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= 002290
(941 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 532 bits (1371), Expect = e-151, Method: Compositional matrix adjust.
Identities = 249/499 (49%), Positives = 371/499 (74%), Gaps = 3/499 (0%)
Query: 81 SPRIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFK 140
+P++ + + +EM S++ Y+MSV++ RALPDVRDGLKPVHRRIL+AM++LG++S KP+K
Sbjct: 6 TPQVREINISQEMRTSFLDYAMSVIVSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYK 65
Query: 141 KCARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTE 200
K AR+VGEV+GK+HPHGD+AVY+S+VRMAQDF+ RY L+ GHGNFGS+D D AAAMRYTE
Sbjct: 66 KSARIVGEVIGKYHPHGDSAVYESMVRMAQDFNYRYMLVDGHGNFGSVDGDSAAAMRYTE 125
Query: 201 CRLEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIP 260
R+ +S +L DI +DT+++ N+D S++E NGA+GIAVGMATNIP
Sbjct: 126 ARMSKIS-MEILRDITKDTIDYQDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIP 184
Query: 261 PHNLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVR 320
PH LGE++D + A+ NP+ T+ EL+E +PGPDFPT G I+G GI AY +GRG IT+R
Sbjct: 185 PHQLGEIIDGVLAVSENPDITIPELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIR 244
Query: 321 GKTEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSGMR 380
K E+E S +R +I+ E+PYQ NK+ L+EKIA+LV +K ++GI+D+RDESDR+GMR
Sbjct: 245 AKAEIEQTSSGKER--IIVTELPYQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMR 302
Query: 381 IVIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVV 440
IVIE++R A+ ++++N+LY+ TALQ+SF N++ ++DGQPK + LK+ L+ +LD + V+
Sbjct: 303 IVIEIRRDANANVILNNLYKQTALQTSFGINLLALVDGQPKVLTLKQCLEHYLDHQKVVI 362
Query: 441 ERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQAD 500
RR ++L + + R HI+EG+ V LD+LD VI ++R + + A L ++F L+EKQA
Sbjct: 363 RRRTAYELRKAEARAHILEGLRVALDHLDAVISLIRNSQTAEIARTGLIEQFSLTEKQAQ 422
Query: 501 AILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTP 560
AILDM L+RLT LER+K +E ++L++ I +L+++L++ +L++I +E+ E+K RF+
Sbjct: 423 AILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILANEYKVLEIIREELTEIKERFNDE 482
Query: 561 RLSMLEDADSGQLDDIDII 579
R + + + ++D D+I
Sbjct: 483 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 = 493 bits (1268), Expect = e-139, Method: Compositional matrix adjust.
Identities = 234/485 (48%), Positives = 350/485 (72%), Gaps = 4/485 (0%)
Query: 83 RIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKC 142
RI + EM S++ Y+MSV++ RALPDVRDGLKPVHRRIL+ ++E G++ K +KK
Sbjct: 243 RINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKS 302
Query: 143 ARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECR 202
AR+VG+V+GK+HPHGD+++Y+++VRMAQDFS RYPL+ G GNFGS+D D AAAMRYTE R
Sbjct: 303 ARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEAR 362
Query: 203 LEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPH 262
+ ++ LL DI++DT++F+ N+D +++E NGASGIAVGMATNIPPH
Sbjct: 363 MTKIT-LELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPH 421
Query: 263 NLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGK 322
NL EL++ + +L NP+ ++ EL+E + GPDFPT GLI+G GI AY TGRG I +R +
Sbjct: 422 NLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSR 481
Query: 323 TEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESD-RSGMRI 381
+E + R +++ EIP+Q NK+ ++EKIAELV +K +DGI+D+RDE+ R+G+R+
Sbjct: 482 AVIE--ERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRV 539
Query: 382 VIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVE 441
VI++++ A+ S+++N+LY+ T LQ+SF NM+ +++G+PK + LKE L +L+ + +VV
Sbjct: 540 VIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVR 599
Query: 442 RRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADA 501
RR ++ L + K+R HI+EG+ + LD++D +I +RE+ ++ A +L+ FKLSEKQA A
Sbjct: 600 RRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQA 659
Query: 502 ILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
ILDM LRRLT LER K E L+ I +LE +L+ + +LQL+ E+ E+++RF R
Sbjct: 660 ILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDR 719
Query: 562 LSMLE 566
+ ++
Sbjct: 720 RTEIQ 724
>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 = 491 bits (1264), Expect = e-139, Method: Compositional matrix adjust.
Identities = 233/485 (48%), Positives = 350/485 (72%), Gaps = 4/485 (0%)
Query: 83 RIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKC 142
RI + EM S++ Y+MSV++ RALPDVRDGLKPVHRRIL+ ++E G++ K +KK
Sbjct: 243 RINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKS 302
Query: 143 ARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECR 202
AR+VG+V+GK+HPHGD+++Y+++VRMAQDFS RYPL+ G GNFGS+D D AAAMR+TE R
Sbjct: 303 ARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEAR 362
Query: 203 LEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPH 262
+ ++ LL DI++DT++F+ N+D +++E NGASGIAVGMATNIPPH
Sbjct: 363 MTKIT-LELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPH 421
Query: 263 NLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGK 322
NL EL++ + +L NP+ ++ EL+E + GPDFPT GLI+G GI AY TGRG I +R +
Sbjct: 422 NLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSR 481
Query: 323 TEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESD-RSGMRI 381
+E + R +++ EIP+Q NK+ ++EKIAELV +K +DGI+D+RDE+ R+G+R+
Sbjct: 482 AVIE--ERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRV 539
Query: 382 VIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVE 441
VI++++ A+ S+++N+LY+ T LQ+SF NM+ +++G+PK + LKE L +L+ + +VV
Sbjct: 540 VIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVR 599
Query: 442 RRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADA 501
RR ++ L + K+R HI+EG+ + LD++D +I +RE+ ++ A +L+ FKLSEKQA A
Sbjct: 600 RRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQA 659
Query: 502 ILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
ILDM LRRLT LER K E L+ I +LE +L+ + +LQL+ E+ E+++RF R
Sbjct: 660 ILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDR 719
Query: 562 LSMLE 566
+ ++
Sbjct: 720 RTEIQ 724
>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 = 491 bits (1263), Expect = e-139, Method: Compositional matrix adjust.
Identities = 233/485 (48%), Positives = 350/485 (72%), Gaps = 4/485 (0%)
Query: 83 RIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKC 142
RI + EM S++ Y+MSV++ RALPDVRDGLKPVHRRIL+ ++E G++ K +KK
Sbjct: 209 RINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKS 268
Query: 143 ARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECR 202
AR+VG+V+GK+HPHGD+++Y+++VRMAQDFS RYPL+ G GNFGS+D D AAAMR+TE R
Sbjct: 269 ARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEAR 328
Query: 203 LEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPH 262
+ ++ LL DI++DT++F+ N+D +++E NGASGIAVGMATNIPPH
Sbjct: 329 MTKIT-LELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPH 387
Query: 263 NLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGK 322
NL EL++ + +L NP+ ++ EL+E + GPDFPT GLI+G GI AY TGRG I +R +
Sbjct: 388 NLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSR 447
Query: 323 TEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESD-RSGMRI 381
+E + R +++ EIP+Q NK+ ++EKIAELV +K +DGI+D+RDE+ R+G+R+
Sbjct: 448 AVIE--ERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRV 505
Query: 382 VIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVE 441
VI++++ A+ S+++N+LY+ T LQ+SF NM+ +++G+PK + LKE L +L+ + +VV
Sbjct: 506 VIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVR 565
Query: 442 RRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADA 501
RR ++ L + K+R HI+EG+ + LD++D +I +RE+ ++ A +L+ FKLSEKQA A
Sbjct: 566 RRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQA 625
Query: 502 ILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
ILDM LRRLT LER K E L+ I +LE +L+ + +LQL+ E+ E+++RF R
Sbjct: 626 ILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDELTEIRDRFGDDR 685
Query: 562 LSMLE 566
+ ++
Sbjct: 686 RTEIQ 690
>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 = 487 bits (1253), Expect = e-137, Method: Compositional matrix adjust.
Identities = 248/517 (47%), Positives = 351/517 (67%), Gaps = 36/517 (6%)
Query: 79 NVSPRIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKP 138
+++ I PV + EE+ SY+ Y+MSV++GRALPDVRDGLKPVHRR+L+AM+ LG K
Sbjct: 2 DLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKA 61
Query: 139 FKKCARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRY 198
+KK ARVVG+V+GK+HPHGD+AVYD++VRMAQ FSLRY L+ G GNFGSID D AAAMRY
Sbjct: 62 YKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRY 121
Query: 199 TECRLEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATN 258
TE RL ++ L+AD++++TV+FV N+D ++K NG+SGIAVGMATN
Sbjct: 122 TEIRLAKIAHE-LMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATN 180
Query: 259 IPPHNLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRIT 318
IPPHNL E+++ A I + + +++ L+E++PGPDFPT +I G GI +AYRTGRG++
Sbjct: 181 IPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVY 240
Query: 319 VRGKTEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSG 378
+R + EVE +D+K+ R +I+ EIPYQ NK+ L+EKIAELV+ K ++GIS +RDESD+ G
Sbjct: 241 IRARAEVE-VDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDG 299
Query: 379 MRIVIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCS 438
MRIVIE+KR A +V+N+LY T LQ SF NMV + GQPK M LK+++ AF+ R
Sbjct: 300 MRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRRE 359
Query: 439 VVERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAA----------- 487
VV RR F+L + ++R HI+E + V L N+D +I ++R AP+ + A A
Sbjct: 360 VVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNV 419
Query: 488 ----------------LKDEF-------KLSEKQADAILDMNLRRLTMLERKKFVDESKT 524
L+ EF L+E+QA AILD+ L++LT LE +K +DE K
Sbjct: 420 AAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE 479
Query: 525 LMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
L++QI +L +L S ++++I +E+ ++ +F R
Sbjct: 480 LLDQIAELLRILGSADRLMEVIREELELVREQFGDKR 516
>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 = 463 bits (1191), Expect = e-130, Method: Compositional matrix adjust.
Identities = 241/517 (46%), Positives = 341/517 (65%), Gaps = 36/517 (6%)
Query: 79 NVSPRIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKP 138
+++ I PV + EE+ SY+ Y+ SV++GRALPDVRDGLKPVHRR+L+A + LG K
Sbjct: 3 DLAREITPVNIEEELKSSYLDYAXSVIVGRALPDVRDGLKPVHRRVLYAXNVLGNDWNKA 62
Query: 139 FKKCARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRY 198
+KK ARVVG+V+GK+HPHGD+AVYD++VR AQ FSLRY L+ G GNFGSID D AAA RY
Sbjct: 63 YKKSARVVGDVIGKYHPHGDSAVYDTIVRXAQPFSLRYXLVDGQGNFGSIDGDSAAAXRY 122
Query: 199 TECRLEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATN 258
TE RL ++ L AD++++TV+FV N+D ++K NG+SGIAVG ATN
Sbjct: 123 TEIRLAKIAHE-LXADLEKETVDFVDNYDGTEKIPDVXPTKIPNLLVNGSSGIAVGXATN 181
Query: 259 IPPHNLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRIT 318
IPPHNL E+++ A I + + +++ L E++PGPDFPT +I G GI +AYRTGRG++
Sbjct: 182 IPPHNLTEVINGCLAYIDDEDISIEGLXEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVY 241
Query: 319 VRGKTEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSG 378
+R + EVE +D+K+ R +I+ EIPYQ NK+ L+EKIAELV+ K ++GIS +RDESD+ G
Sbjct: 242 IRARAEVE-VDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDG 300
Query: 379 MRIVIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCS 438
RIVIE+KR A +V+N+LY T LQ SF N V + GQPK LK+++ AF+ R
Sbjct: 301 XRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINXVALHHGQPKIXNLKDIIAAFVRHRRE 360
Query: 439 VVERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAA----------- 487
VV RR F+L + ++R HI+E + V L N+D +I ++R AP+ + A A
Sbjct: 361 VVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNV 420
Query: 488 ----------------LKDEF-------KLSEKQADAILDMNLRRLTMLERKKFVDESKT 524
L+ EF L+E+QA AILD+ L++LT LE +K +DE K
Sbjct: 421 AAXLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKE 480
Query: 525 LMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
L++QI +L +L S + ++I +E+ ++ +F R
Sbjct: 481 LLDQIAELLRILGSADRLXEVIREELELVREQFGDKR 517
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 460 bits (1184), Expect = e-129, Method: Compositional matrix adjust.
Identities = 237/490 (48%), Positives = 332/490 (67%), Gaps = 36/490 (7%)
Query: 106 LGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSL 165
+GRALPDVRDGLKPVHRR+L+AM+ LG K +KK ARVVG+V+GK+HPHGD+AVYD++
Sbjct: 1 VGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTI 60
Query: 166 VRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECRLEALSEAMLLADIDQDTVNFVPN 225
VRMAQ FSLRY L+ G GNFGSID D AAAMRYTE RL ++ L+AD++++TV+FV N
Sbjct: 61 VRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHE-LMADLEKETVDFVDN 119
Query: 226 FDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEATLQEL 285
+D ++K NG+SGIAVGMATNIPPHNL E+++ A I + + +++ L
Sbjct: 120 YDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGL 179
Query: 286 LEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVIIKEIPYQ 345
+E++PGPDFPT +I G GI +AYRTGRG++ +R + EVE+ D+K+ R +I+ EIPYQ
Sbjct: 180 MEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEV-DAKTGRETIIVHEIPYQ 238
Query: 346 TNKSMLVEKIAELVENKTLDGISDIRDESDRSGMRIVIELKRGADPSIVVNSLYRLTALQ 405
NK+ L+EKIAELV+ K ++GIS +RDESD+ GMRIVIE+KR A +V+N+LY T LQ
Sbjct: 239 VNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQ 298
Query: 406 SSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKLSQVKERRHIVEGIMVGL 465
SF NMV + GQPK M LK+++ AF+ R VV RR F+L + ++R HI+E + V L
Sbjct: 299 VSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVAL 358
Query: 466 DNLDRVIRIVREAPSNSTASAA---------------------------LKDEF------ 492
N+D +I ++R AP+ + A A L+ EF
Sbjct: 359 ANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGL 418
Query: 493 -KLSEKQADAILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVI 551
L+E+QA AILD+ L++LT LE +K +DE K L++QI +L +L S ++++I +E+
Sbjct: 419 YYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELE 478
Query: 552 ELKNRFSTPR 561
++ +F R
Sbjct: 479 LVREQFGDKR 488
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 452 bits (1162), Expect = e-127, Method: Compositional matrix adjust.
Identities = 225/488 (46%), Positives = 328/488 (67%), Gaps = 36/488 (7%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
RALPDVRDGLKPVHRR+LFAM LG K +KK ARVVG+V+GK+HPHGD AVYD++VR
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVVGDVIGKYHPHGDTAVYDTIVR 61
Query: 168 MAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECRLEALSEAMLLADIDQDTVNFVPNFD 227
MAQ FSLRY L+ G GNFGS+D D AAAMRYTE R+ ++ + +LAD+D++TV+FVPN+D
Sbjct: 62 MAQPFSLRYMLVDGQGNFGSVDGDSAAAMRYTEIRMSKIAHS-ILADLDKETVDFVPNYD 120
Query: 228 ESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEATLQELLE 287
++ NG SGIAVGMATNIPPHNL E+++ ALI N E T +E+LE
Sbjct: 121 GTEHIPAVMPTRVPNLLVNGTSGIAVGMATNIPPHNLTEVINACLALIDNSELTFEEILE 180
Query: 288 YMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVIIKEIPYQTN 347
++PGPDFPT G+I G GI +AYRTGRG+I +R + +++ ++ K +I+ E+PYQ N
Sbjct: 181 HIPGPDFPTAGIISGRAGIEEAYRTGRGKIKIRARASIDVHETTGKET-IIVHELPYQVN 239
Query: 348 KSMLVEKIAELVENKTLDGISDIRDESDRSGMRIVIELKRGADPSIVVNSLYRLTALQSS 407
K+ L+EK+AELV++K L+GIS +RDESD+ GMR+VIE+KRG +V+N+LY+LT +Q S
Sbjct: 240 KARLIEKMAELVKDKRLEGISALRDESDKDGMRMVIEIKRGEVGEVVLNNLYKLTQMQVS 299
Query: 408 FSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKLSQVKERRHIVEGIMVGLDN 467
F NMV + +GQPK +KE+L+AF+ R VV RR F+L + ++R HI+EG+ + L N
Sbjct: 300 FGLNMVALTNGQPKIFNIKEMLEAFVLHRREVVTRRTIFELRKARDRAHILEGLSIALAN 359
Query: 468 LDRVIRIVR---------------------------EAPSNSTASAALKDE-------FK 493
+D +I +++ EA +++ L+ E +
Sbjct: 360 IDPIIEMIKNSNNRKESEEKLISQGWELGNVANMLSEAGNDAARPEWLEPEYGIRDGLYY 419
Query: 494 LSEKQADAILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIEL 553
L+ +QA AI+D+ L +L+ +E K + E K L++ I +L +L++ ++++I +E++ +
Sbjct: 420 LTAEQAKAIVDLQLYKLSGMEHDKILSEYKALLDLIAELMHILATPARLMEVICEELVAI 479
Query: 554 KNRFSTPR 561
++ F R
Sbjct: 480 RDEFGDER 487
>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 = 439 bits (1129), Expect = e-123, Method: Compositional matrix adjust.
Identities = 225/484 (46%), Positives = 315/484 (65%), Gaps = 8/484 (1%)
Query: 83 RIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKC 142
RI PV++ +EM SYI Y+MSV++GRALP+VRDGLKPVHRR+L+AM + G + K
Sbjct: 14 RIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKS 73
Query: 143 ARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECR 202
AR V E +G +HPHGD ++YDSLVRMAQ +SLRYPL+ G GNFGS DP AAMRYTE R
Sbjct: 74 ARSVAETMGNYHPHGDASIYDSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEAR 133
Query: 203 LEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPH 262
L L+ M L +ID++TV+F+PN+D +E NG+ GIAVGMATNIPPH
Sbjct: 134 LTPLAMEM-LREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPH 192
Query: 263 NLGELVDVLCALIHNPEA----TLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRIT 318
NL EL D + + N +A TL ++ + GPDFPT GLI+G+ G DAY+TGRG I
Sbjct: 193 NLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIR 252
Query: 319 VRGKTEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDE-SDRS 377
+RG EVE + R ++I E+PYQ N + IAE V + L GIS+I D+ SDR
Sbjct: 253 MRGVVEVE--EDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRV 310
Query: 378 GMRIVIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRC 437
G+RIVIE+KR A +V+N+LY+ T LQ+SF NM+ I+DG P+ + L ++++ ++D +
Sbjct: 311 GLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQL 370
Query: 438 SVVERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEK 497
V+ RR ++L + ER HI+ G++ LD LD VI ++R + + A A L + + E
Sbjct: 371 DVIVRRTTYRLRKANERAHILRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEI 430
Query: 498 QADAILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRF 557
QA AILDM LRRL LER++ +D+ + +I LE++L+ + ++ E+ E+ +R
Sbjct: 431 QAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRH 490
Query: 558 STPR 561
R
Sbjct: 491 GDDR 494
>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 = 416 bits (1070), Expect = e-116, Method: Compositional matrix adjust.
Identities = 214/464 (46%), Positives = 300/464 (64%), Gaps = 8/464 (1%)
Query: 103 SVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVY 162
SV++GRALP+VRDGLKPVHRR+L+AM + G + K AR V E +G +HPHGD ++Y
Sbjct: 4 SVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIY 63
Query: 163 DSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECRLEALSEAMLLADIDQDTVNF 222
DSLVRMAQ +SLRYPL+ G GNFGS DP AAMRYTE RL L+ ML +ID++TV+F
Sbjct: 64 DSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEML-REIDEETVDF 122
Query: 223 VPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEA-- 280
+PN+D +E NG+ GIAVGMATNIPPHNL EL D + + N +A
Sbjct: 123 IPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADE 182
Query: 281 --TLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVI 338
TL ++ + GPDFPT GLI+G+ G DAY+TGRG I +RG EVE + R ++
Sbjct: 183 EETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVE--EDSRGRTSLV 240
Query: 339 IKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDES-DRSGMRIVIELKRGADPSIVVNS 397
I E+PYQ N + IAE V + L GIS+I D+S DR G+RIVIE+KR A +V+N+
Sbjct: 241 ITELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINN 300
Query: 398 LYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKLSQVKERRHI 457
LY+ T LQ+SF NM+ I+DG P+ + L ++++ ++D + V+ RR ++L + ER HI
Sbjct: 301 LYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHI 360
Query: 458 VEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADAILDMNLRRLTMLERKK 517
+ G++ LD LD VI ++R + + A A L + + E QA AILDM LRRL LER++
Sbjct: 361 LRGLVKALDALDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQR 420
Query: 518 FVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPR 561
+D+ + +I LE++L+ + ++ E+ E+ +R R
Sbjct: 421 IIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDR 464
>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
Subunit A (Grla) From Staphylococcus Aureus
Length = 514
Score = 414 bits (1063), Expect = e-115, Method: Compositional matrix adjust.
Identities = 215/487 (44%), Positives = 327/487 (67%), Gaps = 3/487 (0%)
Query: 80 VSPRIVPVELHEEMTGSYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPF 139
VS I + L + + + YS ++ RALPDVRDGLKPV RRIL+AM+ G + K F
Sbjct: 24 VSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNF 83
Query: 140 KKCARVVGEVLGKFHPHGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYT 199
+K A+ VG+V+G++HPHGD++VY+++VR++QD+ LR+ LI HGN GSID DP AAMRYT
Sbjct: 84 RKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYT 143
Query: 200 ECRLEALSEAMLLADIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNI 259
E +L L+E LL DI+++TV+F+PN+D++ E NG++GI+ G AT+I
Sbjct: 144 EAKLSLLAEE-LLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDI 202
Query: 260 PPHNLGELVDVLCALIHNPEATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITV 319
PPHNL E++ I NP+ T+ +L++Y+ GPDFPTGG+I G GI AY +G+GRI V
Sbjct: 203 PPHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRIIV 262
Query: 320 RGKTEVELLDSKSKRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSGM 379
R K E E L ++ R +II EIPY+ NKS LV++I EL +K +DGI ++RDE+DR+G+
Sbjct: 263 RSKVEEETL--RNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGL 320
Query: 380 RIVIELKRGADPSIVVNSLYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSV 439
RI IELK+ + + N LY+ + LQ S++ NMV I DG+PK MG+++++ ++L+ + V
Sbjct: 321 RIAIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIEV 380
Query: 440 VERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQA 499
V R +F+L ++R HIVEG++ L LD+VI ++R + + A L + ++ +E+QA
Sbjct: 381 VANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEVYEFTEEQA 440
Query: 500 DAILDMNLRRLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFST 559
+AI+ + L RLT + E K L I +L +L + +L +I++E+ E+K +F +
Sbjct: 441 EAIVMLQLYRLTNTDIVALEGEHKELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKS 500
Query: 560 PRLSMLE 566
RLS++E
Sbjct: 501 ERLSLIE 507
>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 = 410 bits (1054), Expect = e-114, Method: Compositional matrix adjust.
Identities = 201/468 (42%), Positives = 311/468 (66%), Gaps = 3/468 (0%)
Query: 100 YSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDN 159
YS ++ RALPD+RDGLKPV RRIL++M++ + K ++K A+ VG ++G FHPHGD+
Sbjct: 20 YSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDS 79
Query: 160 AVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPAAAMRYTECRLEALSEAMLLADIDQDT 219
++YD++VRM+Q++ R L+ HGN GS+D DP AAMRYTE RL ++ LL DI++ T
Sbjct: 80 SIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIA-GYLLQDIEKKT 138
Query: 220 VNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPE 279
V F NFD+++KE NG++GI+ G AT+IPPHNL E++D +I +P
Sbjct: 139 VPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPT 198
Query: 280 ATLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVII 339
A + +L+E++PGPDFPTG +I G I AY TG+GR+ VR KTE+E L K + ++I
Sbjct: 199 AKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKL--KGGKEQIVI 256
Query: 340 KEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSGMRIVIELKRGADPSIVVNSLY 399
EIPY+ NK+ LV+KI ++ N + GI+++RDESDR G+RI IELK+ A+ +V+N L+
Sbjct: 257 TEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLF 316
Query: 400 RLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKLSQVKERRHIVE 459
+ T LQ +++ NMV I + P+Q+G+ +L +++ R V+ R+RF + ++R HIVE
Sbjct: 317 KYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVE 376
Query: 460 GIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADAILDMNLRRLTMLERKKFV 519
G++ + LD VI ++R + + + A LK + +E+QA+AI+ + L RLT +
Sbjct: 377 GLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQ 436
Query: 520 DESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPRLSMLED 567
+E L E+I L ++ + + L+++E+ E+K +F+TPRLS LED
Sbjct: 437 EEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFATPRLSSLED 484
>pdb|1ZVU|A Chain A, Structure Of The Full-Length E. Coli Parc Subunit
Length = 716
Score = 352 bits (904), Expect = 5e-97, Method: Compositional matrix adjust.
Identities = 219/602 (36%), Positives = 338/602 (56%), Gaps = 34/602 (5%)
Query: 106 LGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSL 165
+ RALP + DGLKPV RRI++AM ELGL++ FKK AR VG+VLGK+HPHGD+A Y+++
Sbjct: 1 MDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAM 60
Query: 166 VRMAQDFSLRYPLIRGHGNFGSIDADPA--AAMRYTECRLEALSEAMLLADIDQDTVNFV 223
V MAQ FS RYPL+ G GN+G+ D DP AAMRYTE RL SE +LL+++ Q T ++V
Sbjct: 61 VLMAQPFSYRYPLVDGQGNWGAPD-DPKSFAAMRYTESRLSKYSE-LLLSELGQGTADWV 118
Query: 224 PNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEATLQ 283
PNFD + +E NG +GIAVGMAT+IPPHNL E+ ALI P+ TL
Sbjct: 119 PNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLD 178
Query: 284 ELLEYMPGPDFPT-GGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVIIKEI 342
+LL+ + GPD+PT +I I Y GRG + +R K + V+I +
Sbjct: 179 QLLDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVW-------KKEDGAVVISAL 231
Query: 343 PYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSG-MRIVIELKRG-ADPSIVVNSLYR 400
P+Q + + ++E+IA + NK L + D+RDESD R+VI + D V+N L+
Sbjct: 232 PHQVSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFA 291
Query: 401 LTALQSSF--SCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKLSQVKERRHIV 458
T L+ S+ + NM+G LDG+P L E+L +L FR V RR ++L +V +R HI+
Sbjct: 292 TTDLEKSYRINLNMIG-LDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHIL 350
Query: 459 EGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADAILDMNLRRLTMLERKKF 518
EG++V N+D VI I+R + AL F L+E QA+AIL++ LR L LE K
Sbjct: 351 EGLLVAFLNIDEVIEIIR---NEDEPKPALMSRFGLTETQAEAILELKLRHLAKLEEMKI 407
Query: 519 VDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPRLSMLEDADSGQ-LDDID 577
E L ++ +L+ +L+S + + L+++E+ + R S L++ + + + + D
Sbjct: 408 RGEQSELEKERDQLQGILASERKMNNLLKKELQADAQAYGDDRRSPLQEREEAKAMSEHD 467
Query: 578 IIPNDEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLY 637
++P++ + + +S+ G+V+ K + + + D+ + +++ V++
Sbjct: 468 MLPSEPVTIVLSQMGWVRSAKGHDIDAPGL--------NYKAGDSFKAAVKGKSNQPVVF 519
Query: 638 FSDRGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMN 697
G Y+ +P G PL L+L G + ++ S+ DQ L+M +
Sbjct: 520 VDSTGRSYAIDPITLPSA--RGQGEPLTGKLTLPPGATVDHMLMESD---DQKLLMASDA 574
Query: 698 GY 699
GY
Sbjct: 575 GY 576
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 336 bits (862), Expect = 3e-92, Method: Compositional matrix adjust.
Identities = 198/493 (40%), Positives = 297/493 (60%), Gaps = 21/493 (4%)
Query: 96 SYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHP 155
+Y+ Y+M V++ RALP + DGLKPV RRI++AM ELGL S KK AR VG+VLGK+HP
Sbjct: 285 AYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHP 344
Query: 156 HGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPA--AAMRYTECRLEALSEAMLLA 213
HGD+A Y+++V MAQ FS RYPLI G GN+GS D DP AAMRYTE +L A SE +LL+
Sbjct: 345 HGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPD-DPKSFAAMRYTEAKLSAYSE-LLLS 402
Query: 214 DIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCA 273
++ Q T + NFD S KE NG +GIAVGMAT+IPPHNL E+V A
Sbjct: 403 ELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIA 462
Query: 274 LIHNPEATLQELLEYMPGPDFPTGG-LIMGNLGILDAYRTGRGRITVRGKTEVELLDSKS 332
LI NP+ + ++L EY+P PD PT +I +L TGRG +R +E
Sbjct: 463 LIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIE------ 516
Query: 333 KRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSG-MRIVIELKRG-AD 390
+ ++I E+PYQ + S ++ +IA+ ++ K L + D+RDESD R+VI L+ D
Sbjct: 517 -KNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRID 575
Query: 391 PSIVVNSLYRLTALQSSF--SCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKL 448
V++ L+ T L+SS+ + NM+G DG+P+ ++ +L +++ R V RR ++ L
Sbjct: 576 AEAVMSHLFATTDLESSYRVNLNMIG-EDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHL 634
Query: 449 SQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADAILDMNLR 508
+++++R HI+ G+++ ++D VIRI+RE L + F + E QA+AIL++ LR
Sbjct: 635 NRIEKRLHILAGLLIAYLDIDTVIRIIRE---EDQPKPVLMEHFNIDEIQAEAILELKLR 691
Query: 509 RLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPRLS-MLED 567
L LE + E L + + E L + +++ LI E+ E +F R S ++
Sbjct: 692 HLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVAR 751
Query: 568 ADSGQLDDIDIIP 580
A++ Q+ + D++P
Sbjct: 752 AEAVQIKEQDLMP 764
>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 = 333 bits (853), Expect = 3e-91, Method: Compositional matrix adjust.
Identities = 197/493 (39%), Positives = 296/493 (60%), Gaps = 21/493 (4%)
Query: 96 SYITYSMSVLLGRALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHP 155
+Y+ Y+M V++ RALP + DGLKPV RRI++AM ELGL S KK AR VG+VLGK+HP
Sbjct: 285 AYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHP 344
Query: 156 HGDNAVYDSLVRMAQDFSLRYPLIRGHGNFGSIDADPA--AAMRYTECRLEALSEAMLLA 213
HGD+A Y+++V MAQ FS RYPLI G GN+GS D DP AAMR TE +L A SE +LL+
Sbjct: 345 HGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPD-DPKSFAAMRXTEAKLSAYSE-LLLS 402
Query: 214 DIDQDTVNFVPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCA 273
++ Q T + NFD S KE NG +GIAVGMAT+IPPHNL E+V A
Sbjct: 403 ELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIA 462
Query: 274 LIHNPEATLQELLEYMPGPDFPTGG-LIMGNLGILDAYRTGRGRITVRGKTEVELLDSKS 332
LI NP+ + ++L EY+P PD PT +I +L TGRG +R +E
Sbjct: 463 LIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIE------ 516
Query: 333 KRMGVIIKEIPYQTNKSMLVEKIAELVENKTLDGISDIRDESDRSG-MRIVIELKRG-AD 390
+ ++I E+PYQ + S ++ +IA+ ++ K L + D+RDESD R+VI L+ D
Sbjct: 517 -KNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRID 575
Query: 391 PSIVVNSLYRLTALQSSF--SCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARFKL 448
V++ L+ T L+SS+ + NM+G DG+P+ ++ +L +++ R V RR ++ L
Sbjct: 576 AEAVMSHLFATTDLESSYRVNLNMIG-EDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHL 634
Query: 449 SQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAALKDEFKLSEKQADAILDMNLR 508
+++++R HI+ G+++ ++D VIRI+RE L + F + E QA+AIL++ LR
Sbjct: 635 NRIEKRLHILAGLLIAYLDIDTVIRIIRE---EDQPKPVLMEHFNIDEIQAEAILELKLR 691
Query: 509 RLTMLERKKFVDESKTLMEQILKLEELLSSRKNILQLIEQEVIELKNRFSTPRLS-MLED 567
L LE + E L + + E L + +++ LI E+ E +F R S ++
Sbjct: 692 HLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDERRSPIVAR 751
Query: 568 ADSGQLDDIDIIP 580
A++ Q+ + D++P
Sbjct: 752 AEAVQIKEQDLMP 764
>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 = 179 bits (455), Expect = 5e-45, Method: Compositional matrix adjust.
Identities = 109/319 (34%), Positives = 175/319 (54%), Gaps = 28/319 (8%)
Query: 581 NDEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSD 640
+++++ +S +GYVK + + Q RG GKS +++ D + +V HDH+L FS
Sbjct: 2 QEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSS 61
Query: 641 RGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMNGYI 700
RG VYS + Y++PE TR A G P+V +L L ERIT+I+PV+EF + M T NG +
Sbjct: 62 RGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTV 121
Query: 701 KKVSLNLFSSIRTTGIIAIQLVPGDELKWVRCCTNDDLVAMASQNGMVILSSCDIIRSLS 760
KK L F+ +RT G +AI+LV GDEL V + +D V + S G V+ +R++
Sbjct: 122 KKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMG 181
Query: 761 RNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGSSGPWLLFVSESGHGK 820
NT G +RL +GDK+ S+ I+P +G +L +++G+GK
Sbjct: 182 CNTTGVRGIRLGEGDKVVSL-IVP------------------RGDGA--ILTATQNGYGK 220
Query: 821 RVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAEDGESDEQVVLVSQSGTVNRI 880
R ++ + G+I K + + L VVG +D +Q+++++ +GT+ R
Sbjct: 221 RTAVAEYPTKSRATKGVISIKVTERNGL----VVGAVQVDDC---DQIMMITDAGTLVRT 273
Query: 881 KVRDISIQARYARGVILMR 899
+V +ISI R +GVIL+R
Sbjct: 274 RVSEISIVGRNTQGVILIR 292
Score = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 48/193 (24%), Positives = 86/193 (44%), Gaps = 13/193 (6%)
Query: 592 GYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSDRGIVYSARAYK 651
G VK+ FN T GK KL D + + D V+ FS G V +
Sbjct: 119 GTVKKTVLTEFNRLR--TAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESS 176
Query: 652 IPECTRNAAGTPLVQILSLSDGERITS-IIPVSEFAGDQFLVMLTMNGYIKKVSLNLF-- 708
+ N G V+ + L +G+++ S I+P GD ++ T NGY K+ ++ +
Sbjct: 177 VRAMGCNTTG---VRGIRLGEGDKVVSLIVP----RGDGAILTATQNGYGKRTAVAEYPT 229
Query: 709 SSIRTTGIIAIQLVPGDELKWVRCCTND-DLVAMASQNGMVILSSCDIIRSLSRNTRGSV 767
S T G+I+I++ + L +D D + M + G ++ + I + RNT+G +
Sbjct: 230 KSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVI 289
Query: 768 AMRLKDGDKMASM 780
+R + + + +
Sbjct: 290 LIRTAEDENVVGL 302
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 35/177 (19%), Positives = 73/177 (41%), Gaps = 7/177 (3%)
Query: 546 IEQEVIELKNRFSTPRLSMLEDADSGQLDDIDIIPNDEMLLAISEKGYVKRMKPNTFNLQ 605
+++ V+ NR T ++ D +L +D+ ++ ++ S +G V R K ++
Sbjct: 121 VKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAM 180
Query: 606 NRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSDRGIVYSARAYKIPECTRNAAGTPLV 665
T G +L D + IV R +L + G + P +R G
Sbjct: 181 GCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKG---- 236
Query: 666 QILSLSDGERITSIIPVSEFAGDQFLVMLTMNGYIKKVSLNLFSSI--RTTGIIAIQ 720
++S+ ER ++ + ++M+T G + + ++ S + T G+I I+
Sbjct: 237 -VISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIR 292
>pdb|3UC1|A Chain A, Mycobacterium Tuberculosis Gyrase Type Iia Topoisomerase
C-Terminal Domain
Length = 327
Score = 145 bits (367), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 95/321 (29%), Positives = 154/321 (47%), Gaps = 30/321 (9%)
Query: 582 DEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSDR 641
+++++ I+E GY KR K + + Q RG G L+ +D ++ F VC HD +L+F+ +
Sbjct: 3 EDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQ 62
Query: 642 GIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMNGYIK 701
G VY A+AY +PE +R A G + +L+ ERI +I + + +LV+ T NG +K
Sbjct: 63 GRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQIRGYTDAPYLVLATRNGLVK 122
Query: 702 KVSLNLFSSIRTTGIIAIQLVPGDEL-KWVRCCTNDDLVAMASQNGMVILSSCD-IIRSL 759
K L F S R+ GI+A+ L DEL V C DDL+ +++ + S+ D +R +
Sbjct: 123 KSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPM 182
Query: 760 SRNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGSSGPWLLFVSESGHG 819
R T G MR D++ S++++ G +LL + G+
Sbjct: 183 GRATSGVQGMRFNIDDRLLSLNVV---------------------REGTYLLVATSGGYA 221
Query: 820 KRVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAEDGESDEQVVLVSQSGTVNR 879
KR + + P+ G G DR +VG + +D D ++ V+ G V R
Sbjct: 222 KRTAIEEY---PVQGRGGKGVLTVMYDRRRG-RLVGALIVDD---DSELYAVTSGGGVIR 274
Query: 880 IKVRDISIQARYARGVILMRL 900
R + R +GV LM L
Sbjct: 275 TAARQVRKAGRQTKGVRLMNL 295
Score = 42.7 bits (99), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 54/227 (23%), Positives = 97/227 (42%), Gaps = 22/227 (9%)
Query: 585 LLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSDRG-- 642
L+ + G VK+ K F+ G I LR ND + ++C A D +L S G
Sbjct: 112 LVLATRNGLVKKSKLTDFDSNRSGGI--VAVNLRDNDELVGAVLCSAGDDLLLVSANGQS 169
Query: 643 IVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMNGYIKK 702
I +SA + R +G VQ + + +R+ S+ V E +L++ T GY K+
Sbjct: 170 IRFSATDEALRPMGRATSG---VQGMRFNIDDRLLSLNVVRE---GTYLLVATSGGYAKR 223
Query: 703 VSLNLFSSIRTTGIIAIQLVPGDE----LKWVRCCTNDDLVAMASQNGMVILSSCDIIRS 758
++ + ++ G + V D L +D + + G VI ++ +R
Sbjct: 224 TAIEEYP-VQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRK 282
Query: 759 LSRNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGS 805
R T+G M L +GD + A+ ++ E + +D+ + G+
Sbjct: 283 AGRQTKGVRLMNLGEGDTL-------LAIARNAEESGDDNAVDANGA 322
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 57/124 (45%), Gaps = 24/124 (19%)
Query: 576 IDIIPNDEMLLAISEKGYVKRMKPNTFNLQNRG-----TI------GKSVGKLRVNDAMS 624
++++ LL + GY KR + +Q RG T+ G+ VG L V+D
Sbjct: 203 LNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSE 262
Query: 625 DFIVCRAHDHVLYFSDRGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSE 684
+ V S G++ +A A ++ + R G V++++L +G+ + +I +E
Sbjct: 263 LYAVT---------SGGGVIRTA-ARQVRKAGRQTKG---VRLMNLGEGDTLLAIARNAE 309
Query: 685 FAGD 688
+GD
Sbjct: 310 ESGD 313
>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 = 141 bits (356), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 101/360 (28%), Positives = 179/360 (49%), Gaps = 25/360 (6%)
Query: 576 IDIIPNDEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHV 635
+D+I +++++ +S GY KR + + Q RG G+S + D + + HD +
Sbjct: 1 MDLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTL 60
Query: 636 LYFSDRGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLT 695
L F+ G V+ +++PE NA G P++ + L GER+ +++PV E+A ++++ M T
Sbjct: 61 LTFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPVREYADNRYVFMAT 120
Query: 696 MNGYIKKVSLNLFSSIRTTGIIAIQLVPGDELKWVRCCTNDDLVAMASQNGMVILSSCDI 755
NG +KK L+ F+ G IAI L GD L V D V + + NG +
Sbjct: 121 RNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFGEST 180
Query: 756 IRSLSRNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGSSG-------- 807
+RS+ R G +RL G+++ S+ + A + E E + V+ + G
Sbjct: 181 VRSMGRTATGVRGIRLAKGEEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDV 240
Query: 808 ------PWLLFVSESGHGKRVPLSSFRKLPLNRVGLIGYKFSAED-RLAAVFVVGFSLAE 860
++L +E+G+GKR PL+ + + G+IG + + + +L ++G
Sbjct: 241 ADNGDVAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLG----- 295
Query: 861 DGESDEQVVLVSQSGTVNRIKVRDISIQARYARGVILMRLELSGKIQSASLI--SVTEPE 918
S ++V+L+S GT+ R + +IS R +GV L+RL K+Q+ + S+ EPE
Sbjct: 296 ---STDEVMLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERLDASLEEPE 352
>pdb|1SUU|A Chain A, Structure Of Dna Gyrase A C-Terminal Domain
Length = 312
Score = 126 bits (317), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 91/342 (26%), Positives = 168/342 (49%), Gaps = 37/342 (10%)
Query: 577 DIIPNDEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFI-VC-RAHDH 634
D++ + +++ +++KG++KR+ N + LQ GT GK + +ND I +C HD+
Sbjct: 3 DLMQKENIVVMLTKKGFLKRLSQNEYKLQ--GTGGKGLSSFDLNDGDEIVIALCVNTHDY 60
Query: 635 VLYFSDRGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVML 694
+ S+ G +Y AY+I + +R + G + ++++L D E I +I + D +L++
Sbjct: 61 LFMISNEGKLYLINAYEIKDSSRASKGQNISELINLGDQEEILTIKNSKDLTDDAYLLLT 120
Query: 695 TMNGYIKKVSLNLFSSIRTTGIIAIQLVPGDELKWVRCCTNDDLVAMASQNGMVILSSCD 754
T +G I + F ++++ G+I I+L D + D+ V S+ G + +
Sbjct: 121 TASGKIARFESTDFKAVKSRGVIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIFNSR 180
Query: 755 IIRSLSRNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGSSGPWLLFVS 814
+R +R T+G M+LK+GD + + P+LL VS
Sbjct: 181 DVRLTNRGTQGVCGMKLKEGDLFVKVLSVK---------------------ENPYLLIVS 219
Query: 815 ESGHGKRVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAEDGESDEQVVLVSQS 874
E+G+GKR+ +S +L G YK S D+ A V +++ED E ++LVS+
Sbjct: 220 ENGYGKRLNMSKISELKRGATGYTSYKKS--DKKAGSVVDAIAVSEDDE----ILLVSKR 273
Query: 875 GTVNRIKVRDISIQARYARGVILMRLELSGKIQSASLISVTE 916
R +S Q + ARG+ ++ L+ + SL+SV++
Sbjct: 274 SKALRTVAGKVSEQGKDARGIQVLFLD------NDSLVSVSK 309
>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 = 82.4 bits (202), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 87/352 (24%), Positives = 161/352 (45%), Gaps = 41/352 (11%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEV--LGKFHPHGDNAVYDSL 165
R++P + DG KP R++LF + + K K A++ G V + +H HG+ A+ ++
Sbjct: 311 RSIPSLVDGFKPGQRKVLFTCFK---RNDKREVKVAQLAGSVAEMSAYH-HGEQALMMTI 366
Query: 166 VRMAQDF--SLRYPLIRGHGNFGS--IDADPAAAMRYTECRLEALSEAMLLADIDQDTVN 221
V +AQ+F S L++ G FG+ AA+ RY L L+ +L +D + +
Sbjct: 367 VNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLAR-LLFPAVDDNLLK 425
Query: 222 FVPNFDESQK-EXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEA 280
F+ +D++Q+ E NGA GI G A +P ++ E+V+ + ++ +
Sbjct: 426 FL--YDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLD- 482
Query: 281 TLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVIIK 340
P P P G + L G+ + V G E+ ++D R V I
Sbjct: 483 ---------PHPMLPNYKNFKGTIQEL-----GQNQYAVSG--EIFVVD----RNTVEIT 522
Query: 341 EIPYQTNKSMLVEKIAELVEN---KTLDGISDIRDESDRSGMRIVIELKRGADPSIVVNS 397
E+P +T + E++ E + N KT ISD ++ + ++ V+++
Sbjct: 523 ELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAG 582
Query: 398 LYRLTALQSSFSCNMVGILDGQ---PKQMGLKEVLQAFLDFRCSVVERRARF 446
L+++ LQ++ +CN + + D K ++++L+ F D R S R +
Sbjct: 583 LHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEW 634
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 72.8 bits (177), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 85/349 (24%), Positives = 157/349 (44%), Gaps = 42/349 (12%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEV--LGKFHPHGDNAVYDSL 165
R++P + DGLKP R++LF + + K K A++ G V + +H HG+ ++ ++
Sbjct: 283 RSIPSMVDGLKPGQRKVLFTCFK---RNDKREVKVAQLAGSVAEMSSYH-HGEMSLMMTI 338
Query: 166 VRMAQDF--SLRYPLIRGHGNFGS--IDADPAAAMRYTECRLEALSEAMLLADIDQDTVN 221
+ +AQ+F S L++ G FG+ +A+ RY L +L+ +L D T+
Sbjct: 339 INLAQNFVGSNNLNLLQPIGQFGTRLHGGKDSASPRYIFTMLSSLAR-LLFPPKDDHTLK 397
Query: 222 FVPNFDESQK-EXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEA 280
F+ +D++Q+ E NGA GI G + IP ++ E+V+ + L+ E
Sbjct: 398 FL--YDDNQRVEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEE- 454
Query: 281 TLQELLEYMPGPDFPTGGLIMGNLGILDAYRTGRGRITVRGKTEVELLDSKSKRMGVIIK 340
P P P+ G + L + + G EV +L+S + + I
Sbjct: 455 ---------PLPMLPSYKNFKGTIEEL-----APNQYVISG--EVAILNSTT----IEIS 494
Query: 341 EIPYQTNKSMLVEKIAELVEN---KTLDGISDIRDESDRSGMRIVIELKRGADPSIVVNS 397
E+P +T E++ E + N KT I+D R+ + ++ V+++
Sbjct: 495 ELPVRTWTQTYKEQVLEPMLNGTEKTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVG 554
Query: 398 LYRLTALQSSFSCNMVGILDGQPKQMGLKEVLQAFLDFRCSVVERRARF 446
L+++ LQ+S +CN + + D +G + LD E R ++
Sbjct: 555 LHKVFKLQTSLTCNSMVLFD----HVGCLKKYDTVLDILRDFFELRLKY 599
>pdb|4ELY|A Chain A, Ccdbvfi:gyra14ec
pdb|4ELY|B Chain B, Ccdbvfi:gyra14ec
Length = 156
Score = 70.9 bits (172), Expect = 3e-12, Method: Composition-based stats.
Identities = 46/137 (33%), Positives = 71/137 (51%), Gaps = 34/137 (24%)
Query: 436 RCSVVERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAAL------- 488
R S + RR F+L + ++R HI+E + V L N+D +I ++R AP+ + A AL
Sbjct: 17 RGSHMTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQL 76
Query: 489 --------------------KDEFK-------LSEKQADAILDMNLRRLTMLERKKFVDE 521
+ EF L+E+QA AILD+ L++LT LE +K +DE
Sbjct: 77 GNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDE 136
Query: 522 SKTLMEQILKLEELLSS 538
K L++QI +L +L S
Sbjct: 137 YKELLDQIAELLRILGS 153
>pdb|1WP5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Dna
Topoisomerase Iv
Length = 323
Score = 69.7 bits (169), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 64/331 (19%), Positives = 141/331 (42%), Gaps = 32/331 (9%)
Query: 579 IPNDEMLLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYF 638
+ ++++++ +++ GYVKR ++ N G+ + D + + D +L F
Sbjct: 2 VASEDVIVTVTKDGYVKRTSLRSYAASN----GQDFAX-KDTDRLLAXLEXNTKDVLLLF 56
Query: 639 SDRGIVYSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMNG 698
+++G +++P+ G + I+ + E I IP+++F + + + +T NG
Sbjct: 57 TNKGNYLYCPVHELPDIRWKDLGQHIANIIPIDRDEEIIKAIPINDFELNGYFLFVTRNG 116
Query: 699 YIKKVSLNLFSSIRTTG-IIAIQLVPGDELKWVRCCTNDDLVAMASQNGMVILSSCDIIR 757
+KK L + + R + + I L D++ V + + + + NG + +
Sbjct: 117 XVKKTELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGXNELFLVTHNGYALWFDESEVS 176
Query: 758 SLSRNTRGSVAMRLKDGDKMASMDIIPAALHKDLERTPEDSHSNVKGSSGPWLLFVSESG 817
+ G LK+GD + S +I S ++ ++ G
Sbjct: 177 IVGVRAAGVKGXNLKEGDYIVSGQLIT--------------------SKDESIVVATQRG 216
Query: 818 HGKRVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAEDGESDEQVVLVSQSGTV 877
K+ L+ F K + G++ + E + + GF +A+D ++ + L ++ +
Sbjct: 217 AVKKXKLTEFEKATRAKRGVVILR---ELKANPHRISGFVVAQDSDT---IYLQTEKSFI 270
Query: 878 NRIKVRDISIQARYARGVILMRLELSGKIQS 908
IKV DI RY+ G ++ E +G++ S
Sbjct: 271 ETIKVGDIRFSDRYSNGSFVLDEEENGRVIS 301
>pdb|1X75|A Chain A, Ccdb:gyra14 Complex
pdb|1X75|B Chain B, Ccdb:gyra14 Complex
Length = 132
Score = 69.7 bits (169), Expect = 7e-12, Method: Composition-based stats.
Identities = 44/131 (33%), Positives = 68/131 (51%), Gaps = 34/131 (25%)
Query: 442 RRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAAL------------- 488
RR F+L + ++R HI+E + V L N+D +I ++R AP+ + A AL
Sbjct: 2 RRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAM 61
Query: 489 --------------KDEFK-------LSEKQADAILDMNLRRLTMLERKKFVDESKTLME 527
+ EF L+E+QA AILD+ L++LT LE +K +DE K L++
Sbjct: 62 LERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLD 121
Query: 528 QILKLEELLSS 538
QI +L +L S
Sbjct: 122 QIAELLRILGS 132
>pdb|4ELZ|A Chain A, Ccdbvfi:gyra14vfi
pdb|4ELZ|B Chain B, Ccdbvfi:gyra14vfi
Length = 153
Score = 68.9 bits (167), Expect = 1e-11, Method: Composition-based stats.
Identities = 41/137 (29%), Positives = 71/137 (51%), Gaps = 34/137 (24%)
Query: 436 RCSVVERRARFKLSQVKERRHIVEGIMVGLDNLDRVIRIVREAPSNSTASAAL------- 488
R S + RR F+L + ++R HI+EG+ + L N+D +I +++ AP+ + A L
Sbjct: 17 RGSHMTRRTIFELRKARDRAHILEGLALALANIDEIIELIKNAPTPAEAKEGLISRGWDL 76
Query: 489 ---------------------------KDEFKLSEKQADAILDMNLRRLTMLERKKFVDE 521
+ ++ L+E+QA AIL++ L RLT LE +K +DE
Sbjct: 77 GNVASMLERAGTDAARPDWLEPEFGIREGKYFLTEQQAQAILELRLHRLTGLEHEKILDE 136
Query: 522 SKTLMEQILKLEELLSS 538
K L+++I +L +L+S
Sbjct: 137 YKALLDEIAELMHILAS 153
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 65.9 bits (159), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/176 (28%), Positives = 81/176 (46%), Gaps = 8/176 (4%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
R++P+V DG KP R++L+ + L S + A V E +H HG+ ++ +++
Sbjct: 272 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 329
Query: 168 MAQDF--SLRYPLIRGHGNFGS--IDADPAAAMRYTECRLEALSEAMLLADIDQDTVNFV 223
+AQ+F S L+ +G FG+ AAA RY L L+ + D ++
Sbjct: 330 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRK-IFHPADDPLYKYI 388
Query: 224 PNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPE 279
DE E NGA GI G +T IPP N E++ + L+++ E
Sbjct: 389 QE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 443
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 65.5 bits (158), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 50/176 (28%), Positives = 81/176 (46%), Gaps = 8/176 (4%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
R++P+V DG KP R++L+ + L S + A V E +H HG+ ++ +++
Sbjct: 282 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 339
Query: 168 MAQDF--SLRYPLIRGHGNFGS--IDADPAAAMRYTECRLEALSEAMLLADIDQDTVNFV 223
+AQ+F S L+ +G FG+ AAA RY L L+ + D ++
Sbjct: 340 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRK-IFHPADDPLYKYI 398
Query: 224 PNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPE 279
DE E NGA GI G +T IPP N E++ + L+++ E
Sbjct: 399 QE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 453
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 11/189 (5%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
R++P+V DG KP R++L+ + L S + A V E +H HG+ ++ +++
Sbjct: 651 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 708
Query: 168 MAQDF--SLRYPLIRGHGNFGSIDA---DPAAAMRYTECRLEALSEAMLLADIDQDTVNF 222
+AQ+F S L+ +G FG+ D AAA Y L L+ + D +
Sbjct: 709 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRK-IFHPADDPLYKY 767
Query: 223 VPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEATL 282
+ DE E NGA GI G +T IPP N E++ + L+++ E L
Sbjct: 768 IQE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE--L 824
Query: 283 QELLEYMPG 291
+++ + G
Sbjct: 825 EQMHPWFRG 833
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 52/189 (27%), Positives = 87/189 (46%), Gaps = 11/189 (5%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
R++P+V DG KP R++L+ + L S + A V E +H HG+ ++ +++
Sbjct: 647 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 704
Query: 168 MAQDF--SLRYPLIRGHGNFGSIDA---DPAAAMRYTECRLEALSEAMLLADIDQDTVNF 222
+AQ+F S L+ +G FG+ D AAA Y L L+ + D +
Sbjct: 705 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRK-IFHPADDPLYKY 763
Query: 223 VPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPEATL 282
+ DE E NGA GI G +T IPP N E++ + L+++ E L
Sbjct: 764 IQE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE--L 820
Query: 283 QELLEYMPG 291
+++ + G
Sbjct: 821 EQMHPWFRG 829
>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 = 64.3 bits (155), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 50/177 (28%), Positives = 81/177 (45%), Gaps = 9/177 (5%)
Query: 108 RALPDVRDGLKPVHRRILFAMHELGLSSRKPFKKCARVVGEVLGKFHPHGDNAVYDSLVR 167
R++P+V DG KP R++L+ + L S + A V E +H HG+ ++ +++
Sbjct: 270 RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTA-YH-HGEQSLAQTIIG 327
Query: 168 MAQDF--SLRYPLIRGHGNFGSIDA---DPAAAMRYTECRLEALSEAMLLADIDQDTVNF 222
+AQ+F S L+ +G FG+ D AAA Y L L+ + D +
Sbjct: 328 LAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRK-IFHPADDPLYKY 386
Query: 223 VPNFDESQKEXXXXXXXXXXXXXNGASGIAVGMATNIPPHNLGELVDVLCALIHNPE 279
+ DE E NGA GI G +T IPP N E++ + L+++ E
Sbjct: 387 IQE-DEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEE 442
>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 = 38.9 bits (89), Expect = 0.015, Method: Composition-based stats.
Identities = 31/120 (25%), Positives = 56/120 (46%), Gaps = 9/120 (7%)
Query: 585 LLAISEKGYVKRMKPNTFNLQNRGTIGKSVGKLRVNDAMSDFIVCRAHDHVLYFSDRGIV 644
LL ++KGYVK++ F + +G + KL D + H+L F+ +G V
Sbjct: 83 LLLATKKGYVKKIPLAEFEYKAQGM---PIIKLTEGDEVVSIASSVDETHILLFTKKGRV 139
Query: 645 YSARAYKIPECTRNAAGTPLVQILSLSDGERITSIIPVSEFAGDQFLVMLTMNGYIKKVS 704
++P T A G VQ + L + + + + G+ +L+++T G +KK+S
Sbjct: 140 ARFSVREVPPSTPGARG---VQGIKLEKNDETSGL---RIWNGEPYLLVITAKGRVKKIS 193
Score = 35.0 bits (79), Expect = 0.22, Method: Composition-based stats.
Identities = 41/188 (21%), Positives = 79/188 (42%), Gaps = 30/188 (15%)
Query: 660 AGTPLVQILSLSDGERITSIIPVSEFAGDQF---LVMLTMNGYIKKVSLNLFSSIRTTGI 716
AG+ +Q +S R I V F ++F L++ T GY+KK+ L F + G+
Sbjct: 51 AGSQALQGSKVSLKSREEKI--VGAFIREKFGNRLLLATKKGYVKKIPLAEF-EYKAQGM 107
Query: 717 IAIQLVPGDELKWVRCCTNDDLVAMASQNGMVILSSCDIIRSLSRNTRGSVAMRLKDGDK 776
I+L GDE+ + ++ + + ++ G V S + + RG ++L+ D+
Sbjct: 108 PIIKLTEGDEVVSIASSVDETHILLFTKKGRVARFSVREVPPSTPGARGVQGIKLEKNDE 167
Query: 777 MASMDIIPAALHKDLERTPEDSHSNVKGSSGPWLLFVSESGHGKRVPLSSFRKLPLNRVG 836
+ + I + P+LL ++ G K++ S ++P G
Sbjct: 168 TSGLRI---------------------WNGEPYLLVITAKGRVKKI---SHEEIPKTNRG 203
Query: 837 LIGYKFSA 844
+ G + S
Sbjct: 204 VKGTEVSG 211
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 11/95 (11%)
Query: 807 GPWLLFVSESGHGKRVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAEDGESDE 866
G LL ++ G+ K++PL+ F G+ K + D + ++ +
Sbjct: 80 GNRLLLATKKGYVKKIPLAEFE---YKAQGMPIIKLTEGDEVVSI--------ASSVDET 128
Query: 867 QVVLVSQSGTVNRIKVRDISIQARYARGVILMRLE 901
++L ++ G V R VR++ ARGV ++LE
Sbjct: 129 HILLFTKKGRVARFSVREVPPSTPGARGVQGIKLE 163
>pdb|4B0T|A Chain A, Structure Of The Pup Ligase Pafa Of The Prokaryotic
Ubiquitin-Like Modification Pathway In Complex With Adp
pdb|4B0T|B Chain B, Structure Of The Pup Ligase Pafa Of The Prokaryotic
Ubiquitin-Like Modification Pathway In Complex With Adp
Length = 493
Score = 30.0 bits (66), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 756 IRSLSRNTRGSVAMRLKDGDKMASMDIIPAALH---KDLERTPEDSHSNVKGS 805
IR +SR+ GS + LKDG M ++ I K LE+ PE S +
Sbjct: 266 IREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQRPEPEFSGTSNT 318
>pdb|2O8S|A Chain A, X-ray Crystal Structure Of Protein Agr_c_984 From
Agrobacterium Tumefaciens. Northeast Structural Genomics
Consortium Target Atr120.
pdb|2O8S|B Chain B, X-ray Crystal Structure Of Protein Agr_c_984 From
Agrobacterium Tumefaciens. Northeast Structural Genomics
Consortium Target Atr120
Length = 323
Score = 29.6 bits (65), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 13/99 (13%)
Query: 815 ESGHGKRVPLSSFRKLPLNRVGLIGYKFSAEDRLAAVFVVGFSLAE---DGESDEQVVLV 871
+ +G R+ L RK P + GL F A+D LA VF F+L + + D+Q L+
Sbjct: 191 DDNNGVRLALYFERKAPTIKSGL---DFLADDALAQVFRTTFNLPDAFAAADVDKQAALI 247
Query: 872 SQSGTVNRIKVRDISIQARYARGVILMRLELSGKIQSAS 910
+S I ++D +Q G +L R + + Q+ S
Sbjct: 248 EKS-----INIKD--LQDPEKVGKLLERFTIXWEXQNPS 279
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
0.319 0.135 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,917,085
Number of Sequences: 62578
Number of extensions: 996427
Number of successful extensions: 2293
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2165
Number of HSP's gapped (non-prelim): 58
length of query: 941
length of database: 14,973,337
effective HSP length: 108
effective length of query: 833
effective length of database: 8,214,913
effective search space: 6843022529
effective search space used: 6843022529
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)