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= 007002
(622 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 279 bits (713), Expect = 4e-75, Method: Compositional matrix adjust.
Identities = 137/237 (57%), Positives = 169/237 (71%), Gaps = 1/237 (0%)
Query: 386 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 445
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 446 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 505
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 506 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 565
L + G +Y+ PPLYK+ +GKQ Y Y+D EL K+KS +SI R+KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQ 182
Query: 566 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 622
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 183 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 239
>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 = 279 bits (713), Expect = 4e-75, Method: Compositional matrix adjust.
Identities = 137/237 (57%), Positives = 169/237 (71%), Gaps = 1/237 (0%)
Query: 386 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 445
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 446 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 505
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 506 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 565
L + G +Y+ PPLYK+ +GKQ Y Y+D EL K+KS +SI R+KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQ 182
Query: 566 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 622
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 183 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 239
>pdb|1EI1|A Chain A, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
pdb|1EI1|B Chain B, Dimerization Of E. Coli Dna Gyrase B Provides A Structural
Mechanism For Activating The Atpase Catalytic Center
Length = 391
Score = 258 bits (658), Expect = 9e-69, Method: Compositional matrix adjust.
Identities = 136/352 (38%), Positives = 207/352 (58%), Gaps = 13/352 (3%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 24 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 83
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + R+G +
Sbjct: 84 EEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVV--NALSQKLELVIQREGKIHR 141
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FL+
Sbjct: 142 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLD 197
Query: 180 PKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-DVVGFRKDVDGITIDL 238
++I LR D + + + + GG++ +V++LN +K P+H ++ F + DGI +++
Sbjct: 198 SGVSIRLR----DKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEV 253
Query: 239 ALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGE 298
ALQW +D + + + + N+I DGGTH+ G +A++TRTLN+ K K +S +G+
Sbjct: 254 ALQW-NDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGD 312
Query: 299 HVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHP 350
REGL ++SV+VP+P+F QTK +L + EV+ V+Q + E L EYL +P
Sbjct: 313 DAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENP 364
>pdb|3FOE|C Chain C, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOE|D Chain D, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|C Chain C, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|D Chain D, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3K9F|C Chain C, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3K9F|D Chain D, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3KSA|C Chain C, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSA|D Chain D, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSB|C Chain C, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3KSB|D Chain D, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3LTN|C Chain C, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3LTN|D Chain D, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3RAF|C Chain C, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAF|D Chain D, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|C Chain C, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|D Chain D, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|C Chain C, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|D Chain D, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
Length = 268
Score = 239 bits (611), Expect = 3e-63, Method: Compositional matrix adjust.
Identities = 119/227 (52%), Positives = 159/227 (70%), Gaps = 7/227 (3%)
Query: 388 LPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMY 447
L GKL S P ++E+++VEGDSAGGSAKQGRDR+FQAILPLRGK++N + A +
Sbjct: 33 LSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADIL 92
Query: 448 KNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 507
KNEEI +I +G GV G DF E Y KIII+TDAD DGAHI+TLLLTFFYRY + L
Sbjct: 93 KNEEINTMIYTIGAGV-GADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLV 151
Query: 508 DEGCIYVGVPPLYKVERGK----QVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMP 563
+ G +Y+ +PPLYK+ +GK +V Y + D EL++++ F A ++QR+KGLGEM
Sbjct: 152 EAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGA--TLQRYKGLGEMNA 209
Query: 564 VQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 610
QLWETT+NPE R L ++ IED A A + LMG +V+ R++ I++
Sbjct: 210 DQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIED 256
>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 = 229 bits (584), Expect = 4e-60, Method: Compositional matrix adjust.
Identities = 120/237 (50%), Positives = 147/237 (62%), Gaps = 35/237 (14%)
Query: 386 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 445
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 446 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 505
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 506 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 565
L + G +Y+ PP +KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPP----------------------------------TGYKGLGEMNADQ 148
Query: 566 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 622
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 149 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 205
>pdb|1KIJ|A Chain A, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
pdb|1KIJ|B Chain B, Crystal Structure Of The 43k Atpase Domain Of Thermus
Thermophilus Gyrase B In Complex With Novobiocin
Length = 390
Score = 209 bits (532), Expect = 3e-54, Method: Compositional matrix adjust.
Identities = 129/353 (36%), Positives = 189/353 (53%), Gaps = 11/353 (3%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIG TG G HHL EILDNAVDEA AGYA+ I V L D S++V DNGRGIP+DL P
Sbjct: 23 MYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLNEDGSLTVEDNGRGIPVDLMPE 82
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
K A+E + LH+ NALSE V V+R+G +
Sbjct: 83 EGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVV--NALSEWTVVEVFREGKHHRI 140
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+SRG+ T V+ + + GTR+ F PD ++F ++FD + I R+RE+A+L
Sbjct: 141 AFSRGE--VTEPLRVVGEAPRGKTGTRVTFKPDPEIFGN-LRFDPSKIRARLREVAYLVA 197
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDG-ITIDLA 239
L + + D + + + GG+ + + L + L++ + G + +++
Sbjct: 198 GLKLVFQ----DRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVEVEVG 253
Query: 240 LQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEH 299
+ Y+ +L YAN I T DGGTH+ K++ +R LN KK+ K+K +G+
Sbjct: 254 F-LHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTGDD 312
Query: 300 VREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPDV 352
+ EGL ++SV++PNP+FEGQTK +L NPE V Q V E L E LE +P +
Sbjct: 313 LLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEILEENPRI 365
>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 = 207 bits (527), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 109/242 (45%), Positives = 151/242 (62%), Gaps = 3/242 (1%)
Query: 377 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 436
V +K ++ +LPGKLADC T EESE+FIVEGDSAGGSAKQ RD+ FQAI+P+RGKIL
Sbjct: 18 VERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKIL 77
Query: 437 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 496
N + ++E+ ++ A+G+ +D + LRY KI IL DAD DG HI TLL
Sbjct: 78 NTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE--LRYGKICILADADSDGLHIATLLC 135
Query: 497 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 556
F ++ L +EG +YV +PPL++++ GK V Y DD EL+ + + N I RFK
Sbjct: 136 ALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKGNKNPQITRFK 195
Query: 557 GLGEMMPVQLWETTLNPEQRMLKQLVIEDA-AEANVVFSSLMGARVDTRKELIQNAANLV 615
GLGEM +QL ETT++P R L QL ++DA A ++ L R RK+ ++ NL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLA 255
Query: 616 NL 617
++
Sbjct: 256 DI 257
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 207 bits (527), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 109/242 (45%), Positives = 151/242 (62%), Gaps = 3/242 (1%)
Query: 377 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 436
V +K ++ +LPGKLADC T EESE+FIVEGDSAGGSAKQ RD+ FQAI+P+RGKIL
Sbjct: 18 VERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKIL 77
Query: 437 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 496
N + ++E+ ++ A+G+ +D + LRY KI IL DAD DG HI TLL
Sbjct: 78 NTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE--LRYGKICILADADSDGLHIATLLC 135
Query: 497 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 556
F ++ L +EG +YV +PPL++++ GK V Y DD EL+ + + N I RFK
Sbjct: 136 ALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKGNKNPQITRFK 195
Query: 557 GLGEMMPVQLWETTLNPEQRMLKQLVIEDA-AEANVVFSSLMGARVDTRKELIQNAANLV 615
GLGEM +QL ETT++P R L QL ++DA A ++ L R RK+ ++ NL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLA 255
Query: 616 NL 617
++
Sbjct: 256 DI 257
>pdb|3IG0|A Chain A, Crystal Structure Of The Second Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Toprim Domain
At 2.1 A Resolution
pdb|3M4I|A Chain A, Crystal Structure Of The Second Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Toprim Domain
At 1.95 A Resolution
Length = 242
Score = 195 bits (496), Expect = 5e-50, Method: Compositional matrix adjust.
Identities = 110/228 (48%), Positives = 152/228 (66%), Gaps = 8/228 (3%)
Query: 398 TTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIR 457
T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+ + KN E+Q +I
Sbjct: 15 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIIT 74
Query: 458 ALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 517
ALG G+ E F LRYHKI+++ DADVDG HI TLLLT +R+ + L + G +++ P
Sbjct: 75 ALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 133
Query: 518 PLYKVE-RGKQVQYCYDDAEL-----KKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTL 571
PLYK++ + ++ Y D E +K+ N IQR+KGLGEM +LWETT+
Sbjct: 134 PLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTM 193
Query: 572 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-QNAANLVNLD 618
+P R+L+Q+ ++DAA A+ +FS LMG VD R+ I +NA ++ LD
Sbjct: 194 DPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLD 241
>pdb|2ZJT|A Chain A, Crystal Structure Of Dna Gyrase B' Domain Sheds Lights On
The Mechanism For T-Segment Navigation
pdb|2ZJT|B Chain B, Crystal Structure Of Dna Gyrase B' Domain Sheds Lights On
The Mechanism For T-Segment Navigation
Length = 247
Score = 195 bits (495), Expect = 6e-50, Method: Compositional matrix adjust.
Identities = 110/228 (48%), Positives = 152/228 (66%), Gaps = 8/228 (3%)
Query: 398 TTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIR 457
T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+ + KN E+Q +I
Sbjct: 7 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIIT 66
Query: 458 ALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 517
ALG G+ E F LRYHKI+++ DADVDG HI TLLLT +R+ + L + G +++ P
Sbjct: 67 ALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 125
Query: 518 PLYKVE-RGKQVQYCYDDAEL-----KKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTL 571
PLYK++ + ++ Y D E +K+ N IQR+KGLGEM +LWETT+
Sbjct: 126 PLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTM 185
Query: 572 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-QNAANLVNLD 618
+P R+L+Q+ ++DAA A+ +FS LMG VD R+ I +NA ++ LD
Sbjct: 186 DPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLD 233
>pdb|3NUH|B Chain B, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold
That Plays A Critical Role In Gyrase Function
Length = 420
Score = 188 bits (478), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 90/158 (56%), Positives = 114/158 (72%)
Query: 377 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 436
R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGR+R+ QAILPL+GKIL
Sbjct: 8 TRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKIL 67
Query: 437 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 496
NVE+ ++E+ LI ALG G+ +++ + LRYH III TDADVDG+HIRTLLL
Sbjct: 68 NVEKARFDKXLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIXTDADVDGSHIRTLLL 127
Query: 497 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDD 534
TFFYR + + G +Y+ PPLYKV++GKQ QY DD
Sbjct: 128 TFFYRQXPEIVERGHVYIAQPPLYKVKKGKQEQYIKDD 165
Score = 66.2 bits (160), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 551 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-Q 609
SIQR+KGLGE P QLWETT +PE R ++ ++DA A+ +F++L G V+ R+ I +
Sbjct: 351 SIQRYKGLGEXNPEQLWETTXDPESRRXLRVTVKDAIAADQLFTTLXGDAVEPRRAFIEE 410
Query: 610 NAANLVNLD 618
NA N+D
Sbjct: 411 NALKAANID 419
>pdb|4HXZ|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HXZ|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HY1|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HY1|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYM|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYM|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 390
Score = 161 bits (408), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 110/352 (31%), Positives = 166/352 (47%), Gaps = 14/352 (3%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY P +HL+ EI+DN+VDE AG+AS I + L DNS+ VAD+GRG+P+D+HP
Sbjct: 24 MYTNIENP---NHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPE 80
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
S +E ++T LH+ NALS LE + RDG YH
Sbjct: 81 HKMSGIELIMTKLHS--GGKFSNKNYTHSGGLHGVGVSVVNALSTRLEAEIKRDGNVYHI 138
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+ G T ++ K GT+IRFWP+K+ F I+ + + + A L
Sbjct: 139 VFEDG--FKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDD-IKVNFKALKNLLEAKAILCK 195
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAGGLEEYV-QWLNTDKKPLHDVVGFRKDVDGITIDLA 239
LTI E K + + F GL+ Y+ L + P + +D
Sbjct: 196 ALTIKYSNE----IKKEKLTWHFETGLKGYLDHKLEAETLPAEPFIIDNFSNGDSYLDAV 251
Query: 240 LQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEH 299
WC D Y N I T GTH+ G+K + + + +K+ ++ K+I ++
Sbjct: 252 FCWCEDPSESIKNSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKN-SLSVKNIKITAND 310
Query: 300 VREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYLELHPD 351
L +ISV++ NP+F GQTK +L N +V V +V++ LT +L +PD
Sbjct: 311 SFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPD 362
>pdb|4GEE|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4GFN|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic
pdb|4GGL|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HXW|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 215
Score = 157 bits (398), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 86/205 (41%), Positives = 120/205 (58%), Gaps = 8/205 (3%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGST GLHHLV+EI+DN++DEA AG+A +I+V + D+S++V D+GRGIP+ +
Sbjct: 11 MYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDGRGIPVGIQAK 70
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
T + A+ETV TVLHA NALS SL+V V++DG Y+Q
Sbjct: 71 TGRPAVETVFTVLHA--GGKFGGGGYKVSGGLHGVGSSVVNALSTSLDVRVYKDGKVYYQ 128
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+Y RG V L ++ DR GT + F PD ++FT +D + +A R+RELAFLN
Sbjct: 129 EYRRGAVVDDLKV----IEETDRHGTTVHFIPDPEIFTETTVYDFDKLATRVRELAFLNR 184
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAG 205
L I++ ED + EY + G
Sbjct: 185 GLHISI--EDRREGQEDKKEYHYEG 207
>pdb|3TTZ|A Chain A, Crystal Structure Of A Topoisomerase Atpase Inhibitor
pdb|3TTZ|B Chain B, Crystal Structure Of A Topoisomerase Atpase Inhibitor
pdb|3U2D|A Chain A, S. Aureus Gyrb Atpase Domain In Complex With Small
Molecule Inhibitor
pdb|3U2D|B Chain B, S. Aureus Gyrb Atpase Domain In Complex With Small
Molecule Inhibitor
pdb|3U2K|A Chain A, S. Aureus Gyrb Atpase Domain In Complex With A Small
Molecule Inhibitor
pdb|3U2K|B Chain B, S. Aureus Gyrb Atpase Domain In Complex With A Small
Molecule Inhibitor
Length = 198
Score = 154 bits (390), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 87/207 (42%), Positives = 115/207 (55%), Gaps = 30/207 (14%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGST RGLHHLV+EI+DN++DEA AGYA+ IEV + DN + V DNGRGIP+D+
Sbjct: 22 MYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEK 81
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
+ A+E +LT NALS+ LEV V R+ YHQ
Sbjct: 82 MGRPAVEVILT-------------------------SSVVNALSQDLEVYVHRNETIYHQ 116
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
Y +G P L V + D+ GT IRF D ++FT +++ T+ RIRELAFLN
Sbjct: 117 AYKKGVPQFDLK----EVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNK 172
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAGGL 207
+ I LR E D E + + Y + GG+
Sbjct: 173 GIQITLRDE-RDEENVREDSYHYEGGI 198
>pdb|3LNU|A Chain A, Crystal Structure Of Pare Subunit
pdb|3LPS|A Chain A, Crystal Structure Of Pare
Length = 408
Score = 151 bits (382), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 104/349 (29%), Positives = 172/349 (49%), Gaps = 19/349 (5%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY + P +HL E++DN+VDEA AG+A IEV L D S V+D+GRG+P+D+HP
Sbjct: 44 MYTDTARP---NHLAQEVIDNSVDEALAGHAKQIEVTLYKDGSCEVSDDGRGMPVDIHPE 100
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
+E +LT LHA NALS +E+ + R+G E+
Sbjct: 101 EKIPGVELILTRLHA--GGKFNNRNYTFSGGLHGVGVSVVNALSTKVELFIKREGSEHRM 158
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
++ G + L V+ K GTR+RFW D + F T +F+ + +R A L P
Sbjct: 159 EFRDGNAASKL--EVVGTVGKKNTGTRLRFWADPKYFDTP-KFNVRALRHLLRAKAVLCP 215
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK--PLHDVVG-FRKDVDGITID 237
LT+ L E + + + ++F GL +Y++ + + P VG +KD + +D
Sbjct: 216 GLTVKLHDEAT----GEQDSWYFENGLRDYLKGEMAEHEMLPADLFVGSLKKDTE--IVD 269
Query: 238 LALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSG 297
A W + Y N I T GTH+ G+++ LT L + + + + L+
Sbjct: 270 WAAGWVPEG-ELVQESYVNLIPTAQHGTHVNGLRSGLTDALREFC-DFRNLLPRGVKLAP 327
Query: 298 EHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYL 346
E V + +T ++S+++ +P+F GQTK RL + + ++ + + + YL
Sbjct: 328 EDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGAAHDAFSLYL 376
>pdb|3G75|A Chain A, Crystal Structure Of Staphylococcus Aureus Gyrase B Co-
Complexed With Inhibitor
pdb|3G75|B Chain B, Crystal Structure Of Staphylococcus Aureus Gyrase B Co-
Complexed With Inhibitor
pdb|3G7B|A Chain A, Staphylococcus Aureus Gyrase B Co-Complex With Inhibitor
pdb|3G7B|B Chain B, Staphylococcus Aureus Gyrase B Co-Complex With Inhibitor
Length = 184
Score = 149 bits (376), Expect = 4e-36, Method: Compositional matrix adjust.
Identities = 85/203 (41%), Positives = 112/203 (55%), Gaps = 30/203 (14%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGST RGLHHLV+EI+DN++DEA AGYA+ IEV + DN + V DNGRGIP+D+
Sbjct: 11 MYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEK 70
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
+ A+E +LT NALS+ LEV V R+ YHQ
Sbjct: 71 MGRPAVEVILT-------------------------SSVVNALSQDLEVYVHRNETIYHQ 105
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
Y +G P L V + D+ GT IRF D ++FT +++ T+ RIRELAFLN
Sbjct: 106 AYKKGVPQFDLK----EVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNK 161
Query: 181 KLTIALRKEDSDPEKNQYNEYFF 203
+ I LR E D E + + Y +
Sbjct: 162 GIQITLRDE-RDEENVREDSYHY 183
>pdb|1S16|A Chain A, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
pdb|1S16|B Chain B, Crystal Structure Of E. Coli Topoisomerase Iv Pare 43kda
Subunit Complexed With Adpnp
Length = 390
Score = 149 bits (376), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 106/351 (30%), Positives = 171/351 (48%), Gaps = 22/351 (6%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+GRG+P+D+HP
Sbjct: 25 MYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPE 81
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
A+E +L LHA NALS+ +EV V RDG Y+
Sbjct: 82 EGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNI 139
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+ G+ V L V+ K GT + FWPD+ F + +F + + ++ A L P
Sbjct: 140 AFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSRLTHVLKAKAVLCP 196
Query: 181 KLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQWLNT-DKKPLHDVVGFRKDVDGIT 235
+ I + E ++ E+ + + GL +Y V L T +KP + F D +
Sbjct: 197 GVEITFKDEINNTEQ----RWCYQDGLNDYLAEAVNGLPTLPEKPF--IGNFAGDTE--A 248
Query: 236 IDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISL 295
+D AL W + Y N I T+ GGTH+ G++ L + + + + + + L
Sbjct: 249 VDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFC-EYRNILPRGVKL 307
Query: 296 SGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLTEYL 346
S E + + ++SV++ +P+F GQTK RL + + V V++ +L
Sbjct: 308 SAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAFILWL 358
>pdb|4HYP|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|C Chain C, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HYP|D Chain D, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 215
Score = 143 bits (360), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 82/209 (39%), Positives = 113/209 (54%), Gaps = 12/209 (5%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 12 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 71
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + R+G +
Sbjct: 72 EEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHR 129
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FLN
Sbjct: 130 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLN 185
Query: 180 PKLTIALRKEDSDPEKNQYNEYFFAGGLE 208
++I LR + E ++F GLE
Sbjct: 186 SGVSIRLRDKRDGKE-----DHFHYEGLE 209
>pdb|4DUH|A Chain A, Crystal Structure Of 24 Kda Domain Of E. Coli Dna Gyrase B
In Complex With Small Molecule Inhibitor
pdb|4DUH|B Chain B, Crystal Structure Of 24 Kda Domain Of E. Coli Dna Gyrase B
In Complex With Small Molecule Inhibitor
Length = 220
Score = 142 bits (359), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 80/200 (40%), Positives = 109/200 (54%), Gaps = 8/200 (4%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 25 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 84
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + R+G +
Sbjct: 85 EEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHR 142
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FLN
Sbjct: 143 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLN 198
Query: 180 PKLTIALR-KEDSDPEKNQY 198
++I LR K D + Y
Sbjct: 199 SGVSIRLRDKRDGKEDHFHY 218
>pdb|1KZN|A Chain A, Crystal Structure Of E. Coli 24kda Domain In Complex With
Clorobiocin
Length = 205
Score = 142 bits (359), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 80/200 (40%), Positives = 109/200 (54%), Gaps = 8/200 (4%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 11 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 70
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + R+G +
Sbjct: 71 EEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHR 128
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FLN
Sbjct: 129 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLN 184
Query: 180 PKLTIALR-KEDSDPEKNQY 198
++I LR K D + Y
Sbjct: 185 SGVSIRLRDKRDGKEDHFHY 204
>pdb|3G7E|A Chain A, Crystal Structure Of E. Coli Gyrase B Co-Complexed With
Inhibitor
Length = 203
Score = 142 bits (357), Expect = 8e-34, Method: Compositional matrix adjust.
Identities = 77/188 (40%), Positives = 105/188 (55%), Gaps = 7/188 (3%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 11 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 70
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + R+G +
Sbjct: 71 EEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHR 128
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FLN
Sbjct: 129 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLN 184
Query: 180 PKLTIALR 187
++I LR
Sbjct: 185 SGVSIRLR 192
>pdb|1AJ6|A Chain A, Novobiocin-resistant Mutant (r136h) Of The N-terminal 24
Kda Fragment Of Dna Gyrase B Complexed With Novobiocin
At 2.3 Angstroms Resolution
Length = 219
Score = 140 bits (354), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 79/200 (39%), Positives = 108/200 (54%), Gaps = 8/200 (4%)
Query: 1 MYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHP 59
MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+GRGIP +HP
Sbjct: 24 MYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHP 83
Query: 60 ATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYH 119
SA E ++TVLHA NALS+ LE+ + +G +
Sbjct: 84 EEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQHEGKIHR 141
Query: 120 QKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
Q Y G P L ++ GT +RFWP + FT +F++ +A R+REL+FLN
Sbjct: 142 QIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLN 197
Query: 180 PKLTIALR-KEDSDPEKNQY 198
++I LR K D + Y
Sbjct: 198 SGVSIRLRDKRDGKEDHFHY 217
>pdb|4HZ5|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|C Chain C, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|D Chain D, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|E Chain E, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|F Chain F, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|G Chain G, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|H Chain H, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
pdb|4HZ5|J Chain J, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 216
Score = 140 bits (352), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 84/198 (42%), Positives = 111/198 (56%), Gaps = 8/198 (4%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGST RGLHHLVYEI+DNAVDEA +GY + I V + DNS+ VAD+GRG+P +H A
Sbjct: 12 MYIGSTDSRGLHHLVYEIVDNAVDEALSGYGNEINVTIQKDNSICVADSGRGMPTGMH-A 70
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
+ +E + TVLHA NALS+ LEV + RDG+EY +
Sbjct: 71 SGIPTVEVIFTVLHA--GGKFGQGGYKTSGGLHGVGASVVNALSKWLEVHIVRDGVEYME 128
Query: 121 KYS-RGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
++ GKPV TL +K R GT + F PD +F+T F + +A R+RE AFL
Sbjct: 129 RFEDGGKPVGTLKK---IGKTKKRNGTSVTFLPDDTIFSTT-NFSYEILAERLRESAFLL 184
Query: 180 PKLTIALRKEDSDPEKNQ 197
+ I L E + K +
Sbjct: 185 KGVKITLTDERGEEPKEE 202
>pdb|4B6C|A Chain A, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
pdb|4B6C|B Chain B, Structure Of The M. Smegmatis Gyrb Atpase Domain In
Complex With An Aminopyrazinamide
Length = 196
Score = 138 bits (348), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 79/189 (41%), Positives = 106/189 (56%), Gaps = 29/189 (15%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGSTG RGLHHL++E++DNAVDEA AG+A+ ++V + AD SV V D+GRGIP+++H A
Sbjct: 25 MYIGSTGERGLHHLIWEVVDNAVDEAMAGFATRVDVKIHADGSVEVRDDGRGIPVEMH-A 83
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
T ++ V+T + NALS LE TV RDG E+ Q
Sbjct: 84 TGMPTIDVVMTQVGV----------------------SVVNALSTRLEATVLRDGYEWFQ 121
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
Y R P + GT IRFW D ++F T ++ T+A R++E+AFLN
Sbjct: 122 YYDRSVP-----GKLKQGGETKETGTTIRFWADPEIFETT-DYNFETVARRLQEMAFLNK 175
Query: 181 KLTIALRKE 189
LTI L E
Sbjct: 176 GLTIELTDE 184
>pdb|4EM7|A Chain A, Crystal Structure Of A Topoisomerase Atp Inhibitor
pdb|4EMV|A Chain A, Crystal Structure Of A Topoisomerase Atp Inhibitor
Length = 226
Score = 131 bits (330), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 78/193 (40%), Positives = 109/193 (56%), Gaps = 7/193 (3%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MYIGST GLHHLV+EI+DNAVDEA +G+ I+V + D S++V D+GRG+P +H A
Sbjct: 31 MYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDVTINKDGSLTVQDHGRGMPTGMH-A 89
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
+E + T+LHA NALS LEV + RDG Y Q
Sbjct: 90 MGIPTVEVIFTILHA--GGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQ 147
Query: 121 KYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLN 179
++ GKPVTTL + K + GT++ F PD +F+T F +NTI+ R+ E AFL
Sbjct: 148 RFENGGKPVTTLKK--IGTALKSKTGTKVTFMPDATIFSTT-DFKYNTISERLNESAFLL 204
Query: 180 PKLTIALRKEDSD 192
+T++L + +D
Sbjct: 205 KNVTLSLTDKRTD 217
>pdb|3CWV|A Chain A, Crystal Structure Of B-Subunit Of The Dna Gyrase From
Myxococcus Xanthus
pdb|3CWV|B Chain B, Crystal Structure Of B-Subunit Of The Dna Gyrase From
Myxococcus Xanthus
Length = 369
Score = 128 bits (322), Expect = 8e-30, Method: Compositional matrix adjust.
Identities = 98/369 (26%), Positives = 160/369 (43%), Gaps = 60/369 (16%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGR--------- 51
MY G G GLHHLVY +LD A +EA+ G ++ + + D S+++ R
Sbjct: 21 MYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSRTVTAENLVR 80
Query: 52 ---GIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLE 108
G P + +++L V ALS +
Sbjct: 81 VATGAGFLGRPPGDGWGWDSMLVV---------------------------SLALSSRYQ 113
Query: 109 VTVWRDGMEYHQKYSRGKP----VTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFD 164
V +W DG ++ G P +PV ++ +G R+ F PD +F + FD
Sbjct: 114 VDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAE--RGVRVHFVPDATIFEV-LAFD 170
Query: 165 HNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-D 223
++ R ELA L P L ++ +D ++ + + GG+ ++ L + LH +
Sbjct: 171 RARLSRRCNELAALAPGLRVSF----ADLQRGERTLWHLPGGVAQWAHVLTEARPQLHPE 226
Query: 224 VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGK 283
V F DG+ + ALQWC D S T+L +AN++RT+ G H++GV +L L L
Sbjct: 227 PVVFDFTWDGLRVQCALQWCEDEDS-TLLSFANAVRTVRHGAHVKGVTQALRGALAKLSG 285
Query: 284 KSKTVKDKDISLSGEHVREGLTCIISVRVPNPE--FEGQTKTRLGNPEVRKVVDQSVQEY 341
+++ + V +GLT I++V P + F G TK L P + + + + +Q
Sbjct: 286 ETRG------AFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPL 339
Query: 342 LTEYLELHP 350
E L HP
Sbjct: 340 FIELLREHP 348
>pdb|4HZ0|A Chain A, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity.
pdb|4HZ0|B Chain B, Pyrrolopyrimidine Inhibitors Of Dna Gyrase B And
Topoisomerase Iv, Part I: Structure Guided Discovery And
Optimization Of Dual Targeting Agents With Potent,
Broad-spectrum Enzymatic Activity
Length = 213
Score = 104 bits (259), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 66/195 (33%), Positives = 100/195 (51%), Gaps = 8/195 (4%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+GRG+P+D+HP
Sbjct: 14 MYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPE 70
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
A+E +L LHA NALS+ +EV V RDG Y+
Sbjct: 71 EGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNI 128
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+ G+ V L V+ K GT + FWPD+ F + +F + + ++ A L P
Sbjct: 129 AFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSRLTHVLKAKAVLCP 185
Query: 181 KLTIALRKEDSDPEK 195
+ I + E ++ E+
Sbjct: 186 GVEITFKDEINNTEQ 200
>pdb|3FV5|A Chain A, Crystal Structure Of E. Coli Topoisomerase Iv Co-Complexed
With Inhibitor
pdb|3FV5|B Chain B, Crystal Structure Of E. Coli Topoisomerase Iv Co-Complexed
With Inhibitor
Length = 201
Score = 103 bits (258), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 66/195 (33%), Positives = 100/195 (51%), Gaps = 8/195 (4%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+GRG+P+D+HP
Sbjct: 11 MYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPE 67
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
A+E +L LHA NALS+ +EV V RDG Y+
Sbjct: 68 EGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNVRRDGQVYNI 125
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+ G+ V L V+ K GT + FWPD+ F + +F + + ++ A L P
Sbjct: 126 AFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSRLTHVLKAKAVLCP 182
Query: 181 KLTIALRKEDSDPEK 195
+ I + E ++ E+
Sbjct: 183 GVEITFKDEINNTEQ 197
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 102 bits (255), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 73/228 (32%), Positives = 113/228 (49%), Gaps = 17/228 (7%)
Query: 394 DCSSTTPEESEIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYK 448
D E + + EGDSA G GRD+ + PLRGKILNV + +
Sbjct: 16 DAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDK--YGVFPLRGKILNVREASHKQIME 73
Query: 449 NEEIQNLIRALGLGVKGEDFKKE----ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 504
N EI N+I+ +GL K ++++ E LRY KI+I+TD D DG+HI+ LL+ F +
Sbjct: 74 NAEINNIIKIVGLQYK-KNYEDEDSLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWP 132
Query: 505 TLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPV 564
+L + + P+ KV + KQ Y E ++ KSS P++ + ++ +KGLG
Sbjct: 133 SLLRHRFLEEFITPIVKVSKNKQEMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSK 192
Query: 565 QLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 610
+ E + + K ED A ++ FS ++D RKE + N
Sbjct: 193 EAKEYFADMKRHRIQFKYSGPEDDAAISLAFSK---KQIDDRKEWLTN 237
>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 = 100 bits (250), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 72/221 (32%), Positives = 105/221 (47%), Gaps = 19/221 (8%)
Query: 402 ESEIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLI 456
E + + EGDSA G GRDR + PLRGKILNV + +N EI N+I
Sbjct: 52 ECTLILTEGDSAKSLAVSGLGVIGRDR--YGVFPLRGKILNVREASHKQIMENAEINNII 109
Query: 457 RALGLGVK-----GEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGC 511
+ +GL K E K LRY KI+I+TD D DG+HI+ LL+ F + +L G
Sbjct: 110 KIVGLQYKKSYDDAESLK--TLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGF 167
Query: 512 IYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTL 571
+ + P+ K + KQ Y E + K + + I+ +KGLG + E
Sbjct: 168 LEEFITPIVKASKNKQELSFYSIPEFDEWKKHIENQKAWKIKYYKGLGTSTAKEAKEYFA 227
Query: 572 NPEQR--MLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 610
+ E+ + + ED A + FS ++D RKE + N
Sbjct: 228 DMERHRILFRYAGPEDDAAITLAFSK---KKIDDRKEWLTN 265
>pdb|1S14|A Chain A, Crystal Structure Of Escherichia Coli Topoisomerase Iv
Pare 24kda Subunit
pdb|1S14|B Chain B, Crystal Structure Of Escherichia Coli Topoisomerase Iv
Pare 24kda Subunit
Length = 194
Score = 99.4 bits (246), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 63/195 (32%), Positives = 98/195 (50%), Gaps = 31/195 (15%)
Query: 1 MYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGRGIPIDLHPA 60
MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+GRG+P+D+HP
Sbjct: 25 MYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPE 81
Query: 61 TNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQ 120
A+E +L + NALS+ +EV V RDG Y+
Sbjct: 82 EGVPAVELILCI-------------------------SVVNALSKRVEVNVRRDGQVYNI 116
Query: 121 KYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAGRIRELAFLNP 180
+ G+ V L V+ K GT + FWPD+ F + +F + + ++ A L P
Sbjct: 117 AFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSRLTHVLKAKAVLCP 173
Query: 181 KLTIALRKEDSDPEK 195
+ I + E ++ E+
Sbjct: 174 GVEITFKDEINNTEQ 188
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 83.6 bits (205), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 130/538 (24%), Positives = 216/538 (40%), Gaps = 84/538 (15%)
Query: 10 GLHHLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALE 67
GL + EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E
Sbjct: 53 GLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPE 112
Query: 68 TVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQKYSRGKP 127
+ L + LE G +Y QK+
Sbjct: 113 MIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMS 172
Query: 128 VTTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL 175
+ CH + S K T++ F PD F + D++ I G +R++
Sbjct: 173 I----CHPPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDI 227
Query: 176 -AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGI 234
+LN K ++ +R F +E Y++ L L++ + R +V
Sbjct: 228 NVYLNGK-SLKIRN--------------FKNYVELYLKSL--IPTILYERINNRWEVAFA 270
Query: 235 TIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDIS 294
D++ Q S + NSI T GGTH+ + + + ++ + KK K K
Sbjct: 271 VSDISFQQIS---------FVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSF- 320
Query: 295 LSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD-QSVQEYLTEYLELHPDVX 353
++ + I+ + NP F QTK +L +V D S E EY+
Sbjct: 321 ----QIKNNMFIFINCLIENPAFTSQTKEQL----TTRVKDFGSRCEIPLEYIN------ 366
Query: 354 XXXXXXXXXXXXXXXXXXXXXXXVRQKSVLRSSSLPGKLADCSSTTPEE---SEIFIVEG 410
+ + R ++ P KL D + +E + + EG
Sbjct: 367 ----------KIMKTDLATRMFEIADANESRITNYP-KLEDANKAGTKEGYKCTLVLTEG 415
Query: 411 DSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKG 465
DSA G A GRD + PLRGK+LNV + KN EIQ + + +GL +
Sbjct: 416 DSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRK 473
Query: 466 EDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV 522
+ ++LRY ++I+TD D DG+HI+ L++ F L D +G + + P+ KV
Sbjct: 474 KYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKV 531
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 82.0 bits (201), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 131/540 (24%), Positives = 217/540 (40%), Gaps = 92/540 (17%)
Query: 10 GLHHLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALE 67
GL + EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E
Sbjct: 53 GLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPE 112
Query: 68 TVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVTVWRDGMEYHQKYSRGKP 127
+ L + LE G +Y QK+
Sbjct: 113 MIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMS 172
Query: 128 VTTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL 175
+ CH + S K T++ F PD F + D++ I G +R++
Sbjct: 173 I----CHPPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDI 227
Query: 176 -AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGI 234
+LN K ++ +R F +E Y++ L L++ + R +V
Sbjct: 228 NVYLNGK-SLKIRN--------------FKNYVELYLKSL--IPTILYERINNRWEVAFA 270
Query: 235 TIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDIS 294
D++ Q S + NSI T GGTH+ + + + ++ + KK K K
Sbjct: 271 VSDISFQQIS---------FVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSF- 320
Query: 295 LSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD-QSVQEYLTEYLE--LHPD 351
++ + I+ + NP F QTK +L +V D S E EY+ + D
Sbjct: 321 ----QIKNNMFIFINCLIENPAFTSQTKEQL----TTRVKDFGSRCEIPLEYINKIMKTD 372
Query: 352 VXXXXXXXXXXXXXXXXXXXXXXXXVRQKSVLRSSSLPGKLADCSSTTPEE---SEIFIV 408
+ R ++ P KL D + +E + +
Sbjct: 373 LATRMFEIAS----------------------RITNYP-KLEDANKAGTKEGYKCTLVLT 409
Query: 409 EGDSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGV 463
EGDSA G A GRD + PLRGK+LNV + KN EIQ + + +GL
Sbjct: 410 EGDSALSLAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQH 467
Query: 464 KGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV 522
+ + ++LRY ++I+TD D DG+HI+ L++ F L D +G + + P+ KV
Sbjct: 468 RKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKV 527
>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 = 74.7 bits (182), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 384 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 435
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 2 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 58
Query: 436 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 495
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 59 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 118
Query: 496 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 551
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 119 INFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 178
Query: 552 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 609
+ +KGLG + ++ E + L+ ++ L D ++ FS + D RKE ++
Sbjct: 179 QKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSK---KKADDRKEWLR 235
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 74.7 bits (182), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 384 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 435
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 14 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 70
Query: 436 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 495
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 71 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 130
Query: 496 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 551
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 131 INFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 190
Query: 552 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 609
+ +KGLG + ++ E + L+ ++ L D ++ FS + D RKE ++
Sbjct: 191 QKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSK---KKADDRKEWLR 247
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 384 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 435
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 4 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 60
Query: 436 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 495
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 61 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 120
Query: 496 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 551
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 121 INFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 180
Query: 552 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 609
+ +KGLG + ++ E + L+ ++ L D ++ FS + D RKE ++
Sbjct: 181 QKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSK---KKADDRKEWLR 237
>pdb|1QZR|A Chain A, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii Bound To Icrf-187
(Dexrazoxane)
pdb|1QZR|B Chain B, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii Bound To Icrf-187
(Dexrazoxane)
Length = 418
Score = 37.4 bits (85), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 77/341 (22%), Positives = 132/341 (38%), Gaps = 54/341 (15%)
Query: 10 GLHHLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALE 67
GL + EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E
Sbjct: 64 GLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPE 123
Query: 68 TVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRG 125
+ H N S LE G +Y QK+
Sbjct: 124 MIFG--HLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 126 KPVTTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIR 173
+ CH + S K T++ F PD F + D++ I G +R
Sbjct: 182 MSI----CHPPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVR 236
Query: 174 EL-AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP--------LHDV 224
++ +LN K ++ +R + E + LE+ Q N + L++
Sbjct: 237 DINVYLNGK-SLKIRNFKNYVE-------LYLKSLEKKRQLDNGEDGAAKSDIPTILYER 288
Query: 225 VGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKK 284
+ R +V D++ Q S + NSI T GGTH+ + + + ++ + KK
Sbjct: 289 INNRWEVAFAVSDISFQQIS---------FVNSIATTMGGTHVNYITDQIVKKISEILKK 339
Query: 285 SKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRL 325
K K ++ + I+ + NP F QTK +L
Sbjct: 340 KKKKSVKSF-----QIKNNMFIFINCLIENPAFTSQTKEQL 375
>pdb|1PVG|A Chain A, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii
pdb|1PVG|B Chain B, Crystal Structure Of The Atpase Region Of Saccharomyces
Cerevisiae Topoisomerase Ii
Length = 418
Score = 37.0 bits (84), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 76/341 (22%), Positives = 131/341 (38%), Gaps = 54/341 (15%)
Query: 10 GLHHLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALE 67
GL + EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E
Sbjct: 64 GLFKIFDEILVNAADNKVRDPSXKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPE 123
Query: 68 TVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRG 125
+ H N S LE G +Y QK+
Sbjct: 124 XIFG--HLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENN 181
Query: 126 KPVTTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIR 173
+ CH + S K T++ F PD F + D++ I G +R
Sbjct: 182 XSI----CHPPKITSYKKGPSYTKVTFKPDLTRFGXK-ELDNDILGVXRRRVYDINGSVR 236
Query: 174 EL-AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP--------LHDV 224
++ +LN K ++ +R + E + LE+ Q N + L++
Sbjct: 237 DINVYLNGK-SLKIRNFKNYVE-------LYLKSLEKKRQLDNGEDGAAKSDIPTILYER 288
Query: 225 VGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKK 284
+ R +V D++ Q + + NSI T GGTH+ + + + ++ + KK
Sbjct: 289 INNRWEVAFAVSDISFQ---------QISFVNSIATTXGGTHVNYITDQIVKKISEILKK 339
Query: 285 SKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRL 325
K K ++ I+ + NP F QTK +L
Sbjct: 340 KKKKSVKSF-----QIKNNXFIFINCLIENPAFTSQTKEQL 375
>pdb|1ZXM|A Chain A, Human Topo Iia Atpase/amp-pnp
pdb|1ZXM|B Chain B, Human Topo Iia Atpase/amp-pnp
pdb|1ZXN|A Chain A, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|B Chain B, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|C Chain C, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|D Chain D, Human Dna Topoisomerase Iia AtpaseADP
Length = 400
Score = 35.8 bits (81), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 252 LGYANSIRTIDGGTHIEGVKASL-TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 310
+ + NSI T GG H++ V + T+ ++ + KK+K +++ V+ + ++
Sbjct: 283 ISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKNKG----GVAVKAHQVKNHMWIFVNA 338
Query: 311 RVPNPEFEGQTKTRL 325
+ NP F+ QTK +
Sbjct: 339 LIENPTFDSQTKENM 353
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 10 GLHHLVYEILDNAVDEAQAG-YASNIEVALLADNS-VSVADNGRGIPIDLH 58
GL+ + EIL NA D Q S I V + +N+ +S+ +NG+GIP+ H
Sbjct: 52 GLYKIFDEILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEH 102
>pdb|2B26|A Chain A, The Crystal Structure Of The Protein Complex Of Yeast
Hsp40 Sis1 And Hsp70 Ssa1
pdb|2B26|B Chain B, The Crystal Structure Of The Protein Complex Of Yeast
Hsp40 Sis1 And Hsp70 Ssa1
pdb|2B26|C Chain C, The Crystal Structure Of The Protein Complex Of Yeast
Hsp40 Sis1 And Hsp70 Ssa1
Length = 173
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 227 FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT----HIEGVKASLTRTLNSLG 282
F++D D + L L ++ +++LG++ +I+TIDG T ++ V+ S T T G
Sbjct: 82 FKRDGDDLIYTLPL-----SFKESLLGFSKTIQTIDGRTLPLSRVQPVQPSQTSTYPGQG 136
>pdb|1C3G|A Chain A, S. Cerevisiae Heat Shock Protein 40 Sis1
Length = 170
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 227 FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT----HIEGVKASLTRTLNSLG 282
F++D D + L L ++ +++LG++ +I+TIDG T ++ V+ S T T G
Sbjct: 82 FKRDGDDLIYTLPL-----SFKESLLGFSKTIQTIDGRTLPLSRVQPVQPSQTSTYPGQG 136
>pdb|2ZBK|B Chain B, Crystal Structure Of An Intact Type Ii Dna
Topoisomerase: Insights Into Dna Transfer Mechanisms
pdb|2ZBK|D Chain D, Crystal Structure Of An Intact Type Ii Dna
Topoisomerase: Insights Into Dna Transfer Mechanisms
pdb|2ZBK|F Chain F, Crystal Structure Of An Intact Type Ii Dna
Topoisomerase: Insights Into Dna Transfer Mechanisms
pdb|2ZBK|H Chain H, Crystal Structure Of An Intact Type Ii Dna
Topoisomerase: Insights Into Dna Transfer Mechanisms
Length = 530
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 9 RGLHHLVYEILDNAVDEAQA-GYASNIEVAL-LADNS-----VSVADNGRGIP 54
R L+ V E+++N++D G NI++ + L D++ V+V DNG GIP
Sbjct: 30 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 82
>pdb|1Z5A|A Chain A, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5A|B Chain B, Topoisomerase Vi-B, Adp-Bound Dimer Form
pdb|1Z5B|A Chain A, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|1Z5B|B Chain B, Topoisomerase Vi-B, Adp Alf4- Bound Dimer Form
pdb|2HKJ|A Chain A, Topoisomerase Vi-B Bound To Radicicol
Length = 469
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 9 RGLHHLVYEILDNAVDEAQA-GYASNIEVAL-LADNS-----VSVADNGRGIP 54
R L+ V E+++N++D G NI++ + L D++ V+V DNG GIP
Sbjct: 29 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 81
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 9 RGLHHLVYEILDNAVDEAQA-GYASNIEVAL-LADNS-----VSVADNGRGIP 54
R L+ V E+++N++D G NI++ + L D++ V+V DNG GIP
Sbjct: 31 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 83
>pdb|1Z59|A Chain A, Topoisomerase Vi-B, Adp-Bound Monomer Form
pdb|1Z5C|A Chain A, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
pdb|1Z5C|B Chain B, Topoisomerase Vi-B, Adp Pi Bound Dimer Form
Length = 469
Score = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 9 RGLHHLVYEILDNAVDEAQA-GYASNIEVAL-LADNS-----VSVADNGRGIP 54
R L+ V E+++N++D G NI++ + L D++ V+V DNG GIP
Sbjct: 29 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 81
>pdb|1MX0|A Chain A, Structure Of Topoisomerase Subunit
pdb|1MX0|B Chain B, Structure Of Topoisomerase Subunit
pdb|1MX0|C Chain C, Structure Of Topoisomerase Subunit
pdb|1MX0|D Chain D, Structure Of Topoisomerase Subunit
pdb|1MX0|E Chain E, Structure Of Topoisomerase Subunit
pdb|1MX0|F Chain F, Structure Of Topoisomerase Subunit
Length = 472
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 31/53 (58%), Gaps = 7/53 (13%)
Query: 9 RGLHHLVYEILDNAVDEAQA-GYASNIEVAL-LADNS-----VSVADNGRGIP 54
R L+ V E+++N++D G NI++ + L D++ V+V DNG GIP
Sbjct: 32 RALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 84
>pdb|3HN0|A Chain A, Crystal Structure Of An Abc Transporter (bdi_1369) From
Parabacteroides Distasonis At 1.75 A Resolution
pdb|3HN0|B Chain B, Crystal Structure Of An Abc Transporter (bdi_1369) From
Parabacteroides Distasonis At 1.75 A Resolution
Length = 283
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 151 WPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDS 191
+P F TA + +AG++ P L+IALRK+ S
Sbjct: 123 YPLNYAFNTAGEITQGILAGKVNRAVLGEPFLSIALRKDSS 163
>pdb|2Q8F|A Chain A, Structure Of Pyruvate Dehydrogenase Kinase Isoform 1
pdb|2Q8G|A Chain A, Structure Of Pyruvate Dehydrogenase Kinase Isoform 1 In
Complex With Glucose-Lowering Drug Azd7545
pdb|2Q8H|A Chain A, Structure Of Pyruvate Dehydrogenase Kinase Isoform 1 In
Complex With Dichloroacetate (Dca)
Length = 407
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 8 PRGLHHLVYEILDNAV-----DEAQAGYASNIEVALLADN---SVSVADNGRGIPI 55
P L+H+V+E+ NA+ A G I+V + N +V ++D G G+P+
Sbjct: 241 PSHLYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPL 296
>pdb|2E0A|A Chain A, Crystal Structure Of Human Pyruvate Dehydrogenase Kinase 4
In Complex With Amppnp
pdb|2E0A|B Chain B, Crystal Structure Of Human Pyruvate Dehydrogenase Kinase 4
In Complex With Amppnp
pdb|2ZDX|A Chain A, Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase
Kinase 4
pdb|2ZDX|B Chain B, Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase
Kinase 4
pdb|2ZDY|A Chain A, Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase
Kinase 4
pdb|2ZDY|B Chain B, Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase
Kinase 4
Length = 394
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 8 PRGLHHLVYEILDNAVD---EAQAGYAS--NIEVALL---ADNSVSVADNGRGIPI 55
P LHH+++E+ NA+ E Q S IEV ++ D ++ ++D G G+P+
Sbjct: 228 PSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPL 283
>pdb|2ZKJ|A Chain A, Crystal Structure Of Human Pdk4-Adp Complex
pdb|2ZKJ|B Chain B, Crystal Structure Of Human Pdk4-Adp Complex
pdb|3D2R|A Chain A, Crystal Structure Of Pyruvate Dehydrogenase Kinase Isoform
4 In Complex With Adp
pdb|3D2R|B Chain B, Crystal Structure Of Pyruvate Dehydrogenase Kinase Isoform
4 In Complex With Adp
Length = 394
Score = 29.6 bits (65), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 8 PRGLHHLVYEILDNAVD---EAQAGYAS--NIEVALL---ADNSVSVADNGRGIPI 55
P LHH+++E+ NA+ E Q S IEV ++ D ++ ++D G G+P+
Sbjct: 228 PSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPL 283
>pdb|2BZR|A Chain A, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
pdb|2BZR|B Chain B, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
pdb|2BZR|C Chain C, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
pdb|2BZR|D Chain D, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
pdb|2BZR|E Chain E, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
pdb|2BZR|F Chain F, Crystal Structure Of Accd5 (Rv3280), An Acyl-Coa
Carboxylase Beta-Subunit From Mycobacterium Tuberculosis
Length = 548
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 8 PRGLHHLVYEILDNAVDEAQAGYASNIEVAL 38
P +H ++ +LD+ E QAGYA NI V
Sbjct: 311 PYDMHEVITRLLDDEFLEIQAGYAQNIVVGF 341
>pdb|2A7S|A Chain A, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
pdb|2A7S|B Chain B, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
pdb|2A7S|C Chain C, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
pdb|2A7S|D Chain D, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
pdb|2A7S|E Chain E, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
pdb|2A7S|F Chain F, Crystal Structure Of The Acyl-Coa Carboxylase, Accd5, From
Mycobacterium Tuberculosis
Length = 548
Score = 29.6 bits (65), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 8 PRGLHHLVYEILDNAVDEAQAGYASNIEVAL 38
P +H ++ +LD+ E QAGYA NI V
Sbjct: 311 PYDMHEVITRLLDDEFLEIQAGYAQNIVVGF 341
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
0.317 0.135 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,871,047
Number of Sequences: 62578
Number of extensions: 666905
Number of successful extensions: 1840
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1712
Number of HSP's gapped (non-prelim): 69
length of query: 622
length of database: 14,973,337
effective HSP length: 105
effective length of query: 517
effective length of database: 8,402,647
effective search space: 4344168499
effective search space used: 4344168499
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)