met Pro Ala Ala Cys Trp Arg Arg Ser 35 40 45
Ala Thr Trp Arg Ser Ala Arg Cys Ser Pro Phe Arg Ala Pro Pro Arg
50 55 60
Cys Pro Ser Lys Val Ser Val Val Pro Leu Leu Gly Glu Glu Ala Ala 65 70 75 80 Arg Arg Cys Ser Ser Thr Ala Trp Arg Thr Ser Ser Ser Pro Trp Pro
85 90 95
Ser Pro Ser Thr Pro Val Ala Cys Trp Thr Pro Ser Asp Ala Ser Ser 100 105 110 Pro Arg
(2) INFORMATION FOR SEQ ID NO: 195: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:195: TATACCATGG TGGGCGCTAA 20
(2) INFORMATION FOR SEQ ID NO: 196: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTT-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 196: ATGAATTCGA GTAAGGATTT TTG 23
(2) INFORMATION FOR SEQ ID NO:197:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 197:
TTAACCATGG TGAAAAGCGA TA 22
(2) INFORMATION FOR SEQ ID NO: 198:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 198:
TAGAATTCGC ATAACGATCA ATC 23
(2) INFORMATION FOR SEQ ID NO: 199: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 199: ATATCCATGG TGAGTTTGAT GA 22 (2) INFORMATION FOR SEQ ID NO: 200:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 200: ATGAATTCAA TTTTTTATTT TGCCA 25 (2) INFORMATION FOR SEQ ID NO: 201:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 201:
AATTCCATGG TGGGGGCTAT G 21
(2) INFORMATION FOR SEQ ID NO:202:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:202:
ATGAATTCTC GATAGCCAAA ATC 23
(2) INFORMATION FOR SEQ ID J:203:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 203: AATTCCATGG TGCATAACTT CCATT 25
(2) INFORMATION FOR SEQ ID NO: 204:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:204: AAGAATTCTC TAGCATCCAA ATGGA 25
(2) INFORMATION FOR SEQ ID NO: 205:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 205: ATTTCCATGG TCATGTCTCA TATT 24
(2) INFORMATION FOR SEQ ID NO: 206: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 206: ATGAATTCCA TCTTTTATTC CAC 23
(2) INFORMATION FOR SEQ ID NO: 207: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 27 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...27 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:207:
AACCATGGTG ATTTTAAGCA TTGAAAG 27
(2) INFORMATION FOR SEQ ID NO: 208:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 28 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...28 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:208:
AAGAATTCCA CTCAAAATTT TTTAACAG 28
(2) INFORMATION FOR SEQ ID NO: 209:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:209: GATCATCCAT ATGTTATCTT CTAAT 25 (2) INFORMATION FOR SEQ ID NO:210:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:210:
TGAATTCAAC CATTTTAACC CTG 23 (2) INFORMATION FOR SEQ ID NO: 211:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 27 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: ( ) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...27
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 211: TATACCATGG TGAAATTTTT TCTTTTA 27 (2) INFORMATION FOR SEQ ID NO:212:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 212:
AGAATTCAAT TGCGTCTTGT AAAAG 25
(2) INFORMATION FOR SEQ ID NO: 213:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:213:
TATACCATGG TGATGGACAA ACTC 24
(2) INFORMATION FOR SEQ ID NO: 214:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 214: ATGAATTCCC ACTTGGGGCG ATA 23
(2) INFORMATION FOR SEQ ID NO:215:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:215: TTATGGATCC AAACCAATTA AAACT 25
(2) INFORMATION FOR SEQ ID NO:216:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 216: TATCTCGAGT TATAGAGAAG GGC 23
(2) INFORMATION FOR SEQ ID NO: 217: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 217: TTAACCATGG TGAAAAGCGA TA 22
(2) INFORMATION FOR SEQ ID NO: 218: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 24 ^a je pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO ( iv) ANTI - SENSE : NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:218:
TAGAATTCGC CTCTAAAACT TTAG 24
(2) INFORMATION FOR SEQ ID NO: 219:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 219:
TTAACCATGG TGAAAAGCGA TA 22
(2) INFORMATION FOR SEQ ID NO: 220:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 220:
TAGAATTCGC ATAACGATCA ATC 23 (2) INFORMATION FOR SEQ ID NO:221:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 221: ATATCCATGG TGAGTTTGAT GA 22 (2) INFORMATION FOR SEQ ID NO: 222:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 222: ATGAATTCAA TTTTTTATTT TGCCA 25
(2) INFORMATION FOR SEQ ID NO: 223:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 223:
AATTCCATGG CTATCCAAAT CCG 23
(2) INFORMATION FOR SEQ ID NO: 224:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylor-.
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 224:
ATGAATTCGC CAAAATCGTA GTATT 25 (2) INFORMATION FOR SEQ ID NO: 225:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 225: GATACCATGG AATTTATGAA AAAG 24
(2) INFORMATION FOR SEQ ID NO:226:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KτϊY: misc_feature
Figure imgf000295_0001
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 226: TGAATTCGAA AAAGTGTAGT TATAC 25
(2) INFORMATION FOR SEQ ID NO: 227:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 227: CCCTTCATTT TAGAAATCG 19
(2) INFORMATION FOR SEQ ID NO: 228: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 228: ATTTCAACCA ATTCAATGCG 20
(2) INFORMATION FOR SEQ ID NO: 229: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...20 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 229:
GCCCCTTTTG ATTTGAAGCT 20
(2) INFORMATION FOR SEQ ID NO: 230:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:230:
TCGCTCCAAG ATACCAAGAA GT 22
(2) INFORMATION FOR SEQ ID NO: 231:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO ( iv) ANTI - SENSE : NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 231: CTTGAATTAG GGGCAAAGAT CG 22 (2) INFORMATION FOR SEQ ID NO: 232:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:232:
ATGCGTTTTT ACCCAAAGAA GT 22 (2) INFORMATION FOR SEQ ID NO:233:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 233:
ATAACGCCAC TTCCTTATTG GT 22
(2) INFORMATION FOR SEQ ID NO:234:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:234:
CTTTGGGTAA AAACGCATC 19
(2) INFORMATION FOR SEQ ID NO: 235:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 20 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) Ϊ.- JTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B ) LOCATION 1 . . . 20
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:235: CGATCTTTGA TCCTAATTCA 20
(2) INFORMATION FOR SEQ ID NO: 236:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 236: ATCAAGTTGC CTATGCTGA 19
(2) INFORMATION FOR SEQ ID NO: 237:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 237: TTGAACACTT TTGATTATGC GG 22
(2) INFORMATION FOR SEQ ID NO: 238: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 23 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:238: GGATTATGCG ATTGTTTTAC AAG 23
(2) INFORMATION FOR SEQ ID NO: 239: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS : double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc__feature
(B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 239: GTCTTTAGCA AAAATGGCGT C 21
(2) INFORMATION FOR SEQ ID NO: 240: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...21 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:240:
AATGAGCGTA AGAGAGCCTT C 21
(2) INFORMATION FOR SEQ ID NO: 241:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...18 (xi) SEQUENCE DESCRIPTION SEQ ID NO: 241:
CTTATGGGGG TATTGTCA 18
(2) INFORMATION FOR SEQ ID NO:242:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...18
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:242: AGCATGTGGG TATCCAGC 18 (2) INFORMATION FOR SEQ ID NO:243:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:243: AGGTTGTTGC CTAAAGACT 19 (2) INFORMATION FOR SEQ ID NO:244:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...18
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 244:
CTGCCTCCAC CTTTGATC 18
(2) INFORMATION FOR SEQ ID NO: 245:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:245:
ACCAATATCA ATTGGCACT 19
(2) INFORMATION FOR SEQ ID NO:246:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...18
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 246: ACTTGGAAAA GCTCTGCA 18
(2) INFORMATION FOR SEQ ID NO: 247:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 19 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...19
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 47: CTTGCTTGTC ATATCTAGC 19
(2) INFORMATION FOR SEQ ID NO: 248:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...18
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:248:
GTTGAAGTGT TGGTGCTA 18
(2) INFORMATION FOR SEQ ID NO: 249: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 249: CAAGCAAGTG GTTTGGTTTT AG 22
(2) INFORMATION FOR SEQ ID NO: 250: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 22 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE:
Figure imgf000306_0001
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...22
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 250: TGGAAAGAGC AAATCATTGA AG 22
(2) INFORMATION FOR SEQ ID NO: 251:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...21 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 251:
GCCCATAATC AAAAAGCCCA T 21
(2) INFORMATION FOR SEQ ID NO:252:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 24 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...24 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 252:
CTAAAACCAA ACCACTTGCT TGTC 24
(2) INFORMATION FOR SEQ ID NO:253: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 16 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...16
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 253: GTAAAACGAC GGCCAG 16 (2) INFORMATION FOR SEQ ID NO:254:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 17 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...17
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 254: CAGGAAACAG CTATGAC 17 (2) INFORMATION FOR SEQ ID NO:255:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 21 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:255:
ATCTTACCTA TCACCTCAAA T 21
(2) INFORMATION FOR SEQ ID NO:256:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 21 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...21
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:256:
AGACAGCAAC ATCTTTGTGA A 21
(2) INFORMATION FOR SEQ ID NO: 257:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...50
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 257: CGCGGATCCA TATGGCTGAA AAAACGCCTT TTTTTAAAAC TAAAAACCAC 50
(2) INFORMATION FOR SEQ ID NO: 258:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 34 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...34
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 258: CCGGAATTCA TCAGTATTCA ATGGGAATAA AGCC 34
(2) INFORMATION FOR SEQ ID NO: 259:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs
*3' TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...50
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 259: CGCGGATCCA TATGAAAGAA GAAGAAAAAG AAGAAAAAAA GACAGAAAGG 50
(2) INFORMATION FOR SEQ ID NO: 260: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 37 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...37
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 260: CCGGAATTCG CTTAAAAGAA AATAGTCCCC CAAACGC (2) INFORMATION FOR SEQ ID NO: 261: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 43 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...43 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:261:
CGCGGATCCA TATGAAAGAG GTCATTCCCA CCCCTTCAAC CCC 43
(2) INFORMATION FOR SEQ ID NO:262:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 36 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...36 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 262:
CCGGAATTCA TATAAATATC ATATAGGCAG AAAAAC 36
(2) INFORMATION FOR SEQ ID NO:263:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 37 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...37 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:263: CGCGGATCCA TATGGAGGCA GAGCTTGATG AAAAATC 37 (2) INFORMATION FOR SEQ ID NO:264:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 36 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...36
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 264:
CCGGAATTCG ATTGATTTTG TCAAATCTAA AATCCC 36 (2) INFORMATION FOR SEQ ID NO: 265:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 25 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 265: TATTATACAT ATGGAAGAAG ATGGG 25 (2) INFORMATION FOR SEQ ID NO:266:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 23 base pairs ) (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...23
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:266:
TAATCTCGAG TTTAGAAGGC GTA 23
(2) INFORMATION FOR SEQ ID NO: 267:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 25 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature (B) LOCATION 1...25
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 267:
TTATATTCAT ATGGAAGACG ATGGC 25
(2) INFORMATION FOR SEQ ID NO: 268:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 24 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...24
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:268: AATTCTCGAG CCTCTTTATA AGCC 24
(2) INFORMATION FOR SEQ ID NO: 269:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 46 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO (iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE: (A) NAME/KEY: misc_feature
(B) LOCATION 1...46
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 269: CGCGGATCCA TATGGTAGAA GCCTTTCAAA AACACCAAAA AGACGG 46
(2) INFORMATION FOR SEQ ID NO: 270:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 32 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular (ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...32
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 270: CCGGAATTCG GAGCCAATAG GGAGCTAAAG CC 32
(2) INFORMATION FOR SEQ ID NO: 271: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 31 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO (iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori (ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...31
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 271: CGGGATCCGA AGGTGATGGT GTTTATATAG G 31
(2) INFORMATION FOR SEQ ID NO:272: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 32 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO ( iv) ANTI - SENSE : NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...32 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:272:
CGCATATGGA AGGTGATGGT GTTTATATAG GG 32
(2) INFORMATION FOR SEQ ID NO:273:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 37 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...37 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:273:
GCGAATTCTC ACTCTTTCCA ATAGTTTGCT GCAGAGC 37
(2) INFORMATION FOR SEQ ID NO: 274:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 37 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(A) ORGANISM: Helicobacter pylori ( ix) FEATURE :
(A) NAME/KEY: misc_feature
(B) LOCATION 1...37
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 274:
CCGGAATTCT TAATCCCGTT TCAAATGGTA ATAAAGG 37 (2) INFORMATION FOR SEQ ID NO: 275:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 36 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: circular
(ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL: NO
(iv) ANTI -SENSE: NO
(vi) ORIGINAL SOURCE: (A) ORGANISM: Helicobacter pylori
(ix) FEATURE:
(A) NAME/KEY: misc_feature
(B) LOCATION 1...36
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 275: GCGAATTCCC TTTTATTTAA AAAGTGTAGT TATACC 36

Claims

1. An isolated nucleic acid comprising a nucleotide sequence encoding an
H pylori polypeptide at least about 60% homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
2. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID
NO: 194.
3. An isolated nucleic acid which encodes an H. pylori polypeptide, comprising a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
4. The isolated nucleic acid of claim 1, comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
5. An isolated nucleic acid molecule encoding an H pylori polypeptide, comprising a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
6. An isolated nucleic acid comprising a nucleotide sequence of at least 8 nucleotides in length, wherein the sequence hybridizes under stringent hybridization conditions to a nucleic acid having a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
7. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori cell envelope polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 60, SEQ ID NO: 69, and SEQ ID NO: 83, or a complement thereof.
8. The isolated nucleic acid of claim 7, wherein said H pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof comrising a nucleotide sequence of SEQ ID NO: 63, or a complement thereof.
9. The isolated nucleic acid of claim 7, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, and SEQ ID NO: 39, or a complement thereof.
10. The isolated nucleic acid of claim 9, wherein said H pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44, or a complement thereof.
11. The isolated nucleic acid of claim 7, wherein said H pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66, or a complement thereof.
12. The isolated nucleic acid of claim 11 , wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94, or a complement thereof.
13. The isolated nucleic acid of claim 12, wherein said H pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C-terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11 , SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52, or a complement thereof.
14. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori cell envelope polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 160, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 103, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ ID NO: 180.
15. The isolated nucleic acid of claim 14, wherein said H pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof comprising an amino acid sequence of SEQ ID NO: 160.
16. The isolated nucleic acid of claim 14, wherein said H pylori cell envelope polypeptide or a fragment thereof is an H pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, and SEQ ID NO: 136.
17. The isolated nucleic acid of claim 16, wherein said H pylori inner membrane polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 1 15, SEQ ID NO: 116, SEQ ID NO: 140, and SEQ ID NO: 141.
18. The isolated nucleic acid of claim 14, wherein said H pylori cell envelope polypeptide or a fragment thereof is an H pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, and SEQ ID NO: 163.
19. The isolated nucleic acid of claim 18, wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
20. The isolated nucleic acid of claim 19, wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C-terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
21. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93, or a complement thereof.
22. The isolated nucleic acid of claim 21 , wherein said H pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in mRNA translation, said nucleic acid selected from the group consisting of SEQ ID NO: 57 and SEQ ID NO: 58, or a complement thereof.
23. The isolated nucleic acid of claim 21 , wherein said H pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, said nucleic acid selected from the group consisting of SEQ ID NO: 86 and SEQ ID NO: 87, or a complement thereof.
24. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori cytoplasmic polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190.
25. The isolated nucleic acid of claim 24, wherein said H pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
26. The isolated nucleic acid of claim 24, wherein said H. pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184.
27. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori secreted polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 77, SEQ ΪD NO: 78, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID NO: 95, and SEQ ID NO: 97, or a complement thereof.
28. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori secreted polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 1 17, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
29. An isolated nucleic acid comprising a nucleotide sequence encoding an H. pylori cellular polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96, or a complement thereof.
30. An isolated nucleic acid comprising a nucleotide sequence encoding an
H. pylori cellular polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 118, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151 , SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
31. A probe comprising a nucleotide sequence consisting of at least 8 nucleotides of a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
32. A recombinant expression vector comprising the nucleic acid of any of claims 1, 2, 3, 4, 5, 6, 7, 14, 21, 24, 27, 28, 29 or 30 operably linked to a transcription regulatory element.
33. A cell comprising a recombinant expression vector of claim 32.
34. A method for producing an H pylori polypeptide comprising culturing a cell of claim 33 under conditions that permit expression of the polypeptide.
35. The method of claim 34, further comprising purifying the polypeptide from the cell.
36. A method for detecting the presence oϊ a. Helicobacter nucleic acid in a sample comprising: (a) contacting a sample with a nucleic acid of any of claims 6 or 31 so that a hybrid can form between the probe and a Helicobacter nucleic acid in the sample; and
(b) detecting the hybrid formed in step (a), wherein detection of a hybrid indicates the presence of a Helicobacter nucleic acid in the sample.
37. An isolated H pylori polypeptide comprising an amino acid sequence at least about 60% homologous to an H pylori polypeptide selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194.
38. An isolated H pylori polypeptide which is encoded by a nucleic acid comprising a nucleotide sequence at least about 60% homologous to a nucleotide sequence selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97.
39. The isolated H. pylori polypeptide of claim 28, wherein said polypeptide is encoded by a nucleotide sequence selected from the group consisting of SEQ ID NO:
1-SEQ ID NO: 97.
40. An isolated H pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid selected from the group consisting of SEQ ID NO: 1-SEQ ID NO: 97, or a complement thereof.
41. An isolated H. pylori polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 97-SEQ ID NO: 194.
42. An isolated H pylori cell envelope polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 160,
SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 103, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 157, SEQ ID NO: 166, and SEQ ID NO: 180.
43. The isolated polypeptide of claim 42, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori flagella-associated polypeptide or a fragment thereof comprising an amino acid sequence of SEQ ID NO: 160.
44. The isolated polypeptide of claim 43, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 1 14, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 135, SEQ ID NO: 136.
45. The isolated polypeptide of claim 44, wherein said H. pylori inner membrane polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in transport selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 140, and SEQ ID NO: 141.
46. The isolated polypeptide of claim 43, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 110, SEQ ID NO: 1 11, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, SEQ ID NO: 191, SEQ ID NO: 102, SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 149, SEQ ID NO: 119, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 162, and SEQ ID NO: 163.
47. The isolated polypeptide of claim 46, wherein said H pylori outer membrane polypeptide or a fragment thereof is an H pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 133, SEQ ID NO: 139, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 158, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 188, and SEQ ID NO: 191.
48. The isolated polypeptide of claim 47, wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C-terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 108, SEQ ID NO: 123, SEQ ID NO: 133, SEQ ID NO: 139, and SEQ ID NO: 149.
49. An isolated H pylori cell envelope polypeptide or a fragment thereof, wherein said polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 63, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11 , SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 60, SEQ ID NO: 69, and SEQ ID NO: 83.
50. The isolated polypeptide of claim 49, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H pylori flagella-associated polypeptide or a fragment thereof encoded by a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 63.
51. The isolated polypeptide of claim 49, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H pylori inner membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 38, SEQ ID NO: 39.
52. The isolated polypeptide of claim 51 , wherein said H pylori inner membrane polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in transport encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 43, and SEQ ID NO: 44.
53. The isolated polypeptide of claim 49, wherein said H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, SEQ ID NO: 94, SEQ ID NO: 5, SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 52, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 65, and SEQ ID NO: 66.
54. The isolated polypeptide of claim 53, wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H pylori polypeptide having a terminal phenylalanine residur or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 36, SEQ ID NO: 42, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 61, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 91, and SEQ ID NO: 94.
55. The isolated polypeptide of claim 54, wherein said H. pylori outer membrane polypeptide or a fragment thereof is an H pylori polypeptide having a terminal phenylalanine residue and a C-terminal tyrosine cluster or a fragment thereof encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 11, SEQ ID NO: 26, SEQ ID NO: 36, SEQ ID NO: 42, and SEQ ID NO: 52.
56. An isolated H. pylori cytoplasmic polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 189, and SEQ ID NO: 190.
57. The isolated polypeptide of claim 56, wherein said H. pylori cytoplasmic polypeptide or a fragment thereof is an H pylori polypeptide or a fragment thereof involved in mRNA translation selected from the group consisting of SEQ ID NO: 154 and SEQ ID NO: 155.
58. The isolated polypeptide of claim 56, wherein said H pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair selected from the group consisting of SEQ ID NO: 183 and SEQ ID NO: 184.
59. An isolated H. pylori cytoplasmic polypeptide or a fragment thereof, wherein said polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 92, and SEQ ID NO: 93.
60. The isolated polypeptide of claim 59, wherein said H. pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in mRNA translation, said polypeptide encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 57 and SEQ ID NO: 58.
61. The isolated polypeptide of claim 59, wherein said H pylori cytoplasmic polypeptide or a fragment thereof is an H. pylori polypeptide or a fragment thereof involved in genome replication, transcription, recombination and repair, said polypeptide encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 86 and SEQ ID NO: 87.
62. An isolated H. pylori cellular polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 118, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 144, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 156, SEQ ID NO: 159, SEQ ID NO: 165, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, and SEQ ID NO: 193.
63. An isolated H. pylori cellular polypeptide or a fragment thereof, wherein said polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 21, SEQ ID NO: 33, SEQ ID NO: 37, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 47, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56 SEQ ID NO: 59, SEQ ID NO: 62, SEQ ID NO: 68, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, and SEQ ID NO: 96.
64. An isolated H pylori secreted polypeptide or a fragment thereof, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 1 17, SEQ ID NO: 122, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 150 SEQ ID NO: 161, SEQ ID NO: 164, SEQ ID NO: 167, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 187, SEQ ID NO: 192, and SEQ ID NO: 194.
65. An isolated H. pylori secreted polypeptide or a fragment thereof, wherein said polypeptide is encoded by a nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 20, SEQ ID NO: 25, SEQ ID NO: 31 , SEQ ID NO: 32, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 53 SEQ ID NO: 64, SEQ ID NO: 67, SEQ ID NO: 70, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 81 , SEQ ID NO: 82, SEQ ID NO: 90, SEQ ID NO: 95, ana SEQ ID NO: 97.
66. A fusion protein comprising an H pylori polypeptide which comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 98-SEQ ID NO:
194 operatively linked to a non-H. pylori polypeptide.
67. A vaccine formulation for prophylactic or therapeutic treatment of an H. pylori infection comprising an effective amount of at least one isolated nucleic acid of any of claims 1, 2, 3, 4, 5, 6, 7, 14, 21, 24, 27, 28, 29 or 30.
68. A vaccine formulation for prophylactic or therapeutic treatment of an H pylori infection comprising an effective amount of at least one H pylori polypeptide or a fragment thereof of any of claims 37, 38, 40, 41, 42, 49, 56, 59, 62, 63, 64 or 65. .
69. A vaccine formulation of claim 67, further comprising a pharmaceutically acceptable carrier.
70. A vaccine formulation of claim 68, further comprising a pharmaceutically acceptable carrier.
71. A vaccine formulation of claim 69, wherein the pharmaceutically acceptable carrier comprises an adjuvant.
72. A vaccine formulation of claim 70, wherein the pharmaceutically acceptable carrier comprises an adjuvant.
73. A vaccine formulation of claim 69, wherein the pharmaceutically acceptable carrier comprises a delivery system.
74. A vaccine formulation of claim 70, wherein the pharmaceutically acceptable carrier comprises a delivery system.
75. A vaccine formulation of claim 73, wherein the delivery system comprises a live vector.
76. A vaccine formulation of claim 74, wherein the delivery system comprises a live vector.
77. A vaccine formulation of claim 75, wherein the live vector is a bacteria or a virus.
78. A vaccine formulation of claim 76, wherein the live vector is a bacteria or a virus.
79. A vaccine formulation of claim 73, wherein the pharmaceutically acceptable carrier further comprises an adjuvant.
80. A vaccine formulation of claim 74, wherein the pharmaceutically acceptable carrier further comprises an adjuvant.
81. A vaccine formulation for prophylactic or therapeutic treatment of an H pylori infection comprising an effective amount of at least one isolated nucleic acid encoding an H pylori outer membrane polypeptide or a fragment thereof, said nucleic acid selected from the group consisting of SEQ ID NO: 28, SEQ ID NO: 50, SEQ ID NO: 24, SEQ ID NO: 11, SEQ ID NO: 52, SEQ ID NO: 42 and SEQ ID NO: 79.
82. The vaccine formulation of claim 81 , wherein said nucleic acid comprises a nucleotide sequence of SEQ ID NO: 52.
83. A vaccine formulation for prophylactic or therapeutic treatment of an H pylori infection comprising an effective amount of at least one H. pylori outer membrane polypeptide or a fragment thereof, said polypeptide selected from the group consisting of SEQ ID NO: 125, SEQ ID NO: 147, SEQ ID NO: 121, SEQ ID NO: 108, SEQ ID NO: 149, SEQ ID NO: 139 and SEQ ID NO: 176.
84. The vaccine formulation of claim 81, wherein said polypeptide comprises an amino acid sequence of SEQ ID NO: 149.
85. A vaccine formulation of claims 81 or 83, further comprising a pharmaceutically acceptable carrier.
86. A vaccine formulation of claim 85, wherein the pharmaceutically acceptable carrier comprises an adjuvant.
87. A vaccine formulation of claim 85, wherein the pharmaceutically acceptable carrier comprises a delivery system.
88. A vaccine formulation of claim 87, wherein the delivery system comprises a live vector.
89. A vaccine formulation of claim 88, wherein the live vector is a bacteria or a virus.
90. A vaccine formulation of claim 86, wherein the pharmaceutically acceptable carrier further comprises an adjuvant.
91. A method of treating or reducing a risk ofH. pylori infection in a subject comprising administering to a subject a vaccine formulation of claim 67, such that treatment or reduction of risk ofH pylori infection occurs.
92. A method of treating or reducing a risk ofH pylori infection in a subject comprising administering to a subject a vaccine formulation of claim 68, such that treatment or reduction of risk ofH pylori infection occurs.
93. A method of treating or reducing a risk ofH pylori infection in a subject comprising administering to a subject a vaccine formulation of claim 81, such that treatment or reduction of risk ofH pylori infection occurs.
94. A method of treating or reducing a risk ofH. pylori infection in a subject comprising administering to a subject a vaccine formulation of claim 83, such that treatment or reduction of risk ofH. pylori infection occurs.
95. A method of producing a vaccine formulation comprising: combining at least one isolated H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194 with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
96. A method of producing a vaccine formulation comprising:
(a) providing at least one isolated H. pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194; and
(b) combining at least one said isolated H. pylori polypeptide or a fragment thereof with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
97. A method of producing a vaccine formulation comprising:
(a) culturing a cell under condition that permit expression of an H pylori polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 98-SEQ ID NO: 194;
(b) isolating said H pylori polypeptide or a fragment thereof from said cell; and
(c) combining at least one said isolated H. pylori polypeptide or a fragment thereof with a pharmaceutically acceptable carrier to thereby form a vaccine formulation.
98. A chimeric H. pylori polypeptide comprising at least two H pylori polypeptides or fragments thereof, wherein said polypeptides are encoded by nucleic acid sequences selected from the group consisting of SEQ ID NO: 1-SEQ ID NO:97.
99. A chimeric H. pylori polypeptide comprising at least two H pylori polypeptides or fragments thereof, wherein said polypeptides are selected from the group consisting of SEQ ID NO:98-SEQ ID NO: 194.
PCT/US1997/022104 1996-11-15 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof WO1998024475A1 (en)

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BR9714133-0A BR9714133A (en) 1996-12-05 1997-12-05 isolated nucleic acid, molecule thereof, probe, recombinant expression vector, cell, polypeptide, fusion protein vaccine formulation and processes for producing a h. pylori, to detect the presence of a helicobacter nucleic acid in a sample, to treat or reduce a risk of infection by h. pylori in an individual and to produce a vaccine formulation
AU58954/98A AU739641B2 (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
EEP199900226A EE9900226A (en) 1996-12-05 1997-12-05 Nucleic and amino acid sequences associated with Helicobacter pylori and their vaccine compositions
EP97954525A EP0964699A4 (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
NZ335633A NZ335633A (en) 1996-12-05 1997-12-05 Production of recombinant H. pylori polypeptides for treatment and diagnosis of H. pylori related diseases
SK579-99A SK57999A3 (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
CA002273199A CA2273199A1 (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
JP52575898A JP2001510992A (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences related to Helicobacter pylori and vaccine compositions thereof
IL12974697A IL129746A0 (en) 1996-12-05 1997-12-05 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
NO992158A NO992158L (en) 1996-12-05 1999-05-04 Nucleic acid and amino acid sequences associated with Heliobacter Pylori and vaccine preparations thereof.
IS5047A IS5047A (en) 1996-12-05 1999-05-10 Nucleic and amino acid sequences related to Helicobacter pylori and their vaccines
US10/335,977 US20040052799A1 (en) 1996-11-15 2002-12-30 Nucleic acid and amino acid sequences relating to Helicobacter pylori for diagnostics and therapeutics

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Cited By (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002031128A1 (en) * 2000-10-06 2002-04-18 Smithkline Beecham Corporation Methods of agonizing and antagonizing fabk
WO2002066502A1 (en) * 2001-02-21 2002-08-29 Boren Thomas Helicobacter pylori sialic acid binding adhesin, saba and saba - gene
JP2002528076A (en) * 1998-10-26 2002-09-03 ノボザイムス アクティーゼルスカブ Construction and screening of DNA libraries of interest in filamentous cells
US6951729B1 (en) 1999-10-27 2005-10-04 Affinium Pharmaceuticals, Inc. High throughput screening method for biological agents affecting fatty acid biosynthesis
US7034132B2 (en) 2001-06-04 2006-04-25 Anderson David W Therapeutic polypeptides, nucleic acids encoding same, and methods of use
US7048926B2 (en) 2000-10-06 2006-05-23 Affinium Pharmaceuticals, Inc. Methods of agonizing and antagonizing FabK
US7786260B1 (en) * 1999-10-15 2010-08-31 Csl Limited Polypeptide fragments comprising c terminal portion of helicobacter catalase
EP2344152A2 (en) * 2008-10-08 2011-07-20 Immune Solutions Limited Oral vaccines for producing mucosal immunity
WO2017102779A1 (en) * 2015-12-14 2017-06-22 Technische Universität München Helicobacter pylori vaccines

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN110343697A (en) * 2019-08-05 2019-10-18 湖州三零科技股份有限公司 A kind of plant disease fungus Total DNA extraction method
CN113435168B (en) * 2021-06-10 2024-03-22 上海美吉生物医药科技有限公司 Automatic editing method, system, terminal and medium for glue pattern
CN114057854B (en) * 2021-09-30 2022-07-15 河北医科大学第四医院 Helicobacter pylori CD4+T cell tolerance polypeptide fusion antigen and application thereof

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SE9300139L (en) * 1993-01-19 1994-07-20 Medicarb Ab Preparation of a new drug

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
HIRSCHL A.M. et al., "Comparison of ELISA Antigen Preparation Alone or in Combination for Serodiagnosing Helicobacter Pylori Infection", 1990, Vol. 43, pages 511-513. *

Cited By (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2002528076A (en) * 1998-10-26 2002-09-03 ノボザイムス アクティーゼルスカブ Construction and screening of DNA libraries of interest in filamentous cells
US7786260B1 (en) * 1999-10-15 2010-08-31 Csl Limited Polypeptide fragments comprising c terminal portion of helicobacter catalase
US6951729B1 (en) 1999-10-27 2005-10-04 Affinium Pharmaceuticals, Inc. High throughput screening method for biological agents affecting fatty acid biosynthesis
WO2002031128A1 (en) * 2000-10-06 2002-04-18 Smithkline Beecham Corporation Methods of agonizing and antagonizing fabk
US7048926B2 (en) 2000-10-06 2006-05-23 Affinium Pharmaceuticals, Inc. Methods of agonizing and antagonizing FabK
WO2002066502A1 (en) * 2001-02-21 2002-08-29 Boren Thomas Helicobacter pylori sialic acid binding adhesin, saba and saba - gene
US7034132B2 (en) 2001-06-04 2006-04-25 Anderson David W Therapeutic polypeptides, nucleic acids encoding same, and methods of use
EP2344152A2 (en) * 2008-10-08 2011-07-20 Immune Solutions Limited Oral vaccines for producing mucosal immunity
EP2344152A4 (en) * 2008-10-08 2013-04-03 Immune Solutions Ltd Oral vaccines for producing mucosal immunity
WO2017102779A1 (en) * 2015-12-14 2017-06-22 Technische Universität München Helicobacter pylori vaccines
US10828358B2 (en) 2015-12-14 2020-11-10 Technische Universität München Helicobacter pylori vaccines
AU2016374289B2 (en) * 2015-12-14 2023-08-03 MAX-PLANCK-Gesellschaft zur Förderung der Wissenschaften e.V. Helicobacter pylori vaccines

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