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|15645240|ref|NP_207410.1| DNA ligase (lig)
[Helicobacter pylori 26695]
(656 letters)
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
13,198 sequences; 2,899,336 total letters
Searching...........................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1DGT|B Chain B, Crystal Structure Of Nad+-Dependent Dna... 410 e-115
pdb|1B04|B Chain B, Structure Of The Adenylation Domain Of ... 194 3e-50
pdb|1KWH|A Chain A, Structure Analysis Algq2, A Macromolecu... 30 0.85
pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase... 29 1.4
pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carbox... 28 4.2
pdb|1HDH|A Chain A, Arylsulfatase From Pseudomonas Aerugino... 28 4.2
pdb|1H3F|A Chain A, Tyrosyl-Trna Synthetase From Thermus Th... 28 4.2
pdb|1KJU|A Chain A, Ca2+-Atpase In The E2 State >gi|2320015... 27 5.5
pdb|1JXL|A Chain A, Crystal Structure Of A Y-Family Dna Pol... 27 7.2
pdb|1THG| Lipase (E.C.3.1.1.3) Triacylglycerol Hydrolase 27 7.2
pdb|1NAR| Narbonin 27 9.4
pdb|1OJT| Structure Of Dihydrolipoamide Dehydrogenase 27 9.4
pdb|1BHY| Low Temperature Middle Resolution Structure Of ... 27 9.4
>pdb|1DGT|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase
pdb|1DGS|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGS|B Chain B, Crystal Structure Of Nad+-Dependent Dna Ligase From T.
Filiformis
pdb|1DGT|A Chain A, Crystal Structure Of Nad+-Dependent Dna Ligase
Length = 667
Score = 410 bits (1053), Expect = e-115
Identities = 260/665 (39%), Positives = 389/665 (58%), Gaps = 20/665 (3%)
Query: 4 SQKEYLERIAYLNTL----SHHYYNLDEPIVSDAIYDELYQELKAYEEKNPNGIQANSPT 59
+++E RI L L ++ YY L +P +SDA YD L +ELK EE+ P +SPT
Sbjct: 2 TREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPT 61
Query: 60 QKVGATTTN-SFNKNPHLMRMWSLDDVFNQSELQAWLQRILKAYPSAS-FVCSPKLDGVS 117
++VGA +F H RM+SLD+ F E+ A+ +R+ + + S + K+DG+S
Sbjct: 62 EQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGLS 121
Query: 118 LNLLYQHGKLVKATTRGNGLEGELVSANAKHIANIPHAI-AYNGEIEIRGEVIISKKDFD 176
+ L Y+ G V +T G+G GE V+ N I IP + +E+RGEV + + F
Sbjct: 122 V-LYYEEG--VWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFL 178
Query: 177 ALNQERLNANEPLFANPRNAASGSLRQLDSEITKKRKLQF----IPWGVGKHSLNFLSFK 232
LN+E E +F NPRNAA+GSLRQ D +T KR L+ + G+G S
Sbjct: 179 RLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQY 238
Query: 233 ECLDFIVSLGFSAIQYLSLNKNHQEIEDNYHTLIREREGFFALLDGMVIVVNELNIQKEL 292
E L ++ GF + +E+ Y + +R DG+V+ +++L + EL
Sbjct: 239 ELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGEL 298
Query: 293 GYTQKSPKFACAYKFPALEKHTKIVGVINQVGRSGAITPVALLEPVEIAGAMINRATLHN 352
GYT ++P+FA AYKFPA EK T+++ V+ QVGR+G +TPV +LEPV I G+ ++R TLHN
Sbjct: 299 GYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHN 358
Query: 353 YSEIEKKNIMLSDRVVVIRSGDVIPKIIKPLESYRDGSQHKIERPKVCPICSHELLCEEI 412
S IE+ +I + D V+V ++G VIP++++ L+ R G + I P+ CP C H L+ E
Sbjct: 359 ESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGK 418
Query: 413 FTYCQNLNCPARLKESLIHFASKDALNIQGLGDKVIEQLFEEKLIFNALDLYALKLEDLM 472
C N CPA+ E++ H+AS+ A++I+GLG+K+IE+L E+ L+ + DLY L+ EDL+
Sbjct: 419 VHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLL 478
Query: 473 RLDKFKIKKAQNLLDAILKSKNPPLWRLINALGIEHIGKGASKTLA-KYGL--NVLEKSE 529
L++ K AQNLL I +SK+ L RL+ ALG+ +G+ ++ LA ++G +LE S
Sbjct: 479 GLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASL 538
Query: 530 AEFLEMEGFGVEMARSLVNFYASNQEFIRSLFELLNPKNSDMAEEKQKSSSVFNNKTIVL 589
E +E+E G AR+++ R L L M E K++ S + + T VL
Sbjct: 539 EELIEVEEVGELTARAILE--TLKDPAFRDLVRRLKEAGVSM-ESKEEVSDLLSGLTFVL 595
Query: 590 TGTLSKPRQEYAQMLENLGAKISSSVSAKTDFLIAGENPGSKLALAQKHGVSVLNEEELL 649
TG LS+PR+E +L LGAK++ SVS KT +L+ GENPGSKL A+ GV+VL EEE
Sbjct: 596 TGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFW 655
Query: 650 KRLKE 654
+ LKE
Sbjct: 656 RFLKE 660
>pdb|1B04|B Chain B, Structure Of The Adenylation Domain Of An Nad+ Dependent
Ligase
pdb|1B04|A Chain A, Structure Of The Adenylation Domain Of An Nad+ Dependent
Ligase
Length = 318
Score = 194 bits (492), Expect = 3e-50
Identities = 114/310 (36%), Positives = 171/310 (54%), Gaps = 1/310 (0%)
Query: 3 KSQKEYLERIAYLNTLSHHYYNLDEPIVSDAIYDELYQELKAYEEKNPNGIQANSPTQKV 62
++++ E LN + YY LD P V DA YD L QEL A EE+ P ++SPTQ++
Sbjct: 5 QAERRAAELRELLNRYGYEYYVLDRPSVPDAEYDRLMQELIAIEEQYPELKTSDSPTQRI 64
Query: 63 GATTTNSFNKNPHLMRMWSLDDVFNQSELQAWLQRILKAYPSASFVCSPKLDGVSLNLLY 122
G +F K H + M SL + F + +L+ + +R+ + A++VC +DG+++++ Y
Sbjct: 65 GGPPLEAFRKVAHRVPMMSLANAFGEGDLRDFDRRVRQEVGEAAYVCELAIDGLAVSVRY 124
Query: 123 QHGKLVKATTRGNGLEGELVSANAKHIANIPHAIAYNGEIEIRGEVIISKKDFDALNQER 182
+ G V+ TRG+G GE ++ N K I ++P + +E RGE + K F LN+ER
Sbjct: 125 EDGYFVQGATRGDGTTGEDITENLKTIRSLPLRLKEPVSLEARGEAFMPKASFLRLNEER 184
Query: 183 LNANEPLFANPRNAASGSLRQLDSEITKKRKLQFIPWGVG-KHSLNFLSFKECLDFIVSL 241
E LFANPRNAA+GSLRQLD ++ R+L +G+ +L S E LD++ +L
Sbjct: 185 KARGEELFANPRNAAAGSLRQLDPKVAASRQLDLFVYGLADAEALGIASHSEALDYLQAL 244
Query: 242 GFSAIQYLSLNKNHQEIEDNYHTLIREREGFFALLDGMVIVVNELNIQKELGYTQKSPKF 301
GF N E+ +R +DG+VI V+ Q+ LG T KSP++
Sbjct: 245 GFKVNPERRRCANIDEVIAFVSEWHDKRPQLPYEIDGIVIKVDSFAQQRALGATAKSPRW 304
Query: 302 ACAYKFPALE 311
A AYKFPA E
Sbjct: 305 AIAYKFPAEE 314
>pdb|1KWH|A Chain A, Structure Analysis Algq2, A
Macromolecule(Alginate)-Binding Periplasmic Protein Of
Sphingomonas Sp. A1
Length = 492
Score = 30.0 bits (66), Expect = 0.85
Identities = 12/17 (70%), Positives = 15/17 (87%)
Query: 36 DELYQELKAYEEKNPNG 52
DELY LKA++EK+PNG
Sbjct: 158 DELYTVLKAFKEKDPNG 174
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
Length = 1524
Score = 29.3 bits (64), Expect = 1.4
Identities = 22/70 (31%), Positives = 35/70 (49%), Gaps = 12/70 (17%)
Query: 443 LGDKVIEQLFEEKLIFNALDLYALKLEDL------MRLDKFKIKKAQNLLDAILKSKNPP 496
+G + I+QL +E LDL AL+ E L R + K +K ++ A L S N P
Sbjct: 456 MGAEAIQQLLKE------LDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRP 509
Query: 497 LWRLINALGI 506
W ++ A+ +
Sbjct: 510 EWMILEAVPV 519
>pdb|1K9X|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|B Chain B, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|C Chain C, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1K9X|D Chain D, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Yb
pdb|1KA2|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Apo-Mg
pdb|1KA4|A Chain A, Structure Of Pyrococcus Furiosus Carboxypeptidase Nat-Pb
Length = 499
Score = 27.7 bits (60), Expect = 4.2
Identities = 18/65 (27%), Positives = 30/65 (45%), Gaps = 1/65 (1%)
Query: 207 EITKKRKLQFIPWGVGKHSLNFLSFKECLDFIVSLGFSAIQYLSLNKN-HQEIEDNYHTL 265
E+++ L W K +F F+ LD I+SL A +YL + + + D Y
Sbjct: 107 EVSETTSLATKAWEEAKAKDDFSKFEPWLDKIISLAKRAAEYLGYEEEPYDALLDLYEEG 166
Query: 266 IRERE 270
+R R+
Sbjct: 167 LRTRD 171
>pdb|1HDH|A Chain A, Arylsulfatase From Pseudomonas Aeruginosa
pdb|1HDH|B Chain B, Arylsulfatase From Pseudomonas Aeruginosa
Length = 536
Score = 27.7 bits (60), Expect = 4.2
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 8 YLERIAYLNTLSHHYYNLDEPIVSDAIYDELYQELKAYEEKNP 50
Y+E YL+TL +Y+ SDA D+L Q LK ++ P
Sbjct: 164 YVEDERYLDTLPEGFYS------SDAFGDKLLQYLKERDQSRP 200
>pdb|1H3F|A Chain A, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Tyrosinol
pdb|1H3F|B Chain B, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Tyrosinol
pdb|1H3E|A Chain A, Tyrosyl-Trna Synthetase From Thermus Thermophilus
Complexed With Wild-Type Trnatyr(Gua) And With Atp And
Tyrosinol
Length = 432
Score = 27.7 bits (60), Expect = 4.2
Identities = 13/30 (43%), Positives = 18/30 (59%)
Query: 625 GENPGSKLALAQKHGVSVLNEEELLKRLKE 654
G P LAL ++ ++ EEELL +LKE
Sbjct: 5 GHTPEEALALLKRGAEEIVPEEELLAKLKE 34
>pdb|1KJU|A Chain A, Ca2+-Atpase In The E2 State
pdb|1IWO|A Chain A, Crystal Structure Of The Sr Ca2+-Atpase In The Absence Of
Ca2+
pdb|1IWO|B Chain B, Crystal Structure Of The Sr Ca2+-Atpase In The Absence Of
Ca2+
pdb|1EUL|A Chain A, Crystal Structure Of Calcium Atpase With Two Bound Calcium
Ions
Length = 994
Score = 27.3 bits (59), Expect = 5.5
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 14/86 (16%)
Query: 566 PKNSDMA-EEKQKSSSVFNNKTIV-LTGTLSKPRQEYA---QMLENLGAKISSSVSAKTD 620
PK +M ++ + + T V + G L PR+E Q+ + G ++
Sbjct: 571 PKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRV--------- 621
Query: 621 FLIAGENPGSKLALAQKHGVSVLNEE 646
+I G+N G+ +A+ ++ G+ NEE
Sbjct: 622 IMITGDNKGTAIAICRRIGIFGENEE 647
>pdb|1JXL|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A
Ternary Complex With Dna Substrates And An Incoming
Nucleotide
Length = 352
Score = 26.9 bits (58), Expect = 7.2
Identities = 16/57 (28%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 606 NLGAKISSSVSAKTDFL----IAGENPGSKLA--LAQKHGVSVLNEEELLKRLKELD 656
NLG +I + + K I+ +K+A +A+ +G+ V+++EE+ + ++ELD
Sbjct: 123 NLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELD 179
>pdb|1THG| Lipase (E.C.3.1.1.3) Triacylglycerol Hydrolase
Length = 544
Score = 26.9 bits (58), Expect = 7.2
Identities = 34/109 (31%), Positives = 49/109 (44%), Gaps = 15/109 (13%)
Query: 26 DEPIVSDAIYDELYQELKAYEEKNPNGIQANSPTQ----KVGATTTNSFNKNPHLMRMWS 81
D I+ DA Y EL++ + + +G Q + T + ATTT PH+ + W
Sbjct: 324 DGNIIPDAAY-ELFRSGRYAKVPYISGNQEDEGTAFAPVALNATTT------PHVKK-WL 375
Query: 82 LDDVFNQSELQAWLQRILKAYPSASFVCSPKLDGVSLNLLYQHGKLVKA 130
++ SE A + R+L YP V SP G+ LN L K V A
Sbjct: 376 QYIFYDASE--ASIDRVLSLYPQTLSVGSPFRTGI-LNALTPQFKRVAA 421
>pdb|1NAR| Narbonin
Length = 290
Score = 26.6 bits (57), Expect = 9.4
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 5 QKEYLERIAYLNTLSHHYYNLDEPIVSDAIYDELYQELK 43
QK Y + Y+N + + + N +P+ +D + E+++ L+
Sbjct: 175 QKLYNAKKDYINWVDYQFSNQQKPVSTDDAFVEIFKSLE 213
>pdb|1OJT| Structure Of Dihydrolipoamide Dehydrogenase
Length = 482
Score = 26.6 bits (57), Expect = 9.4
Identities = 25/105 (23%), Positives = 46/105 (43%), Gaps = 2/105 (1%)
Query: 539 GVEMARSLVNFYASNQEFIRSLFELLNPKNSDMAEEKQKSSSVFNNKTIVLTGTLSKPRQ 598
G+EM ++ + S + + + L+ + D+ + QK + + +V T T++ +
Sbjct: 197 GLEMG-TVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYRFDNIMVNTKTVAVEPK 255
Query: 599 EYAQMLENLGAKISSSVSAKTDFLIA-GENPGSKLALAQKHGVSV 642
E + GA L+A G P KL A+K GV+V
Sbjct: 256 EDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGKLISAEKAGVAV 300
>pdb|1BHY| Low Temperature Middle Resolution Structure Of P64k From Masc Data
Length = 482
Score = 26.6 bits (57), Expect = 9.4
Identities = 25/105 (23%), Positives = 46/105 (43%), Gaps = 2/105 (1%)
Query: 539 GVEMARSLVNFYASNQEFIRSLFELLNPKNSDMAEEKQKSSSVFNNKTIVLTGTLSKPRQ 598
G+EM ++ + S + + + L+ + D+ + QK + + +V T T++ +
Sbjct: 197 GLEMG-TVYSTLGSRLDVVEMMDGLMQGADRDLVKVWQKQNEYRFDNIMVNTKTVAVEPK 255
Query: 599 EYAQMLENLGAKISSSVSAKTDFLIA-GENPGSKLALAQKHGVSV 642
E + GA L+A G P KL A+K GV+V
Sbjct: 256 EDGVYVTFEGANAPKEPQRYDAVLVAAGRAPNGKLISAEKAGVAV 300
Database: /var/www/html/HP/blast_new/blast/db/pdbaa
Posted date: Dec 20, 2002 11:08 AM
Number of letters in database: 2,899,336
Number of sequences in database: 13,198
Lambda K H
0.317 0.135 0.378
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,620,590
Number of Sequences: 13198
Number of extensions: 146492
Number of successful extensions: 421
Number of sequences better than 10.0: 13
Number of HSP's better than 10.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 408
Number of HSP's gapped (non-prelim): 14
length of query: 656
length of database: 2,899,336
effective HSP length: 94
effective length of query: 562
effective length of database: 1,658,724
effective search space: 932202888
effective search space used: 932202888
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.6 bits)