Table 1.

Comparison of OM proteins from H. pylori J99 (JHP) and 26695 (HP)

Protein groupGene no.Length (aa)% Size variation (aa)C-terminal residues% IdentityGene namea
Family 1 (major outer membrane protein family)
 Hop proteins70009669b 672b 0.1 (1c)FAY95.194.3 hopZ
2100256907113 (21)FAY85.285.8 hopD
21202276966910.7 (5)FAY81.683.7 hopM
21402294834830LAY91.592.3 hopA
23702524794871.6 (8)VGF95.193.5 hopF
2380253/0254471471e 0IGF98.196.8 hopG
42904773713671.1 (4)YSF88.188.9 hopJ
58106383073050c NKH92.894.5 hopH
64507062702730f YTF96.794.3 hopE
6590722638b 644b 1.2 (8c)FAY87.890.9 hopO
6620725651b 653b 0.6 (4c)FAY91.792.3 hopP
83312437447331.5 (11)FAY92.291.0 babA (hopS)
84809125205151 (5)YSF96.596.2 hopC
84909135275290.4 (2)YAF95.394.7 hopB
85709233663690.8 (3)YSF89.289.5 hopK
108311566976960.1 (1)IGF95.495.1 hopI
108411571,2371,2300.6 (7)MGF93.293.8 hopL
116408967037080.4 (3c)FAY91.890.2 babB (hopT)
110311776436410.3 (2)FAY87.689.3 hopQ
126113426966910.7 (5)FAY81.683.7 hopN
NAd 0317NAd 745NAd FAYNAd NAd hopU
 Hor proteins730078/0079255684e 62.7 (429)IN(L/Fg)94.1h 96.2h horA
11701272862860VSF99.097.3 horB
30703242452540f YHF90.689.3 horC
35910662002000WHF99.595.0 horD
42404721861860FTF99.596.6 horE
61406712702700YNF98.195.7 horF
73207962782780YDF92.492.6 horG
103411072202300f YNF91.790.8 horH
104011132772770YSF93.194.5 horI
136214692482480RDF94.894.6 horJ
139415013883880YTF97.995.6 horK
143213952422420FTF90.990.4 horL
Family 2 (Hof family of outer membrane proteins)19502094384500f YRF91.391.7 hofA
34210834794790AKF95.693.8 hofB
43804865285280YSF95.193.1 hofC
43904874654800f RIY95.492.1 hofD
71907824554550FFF89.790.6 hofE
72507884994990WKL97.295.2 hofF
85009145145140LKF98.195.8 hofG
109411674714710ASF96.494.9 hofH
Family 3 (Hom family of outer membrane proteins)64907106576600.5 (3)WVF95.294.3 homA
870NAd 668NAd NAd WVFNAd NAd homB
100803737517006.8 (51)WVF75.379.3 homC
134614537447460.3 (2)WIF94.993.0 homD
Family 4 (iron-regulated outer membrane proteins)
 FecA-like proteins62606867677670YEF93.192.6 fecA-1
74308077927870.6 (5)i YNF93.393.5 fecA-2
142614008418420f YTF99.097.0 fecA-3
 FrpB-like proteins81008767917910YKW97.694.9 frpB-1
8510915/0916815812e 0.4 (3)YKF96.293.7 frpB-2
140515128798770.2 (2)YQF97.495.3 frpB-3
Family 5 (efflux pump outer membrane proteins)55206054774770YVH98.396.5 hefA
90509714314130.4 (2f)VLH92.391.2 hefD
124713274124120GLE93.793.4 hefG
Other outer membrane proteins45605064064030.7 (3)EGF96.693.9
60006559069161.1 (10)TRF96.494.7
634069433625723.5 (79)j FAF73.873.2
30803252372370MPY98.396.8 flgH
105411251791790LVK95.596.3 palA
134914561751750VKK10096.6 lpp20
  • a Those with Hop-like motifs have been named hop genes, with the original hopA-E gene names being assigned to those previous identified (17, 22). Proteins related to the hop family but lacking the N-terminal motif have been called hor (hop related) genes. The family of 50-kDa outer membrane protein genes has been calledhof (Helicobacter OMP family) genes. The smaller family of outer membrane protein genes has been called hom(Helicobacter outer membrane) genes.

  • b Out of frame due to a CT dinucleotide repeat in the signal sequence. Protein size was determined by adjusting the coding sequence by the addition or removal of a single dinucleotide repeat.

  • c The size variation does not include the differences caused by the different numbers of CT dinucleotide repeats in the coding sequence.

  • d NA, not applicable.

  • e The HP0253 and HP0254 genes, the HP0078 and HP0079 genes, and the HP0915 and HP0916 genes were joined by the addition or removal of a single nucleotide.

  • f Size difference due to difference in prediction of initiation codons between H. pylori J99 and 26695.

  • g Protein terminates with an F residue in 26695 and an L in J99.

  • h The identity was calculated over the aligned portion of the proteins only.

  • i There is significant difference in the C-terminal 20 amino acids. The C terminus of JHP743 is found in a different reading frame in H. pylori 26695 and likely represents a frameshift in HP0807.

  • j The remainder of JHP634 is found in a different reading frame in H. pylori 26695 after a frameshift.