BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy14505
(1619 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Y3P|A Chain A, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
pdb|2Y3P|B Chain B, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
Length = 522
Score = 600 bits (1546), Expect = e-171, Method: Compositional matrix adjust.
Identities = 288/525 (54%), Positives = 387/525 (73%), Gaps = 5/525 (0%)
Query: 2 NQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNR 61
+ A+E+ + +EEE+ SYLDYAMSVIVGRALPDVRDGLKPVHRRVL+AM+ + N WN+
Sbjct: 1 SDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNK 60
Query: 62 PFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMR 121
+ K ARVVG+ +GKYHPHGD ++YD +VRMAQ FSLR LVDGQGNFGSIDGDSAAAMR
Sbjct: 61 AYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMR 120
Query: 122 YTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATN 181
YTE RL KI++EL+ DL+KET+DF+ NYDG EK P V+PT+IPNLL+NGSSGIAVGMATN
Sbjct: 121 YTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATN 180
Query: 182 IPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVI 241
IPPHNLTEVI+G L + + + SI L++ IP PDFPTA II G + + Y TG+G+V
Sbjct: 181 IPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVY 240
Query: 242 IRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGM 301
IRA+ +E + R II+ E+PYQVNK L+EKI++LVKEK++E IS LRDESDK GM
Sbjct: 241 IRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGM 300
Query: 302 RIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEV 361
RIVIE+KR+ + E+VLN LY QTQLQ +FG+NM+AL +GQPK++NLK+I+ F+ HR+EV
Sbjct: 301 RIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREV 360
Query: 362 IKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVS 421
+ RRTIFELRKAR+ AHILE L +AL NID I++IR TP EAK ++ + W L +V+
Sbjct: 361 VTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVA 420
Query: 422 KIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYEN 481
++ + + +++ +Y L++ QAQ IL + LQ+LT +E +K++++Y+
Sbjct: 421 AMLERAGDDAARPEWLEPEFGVRDG-LYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE 479
Query: 482 VIKKVIDLTDILSNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEI 526
++ ++ +L IL ++ R + ++G RR+EI
Sbjct: 480 LLDQIAELLRILGSADRLMEVIREELELVREQFGDK----RRTEI 520
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 568 bits (1464), Expect = e-162, Method: Compositional matrix adjust.
Identities = 273/497 (54%), Positives = 366/497 (73%), Gaps = 5/497 (1%)
Query: 30 VGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDAL 89
VGRALPDVRDGLKPVHRRVL+AM+ + N WN+ + K ARVVG+ +GKYHPHGD ++YD +
Sbjct: 1 VGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTI 60
Query: 90 VRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNY 149
VRMAQ FSLR LVDGQGNFGSIDGDSAAAMRYTE RL KI++EL+ DL+KET+DF+ NY
Sbjct: 61 VRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNY 120
Query: 150 DGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLI 209
DG EK P V+PT+IPNLL+NGSSGIAVGMATNIPPHNLTEVI+G L + + + SI L+
Sbjct: 121 DGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLM 180
Query: 210 KIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVN 269
+ IP PDFPTA II G + + Y TG+G+V IRA+ +E + R II+ E+PYQVN
Sbjct: 181 EHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVN 240
Query: 270 KKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNT 329
K L+EKI++LVKEK++E IS LRDESDK GMRIVIE+KR+ + E+VLN LY QTQLQ +
Sbjct: 241 KARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVS 300
Query: 330 FGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALTN 389
FG+NM+AL +GQPK++NLK+I+ F+ HR+EV+ RRTIFELRKAR+ AHILE L +AL N
Sbjct: 301 FGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALAN 360
Query: 390 IDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMY 449
ID I++IR TP EAK ++ + W L +V+ ++ + + +++ +Y
Sbjct: 361 IDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDG-LY 419
Query: 450 KLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRXXXXXXXXXXX 509
L++ QAQ IL + LQ+LT +E +K++++Y+ ++ ++ +L IL ++ R
Sbjct: 420 YLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELEL 479
Query: 510 XKNKYGSHKKNIRRSEI 526
+ ++G RR+EI
Sbjct: 480 VREQFGDK----RRTEI 492
>pdb|3NUH|A Chain A, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold
That Plays A Critical Role In Gyrase Function
Length = 525
Score = 561 bits (1445), Expect = e-159, Method: Composition-based stats.
Identities = 283/529 (53%), Positives = 378/529 (71%), Gaps = 5/529 (0%)
Query: 2 NQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNR 61
+ A+E+ + +EEE+ SYLDYA SVIVGRALPDVRDGLKPVHRRVL+A + + N WN+
Sbjct: 2 SDLAREITPVNIEEELKSSYLDYAXSVIVGRALPDVRDGLKPVHRRVLYAXNVLGNDWNK 61
Query: 62 PFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMR 121
+ K ARVVG+ +GKYHPHGD ++YD +VR AQ FSLR LVDGQGNFGSIDGDSAAA R
Sbjct: 62 AYKKSARVVGDVIGKYHPHGDSAVYDTIVRXAQPFSLRYXLVDGQGNFGSIDGDSAAAXR 121
Query: 122 YTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATN 181
YTE RL KI++EL DL+KET+DF+ NYDG EK P V PT+IPNLL+NGSSGIAVG ATN
Sbjct: 122 YTEIRLAKIAHELXADLEKETVDFVDNYDGTEKIPDVXPTKIPNLLVNGSSGIAVGXATN 181
Query: 182 IPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVI 241
IPPHNLTEVI+G L + + + SI L + IP PDFPTA II G + + Y TG+G+V
Sbjct: 182 IPPHNLTEVINGCLAYIDDEDISIEGLXEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVY 241
Query: 242 IRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGM 301
IRA+ +E + R II+ E+PYQVNK L+EKI++LVKEK++E IS LRDESDK G
Sbjct: 242 IRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGX 301
Query: 302 RIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEV 361
RIVIE+KR+ + E+VLN LY QTQLQ +FG+N +AL +GQPK+ NLK+I+ F+ HR+EV
Sbjct: 302 RIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINXVALHHGQPKIXNLKDIIAAFVRHRREV 361
Query: 362 IKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVS 421
+ RRTIFELRKAR+ AHILE L +AL NID I++IR TP EAK ++ + W L +V+
Sbjct: 362 VTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVA 421
Query: 422 KIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYEN 481
+ + + +++ +Y L++ QAQ IL + LQ+LT +E +K++++Y+
Sbjct: 422 AXLERAGDDAARPEWLEPEFGVRDG-LYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE 480
Query: 482 VIKKVIDLTDILSNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEIILNA 530
++ ++ +L IL ++ R + ++G RR+EI N+
Sbjct: 481 LLDQIAELLRILGSADRLXEVIREELELVREQFGDK----RRTEITANS 525
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 555 bits (1431), Expect = e-158, Method: Compositional matrix adjust.
Identities = 264/497 (53%), Positives = 365/497 (73%), Gaps = 5/497 (1%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
RALPDVRDGLKPVHRRVLFAM + N WN+ + K ARVVG+ +GKYHPHGD ++YD +VR
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVVGDVIGKYHPHGDTAVYDTIVR 61
Query: 92 MAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNYDG 151
MAQ FSLR LVDGQGNFGS+DGDSAAAMRYTE R++KI++ +L DLDKET+DF+ NYDG
Sbjct: 62 MAQPFSLRYMLVDGQGNFGSVDGDSAAAMRYTEIRMSKIAHSILADLDKETVDFVPNYDG 121
Query: 152 KEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLIKI 211
E P+V+PTR+PNLL+NG+SGIAVGMATNIPPHNLTEVI+ L ++ N E + ++++
Sbjct: 122 TEHIPAVMPTRVPNLLVNGTSGIAVGMATNIPPHNLTEVINACLALIDNSELTFEEILEH 181
Query: 212 IPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNKK 271
IP PDFPTAGII G + + + Y TG+G++ IRA+ I+ + II+ ELPYQVNK
Sbjct: 182 IPGPDFPTAGIISGRAGIEEAYRTGRGKIKIRARASIDVHETTGKETIIVHELPYQVNKA 241
Query: 272 SLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNTFG 331
L+EK+++LVK+K+LE IS LRDESDK GMR+VIE+KR E+ E+VLN LYK TQ+Q +FG
Sbjct: 242 RLIEKMAELVKDKRLEGISALRDESDKDGMRMVIEIKRGEVGEVVLNNLYKLTQMQVSFG 301
Query: 332 MNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNID 391
+NM+AL NGQPK+ N+KE+L F+LHR+EV+ RRTIFELRKAR+ AHILEGL+IAL NID
Sbjct: 302 LNMVALTNGQPKIFNIKEMLEAFVLHRREVVTRRTIFELRKARDRAHILEGLSIALANID 361
Query: 392 NFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKL 451
I++I++++ +E++ K+I W L +V+ ++ + + +++ +Y L
Sbjct: 362 PIIEMIKNSNNRKESEEKLISQGWELGNVANMLSEAGNDAARPEWLEPEYGIRDG-LYYL 420
Query: 452 SDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRXXXXXXXXXXXXK 511
+ QA+ I+ + L +L+ ME KI+++Y+ ++ + +L IL+ R +
Sbjct: 421 TAEQAKAIVDLQLYKLSGMEHDKILSEYKALLDLIAELMHILATPARLMEVICEELVAIR 480
Query: 512 NKYGSHKKNIRRSEIIL 528
+++G RR+EI L
Sbjct: 481 DEFGDE----RRTEITL 493
>pdb|4DDQ|A Chain A, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|B Chain B, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|C Chain C, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|D Chain D, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|E Chain E, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|F Chain F, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
Length = 502
Score = 545 bits (1403), Expect = e-155, Method: Compositional matrix adjust.
Identities = 269/538 (50%), Positives = 373/538 (69%), Gaps = 41/538 (7%)
Query: 3 QFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRP 62
Q +V I + +EM S+LDYAMSVIV RALPDVRDGLKPVHRR+L+AM+++ ++P
Sbjct: 4 QNTPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKP 63
Query: 63 FVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRY 122
+ K AR+VGE +GKYHPHGD ++Y+++VRMAQ F+ R LVDG GNFGS+DGDSAAAMRY
Sbjct: 64 YKKSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRY 123
Query: 123 TECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNI 182
TE R++KIS E+L D+ K+TID+ NYDG E+EP V+P+R PNLL+NG++GIAVGMATNI
Sbjct: 124 TEARMSKISMEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNI 183
Query: 183 PPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVII 242
PPH L E+IDGVL V NP+ +I +L+++IP PDFPTAG I G S + Y +G+G + I
Sbjct: 184 PPHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITI 243
Query: 243 RAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMR 302
RAK IE+ + + II+ ELPYQVNK L+EKI+ LV++KK+E I++LRDESD++GMR
Sbjct: 244 RAKAEIEQTS-SGKERIIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMR 302
Query: 303 IVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVI 362
IVIE++R+ ++LN LYKQT LQ +FG+N+LALV+GQPK+L LK+ L +++ H+K VI
Sbjct: 303 IVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVI 362
Query: 363 KRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSK 422
+RRT +ELRKA AHILEGL +AL ++D I +IR++ T + A+ +IE
Sbjct: 363 RRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQ--------- 413
Query: 423 IIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENV 482
+ L++ QAQ IL M LQRLT +E++KI +Y+++
Sbjct: 414 --------------------------FSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSL 447
Query: 483 IKKVIDLTDILSNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEIILNAINP-STEDLI 539
+K + +L DIL+N + K ++ RR+EI+ + + EDLI
Sbjct: 448 VKLIAELKDILANEYKVLEIIREELTEIKERFNDE----RRTEIVTSGLETIEDEDLI 501
>pdb|2XCO|A Chain A, The 3.1a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase
pdb|2XCQ|A Chain A, The 2.98a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase
Length = 726
Score = 509 bits (1312), Expect = e-144, Method: Compositional matrix adjust.
Identities = 259/514 (50%), Positives = 356/514 (69%), Gaps = 41/514 (7%)
Query: 16 EMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMG 75
EM +S+LDYAMSVIV RALPDVRDGLKPVHRR+L+ ++E ++ + K AR+VG+ MG
Sbjct: 252 EMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMG 311
Query: 76 KYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELL 135
KYHPHGD SIY+A+VRMAQ FS R LVDGQGNFGS+DGD AAAMRYTE R+ KI+ ELL
Sbjct: 312 KYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELL 371
Query: 136 IDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVL 195
D++K+TIDFI NYDG E+EPSVLP R PNLL NG+SGIAVGMATNIPPHNLTE+I+GVL
Sbjct: 372 RDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVL 431
Query: 196 YVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNREN 255
+ NP+ SI +L++ I PDFPTAG+I G S + Y TG+G + +R++ IEE
Sbjct: 432 SLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERG-GG 490
Query: 256 RTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEIPE 314
R I++ E+P+QVNK ++EKI++LV++KK++ I++LRDE+ ++G+R+VI+++++
Sbjct: 491 RQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANAS 550
Query: 315 IVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAR 374
++LN LYKQT LQ +FG+NM+ALVNG+PKL+NLKE L +++ H+K V++RRT + LRKA+
Sbjct: 551 VILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAK 610
Query: 375 EYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTI 434
+ AHILEGL IAL +ID I IR + T + A
Sbjct: 611 DRAHILEGLRIALDHIDEIISTIRESDTDKVA---------------------------- 642
Query: 435 SKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILS 494
+ LQ +KLS+ QAQ IL M L+RLT +E+ KI +Y ++ + +L IL+
Sbjct: 643 -----MESLQQR--FKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILA 695
Query: 495 NSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEIIL 528
+ + ++++G RR+EI L
Sbjct: 696 DEEVLLQLVRDELTEIRDRFGDD----RRTEIQL 725
>pdb|2XCS|B Chain B, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCS|D Chain D, The 2.1a Crystal Structure Of S. Aureus Gyrase Complex
With Gsk299423 And Dna
pdb|2XCT|B Chain B, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|D Chain D, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|S Chain S, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
pdb|2XCT|U Chain U, The Twinned 3.35a Structure Of S. Aureus Gyrase Complex
With Ciprofloxacin And Dna
Length = 692
Score = 509 bits (1310), Expect = e-144, Method: Compositional matrix adjust.
Identities = 258/514 (50%), Positives = 356/514 (69%), Gaps = 41/514 (7%)
Query: 16 EMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMG 75
EM +S+LDYAMSVIV RALPDVRDGLKPVHRR+L+ ++E ++ + K AR+VG+ MG
Sbjct: 218 EMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMG 277
Query: 76 KYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELL 135
KYHPHGD SIY+A+VRMAQ FS R LVDGQGNFGS+DGD AAAMR+TE R+ KI+ ELL
Sbjct: 278 KYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELL 337
Query: 136 IDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVL 195
D++K+TIDFI NYDG E+EPSVLP R PNLL NG+SGIAVGMATNIPPHNLTE+I+GVL
Sbjct: 338 RDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVL 397
Query: 196 YVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNREN 255
+ NP+ SI +L++ I PDFPTAG+I G S + Y TG+G + +R++ IEE
Sbjct: 398 SLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERG-GG 456
Query: 256 RTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEIPE 314
R I++ E+P+QVNK ++EKI++LV++KK++ I++LRDE+ ++G+R+VI+++++
Sbjct: 457 RQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANAS 516
Query: 315 IVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAR 374
++LN LYKQT LQ +FG+NM+ALVNG+PKL+NLKE L +++ H+K V++RRT + LRKA+
Sbjct: 517 VILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAK 576
Query: 375 EYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTI 434
+ AHILEGL IAL +ID I IR + T + A
Sbjct: 577 DRAHILEGLRIALDHIDEIISTIRESDTDKVA---------------------------- 608
Query: 435 SKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILS 494
+ LQ +KLS+ QAQ IL M L+RLT +E+ KI +Y ++ + +L IL+
Sbjct: 609 -----MESLQQR--FKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILA 661
Query: 495 NSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEIIL 528
+ + ++++G RR+EI L
Sbjct: 662 DEEVLLQLVRDELTEIRDRFGDD----RRTEIQL 691
>pdb|2XCR|B Chain B, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|D Chain D, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|S Chain S, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
pdb|2XCR|U Chain U, The 3.5a Crystal Structure Of The Catalytic Core (B'a'
Region) Of Staphylococcus Aureus Dna Gyrase Complexed
With Gsk299423 And Dna
Length = 726
Score = 508 bits (1308), Expect = e-143, Method: Compositional matrix adjust.
Identities = 258/514 (50%), Positives = 356/514 (69%), Gaps = 41/514 (7%)
Query: 16 EMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMG 75
EM +S+LDYAMSVIV RALPDVRDGLKPVHRR+L+ ++E ++ + K AR+VG+ MG
Sbjct: 252 EMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMG 311
Query: 76 KYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELL 135
KYHPHGD SIY+A+VRMAQ FS R LVDGQGNFGS+DGD AAAMR+TE R+ KI+ ELL
Sbjct: 312 KYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARMTKITLELL 371
Query: 136 IDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVL 195
D++K+TIDFI NYDG E+EPSVLP R PNLL NG+SGIAVGMATNIPPHNLTE+I+GVL
Sbjct: 372 RDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVL 431
Query: 196 YVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNREN 255
+ NP+ SI +L++ I PDFPTAG+I G S + Y TG+G + +R++ IEE
Sbjct: 432 SLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERG-GG 490
Query: 256 RTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEIPE 314
R I++ E+P+QVNK ++EKI++LV++KK++ I++LRDE+ ++G+R+VI+++++
Sbjct: 491 RQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANAS 550
Query: 315 IVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAR 374
++LN LYKQT LQ +FG+NM+ALVNG+PKL+NLKE L +++ H+K V++RRT + LRKA+
Sbjct: 551 VILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAK 610
Query: 375 EYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTI 434
+ AHILEGL IAL +ID I IR + T + A
Sbjct: 611 DRAHILEGLRIALDHIDEIISTIRESDTDKVA---------------------------- 642
Query: 435 SKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILS 494
+ LQ +KLS+ QAQ IL M L+RLT +E+ KI +Y ++ + +L IL+
Sbjct: 643 -----MESLQQR--FKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELETILA 695
Query: 495 NSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEIIL 528
+ + ++++G RR+EI L
Sbjct: 696 DEEVLLQLVRDELTEIRDRFGDD----RRTEIQL 725
>pdb|3IFZ|A Chain A, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
pdb|3IFZ|B Chain B, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
Length = 508
Score = 464 bits (1195), Expect = e-130, Method: Composition-based stats.
Identities = 245/520 (47%), Positives = 334/520 (64%), Gaps = 45/520 (8%)
Query: 13 LEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGE 72
+E+EM +SY+DYAMSVIVGRALP+VRDGLKPVHRRVL+AM + +R K AR V E
Sbjct: 20 IEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAE 79
Query: 73 TMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISN 132
TMG YHPHGD SIYD+LVRMAQ +SLR LVDGQGNFGS D AAMRYTE RL ++
Sbjct: 80 TMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAM 139
Query: 133 ELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVID 192
E+L ++D+ET+DFI NYDG+ +EP+VLP+R PNLL NGS GIAVGMATNIPPHNL E+ D
Sbjct: 140 EMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELAD 199
Query: 193 GVLYVLHN----PECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHI 248
V + L N E ++ ++ + PDFPTAG+I G D Y TG+G + +R +
Sbjct: 200 AVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEV 259
Query: 249 EEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDE-SDKSGMRIVIEL 307
EE +R RT+++I ELPYQVN + + I++ V++ KL ISN+ D+ SD+ G+RIVIE+
Sbjct: 260 EEDSR-GRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEI 318
Query: 308 KRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTI 367
KR+ + ++V+N LYK TQLQ +FG NMLA+V+G P+ L L +++ Y++ H+ +VI RRT
Sbjct: 319 KRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTT 378
Query: 368 FELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFN 427
+ LRKA E AHIL GL AL +D I +IR++ T A+ +IE
Sbjct: 379 YRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIE--------------- 423
Query: 428 KKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVI 487
+ + +IQAQ IL M L+RL +E+++II+ + ++
Sbjct: 424 --------------------LLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIA 463
Query: 488 DLTDILSNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEII 527
DL DIL+ +R +++G RR+ II
Sbjct: 464 DLEDILAKPERQRGIVRDELAEIVDRHGDD----RRTRII 499
>pdb|3ILW|A Chain A, Structure Of Dna Gyrase Subunit A N-Terminal Domain
pdb|3ILW|B Chain B, Structure Of Dna Gyrase Subunit A N-Terminal Domain
Length = 470
Score = 443 bits (1139), Expect = e-124, Method: Composition-based stats.
Identities = 236/506 (46%), Positives = 321/506 (63%), Gaps = 45/506 (8%)
Query: 27 SVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIY 86
SVIVGRALP+VRDGLKPVHRRVL+AM + +R K AR V ETMG YHPHGD SIY
Sbjct: 4 SVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIY 63
Query: 87 DALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFI 146
D+LVRMAQ +SLR LVDGQGNFGS D AAMRYTE RL ++ E+L ++D+ET+DFI
Sbjct: 64 DSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFI 123
Query: 147 SNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHN----PE 202
NYDG+ +EP+VLP+R PNLL NGS GIAVGMATNIPPHNL E+ D V + L N E
Sbjct: 124 PNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEE 183
Query: 203 CSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIID 262
++ ++ + PDFPTAG+I G D Y TG+G + +R +EE +R RT+++I
Sbjct: 184 ETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSR-GRTSLVIT 242
Query: 263 ELPYQVNKKSLLEKISQLVKEKKLECISNLRDE-SDKSGMRIVIELKRNEIPEIVLNKLY 321
ELPYQVN + + I++ V++ KL ISN+ D+ SD+ G+RIVIE+KR+ + ++V+N LY
Sbjct: 243 ELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLY 302
Query: 322 KQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILE 381
K TQLQ +FG NMLA+V+G P+ L L +++ Y++ H+ +VI RRT + LRKA E AHIL
Sbjct: 303 KHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILR 362
Query: 382 GLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNIS 441
GL AL +D I +IR++ T A+ +IE
Sbjct: 363 GLVKALDALDEVIALIRASETVDIARAGLIE----------------------------- 393
Query: 442 KLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRXXX 501
+ + +IQAQ IL M L+RL +E+++II+ + ++ DL DIL+ +R
Sbjct: 394 ------LLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRG 447
Query: 502 XXXXXXXXXKNKYGSHKKNIRRSEII 527
+++G RR+ II
Sbjct: 448 IVRDELAEIVDRHGDD----RRTRII 469
>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
Subunit A (Grla) From Staphylococcus Aureus
Length = 514
Score = 391 bits (1005), Expect = e-108, Method: Compositional matrix adjust.
Identities = 213/521 (40%), Positives = 322/521 (61%), Gaps = 37/521 (7%)
Query: 7 EVISIL-LEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVK 65
E+I L LE+ + + Y+ +I RALPDVRDGLKPV RR+L+AM+ N ++ F K
Sbjct: 26 EIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRK 85
Query: 66 CARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTEC 125
A+ VG+ +G+YHPHGD S+Y+A+VR++Q + LR L++ GN GSID D AAMRYTE
Sbjct: 86 SAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYTEA 145
Query: 126 RLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPH 185
+L+ ++ ELL D++KET+ FI NYD EP VLP+R PNLL+NGS+GI+ G AT+IPPH
Sbjct: 146 KLSLLAEELLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIPPH 205
Query: 186 NLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAK 245
NL EVI L + NP+ ++N L+K I PDFPT GII G+ + Y +GKGR+I+R+K
Sbjct: 206 NLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRIIVRSK 265
Query: 246 THIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVI 305
EE R R +II E+PY+VNK SL+++I +L +KK++ I +RDE+D++G+RI I
Sbjct: 266 VE-EETLRNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGLRIAI 324
Query: 306 ELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRR 365
ELK++ E + N LYK + LQ ++ NM+A+ +G+PKL+ +++I+ ++ H+ EV+ R
Sbjct: 325 ELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIEVVANR 384
Query: 366 TIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIG 425
T FEL A + HI+EGL AL+ +D I++IRS+ ++AK +IE
Sbjct: 385 TKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIE------------- 431
Query: 426 FNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKK 485
+Y+ ++ QA+ I+ + L RLTN + + +++ +
Sbjct: 432 ----------------------VYEFTEEQAEAIVMLQLYRLTNTDIVALEGEHKELEAL 469
Query: 486 VIDLTDILSNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEI 526
+ L IL N K K+ S + ++ +EI
Sbjct: 470 IKQLRHILDNHDALLNVIKEELNEIKKKFKSERLSLIEAEI 510
>pdb|2NOV|A Chain A, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|B Chain B, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|C Chain C, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|D Chain D, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|3FOE|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOE|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3K9F|A Chain A, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3K9F|B Chain B, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3KSA|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSA|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSB|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3KSB|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3LTN|A Chain A, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3LTN|B Chain B, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3RAF|A Chain A, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAF|B Chain B, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|A Chain A, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|B Chain B, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|A Chain A, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|B Chain B, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
Length = 496
Score = 387 bits (993), Expect = e-107, Method: Compositional matrix adjust.
Identities = 185/398 (46%), Positives = 274/398 (68%), Gaps = 1/398 (0%)
Query: 13 LEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGE 72
LE+ M + + Y+ +I RALPD+RDGLKPV RR+L++M++ +N +++ + K A+ VG
Sbjct: 9 LEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGN 68
Query: 73 TMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISN 132
MG +HPHGD SIYDA+VRM+Q++ R LV+ GN GS+DGD AAMRYTE RL++I+
Sbjct: 69 IMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAG 128
Query: 133 ELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVID 192
LL D++K+T+ F N+D EKEP+VLP PNLL+NGS+GI+ G AT+IPPHNL EVID
Sbjct: 129 YLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVID 188
Query: 193 GVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFN 252
+Y++ +P I+ L++ +P PDFPT II G + Y TGKGRV++R+KT IE+
Sbjct: 189 AAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKL- 247
Query: 253 RENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEI 312
+ + I+I E+PY++NK +L++KI + K+ I+ +RDESD+ G+RI IELK++
Sbjct: 248 KGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDAN 307
Query: 313 PEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRK 372
E+VLN L+K T LQ + NM+A+ N P+ + + IL +I HR+EVI R+ F+ K
Sbjct: 308 TELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEK 367
Query: 373 AREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKI 410
A + HI+EGL ++ +D I +IR++ +AK +
Sbjct: 368 AEKRLHIVEGLIRVISILDEVIALIRASENKADAKENL 405
>pdb|1ZVU|A Chain A, Structure Of The Full-Length E. Coli Parc Subunit
Length = 716
Score = 337 bits (863), Expect = 4e-92, Method: Compositional matrix adjust.
Identities = 215/691 (31%), Positives = 366/691 (52%), Gaps = 71/691 (10%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
RALP + DGLKPV RR+++AM E+ + F K AR VG+ +GKYHPHGD + Y+A+V
Sbjct: 3 RALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAMVL 62
Query: 92 MAQSFSLRCTLVDGQGNFGSIDGD-SAAAMRYTECRLNKISNELLIDLDKETIDFISNYD 150
MAQ FS R LVDGQGN+G+ D S AAMRYTE RL+K S LL +L + T D++ N+D
Sbjct: 63 MAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPNFD 122
Query: 151 GKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLIK 210
G +EP +LP R+PN+L+NG++GIAVGMAT+IPPHNL EV + ++ P+ +++ L+
Sbjct: 123 GTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQLLD 182
Query: 211 IIPAPDFPT-AGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVN 269
I+ PD+PT A II + + Y G+G V +RA E+ A++I LP+QV+
Sbjct: 183 IVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKED------GAVVISALPHQVS 236
Query: 270 KKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEIP-EIVLNKLYKQTQLQ 327
+LE+I+ ++ KKL + +LRDESD ++ R+VI + N + + V+N L+ T L+
Sbjct: 237 GARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTDLE 296
Query: 328 NTF--GMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTI 385
++ +NM+ L +G+P + NL EIL +++ R++ ++RR + L K + HILEGL +
Sbjct: 297 KSYRINLNMIGL-DGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLLV 355
Query: 386 ALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQN 445
A NID I+IIR+ P+ A +S+
Sbjct: 356 AFLNIDEVIEIIRNEDEPKPA--------------------------LMSR--------- 380
Query: 446 NDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRXXXXXXX 505
+ L++ QA+ IL++ L+ L +E+ KI + + K+ L IL++ ++
Sbjct: 381 ---FGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLKK 437
Query: 506 XXXXXKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMVITLSNLGYIKSQPISEYRAQ 565
YG +++ + A+ S D++ S+ + I LS +G+++S + A
Sbjct: 438 ELQADAQAYGDDRRSPLQEREEAKAM--SEHDMLPSEPVTIVLSQMGWVRSAKGHDIDA- 494
Query: 566 KRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYWLKVWQIPQGSRNSRGKPII 625
+ K D ++ ++ + GR Y + +P S +G+P+
Sbjct: 495 -------PGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLP--SARGQGEPLT 545
Query: 626 NMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKTLLSNFSNPRKSGIIAVNL 685
+L + +L S++++ + M++ G ++ ++G + L
Sbjct: 546 GKLTLPPGATVDHMLMESDDQK-------LLMASDAGYGFVCTFNDLVARNRAGKALITL 598
Query: 686 SNEDFLIGAALTDGSYDIML-FSDSGKAVRF 715
++ + + + D++L + +G+ + F
Sbjct: 599 PENAHVMPPVVIEDASDMLLAITQAGRMLMF 629
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 317 bits (813), Expect = 3e-86, Method: Compositional matrix adjust.
Identities = 194/531 (36%), Positives = 301/531 (56%), Gaps = 55/531 (10%)
Query: 19 KSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYH 78
++YL+YAM VI+ RALP + DGLKPV RR+++AM E+ + K AR VG+ +GKYH
Sbjct: 284 QAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYH 343
Query: 79 PHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGD-SAAAMRYTECRLNKISNELLID 137
PHGD + Y+A+V MAQ FS R L++GQGN+GS D S AAMRYTE +L+ S LL +
Sbjct: 344 PHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSE 403
Query: 138 LDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYV 197
L + T ++ N+DG KEP LP R+PN+L+NG++GIAVGMAT+IPPHNL EV+ G + +
Sbjct: 404 LGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIAL 463
Query: 198 LHNPECSINDLIKIIPAPDFPT-AGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENR 256
+ NP+ S L + IPAPD PT A II + TG+G +RA IE +
Sbjct: 464 IRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIE------K 517
Query: 257 TAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEI-PE 314
I+I ELPYQV+ ++ +I+ ++ KKL + ++RDESD ++ R+VI L+ N I E
Sbjct: 518 NEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAE 577
Query: 315 IVLNKLYKQTQLQNTFGMNM-LALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKA 373
V++ L+ T L++++ +N+ + +G+P++ +++ IL +I RK+ + RR + L +
Sbjct: 578 AVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRI 637
Query: 374 REYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNT 433
+ HIL GL IA +ID I+IIR P K ++E
Sbjct: 638 EKRLHILAGLLIAYLDIDTVIRIIREEDQP---KPVLMEH-------------------- 674
Query: 434 ISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDIL 493
+ + +IQA+ IL++ L+ L +E+ +I ++ + + K + + L
Sbjct: 675 ---------------FNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQL 719
Query: 494 SNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEII--LNAINPSTEDLIASQ 542
N + K+G RRS I+ A+ +DL+ ++
Sbjct: 720 ENPESLKNLIISELKEDAKKFGDE----RRSPIVARAEAVQIKEQDLMPAE 766
>pdb|2XKK|A Chain A, Crystal Structure Of Moxifloxacin, Dna, And A. Baumannii
Topo Iv (Pare-Parc Fusion Truncate)
pdb|2XKK|C Chain C, Crystal Structure Of Moxifloxacin, Dna, And A. Baumannii
Topo Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 314 bits (804), Expect = 3e-85, Method: Compositional matrix adjust.
Identities = 193/531 (36%), Positives = 300/531 (56%), Gaps = 55/531 (10%)
Query: 19 KSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYH 78
++YL+YAM VI+ RALP + DGLKPV RR+++AM E+ + K AR VG+ +GKYH
Sbjct: 284 QAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYH 343
Query: 79 PHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGD-SAAAMRYTECRLNKISNELLID 137
PHGD + Y+A+V MAQ FS R L++GQGN+GS D S AAMR TE +L+ S LL +
Sbjct: 344 PHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRXTEAKLSAYSELLLSE 403
Query: 138 LDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYV 197
L + T ++ N+DG KEP LP R+PN+L+NG++GIAVGMAT+IPPHNL EV+ G + +
Sbjct: 404 LGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIAL 463
Query: 198 LHNPECSINDLIKIIPAPDFPT-AGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENR 256
+ NP+ S L + IPAPD PT A II + TG+G +RA IE +
Sbjct: 464 IRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIE------K 517
Query: 257 TAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIELKRNEI-PE 314
I+I ELPYQV+ ++ +I+ ++ KKL + ++RDESD ++ R+VI L+ N I E
Sbjct: 518 NEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAE 577
Query: 315 IVLNKLYKQTQLQNTFGMNM-LALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKA 373
V++ L+ T L++++ +N+ + +G+P++ +++ IL +I RK+ + RR + L +
Sbjct: 578 AVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRI 637
Query: 374 REYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNT 433
+ HIL GL IA +ID I+IIR P K ++E
Sbjct: 638 EKRLHILAGLLIAYLDIDTVIRIIREEDQP---KPVLMEH-------------------- 674
Query: 434 ISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDIL 493
+ + +IQA+ IL++ L+ L +E+ +I ++ + + K + + L
Sbjct: 675 ---------------FNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQL 719
Query: 494 SNSKRXXXXXXXXXXXXKNKYGSHKKNIRRSEII--LNAINPSTEDLIASQ 542
N + K+G RRS I+ A+ +DL+ ++
Sbjct: 720 ENPESLKNLIISELKEDAKKFGDE----RRSPIVARAEAVQIKEQDLMPAE 766
>pdb|1ZI0|A Chain A, A Superhelical Spiral In Escherichia Coli Dna Gyrase A C-
Terminal Domain Imparts Unidirectional Supercoiling Bias
pdb|1ZI0|B Chain B, A Superhelical Spiral In Escherichia Coli Dna Gyrase A C-
Terminal Domain Imparts Unidirectional Supercoiling Bias
Length = 307
Score = 310 bits (795), Expect = 3e-84, Method: Composition-based stats.
Identities = 157/310 (50%), Positives = 223/310 (71%), Gaps = 5/310 (1%)
Query: 542 QDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNY 601
+D+V+TLS+ GY+K QP+SEY AQ+RGG+GK A K+ED+I++L +ANTHD+ILCFS+
Sbjct: 3 EDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSR 62
Query: 602 GRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSL 661
GR+Y +KV+Q+P+ +R +RG+PI+N+ L+ E+IT ILP++ +F + VFM+T+
Sbjct: 63 GRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVT----EFEEGVKVFMATAN 118
Query: 662 GIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVR 721
G VKKT+L+ F+ R +G +A+ L + D LIG LT G ++MLFS GK VRF E+SVR
Sbjct: 119 GTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVR 178
Query: 722 AMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGI 781
AMG + GV G+RL + KV++L+V ++LTAT+NGYGKRT + EY +R TKG+
Sbjct: 179 AMGCNTTGVRGIRLGEGDKVVSLIVPRGDG-AILTATQNGYGKRTAVAEYPTKSRATKGV 237
Query: 782 ISIKTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKS 841
ISIK +RNG VV A V+ +IM+IT G L+RTRVSEI +GR+TQGVILI
Sbjct: 238 ISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDE 297
Query: 842 KLCGVQRLCK 851
+ G+QR+ +
Sbjct: 298 NVVGLQRVAE 307
>pdb|3L6V|A Chain A, Crystal Structure Of The Xanthomonas Campestris Gyrase A
C- Terminal Domain
pdb|3L6V|B Chain B, Crystal Structure Of The Xanthomonas Campestris Gyrase A
C- Terminal Domain
Length = 370
Score = 294 bits (752), Expect = 3e-79, Method: Composition-based stats.
Identities = 163/347 (46%), Positives = 228/347 (65%), Gaps = 38/347 (10%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYIL 596
DLIA +D+V+TLS+ GY K QP+S YRAQ+RGGRG+ A TK+ED+I+QL++ NTHD +L
Sbjct: 2 DLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLL 61
Query: 597 CFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVF 656
F++ G+++WL V Q+P+ N+RG+PIIN L++ E++ +LP+ R++ N YVF
Sbjct: 62 TFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPV----REYADNRYVF 117
Query: 657 MSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFN 716
M+T G VKKT LS F+ G IA+NL D L+G ALTDG D++LF+ +GK VRF
Sbjct: 118 MATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFG 177
Query: 717 ENSVRAMGRSARGVIGMRLEKKQKVIALLVS----------------------------- 747
E++VR+MGR+A GV G+RL K ++V++L+VS
Sbjct: 178 ESTVRSMGRTATGVRGIRLAKGEEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAV 237
Query: 748 -----NNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVNRY 802
N +LTATENGYGKRT + EY + RGT+G+I I+T +RNGK+V A L+
Sbjct: 238 IDVADNGDVAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGST 297
Query: 803 HEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRL 849
E+MLI+ GG L+RTR SEI ++GR+TQGV LI + KL V+RL
Sbjct: 298 DEVMLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERL 344
>pdb|3UC1|A Chain A, Mycobacterium Tuberculosis Gyrase Type Iia Topoisomerase
C-Terminal Domain
Length = 327
Score = 218 bits (554), Expect = 3e-56, Method: Composition-based stats.
Identities = 110/310 (35%), Positives = 189/310 (60%), Gaps = 7/310 (2%)
Query: 541 SQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSN 600
++D+V+T++ GY K YR+QKRGG+G + K +D + F+ +THD IL F+
Sbjct: 2 AEDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTT 61
Query: 601 YGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTS 660
GR+Y K + +P+ SR +RG+ + N+ + + +E+I ++ + R + Y+ ++T
Sbjct: 62 QGRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQI----RGYTDAPYLVLATR 117
Query: 661 LGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFN--EN 718
G+VKK+ L++F + R GI+AVNL + D L+GA L D++L S +G+++RF+ +
Sbjct: 118 NGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDE 177
Query: 719 SVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGT 778
++R MGR+ GV GMR ++++L V + +L AT GY KRT I+EY RG
Sbjct: 178 ALRPMGRATSGVQGMRFNIDDRLLSLNVV-REGTYLLVATSGGYAKRTAIEEYPVQGRGG 236
Query: 779 KGIISIKTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVE 838
KG++++ ++R G++V A +V+ E+ +T+GG +IRT ++RK GR T+GV L+ +
Sbjct: 237 KGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLG 296
Query: 839 NKSKLCGVQR 848
L + R
Sbjct: 297 EGDTLLAIAR 306
Score = 41.6 bits (96), Expect = 0.003, Method: Composition-based stats.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 6/111 (5%)
Query: 749 NQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVNRYHEIML- 807
N + V+T TE GY KRT Y RG KG+ + +VA V H+++L
Sbjct: 1 NAEDVVVTITETGYAKRTKTDLYRSQKRGGKGVQG--AGLKQDDIVAHFFVCSTHDLILF 58
Query: 808 ITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRLCKITMIKKY 858
TT G + R + ++ + R+ +G V N +R+ ++ I+ Y
Sbjct: 59 FTTQGRVYRAKAYDLPEASRTARGQ---HVANLLAFQPEERIAQVIQIRGY 106
>pdb|2CMK|A Chain A, Cytidine Monophosphate Kinase In Complex With Cytidine-Di-
Phosphate
pdb|1KDO|A Chain A, Cytidine Monophosphate Kinase From E. Coli In Complex With
Cytidine Monophosphate
pdb|1KDO|B Chain B, Cytidine Monophosphate Kinase From E. Coli In Complex With
Cytidine Monophosphate
pdb|1KDP|A Chain A, Cytidine Monophosphate Kinase From E. Coli In Complex With
2'-Deoxy-Cytidine Monophosphate
pdb|1KDP|B Chain B, Cytidine Monophosphate Kinase From E. Coli In Complex With
2'-Deoxy-Cytidine Monophosphate
pdb|1KDR|A Chain A, Cytidine Monophosphate Kinase From E.Coli In Complex With
Ara-Cytidine Monophosphate
pdb|1KDR|B Chain B, Cytidine Monophosphate Kinase From E.Coli In Complex With
Ara-Cytidine Monophosphate
pdb|1KDT|A Chain A, Cytidine Monophosphate Kinase From E.Coli In Complex With
2',3'-Dideoxy-Cytidine Monophosphate
pdb|1KDT|B Chain B, Cytidine Monophosphate Kinase From E.Coli In Complex With
2',3'-Dideoxy-Cytidine Monophosphate
Length = 227
Score = 187 bits (475), Expect = 4e-47, Method: Composition-based stats.
Identities = 94/212 (44%), Positives = 143/212 (67%), Gaps = 4/212 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
PVITIDGP+ +GKGT+ + +A L +H LDSGA+YR++ L+A+++++ + +E LV L
Sbjct: 6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLAS 65
Query: 920 KLNYNFLGK----EVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ F+ EV L G +V+ IR ++V+N AS++A F +R+ L + Q FR+ PG
Sbjct: 66 HLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPG 125
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
L+ADGRDMGT VFPDA +KIFL A ++R RR QL +KGFSV+ LL + +RD RD
Sbjct: 126 LIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRD 185
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
+ R ++PL A +L+++ ++I QV+ + L
Sbjct: 186 RNRAVAPLVPAADALVLDSTTLSIEQVIEKAL 217
>pdb|1CKE|A Chain A, Cmp Kinase From Escherichia Coli Free Enzyme Structure
Length = 227
Score = 186 bits (471), Expect = 1e-46, Method: Composition-based stats.
Identities = 94/212 (44%), Positives = 142/212 (66%), Gaps = 4/212 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
PVITIDGP+ +GKGT+ + +A L +H LDSGA+YR++ L+A+++++ + +E LV L
Sbjct: 6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLAS 65
Query: 920 KLNYNFLGK----EVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ F+ EV L G +V+ IR ++V+N AS++A F +R+ L + Q FR+ PG
Sbjct: 66 HLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPG 125
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
L+ADGRDMGT VFPDA +KIFL A ++R RR QL KGFSV+ LL + +RD RD
Sbjct: 126 LIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQVKGFSVNFERLLAEIKERDDRD 185
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
+ R ++PL A +L+++ ++I QV+ + L
Sbjct: 186 RNRAVAPLVPAADALVLDSTTLSIEQVIEKAL 217
>pdb|2FEM|A Chain A, Mutant R188m Of The Cytidine Monophosphate Kinase From E.
Coli
pdb|2FEO|A Chain A, Mutant R188m Of The Cytidine Monophosphate Kinase From E.
Coli Complexed With Dcmp
Length = 227
Score = 184 bits (468), Expect = 3e-46, Method: Composition-based stats.
Identities = 93/212 (43%), Positives = 142/212 (66%), Gaps = 4/212 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
PVITIDGP+ +GKGT+ + +A L +H LDSGA+YR++ L+A+++++ + +E LV L
Sbjct: 6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLAS 65
Query: 920 KLNYNFLGK----EVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ F+ EV L G +V+ IR ++V+N AS++A F +R+ L + Q FR+ PG
Sbjct: 66 HLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPG 125
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
L+ADGRDMGT VFPDA +KIFL A ++R RR QL +KGFSV+ LL + +RD RD
Sbjct: 126 LIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRD 185
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
+ ++PL A +L+++ ++I QV+ + L
Sbjct: 186 RNMAVAPLVPAADALVLDSTTLSIEQVIEKAL 217
>pdb|4E22|A Chain A, Structure Of Cytidine Monophosphate Kinase From Yersinia
Pseudotuberculosis
Length = 252
Score = 184 bits (467), Expect = 3e-46, Method: Composition-based stats.
Identities = 92/212 (43%), Positives = 139/212 (65%), Gaps = 4/212 (1%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
PVIT+DGP+ +GKGT+ + +A L + LDSGA+YR++ L+A+++ + + E LV L
Sbjct: 28 PVITVDGPSGAGKGTLCKALAESLNWRLLDSGAIYRVLALAALHHQVDISTEEALVPLAA 87
Query: 920 KLNYNFLGK----EVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
L+ F+ + +V L G +V+ IR E V N AS+ A F +R+ L + Q FR+ PG
Sbjct: 88 HLDVRFVSQNGQLQVILEGEDVSNEIRTETVGNTASQAAAFPRVREALLRRQRAFREAPG 147
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
L+ADGRDMGT VFPDA +KIFL A ++R RR QL ++GF+V+ LL + +RD RD
Sbjct: 148 LIADGRDMGTIVFPDAPVKIFLDASSQERAHRRMLQLQERGFNVNFERLLAEIQERDNRD 207
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
+ R+++PL A +L+++ M+I QV+ Q L
Sbjct: 208 RNRSVAPLVPAADALVLDSTSMSIEQVIEQAL 239
>pdb|1SUU|A Chain A, Structure Of Dna Gyrase A C-Terminal Domain
Length = 312
Score = 155 bits (392), Expect = 2e-37, Method: Compositional matrix adjust.
Identities = 93/316 (29%), Positives = 169/316 (53%), Gaps = 7/316 (2%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYIL 596
DL+ +++V+ L+ G++K +EY+ Q GG+G + D D I NTHDY+
Sbjct: 3 DLMQKENIVVMLTKKGFLKRLSQNEYKLQGTGGKGLSSFDLNDGDEIVIALCVNTHDYLF 62
Query: 597 CFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVF 656
SN G+LY + ++I SR S+G+ I + +L ++E+I I N +D + Y+
Sbjct: 63 MISNEGKLYLINAYEIKDSSRASKGQNISELINLGDQEEILTI----KNSKDLTDDAYLL 118
Query: 657 MSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFN 716
++T+ G + + ++F + G+I + L+++DF+ A + ++ S G A FN
Sbjct: 119 LTTASGKIARFESTDFKAVKSRGVIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIFN 178
Query: 717 ENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNR 776
VR R +GV GM+L++ + +L S + +L +ENGYGKR + + ++ R
Sbjct: 179 SRDVRLTNRGTQGVCGMKLKEGDLFVKVL-SVKENPYLLIVSENGYGKRLNMSKISELKR 237
Query: 777 GTKGIISI-KTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILI 835
G G S K++K+ G VV A V+ EI+L++ +RT ++ + G+ +G+ ++
Sbjct: 238 GATGYTSYKKSDKKAGSVVDAIAVSEDDEILLVSKRSKALRTVAGKVSEQGKDARGIQVL 297
Query: 836 TVENKSKLCGVQRLCK 851
++N S L V + K
Sbjct: 298 FLDNDS-LVSVSKFIK 312
>pdb|1Q3T|A Chain A, Solution Structure And Function Of An Essential Cmp Kinase
Of Streptococcus Pneumoniae
Length = 236
Score = 151 bits (381), Expect = 3e-36, Method: Composition-based stats.
Identities = 83/210 (39%), Positives = 125/210 (59%), Gaps = 5/210 (2%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKKL 921
I IDGP +SGK TVA+++A GF YLD+GA+YR T A+ N + ++ L+ L+ +
Sbjct: 19 IAIDGPASSGKSTVAKIIAKDFGFTYLDTGAMYRAATYMALKNQLGVEEVEALLALLDQH 78
Query: 922 NYNFLGKE-----VYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGL 976
+F E V++ V++T IR +V+N+ S IA +R++L +Q + + G+
Sbjct: 79 PISFGRSETGDQLVFVGDVDITHPIRENEVTNHVSAIAAIPEVREKLVSLQQEIAQQGGI 138
Query: 977 VADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDK 1036
V DGRD+GT V P A LKIFL A + +R +RRYK+ + KG + L + RD +D
Sbjct: 139 VMDGRDIGTVVLPQAELKIFLVASVDERAERRYKENIAKGIETDLETLKKEIAARDYKDS 198
Query: 1037 TRNLSPLKCPEQAHLLNTSKMNINQVVNQI 1066
R SPLK E A L+T+ +NI +VV +I
Sbjct: 199 HRETSPLKQAEDAVYLDTTGLNIQEVVEKI 228
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 140 bits (352), Expect = 7e-33, Method: Composition-based stats.
Identities = 62/91 (68%), Positives = 79/91 (86%)
Query: 1332 WIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLND 1391
W+ ++ RYP GT+L G+VTNLTDYG FVEIE+G+EGLVH+SEMDW NKN+ PSK+V + D
Sbjct: 21 WVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGD 80
Query: 1392 TVEIMILEINEERRRISLGMKQCKDNPWENF 1422
VE+M+L+I+EERRRISLG+KQCK NPW+ F
Sbjct: 81 VVEVMVLDIDEERRRISLGLKQCKANPWQQF 111
Score = 65.5 bits (158), Expect = 2e-10, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 54/79 (68%), Gaps = 2/79 (2%)
Query: 1256 EGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAW-RRVKHPSEILTIGQDISTKILKY 1313
EG + G V N+TDYG F+++ G++GL+H++++ W + HPS+++ +G + +L
Sbjct: 30 EGTKLTGRVTNLTDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDI 89
Query: 1314 DQEKNRVSLGMKQLGIDPW 1332
D+E+ R+SLG+KQ +PW
Sbjct: 90 DEERRRISLGLKQCKANPW 108
Score = 55.8 bits (133), Expect = 2e-07, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 46/70 (65%)
Query: 1440 TDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIK 1499
TD+G F+ ++ ++GL+H+S++ WT+ + GD +E ++L ID E+ RISLG+K
Sbjct: 42 TDYGCFVEIEEGVEGLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLK 101
Query: 1500 QLEGDPFNNY 1509
Q + +P+ +
Sbjct: 102 QCKANPWQQF 111
>pdb|2H92|A Chain A, Crystal Structure Of Staphylococcus Aureus Cytidine
Monophosphate Kinase In Complex With Cytidine-5'-
Monophosphate
pdb|2H92|B Chain B, Crystal Structure Of Staphylococcus Aureus Cytidine
Monophosphate Kinase In Complex With Cytidine-5'-
Monophosphate
pdb|2H92|C Chain C, Crystal Structure Of Staphylococcus Aureus Cytidine
Monophosphate Kinase In Complex With Cytidine-5'-
Monophosphate
Length = 219
Score = 129 bits (323), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 72/211 (34%), Positives = 120/211 (56%), Gaps = 9/211 (4%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKKL 921
I +DGP A+GK T+A+ VAS+L Y+D+GA+YR +T ++L+ + L+ +
Sbjct: 6 IALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTY----KYLKLNKTEDFAKLVDQT 61
Query: 922 NYNFL-----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGL 976
+ G+ V L+ +VT +RN V+ + S +A + +R K Q + G+
Sbjct: 62 TLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGI 121
Query: 977 VADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDK 1036
V DGRD+GT V PDA LK+++ A +++R +RRYK +G + DL ++ RD D
Sbjct: 122 VMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDM 181
Query: 1037 TRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
R +SPL+ + A L+T+ +I +V ++IL
Sbjct: 182 NREISPLRKADDAVTLDTTGKSIEEVTDEIL 212
>pdb|3R8C|A Chain A, Crystal Structure Of Cytidylate Kinase (Cmk) From
Mycobacterium Abscessus
pdb|3R8C|B Chain B, Crystal Structure Of Cytidylate Kinase (Cmk) From
Mycobacterium Abscessus
pdb|4DIE|A Chain A, Crystal Structure Of A Cytidylate Kinase Cmk From
Mycobacterium Abscessus Bound To
Cytidine-5'-Monophosphate
pdb|4DIE|B Chain B, Crystal Structure Of A Cytidylate Kinase Cmk From
Mycobacterium Abscessus Bound To
Cytidine-5'-Monophosphate
pdb|4DIE|C Chain C, Crystal Structure Of A Cytidylate Kinase Cmk From
Mycobacterium Abscessus Bound To
Cytidine-5'-Monophosphate
pdb|4DIE|D Chain D, Crystal Structure Of A Cytidylate Kinase Cmk From
Mycobacterium Abscessus Bound To
Cytidine-5'-Monophosphate
Length = 228
Score = 125 bits (314), Expect = 2e-28, Method: Composition-based stats.
Identities = 73/217 (33%), Positives = 120/217 (55%), Gaps = 5/217 (2%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
V+ +DGP+ +GK +VA+ +A +LG YLD+GA+YR+VTL + + L + + +
Sbjct: 6 VVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDLTDPAAIAAATDQ 65
Query: 921 LNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG- 975
+ + + L G +V+ IR +V+ S ++ +R+ L + Q + + G
Sbjct: 66 VPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVSAVPAVRERLVRQQRELAESSGA 125
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
+V +GRD+GT V PDA +KI+LTA + R +RR Q + G +L ++ +RD D
Sbjct: 126 VVVEGRDIGTVVLPDADVKIYLTASAQARAQRRNAQNVSGGGDDEYEKVLADVQRRDHLD 185
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQILDCFAT 1072
TR +SPL+ E A ++TS M QVV +LD T
Sbjct: 186 STRAVSPLRPAEDALEVDTSDMTQEQVVAHLLDLVRT 222
>pdb|3R20|A Chain A, Crystal Structure Of Cytidylate Kinase From Mycobacterium
Smegmatis
Length = 233
Score = 125 bits (314), Expect = 2e-28, Method: Composition-based stats.
Identities = 72/214 (33%), Positives = 119/214 (55%), Gaps = 7/214 (3%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
V+ +DGP +GK +V++ +A LG YLD+GA+YR+ TL+ + L + +
Sbjct: 11 VVAVDGPAGTGKSSVSRGLARALGARYLDTGAMYRIATLAVLRAGADLTDPAAIEKAAAD 70
Query: 921 LNYNFLGKE-----VYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPG 975
+G + +L G +V++ IR + V+ S ++ +R L IQ K G
Sbjct: 71 AEIG-VGSDPDVDAAFLAGEDVSSEIRGDAVTGAVSAVSAVPAVRTRLVDIQRKLATEGG 129
Query: 976 -LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIR 1034
+V +GRD+GT V PDA +KIFLTA ++R +RR Q + G + +L ++ +RD
Sbjct: 130 RVVVEGRDIGTVVLPDADVKIFLTASAEERARRRNAQNVANGLPDDYATVLADVQRRDHL 189
Query: 1035 DKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
D TR +SPL+ + A +++TS M+ QV+ +LD
Sbjct: 190 DSTRPVSPLRAADDALVVDTSDMDQAQVIAHLLD 223
>pdb|1WP5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Dna
Topoisomerase Iv
Length = 323
Score = 124 bits (311), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 82/313 (26%), Positives = 156/313 (49%), Gaps = 11/313 (3%)
Query: 539 IASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCF 598
+AS+D+++T++ GY+K + Y A + KD D + NT D +L F
Sbjct: 2 VASEDVIVTVTKDGYVKRTSLRSYAAS-----NGQDFAXKDTDRLLAXLEXNTKDVLLLF 56
Query: 599 SNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMS 658
+N G + V ++P G+ I N+ + E+I +P++ DF N Y
Sbjct: 57 TNKGNYLYCPVHELPDIRWKDLGQHIANIIPIDRDEEIIKAIPIN----DFELNGYFLFV 112
Query: 659 TSLGIVKKTLLSNFSNPRKSG-IIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNE 717
T G VKKT L ++ R S + +NL N+D ++ LTDG ++ L + +G A+ F+E
Sbjct: 113 TRNGXVKKTELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGXNELFLVTHNGYALWFDE 172
Query: 718 NSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRG 777
+ V +G A GV G L++ +++ + ++ +S++ AT+ G K+ + E+ K R
Sbjct: 173 SEVSIVGVRAAGVKGXNLKEGDYIVSGQLITSKDESIVVATQRGAVKKXKLTEFEKATRA 232
Query: 778 TKGIISIKTNKRNGKVVAATLVNRYHEIMLITTGGILIRT-RVSEIRKMGRSTQGVILIT 836
+G++ ++ K N ++ +V + + + + T I T +V +IR R + G ++
Sbjct: 233 KRGVVILRELKANPHRISGFVVAQDSDTIYLQTEKSFIETIKVGDIRFSDRYSNGSFVLD 292
Query: 837 VENKSKLCGVQRL 849
E ++ V ++
Sbjct: 293 EEENGRVISVWKV 305
>pdb|4ELY|A Chain A, Ccdbvfi:gyra14ec
pdb|4ELY|B Chain B, Ccdbvfi:gyra14ec
Length = 156
Score = 100 bits (250), Expect = 5e-21, Method: Composition-based stats.
Identities = 52/144 (36%), Positives = 90/144 (62%), Gaps = 1/144 (0%)
Query: 355 ILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIEST 414
++ R + RRTIFELRKAR+ AHILE L +AL NID I++IR TP EAK ++ +
Sbjct: 14 LVPRGSHMTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANP 73
Query: 415 WNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKK 474
W L +V+ ++ + + +++ +Y L++ QAQ IL + LQ+LT +E +K
Sbjct: 74 WQLGNVAAMLERAGDDAARPEWLEPEFGVRDG-LYYLTEQQAQAILDLRLQKLTGLEHEK 132
Query: 475 IINKYENVIKKVIDLTDILSNSKR 498
++++Y+ ++ ++ +L IL ++ R
Sbjct: 133 LLDEYKELLDQIAELLRILGSADR 156
>pdb|4ELZ|A Chain A, Ccdbvfi:gyra14vfi
pdb|4ELZ|B Chain B, Ccdbvfi:gyra14vfi
Length = 153
Score = 100 bits (248), Expect = 1e-20, Method: Composition-based stats.
Identities = 55/144 (38%), Positives = 92/144 (63%), Gaps = 7/144 (4%)
Query: 355 ILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIEST 414
++ R + RRTIFELRKAR+ AHILEGL +AL NID I++I++ TP EAK +I
Sbjct: 14 LVPRGSHMTRRTIFELRKARDRAHILEGLALALANIDEIIELIKNAPTPAEAKEGLISRG 73
Query: 415 WNLPDVSKII---GFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNME 471
W+L +V+ ++ G + + + I + + Y L++ QAQ IL++ L RLT +E
Sbjct: 74 WDLGNVASMLERAGTDAARPDWLEPEFGIREGK----YFLTEQQAQAILELRLHRLTGLE 129
Query: 472 QKKIINKYENVIKKVIDLTDILSN 495
+KI+++Y+ ++ ++ +L IL++
Sbjct: 130 HEKILDEYKALLDEIAELMHILAS 153
>pdb|1X75|A Chain A, Ccdb:gyra14 Complex
pdb|1X75|B Chain B, Ccdb:gyra14 Complex
Length = 132
Score = 97.4 bits (241), Expect = 5e-20, Method: Composition-based stats.
Identities = 50/132 (37%), Positives = 84/132 (63%), Gaps = 1/132 (0%)
Query: 364 RRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKI 423
RRTIFELRKAR+ AHILE L +AL NID I++IR TP EAK ++ + W L +V+ +
Sbjct: 2 RRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAM 61
Query: 424 IGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVI 483
+ + + +++ +Y L++ QAQ IL + LQ+LT +E +K++++Y+ ++
Sbjct: 62 LERAGDDAARPEWLEPEFGVRDG-LYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELL 120
Query: 484 KKVIDLTDILSN 495
++ +L IL +
Sbjct: 121 DQIAELLRILGS 132
>pdb|3AKC|A Chain A, Crystal Structure Of Cmp Kinase In Complex With Cdp And Adp
From Thermus Thermophilus Hb8
pdb|3AKD|A Chain A, Crystal Structure Of Cmp Kinase In Complex With Cdp From
Thermus Thermophilus Hb8
pdb|3AKE|A Chain A, Crystal Structure Of Cmp Kinase In Complex With Cmp From
Thermus Thermophilus Hb8
Length = 208
Score = 95.9 bits (237), Expect = 2e-19, Method: Composition-based stats.
Identities = 73/212 (34%), Positives = 120/212 (56%), Gaps = 17/212 (8%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
++TIDGP+ASGK +VA+ VA+ LG YL SG LYR A+ + +E L+ L++
Sbjct: 4 IVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLEG 63
Query: 921 LNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKF-PG 975
L L G V +G ++T+ + +V S +A+ +R + + ++ P
Sbjct: 64 LGVRLLAQAEGNRVLADGEDLTSFLHTPEVDRVVSAVARLPGVRAW---VNRRLKEVPPP 120
Query: 976 LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRD 1035
VA+GRDMGT VFP+A K +LTA + R RR ++ Q + ++L +L++RD RD
Sbjct: 121 FVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQ-----AYEEVLRDLLRRDERD 175
Query: 1036 KTRNLSPLKCPEQAHLLNTSKMNINQVVNQIL 1067
K ++ +P P+ A +L+T M +++VV +L
Sbjct: 176 KAQS-AP--APD-ALVLDTGGMTLDEVVAWVL 203
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 95.5 bits (236), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 83/318 (26%), Positives = 147/318 (46%), Gaps = 36/318 (11%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGET--MGKYHPHGDVSIYDAL 89
R++P + DGLKP R+VLF + N+ + VK A++ G M YH HG++S+ +
Sbjct: 283 RSIPSMVDGLKPGQRKVLFTCFKRND---KREVKVAQLAGSVAEMSSYH-HGEMSLMMTI 338
Query: 90 VRMAQSF--SLRCTLVDGQGNFGS--IDGDSAAAMRYTECRLNKISNELLIDLDKETIDF 145
+ +AQ+F S L+ G FG+ G +A+ RY L+ ++ L D T+ F
Sbjct: 339 INLAQNFVGSNNLNLLQPIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDDHTLKF 398
Query: 146 ISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSI 205
+ + D + EP IP +LING+ GI G + IP ++ E+++ + ++ E
Sbjct: 399 LYD-DNQRVEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEE--- 454
Query: 206 NDLIKIIPAPDFPTAGIIYG-LSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDEL 264
P P P+ G + + Y G V I N T I I EL
Sbjct: 455 -------PLPMLPSYKNFKGTIEELAPNQYVISGEVAIL-----------NSTTIEISEL 496
Query: 265 PYQVNKKSLLEKISQLV---KEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLY 321
P + ++ E++ + + EK I++ R+ + ++ V+++ ++ E L+
Sbjct: 497 PVRTWTQTYKEQVLEPMLNGTEKTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVGLH 556
Query: 322 KQTQLQNTFGMNMLALVN 339
K +LQ + N + L +
Sbjct: 557 KVFKLQTSLTCNSMVLFD 574
>pdb|3QX3|A Chain A, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
pdb|3QX3|B Chain B, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
Length = 803
Score = 89.0 bits (219), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 82/319 (25%), Positives = 144/319 (45%), Gaps = 38/319 (11%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGET--MGKYHPHGDVSIYDAL 89
R++P + DG KP R+VLF + N+ + VK A++ G M YH HG+ ++ +
Sbjct: 311 RSIPSLVDGFKPGQRKVLFTCFKRND---KREVKVAQLAGSVAEMSAYH-HGEQALMMTI 366
Query: 90 VRMAQSF--SLRCTLVDGQGNFGS--IDGDSAAAMRYTECRLNKISNELLIDLDKETIDF 145
V +AQ+F S L+ G FG+ G AA+ RY L+ ++ L +D + F
Sbjct: 367 VNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKF 426
Query: 146 ISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSI 205
+ + D + EP IP +LING+ GI G A +P ++ E+++ V +L
Sbjct: 427 LYD-DNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDG----- 480
Query: 206 NDLIKIIPAPDFPTAGIIYG-LSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDEL 264
+ P P P G + + Y G + + +R + I EL
Sbjct: 481 -----LDPHPMLPNYKNFKGTIQELGQNQYAVSGEIFVV-----------DRNTVEITEL 524
Query: 265 PY----QVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKL 320
P QV K+ +LE + +K IS+ ++ + ++ V+++ ++ + L
Sbjct: 525 PVRTWTQVYKEQVLEPMLNGT-DKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGL 583
Query: 321 YKQTQLQNTFGMNMLALVN 339
+K +LQ T N + L +
Sbjct: 584 HKVFKLQTTLTCNSMVLFD 602
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/175 (32%), Positives = 89/175 (50%), Gaps = 7/175 (4%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
R++P+V DG KP R+VL+ + N + A V E YH HG+ S+ ++
Sbjct: 272 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 329
Query: 92 MAQSF--SLRCTLVDGQGNFG--SIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFIS 147
+AQ+F S L+ G FG + G AAA RY LNK++ ++ D +I
Sbjct: 330 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQ 389
Query: 148 NYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE 202
D K EP +P +L+NG+ GI G +T IPP N E+I + +++++ E
Sbjct: 390 E-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 443
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 88.6 bits (218), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 57/175 (32%), Positives = 89/175 (50%), Gaps = 7/175 (4%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
R++P+V DG KP R+VL+ + N + A V E YH HG+ S+ ++
Sbjct: 282 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 339
Query: 92 MAQSF--SLRCTLVDGQGNFG--SIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFIS 147
+AQ+F S L+ G FG + G AAA RY LNK++ ++ D +I
Sbjct: 340 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQ 399
Query: 148 NYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE 202
D K EP +P +L+NG+ GI G +T IPP N E+I + +++++ E
Sbjct: 400 E-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 453
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 84.7 bits (208), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 56/176 (31%), Positives = 89/176 (50%), Gaps = 8/176 (4%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
R++P+V DG KP R+VL+ + N + A V E YH HG+ S+ ++
Sbjct: 647 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 704
Query: 92 MAQSF--SLRCTLVDGQGNFGSIDG---DSAAAMRYTECRLNKISNELLIDLDKETIDFI 146
+AQ+F S L+ G FG+ D+AAA Y LNK++ ++ D +I
Sbjct: 705 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRKIFHPADDPLYKYI 764
Query: 147 SNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE 202
D K EP +P +L+NG+ GI G +T IPP N E+I + +++++ E
Sbjct: 765 QE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 819
>pdb|3L4J|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Apo
pdb|3L4K|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Metal-Bound
Length = 722
Score = 84.7 bits (208), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 56/176 (31%), Positives = 89/176 (50%), Gaps = 8/176 (4%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
R++P+V DG KP R+VL+ + N + A V E YH HG+ S+ ++
Sbjct: 270 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 327
Query: 92 MAQSF--SLRCTLVDGQGNFGSI---DGDSAAAMRYTECRLNKISNELLIDLDKETIDFI 146
+AQ+F S L+ G FG+ D+AAA Y LNK++ ++ D +I
Sbjct: 328 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRKIFHPADDPLYKYI 387
Query: 147 SNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE 202
D K EP +P +L+NG+ GI G +T IPP N E+I + +++++ E
Sbjct: 388 QE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 442
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 84.7 bits (208), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 56/176 (31%), Positives = 89/176 (50%), Gaps = 8/176 (4%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
R++P+V DG KP R+VL+ + N + A V E YH HG+ S+ ++
Sbjct: 651 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 708
Query: 92 MAQSF--SLRCTLVDGQGNFGSIDG---DSAAAMRYTECRLNKISNELLIDLDKETIDFI 146
+AQ+F S L+ G FG+ D+AAA Y LNK++ ++ D +I
Sbjct: 709 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRKIFHPADDPLYKYI 768
Query: 147 SNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE 202
D K EP +P +L+NG+ GI G +T IPP N E+I + +++++ E
Sbjct: 769 QE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 823
>pdb|3NO0|A Chain A, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|B Chain B, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
pdb|3NO0|C Chain C, Aquifex Aeolicus Type Iia Topoisomerase C-Terminal Domain
Length = 276
Score = 70.5 bits (171), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 60/201 (29%), Positives = 91/201 (45%), Gaps = 24/201 (11%)
Query: 583 INQLFIANTHDYILCFSNYGRLYWLKVWQIPQGSR---NSRGKPIINMFSLKNKEKITVI 639
+N L + T L SN GR+YW+ Q QGS+ SR + I+ F +EK
Sbjct: 27 VNILRVPFTEGLFLV-SNRGRVYWIAGSQALQGSKVSLKSREEKIVGAFI---REKF--- 79
Query: 640 LPLSNNKRDFPKNNYVFMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDG 699
N + ++T G VKK L+ F + G+ + L+ D ++ A +
Sbjct: 80 ------------GNRLLLATKKGYVKKIPLAEFEY-KAQGMPIIKLTEGDEVVSIASSVD 126
Query: 700 SYDIMLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATE 759
I+LF+ G+ RF+ V ARGV G++LEK + L + N + +L T
Sbjct: 127 ETHILLFTKKGRVARFSVREVPPSTPGARGVQGIKLEKNDETSGLRIWNGEPY-LLVITA 185
Query: 760 NGYGKRTLIKEYTKHNRGTKG 780
G K+ +E K NRG KG
Sbjct: 186 KGRVKKISHEEIPKTNRGVKG 206
Score = 32.7 bits (73), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 76/165 (46%), Gaps = 21/165 (12%)
Query: 552 GYIKSQPISE--YRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYWLKV 609
GY+K P++E Y+AQ G + + D + + + +IL F+ GR+ V
Sbjct: 90 GYVKKIPLAEFEYKAQ-----GMPIIKLTEGDEVVSIASSVDETHILLFTKKGRVARFSV 144
Query: 610 WQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKTLL 669
++P + +RG I + KN E ++ R + Y+ + T+ G VKK +
Sbjct: 145 REVPPSTPGARGVQGIKL--EKNDE--------TSGLRIWNGEPYLLVITAKGRVKK--I 192
Query: 670 SNFSNPRKS-GIIAVNLS-NEDFLIGAALTDGSYDIMLFSDSGKA 712
S+ P+ + G+ +S +D L+ ++++ + +GKA
Sbjct: 193 SHEEIPKTNRGVKGTEVSGTKDTLVDLIPIKEEVELLITTKNGKA 237
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 57/84 (67%), Gaps = 4/84 (4%)
Query: 1246 ERQKLIETLKE---GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILT 1301
E Q+ +E+LK+ G ++GVV N+T++GAF+D+G DGL+HI+ ++ + VK P E++
Sbjct: 641 EFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVK 700
Query: 1302 IGQDISTKILKYDQEKNRVSLGMK 1325
G + K+++ D +NRV L M+
Sbjct: 701 AGDIVKVKVMEVDIPRNRVGLSMR 724
Score = 52.8 bits (125), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/80 (40%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEI 1400
G L G VTN+T++GAFV+I +GLVHIS + K V P ++V+ D V++ ++E+
Sbjct: 655 GMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALS--EKFVKDPYEVVKAGDIVKVKVMEV 712
Query: 1401 NEERRRISLGMKQCKDNPWE 1420
+ R R+ L M+ D P E
Sbjct: 713 DIPRNRVGLSMRMS-DTPGE 731
Score = 37.7 bits (86), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 7/63 (11%)
Query: 1440 TDFGIFIGLDGNIDGLIHLSDLSW---TDPGEEIIRNFKKGDEIEAIILSIDVEKERISL 1496
T+FG F+ + + DGL+H+S LS DP E + K GD ++ ++ +D+ + R+ L
Sbjct: 666 TNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVV----KAGDIVKVKVMEVDIPRNRVGL 721
Query: 1497 GIK 1499
++
Sbjct: 722 SMR 724
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 65.5 bits (158), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 33/84 (39%), Positives = 57/84 (67%), Gaps = 4/84 (4%)
Query: 1246 ERQKLIETLKE---GCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILT 1301
E Q+ +E+LK+ G ++GVV N+T++GAF+D+G DGL+HI+ ++ + VK P E++
Sbjct: 642 EFQEGVESLKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVK 701
Query: 1302 IGQDISTKILKYDQEKNRVSLGMK 1325
G + K+++ D +NRV L M+
Sbjct: 702 AGDIVKVKVMEVDIPRNRVGLSMR 725
Score = 52.8 bits (125), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/80 (40%), Positives = 49/80 (61%), Gaps = 4/80 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEI 1400
G L G VTN+T++GAFV+I +GLVHIS + K V P ++V+ D V++ ++E+
Sbjct: 656 GMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALS--EKFVKDPYEVVKAGDIVKVKVMEV 713
Query: 1401 NEERRRISLGMKQCKDNPWE 1420
+ R R+ L M+ D P E
Sbjct: 714 DIPRNRVGLSMRMS-DTPGE 732
Score = 37.7 bits (86), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 7/63 (11%)
Query: 1440 TDFGIFIGLDGNIDGLIHLSDLSW---TDPGEEIIRNFKKGDEIEAIILSIDVEKERISL 1496
T+FG F+ + + DGL+H+S LS DP E + K GD ++ ++ +D+ + R+ L
Sbjct: 667 TNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVV----KAGDIVKVKVMEVDIPRNRVGL 722
Query: 1497 GIK 1499
++
Sbjct: 723 SMR 725
>pdb|2KHJ|A Chain A, Nmr Structure Of The Domain 6 Of The E. Coli Ribosomal
Protein S1
Length = 109
Score = 55.1 bits (131), Expect = 3e-07, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 5/79 (6%)
Query: 1506 FNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGE 1561
FNN+V +N KG++V G + ++D KGA ++L++ VEGYLR SE + L +G+
Sbjct: 22 FNNWVALNKKGAIVTGKVTAVDA-KGATVELADGVEGYLRASEASRDRVEDATLVLSVGD 80
Query: 1562 NIDVLTVLIDHKTRYIQLS 1580
++ +D K R I LS
Sbjct: 81 EVEAKFTGVDRKNRAISLS 99
Score = 35.4 bits (80), Expect = 0.28, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 1332 WIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLND 1391
W+ L+ +G + GKVT + GA VE+ G+EG + SE ++ + ++ + D
Sbjct: 25 WVALN---KKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASR-DRVEDATLVLSVGD 80
Query: 1392 TVEIMILEINEERRRISLGMK 1412
VE ++ + R ISL ++
Sbjct: 81 EVEAKFTGVDRKNRAISLSVR 101
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 53.1 bits (126), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 52/80 (65%), Gaps = 2/80 (2%)
Query: 1248 QKLIETLKEGCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEILTIGQDI 1306
+++ ++ G G V I D+GAF+ +GG +GL+HI+ IA +RV+ ++ L +GQ++
Sbjct: 619 EEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEV 678
Query: 1307 STKILKYDQEKNRVSLGMKQ 1326
K+L+ D++ R+ L +K+
Sbjct: 679 PVKVLEVDRQ-GRIRLSIKE 697
Score = 46.6 bits (109), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 4/72 (5%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTP-SKIVQLNDTVEIMILEINEERR 1405
GKVT + D+GAFV I G EGLVHIS++ +K V + +Q+ V + +LE++ +
Sbjct: 633 GKVTRIVDFGAFVAIGGGKEGLVHISQI--ADKRVEKVTDYLQMGQEVPVKVLEVDRQ-G 689
Query: 1406 RISLGMKQCKDN 1417
RI L +K+ +
Sbjct: 690 RIRLSIKEATEQ 701
Score = 35.0 bits (79), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1441 DFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQ 1500
DFG F+ + G +GL+H+S ++ E++ + G E+ +L +D + RI L IK+
Sbjct: 640 DFGAFVAIGGGKEGLVHISQIADKRV-EKVTDYLQMGQEVPVKVLEVD-RQGRIRLSIKE 697
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 52.8 bits (125), Expect = 1e-06, Method: Composition-based stats.
Identities = 21/24 (87%), Positives = 23/24 (95%)
Query: 1440 TDFGIFIGLDGNIDGLIHLSDLSW 1463
TDFGIFIGLDG IDGL+HLSD+SW
Sbjct: 73 TDFGIFIGLDGGIDGLVHLSDISW 96
Score = 48.9 bits (115), Expect = 2e-05, Method: Composition-based stats.
Identities = 21/41 (51%), Positives = 33/41 (80%), Gaps = 1/41 (2%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVK 1294
++G V+G +K+ITD+G FI L GGIDGL+H++DI+W + +
Sbjct: 60 QQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQAE 100
Score = 46.2 bits (108), Expect = 2e-04, Method: Composition-based stats.
Identities = 16/36 (44%), Positives = 29/36 (80%)
Query: 1341 RGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW 1376
+G R+ GK+ ++TD+G F+ ++ GI+GLVH+S++ W
Sbjct: 61 QGDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISW 96
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 51.2 bits (121), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/71 (38%), Positives = 47/71 (66%), Gaps = 2/71 (2%)
Query: 1257 GCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G G V I D+GAF+ +GG +GL+HI+ IA +RV+ ++ L +GQ++ K+L+ D+
Sbjct: 6 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDR 65
Query: 1316 EKNRVSLGMKQ 1326
+ R+ L +K+
Sbjct: 66 Q-GRIRLSIKE 75
Score = 45.1 bits (105), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/68 (41%), Positives = 43/68 (63%), Gaps = 4/68 (5%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTP-SKIVQLNDTVEIMILEINEERR 1405
GKVT + D+GAFV I G EGLVHIS++ +K V + +Q+ V + +LE++ +
Sbjct: 11 GKVTRIVDFGAFVAIGGGKEGLVHISQI--ADKRVEKVTDYLQMGQEVPVKVLEVDRQ-G 67
Query: 1406 RISLGMKQ 1413
RI L +K+
Sbjct: 68 RIRLSIKE 75
Score = 35.0 bits (79), Expect = 0.36, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 1441 DFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQ 1500
DFG F+ + G +GL+H+S ++ E++ + G E+ +L +D + RI L IK+
Sbjct: 18 DFGAFVAIGGGKEGLVHISQIA-DKRVEKVTDYLQMGQEVPVKVLEVD-RQGRIRLSIKE 75
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 51.2 bits (121), Expect = 5e-06, Method: Composition-based stats.
Identities = 29/89 (32%), Positives = 54/89 (60%), Gaps = 11/89 (12%)
Query: 1335 LSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW-----INKNVTPSKIVQL 1389
++ ++ G+ GKVT L YGAFV +++ +GLVHISE+ IN++++ +
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLS------V 54
Query: 1390 NDTVEIMILEINEERRRISLGMKQCKDNP 1418
D V++ +L ++EE+ +ISL ++ + P
Sbjct: 55 GDEVQVKVLAVDEEKGKISLSIRATQAAP 83
Score = 46.2 bits (108), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 1257 GCTVKGVVKNITDYGAFIDLGG-IDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G G V + YGAF+ L GL+HI+++ VK +E L++G ++ K+L D+
Sbjct: 8 GSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVDE 67
Query: 1316 EKNRVSLGMKQLGIDP 1331
EK ++SL ++ P
Sbjct: 68 EKGKISLSIRATQAAP 83
Score = 42.7 bits (99), Expect = 0.002, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 1442 FGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQL 1501
+G F+ LD GL+H+S+++ ++I + GDE++ +L++D EK +ISL I+
Sbjct: 21 YGAFVALDEETQGLVHISEVT-HGFVKDINEHLSVGDEVQVKVLAVDEEKGKISLSIRAT 79
Query: 1502 EGDP 1505
+ P
Sbjct: 80 QAAP 83
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 1262 GVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
G V + D+GAF++ G DGL+H++ I+ RV PS++L GQ + K+L +D ++ +
Sbjct: 643 GKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD-DRGKT 701
Query: 1321 SLGMK 1325
L MK
Sbjct: 702 KLSMK 706
Score = 37.7 bits (86), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEINEERR 1405
GKV + D+GAFV +GLVH+S++ N+ V PS +++ V++ +L + +R
Sbjct: 643 GKVVKVVDFGAFVNFFGAKDGLVHVSQIS--NERVAKPSDVLKEGQMVKVKLLGFD-DRG 699
Query: 1406 RISLGMKQCKDNPWENF 1422
+ L MK E+
Sbjct: 700 KTKLSMKVVDQETGEDL 716
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQ 1315
G G V + D+GAF++ G DGL+H++ I+ RV PS++L GQ + K+L +D
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD- 696
Query: 1316 EKNRVSLGMK 1325
++ + L MK
Sbjct: 697 DRGKTKLSMK 706
Score = 37.7 bits (86), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEINEERR 1405
GKV + D+GAFV +GLVH+S++ N+ V PS +++ V++ +L + +R
Sbjct: 643 GKVVKVVDFGAFVNFFGAKDGLVHVSQIS--NERVAKPSDVLKEGQMVKVKLLGFD-DRG 699
Query: 1406 RISLGMKQCKDNPWENF 1422
+ L MK E+
Sbjct: 700 KTKLSMKVVDQETGEDL 716
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 50.4 bits (119), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 1262 GVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
G V + D+GAF++ G DGL+H++ I+ RV PS++L GQ + K+L +D ++ +
Sbjct: 634 GKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD-DRGKT 692
Query: 1321 SLGMK 1325
L MK
Sbjct: 693 KLSMK 697
Score = 37.7 bits (86), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 1347 GKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT-PSKIVQLNDTVEIMILEINEERR 1405
GKV + D+GAFV +GLVH+S++ N+ V PS +++ V++ +L + +R
Sbjct: 634 GKVVKVVDFGAFVNFFGAKDGLVHVSQIS--NERVAKPSDVLKEGQMVKVKLLGFD-DRG 690
Query: 1406 RISLGMKQCKDNPWENF 1422
+ L MK E+
Sbjct: 691 KTKLSMKVVDQETGEDL 707
>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Hypothetical Protein Flj11067
Length = 119
Score = 49.3 bits (116), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 5/84 (5%)
Query: 1247 RQKLIETLKEGCTV-KGVVKNITDYGAFIDLGGI--DGLLHITDIAWRRVKHPSEILTIG 1303
R + +E L T+ +G V +TDYGAFI + G GL+H T ++ RV PSEI+ +G
Sbjct: 12 RPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVG 71
Query: 1304 QDISTKILKYDQEKNR--VSLGMK 1325
+ K++ + + +R VSL MK
Sbjct: 72 DKVWVKLIGREMKNDRIKVSLSMK 95
Score = 40.8 bits (94), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 4/73 (5%)
Query: 1343 TRLLGKVTNLTDYGAFVEIEKG-IEGLVHISEMDWINKNVTPSKIVQLNDTVEIMIL--E 1399
T G+V +TDYGAF++I +GLVH + M + PS+IV + D V + ++ E
Sbjct: 24 TIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVD-KPSEIVDVGDKVWVKLIGRE 82
Query: 1400 INEERRRISLGMK 1412
+ +R ++SL MK
Sbjct: 83 MKNDRIKVSLSMK 95
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 45.4 bits (106), Expect = 3e-04, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 1248 QKLIETLKEGCTVKGVVKNITDYGAFIDLG---GIDGLLHITDIAWRRVKHPSEILTIGQ 1304
+K E +EG V VK I +YGAF++L G + +HI+++A V++ + L GQ
Sbjct: 3 RKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQ 62
Query: 1305 DISTKILKYDQEKNRVSLGMKQL 1327
+ K+++ D K + L ++++
Sbjct: 63 KVVAKVIRVDPRKGHIDLSLRRV 85
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 44.7 bits (104), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 3/79 (3%)
Query: 1252 ETLKEGCTVKGVVKNITDYGAFIDLG---GIDGLLHITDIAWRRVKHPSEILTIGQDIST 1308
E +EG V VK I +YGAF++L G + +HI+++A V++ + L GQ +
Sbjct: 6 EYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVA 65
Query: 1309 KILKYDQEKNRVSLGMKQL 1327
K+++ D K + L ++++
Sbjct: 66 KVIRVDPRKGHIDLSLRRV 84
>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2
Length = 308
Score = 44.7 bits (104), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 51/82 (62%), Gaps = 3/82 (3%)
Query: 1264 VKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
V++I + GA++ L I+G++H+++++ RR++ ++++ IG++ K+++ D+EK +
Sbjct: 21 VRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIRVDKEKGYI 80
Query: 1321 SLGMKQLGIDPWIGLSFRYPRG 1342
L +++ + I ++ +
Sbjct: 81 DLSKRRVSPEEAIKCEDKFTKS 102
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 40.0 bits (92), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGLLHITDI----AWRRVKHPSEILTIGQDISTKIL 1311
G + G V T +GAF+ L G DGLLHI+ I +RV++ ++L +GQ + +I
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 1312 KYDQEKNRVSL 1322
+ D + ++SL
Sbjct: 728 EIDS-RGKLSL 737
Score = 38.1 bits (87), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 8/73 (10%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWIN-----KNVTPSKIVQLNDTVEIM 1396
G R+LG V T +GAFV + G +GL+HIS++ + +NV ++ + V++
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENV--EDVLGVGQKVQVE 725
Query: 1397 ILEINEERRRISL 1409
I EI+ R ++SL
Sbjct: 726 IAEID-SRGKLSL 737
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 39.7 bits (91), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 1257 GCTVKGVVKNITDYGAFIDL-GGIDGLLHITDI----AWRRVKHPSEILTIGQDISTKIL 1311
G + G V T +GAF+ L G DGLLHI+ I +RV++ ++L +GQ + +I
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 1312 KYDQEKNRVSL 1322
+ D + ++SL
Sbjct: 728 EIDS-RGKLSL 737
Score = 38.1 bits (87), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 8/73 (10%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWIN-----KNVTPSKIVQLNDTVEIM 1396
G R+LG V T +GAFV + G +GL+HIS++ + +NV ++ + V++
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENV--EDVLGVGQKVQVE 725
Query: 1397 ILEINEERRRISL 1409
I EI+ R ++SL
Sbjct: 726 IAEID-SRGKLSL 737
>pdb|2AHO|B Chain B, Structure Of The Archaeal Initiation Factor Eif2 Alpha-
Gamma Heterodimer From Sulfolobus Solfataricus Complexed
With Gdpnp
pdb|3CW2|C Chain C, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|D Chain D, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|G Chain G, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3CW2|H Chain H, Crystal Structure Of The Intact Archaeal Translation
Initiation Factor 2 From Sulfolobus Solfataricus .
pdb|3V11|B Chain B, Structure Of The Ternary Initiation Complex
Aif2:gdpnp:methionylated Initiator Trna
Length = 266
Score = 39.3 bits (90), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 44/78 (56%), Gaps = 3/78 (3%)
Query: 1256 EGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
EG + VK + DYG+++ L GG+ L ++++ + VK+ ++L + + K+++
Sbjct: 11 EGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVIR 70
Query: 1313 YDQEKNRVSLGMKQLGID 1330
D+ K V + +K++ D
Sbjct: 71 VDRRKGTVDVSLKKVTDD 88
Score = 33.5 bits (75), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 47/93 (50%), Gaps = 8/93 (8%)
Query: 1162 SLEKAMESGEIITGTINGKVKGGLTVLTN---GLKAFLPGSLVDIRPVKDTTPF--EGKT 1216
S K GEI+ T+ G V + GL+AFLP S V + VK+ E +
Sbjct: 4 SRSKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRK 63
Query: 1217 MDFKVIKLDRKRNNVVLSHRAVIEESMGEERQK 1249
+ KVI++DR++ V +S + V ++ E R+K
Sbjct: 64 VIVKVIRVDRRKGTVDVSLKKVTDD---ERRKK 93
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|T Chain T, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|E Chain E, Rnap At 3.2ang
pdb|4B1O|E Chain E, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|T Chain T, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 180
Score = 37.7 bits (86), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 1266 NITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL-KYDQEKNRV-SLG 1323
+ +YG F++LG +DGL+HI+ I +K+ + I + S K++ K D+ + RV S+
Sbjct: 91 QVDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 1324 MKQLGIDPWIGLSFRYPRGTRLLGKVTNLT 1353
G P I L+ R P LGK+ +T
Sbjct: 151 STVTGRLPRIALTMRQP----YLGKLEWIT 176
>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Atp-Dependent Rna Helicase Dhx8
Length = 103
Score = 37.4 bits (85), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 1347 GKVTNLTDYGAFVEIE---KGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEE 1403
GKVT++ +G FV++E K EGLVHISE+ + + +V V++ +L
Sbjct: 18 GKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGT 77
Query: 1404 RRRISLGMKQCKDNPWENF 1422
+ SL MK E+
Sbjct: 78 --KTSLSMKDVDQETGEDL 94
>pdb|2AR7|A Chain A, Crystal Structure Of Human Adenylate Kinase 4, Ak4
pdb|2AR7|B Chain B, Crystal Structure Of Human Adenylate Kinase 4, Ak4
pdb|2BBW|A Chain A, Crystal Structure Of Human Adenylate Kinase 4 (Ak4) In
Complex With Diguanosine Pentaphosphate
pdb|2BBW|B Chain B, Crystal Structure Of Human Adenylate Kinase 4 (Ak4) In
Complex With Diguanosine Pentaphosphate
Length = 246
Score = 37.4 bits (85), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 845 GVQRLCKITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G + L +M K + + + GP SGKGTV Q +A G +L SG R
Sbjct: 14 GTENLYFQSMASKLLRAVIL-GPPGSGKGTVCQRIAQNFGLQHLSSGHFLR 63
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|T Chain T, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 180
Score = 37.0 bits (84), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 1266 NITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL-KYDQEKNRV-SLG 1323
+ +YG F++LG +DGL+HI+ I +K+ + I + S K++ K D+ + RV S+
Sbjct: 91 QVDNYGIFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 1324 MKQLGIDPWIGLSFRYPRGTRLLGKVTNLT 1353
G P I L+ R P LGK+ +T
Sbjct: 151 STVTGRLPRIALTMRQP----YLGKLEWIT 176
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|T Chain T, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|E Chain E, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|Q Chain Q, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 180
Score = 37.0 bits (84), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 1266 NITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL-KYDQEKNRV-SLG 1323
+ +YG F++LG +DGL+HI+ I +K+ + I + S K++ K D+ + RV S+
Sbjct: 91 QVDNYGIFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVA 150
Query: 1324 MKQLGIDPWIGLSFRYPRGTRLLGKVTNLT 1353
G P I L+ R P LGK+ +T
Sbjct: 151 STVTGRLPRIALTMRQP----YLGKLEWIT 176
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 36.6 bits (83), Expect = 0.11, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 51/92 (55%), Gaps = 18/92 (19%)
Query: 1260 VKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRV-----------KHPSEILTIGQDIST 1308
++G V ++ ++G+F+ LG +DGL+H++ I V K ++L IG +
Sbjct: 85 IEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRA 144
Query: 1309 KI----LKYDQEK-NRVSLGMKQ--LGIDPWI 1333
+I LK ++++ ++++L M+Q LG WI
Sbjct: 145 RIVAISLKAERKRGSKIALTMRQPYLGKLEWI 176
Score = 31.2 bits (69), Expect = 5.4, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 16/75 (21%)
Query: 1441 DFGIFIGLDGNIDGLIHLS----DLSWTDP------GEEIIRNFKKGDEIEAIILSIDVE 1490
+FG F+ L G +DGLIH+S D DP G+E + + GD + A I++I ++
Sbjct: 94 EFGSFVRL-GPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK 152
Query: 1491 KER-----ISLGIKQ 1500
ER I+L ++Q
Sbjct: 153 AERKRGSKIALTMRQ 167
>pdb|3NDP|A Chain A, Crystal Structure Of Human Ak4(L171p)
pdb|3NDP|B Chain B, Crystal Structure Of Human Ak4(L171p)
Length = 231
Score = 36.2 bits (82), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 864 IDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
I GP SGKGTV Q +A G +L SG R
Sbjct: 10 ILGPPGSGKGTVCQRIAQNFGLQHLSSGHFLR 41
>pdb|1Q46|A Chain A, Crystal Structure Of The Eif2 Alpha Subunit From
Saccharomyces Cerevisia
Length = 175
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 1264 VKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
V+ I + GA++ L I+G++ +++++ RR++ +++ +G++ +L+ D+EK +
Sbjct: 23 VQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYI 82
Query: 1321 SLGMKQLGIDPWIGLSFRYPRG 1342
L +++ + I +Y +
Sbjct: 83 DLSKRRVSSEDIIKCEEKYQKS 104
>pdb|2A19|A Chain A, Pkr Kinase Domain- Eif2alpha- Amp-Pnp Complex.
pdb|2A1A|A Chain A, Pkr Kinase Domain-Eif2alpha Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 1264 VKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
V+ I + GA++ L I+G++ +++++ RR++ +++ +G++ +L+ D+EK +
Sbjct: 23 VQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYI 82
Query: 1321 SLGMKQLGIDPWIGLSFRYPRG 1342
L +++ + I +Y +
Sbjct: 83 DLSKRRVSSEDIIKCEEKYQKS 104
>pdb|3L0P|A Chain A, Crystal Structures Of Iron Containing Adenylate Kinase
From Desulfovibrio Gigas
pdb|3L0S|A Chain A, Crystal Structures Of Zinc, Cobalt And Iron Containing
Adenylate Kinase From Gram-Negative Bacteria
Desulfovibrio Gigas
pdb|3L0S|C Chain C, Crystal Structures Of Zinc, Cobalt And Iron Containing
Adenylate Kinase From Gram-Negative Bacteria
Desulfovibrio Gigas
Length = 223
Score = 33.9 bits (76), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
I I GP SGKGT LV K +++SG ++R
Sbjct: 3 ILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFR 36
>pdb|2XB4|A Chain A, Crystal Structures Of Zinc Containing Adenylate Kinase
From Desulfovibrio Gigas
Length = 223
Score = 33.9 bits (76), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
I I GP SGKGT LV K +++SG ++R
Sbjct: 3 ILIFGPNGSGKGTQGNLVKDKYSLAHIESGGIFR 36
>pdb|1KL9|A Chain A, Crystal Structure Of The N-Terminal Segment Of Human
Eukaryotic Initiation Factor 2alpha
Length = 182
Score = 33.5 bits (75), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 42/67 (62%), Gaps = 3/67 (4%)
Query: 1265 KNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRVS 1321
++I + GA++ L I+G + +++++ RR++ ++++ IG++ +++ D+EK +
Sbjct: 24 RSIAEXGAYVSLLEYNNIEGXILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYID 83
Query: 1322 LGMKQLG 1328
L +++
Sbjct: 84 LSKRRVS 90
>pdb|1EG1|A Chain A, Endoglucanase I From Trichoderma Reesei
pdb|1EG1|C Chain C, Endoglucanase I From Trichoderma Reesei
Length = 371
Score = 32.0 bits (71), Expect = 3.2, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 11/77 (14%)
Query: 1109 SEAFIPIEEFKNDNGELEVKIGDFVSVAIESLENGF--------GDTILSRDKAKRLASW 1160
S+ F I +F DNG G+ VS+ + +NG GDTI S A
Sbjct: 246 SKTFTIITQFNTDNGSPS---GNLVSITRKYQQNGVDIPSAQPGGDTISSCPSASAYGGL 302
Query: 1161 LSLEKAMESGEIITGTI 1177
++ KA+ SG ++ +I
Sbjct: 303 ATMGKALSSGMVLVFSI 319
>pdb|3CM0|A Chain A, Crystal Structure Of Adenylate Kinase From Thermus
Thermophilus Hb8
Length = 186
Score = 31.6 bits (70), Expect = 3.6, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A +A +LGF L +G + R
Sbjct: 11 GPPGAGKGTQASRLAQELGFKKLSTGDILR 40
>pdb|2K52|A Chain A, Structure Of Uncharacterized Protein Mj1198 From
Methanocaldococcus Jannaschii. Northeast Structural
Genomics Target Mjr117b
Length = 80
Score = 31.6 bits (70), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
++ G KGVV I YGAFI+L + GLL D+ R+++ L +G +I + +
Sbjct: 3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAID 58
Query: 1313 YDQEKNRVSL 1322
EK +
Sbjct: 59 VRPEKREIDF 68
>pdb|2BWJ|A Chain A, Structure Of Adenylate Kinase 5
pdb|2BWJ|B Chain B, Structure Of Adenylate Kinase 5
pdb|2BWJ|C Chain C, Structure Of Adenylate Kinase 5
pdb|2BWJ|D Chain D, Structure Of Adenylate Kinase 5
pdb|2BWJ|E Chain E, Structure Of Adenylate Kinase 5
pdb|2BWJ|F Chain F, Structure Of Adenylate Kinase 5
Length = 199
Score = 31.2 bits (69), Expect = 4.6, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 848 RLCKITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
R CKI I I GP SGKGT + + K GF +L +G L R
Sbjct: 10 RKCKIIFI--------IGGP-GSGKGTQCEKLVEKYGFTHLSTGELLR 48
>pdb|2CDN|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Adenylate
Kinase Complexed With Two Molecules Of Adp And Mg
Length = 201
Score = 31.2 bits (69), Expect = 5.3, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A +A KLG + +G L+R
Sbjct: 27 GPPGAGKGTQAVKLAEKLGIPQISTGELFR 56
>pdb|1P4S|A Chain A, Solution Structure Of Mycobacterium Tuberculosis Adenylate
Kinase
Length = 181
Score = 30.8 bits (68), Expect = 5.9, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A +A KLG + +G L+R
Sbjct: 7 GPPGAGKGTQAVKLAEKLGIPQISTGELFR 36
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.137 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,275,319
Number of Sequences: 62578
Number of extensions: 1925091
Number of successful extensions: 5280
Number of sequences better than 100.0: 79
Number of HSP's better than 100.0 without gapping: 69
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 5030
Number of HSP's gapped (non-prelim): 147
length of query: 1619
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1507
effective length of database: 7,964,601
effective search space: 12002653707
effective search space used: 12002653707
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: 58 (26.9 bits)