BLASTP 2.2.1 [Apr-13-2001]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|15644666|ref|NP_206835.1| ATP-dependent C1p protease
(clpA) [Helicobacter pylori 26695]
(741 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_222751.1| ATP-DEPENDENT PROTEASE,ATP-BINDING SUBUNIT... 1290 0.0
ref|NP_222970.1| HEAT SHOCK PROTEIN [Helicobacter pylori J99] 263 9e-72
ref|NP_222992.1| ATP-DEPENDENT ZINC METALLOPEPTIDASE [Helic... 54 1e-08
ref|NP_224006.1| ATP-DEPENDENT PROTEASE,ATP-BINDING SUBUNIT... 51 9e-08
ref|NP_224011.1| ATP-DEPENDENT PROTEASE LA [Helicobacter py... 50 2e-07
ref|NP_223183.1| HEAT SHOCK PROTEIN [Helicobacter pylori J99] 39 6e-04
ref|NP_223085.1| HOLLIDAY JUNCTION DNA HELICASE RUVB [Helic... 37 0.002
ref|NP_223117.1| putative [Helicobacter pylori J99] 33 0.026
ref|NP_223075.1| ATP-DEPENDENT ZINC METALLOPEPTIDASE [Helic... 32 0.044
ref|NP_223361.1| putative TRANSCRIPTIONAL REGULATOR [Helico... 32 0.058
ref|NP_223108.1| putative FLAGELLAR BIOSYNTHESIS PROTEIN [H... 32 0.075
ref|NP_222839.1| putative [Helicobacter pylori J99] 31 0.099
ref|NP_222917.1| 90kDa chaperone [Helicobacter pylori J99] 31 0.13
ref|NP_224135.1| CHROMOSOMAL REPLICATION INITIATOR PROTEIN ... 30 0.29
ref|NP_223479.1| HOMOSERINE DEHYDROGENASE [Helicobacter pyl... 30 0.29
ref|NP_222727.1| OROTIDINE 5'-PHOSPHATE DECARBOXYLASE [Heli... 30 0.29
ref|NP_222866.1| SHIKIMATE KINASE I [Helicobacter pylori J99] 29 0.49
ref|NP_223399.1| putative [Helicobacter pylori J99] 28 0.64
ref|NP_223194.1| cag island protein [Helicobacter pylori J99] 28 0.83
ref|NP_222770.1| Proline/pyrroline-5-carboxylate dehydrogen... 28 0.83
ref|NP_223626.1| 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPH... 27 1.4
ref|NP_222785.1| UREASE ACCESSORY PROTEIN [Helicobacter pyl... 27 1.4
ref|NP_224119.1| putative ferredoxin-like protein [Helicoba... 27 1.9
ref|NP_223859.1| putative ABC transporter, ATP-binding prot... 27 1.9
ref|NP_223359.1| DNA GYRASE SUBUNIT A [Helicobacter pylori ... 27 1.9
ref|NP_224176.1| TRANSCRIPTION-REPAIR COUPLING FACTOR [Heli... 27 2.4
ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT ... 27 2.4
ref|NP_223507.1| putative abc transporter, ATP-binding prot... 27 2.4
ref|NP_223797.1| VALYL-TRNA SYNTHETASE [Helicobacter pylori... 26 3.2
ref|NP_223777.1| ATP synthase F1, subunit beta [Helicobacte... 26 3.2
ref|NP_223215.1| TRANSCRIPTION TERMINATION FACTOR [Helicoba... 26 4.1
ref|NP_223148.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRA... 26 4.1
ref|NP_222759.1| phosphomannose isomerase/GDP-mannose pyrop... 26 4.1
ref|NP_223406.1| putative FLAGELLIN PROTEIN [Helicobacter p... 25 5.4
ref|NP_222996.1| DIAMINOPIMELATE DECARBOXYLASE [Helicobacte... 25 5.4
ref|NP_222962.1| putative [Helicobacter pylori J99] 25 5.4
ref|NP_223990.1| putative [Helicobacter pylori J99] 25 7.1
ref|NP_223180.1| putative [Helicobacter pylori J99] 25 7.1
ref|NP_223007.1| DIPEPTIDE TRANSPORT SYSTEM ATP-BINDING PRO... 25 7.1
ref|NP_222956.1| ABC transporter, ATP-binding protein [Heli... 25 7.1
ref|NP_224208.1| PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN A... 25 9.2
ref|NP_224127.1| putative TYPE II DNA MODIFICATION ENZYME (... 25 9.2
ref|NP_223603.1| putative [Helicobacter pylori J99] 25 9.2
ref|NP_223491.1| putative [Helicobacter pylori J99] 25 9.2
ref|NP_223279.1| ADENYLATE KINASE [Helicobacter pylori J99] 25 9.2
ref|NP_223242.1| METHYLENETETRAHYDROFOLATE DEHYDROGENASE/ME... 25 9.2
>ref|NP_222751.1| ATP-DEPENDENT PROTEASE,ATP-BINDING SUBUNIT [Helicobacter pylori
J99]
Length = 742
Score = 1290 bits (3338), Expect = 0.0
Identities = 667/745 (89%), Positives = 696/745 (92%), Gaps = 7/745 (0%)
Query: 1 MAKFNQDLNEVLNQALNLALDLNHALCTTEHVLLVILEHESGEKIIGTLERDDYDKLKQI 60
M KFN+DLNEVL+ AL+LALD NH LCTTEHVLL ILEH G +I TLE D Y K++QI
Sbjct: 1 MDKFNKDLNEVLSHALDLALDFNHVLCTTEHVLLAILEHGIGIRIFNTLEEDGYHKMEQI 60
Query: 61 LKDYLLQYVPLKSDPAKMPARSFVLLRMLKRMYASCFESVGVEELLILMLDHPDCYASKL 120
LKDYL QY+PLK+DP K+P RS VL R+ K+MYAS +SVGVEELLI +L++ DCYASKL
Sbjct: 61 LKDYLQQYIPLKNDPTKIPDRSPVLARVFKKMYASYLDSVGVEELLIFILEYDDCYASKL 120
Query: 121 MDSFGIARLYSNPALLDLDNHGIPNDINDN----EEAPKNTPLKKYAKNLSALAQDNALD 176
+DSFGI R Y ALLD DN PNDINDN EEAPK+TPLKKY KNLSALAQ+NALD
Sbjct: 121 LDSFGITRSYFKSALLDFDN---PNDINDNDINNEEAPKSTPLKKYTKNLSALAQNNALD 177
Query: 177 PVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVY 236
PVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVY
Sbjct: 178 PVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVY 237
Query: 237 SLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLGTGSSNAGSLDAANI 296
SLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLG GSSNAGSLDAANI
Sbjct: 238 SLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLGAGSSNAGSLDAANI 297
Query: 297 LKPVLTDGSLKCLGATTFEEYRSVFEKDKAFNRRFSVIKVEEPSKEACYLILKKIAPLYE 356
LKPVLTDGSLKCLGATTFEEYRSVFEKDKAFNRRFS++ VEEPSKEACYLILK IAPLYE
Sbjct: 298 LKPVLTDGSLKCLGATTFEEYRSVFEKDKAFNRRFSIVNVEEPSKEACYLILKNIAPLYE 357
Query: 357 EHHQVRYDESVFKACVDLTSDYMHDKFLPDKAIELLDEVGSRKKISPKKGKKIGVDDVKE 416
EHHQVRY+ESVFKACVDLTS YMHDKFLPDKAIELLDEVGSRKKI+PKKGKKI VDDV+E
Sbjct: 358 EHHQVRYNESVFKACVDLTSYYMHDKFLPDKAIELLDEVGSRKKINPKKGKKISVDDVQE 417
Query: 417 TLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKNKPV 476
TLALKLKIPKMRL+SDKKALLRNLEKSLKNKIFAQ EAI+LVSNAIKIQHCGLSAKNKPV
Sbjct: 418 TLALKLKIPKMRLNSDKKALLRNLEKSLKNKIFAQTEAINLVSNAIKIQHCGLSAKNKPV 477
Query: 477 GSFLFVGPSGVGKTELAKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGL 536
GSFLFVGPSGVGKTELAKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGL
Sbjct: 478 GSFLFVGPSGVGKTELAKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGL 537
Query: 537 LVNAIKKHPHCLLLLDEIEKAHSNVYDLLLQVMDNATLSDNLGNQASFKHVILIMTSNVG 596
LVNAIKKHPHCLLLLDEIEKAH NVYDLLLQVMDNATLSDNLGN+ASFKHVILIMTSNVG
Sbjct: 538 LVNAIKKHPHCLLLLDEIEKAHPNVYDLLLQVMDNATLSDNLGNKASFKHVILIMTSNVG 597
Query: 597 SKDKDTLGFFSAKNTKYDKAVKELLTPELRSRIDAIVPFNALSLEDFERIVSVELDKLKA 656
SKDKDTLGFFS KN KYD+AVKELLTPELRSRIDAIVPFNALSLEDFERIVSVELDKLKA
Sbjct: 598 SKDKDTLGFFSTKNAKYDRAVKELLTPELRSRIDAIVPFNALSLEDFERIVSVELDKLKA 657
Query: 657 LALEQDITLKFHKEVVKFIAQKSYQTTLGAREIKKIIHNEIKTKLSDILLLQSFKKPCKI 716
LALEQ + LKFHKEVVK IAQKSYQTTLGAREIKKIIHNEIKT+LSDILLLQSFKKPCKI
Sbjct: 658 LALEQGVILKFHKEVVKCIAQKSYQTTLGAREIKKIIHNEIKTQLSDILLLQSFKKPCKI 717
Query: 717 ACLLEKNQLVLKEIKRAQKVKENDF 741
ACLLEKNQLVLKEIKRAQKVKENDF
Sbjct: 718 ACLLEKNQLVLKEIKRAQKVKENDF 742
>ref|NP_222970.1| HEAT SHOCK PROTEIN [Helicobacter pylori J99]
Length = 856
Score = 263 bits (673), Expect = 9e-72
Identities = 171/473 (36%), Positives = 263/473 (55%), Gaps = 41/473 (8%)
Query: 3 KFNQDLNEVLNQALNLALDLNHALCTTEHVLLVILEHESGEKIIGTLERDDYDKLKQILK 62
K L+E L+ A+ LAL +A T H+L +L + G I
Sbjct: 6 KMTDQLHETLDSAIALALHHKNAEVTPMHMLFAMLNNSQGILI----------------- 48
Query: 63 DYLLQYVPLKSDPAKMPARSFVLLRMLKRMYASCFESVGVEELLILMLDHPDCYASKLMD 122
LQ +P+ + K+ +S L ++ +++ + + LI L++ +K D
Sbjct: 49 -QALQKMPVDIEALKLSVQSE--LNKFAKVSQISKQNIQLNQALIQSLENAQGLMAKRGD 105
Query: 123 SFGI--ARLYSNPALLD---------------LDNHGIPNDINDNEEAPKNTPLKKYAKN 165
SF A L +N L + L++ I D + L+K+ +
Sbjct: 106 SFIATDAYLLANMNLFESVLKPYLDTKELQKTLESLRKGRTIQDKNDDSNLESLEKFGID 165
Query: 166 LSALAQDNALDPVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKE 225
L+ A +N LDPVIGR+EEI+R+++IL R+ KNNP+L+GE GVGKT++ E LA +I KE
Sbjct: 166 LTQKALENKLDPVIGRDEEIIRMMQILIRKTKNNPILLGEPGVGKTAVVEGLAQRIVNKE 225
Query: 226 VPEFLQEYEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLGTGS 285
VP+ L V +LDL+L+VAGAKYRG+FE+RLKK ++E++++ +ILFIDEIHT++G G+
Sbjct: 226 VPKTLLNKRVVALDLSLLVAGAKYRGEFEERLKKVIEEVKKSANVILFIDEIHTIVGAGA 285
Query: 286 SNAGSLDAANILKPVLTDGSLKCLGATTFEEYRSVFEKDKAFNRRFSVIKVEEPSKEACY 345
S G +DAANILKP L G L +GATT +EYR FEKD A RRF I + EPS
Sbjct: 286 SE-GGMDAANILKPALARGELHTIGATTLKEYRKYFEKDMALQRRFQPILLNEPSINEAL 344
Query: 346 LILKKIAPLYEEHHQVRYDESVFKACVDLTSDYMHDKFLPDKAIELLDEVGSRKKISPKK 405
IL+ + E HH + ++S A L+S Y+ D+FLPDKAI+L+DE ++ K+ +
Sbjct: 345 QILRGLKETLETHHNITINDSALIASAKLSSRYITDRFLPDKAIDLIDEGAAQLKMQ-ME 403
Query: 406 GKKIGVDDVKETLALKLKIPKMRLS-SDKKALLRNLEKSLKNKIFAQAEAISL 457
+ + VK ++ +L++ K L +K++ + +++ LK + E I L
Sbjct: 404 SEPAKLSSVKRSIQ-RLEMEKQALEMENKESNHKRMQEILKELSDLKEEKIQL 455
Score = 222 bits (566), Expect = 2e-59
Identities = 118/321 (36%), Positives = 197/321 (60%), Gaps = 4/321 (1%)
Query: 412 DDVKETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSA 471
+++ E ++ IP ++ +K + N+E L+ ++ Q +A+ ++ AIK GLS
Sbjct: 534 NNIAEIVSQWTHIPVQKMLQSEKNRVLNIESELQKRVVGQEKALKAIAKAIKRNKAGLSD 593
Query: 472 KNKPVGSFLFVGPSGVGKTELAKELALNL---NLHFERFDMSEYKEAHSVAKLIGSPSGY 528
NKP+GSFLF+GP+GVGKTE AK LA L + + R DMSEY E H++++LIG+ GY
Sbjct: 594 SNKPIGSFLFLGPTGVGKTESAKALAQFLFDSDKNLIRIDMSEYMEKHAISRLIGAAPGY 653
Query: 529 VGFEQGGLLVNAIKKHPHCLLLLDEIEKAHSNVYDLLLQVMDNATLSDNLGNQASFKHVI 588
VG+E+GG L A+++ P+ ++LLDE+EKAH +V++LLLQV+D L+D+ G + FK+ I
Sbjct: 654 VGYEEGGQLTEAVRRKPYSVVLLDEVEKAHPDVFNLLLQVLDEGHLTDSKGVRVDFKNTI 713
Query: 589 LIMTSNVGSKDKDTLGFFSAKNTKYDK-AVKELLTPELRSRIDAIVPFNALSLEDFERIV 647
LI+TSNV S A K K ++++ PE +R+D I+ FNAL IV
Sbjct: 714 LILTSNVASGALLEEDLSEADKQKAIKESLRQFFKPEFLNRLDEIISFNALDSHAIINIV 773
Query: 648 SVELDKLKALALEQDITLKFHKEVVKFIAQKSYQTTLGAREIKKIIHNEIKTKLSDILLL 707
+ + ++ ALE+ I + ++ + IA+ + GAR +K+ ++ ++ KL++++L
Sbjct: 774 GILFENVQKKALERGINITLDEKAKELIAEAGFDRFYGARPLKRALYEMVEDKLAELILE 833
Query: 708 QSFKKPCKIACLLEKNQLVLK 728
K+ +A ++E N++V K
Sbjct: 834 DKIKENDSVAFVVENNEIVPK 854
Score = 29.6 bits (65), Expect = 0.29
Identities = 34/145 (23%), Positives = 67/145 (45%), Gaps = 31/145 (21%)
Query: 178 VIGREEEILRVIEILGRRK-----KNNP----LLIGEAGVGKTSIAEALA-------LKI 221
V+G+E+ + + + + R K N P L +G GVGKT A+ALA +
Sbjct: 570 VVGQEKALKAIAKAIKRNKAGLSDSNKPIGSFLFLGPTGVGKTESAKALAQFLFDSDKNL 629
Query: 222 AQKEVPEFLQEYEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLL 281
+ ++ E+++++ + L+ A Y G +E+ + T + +++ ++ +DE+
Sbjct: 630 IRIDMSEYMEKHAI----SRLIGAAPGYVG-YEEGGQLT-EAVRRKPYSVVLLDEV---- 679
Query: 282 GTGSSNAGSLDAANILKPVLTDGSL 306
D N+L VL +G L
Sbjct: 680 -----EKAHPDVFNLLLQVLDEGHL 699
>ref|NP_222992.1| ATP-DEPENDENT ZINC METALLOPEPTIDASE [Helicobacter pylori J99]
Length = 550
Score = 53.9 bits (128), Expect = 1e-08
Identities = 89/320 (27%), Positives = 135/320 (41%), Gaps = 57/320 (17%)
Query: 182 EEEILRVIEILGRRKK---------NNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQE 232
+EE+L VI+ L KK LL+G GVGKT IA+ALA ++ VP F +
Sbjct: 171 KEELLEVIDYLKNPKKYQDLGIFLPKGVLLVGPPGVGKTMIAKALA---SEARVPFFYES 227
Query: 233 YEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLGTGSSNAGSLD 292
+S Y G K++ + +++ I+FIDEI LG S +
Sbjct: 228 GSAFS---------QIYVGAGAKKVHELFMHAKKHAPSIIFIDEIDA-LGKARGGHRSDE 277
Query: 293 AANILKPVLT--DGSLK-----CLGATT-FEEYRSVFEKDKAFNRRFSVIKVEEPSKEAC 344
L +LT DG L+ +GAT E + K F+RR I + P
Sbjct: 278 REATLNQLLTEMDGFLQNDEVVVIGATNQMEVMDEALLRSKRFDRR---IFISLPDLLER 334
Query: 345 YLILKKIAPLYEEHHQVRYDESVFKACVDLTSDYMHDKFLPDKAIELL----------DE 394
IL+K+ L + H + Y + K CV S M + + A+ L D
Sbjct: 335 QSILEKL--LENKKHALDY-LKIAKICVGF-SGAMLATLINESALNALKHQRKEITHGDI 390
Query: 395 VGSRKKISPKKGKKIGVDD-VKETLAL-----KLKIPKMRLSSDKKALLRNLEKSLKNKI 448
+ + KI+ K K +D+ KE +AL L + + DK +LL +NKI
Sbjct: 391 LEVKDKIAYGKKKPQTLDENQKELVALYQSAKALSAYWLEIEFDKASLLGEFIAFNENKI 450
Query: 449 FAQAEAISLVSNAIKIQHCG 468
+++E + N IK+ G
Sbjct: 451 HSESE----IKNYIKVYLSG 466
Score = 35.4 bits (80), Expect = 0.005
Identities = 32/103 (31%), Positives = 45/103 (43%), Gaps = 14/103 (13%)
Query: 453 EAISLVSNAIKIQHCGLSAKNKPVGSFLFVGPSGVGKTELAKELALNLNLHFERFDMSEY 512
E I + N K Q G+ P G L VGP GVGKT +AK LA + F S +
Sbjct: 176 EVIDYLKNPKKYQDLGIFL---PKG-VLLVGPPGVGKTMIAKALASEARVPFFYESGSAF 231
Query: 513 KEAHSVAKLIGSPSGYVGFEQGGLLVNAIKKHPHCLLLLDEIE 555
+ + A G ++ L KKH ++ +DEI+
Sbjct: 232 SQIYVGA----------GAKKVHELFMHAKKHAPSIIFIDEID 264
>ref|NP_224006.1| ATP-DEPENDENT PROTEASE,ATP-BINDING SUBUNIT [Helicobacter pylori
J99]
Length = 452
Score = 51.2 bits (121), Expect = 9e-08
Identities = 87/396 (21%), Positives = 163/396 (40%), Gaps = 98/396 (24%)
Query: 412 DDVKETLALKL-KIPKMRLSSDKKALL-------RNLEKSLKNKIFAQAEAISLVSNAIK 463
D + LALK ++ +M S+ ++ L + L+ L N + Q +A + S A+
Sbjct: 55 DRMDSLLALKRDRLRRMESSAYEEEFLLSRIPAPKELKAVLDNYVIGQEQAKKVFSVAVY 114
Query: 464 IQHCGLSAKNK---------------------PVGSFLFVGPSGVGKTELAKELALNLNL 502
+ LS K K + L +GP+G GKT +A+ LA +L++
Sbjct: 115 NHYKRLSFKEKLKKQDNQDSDLELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDI 174
Query: 503 HFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGLLVNA-------IKKHPHCLLLLDEIE 555
D + EA GYVG + +L ++K ++ +DEI+
Sbjct: 175 PIAISDATSLTEA-----------GYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEID 223
Query: 556 K--------------AHSNVYDLLLQVMDNATLSDNLGNQASFKH----VILIMTSNV-- 595
K + V LL++++ + + N+ + KH I I TS++
Sbjct: 224 KISRLSEHRSITRDVSGEGVQQALLKIVEGSLV--NIPPKGGRKHPEGNFIQIDTSDILF 281
Query: 596 ---GSKD-----------KDTLGFFSAKNTKYD-KAVKEL----------LTPELRSRID 630
G+ D ++ LGF K +K + +A+ L L PEL R+
Sbjct: 282 ICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIGRLP 341
Query: 631 AIVPFNALSLEDFERIV----SVELDKLKALALEQDITLKFHKEVVKFIAQKSYQTTLGA 686
+ +++SLE I+ + + + + L ++ L F +E +K IA+ + + GA
Sbjct: 342 VLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAKLALERKTGA 401
Query: 687 REIKKIIHNEIKTKLSDILLLQSFKKPCKIACLLEK 722
R ++ II + + D+ L+ + C+L++
Sbjct: 402 RGLRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQ 437
Score = 32.3 bits (72), Expect = 0.044
Identities = 33/101 (32%), Positives = 50/101 (48%), Gaps = 20/101 (19%)
Query: 182 EEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVYSLDLA 241
E E L +E+ K+N LLIG G GKT +A+ LA + ++P + + A
Sbjct: 137 ELEHLEEVEL----SKSNILLIGPTGSGKTLMAQTLAKHL---DIPIAISD--------A 181
Query: 242 LMVAGAKYRG-DFEKRLKKTLK----EIQQNGRIILFIDEI 277
+ A Y G D E L + L+ +Q+ + I+FIDEI
Sbjct: 182 TSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEI 222
>ref|NP_224011.1| ATP-DEPENDENT PROTEASE LA [Helicobacter pylori J99]
Length = 831
Score = 50.4 bits (119), Expect = 2e-07
Identities = 61/228 (26%), Positives = 103/228 (44%), Gaps = 32/228 (14%)
Query: 416 ETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKNKP 475
E AL +K K +L +D +L R E+ ++ FA + + + K+K
Sbjct: 307 EKKALDIKHVKEQLDNDHYSLKRPKERIVE--YFATMQLLEMRHKKKP------EKKDKT 358
Query: 476 VGSFL-FVGPSGVGKTELAKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQG 534
G+ L F GP GVGKT LA +A + R + ++ V +L G Y+G G
Sbjct: 359 KGTILCFYGPPGVGKTSLANSIAKAIERPLVRIALGGLED---VNELRGHRRTYIGSMPG 415
Query: 535 GL---LVNAIKKHPHCLLLLDEIEKAHSNV----YDLLLQVMD---NATLSDNLGN-QAS 583
+ L+ A K +P +++LDEI+K +V LL+++D N D+ N
Sbjct: 416 RIVQGLIEAKKMNP--VMVLDEIDKVDRSVRGDPASALLEILDPEQNIAFRDHYANFSID 473
Query: 584 FKHVILIMTSN----VGSKDKDTLGFFSAKN---TKYDKAVKELLTPE 624
VI I T+N + + +D + F S + ++ ++ K L P+
Sbjct: 474 LSQVIFIATANNIDRIPAPLRDRMEFISVSSYTPSEKEEIAKNYLIPQ 521
>ref|NP_223183.1| HEAT SHOCK PROTEIN [Helicobacter pylori J99]
Length = 443
Score = 38.5 bits (88), Expect = 6e-04
Identities = 59/274 (21%), Positives = 111/274 (39%), Gaps = 56/274 (20%)
Query: 438 RNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKNK-----PVGSFLFVGPSGVGKTEL 492
R + L I Q EA ++ A++ ++ L + + L +G +GVGKTE+
Sbjct: 9 REIVAYLDEYIIEQKEAKKFIAIALRNRYRRLQLEKSLQEEITPKNILMIGSTGVGKTEI 68
Query: 493 AKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGLLVNAIKKHPHCLLLLD 552
A+ +A + L F + + S+Y E G+VG + ++ + + + +LL++
Sbjct: 69 ARRMAKIMKLPFVKVEASKYTEV-----------GFVGRDVESMVRDLVN---NSVLLVE 114
Query: 553 EIEKAHSNVYDLLLQVMDNATLSDNLGNQASFKHVILIMTSNVGSKDKDTLGFFSAKNTK 612
K + L ++ A + + K ++ + S V + K
Sbjct: 115 NEHK------ERLKDKIEEAVV------EKIAKKLLPPLPSGVSEEKKQEYA------NS 156
Query: 613 YDKAVKELLTPELRSRIDAIVPFNALSLEDFERIVSVELDK---LKALALEQDITLKFHK 669
K + + EL SR +E R S+E+D + L +++++ FHK
Sbjct: 157 LLKMQQRIAQGELDSR----------EIEIEVRKKSIEIDSNVPPEILRVQENLIKVFHK 206
Query: 670 EVVKFIAQKSYQTTLGAREIKKIIHNEIKTKLSD 703
E Q + TL +E K+ + EI L D
Sbjct: 207 E------QDKVKKTLSVKEAKEALKAEISDTLLD 234
Score = 26.9 bits (58), Expect = 1.9
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 199 NPLLIGEAGVGKTSIAEALA 218
N L+IG GVGKT IA +A
Sbjct: 54 NILMIGSTGVGKTEIARRMA 73
>ref|NP_223085.1| HOLLIDAY JUNCTION DNA HELICASE RUVB [Helicobacter pylori J99]
Length = 336
Score = 36.6 bits (83), Expect = 0.002
Identities = 29/140 (20%), Positives = 58/140 (40%), Gaps = 18/140 (12%)
Query: 441 EKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKNKPVGSFLFVGPSGVGKTELAKELALNL 500
E SL+ ++ + + ++I C + + + LF GP G+GKT ++ +A
Sbjct: 18 EVSLRPNLWEDFIGQEKIKSNLQISICAAKKRQESLDHMLFFGPPGLGKTSISHIIA--- 74
Query: 501 NLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGLLVNAIKKHPHCLLLLDEIEKAHSN 560
KE + K+ +P + +L N K +L +DEI +
Sbjct: 75 ------------KEMETNIKITAAPMIEKSGDLAAILTNLQAKD---ILFIDEIHRLSPA 119
Query: 561 VYDLLLQVMDNATLSDNLGN 580
+ ++L M++ L +G+
Sbjct: 120 IEEVLYPAMEDFRLDIIIGS 139
Score = 25.0 bits (53), Expect = 7.1
Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 25/113 (22%)
Query: 173 NALDPVIGREEEILRV-IEILGRRKK----NNPLLIGEAGVGKTSIAEALALKIAQKEVP 227
N + IG+E+ + I I +K+ ++ L G G+GKTSI+ +A KE+
Sbjct: 24 NLWEDFIGQEKIKSNLQISICAAKKRQESLDHMLFFGPPGLGKTSISHIIA-----KEME 78
Query: 228 EFLQEYEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTL 280
++ + A M+ + GD L L +Q + ILFIDEIH L
Sbjct: 79 TNIK------ITAAPMI---EKSGD----LAAILTNLQ--AKDILFIDEIHRL 116
>ref|NP_223117.1| putative [Helicobacter pylori J99]
Length = 391
Score = 33.1 bits (74), Expect = 0.026
Identities = 43/197 (21%), Positives = 83/197 (41%), Gaps = 35/197 (17%)
Query: 165 NLSALAQDNALDPVIGREEEILR---VIEILGRRKKNNPLLIGEAGVGKTSIAEALALKI 221
+L+ L +L+ +G+E I + + + L + + G GVGKTS+A+ +A +
Sbjct: 2 SLTVLLNPKSLEEFLGQEHLIGKDAPLFKALQSKHFPHAFFYGPPGVGKTSLAQIIARSL 61
Query: 222 AQKEVPEFLQEYEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLL 281
+ + ++++ L L L K + TL + ++FIDE H L
Sbjct: 62 KRPILSFNATDFKLEDLRLKL------------KNYQNTLL------KPVVFIDETHRLN 103
Query: 282 GTGSSNAGSLDAANILKPVLTDGSLKCLGATTFEEYRSVFE--KDKAFNRRFSVIKVEEP 339
T L P++ LGA+T + S+ + ++F + +K +
Sbjct: 104 KT---------QQEFLLPIMEKNRALILGASTQDPNYSLSHAIRSRSFTFELTPLKKSDL 154
Query: 340 SK---EACYLILKKIAP 353
+ +A L+ K+I P
Sbjct: 155 DRLCDKALTLLKKQIEP 171
Score = 30.4 bits (67), Expect = 0.17
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 481 FVGPSGVGKTELAKELALNLNLHFERFDMSEYK 513
F GP GVGKT LA+ +A +L F+ +++K
Sbjct: 42 FYGPPGVGKTSLAQIIARSLKRPILSFNATDFK 74
>ref|NP_223075.1| ATP-DEPENDENT ZINC METALLOPEPTIDASE [Helicobacter pylori J99]
Length = 632
Score = 32.3 bits (72), Expect = 0.044
Identities = 45/183 (24%), Positives = 75/183 (40%), Gaps = 36/183 (19%)
Query: 182 EEEILRVIEIL---------GRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQE 232
+EE++ +++ L G + LL+G G GKT +A+A+A + VP F
Sbjct: 179 KEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVA---GEAHVPFFSMG 235
Query: 233 YEVYSLDLALMVAGAKYRGDFEKRLKKT-----LKEIQQNGR------IILFIDEIHTLL 281
+ +++ + + ++ R FE K+ + EI G+ +I DE L
Sbjct: 236 GSSF-IEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGMISGNDEREQTL 294
Query: 282 --------GTGSSNAGSLDAANILKPVLTDGSLKCLGATTFEEYRSVFEKDKAFNRRFSV 333
G GS NA + A +P + D +L G R V FN R +
Sbjct: 295 NQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFD----RQVLVDKPDFNGRVEI 350
Query: 334 IKV 336
+KV
Sbjct: 351 LKV 353
Score = 28.5 bits (62), Expect = 0.64
Identities = 22/76 (28%), Positives = 34/76 (43%), Gaps = 10/76 (13%)
Query: 480 LFVGPSGVGKTELAKELALNLNLHFERFDMSEYKEAHSVAKLIGSPSGYVGFEQGGLLVN 539
L VGP G GKT LAK +A ++ F S + + +G +G + L
Sbjct: 207 LLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSF-----IEMFVG-----LGASRVRDLFE 256
Query: 540 AIKKHPHCLLLLDEIE 555
KK ++ +DEI+
Sbjct: 257 TAKKQAPSIIFIDEID 272
>ref|NP_223361.1| putative TRANSCRIPTIONAL REGULATOR [Helicobacter pylori J99]
Length = 381
Score = 32.0 bits (71), Expect = 0.058
Identities = 40/135 (29%), Positives = 55/135 (40%), Gaps = 31/135 (22%)
Query: 154 PKNTPLKKYAKNLSALAQDNALDPVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSI 213
P PLKK K+ S LA AL+ + + L+V N +L+GE+GVGK
Sbjct: 123 PLEKPLKKAPKH-SFLATSKALEET---KRQALKVAST-----DANVMLLGESGVGKEVF 173
Query: 214 AEAL----------ALKIAQKEVPEFLQEYEVYSLDL-ALMVAGAKYRGDFEKRLKKTLK 262
A + + I +PE L E E++ A A A G FE K T
Sbjct: 174 AHFIHQHSQRSKHPFIAINMSAIPEHLLESELFGYQKGAFTDATAPKMGLFESANKGT-- 231
Query: 263 EIQQNGRIILFIDEI 277
+F+DEI
Sbjct: 232 ---------IFLDEI 237
>ref|NP_223108.1| putative FLAGELLAR BIOSYNTHESIS PROTEIN [Helicobacter pylori J99]
Length = 455
Score = 31.6 bits (70), Expect = 0.075
Identities = 31/142 (21%), Positives = 58/142 (40%), Gaps = 19/142 (13%)
Query: 356 EEHHQVRYDESVFKACVDLTSDYMHDKFLPDKAIELLDEVGSRKKISPKKGKKIGVDDVK 415
EE + S + + L + D+ P+ ++ + E K++ + G K D
Sbjct: 151 EEIKDINAQLSKIRDSLKLIQNMFWDEKNPN-SVNIPQEFAEIYKLAKQSGMKSSHLD-- 207
Query: 416 ETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKNKP 475
E + L L++ +R+ + + R + L+ I + E ++L I
Sbjct: 208 EIMQLSLELMPLRMRENSVTIKRYFREVLRKIILCRPEDLNLRQKRI------------- 254
Query: 476 VGSFLFVGPSGVGKTELAKELA 497
+ VGP+GVGKT +LA
Sbjct: 255 ---LMLVGPTGVGKTTTLAKLA 273
Score = 27.3 bits (59), Expect = 1.4
Identities = 17/45 (37%), Positives = 25/45 (54%), Gaps = 5/45 (11%)
Query: 184 EILRVI-----EILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQ 223
E+LR I E L R+K +L+G GVGKT+ LA + ++
Sbjct: 234 EVLRKIILCRPEDLNLRQKRILMLVGPTGVGKTTTLAKLAARYSR 278
>ref|NP_222839.1| putative [Helicobacter pylori J99]
Length = 143
Score = 31.2 bits (69), Expect = 0.099
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 220 KIAQKEVPEFLQEYEVYSLDLALMVAGAKYRGDFEKRLKKTLKEIQQNGR 269
K+A EVPEF E L+ KY+ DF+K + K L + Q R
Sbjct: 38 KVAPSEVPEFRTEVNK-RLEAMKEEERQKYKADFKKAMDKNLASLSQEDR 86
>ref|NP_222917.1| 90kDa chaperone [Helicobacter pylori J99]
Length = 621
Score = 30.8 bits (68), Expect = 0.13
Identities = 91/390 (23%), Positives = 147/390 (37%), Gaps = 51/390 (13%)
Query: 189 IEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVYSLDLALMVAGAK 248
+ L KK + LIG+ GVG S A +A K V +Q +V S V+ K
Sbjct: 105 LSALSGDKKKDSALIGQFGVGFYS-----AFMVASKIV---VQTKKVTSHQAYAWVSDGK 156
Query: 249 YRGDFEKRLKKTLKEIQQNGRIILFIDEIHTLLGTGSSNAGSLDAANILKPVLTDGSLKC 308
G FE + + +KE +Q I LF+ E S A + +++K
Sbjct: 157 --GKFE--ISECVKE-EQGTEITLFLKE------EDSHFASRWEIDSVVKKYSEHIPFPI 205
Query: 309 LGATTFEEYRSVFEKDKAFNRRFSVIKVEEPSKEACYLILKKIAPLYEEHHQVRYDESVF 368
T ++ + K K ++ ++ + + K + L E+ ++ Y
Sbjct: 206 FLTYTDTKFEGEGDNKKEVKEE----KCDQINQASALWKMNK-SELKEKDYKDFYQSFAH 260
Query: 369 KACVDLTSDYMHDK-----------FLPDKAIELLDEVGSRKKISPKKGKKIGVDDVKET 417
L+ Y+H+K ++P KA L V + + + DD KE
Sbjct: 261 DNSEPLS--YIHNKVEGSLEYTTLFYIPSKAPFDLFRVDYKSGVKLYVKRVFITDDDKEL 318
Query: 418 LALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKN---- 473
L L+ K + S+ L + E +NKI A + S+ +I+ KN
Sbjct: 319 LPSYLRFVKGVIDSEDLPLNVSREILQQNKILANIRSASVKKILSEIERLSKDNKNYHKF 378
Query: 474 -KPVGSFLFVGPSG--VGKTELAKELALNLNLHFERFDMSEYKE-----AHSVAKLIGSP 525
+P G L G G K +L + L E + EYKE S+ L+G
Sbjct: 379 YEPFGKVLKEGLYGDFENKEKLLELLRFYSKDKGEWISLKEYKENLKENQKSIYYLLGEN 438
Query: 526 SGYVGFEQGGLLVNAIKKHPHCLLLLDEIE 555
+ + LL +K LLL DEI+
Sbjct: 439 LDLL--KASPLLEKYAQKGYDVLLLSDEID 466
>ref|NP_224135.1| CHROMOSOMAL REPLICATION INITIATOR PROTEIN [Helicobacter pylori J99]
Length = 457
Score = 29.6 bits (65), Expect = 0.29
Identities = 33/144 (22%), Positives = 65/144 (44%), Gaps = 16/144 (11%)
Query: 355 YEEH-HQVRYDESVFKACVDLTSDYMHDKFL----PDKAIELLDEVGSRKKISPKKGKKI 409
YE + Q++Y+ + K+ D+ Y +KFL K LL E+ S+ K+ +
Sbjct: 26 YENYLSQLKYNPNASKS--DIAFFYAPNKFLCTTITAKYGALLKEILSQNKVGMHLAHSV 83
Query: 410 GVDDVKETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAI-KIQHCG 468
DV+ +A PK+++++ + + S+K+ + + +N + +I
Sbjct: 84 ---DVRIEVA-----PKIQVNAQSNINYKATKTSVKDSYTFENFVVGSCNNTVYEIAKKV 135
Query: 469 LSAKNKPVGSFLFVGPSGVGKTEL 492
+ P LF G +G+GKT +
Sbjct: 136 AQSDTPPYNPVLFYGGTGLGKTHI 159
>ref|NP_223479.1| HOMOSERINE DEHYDROGENASE [Helicobacter pylori J99]
Length = 421
Score = 29.6 bits (65), Expect = 0.29
Identities = 66/282 (23%), Positives = 114/282 (40%), Gaps = 68/282 (24%)
Query: 414 VKETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLVSNAIKIQHCGLSAKN 473
+K+ +++KI KKA++R+++K K F ++ + V I+ G+
Sbjct: 30 IKDRAGVEIKI--------KKAVVRDVKKH-KGYAFEISDDLESV-----IEDKGIDIVV 75
Query: 474 KPVGSFLFVGPSGVGKTELAKELAL----NLNLHFERFDMSEYKEAHSVAKLIGSPSGYV 529
+ +G P + K LAK+ A L + R+++ + +AK +P G+
Sbjct: 76 ELMGGV--EAPYLLAKKTLAKQKAFVTANKAMLAYHRYELEQ------IAK--NTPIGFE 125
Query: 530 GFEQGGL-LVNAIKKHPHCLLLLDEIEKAHSNVYDLLLQVMDNATLSDNLGNQASFKHVI 588
GG+ ++ A+K D + H + +L N LS NQASFK +
Sbjct: 126 ASVCGGIPIIKALK---------DGLSANHILSFKGILNGTSNYILSQMFKNQASFKDAL 176
Query: 589 LIMTSNVGSKDKDTLGF------FSAKNTKYDKAVKELLTPELRSRIDAIVPFNALSLED 642
KD LG+ F K D A K L+ L IDA + +E
Sbjct: 177 ---------KDAQHLGYAELNPEFDIKG--IDAAHKLLILASLAYGIDA--KLEEILIEG 223
Query: 643 FERIVSVELD---------KLKALALEQD--ITLKFHKEVVK 673
E+I +++ KL +A + I L+ H ++K
Sbjct: 224 IEKIEPDDMEFAKEFGYSIKLLGIAKKHQDCIELRVHPSMIK 265
>ref|NP_222727.1| OROTIDINE 5'-PHOSPHATE DECARBOXYLASE [Helicobacter pylori J99]
Length = 227
Score = 29.6 bits (65), Expect = 0.29
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 156 NTPLKKYAKNLSALAQDNALDPVIGREEEILRVIEILGR 194
N PLK A LSA+ +++ +D V+ E L + E LG+
Sbjct: 130 NAPLKTQAITLSAIGKESGIDGVVCSVFESLAIKEALGK 168
>ref|NP_222866.1| SHIKIMATE KINASE I [Helicobacter pylori J99]
Length = 162
Score = 28.9 bits (63), Expect = 0.49
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 16/81 (19%)
Query: 201 LLIGEAGVGKTSIAEALALKIAQKEVPEFLQEYEVYSLDLALMV-AGAKYRGDFEKRLKK 259
+LIG G GK+S+A+ L L + + EV D+ + G RG FE+ +
Sbjct: 5 VLIGFMGSGKSSLAQELGLAL----------KLEVLDTDMIISERVGLSVRGIFEELGED 54
Query: 260 TLKEIQQNGRIILFIDEIHTL 280
+ ++N IDE+ TL
Sbjct: 55 NFRMFEKN-----LIDELKTL 70
>ref|NP_223399.1| putative [Helicobacter pylori J99]
Length = 404
Score = 28.5 bits (62), Expect = 0.64
Identities = 23/87 (26%), Positives = 41/87 (46%), Gaps = 6/87 (6%)
Query: 187 RVIEILGRRK-KNNPLLIGEAGVGKTSIAEALALKI-----AQKEVPEFLQEYEVYSLDL 240
+++E + + K K N LL+G GVGK+S+ AL K K + + L++Y L
Sbjct: 34 KMLEFIKKEKPKMNVLLMGATGVGKSSLINALFGKEITKTGVGKPITQHLEKYIDEEKGL 93
Query: 241 ALMVAGAKYRGDFEKRLKKTLKEIQQN 267
L D+ ++ KE++ +
Sbjct: 94 ILWDTKGIEDKDYHDTMQSIKKEMEDS 120
>ref|NP_223194.1| cag island protein [Helicobacter pylori J99]
Length = 1819
Score = 28.1 bits (61), Expect = 0.83
Identities = 22/74 (29%), Positives = 35/74 (46%), Gaps = 3/74 (4%)
Query: 373 DLTSDYMHDKFLPDKAIE--LLDEVGSRKKISPK-KGKKIGVDDVKETLALKLKIPKMRL 429
D+T Y +K + DK++E L +G KK K KGKK + E+ + + +
Sbjct: 1471 DITKQYETEKTIKDKSLEAKLAKALGGDKKDDDKEKGKKPTAETKAESNKIDKDVAETAK 1530
Query: 430 SSDKKALLRNLEKS 443
+ + AL EKS
Sbjct: 1531 NISEIALKNKKEKS 1544
Score = 25.8 bits (55), Expect = 4.1
Identities = 29/128 (22%), Positives = 54/128 (41%), Gaps = 21/128 (16%)
Query: 608 AKNTKYDKAVKELLTPELRSRIDAIVPFNALSLEDFERIVSVELDKLKALALEQDITLKF 667
A+N K K ++LLTPE R LE+ ++ V LD + E +
Sbjct: 1136 ARNEKEKKECEKLLTPEARK-----------LLEESKKSVKAYLDCVSKAKNEAE----- 1179
Query: 668 HKEVVKFIAQKSYQTTLGAREIKKIIHNEIKTKLSDILLLQSFKKPCKIACLLEKNQLVL 727
KE K + ++ + A+E K + + + + K+ C+ E +L+
Sbjct: 1180 KKECEKLLTPEARKLLEEAKESVKAYKDCVSRARN-----EKEKQECEKLLTPEARKLLE 1234
Query: 728 KEIKRAQK 735
+E+K++ K
Sbjct: 1235 QEVKKSVK 1242
>ref|NP_222770.1| Proline/pyrroline-5-carboxylate dehydrogenase [Helicobacter pylori
J99]
Length = 1185
Score = 28.1 bits (61), Expect = 0.83
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 607 SAKNTKYDKAVKELLTPELRSRIDAIVPFNALSLEDFE---RIVSVELDKLKALALEQD 662
SA+ KY +A+K + +I I F+ +++ DFE + + LD L ALALE++
Sbjct: 156 SARFEKYSQALKSNYIQYISIKITTI--FSQINILDFEYSKKEIVKRLDALYALALEEE 212
>ref|NP_223626.1| 2,3-BISPHOSPHOGLYCERATE-INDEPENDENT PHOSPHOGLYCERATE MUTASE
[Helicobacter pylori J99]
Length = 491
Score = 27.3 bits (59), Expect = 1.4
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 588 ILIMTSNVG-SKDKDTLGFFSAKNTKYDKAVKEL 620
+LI+T +G KD D FF AK YD K L
Sbjct: 6 LLIITDGIGYRKDSDHNAFFHAKKPTYDLMFKTL 39
>ref|NP_222785.1| UREASE ACCESSORY PROTEIN [Helicobacter pylori J99]
Length = 199
Score = 27.3 bits (59), Expect = 1.4
Identities = 26/101 (25%), Positives = 48/101 (46%), Gaps = 9/101 (8%)
Query: 483 GPSGVGKTELAKELALNLNLHFERF----DMSEYKEAHSVAKLIGSP-SGYVGFEQGGLL 537
GP G GKT L + L +++ ++ D+ ++A + K P +G E GG
Sbjct: 8 GPVGSGKTALIEALTRHMSKDYDMAVITNDIYTKEDAEFMCKNSVMPRDRIIGVETGGCP 67
Query: 538 VNAIKKHPHCLLLLDEIEKAHSNVYDLLLQVMDNATLSDNL 578
AI++ + L+ +E+ H +L L ++++ DNL
Sbjct: 68 HTAIRE--DASMNLEAVEEMHGRFPNLELLLIESG--GDNL 104
>ref|NP_224119.1| putative ferredoxin-like protein [Helicobacter pylori J99]
Length = 458
Score = 26.9 bits (58), Expect = 1.9
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 147 INDNEEAPKNTPLKKYAKNLSAL 169
I++ +E+PKNTP K K LS L
Sbjct: 116 ISNKQESPKNTPSYKIRKALSVL 138
>ref|NP_223859.1| putative ABC transporter, ATP-binding protein [Helicobacter pylori
J99]
Length = 228
Score = 26.9 bits (58), Expect = 1.9
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 482 VGPSGVGKTELAKELA-LNLNLHFE 505
+GP+G GKT L K LA LNLN E
Sbjct: 34 LGPNGAGKTTLLKILAGLNLNYQGE 58
>ref|NP_223359.1| DNA GYRASE SUBUNIT A [Helicobacter pylori J99]
Length = 828
Score = 26.9 bits (58), Expect = 1.9
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 17/83 (20%)
Query: 198 NNPLLIGEAGVGKTSIAEA-----------LALKIAQKEVPEFLQEYEVYSLDLALMVAG 246
N L + E G+GK ++AEA + +K+ QK + V +L LM+
Sbjct: 713 NKLLSVSENGLGKQTLAEAYREQSRGGKGVIGMKLTQK-TGNLVSVISVDDENLNLMILT 771
Query: 247 AKYRGDFEKRLKKTLKEIQQNGR 269
A K ++ ++K+I++ GR
Sbjct: 772 AS-----AKMIRVSIKDIRETGR 789
>ref|NP_224176.1| TRANSCRIPTION-REPAIR COUPLING FACTOR [Helicobacter pylori J99]
Length = 1001
Score = 26.6 bits (57), Expect = 2.4
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 612 KYDKAVKELLTPELRSRIDAIVPFNAL-SLEDFERIVSVELDKLKALALEQDITLKFHKE 670
K D+ +KE++ ELR N + S+ + + + KLK L I +E
Sbjct: 675 KNDELLKEIIYRELRRNGQIFYIHNHIASISKVKTKLEDLIPKLKIAILHSQINANESEE 734
Query: 671 VVKFIAQKSYQTTLGAREIKKIIH 694
++ A+ +YQ L ++ IH
Sbjct: 735 IMLEFAKGNYQVLLCTSIVESGIH 758
>ref|NP_223838.1| DNA-DIRECTED RNA POLYMERASE, BETA SUBUNIT [Helicobacter pylori J99]
Length = 2890
Score = 26.6 bits (57), Expect = 2.4
Identities = 22/112 (19%), Positives = 52/112 (45%), Gaps = 19/112 (16%)
Query: 347 ILKKIAPLYEEHHQVRYDESVFKACVDLTSDYMHDKFLPDKAIE--LLDEVGSRKKI--- 401
+ K I P+ +EH+++ + + C ++ K+ +A+E + + + K+
Sbjct: 52 VFKSIFPIQDEHNRITLE---YAGC-----EFGKSKYTVREAMERGITYSIPLKIKVRLI 103
Query: 402 ----SPKKGKKIGVDDVKETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIF 449
K G+K G+ D+KE +IP M + ++ +E+ + N+++
Sbjct: 104 LWEKDTKSGEKNGIKDIKEQSIFIREIPLM--TERTSFIINGVERVVVNQLY 153
>ref|NP_223507.1| putative abc transporter, ATP-binding protein [Helicobacter pylori
J99]
Length = 533
Score = 26.6 bits (57), Expect = 2.4
Identities = 13/32 (40%), Positives = 17/32 (52%)
Query: 469 LSAKNKPVGSFLFVGPSGVGKTELAKELALNL 500
+S K P +GP+GVGK+ L K L L
Sbjct: 340 VSLKVMPKDKIALIGPNGVGKSTLCKILVEEL 371
>ref|NP_223797.1| VALYL-TRNA SYNTHETASE [Helicobacter pylori J99]
Length = 872
Score = 26.2 bits (56), Expect = 3.2
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 570 DNATLSDNLGNQASFKHVILIMTSNVGSKDKDTLGFFSAKNTKYDKAVKELLTPELRSRI 629
+N ++ L N AS+ + KDK+ L + +Y K+ L+T E+R+ +
Sbjct: 577 NNKNFANKLFNAASY-----LKLKQESFKDKERLNEYQTALGRYAKSRLNLVTKEVRNAL 631
Query: 630 D 630
D
Sbjct: 632 D 632
>ref|NP_223777.1| ATP synthase F1, subunit beta [Helicobacter pylori J99]
Length = 469
Score = 26.2 bits (56), Expect = 3.2
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 186 LRVIEILGRRKKNNPL-LIGEAGVGKTSIAEALALKIAQK 224
++VI++L K + L G AGVGKT I L +A K
Sbjct: 136 IKVIDLLAPYSKGGKVGLFGGAGVGKTVIIMELIHNVAYK 175
>ref|NP_223215.1| TRANSCRIPTION TERMINATION FACTOR [Helicobacter pylori J99]
Length = 438
Score = 25.8 bits (55), Expect = 4.1
Identities = 15/26 (57%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 475 PVGS---FLFVGPSGVGKTELAKELA 497
PVG L V P GKTEL KELA
Sbjct: 186 PVGKGQRALIVAPPRTGKTELMKELA 211
>ref|NP_223148.1| TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE) [Helicobacter
pylori J99]
Length = 545
Score = 25.8 bits (55), Expect = 4.1
Identities = 22/72 (30%), Positives = 32/72 (43%), Gaps = 7/72 (9%)
Query: 597 SKDKDTLGFFSAKNTKYDKAVKELLTPELRSRIDAI-------VPFNALSLEDFERIVSV 649
S D +L F ++ N + A LL PE IDA + F SL DF++
Sbjct: 233 SLDSASLFFMASLNCLKENAYLGLLLPESCLNIDAFSKMREMALKFQMRSLIDFDKPFKN 292
Query: 650 ELDKLKALALEQ 661
+ K LAL++
Sbjct: 293 LMTKAVGLALKK 304
>ref|NP_222759.1| phosphomannose isomerase/GDP-mannose pyrophosphorylase
[Helicobacter pylori J99]
Length = 470
Score = 25.8 bits (55), Expect = 4.1
Identities = 26/106 (24%), Positives = 46/106 (42%), Gaps = 18/106 (16%)
Query: 109 MLDHPDCYASKLMDSFGIARL--------------YSNPALLDLDNHGIPNDINDNEEAP 154
+L CY K+++ ARL S A ++LD+ N++ P
Sbjct: 366 VLHESGCYKVKILEVKPNARLSLQKHFHRSEHWVVISGMASVELDHQSFELQANESTYIP 425
Query: 155 KNT--PLKKYAKNLSALAQDNALDPVIGREEEILRVIEILGRRKKN 198
KNT L Y K + + + + +G E++I+RV + R+ +N
Sbjct: 426 KNTLHRLANYGK-IPLIIIEVQVGEYVG-EDDIVRVDDDFNRQNQN 469
>ref|NP_223406.1| putative FLAGELLIN PROTEIN [Helicobacter pylori J99]
Length = 119
Score = 25.4 bits (54), Expect = 5.4
Identities = 15/59 (25%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 8 LNEVLNQALN-LALDLNHALCTTEHVLLVILEHESGEKIIGTLERDDYDKLKQILKDYL 65
L+E LN+ + + D+N + T L+V ++ +G+K+I + + +L Q ++D +
Sbjct: 53 LSERLNEEMKRIGTDINFSYNDTIKGLVVSVKDANGDKVIREIPSKEAVELMQRMRDVI 111
>ref|NP_222996.1| DIAMINOPIMELATE DECARBOXYLASE [Helicobacter pylori J99]
Length = 405
Score = 25.4 bits (54), Expect = 5.4
Identities = 15/40 (37%), Positives = 22/40 (54%), Gaps = 1/40 (2%)
Query: 485 SGVGKTELAKELALNLNLHFERFD-MSEYKEAHSVAKLIG 523
SGVGK+ E AL LN+ F + E K ++A+ +G
Sbjct: 88 SGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLG 127
>ref|NP_222962.1| putative [Helicobacter pylori J99]
Length = 222
Score = 25.4 bits (54), Expect = 5.4
Identities = 21/86 (24%), Positives = 44/86 (50%), Gaps = 2/86 (2%)
Query: 652 DKLKALALEQDITLKFHKEVVKFIAQKSYQTTLGAREIKKIIHNEIKTKLSDILLLQSFK 711
+ L+ L+ ++ E + + +KS +EI + + N + K LQ+ +
Sbjct: 39 EDLRQLSEKEQSLRILQTENARLLDEKSDLLNKKEKEIDEKLKN-LAAKEEAFKTLQTEE 97
Query: 712 KPCKIACLLEKNQLVLKEIKRAQKVK 737
K ++ L+E+N+ +L+EIK+A+ K
Sbjct: 98 KK-RLKNLIEENEGILREIKQAKDSK 122
>ref|NP_223990.1| putative [Helicobacter pylori J99]
Length = 1164
Score = 25.0 bits (53), Expect = 7.1
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 704 ILLLQSFKKPCKIACLLEKNQLVLKEIKRAQKVKEND 740
I+L + +P +I N + KE+ AQ++K+N+
Sbjct: 436 IILTNTLIQPSEIIAYRGLNPIFEKELSNAQEIKKNE 472
>ref|NP_223180.1| putative [Helicobacter pylori J99]
Length = 706
Score = 25.0 bits (53), Expect = 7.1
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 10/103 (9%)
Query: 606 FSAKNTKYDKAVKELLT---PELRSRIDAIVPFNALSLEDFERIVSVELDKLKALALEQD 662
F + K +K +K+L E+ R +V + AL + + + + L++ K +++
Sbjct: 506 FKQSSLKLNKNLKDLEPFGEKEIEKRASDLVDW-ALKIWTYPILEAETLEEYKPKKEKKE 564
Query: 663 ITLKFHKEVVKFIAQK------SYQTTLGAREIKKIIHNEIKT 699
K KE K +K SY+ + +RE+ I+ EIKT
Sbjct: 565 KKEKKEKEEYKLKKEKKVYDLSSYKFSPHSRELFDILRKEIKT 607
>ref|NP_223007.1| DIPEPTIDE TRANSPORT SYSTEM ATP-BINDING PROTEIN [Helicobacter pylori
J99]
Length = 268
Score = 25.0 bits (53), Expect = 7.1
Identities = 13/55 (23%), Positives = 30/55 (53%), Gaps = 2/55 (3%)
Query: 166 LSALAQDNALDPVIGREEEILRVIEILGRRKKNNPLL--IGEAGVGKTSIAEALA 218
+ L + A+D + + + ++ + + + N +L +GE+G GK++ A+ LA
Sbjct: 6 IKELKKSYAIDRGLFKPKRVIHALNGISFEVEQNEVLSIVGESGCGKSTTAKILA 60
>ref|NP_222956.1| ABC transporter, ATP-binding protein [Helicobacter pylori J99]
Length = 516
Score = 25.0 bits (53), Expect = 7.1
Identities = 14/28 (50%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 195 RKKNNPLLIGEAGVGKTSIAEALALKIA 222
+ K N +IGE+G GK+S+A L LK+A
Sbjct: 296 KAKENIGIIGESGSGKSSLALGL-LKLA 322
>ref|NP_224208.1| PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN A [Helicobacter pylori
J99]
Length = 307
Score = 24.6 bits (52), Expect = 9.2
Identities = 17/64 (26%), Positives = 29/64 (44%)
Query: 533 QGGLLVNAIKKHPHCLLLLDEIEKAHSNVYDLLLQVMDNATLSDNLGNQASFKHVILIMT 592
QG L +K H L + + HS + + Q++DNA + L A + L+ +
Sbjct: 14 QGVGLELILKSHKEVSALCEPLYLVHSELLERANQLLDNAYETKTLNAIAIDAPLPLLNS 73
Query: 593 SNVG 596
S +G
Sbjct: 74 STIG 77
>ref|NP_224127.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 1252
Score = 24.6 bits (52), Expect = 9.2
Identities = 16/48 (33%), Positives = 24/48 (49%), Gaps = 5/48 (10%)
Query: 411 VDDVKETLALKLKIPKMRLSSDKKALLRNLEKSLKNKIFAQAEAISLV 458
+ D+K T +L LK PK K L + +EK +K F + SL+
Sbjct: 703 IQDLKNTFSLTLKDPK-----TKAELEKTIEKHIKKYNFFALDDKSLL 745
>ref|NP_223603.1| putative [Helicobacter pylori J99]
Length = 204
Score = 24.6 bits (52), Expect = 9.2
Identities = 20/69 (28%), Positives = 30/69 (42%), Gaps = 11/69 (15%)
Query: 84 VLLRMLKRM--YASCF-------ESVGVEELLILMLDHPDCYASKLMDSFGIARLYSNPA 134
VLL R+ Y SCF SV + + IL HP C +K +D I + +
Sbjct: 127 VLLNFEGRLQSYNSCFLCDAKLERSVALAQGFILA--HPSCLKAKSLDLEKIQAFFRTQS 184
Query: 135 LLDLDNHGI 143
+DL+ +
Sbjct: 185 TIDLETEEV 193
>ref|NP_223491.1| putative [Helicobacter pylori J99]
Length = 462
Score = 24.6 bits (52), Expect = 9.2
Identities = 27/118 (22%), Positives = 54/118 (44%), Gaps = 30/118 (25%)
Query: 172 DNALDPVIGREEEILRVIEILGRRKKNNPLLIGEAGVGKTSIAEALALKIAQKEVPEFLQ 231
+NAL+ +EEEI++V +IG VGK+S+ AL K ++ + +
Sbjct: 189 NNALEET--KEEEIIQVG------------IIGRVNVGKSSLLNALTKK--ERSLVSSVA 232
Query: 232 EYEVYSLDLALMV----------AGAKYRGDF----EKRLKKTLKEIQQNGRIILFID 275
+ +D +++ AG ++RG + L +T K ++++ +L +D
Sbjct: 233 GTTIDPIDETILIGDQKICFVDTAGIRHRGKILGIEKYALDRTQKALEKSHIALLVLD 290
>ref|NP_223279.1| ADENYLATE KINASE [Helicobacter pylori J99]
Length = 191
Score = 24.6 bits (52), Expect = 9.2
Identities = 33/143 (23%), Positives = 58/143 (40%), Gaps = 10/143 (6%)
Query: 201 LLIGEAGVGKTSIAEALALK----IAQKEVPEFLQEYEVYSLDLALMVAGAKYRGD---F 253
L+IG G GKT+ AE +A IA + L+ + L++ +G+
Sbjct: 6 LIIGAPGSGKTTDAELIAKNNSETIAHFSTGDLLRAESAKKTERGLLIEKFTSQGELVPL 65
Query: 254 EKRLKKTLKEIQQNGRIILFIDEIHTLLGTGSSNAGSLDAAN--ILKPVL-TDGSLKCLG 310
E ++ L I+ + + I+ ID + + L+A N ILK V+ + S
Sbjct: 66 EIVVETILSAIKSSSKGIILIDGYPRSVEQMQALDKELNAQNEVILKSVIEVEVSENTAK 125
Query: 311 ATTFEEYRSVFEKDKAFNRRFSV 333
R + ++ F+ R V
Sbjct: 126 ERVLGRSRGADDNERVFHNRMRV 148
>ref|NP_223242.1| METHYLENETETRAHYDROFOLATE DEHYDROGENASE/METHENYLTETRAHYDROFOLATE
CYCLOHYDROLASE [Helicobacter pylori J99]
Length = 290
Score = 24.6 bits (52), Expect = 9.2
Identities = 11/17 (64%), Positives = 13/17 (75%)
Query: 432 DKKALLRNLEKSLKNKI 448
D +AL N+EK LKNKI
Sbjct: 10 DGQALAYNIEKDLKNKI 26
Database: NC_000921.faa
Posted date: Dec 10, 2001 4:36 PM
Number of letters in database: 494,079
Number of sequences in database: 1491
Lambda K H
0.317 0.136 0.374
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 780,862
Number of Sequences: 1491
Number of extensions: 38129
Number of successful extensions: 230
Number of sequences better than 10.0: 46
Number of HSP's better than 10.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 164
Number of HSP's gapped (non-prelim): 80
length of query: 741
length of database: 494,079
effective HSP length: 85
effective length of query: 656
effective length of database: 367,344
effective search space: 240977664
effective search space used: 240977664
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)