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= 005028
(718 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 281 bits (718), Expect = 1e-75, Method: Compositional matrix adjust.
Identities = 147/367 (40%), Positives = 221/367 (60%), Gaps = 13/367 (3%)
Query: 82 IQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSV 140
I+VL+GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSV
Sbjct: 9 IKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSV 68
Query: 141 SVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALS 200
SV D+GRGIP +HP SA E ++TVLHA NALS
Sbjct: 69 SVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVV--NALS 126
Query: 201 ESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFD 260
+ LE+ + R+G + Q Y G P L ++ GT +RFWP + FT +F+
Sbjct: 127 QKLELVIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFE 182
Query: 261 HNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLH-D 319
+ +A R+REL+FL+ ++I LR D + + + + GG++ +V++LN +K P+H +
Sbjct: 183 YEILAKRLRELSFLDSGVSIRLR----DKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPN 238
Query: 320 VVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGK 379
+ F + DGI +++ALQW +D + + + + N+I DGGTH+ G +A++TRTLN+
Sbjct: 239 IFYFSTEKDGIGVEVALQW-NDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMD 297
Query: 380 KSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSVQEYLT 439
K K +S +G+ REGL ++SV+VP+P+F QTK +L + EV+ V+Q + E L
Sbjct: 298 KEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLA 357
Query: 440 EYLELHP 446
EYL +P
Sbjct: 358 EYLLENP 364
>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 = 280 bits (715), Expect = 3e-75, Method: Compositional matrix adjust.
Identities = 137/237 (57%), Positives = 169/237 (71%), Gaps = 1/237 (0%)
Query: 482 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 541
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 542 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 601
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 602 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 661
L + G +Y+ PPLYK+ +GKQ Y Y+D EL K+KS +SI R+KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQ 182
Query: 662 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 718
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 (714), Expect = 3e-75, Method: Compositional matrix adjust.
Identities = 137/237 (57%), Positives = 169/237 (71%), Gaps = 1/237 (0%)
Query: 482 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 541
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 542 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 601
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 602 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 661
L + G +Y+ PPLYK+ +GKQ Y Y+D EL K+KS +SI R+KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQ 182
Query: 662 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 718
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 183 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 239
>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 = 240 bits (612), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 119/227 (52%), Positives = 159/227 (70%), Gaps = 7/227 (3%)
Query: 484 LPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMY 543
L GKL S P ++E+++VEGDSAGGSAKQGRDR+FQAILPLRGK++N + A +
Sbjct: 33 LSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADIL 92
Query: 544 KNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLF 603
KNEEI +I +G GV G DF E Y KIII+TDAD DGAHI+TLLLTFFYRY + L
Sbjct: 93 KNEEINTMIYTIGAGV-GADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLV 151
Query: 604 DEGCIYVGVPPLYKVERGK----QVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMP 659
+ G +Y+ +PPLYK+ +GK +V Y + D EL++++ F A ++QR+KGLGEM
Sbjct: 152 EAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGA--TLQRYKGLGEMNA 209
Query: 660 VQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 706
QLWETT+NPE R L ++ IED A A + LMG +V+ R++ I++
Sbjct: 210 DQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIED 256
>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 = 233 bits (594), Expect = 3e-61, Method: Compositional matrix adjust.
Identities = 141/374 (37%), Positives = 205/374 (54%), Gaps = 11/374 (2%)
Query: 76 TYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALL 135
+Y + I+VL+GLE VR RPAMYIG TG G HHL EILDNAVDEA AGYA+ I V L
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATEILVRLN 61
Query: 136 ADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXX 195
D S++V DNGRGIP+DL P K A+E + LH+
Sbjct: 62 EDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHS--GGKFEQGAYKVSGGLHGVGASV 119
Query: 196 XNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
NALSE V V+R+G + +SRG+ T V+ + + GTR+ F PD ++F
Sbjct: 120 VNALSEWTVVEVFREGKHHRIAFSRGE--VTEPLRVVGEAPRGKTGTRVTFKPDPEIFGN 177
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK 315
++FD + I R+RE+A+L L + + D + + + GG+ + + L +
Sbjct: 178 -LRFDPSKIRARLREVAYLVAGLKLVFQ----DRQHGKEEVFLDKGGVASFAKALAEGED 232
Query: 316 PLHDVVGFRKDVDG-ITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTL 374
L++ + G + +++ + Y+ +L YAN I T DGGTH+ K++ +R L
Sbjct: 233 LLYEKPFLIRGTHGEVEVEVGF-LHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRAL 291
Query: 375 NSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQSV 434
N KK+ K+K +G+ + EGL ++SV++PNP+FEGQTK +L NPE V Q V
Sbjct: 292 NQYAKKAGLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVV 351
Query: 435 QEYLTEYLELHPDV 448
E L E LE +P +
Sbjct: 352 YERLLEILEENPRI 365
>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 (585), Expect = 3e-60, Method: Compositional matrix adjust.
Identities = 120/237 (50%), Positives = 147/237 (62%), Gaps = 35/237 (14%)
Query: 482 SSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAA 541
+SLPGKLADCSS +PEE EIF+VEGDSAGGS K GRD R QAILPLRGKILNVE+
Sbjct: 4 ASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDR 63
Query: 542 MYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKT 601
+ N EI+ +I A G G+ G DF RYHKI+I+TDADVDGAHIRTLLLTFFYR+ +
Sbjct: 64 ILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 602 LFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQ 661
L + G +Y+ PP +KGLGEM Q
Sbjct: 123 LIEAGYVYIAQPP----------------------------------TGYKGLGEMNADQ 148
Query: 662 LWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQNAANLVNLDHLDI 718
LWETT+NPE R L Q+ +EDA EA+ F LMG V+ R++ I++ A NLD ++
Sbjct: 149 LWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAEL 205
>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 = 208 bits (530), Expect = 7e-54, Method: Compositional matrix adjust.
Identities = 109/242 (45%), Positives = 151/242 (62%), Gaps = 3/242 (1%)
Query: 473 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 532
V +K ++ +LPGKLADC T EESE+FIVEGDSAGGSAKQ RD+ FQAI+P+RGKIL
Sbjct: 18 VERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKIL 77
Query: 533 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 592
N + ++E+ ++ A+G+ +D + LRY KI IL DAD DG HI TLL
Sbjct: 78 NTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE--LRYGKICILADADSDGLHIATLLC 135
Query: 593 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 652
F ++ L +EG +YV +PPL++++ GK V Y DD EL+ + + N I RFK
Sbjct: 136 ALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKGNKNPQITRFK 195
Query: 653 GLGEMMPVQLWETTLNPEQRMLKQLVIEDA-AEANVVFSSLMGARVDTRKELIQNAANLV 711
GLGEM +QL ETT++P R L QL ++DA A ++ L R RK+ ++ NL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLA 255
Query: 712 NL 713
++
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 = 208 bits (530), Expect = 7e-54, Method: Compositional matrix adjust.
Identities = 109/242 (45%), Positives = 151/242 (62%), Gaps = 3/242 (1%)
Query: 473 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 532
V +K ++ +LPGKLADC T EESE+FIVEGDSAGGSAKQ RD+ FQAI+P+RGKIL
Sbjct: 18 VERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQAIMPIRGKIL 77
Query: 533 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 592
N + ++E+ ++ A+G+ +D + LRY KI IL DAD DG HI TLL
Sbjct: 78 NTWEVSSDEVLASQEVHDIAIAIGVDPGSDDLSE--LRYGKICILADADSDGLHIATLLC 135
Query: 593 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFK 652
F ++ L +EG +YV +PPL++++ GK V Y DD EL+ + + N I RFK
Sbjct: 136 ALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNVKGNKNPQITRFK 195
Query: 653 GLGEMMPVQLWETTLNPEQRMLKQLVIEDA-AEANVVFSSLMGARVDTRKELIQNAANLV 711
GLGEM +QL ETT++P R L QL ++DA A ++ L R RK+ ++ NL
Sbjct: 196 GLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADRKQWLEQKGNLA 255
Query: 712 NL 713
++
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 = 196 bits (498), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 110/228 (48%), Positives = 152/228 (66%), Gaps = 8/228 (3%)
Query: 494 TTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIR 553
T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+ + KN E+Q +I
Sbjct: 15 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIIT 74
Query: 554 ALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 613
ALG G+ E F LRYHKI+++ DADVDG HI TLLLT +R+ + L + G +++ P
Sbjct: 75 ALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 133
Query: 614 PLYKVE-RGKQVQYCYDDAELK-----KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTL 667
PLYK++ + ++ Y D E +K+ N IQR+KGLGEM +LWETT+
Sbjct: 134 PLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTM 193
Query: 668 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-QNAANLVNLD 714
+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 = 196 bits (497), Expect = 5e-50, Method: Compositional matrix adjust.
Identities = 110/228 (48%), Positives = 152/228 (66%), Gaps = 8/228 (3%)
Query: 494 TTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIR 553
T P +SE+++VEGDSAGGSAK GRD FQAILPLRGKI+NVE+ + KN E+Q +I
Sbjct: 7 TDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIIT 66
Query: 554 ALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIYVGVP 613
ALG G+ E F LRYHKI+++ DADVDG HI TLLLT +R+ + L + G +++ P
Sbjct: 67 ALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 125
Query: 614 PLYKVE-RGKQVQYCYDDAELK-----KVKSSFPSNALYSIQRFKGLGEMMPVQLWETTL 667
PLYK++ + ++ Y D E +K+ N IQR+KGLGEM +LWETT+
Sbjct: 126 PLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTM 185
Query: 668 NPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-QNAANLVNLD 714
+P R+L+Q+ ++DAA A+ +FS LMG VD R+ I +NA ++ LD
Sbjct: 186 DPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLD 233
>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 = 189 bits (480), Expect = 5e-48, Method: Compositional matrix adjust.
Identities = 104/227 (45%), Positives = 133/227 (58%), Gaps = 30/227 (13%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
YG+ QIQVLEGLEAVRKRP MYIGST RGLHHLV+EI+DN++DEA AGYA+ IEV +
Sbjct: 2 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEK 61
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXX 196
DN + V DNGRGIP+D+ + A+E +LT
Sbjct: 62 DNWIKVTDNGRGIPVDIQEKMGRPAVEVILT-------------------------SSVV 96
Query: 197 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 256
NALS+ LEV V R+ YHQ Y +G P L V + D+ GT IRF D ++FT
Sbjct: 97 NALSQDLEVYVHRNETIYHQAYKKGVPQFDLK----EVGTTDKTGTVIRFKADGEIFTET 152
Query: 257 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGL 303
+++ T+ RIRELAFLN + I LR E D E + + Y + GG+
Sbjct: 153 TVYNYETLQQRIRELAFLNKGIQITLRDE-RDEENVREDSYHYEGGI 198
>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 = 189 bits (479), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 90/158 (56%), Positives = 114/158 (72%)
Query: 473 VRQKSVLRSSSLPGKLADCSSTTPEESEIFIVEGDSAGGSAKQGRDRRFQAILPLRGKIL 532
R+K L + LPGKLADC P SE+++VEGDSAGGSAKQGR+R+ QAILPL+GKIL
Sbjct: 8 TRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKIL 67
Query: 533 NVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLLL 592
NVE+ ++E+ LI ALG G+ +++ + LRYH III TDADVDG+HIRTLLL
Sbjct: 68 NVEKARFDKXLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIXTDADVDGSHIRTLLL 127
Query: 593 TFFYRYQKTLFDEGCIYVGVPPLYKVERGKQVQYCYDD 630
TFFYR + + G +Y+ PPLYKV++GKQ QY DD
Sbjct: 128 TFFYRQXPEIVERGHVYIAQPPLYKVKKGKQEQYIKDD 165
Score = 66.2 bits (160), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 1/69 (1%)
Query: 647 SIQRFKGLGEMMPVQLWETTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELI-Q 705
SIQR+KGLGE P QLWETT +PE R ++ ++DA A+ +F++L G V+ R+ I +
Sbjct: 351 SIQRYKGLGEXNPEQLWETTXDPESRRXLRVTVKDAIAADQLFTTLXGDAVEPRRAFIEE 410
Query: 706 NAANLVNLD 714
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 = 184 bits (468), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 120/374 (32%), Positives = 182/374 (48%), Gaps = 14/374 (3%)
Query: 75 KTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
+ Y ++ I+VL GL+ V+KRP MY P +HL+ EI+DN+VDE AG+AS I + L
Sbjct: 2 QNYNAKSIEVLTGLDPVKKRPGMYTNIENP---NHLIQEIIDNSVDEVLAGFASKINITL 58
Query: 135 LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXX 194
DNS+ VAD+GRG+P+D+HP S +E ++T LH+
Sbjct: 59 YEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHS--GGKFSNKNYTHSGGLHGVGVS 116
Query: 195 XXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFT 254
NALS LE + RDG YH + G T ++ K GT+IRFWP+K+ F
Sbjct: 117 VVNALSTRLEAEIKRDGNVYHIVFEDG--FKTKDLEIIDNVGKKNTGTKIRFWPNKKYFD 174
Query: 255 TAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYV-QWLNTD 313
I+ + + + A L LTI E K + + F GL+ Y+ L +
Sbjct: 175 D-IKVNFKALKNLLEAKAILCKALTIKYSNE----IKKEKLTWHFETGLKGYLDHKLEAE 229
Query: 314 KKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRT 373
P + +D WC D Y N I T GTH+ G+K +
Sbjct: 230 TLPAEPFIIDNFSNGDSYLDAVFCWCEDPSESIKNSYVNLIPTPQDGTHVTGLKNGIYDA 289
Query: 374 LNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQS 433
+ + +K+ ++ K+I ++ L +ISV++ NP+F GQTK +L N +V V +
Sbjct: 290 IKAYIEKN-SLSVKNIKITANDSFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATA 348
Query: 434 VQEYLTEYLELHPD 447
V++ LT +L +PD
Sbjct: 349 VKDLLTIWLNQNPD 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 = 177 bits (448), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 95/215 (44%), Positives = 129/215 (60%), Gaps = 8/215 (3%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
GLEAVRKRP MYIGST GLHHLV+EI+DN++DEA AG+A +I+V + D+S++V D+G
Sbjct: 1 GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDG 60
Query: 147 RGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVT 206
RGIP+ + T + A+ETV TVLHA NALS SL+V
Sbjct: 61 RGIPVGIQAKTGRPAVETVFTVLHA--GGKFGGGGYKVSGGLHGVGSSVVNALSTSLDVR 118
Query: 207 VWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG 266
V++DG Y+Q+Y RG V L ++ DR GT + F PD ++FT +D + +A
Sbjct: 119 VYKDGKVYYQEYRRGAVVDDLKV----IEETDRHGTTVHFIPDPEIFTETTVYDFDKLAT 174
Query: 267 RIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAG 301
R+RELAFLN L I++ ED + EY + G
Sbjct: 175 RVRELAFLNRGLHISI--EDRREGQEDKKEYHYEG 207
>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 = 176 bits (447), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 118/375 (31%), Positives = 190/375 (50%), Gaps = 22/375 (5%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV 132
+++TY ++ I+VL GLE VR+RP MY +T P +HL E++DN+VDEA AG+A ++V
Sbjct: 1 MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDV 57
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXX 192
L AD S+ V D+GRG+P+D+HP A+E +L LHA
Sbjct: 58 ILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVG 115
Query: 193 XXXXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQV 252
NALS+ +EV V RDG Y+ + G+ V L V+ K GT + FWPD+
Sbjct: 116 ISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETF 173
Query: 253 FTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEY----VQ 308
F + +F + + ++ A L P + I + E ++ E+ + + GL +Y V
Sbjct: 174 FDSP-RFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQ----RWCYQDGLNDYLAEAVN 228
Query: 309 WLNT-DKKPLHDVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVK 367
L T +KP + F D + +D AL W + Y N I T+ GGTH+ G++
Sbjct: 229 GLPTLPEKPF--IGNFAGDTE--AVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLR 284
Query: 368 ASLTRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVR 427
L + + + + + + LS E + + ++SV++ +P+F GQTK RL + +
Sbjct: 285 QGLLDAMREFC-EYRNILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCA 343
Query: 428 KVVDQSVQEYLTEYL 442
V V++ +L
Sbjct: 344 AFVSGVVKDAFILWL 358
>pdb|3LNU|A Chain A, Crystal Structure Of Pare Subunit
pdb|3LPS|A Chain A, Crystal Structure Of Pare
Length = 408
Score = 172 bits (436), Expect = 6e-43, Method: Compositional matrix adjust.
Identities = 113/369 (30%), Positives = 186/369 (50%), Gaps = 19/369 (5%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
Y + I+VL GL+ V++RP MY + P +HL E++DN+VDEA AG+A IEV L
Sbjct: 24 YNAADIEVLSGLDPVKRRPGMYTDTARP---NHLAQEVIDNSVDEALAGHAKQIEVTLYK 80
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXX 196
D S V+D+GRG+P+D+HP +E +LT LHA
Sbjct: 81 DGSCEVSDDGRGMPVDIHPEEKIPGVELILTRLHA--GGKFNNRNYTFSGGLHGVGVSVV 138
Query: 197 NALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTA 256
NALS +E+ + R+G E+ ++ G + L V+ K GTR+RFW D + F T
Sbjct: 139 NALSTKVELFIKREGSEHRMEFRDGNAASKL--EVVGTVGKKNTGTRLRFWADPKYFDTP 196
Query: 257 IQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKK- 315
+F+ + +R A L P LT+ L E + + + ++F GL +Y++ + +
Sbjct: 197 -KFNVRALRHLLRAKAVLCPGLTVKLHDEAT----GEQDSWYFENGLRDYLKGEMAEHEM 251
Query: 316 -PLHDVVG-FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRT 373
P VG +KD + +D A W + Y N I T GTH+ G+++ LT
Sbjct: 252 LPADLFVGSLKKDTE--IVDWAAGWVPEG-ELVQESYVNLIPTAQHGTHVNGLRSGLTDA 308
Query: 374 LNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVDQS 433
L + + + + L+ E V + +T ++S+++ +P+F GQTK RL + + ++ +
Sbjct: 309 LREFC-DFRNLLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAAGFIEGA 367
Query: 434 VQEYLTEYL 442
+ + YL
Sbjct: 368 AHDAFSLYL 376
>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 = 171 bits (434), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 94/224 (41%), Positives = 128/224 (57%), Gaps = 8/224 (3%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIE 131
+S +Y S I+VL+GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I
Sbjct: 1 MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEII 60
Query: 132 VALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXX 191
V + ADNSVSV D+GRGIP +HP SA E ++TVLHA
Sbjct: 61 VTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGV 118
Query: 192 XXXXXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
NALS+ LE+ + R+G + Q Y G P L ++ GT +RFWP +
Sbjct: 119 GVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLE 174
Query: 252 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALR-KEDSDPEKNQY 294
FT +F++ +A R+REL+FLN ++I LR K D + Y
Sbjct: 175 TFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 218
>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 = 171 bits (432), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 94/211 (44%), Positives = 124/211 (58%), Gaps = 29/211 (13%)
Query: 75 KTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
K YG++ I +LEGLEAVRKRP MYIGSTG RGLHHL++E++DNAVDEA AG+A+ ++V +
Sbjct: 3 KEYGADSITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGFATRVDVKI 62
Query: 135 LADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXX 194
AD SV V D+GRGIP+++H AT ++ V+T +
Sbjct: 63 HADGSVEVRDDGRGIPVEMH-ATGMPTIDVVMTQVGV----------------------S 99
Query: 195 XXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFT 254
NALS LE TV RDG E+ Q Y R P + GT IRFW D ++F
Sbjct: 100 VVNALSTRLEATVLRDGYEWFQYYDRSVP-----GKLKQGGETKETGTTIRFWADPEIFE 154
Query: 255 TAIQFDHNTIAGRIRELAFLNPKLTIALRKE 285
T ++ T+A R++E+AFLN LTI L E
Sbjct: 155 TT-DYNFETVARRLQEMAFLNKGLTIELTDE 184
>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 = 169 bits (427), Expect = 6e-42, Method: Compositional matrix adjust.
Identities = 93/223 (41%), Positives = 126/223 (56%), Gaps = 8/223 (3%)
Query: 74 SKTYGSEQIQVLEGLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEV 132
S +Y S I+VL+GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V
Sbjct: 1 SNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV 60
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXX 192
+ ADNSVSV D+GRGIP +HP SA E ++TVLHA
Sbjct: 61 TIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVG 118
Query: 193 XXXXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQV 252
NALS+ LE+ + +G + Q Y G P L ++ GT +RFWP +
Sbjct: 119 VSVVNALSQKLELVIQHEGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLET 174
Query: 253 FTTAIQFDHNTIAGRIRELAFLNPKLTIALR-KEDSDPEKNQY 294
FT +F++ +A R+REL+FLN ++I LR K D + Y
Sbjct: 175 FTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY 217
>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 = 168 bits (426), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 94/213 (44%), Positives = 121/213 (56%), Gaps = 30/213 (14%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
GLEAVRKRP MYIGST RGLHHLV+EI+DN++DEA AGYA+ IEV + DN + V DNG
Sbjct: 1 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNG 60
Query: 147 RGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVT 206
RGIP+D+ + A+E +LT NALS+ LEV
Sbjct: 61 RGIPVDIQEKMGRPAVEVILT-------------------------SSVVNALSQDLEVY 95
Query: 207 VWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG 266
V R+ YHQ Y +G P L V + D+ GT IRF D ++FT +++ T+
Sbjct: 96 VHRNETIYHQAYKKGVPQFDLK----EVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQ 151
Query: 267 RIRELAFLNPKLTIALRKEDSDPEKNQYNEYFF 299
RIRELAFLN + I LR E D E + + Y +
Sbjct: 152 RIRELAFLNKGIQITLRDE-RDEENVREDSYHY 183
>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 = 161 bits (407), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 92/213 (43%), Positives = 125/213 (58%), Gaps = 7/213 (3%)
Query: 77 YGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLA 136
Y + IQVLEGL+AVRKRP MYIGST GLHHLV+EI+DNAVDEA +G+ I+V +
Sbjct: 11 YNDDAIQVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDVTINK 70
Query: 137 DNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXX 196
D S++V D+GRG+P +H A +E + T+LHA
Sbjct: 71 DGSLTVQDHGRGMPTGMH-AMGIPTVEVIFTILHA--GGKFGQGGYKTSGGLHGVGSSVV 127
Query: 197 NALSESLEVTVWRDGMEYHQKYSR-GKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTT 255
NALS LEV + RDG Y Q++ GKPVTTL + K + GT++ F PD +F+T
Sbjct: 128 NALSSWLEVEITRDGAVYKQRFENGGKPVTTLKK--IGTALKSKTGTKVTFMPDATIFST 185
Query: 256 AIQFDHNTIAGRIRELAFLNPKLTIALRKEDSD 288
F +NTI+ R+ E AFL +T++L + +D
Sbjct: 186 T-DFKYNTISERLNESAFLLKNVTLSLTDKRTD 217
>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 = 161 bits (407), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 90/219 (41%), Positives = 122/219 (55%), Gaps = 12/219 (5%)
Query: 87 GLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADN 145
GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+
Sbjct: 2 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 61
Query: 146 GRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEV 205
GRGIP +HP SA E ++TVLHA NALS+ LE+
Sbjct: 62 GRGIPTGIHPEEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLEL 119
Query: 206 TVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
+ R+G + Q Y G P L ++ GT +RFWP + FT +F++ +A
Sbjct: 120 VIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILA 175
Query: 266 GRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLE 304
R+REL+FLN ++I LR + E ++F GLE
Sbjct: 176 KRLRELSFLNSGVSIRLRDKRDGKE-----DHFHYEGLE 209
>pdb|1KZN|A Chain A, Crystal Structure Of E. Coli 24kda Domain In Complex With
Clorobiocin
Length = 205
Score = 160 bits (405), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 88/210 (41%), Positives = 118/210 (56%), Gaps = 8/210 (3%)
Query: 87 GLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADN 145
GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+
Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60
Query: 146 GRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEV 205
GRGIP +HP SA E ++TVLHA NALS+ LE+
Sbjct: 61 GRGIPTGIHPEEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLEL 118
Query: 206 TVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
+ R+G + Q Y G P L ++ GT +RFWP + FT +F++ +A
Sbjct: 119 VIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILA 174
Query: 266 GRIRELAFLNPKLTIALR-KEDSDPEKNQY 294
R+REL+FLN ++I LR K D + Y
Sbjct: 175 KRLRELSFLNSGVSIRLRDKRDGKEDHFHY 204
>pdb|3G7E|A Chain A, Crystal Structure Of E. Coli Gyrase B Co-Complexed With
Inhibitor
Length = 203
Score = 159 bits (402), Expect = 5e-39, Method: Compositional matrix adjust.
Identities = 85/198 (42%), Positives = 114/198 (57%), Gaps = 7/198 (3%)
Query: 87 GLEAVRKRPAMYIGSTGP-RGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADN 145
GL+AVRKRP MYIG T GLHH+V+E++DNA+DEA AG+ I V + ADNSVSV D+
Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60
Query: 146 GRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEV 205
GRGIP +HP SA E ++TVLHA NALS+ LE+
Sbjct: 61 GRGIPTGIHPEEGVSAAEVIMTVLHA--GGKFDDNSYKVSGGLHGVGVSVVNALSQKLEL 118
Query: 206 TVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
+ R+G + Q Y G P L ++ GT +RFWP + FT +F++ +A
Sbjct: 119 VIQREGKIHRQIYEHGVPQAPLAV----TGETEKTGTMVRFWPSLETFTNVTEFEYEILA 174
Query: 266 GRIRELAFLNPKLTIALR 283
R+REL+FLN ++I LR
Sbjct: 175 KRLRELSFLNSGVSIRLR 192
>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 = 159 bits (402), Expect = 5e-39, Method: Compositional matrix adjust.
Identities = 93/208 (44%), Positives = 120/208 (57%), Gaps = 8/208 (3%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
GLEAVRKRP MYIGST RGLHHLVYEI+DNAVDEA +GY + I V + DNS+ VAD+G
Sbjct: 2 GLEAVRKRPGMYIGSTDSRGLHHLVYEIVDNAVDEALSGYGNEINVTIQKDNSICVADSG 61
Query: 147 RGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVT 206
RG+P +H A+ +E + TVLHA NALS+ LEV
Sbjct: 62 RGMPTGMH-ASGIPTVEVIFTVLHA--GGKFGQGGYKTSGGLHGVGASVVNALSKWLEVH 118
Query: 207 VWRDGMEYHQKYS-RGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIA 265
+ RDG+EY +++ GKPV TL +K R GT + F PD +F+T F + +A
Sbjct: 119 IVRDGVEYMERFEDGGKPVGTLKK---IGKTKKRNGTSVTFLPDDTIFSTT-NFSYEILA 174
Query: 266 GRIRELAFLNPKLTIALRKEDSDPEKNQ 293
R+RE AFL + I L E + K +
Sbjct: 175 ERLRESAFLLKGVKITLTDERGEEPKEE 202
>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 = 140 bits (353), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 104/378 (27%), Positives = 167/378 (44%), Gaps = 60/378 (15%)
Query: 88 LEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNGR 147
+E VRKRP MY G G GLHHLVY +LD A +EA+ G ++ + + D S+++ R
Sbjct: 12 VENVRKRPGMYCGDVGEYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCTSR 71
Query: 148 ------------GIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXX 195
G P + +++L V
Sbjct: 72 TVTAENLVRVATGAGFLGRPPGDGWGWDSMLVV--------------------------- 104
Query: 196 XNALSESLEVTVWRDGMEYHQKYSRGKP----VTTLTCHVLPVDSKDRQGTRIRFWPDKQ 251
ALS +V +W DG ++ G P +PV ++ +G R+ F PD
Sbjct: 105 SLALSSRYQVDIWADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAE--RGVRVHFVPDAT 162
Query: 252 VFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLN 311
+F + FD ++ R ELA L P L ++ +D ++ + + GG+ ++ L
Sbjct: 163 IFEV-LAFDRARLSRRCNELAALAPGLRVSF----ADLQRGERTLWHLPGGVAQWAHVLT 217
Query: 312 TDKKPLH-DVVGFRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASL 370
+ LH + V F DG+ + ALQWC D S T+L +AN++RT+ G H++GV +L
Sbjct: 218 EARPQLHPEPVVFDFTWDGLRVQCALQWCEDEDS-TLLSFANAVRTVRHGAHVKGVTQAL 276
Query: 371 TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISVRVPNPE--FEGQTKTRLGNPEVRK 428
L L +++ + V +GLT I++V P + F G TK L P + +
Sbjct: 277 RGALAKLSGETRG------AFPWARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEE 330
Query: 429 VVDQSVQEYLTEYLELHP 446
+ + +Q E L HP
Sbjct: 331 AIRKQLQPLFIELLREHP 348
>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 = 126 bits (317), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 75/219 (34%), Positives = 117/219 (53%), Gaps = 31/219 (14%)
Query: 73 VSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEV 132
+++TY ++ I+VL GLE VR+RP MY +T P +HL E++DN+VDEA AG+A ++V
Sbjct: 1 MTQTYNADAIEVLTGLEPVRRRPGMYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDV 57
Query: 133 ALLADNSVSVADNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXX 192
L AD S+ V D+GRG+P+D+HP A+E +L +
Sbjct: 58 ILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCI------------------------ 93
Query: 193 XXXXNALSESLEVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQV 252
NALS+ +EV V RDG Y+ + G+ V L V+ K GT + FWPD+
Sbjct: 94 -SVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETF 150
Query: 253 FTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDSDPEK 291
F + +F + + ++ A L P + I + E ++ E+
Sbjct: 151 FDSP-RFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQ 188
>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 = 122 bits (307), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 75/208 (36%), Positives = 110/208 (52%), Gaps = 8/208 (3%)
Query: 84 VLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVA 143
VL GLE VR+RP MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V
Sbjct: 1 VLTGLEPVRRRPGMYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVI 57
Query: 144 DNGRGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESL 203
D+GRG+P+D+HP A+E +L LHA NALS+ +
Sbjct: 58 DDGRGMPVDIHPEEGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVGISVVNALSKRV 115
Query: 204 EVTVWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNT 263
EV V RDG Y+ + G+ V L V+ K GT + FWPD+ F + +F +
Sbjct: 116 EVNVRRDGQVYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSR 172
Query: 264 IAGRIRELAFLNPKLTIALRKEDSDPEK 291
+ ++ A L P + I + E ++ E+
Sbjct: 173 LTHVLKAKAVLCPGVEITFKDEINNTEQ 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 = 119 bits (299), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 73/205 (35%), Positives = 108/205 (52%), Gaps = 8/205 (3%)
Query: 87 GLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASNIEVALLADNSVSVADNG 146
GLE VR+RP MY +T P +HL E++DN+VDEA AG+A ++V L AD S+ V D+G
Sbjct: 1 GLEPVRRRPGMYTDTTRP---NHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDG 57
Query: 147 RGIPIDLHPATNKSALETVLTVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSESLEVT 206
RG+P+D+HP A+E +L LHA NALS+ +EV
Sbjct: 58 RGMPVDIHPEEGVPAVELILCRLHA--GGKFSNKNYQFSGGLHGVGISVVNALSKRVEVN 115
Query: 207 VWRDGMEYHQKYSRGKPVTTLTCHVLPVDSKDRQGTRIRFWPDKQVFTTAIQFDHNTIAG 266
V RDG Y+ + G+ V L V+ K GT + FWPD+ F + +F + +
Sbjct: 116 VRRDGQVYNIAFENGEKVQDL--QVVGTCGKRNTGTSVHFWPDETFFDSP-RFSVSRLTH 172
Query: 267 RIRELAFLNPKLTIALRKEDSDPEK 291
++ A L P + I + E ++ E+
Sbjct: 173 VLKAKAVLCPGVEITFKDEINNTEQ 197
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 103 bits (257), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 73/228 (32%), Positives = 113/228 (49%), Gaps = 17/228 (7%)
Query: 490 DCSSTTPEESEIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYK 544
D E + + EGDSA G GRD+ + PLRGKILNV + +
Sbjct: 16 DAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDK--YGVFPLRGKILNVREASHKQIME 73
Query: 545 NEEIQNLIRALGLGVKGEDFKKE----ALRYHKIIILTDADVDGAHIRTLLLTFFYRYQK 600
N EI N+I+ +GL K ++++ E LRY KI+I+TD D DG+HI+ LL+ F +
Sbjct: 74 NAEINNIIKIVGLQYK-KNYEDEDSLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWP 132
Query: 601 TLFDEGCIYVGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPV 660
+L + + P+ KV + KQ Y E ++ KSS P++ + ++ +KGLG
Sbjct: 133 SLLRHRFLEEFITPIVKVSKNKQEMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSK 192
Query: 661 QLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 706
+ 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 = 101 bits (251), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 71/219 (32%), Positives = 105/219 (47%), Gaps = 15/219 (6%)
Query: 498 ESEIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLI 552
E + + EGDSA G GRDR + PLRGKILNV + +N EI N+I
Sbjct: 52 ECTLILTEGDSAKSLAVSGLGVIGRDR--YGVFPLRGKILNVREASHKQIMENAEINNII 109
Query: 553 RALGLGVKGEDFKKEAL---RYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFDEGCIY 609
+ +GL K E+L RY KI+I+TD D DG+HI+ LL+ F + +L G +
Sbjct: 110 KIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLE 169
Query: 610 VGVPPLYKVERGKQVQYCYDDAELKKVKSSFPSNALYSIQRFKGLGEMMPVQLWETTLNP 669
+ P+ K + KQ Y E + K + + I+ +KGLG + E +
Sbjct: 170 EFITPIVKASKNKQELSFYSIPEFDEWKKHIENQKAWKIKYYKGLGTSTAKEAKEYFADM 229
Query: 670 EQR--MLKQLVIEDAAEANVVFSSLMGARVDTRKELIQN 706
E+ + + ED A + FS ++D RKE + N
Sbjct: 230 ERHRILFRYAGPEDDAAITLAFSK---KKIDDRKEWLTN 265
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 89.7 bits (221), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 142/591 (24%), Positives = 233/591 (39%), Gaps = 111/591 (18%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHLVYEI 114
S++ Q + LE + KRP YIGS + GL + EI
Sbjct: 2 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEI 61
Query: 115 LDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAX 172
L NA D + + I+V + A+ +++ V ++G+GIPI++H N E + H
Sbjct: 62 LVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFG--HLL 119
Query: 173 XXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRGKPVTTLTCH 230
N S LE G +Y QK+ + CH
Sbjct: 120 TSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSI----CH 175
Query: 231 VLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL-AFLNPK 277
+ S K T++ F PD F + D++ I G +R++ +LN K
Sbjct: 176 PPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDINVYLNGK 234
Query: 278 LTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQ 337
++ +R F +E Y++ L L++ + R +V D++ Q
Sbjct: 235 -SLKIRN--------------FKNYVELYLKSLIP--TILYERINNRWEVAFAVSDISFQ 277
Query: 338 WCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVR 397
+ + NSI T GGTH+ + + + ++ + KK K K ++
Sbjct: 278 ---------QISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSF-----QIK 323
Query: 398 EGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD-QSVQEYLTEYLELHPDVXXXXXXXX 456
+ I+ + NP F QTK +L +V D S E EY+
Sbjct: 324 NNMFIFINCLIENPAFTSQTKEQL----TTRVKDFGSRCEIPLEYIN------------- 366
Query: 457 XXXXXXXXXXXXXXXXVRQKSVLRSSSLPGKLADCSSTTPEE---SEIFIVEGDSA---- 509
+ + R ++ P KL D + +E + + EGDSA
Sbjct: 367 ---KIMKTDLATRMFEIADANESRITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLA 422
Query: 510 -GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEA 568
G A GRD + PLRGK+LNV + KN EIQ + + +GL + + ++
Sbjct: 423 VAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKS 480
Query: 569 LRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV 618
LRY ++I+TD D DG+HI+ L++ F L D +G + + P+ KV
Sbjct: 481 LRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKV 531
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 89.0 bits (219), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 143/593 (24%), Positives = 234/593 (39%), Gaps = 119/593 (20%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLHHLVYEI 114
S++ Q + LE + KRP YIGS + GL + EI
Sbjct: 2 ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEI 61
Query: 115 LDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVLTVLHAX 172
L NA D + + I+V + A+ +++ V ++G+GIPI++H N E + H
Sbjct: 62 LVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFG--HLL 119
Query: 173 XXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRGKPVTTLTCH 230
N S LE G +Y QK+ + CH
Sbjct: 120 TSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSI----CH 175
Query: 231 VLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL-AFLNPK 277
+ S K T++ F PD F + D++ I G +R++ +LN K
Sbjct: 176 PPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDINVYLNGK 234
Query: 278 LTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKPLHDVVGFRKDVDGITIDLALQ 337
++ +R F +E Y++ L L++ + R +V D++ Q
Sbjct: 235 -SLKIRN--------------FKNYVELYLKSLIP--TILYERINNRWEVAFAVSDISFQ 277
Query: 338 WCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKTVKDKDISLSGEHVR 397
+ + NSI T GGTH+ + + + ++ + KK K K ++
Sbjct: 278 ---------QISFVNSIATTMGGTHVNYITDQIVKKISEILKKKKKKSVKSF-----QIK 323
Query: 398 EGLTCIISVRVPNPEFEGQTKTRLGNPEVRKVVD-QSVQEYLTEYLE--LHPDVXXXXXX 454
+ I+ + NP F QTK +L +V D S E EY+ + D+
Sbjct: 324 NNMFIFINCLIENPAFTSQTKEQL----TTRVKDFGSRCEIPLEYINKIMKTDLATRMFE 379
Query: 455 XXXXXXXXXXXXXXXXXXVRQKSVLRSSSLPGKLADCSSTTPEE---SEIFIVEGDSA-- 509
R ++ P KL D + +E + + EGDSA
Sbjct: 380 IAS----------------------RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALS 416
Query: 510 ---GGSAKQGRDRRFQAILPLRGKILNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKK 566
G A GRD + PLRGK+LNV + KN EIQ + + +GL + +
Sbjct: 417 LAVAGLAVVGRD--YYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDT 474
Query: 567 EALRYHKIIILTDADVDGAHIRTLLLTFFYRYQKTLFD-EGCIYVGVPPLYKV 618
++LRY ++I+TD D DG+HI+ L++ F L D +G + + P+ KV
Sbjct: 475 KSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKV 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 = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 480 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 531
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 2 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 58
Query: 532 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 591
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 59 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 118
Query: 592 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 647
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 119 INFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 178
Query: 648 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 705
+ +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 = 75.1 bits (183), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 480 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 531
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 14 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 70
Query: 532 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 591
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 71 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 130
Query: 592 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 647
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 131 INFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 190
Query: 648 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 705
+ +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 = 74.7 bits (182), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/240 (27%), Positives = 114/240 (47%), Gaps = 20/240 (8%)
Query: 480 RSSSLPGKLADCSSTTPEES---EIFIVEGDSA-----GGSAKQGRDRRFQAILPLRGKI 531
R ++ P KL D + +E + + EGDSA G A GRD + PLRGK+
Sbjct: 4 RITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRD--YYGCYPLRGKM 60
Query: 532 LNVERKDEAAMYKNEEIQNLIRALGLGVKGEDFKKEALRYHKIIILTDADVDGAHIRTLL 591
LNV + KN EIQ + + +GL + + ++LRY ++I+TD D DG+HI+ L+
Sbjct: 61 LNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLI 120
Query: 592 LTFFYRYQKTLFD-EGCIYVGVPPLYKVERGKQVQYC---YDDAELKKVKSSFPSNALYS 647
+ F L D +G + + P+ KV K + Y+ + +K + +
Sbjct: 121 INFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESHKFTWK 180
Query: 648 IQRFKGLGEMMPVQLWE--TTLNPEQRMLKQLVIEDAAEANVVFSSLMGARVDTRKELIQ 705
+ +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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 91/398 (22%), Positives = 151/398 (37%), Gaps = 80/398 (20%)
Query: 72 PVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLH 108
PVS S++ Q + LE + KRP YIGS + GL
Sbjct: 10 PVS---ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLF 66
Query: 109 HLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVL 166
+ EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E +
Sbjct: 67 KIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIF 126
Query: 167 TVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRGKPV 224
H N S LE G +Y QK+ +
Sbjct: 127 G--HLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSI 184
Query: 225 TTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL- 271
CH + S K T++ F PD F + D++ I G +R++
Sbjct: 185 ----CHPPKITSYKKGPSYTKVTFKPDLTRFGMK-ELDNDILGVMRRRVYDINGSVRDIN 239
Query: 272 AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP--------LHDVVGF 323
+LN K ++ +R + E + LE+ Q N + L++ +
Sbjct: 240 VYLNGK-SLKIRNFKNYVE-------LYLKSLEKKRQLDNGEDGAAKSDIPTILYERINN 291
Query: 324 RKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKT 383
R +V D++ Q S + NSI T GGTH+ + + + ++ + KK K
Sbjct: 292 RWEVAFAVSDISFQQIS---------FVNSIATTMGGTHVNYITDQIVKKISEILKKKKK 342
Query: 384 VKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRL 421
K ++ + I+ + NP F QTK +L
Sbjct: 343 KSVKSF-----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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 90/398 (22%), Positives = 150/398 (37%), Gaps = 80/398 (20%)
Query: 72 PVSKTYGSEQIQVLEGLEAVRKRPAMYIGSTGPR-----------------------GLH 108
PVS S++ Q + LE + KRP YIGS + GL
Sbjct: 10 PVS---ASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCXIEKNVTIVPGLF 66
Query: 109 HLVYEILDNAVD-EAQAGYASNIEVALLAD-NSVSVADNGRGIPIDLHPATNKSALETVL 166
+ EIL NA D + + I+V + A+ +++ V ++G+GIPI++H N E +
Sbjct: 67 KIFDEILVNAADNKVRDPSXKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEXIF 126
Query: 167 TVLHAXXXXXXXXXXXXXXXXXXXXXXXXXNALSES--LEVTVWRDGMEYHQKYSRGKPV 224
H N S LE G +Y QK+ +
Sbjct: 127 G--HLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNXSI 184
Query: 225 TTLTCHVLPVDS--KDRQGTRIRFWPDKQVFTTAIQFDHNT----------IAGRIREL- 271
CH + S K T++ F PD F + D++ I G +R++
Sbjct: 185 ----CHPPKITSYKKGPSYTKVTFKPDLTRFGXK-ELDNDILGVXRRRVYDINGSVRDIN 239
Query: 272 AFLNPKLTIALRKEDSDPEKNQYNEYFFAGGLEEYVQWLNTDKKP--------LHDVVGF 323
+LN K ++ +R + E + LE+ Q N + L++ +
Sbjct: 240 VYLNGK-SLKIRNFKNYVE-------LYLKSLEKKRQLDNGEDGAAKSDIPTILYERINN 291
Query: 324 RKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGTHIEGVKASLTRTLNSLGKKSKT 383
R +V D++ Q + + NSI T GGTH+ + + + ++ + KK K
Sbjct: 292 RWEVAFAVSDISFQ---------QISFVNSIATTXGGTHVNYITDQIVKKISEILKKKKK 342
Query: 384 VKDKDISLSGEHVREGLTCIISVRVPNPEFEGQTKTRL 421
K ++ I+ + NP F QTK +L
Sbjct: 343 KSVKSF-----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 = 0.083, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 348 LGYANSIRTIDGGTHIEGVKASL-TRTLNSLGKKSKTVKDKDISLSGEHVREGLTCIISV 406
+ + NSI T GG H++ V + T+ ++ + KK+K +++ V+ + ++
Sbjct: 283 ISFVNSIATSKGGRHVDYVADQIVTKLVDVVKKKNKG----GVAVKAHQVKNHMWIFVNA 338
Query: 407 RVPNPEFEGQTKTRL 421
+ NP F+ QTK +
Sbjct: 339 LIENPTFDSQTKENM 353
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 40/91 (43%), Gaps = 24/91 (26%)
Query: 88 LEAVRKRPAMYIGS----------------------TGPRGLHHLVYEILDNAVDEAQAG 125
LE + RP YIGS T GL+ + EIL NA D Q
Sbjct: 12 LEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVNAADNKQRD 71
Query: 126 -YASNIEVALLADNS-VSVADNGRGIPIDLH 154
S I V + +N+ +S+ +NG+GIP+ H
Sbjct: 72 PKMSCIRVTIDPENNLISIWNNGKGIPVVEH 102
>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 = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA-GYASNIEVAL-L 135
E+ L E ++ P + R L+ V E+++N++D G NI++ + L
Sbjct: 3 AKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDL 62
Query: 136 ADNS-----VSVADNGRGIP 150
D++ V+V DNG GIP
Sbjct: 63 IDDARQIYKVNVVDNGIGIP 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 = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA-GYASNIEVAL-L 135
E+ L E ++ P + R L+ V E+++N++D G NI++ + L
Sbjct: 2 AKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDL 61
Query: 136 ADNS-----VSVADNGRGIP 150
D++ V+V DNG GIP
Sbjct: 62 IDDARQIYKVNVVDNGIGIP 81
>pdb|1MU5|A Chain A, Structure Of Topoisomerase Subunit
Length = 471
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA-GYASNIEVAL-L 135
E+ L E ++ P + R L+ V E+++N++D G NI++ + L
Sbjct: 4 AKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDL 63
Query: 136 ADNS-----VSVADNGRGIP 150
D++ V+V DNG GIP
Sbjct: 64 IDDARQIYKVNVVDNGIGIP 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 = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA-GYASNIEVAL-L 135
E+ L E ++ P + R L+ V E+++N++D G NI++ + L
Sbjct: 2 AKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDL 61
Query: 136 ADNS-----VSVADNGRGIP 150
D++ V+V DNG GIP
Sbjct: 62 IDDARQIYKVNVVDNGIGIP 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 = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 78 GSEQIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQA-GYASNIEVAL-L 135
E+ L E ++ P + R L+ V E+++N++D G NI++ + L
Sbjct: 5 AKEKFTSLSPAEFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDL 64
Query: 136 ADNS-----VSVADNGRGIP 150
D++ V+V DNG GIP
Sbjct: 65 IDDARQIYKVNVVDNGIGIP 84
>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 = 2.0, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 323 FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT----HIEGVKASLTRTLNSLG 378
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 = 2.1, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 323 FRKDVDGITIDLALQWCSDAYSDTMLGYANSIRTIDGGT----HIEGVKASLTRTLNSLG 378
F++D D + L L ++ +++LG++ +I+TIDG T ++ V+ S T T G
Sbjct: 82 FKRDGDDLIYTLPL-----SFKESLLGFSKTIQTIDGRTLPLSRVQPVQPSQTSTYPGQG 136
>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 = 4.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 247 WPDKQVFTTAIQFDHNTIAGRIRELAFLNPKLTIALRKEDS 287
+P F TA + +AG++ P L+IALRK+ S
Sbjct: 123 YPLNYAFNTAGEITQGILAGKVNRAVLGEPFLSIALRKDSS 163
>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 = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 104 PRGLHHLVYEILDNAVD---EAQAGYAS--NIEVALL---ADNSVSVADNGRGIPI 151
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 = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
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 = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 104 PRGLHHLVYEILDNAVDEAQAGYASNIEVAL 134
P +H ++ +LD+ E QAGYA NI V
Sbjct: 311 PYDMHEVITRLLDDEFLEIQAGYAQNIVVGF 341
>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 = 29.6 bits (65), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 104 PRGLHHLVYEILDNAVD---EAQAGYAS--NIEVALL---ADNSVSVADNGRGIPI 151
P LHH+++E+ NA+ E Q S IEV ++ D ++ ++D G G+P+
Sbjct: 228 PSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPL 283
>pdb|1JM6|A Chain A, Pyruvate Dehydrogenase Kinase, Isozyme 2, Containing Adp
pdb|1JM6|B Chain B, Pyruvate Dehydrogenase Kinase, Isozyme 2, Containing Adp
pdb|3CRK|A Chain A, Crystal Structure Of The Pdhk2-L2 Complex.
pdb|3CRK|B Chain B, Crystal Structure Of The Pdhk2-L2 Complex.
pdb|3CRL|A Chain A, Crystal Structure Of The Pdhk2-L2 Complex.
pdb|3CRL|B Chain B, Crystal Structure Of The Pdhk2-L2 Complex
Length = 407
Score = 29.3 bits (64), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 12/79 (15%)
Query: 81 QIQVLEGLEAVRKRPAMYIGSTGPRGLHHLVYEILDNAVDEAQAGYASN-------IEVA 133
+IQ + A + +Y+ P L+H+++E+ NA+ + S+ I VA
Sbjct: 223 EIQEVNATNATQPIHMVYV----PSHLYHMLFELFKNAMRATVESHESSLTLPPIKIMVA 278
Query: 134 L-LADNSVSVADNGRGIPI 151
L D S+ ++D G G+P+
Sbjct: 279 LGEEDLSIKMSDRGGGVPL 297
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 0.134 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,728,761
Number of Sequences: 62578
Number of extensions: 735970
Number of successful extensions: 2040
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1896
Number of HSP's gapped (non-prelim): 68
length of query: 718
length of database: 14,973,337
effective HSP length: 106
effective length of query: 612
effective length of database: 8,340,069
effective search space: 5104122228
effective search space used: 5104122228
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)