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|15646083|ref|NP_208265.1| thymidylate kinase (tmk)
[Helicobacter pylori 26695]
(191 letters)
Database: NC_000921.faa
1491 sequences; 494,079 total letters
Searching...done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_224085.1| THYMIDYLATE KINASE [Helicobacter pylori J99] 339 3e-95
ref|NP_222996.1| DIAMINOPIMELATE DECARBOXYLASE [Helicobacte... 30 0.054
ref|NP_223788.1| putative [Helicobacter pylori J99] 28 0.12
ref|NP_223062.1| multi-drug resistance protein [Helicobacte... 28 0.21
ref|NP_223024.1| GUANYLATE KINASE [Helicobacter pylori J99] 28 0.21
ref|NP_224141.1| TYPE I RESTRICTION ENZYME (MODIFICATION SU... 26 0.78
ref|NP_224043.1| putative [Helicobacter pylori J99] 25 1.3
ref|NP_223459.1| putative lipopolysaccharide biosynthesis p... 25 1.3
ref|NP_223886.1| putative [Helicobacter pylori J99] 25 1.7
ref|NP_223624.1| GLYCYL-TRNA SYNTHETASE BETA CHAIN [Helicob... 25 1.7
ref|NP_223488.1| putative [Helicobacter pylori J99] 25 1.7
ref|NP_223279.1| ADENYLATE KINASE [Helicobacter pylori J99] 25 1.7
ref|NP_224127.1| putative TYPE II DNA MODIFICATION ENZYME (... 24 2.3
ref|NP_224061.1| putative Inner membrane protein [Helicobac... 24 2.3
ref|NP_223507.1| putative abc transporter, ATP-binding prot... 24 2.3
ref|NP_223323.1| putative [Helicobacter pylori J99] 24 2.3
ref|NP_223388.1| putative [Helicobacter pylori J99] 24 3.0
ref|NP_223037.1| putative [Helicobacter pylori J99] 24 3.0
ref|NP_223423.1| MOLYBDOPTERIN COFACTOR BIOSYNTHETIC PROTEI... 23 3.9
ref|NP_223875.1| putative [Helicobacter pylori J99] 23 5.1
ref|NP_223859.1| putative ABC transporter, ATP-binding prot... 23 5.1
ref|NP_223236.1| putative [Helicobacter pylori J99] 23 5.1
ref|NP_223656.1| putative [Helicobacter pylori J99] 23 6.6
ref|NP_224092.1| putative [Helicobacter pylori J99] 22 8.6
ref|NP_223510.1| putative ADP-D-glycero-D-mannoheptose synt... 22 8.6
>ref|NP_224085.1| THYMIDYLATE KINASE [Helicobacter pylori J99]
Length = 191
Score = 339 bits (869), Expect = 3e-95
Identities = 179/191 (93%), Positives = 183/191 (95%)
Query: 1 MYVVLEGVDGAGKSTQVELLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLF 60
MYVVLEGVDGAGKSTQV LLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLF
Sbjct: 1 MYVVLEGVDGAGKSTQVGLLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLF 60
Query: 61 LSDRAEHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLATQSVLPAKIILLLI 120
LSDRAEH ESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLATQSVLP KIILLLI
Sbjct: 61 LSDRAEHIESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLATQSVLPEKIILLLI 120
Query: 121 DKEGLKQRLSLKSLDKIENQGIEKLLHIQQKLKTHAYALQEKFGCEVLELDAKESVKNLH 180
+KE LKQRLSLKSLDKIENQGIEKLL IQQKLKTHAYALQEKFGCEVLELDA++S KNLH
Sbjct: 121 NKENLKQRLSLKSLDKIENQGIEKLLTIQQKLKTHAYALQEKFGCEVLELDAQKSAKNLH 180
Query: 181 EKIAAFIKCAV 191
EKIA FI+C V
Sbjct: 181 EKIATFIECVV 191
>ref|NP_222996.1| DIAMINOPIMELATE DECARBOXYLASE [Helicobacter pylori J99]
Length = 405
Score = 29.6 bits (65), Expect = 0.054
Identities = 29/111 (26%), Positives = 53/111 (47%), Gaps = 13/111 (11%)
Query: 69 ESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLA--TQSVLPAKIILLLIDKEGLK 126
+ +K +K K++ S + A+ +L+LN+L +S + K I + G+K
Sbjct: 73 QRALKAGIKPYKIVFSG---VGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIK 129
Query: 127 QRLSLKSLDKIENQGIEKLLH--IQQKLKTHAYALQEKFGCEVLELDAKES 175
R+S++ N I+ H I LK + + ++EK E+ L AK+S
Sbjct: 130 ARISIRI-----NPNIDAKTHPYISTGLKENKFGVEEKEALEMF-LWAKKS 174
>ref|NP_223788.1| putative [Helicobacter pylori J99]
Length = 433
Score = 28.5 bits (62), Expect = 0.12
Identities = 36/146 (24%), Positives = 59/146 (39%), Gaps = 18/146 (12%)
Query: 46 ALNENISELARAFLFLSDRAEHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLL 105
A + ++E + E E +K KE++ + A Q S+L L
Sbjct: 42 AFEKEVNEKRAQYQSYFKNLEQKEEALKERAKEQQAQFDE-------AVKQASALALQDE 94
Query: 106 ATQSVLPAKIILLLIDKEGLKQRLSLKSLDKIENQ---------GIEKLLHIQQKLKTHA 156
+ + A+ L ++GL+ L K LD+ Q IE+L + ++
Sbjct: 95 RAKIIEEARKNAFLEQQKGLE--LLQKELDEKSKQVQELHQKEAEIERLKRENNEAESRL 152
Query: 157 YALQEKFGCEVLELDAKESVKNLHEK 182
A EK E LEL+ ++ K LHEK
Sbjct: 153 KAENEKKLNEKLELEREKIEKALHEK 178
>ref|NP_223062.1| multi-drug resistance protein [Helicobacter pylori J99]
Length = 551
Score = 27.7 bits (60), Expect = 0.21
Identities = 28/91 (30%), Positives = 44/91 (47%), Gaps = 15/91 (16%)
Query: 3 VVLEGVDGAGKSTQVEL---LKDRFKNALFTKEPGGTRMGESLRRIALNENISELA-RAF 58
V L+G G+GKS+ V L L + K +F + + ES+ + +L E IS + R F
Sbjct: 366 VALKGESGSGKSSLVNLILRLYEPSKGEIFIND----QKIESITQKSLREKISVVTQRVF 421
Query: 59 LFLSDRAEHT-------ESVIKPALKEKKLI 82
+F AE+ E IK LK+ + +
Sbjct: 422 IFNGSVAENVAYGLEIDEIKIKECLKKAQAL 452
>ref|NP_223024.1| GUANYLATE KINASE [Helicobacter pylori J99]
Length = 206
Score = 27.7 bits (60), Expect = 0.21
Identities = 41/167 (24%), Positives = 71/167 (41%), Gaps = 26/167 (15%)
Query: 3 VVLEGVDGAGKSTQVELLKDRFKNALF-----TKEPGGTRMGESLRRIALNENISELARA 57
++L G GAGKST + L+++ F T++P + E +
Sbjct: 8 LILSGPSGAGKSTLTKYLQEKIPKTHFSLSTTTRKPREGEVDGLHYNFVSEEEFKQGIEK 67
Query: 58 FLFLSDRAEH------TESVIKPALKEKKLIISDRSL----ISGMAYSQFSSLELNLLAT 107
FL H ++ ++ ALKE K++I D + I Y S+ ++
Sbjct: 68 GQFLEWAIVHNHYYGTSKIPVEKALKEGKIVIFDIDVQGHEILKKHYPNACSVFIS-TKN 126
Query: 108 QSVLPAKIILLLID-KEGLKQRL--------SLKSLD-KIENQGIEK 144
Q +L +++L D KE +++RL L+S D I N+ +EK
Sbjct: 127 QEILKERLLLRGTDSKETIEKRLINAYKEMQCLESFDYLIINEDLEK 173
>ref|NP_224141.1| TYPE I RESTRICTION ENZYME (MODIFICATION SUBUNIT) [Helicobacter
pylori J99]
Length = 815
Score = 25.8 bits (55), Expect = 0.78
Identities = 17/64 (26%), Positives = 31/64 (47%)
Query: 19 LLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLFLSDRAEHTESVIKPALKE 78
++KD++ N+L + + ALNE IS + + L L + +ES + LK+
Sbjct: 751 IIKDKWLNSLKNALENKIQKRTNAFASALNEIISSYSNSLLELDKEVKESESKVLEHLKD 810
Query: 79 KKLI 82
L+
Sbjct: 811 LGLM 814
>ref|NP_224043.1| putative [Helicobacter pylori J99]
Length = 357
Score = 25.0 bits (53), Expect = 1.3
Identities = 12/48 (25%), Positives = 25/48 (52%)
Query: 55 ARAFLFLSDRAEHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLEL 102
++ +LF S R HT + +K+KK+ +++ G Y+ S ++
Sbjct: 74 SKKYLFKSLRDNHTFEAVLLKMKDKKIDEETNAVLEGEKYTVCVSCQI 121
>ref|NP_223459.1| putative lipopolysaccharide biosynthesis protein [Helicobacter
pylori J99]
Length = 292
Score = 25.0 bits (53), Expect = 1.3
Identities = 16/62 (25%), Positives = 31/62 (49%), Gaps = 8/62 (12%)
Query: 115 IILLLIDKEGLKQRLSLKSLDKIENQGIEKLLHIQQKLKTHAYALQEKFGCEVLELDAKE 174
I L+ +++ KQ+ +K G+ ++L+ + + T Y L K ++L+ AKE
Sbjct: 163 IRLMHLEENVAKQKTPVK--------GVSQILNFKDGIGTQGYVLAPKAAQKLLKYSAKE 214
Query: 175 SV 176
V
Sbjct: 215 WV 216
>ref|NP_223886.1| putative [Helicobacter pylori J99]
Length = 340
Score = 24.6 bits (52), Expect = 1.7
Identities = 16/59 (27%), Positives = 29/59 (49%)
Query: 4 VLEGVDGAGKSTQVELLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLFLS 62
+++ + G + E++++ KNAL KE G R+ E R L + FL+L+
Sbjct: 274 LMDAKEVLGYAPPKEIVENYAKNALRLKEAGYKRVFEIFRLWHLQSMQGQKELGFLYLT 332
>ref|NP_223624.1| GLYCYL-TRNA SYNTHETASE BETA CHAIN [Helicobacter pylori J99]
Length = 701
Score = 24.6 bits (52), Expect = 1.7
Identities = 26/114 (22%), Positives = 46/114 (39%)
Query: 66 EHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLATQSVLPAKIILLLIDKEGL 125
++ ++ ++KE+ L S+ + + +S +L L + + S+ I
Sbjct: 437 QNENELVALSVKEQYLPASENAPLPSSVFSSIVALSLKIDSLFSLFSVGKIPSGSKDPFA 496
Query: 126 KQRLSLKSLDKIENQGIEKLLHIQQKLKTHAYALQEKFGCEVLELDAKESVKNL 179
+RLS L I + G+E L K + + F EVLE E NL
Sbjct: 497 LRRLSFGLLKIIAHYGLEFDLKADLKNLFEKVGVYQSFDLEVLEKFLLERFHNL 550
Score = 23.5 bits (49), Expect = 3.9
Identities = 9/19 (47%), Positives = 12/19 (62%)
Query: 168 LELDAKESVKNLHEKIAAF 186
LE D K +KNL EK+ +
Sbjct: 513 LEFDLKADLKNLFEKVGVY 531
>ref|NP_223488.1| putative [Helicobacter pylori J99]
Length = 196
Score = 24.6 bits (52), Expect = 1.7
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 7/44 (15%)
Query: 133 SLDKIENQGI-----EKLLHIQQKLKTHAYALQEKFGCEVLELD 171
+L +E+QG +K+ H Q L+ H + ++FG ++LE D
Sbjct: 20 TLKILESQGYKILDADKIAH--QLLQEHRLEIAQRFGSDILEKD 61
>ref|NP_223279.1| ADENYLATE KINASE [Helicobacter pylori J99]
Length = 191
Score = 24.6 bits (52), Expect = 1.7
Identities = 29/138 (21%), Positives = 51/138 (36%), Gaps = 7/138 (5%)
Query: 7 GVDGAGKSTQVELLKDRFKNALFTKEPGGTRMGESLRRIALNENISELARAFLFLSDRAE 66
G G+GK+T EL+ + G ES ++ I +
Sbjct: 9 GAPGSGKTTDAELIAKNNSETIAHFSTGDLLRAESAKKTERGLLIEKFTS-----QGELV 63
Query: 67 HTESVIKPALKEKKLIISDRSLISGMAYS--QFSSLELNLLATQSVLPAKIILLLIDKEG 124
E V++ L K LI G S Q +L+ L A V+ +I + + +
Sbjct: 64 PLEIVVETILSAIKSSSKGIILIDGYPRSVEQMQALDKELNAQNEVILKSVIEVEVSENT 123
Query: 125 LKQRLSLKSLDKIENQGI 142
K+R+ +S +N+ +
Sbjct: 124 AKERVLGRSRGADDNERV 141
>ref|NP_224127.1| putative TYPE II DNA MODIFICATION ENZYME (METHYLTRANSFERASE)
[Helicobacter pylori J99]
Length = 1252
Score = 24.3 bits (51), Expect = 2.3
Identities = 21/69 (30%), Positives = 34/69 (48%), Gaps = 7/69 (10%)
Query: 42 LRRIALNENISELARAF-LFLSD---RAEHTESVIKPALKEKKLIISDRSLISGMAY--- 94
L + L I +L F L L D +AE +++ K K + D+SL+ G+ Y
Sbjct: 694 LNKADLINKIQDLKNTFSLTLKDPKTKAELEKTIEKHIKKYNFFALDDKSLLDGLNYFIP 753
Query: 95 SQFSSLELN 103
S F +L+L+
Sbjct: 754 SLFGTLKLS 762
>ref|NP_224061.1| putative Inner membrane protein [Helicobacter pylori J99]
Length = 549
Score = 24.3 bits (51), Expect = 2.3
Identities = 17/55 (30%), Positives = 24/55 (42%)
Query: 114 KIILLLIDKEGLKQRLSLKSLDKIENQGIEKLLHIQQKLKTHAYALQEKFGCEVL 168
+IIL + +G+ LK L + EK QKL+ H L +K G L
Sbjct: 367 RIILYPLSYKGMVSMQKLKELAPKMKELQEKYKGEPQKLQAHMMQLYKKHGANPL 421
>ref|NP_223507.1| putative abc transporter, ATP-binding protein [Helicobacter pylori
J99]
Length = 533
Score = 24.3 bits (51), Expect = 2.3
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 3 VVLEGVDGAGKSTQVELLKDRFKNALFTKEPGGTRMGESLRRIALNENISE 53
+ L G +G GKST ++L + K + G + G ++ + +N+SE
Sbjct: 350 IALIGPNGVGKSTLCKILVEELK-----PDTGVVKWGATVLKGYFPQNVSE 395
>ref|NP_223323.1| putative [Helicobacter pylori J99]
Length = 335
Score = 24.3 bits (51), Expect = 2.3
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 126 KQRLSLKSLDKIENQGIE---KLLHIQQKLKTHAYALQEKFGCEVLELDAKESVKN 178
K + ++K + + + +E KLLH + K ++ AL+ E LE+ E++KN
Sbjct: 123 KTKDTVKEILRFSPRNVEALLKLLHAYELEKDYSKALETLECLEELEVPKIETIKN 178
>ref|NP_223388.1| putative [Helicobacter pylori J99]
Length = 192
Score = 23.9 bits (50), Expect = 3.0
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 3 VVLEGVDGAGKSTQVELLKDRFK 25
+ G GAGKST +E L+ FK
Sbjct: 69 IAFYGETGAGKSTLIECLRMFFK 91
>ref|NP_223037.1| putative [Helicobacter pylori J99]
Length = 251
Score = 23.9 bits (50), Expect = 3.0
Identities = 13/29 (44%), Positives = 16/29 (54%)
Query: 140 QGIEKLLHIQQKLKTHAYALQEKFGCEVL 168
QG+EK L L + A L+E FGC L
Sbjct: 184 QGVEKDLTKVAYLYSKACELKESFGCGAL 212
>ref|NP_223423.1| MOLYBDOPTERIN COFACTOR BIOSYNTHETIC PROTEIN [Helicobacter pylori
J99]
Length = 321
Score = 23.5 bits (49), Expect = 3.9
Identities = 14/44 (31%), Positives = 24/44 (53%), Gaps = 2/44 (4%)
Query: 129 LSLKSLDKIEN--QGIEKLLHIQQKLKTHAYALQEKFGCEVLEL 170
L + D ++N +GIE+ L + KLK + ++ E+LEL
Sbjct: 129 LKISQKDALKNTLEGIEESLKVGLKLKLNTVVMKGVNDDEILEL 172
>ref|NP_223875.1| putative [Helicobacter pylori J99]
Length = 183
Score = 23.1 bits (48), Expect = 5.1
Identities = 32/123 (26%), Positives = 54/123 (43%), Gaps = 18/123 (14%)
Query: 42 LRRIALNEN-ISELARAFLFLSDRAEHTESVIKPALKEKKLI-ISDRSLISGMAYSQFSS 99
L + EN I E AR L E+T+ + + E++L + R + + F
Sbjct: 42 LEKSVKKENAIDEQARELL-----EENTDEIEFMRMDERQLFWMIKRQIAQKEGFHLFWE 96
Query: 100 LELNLLATQ---SVLPAKIILLLIDKEGLKQRLSLKSLD-------KIENQGIEKLLHIQ 149
+ L+ Q +L +I+ + E L + L KS+D IEN+ EK+ H +
Sbjct: 97 ERCSDLSHQILNKILDEDLIMFSVS-ENLIRNLIYKSIDTYSKAYESIENEVHEKIKHYK 155
Query: 150 QKL 152
+KL
Sbjct: 156 RKL 158
>ref|NP_223859.1| putative ABC transporter, ATP-binding protein [Helicobacter pylori
J99]
Length = 228
Score = 23.1 bits (48), Expect = 5.1
Identities = 35/131 (26%), Positives = 54/131 (40%), Gaps = 25/131 (19%)
Query: 2 YVVLEGVDGAGKSTQVELLKDRFKNALFTKEPGGTRMGESLRRIALNENIS-ELARAFLF 60
++ L G +GAGK+T +++L G + LN+ I E ++ F
Sbjct: 30 FIGLLGPNGAGKTTLLKIL-------------AGLNLNYQGEVKILNQKIGIETKKSVAF 76
Query: 61 LSDRAEHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLELNLLATQSVLPAKIILLLI 120
LSD + P L K I + S S+ LNLL SV P K +
Sbjct: 77 LSD-----GDFLDPKLTPLKAIAFYKDFFSDFDESK----ALNLLKRFSV-PLKREFKAL 126
Query: 121 DKEGLKQRLSL 131
K G++++L L
Sbjct: 127 SK-GMREKLQL 136
>ref|NP_223236.1| putative [Helicobacter pylori J99]
Length = 192
Score = 23.1 bits (48), Expect = 5.1
Identities = 10/17 (58%), Positives = 12/17 (69%)
Query: 143 EKLLHIQQKLKTHAYAL 159
E+LLH + LK H YAL
Sbjct: 153 EELLHALEWLKKHPYAL 169
>ref|NP_223656.1| putative [Helicobacter pylori J99]
Length = 337
Score = 22.7 bits (47), Expect = 6.6
Identities = 15/55 (27%), Positives = 32/55 (57%), Gaps = 2/55 (3%)
Query: 120 IDKEGLKQRLSLKSLDKIENQGIEKLLHIQQKLKTHAYALQEKFGCEVLELDAKE 174
+++E KQ L+L ++K + + E+L +++K A L++KF ++ +KE
Sbjct: 87 VEEEKHKQALNL--INKEDTEDKEELAKKIKEIKEKAKVLRQKFMAFEMKEHSKE 139
>ref|NP_224092.1| putative [Helicobacter pylori J99]
Length = 265
Score = 22.3 bits (46), Expect = 8.6
Identities = 15/46 (32%), Positives = 24/46 (51%), Gaps = 2/46 (4%)
Query: 47 LNENISELARAFLFLSDRAEHTESVIKP--ALKEKKLIISDRSLIS 90
+NE ++ ARA FLS + E + ++ L+E I +LIS
Sbjct: 48 VNEINAQSARAIGFLSQKCEELDLIVSAPVLLEEHSKIYKKIALIS 93
>ref|NP_223510.1| putative ADP-D-glycero-D-mannoheptose synthase [Helicobacter pylori
J99]
Length = 463
Score = 22.3 bits (46), Expect = 8.6
Identities = 14/37 (37%), Positives = 20/37 (53%), Gaps = 3/37 (8%)
Query: 66 EHTESVIKPALKEKKLIISDRSLISGMAYSQFSSLEL 102
E T+++I A K KLI+ D G YS++S L
Sbjct: 154 ELTQTIITLANKHHKLILCDP---KGKDYSKYSHASL 187
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 0.135 0.354
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 185,330
Number of Sequences: 1491
Number of extensions: 7903
Number of successful extensions: 61
Number of sequences better than 10.0: 25
Number of HSP's better than 10.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 37
Number of HSP's gapped (non-prelim): 33
length of query: 191
length of database: 494,079
effective HSP length: 73
effective length of query: 118
effective length of database: 385,236
effective search space: 45457848
effective search space used: 45457848
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: 46 (22.3 bits)