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|15645324|ref|NP_207495.1| DNA gyrase, sub A (gyrA)
[Helicobacter pylori 26695]
(827 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|1AB4| 59kda Fragment Of Gyrase A From E. Coli 497 e-141
pdb|1BJT| Topoisomerase Ii Residues 409 - 1201 >gi|163327... 92 2e-19
pdb|1FEW|A Chain A, Crystal Structure Of SmacDIABLO 30 0.83
pdb|1L5J|A Chain A, Crystal Structure Of E. Coli Aconitase ... 29 1.9
pdb|1MWS|A Chain A, Structure Of Nitrocefin Acyl-Penicillin... 29 2.4
pdb|1MWX|A Chain A, Structure Of Penicillin Binding Protein... 28 4.1
pdb|2DLD|A Chain A, D-Lactate Dehydrogenase Complexed With ... 28 5.4
pdb|1FMI|A Chain A, Crystal Structure Of Human Class I Alph... 27 7.0
pdb|1FD9|A Chain A, Crystal Structure Of The Macrophage Inf... 27 7.0
pdb|1FO2|A Chain A, Crystal Structure Of Human Class I Alph... 27 7.0
pdb|1E4F|T Chain T, Ftsa (Apo Form) From Thermotoga Maritima 27 9.2
>pdb|1AB4| 59kda Fragment Of Gyrase A From E. Coli
Length = 477
Score = 497 bits (1279), Expect = e-141
Identities = 250/486 (51%), Positives = 350/486 (71%), Gaps = 40/486 (8%)
Query: 34 IGRALPDARDGLKPVHRRILYAMHELGLTSKVAYKKSARIVGDVIGKYHPHGDNAVYDAL 93
+GRALPD RDGLKPVHRR+LYAM+ LG AYKKSAR+VGDVIGKYHPHGD+AVYD +
Sbjct: 1 VGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTI 60
Query: 94 VRMAQDFSMRLELVDGQGNFGSIDGDNAAAMRYTEARMTKASEEILRDIDKDTIDFVPNY 153
VRMAQ FS+R LVDGQGNFGSIDGD+AAAMRYTE R+ K + E++ D++K+T+DFV NY
Sbjct: 61 VRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNY 120
Query: 154 DDTLKEPDILPSRLPNLLVNGANGIAVGMATSIPPHRMDEIIDALVHVLENPNAGLDEIL 213
D T K PD++P+++PNLLVNG++GIAVGMAT+IPPH + E+I+ + +++ + ++ ++
Sbjct: 121 DGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLM 180
Query: 214 EFVKGPDFPTGGIIYGKAGIIEAYKTGRGRVKVRAKVHVEKTKNKEIIVLDEMPFQTNKA 273
E + GPDFPT II G+ GI EAY+TGRG+V +RA+ VE E I++ E+P+Q NKA
Sbjct: 181 EHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVE----VETIIVHEIPYQVNKA 236
Query: 274 KLVEQISDLAREKQIEGISEVRDESDREGIRVVIELKRDAMSEIVLNHLYKLTTMETTFS 333
+L+E+I++L +EK++EGIS +RDESD++G+R+VIE E+VLN+LY T ++ +F
Sbjct: 237 RLIEKIAELVKEKRVEGISALRDESDKDGMRIVIE------GEVVLNNLYSQTQLQVSFG 290
Query: 334 IILLAIYNKEPKIFTLLELLHLFLNHRKTIIIRRTIFELEKAKARAHILEGYLIALDNID 393
I ++A+++ +PKI L +++ F+ HR+ ++ RRTIFEL KA+ RAHILE +AL NID
Sbjct: 291 INMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANID 350
Query: 394 EIVRLIKTSQSPEAAKNALMER------------------------------FTLSEIQS 423
I+ LI+ + +P AK AL+ + L+E Q+
Sbjct: 351 PIIELIRHAPTPAEAKTALVANPWQLGNVAAMLEDAARPEWLEPEFGVRDGLYYLTEQQA 410
Query: 424 KAILEMRLQRLTGLERDKIKEEYQNLLELIDDLNGILKSEDRLNGVVKTELLEVKEQFSS 483
+AIL++RLQ+LTGLE +K+ +EY+ LL+ I +L IL S DRL V++ EL V+EQF
Sbjct: 411 QAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGD 470
Query: 484 PRRTEI 489
RRTEI
Sbjct: 471 KRRTEI 476
>pdb|1BJT| Topoisomerase Ii Residues 409 - 1201
pdb|1BGW| Topoisomerase Residues 410 - 1202,
Length = 793
Score = 92.0 bits (227), Expect = 2e-19
Identities = 99/376 (26%), Positives = 176/376 (46%), Gaps = 37/376 (9%)
Query: 14 EVGIDSSIEESYLAYSMSVIIGRALPDARDGLKPVHRRILYAMHELGLTSKVAYKKSARI 73
E+ I I + + +S++ I R++P+ DG KP R++LY + L S++ + A
Sbjct: 261 EIPISDFINKELILFSLADNI-RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPY 319
Query: 74 VGDVIGKYHPHGDNAVYDALVRMAQDF--SMRLELVDGQGNFGS--IDGDNAAAMRYTEA 129
V + YH HG+ ++ ++ +AQ+F S + L+ G FG+ G +AAA RY
Sbjct: 320 VSECTA-YH-HGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYT 377
Query: 130 RMTKASEEILRDIDKDTIDFVPNYDDTLKEPDILPSRLPNLLVNGANGIAVGMATSIPPH 189
+ K + +I D ++ + T++ LP LP +LVNGA GI G +T IPP
Sbjct: 378 ELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPI-LPMILVNGAEGIGTGWSTYIPPF 436
Query: 190 RMDEIIDALVHVLENPNAGLDEILEFVKGPDFPTGGIIYGKAGIIEAYKTGRGRVKVRAK 249
EII + H++ DE LE + P F G G IE + R R+ R
Sbjct: 437 NPLEIIKNIRHLMN------DEELEQMH-PWF------RGWTGTIEEIEPLRYRMYGR-- 481
Query: 250 VHVEKTKNKEIIVLDEMPFQTNKAKLVEQ-ISDLAREKQIEGISEVRDESDREGIRVVIE 308
+E+ ++ + E+P +T + + E + L+ +I+ + +E + I+ +I
Sbjct: 482 --IEQI-GDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKFIIT 538
Query: 309 LKRDAMS---EIVLNHLYKLTTMETTFSIILLAIYNKEPKIFTLLELLHLF-------LN 358
L + M+ +I +KL + + +++ + K K ++ E+L F
Sbjct: 539 LSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQ 598
Query: 359 HRKTIIIRRTIFELEK 374
RK + R +E+EK
Sbjct: 599 KRKDHMSERLQWEVEK 614
>pdb|1FEW|A Chain A, Crystal Structure Of SmacDIABLO
Length = 184
Score = 30.4 bits (67), Expect = 0.83
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 9/69 (13%)
Query: 236 AYKTGRGRVKVRAKVHVEKTKNKEIIVLDEMPFQTNKA--KLVE-QISDLAREKQIEGIS 292
AY+TG + + A+ H++ K + ++E+ + KA KL E QI +L ++ Q EG
Sbjct: 116 AYQTGADQASITARNHIQLVK----LQVEEVHQLSRKAETKLAEAQIEELKQKTQEEG-- 169
Query: 293 EVRDESDRE 301
E R ES++E
Sbjct: 170 EERAESEQE 178
>pdb|1L5J|A Chain A, Crystal Structure Of E. Coli Aconitase B.
pdb|1L5J|B Chain B, Crystal Structure Of E. Coli Aconitase B
Length = 865
Score = 29.3 bits (64), Expect = 1.9
Identities = 31/107 (28%), Positives = 45/107 (41%), Gaps = 10/107 (9%)
Query: 178 IAVGMATSIPPHRMD-EIIDALVHVLENPNAGLDEILEFVKGPDFPTG--GIIYGKAGII 234
+A A I P +D + ALV +L+NP AG +E L + P G Y KAG +
Sbjct: 9 VAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYVKAGFL 68
Query: 235 EAYKTGRGRVKVRAKVHVEKTKNKEIIVLDEMPFQTNKAKLVEQISD 281
A G + + T K I +L M N L++ + D
Sbjct: 69 AAIAKGEAKSPL-------LTPEKAIELLGTMQGGYNIHPLIDALDD 108
>pdb|1MWS|A Chain A, Structure Of Nitrocefin Acyl-Penicillin Binding Protein 2a
From Methicillin Resistant Staphylococcus Aureus Strain
27r At 2.00 A Resolution.
pdb|1MWS|B Chain B, Structure Of Nitrocefin Acyl-Penicillin Binding Protein 2a
From Methicillin Resistant Staphylococcus Aureus Strain
27r At 2.00 A Resolution.
pdb|1MWT|A Chain A, Structure Of Penicillin G Acyl-Penicillin Binding Protein
2a From Methicillin Resistant Staphylococcus Aureus
Strain 27r At 2.45 A Resolution.
pdb|1MWT|B Chain B, Structure Of Penicillin G Acyl-Penicillin Binding Protein
2a From Methicillin Resistant Staphylococcus Aureus
Strain 27r At 2.45 A Resolution.
pdb|1MWU|A Chain A, Structure Of Methicillin Acyl-Penicillin Binding Protein
2a From Methicillin Resistant Staphylococcus Aureus
Strain 27r At 2.60 A Resolution.
pdb|1MWU|B Chain B, Structure Of Methicillin Acyl-Penicillin Binding Protein
2a From Methicillin Resistant Staphylococcus Aureus
Strain 27r At 2.60 A Resolution
Length = 646
Score = 28.9 bits (63), Expect = 2.4
Identities = 25/115 (21%), Positives = 51/115 (43%), Gaps = 12/115 (10%)
Query: 705 VVISDDGNKLLSVSENGLGKQTLAEAYRGQSR--GGKGVIGMKLTQ-KTGNLVG-VISVD 760
++ ++ N L + + K + YR + G G +K+ Q +TG +G IS D
Sbjct: 540 IISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYD 599
Query: 761 DENLDLMILTASAKMIRVSIKDIRETGRNASGVKLINTADKVMYVNSCPKEEEPE 815
+N ++M+ +++KD+++ G + K+ +Y N K + E
Sbjct: 600 KDNPNMMMA--------INVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 646
>pdb|1MWX|A Chain A, Structure Of Penicillin Binding Protein 2a From
Methicillin Resistant Staphylococcus Aureus Strain 27r
At 1.80 A Resolution.
pdb|1MWX|B Chain B, Structure Of Penicillin Binding Protein 2a From
Methicillin Resistant Staphylococcus Aureus Strain 27r
At 1.80 A Resolution
Length = 646
Score = 28.1 bits (61), Expect = 4.1
Identities = 25/115 (21%), Positives = 51/115 (43%), Gaps = 12/115 (10%)
Query: 705 VVISDDGNKLLSVSENGLGKQTLAEAYRGQSR--GGKGVIGMKLTQ-KTGNLVG-VISVD 760
++ ++ N L + + K + YR + G G +K+ Q +TG +G IS D
Sbjct: 540 IISKENINLLNDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYD 599
Query: 761 DENLDLMILTASAKMIRVSIKDIRETGRNASGVKLINTADKVMYVNSCPKEEEPE 815
+N ++M+ +++KD+++ G + K+ +Y N K + E
Sbjct: 600 KDNPNMMMA--------INVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE 646
>pdb|2DLD|A Chain A, D-Lactate Dehydrogenase Complexed With Nadh And Oxamate
pdb|2DLD|B Chain B, D-Lactate Dehydrogenase Complexed With Nadh And Oxamate
Length = 337
Score = 27.7 bits (60), Expect = 5.4
Identities = 35/142 (24%), Positives = 53/142 (36%), Gaps = 15/142 (10%)
Query: 121 AAAMRYTEARMTKASEEILRDIDKDTIDFVPNYDDTLKEPDILPSRLPNLLVNGANGIAV 180
A A+R E +E +DID D Y D L P+ L GA+G+ V
Sbjct: 6 AYAIRKDEEPFLNEWKEAHKDIDVD-------YTDKLLTPETAK------LAKGADGVVV 52
Query: 181 GMATSIPPHRMDEIIDALVHVLENPNAGLDEI-LEFVKGPDFPTGGI-IYGKAGIIEAYK 238
+ + DA V + N G+D I ++ K F + +Y I E
Sbjct: 53 YQQLDYTADTLQALADAGVTKMSLRNVGVDNIDMDKAKELGFQITNVPVYSPNAIAEHAA 112
Query: 239 TGRGRVKVRAKVHVEKTKNKEI 260
RV + K EK +++
Sbjct: 113 IQAARVLRQDKRMDEKMAKRDL 134
>pdb|1FMI|A Chain A, Crystal Structure Of Human Class I Alpha1,2-Mannosidase
Length = 458
Score = 27.3 bits (59), Expect = 7.0
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 67 YKKSARIVGDVIGKYHPHGDNAVYDALVRMAQDFSMRL 104
++ + RI+G ++ YH GD+ +R A+DF RL
Sbjct: 90 FESTIRILGGLLSAYHLSGDS----LFLRKAEDFGNRL 123
>pdb|1FD9|A Chain A, Crystal Structure Of The Macrophage Infectivity
Potentiator Protein (Mip) A Major Virulence Factor From
Legionella Pneumophila
Length = 213
Score = 27.3 bits (59), Expect = 7.0
Identities = 22/100 (22%), Positives = 40/100 (40%), Gaps = 14/100 (14%)
Query: 114 GSIDGDNAAAMRYTEARMTKASEEILRDI-DKDTIDFVPNYDDTLKEPD----------- 161
G D + A + TE +M + +D+ K T +F D+ + +
Sbjct: 41 GMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPG 100
Query: 162 --ILPSRLPNLLVNGANGIAVGMATSIPPHRMDEIIDALV 199
+LPS L ++N NG+ G + ++ +ID V
Sbjct: 101 VVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTV 140
>pdb|1FO2|A Chain A, Crystal Structure Of Human Class I Alpha1,2-Mannosidase In
Complex With 1-Deoxymannojirimycin
pdb|1FO3|A Chain A, Crystal Structure Of Human Class I Alpha1,2-Mannosidase In
Complex With Kifunensine
Length = 460
Score = 27.3 bits (59), Expect = 7.0
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 67 YKKSARIVGDVIGKYHPHGDNAVYDALVRMAQDFSMRL 104
++ + RI+G ++ YH GD+ +R A+DF RL
Sbjct: 90 FESTIRILGGLLSAYHLSGDS----LFLRKAEDFGNRL 123
>pdb|1E4F|T Chain T, Ftsa (Apo Form) From Thermotoga Maritima
Length = 419
Score = 26.9 bits (58), Expect = 9.2
Identities = 38/161 (23%), Positives = 65/161 (39%), Gaps = 16/161 (9%)
Query: 439 RDKIKEEYQNLLELIDDLNGILKSEDRLNGVVKTEL-LEVKEQFSSPRRTEIQESYENID 497
+D +K +Q L+ G+L + ++ GVV L + I+ SY +
Sbjct: 178 QDTVKSPFQLKSSLVSTAEGVLTTPEKDRGVVVVNLGYNFTGLIAYKNGVPIKISYVPVG 237
Query: 498 IEDLIANEPMVVSMSYK---------GYVKRVDLKAYEKQNRGGKGKLSGSTYEDDFIEN 548
++ +I + V+ S++ G DLK E Q RG L G+T + +
Sbjct: 238 MKHVIKDVSAVLDTSFEESERLIITHGNAVYNDLKEEEIQYRG----LDGNTIKTTTAKK 293
Query: 549 FFVANTHDILLFITNKGQLYHLKV-YKIPEASRIAMGKAIV 588
V H L I +K + + +V KI E I + +V
Sbjct: 294 LSVI-IHARLREIMSKSKKFFREVEAKIVEEGEIGIPGGVV 333
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
0.316 0.136 0.367
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,423,868
Number of Sequences: 13198
Number of extensions: 188182
Number of successful extensions: 534
Number of sequences better than 10.0: 11
Number of HSP's better than 10.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 526
Number of HSP's gapped (non-prelim): 13
length of query: 827
length of database: 2,899,336
effective HSP length: 96
effective length of query: 731
effective length of database: 1,632,328
effective search space: 1193231768
effective search space used: 1193231768
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: 58 (26.9 bits)