Helicobacter pylori Genome
Sequence Search
>Query : 217 aa
vs library
using protein matrix
500489 residues in 1577 sequences
statistics exclude scores greater than 73
mean initn score: 26.4 (6.90)
mean init1 score: 25.9 (5.97)
1577 scores better than 1 saved, ktup: 2, variable pamfact
joining threshold: 28
The best scores are: initn init1 opt
HP0642 NAD(P)H-flavin oxidoreductase {Haemophilus infl 1069 1069 1069
HP0954 oxygen-insensitive NAD(P)H nitroreductase {Haem 133 82 183
HP1354 putative adenine specific DNA methyltransferase 67 52 61
HP1142 hypothetical protein 60 36 41
HP1206 multidrug resistance protein (hetA) {Anabaena s 58 47 57
HP0157 shikimic acid kinase I (aroK) {Haemophilus infl 56 46 46
HP0529 cag pathogenicity island protein (cag9) {Helico 56 47 48
HP0555 hypothetical protein 55 44 46
HP0453 hypothetical protein 55 55 57
HP0054 adenine/cytosine DNA methyltransferase {Haemoph 55 45 53
HP1222 D-lactate dehydrogenase (dld) {Haemophilus infl 55 38 44
HP1048 translation initiation factor IF-2 (infB) {Baci 54 43 53
HP0017 virB4 homolog (virB4) {Agrobacterium radiobacte 51 37 41
HP0728 conserved hypothetical protein {Bacillus subtil 50 40 42
HP0604 uroporphyrinogen decarboxylase (hemE) {Escheric 50 50 57
HP1359 hypothetical protein 49 31 67
HP0876 iron-regulated outer membrane protein (frpB) {N 49 40 45
HP1063 glucose-inhibited division protein (gidB) {Esch 49 49 64
HP0112 hypothetical protein 48 38 39
HP0480 GTP-binding protein, fusA-homolog (yihK) {Esche 48 38 41
HP1059 Holliday junction DNA helicase (ruvB) {Haemophi 48 48 51
HP0524 cag pathogenicity island protein (cag5) {Helico 47 34 45
HP0544 cag pathogenicity island protein (cag23) {Helic 47 36 45
HP1274 paralysed flagella protein (pflA) {Campylobacte 47 35 44
HP0269 conserved hypothetical ATP-binding protein {Pse 47 47 75
HP0887 vacuolating cytotoxin {Helicobacter pylori} 47 36 44
HP0285 conserved hypothetical protein {Bacillus subtil 47 47 47
HP0692 3-oxoadipate coA-transferase subunit B (yxjE) { 46 35 40
HP0915 iron-regulated outer membrane protein (frpB) {N 46 46 50
HP0788 hypothetical protein 45 33 42
HP0614 hypothetical protein 45 45 52
HP1240 conserved hypothetical protein {Escherichia col 45 45 45
HP0439 hypothetical protein 45 35 41
HP0260 adenine specific DNA methyltransferase (mod) {E 45 32 32
HP0797 flagellar sheath adhesin hpaA {Helicobacter pyl 45 36 40
HP0044 GDP-D-mannose dehydratase (rfbD) {Vibrio choler 45 33 35
HP1099 2-keto-3-deoxy-6-phosphogluconate aldolase (eda 44 44 52
HP0264 ATP-dependent protease binding subunit (clpB) { 44 35 42
HP1380 prephenate dehydrogenase (tyrA) {Bacillus subti 44 32 40
HP0759 conserved hypothetical integral membrane protei 44 35 35
HP0048 transcriptional regulator (hypF) {Rhodobacter c 44 33 48
HP0655 protective surface antigen D15 {Haemophilus inf 44 44 54
HP1471 type IIS restriction enzyme R protein (BCGIB) { 44 44 62
HP1513 selenocysteine synthase SelA, putative {Escheri 43 43 43
HP1247 hypothetical protein 43 33 48
HP0284 conserved hypothetical integral membrane protei 43 32 34
HP0424 hypothetical protein 43 43 52
HP1450 60 kDa inner-membrane protein {Pseudomonas puti 43 43 46
HP1411 hypothetical protein 43 43 52
HP0447 conserved hypothetical protein {Saccharomyces c 43 34 40
HP0642 NAD(P)H-flavin oxidoreductase {Haemophilus influenzae}
93.5% identity in 217 aa overlap
10 20 30 40 50 60
Query MDREQIIALQHQRFATKKYDPNRRISEKDWEVLVEVGRLAPSSIGLEPWKMLLLKNERMK
X::::..::::::::.::::::::::.::::.::::::::::::::::::::::::::::
HP0642 MDREQVVALQHQRFAAKKYDPNRRISQKDWEALVEVGRLAPSSIGLEPWKMLLLKNERMK
10 20 30 40 50 60
70 80 90 100 110 120
Query EDLKPMAWGGLSSLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTHSRFAQIIKN
:::::::::.: .:::::::::::::::::::::::::::::::::::::.:::::::::
HP0642 EDLKPMAWGALFGLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTNSRFAQIIKN
70 80 90 100 110 120
130 140 150 160 170 180
Query FQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGY
::::::::..:::::::::::::::::::::::::::::::::::::::::::::.::::
HP0642 FQENDMKLNSERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLEEKGY
130 140 150 160 170 180
190 200 210
Query LDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
:.::::::::::.:::::::::::::::::::::::X
HP0642 LNTAEFGVSVMACFGYRNQEITPKTRWKTEVIYEVIE
190 200 210
HP0954 oxygen-insensitive NAD(P)H nitroreductase {Haemophilus influenzae}
23.9% identity in 180 aa overlap
10 20 30 40 50
Query MDREQIIALQHQRFATKKYDPNRRISEKDWEVLVEVGRLAPSSIGLEPWKMLLLKNE
.:.:. .: ..: . :..:.. .:... : ..:..::.::: . .::........
HP0954 MKFLDQEKRRQLLNERHSCKMFDSHYEFSSTELEEIAEIARLSPSSYNTQPWHFVMVTDK
10 20 30 40 50 60
60 70 80 90 100 110
Query RMKEDLKPMAWGGLSSLEGASHFVIY--LARKGVTYDSDYVKKVMHEVKKRDYDTHSRFA
.:... . .. . . ...:: ... : .... ...:.... .: : . ..::
HP0954 DLKKQIAAHSYFNEEMIKSASALMVVCSLRPSELLPHGHYMQNLYPESYK--VRVIPSFA
70 80 90 100 110
120 130 140 150 160 170
Query QIIKNFQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYL
:.. ...:. .. : .: X:..... :.....:.::: :.:.:. :X.. :
HP0954 QMLGVRFNHSMQRLESYIL-----EQCYIAVGQICMGVSLMGLDSCIIGGFDPLKVGEVL
120 130 140 150 160 170
180 190 200 210
Query KEKGYLDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
.:.
HP0954 EERINKPKIACLIALGKRVAEASQKSRKSKVDAITWL
180 190 200 210
HP1354 putative adenine specific DNA methyltransferase {Escherichia coli}
40.0% identity in 15 aa overlap
100 110 120 130 140 150
Query VMHEVKKRDYDTHSRFAQIIKNFQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGI
.....X:.:. :.:X
HP1354 IFEKELSNAQEIKKNENILIITGNPPYSGASENKGLFEWEVKATYGIDPKFQTIEIEKNV
460 470 480 490 500 510
160 170 180 190 200 210
Query DSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
HP1354 KLADKIQTLLSSVQIQKQSGSKNDLKKLKSLHSKYKLQDEKNPKWLLDDYVKFMRFAQNK
520 530 540 550 560 570
HP1142 hypothetical protein
18.5% identity in 54 aa overlap
10 20 30
Query MDREQIIALQHQRFATKKYDPNRRISEKDWEVL
:.. .. .. ..^: . .. .: . .:^
HP1142 KIEVYNKQFKEEQLRNSQVKGIFTLGKKTNENLEKIESKKESINKENEKKIKNEASLQVL
90 100 110 120 130 140
40 50 60 70 80 90
Query VEVGRLAPSSIGLEPWKMLLLKNERMKEDLKPMAWGGLSSLEGASHFVIYLARKGVTYDS
..v . .... :..v :::
HP1142 TQKKEKEEKDFADRCWEKLYKKNEEDFKETLEGFKRKEKFKEKILKEFENDKYNQSEIVG
150 160 170 180 190 200
HP1206 multidrug resistance protein (hetA) {Anabaena sp.}
31.0% identity in 29 aa overlap
10 20 30 40
Query MDREQIIALQHQRFATKKYDPNRRISEKDWEVLVEVGRLAPSS
: : X::: ...::X... . .....
HP1206 FKEKMVFFLLVLMAVFSSFVEVMSLTLLMPFITLASDPNRALDDKDWKMVYDFFHFSSPV
30 40 50 60 70 80
50 60 70 80 90 100
Query IGLEPWKMLLLKNERMKEDLKPMAWGGLSSLEGASHFVIYLARKGVTYDSDYVKKVMHEV
HP1206 RLMYFFSFCLVGIYLFRMFYGVSFTYLKGRFSNKKAYQIKQQLFLQHIKSNYLSHLNHNL
90 100 110 120 130 140
HP0157 shikimic acid kinase I (aroK) {Haemophilus influenzae}
30.0% identity in 40 aa overlap
10 20 30 40 50 60
Query REQIIALQHQRFATKKYDPNRRISEKDWEVLVEVGRLAPSSIGLEPWKMLLLKNERMKED
X: .: ..... .:.. : :: : ...:
HP0157 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTD
10 20 30
70 80 90 100 110 120
Query LKPMAWGGLSSLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTHSRFAQIIKNFQ
. .. ::X
HP0157 MIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGT
40 50 60 70 80 90
HP0529 cag pathogenicity island protein (cag9) {Helicobacter pylori}
40.9% identity in 22 aa overlap
150 160 170 180 190 200
Query YIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGYRNQEIT
.X:. .:: ::. :. :X
HP0529 ALESVVKGADAAVLPAYGVVNLPDIIIGQGSYLDFVSYLIYIVFGIFVFISFMKLRDISS
220 230 240 250 260 270
210
Query PKTRWKTEVIYEVIE
HP0529 NIQINIGFEYMRFVGGTLFKMAMVSFIAYAGFGYLYKISYSIYFGLAGAFGLNQVLFWAL
280 290 300 310 320 330
HP0555 hypothetical protein
46.2% identity in 13 aa overlap
10 20 30 40
Query MDREQIIALQHQRFATKKYDPNRRISEKDWEVLVEVGRLAPSSIGLEP
. X:.: :.:X
HP0555 GENVFSYDLKTEYVLDPNILIETMKRHGFDFVDIRRVSLKEWEYDFSLQEVKLPNARVLV
120 130 140 150 160 170
50 60 70 80 90 100
Query WKMLLLKNERMKEDLKPMAWGGLSSLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDY
HP0555 LSSEPVEFKEASGKYWLSVNQNAYLKISSNNPLWQPKIIFYDENLKIIQIIAKENRQQEI
180 190 200 210 220 230
HP0453 hypothetical protein
37.5% identity in 24 aa overlap
150 160 170 180 190 200
Query QMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGYRNQEITPK
X:....: . .: . :::.:X.
HP0453 MDLEELYAPNHIERLKARSFLRSIAFFDDFSASFEYRDLFSVLE
10 20 30 40
210
Query TRWKTEVIYEVIE
HP0453 NIVQFDYEKKPYKDDLYFLCKFVEPALKAIFSNLNTNIYRKHLKMPLEKAREFDAKCALD
50 60 70 80 90 100
HP0054 adenine/cytosine DNA methyltransferase {Haemophilus paragallinarum}
38.1% identity in 21 aa overlap
40 50 60 70 80 90
Query LVEVGRLAPSSIGLEPWKMLLLKNERMKEDLKPMAWGGLSSLEGASHFVIYLARKGVTYD
X::.::X. .. . : .:
HP0054 VCKEFKDFISALEFFPDFKQEKTLKEVIGSLKPLAWGEYDNTDFYHSFRTYPKHMQEWIK
200 210 220 230 240 250
100 110 120 130 140 150
Query SDYVKKVMHEVKKRDYDTHSRFAQIIKNFQENDMKLTDERSLFDWASKQTYIQMANMMMA
HP0054 DLKEGQSAFENTELNKKPHRIVGSKIVLNVSKNGDKYKRQKYHSVAPCIHTRNDQMASQN
260 270 280 290 300 310
HP1222 D-lactate dehydrogenase (dld) {Haemophilus influenzae}
40.0% identity in 25 aa overlap
140 150 160 170 180 190
Query WASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGY
X: ... :::..:X. :. .:. :
HP1222 KDLSLTPRQRIVIHREVEHLKERVSHGHHEDQVLLDELLKESEYLAHATCAVCHMCSTLC
570 580 590 600 610 620
200 210
Query RNQEITPKTRWKTEVIYEVIE
HP1222 PLEIDTGKIALNYYQKNPKGEKIASKILNHMQTTTSMARFSLKSARLVQNLIGSHNLVSL
630 640 650 660 670 680
HP1048 translation initiation factor IF-2 (infB) {Bacillus stearothermophilus}
21.4% identity in 28 aa overlap
130 140 150 160 170 180
Query QENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYL
.....:... .:. ...: ..::..:.
HP1048 TMTDDQGKSIQNLKPSMVALITGLSEVPPAGSVLIGVENDSIARLQAQKRATYLRQKALS
670 680 690 700 710 720
190 200 210
Query DTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
HP1048 KSTKVSFDELSEMVANKELKNIPVVIKADTQGSLEAIKNSLLELNNEEVAIQVIHSGVGG
730 740 750 760 770 780
HP0017 virB4 homolog (virB4) {Agrobacterium radiobacter}
35.3% identity in 17 aa overlap
30 40 50 60 70 80
Query RRISEKDWEVLVEVGRLAPSSIGLEPWKMLLLKNERMKEDLKPMAWGGLSSLEGASHFVI
:. X: . ..:. .:X.
HP0017 GLKGGYFSFFPERIHLNHRLRFLTSKALACLMVFERQNLGFKANSWGNSPLSVFKNLDYS
360 370 380 390 400 410
90 100 110 120 130 140
Query YLARKGVTYDSDYVKKVMHEVKKRDYDTHSRFAQIIKNFQENDMKLTDERSLFDWASKQT
HP0017 PFLFNFHNQEVSHKNAKEIARVNGHTLIIGATGSGKSTLISFLMMSALKYQNMRLLAFDR
420 430 440 450 460 470
HP0728 conserved hypothetical protein {Bacillus subtilis}
24.3% identity in 37 aa overlap
120 130 140 150 160 170
Query AQIIKNFQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAY
.. . ....: ::. . . X.:.
HP0728 CFRKNYANSLMQDYSKGIIQSFKFLDQEKERLYPLTIVSQMHGITFFKYSQNALFMVDKI
190 200 210 220 230 240
180 190 200 210
Query LKEKGYLDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
::.:::X
HP0728 LKQKGYVLSFSQKEEIKRSFFSLEIAQKFIIESDKEHVFIALKPPKTLSMPKDFKDRARR
250 260 270 280 290 300
HP0604 uroporphyrinogen decarboxylase (hemE) {Escherichia coli}
44.4% identity in 18 aa overlap
60 70 80 90 100 110
Query MKEDLKPMAWGGLSSLEGASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTHSRFAQII
.... X:.::. .:.::X
HP0604 IEYLSLQIQAGVNAVMIFDSWASALEKEAYLKFSWDYLKKISKELKKRYAHIPVILFPKG
190 200 210 220 230 240
120 130 140 150 160 170
Query KNFQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEK
HP0604 IGAYLDSIDGEFDVFGVDWGTPLTAAKKILGGKYVLQGNLEPTRLYDKNALEEGVETILK
250 260 270 280 290 300
HP1359 hypothetical protein
19.8% identity in 106 aa overlap
10 20 30
Query MDREQIIALQHQRFATKKYDPNRRISEKDW-EVLVE
... ..X: .:. . ..: :X . .
HP1359 LSSLMWGLSMHELVLRSQALGFETRLVQCDLSFSYERFISKSKRSLAVLEEFDWLNSGFD
20 30 40 50 60 70
40 50 60 70 80 90
Query VGRLAPSSIGLEPWKMLLLKNERMKEDL---KPMAWGGLSSLEGASHFVIYLARKGVTYD
.::. .. .:: : : .: :.... : . .. . ..... .: .:.: .....
HP1359 FSRLNVENDTLELLKALYFKLEKLESLLLKENLLELEQKDRITALGHGLICLKKSSLIAP
80 90 100 110 120 130
100 110 120 130 140 150
Query SDYVKKVMHEVKKRDYDTHSRFAQIIKNFQENDMKLTDERSLFDWASKQTYIQMANMMMA
.: . . : : ..
HP1359 QTYYGRCVLEGKILAFFGVARDKDFLEITRMHALDIKRYDSFIVHSERKGLKL
140 150 160 170 180
HP0876 iron-regulated outer membrane protein (frpB) {Neisseria meningitidis}
20.0% identity in 35 aa overlap
150 160 170 180 190 200
Query YIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGYRNQEIT
.::....: .:. : . ...: ....
HP0876 RIYGYEVGGTFRYKGVSLNVGVSRTWPTTRGYLMADSYELAASTGNVFIIKLDYTIPKTG
610 620 630 640 650 660
210
Query PKTRWKTEVIYEVIE
. :
HP0876 INLAWLSRFVTGLDYCGFDIYLPDYGTAEKPKTPTDLAKCGSQLGLVHMHKPGYGVSNFY
670 680 690 700 710 720
HP1063 glucose-inhibited division protein (gidB) {Escherichia coli}
21.9% identity in 32 aa overlap
120 130 140 150 160 170
Query NFQENDMKLTDERSLFDWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKG
........ . . ... X: . .::.::
HP1063 KRAAFLNYLKSVLPLKNIEIIKKRLEDYQNLLQVDLITSRAVASSSFLIEKSQRFLKDKG
90 100 110 120 130 140
180 190 200 210
Query YLDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYEVIE
X.
HP1063 YFLFYKGEQLKDEIACKDTECFMHQKRVYFYKSKESLC
150 160 170
HP0112 hypothetical protein
28.6% identity in 28 aa overlap
80 90 100 110 120 130
Query GASHFVIYLARKGVTYDSDYVKKVMHEVKKRDYDTHSRFAQIIKNFQENDMKLTDERSLF
X:: ....... :. :. .: . .:X.
HP0112 YREFLDAKFIAYARPPYSLAYSLRHNRLLPRDYLGYRSLGEEISIFNPKDYDSWQERADT
110 120 130 140 150 160
140 150 160 170 180 190
Query DWASKQTYIQMANMMMAAAMLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFG
HP0112 EILRQLQESKKYFVFIKGCGIFAYHRELSKLMEVFDLIENSCKVLRLGDLMDYCYNDDPR
170 180 190 200 210 220
HP0480 GTP-binding protein, fusA-homolog (yihK) {Escherichia coli}
33.3% identity in 15 aa overlap
160 170 180 190 200 210
Query MLGIDSCPIEGYDQEKVEAYLKEKGYLDTAEFGVSVMASFGYRNQEITPKTRWKTEVIYE
X:...... .::X..
HP0480 DFSGAIIERLGKRKAEMKAMNPMSDGYTRLEFEIPARGLIGYRSEFLTDTKGEGVMNHSF
410 420 430 440 450 460
Query VIE
HP0480 LEFRPFSGSVESRKNGALISMENGEATAFSLFNIQERGTLFINPQTKVYVGMVIGEHSRD
470 480 490 500 510 520
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