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= 000459
(1484 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 1037 bits (2682), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 547/1169 (46%), Positives = 737/1169 (63%), Gaps = 80/1169 (6%)
Query: 31 YQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNA 90
YQK SQLEHIL RPDTYIGS+E Q WIY+EE+ MI + ++ VPGL+KIFDEILVNA
Sbjct: 6 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 65
Query: 91 ADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYD 150
ADNK RDP M + V I E I V N G G+P+EIH +E +Y+PE+IFGHLLTSSNYD
Sbjct: 66 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 125
Query: 151 DNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEG 210
D+ KK TGGRNGYGAKL NIFSTEFI+ETAD +KY Q + NNM P I+ K+G
Sbjct: 126 DDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKG 185
Query: 211 DNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVKSFAEY 270
++TKV+FKPDL +F M L++D++ +M++RV D+ G + + + V LNG + +++F Y
Sbjct: 186 PSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV-RDINVYLNGKSLKIRNFKNY 244
Query: 271 VDMYPKSV--TRFHERVNERWEICVTLSEGQFQQVSFVNGIATIKGGTHVDYVANQXXXX 328
V++Y KS+ T +ER+N RWE+ +S+ FQQ+SFVN IAT GGTHV+Y+ +Q
Sbjct: 245 VELYLKSLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKK 304
Query: 329 XXXXXXXXXXXXXXXXXXXXXXLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSEE 388
+++F+N LI+NPAF SQTKE LT R FGS+CE+ E
Sbjct: 305 ISEILKKKKKKSVKSFQIKNN-MFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLE 363
Query: 389 FLKKVTAKSGIVETLLSWANFKQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTL 448
++ K+ K+ + + A+ +S+ + KLEDAN AG + +CTL
Sbjct: 364 YINKI-MKTDLATRMFEIADANESR------------ITNYPKLEDANKAGTKEGYKCTL 410
Query: 449 ILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVREASSNQVLNNSEIGNIKKILGLK 508
+LTEGDSA +LA+AGL+VVGRD +G +PLRGK+LNVREAS++Q+L N+EI IKKI+GL+
Sbjct: 411 VLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQ 470
Query: 509 QGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQDHDGSHIKGL 568
+Y + KSLRYGHLMIMTDQ DHDGSHIKGL
Sbjct: 471 HRKKYEDTKSLRYGHLMIMTDQ----------------------------DHDGSHIKGL 502
Query: 569 LINFIHSFWPSLLKIPSFLVEFITPIVKA--TNKNGKVLSFYSMPDYEAWKESLGGNASS 626
+INF+ S +P LL I FL+EFITPI+K T ++FY+MPDYE W+E + +
Sbjct: 503 IINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREE-ESHKFT 561
Query: 627 WSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQ 686
W KYY TS ++E +EYF N+ H K F D + I+LAFSKKK + RK+WL Q
Sbjct: 562 WKQKYY----TSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQ 617
Query: 687 FEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFI 746
+EPG LD K I SDF+NKELILFS+AD RSIP+++DG KPGQRK+L+ FK+N
Sbjct: 618 YEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLK 677
Query: 747 KEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKD 806
E KVAQ + YVSE +AYHHGEQSLA TI+G+AQ+FVGSNNI LL PNG FGTR GGKD
Sbjct: 678 SELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKD 737
Query: 807 AASAR-YIFTRLSPITRFLFPXXXXXXXXYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGT 865
AA+AR YI+T L+ +TR +F Y+ ED + +EP WY+PI+P +LVNG+EGIGT
Sbjct: 738 AAAARXYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGT 797
Query: 866 GWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIE 925
GWS+YIP +NP +I+ N+R L+N E +E MHPW+RG+ GTIE+ + Y + G IE
Sbjct: 798 GWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEP----LRYRMYGRIE 853
Query: 926 EVNETTLRIKELPIRRWTQDYREFLESIIDQNDS---FIRGFRQYSDDTTVDFEVFLSEE 982
++ + L I ELP R WT +E+L + ND +I+ + DD + F + LS E
Sbjct: 854 QIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDD-NIKFIITLSPE 912
Query: 983 SMMRTKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKK 1042
M +T++ G ++FKL + IS NM FD G IKKY++ +IL EF+++RLE+Y+KRK
Sbjct: 913 EMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKD 972
Query: 1043 VQXXXXXXXXXXXXXXVRFILGVVNGEIVVNNRKRTDLLLELRQKGFTPFPKNSKSIEAV 1102
V+FI ++ E+ V N+ R ++ EL GF F K K
Sbjct: 973 HMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKP---- 1028
Query: 1103 VAGATDXXXXXXXXXXVVNGVQSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLR 1162
G+ + Y+YLL M I +LT E+ Q LL + + E+++L
Sbjct: 1029 YYGSEELYGT---------------YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLL 1073
Query: 1163 KATPESLWVKDLDALDMQLDELDKSDARA 1191
K + + +W DL A ++ E + DA A
Sbjct: 1074 KLSAKDIWNTDLKAFEVGYQEFLQRDAEA 1102
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 1034 bits (2673), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 546/1169 (46%), Positives = 734/1169 (62%), Gaps = 84/1169 (7%)
Query: 31 YQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNA 90
YQK SQLEHIL RPDTYIGS+E Q WIY+EE+ MI + ++ VPGL+KIFDEILVNA
Sbjct: 6 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 65
Query: 91 ADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYD 150
ADNK RDP M + V I E I V N G G+P+EIH +E +Y+PE+IFGHLLTSSNYD
Sbjct: 66 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 125
Query: 151 DNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEG 210
D+ KK TGGRNGYGAKL NIFSTEFI+ETAD +KY Q + NNM P I+ K+G
Sbjct: 126 DDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKG 185
Query: 211 DNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVKSFAEY 270
++TKV+FKPDL +F M L++D++ +M++RV D+ G + + + V LNG + +++F Y
Sbjct: 186 PSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV-RDINVYLNGKSLKIRNFKNY 244
Query: 271 VDMYPKSV--TRFHERVNERWEICVTLSEGQFQQVSFVNGIATIKGGTHVDYVANQXXXX 328
V++Y KS+ T +ER+N RWE+ +S+ FQQ+SFVN IAT GGTHV+Y+ +Q
Sbjct: 245 VELYLKSLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQIVKK 304
Query: 329 XXXXXXXXXXXXXXXXXXXXXXLWVFVNALIDNPAFDSQTKETLTLRQSSFGSKCELSEE 388
+++F+N LI+NPAF SQTKE LT R FGS+CE+ E
Sbjct: 305 ISEILKKKKKKSVKSFQIKNN-MFIFINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLE 363
Query: 389 FLKKVTAKSGIVETLLSWANFKQSKDLKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTL 448
++ K+ K+ + + A+ + KLEDAN AG + +CTL
Sbjct: 364 YINKI-MKTDLATRMFEIAS----------------RITNYPKLEDANKAGTKEGYKCTL 406
Query: 449 ILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVREASSNQVLNNSEIGNIKKILGLK 508
+LTEGDSA +LA+AGL+VVGRD +G +PLRGK+LNVREAS++Q+L N+EI IKKI+GL+
Sbjct: 407 VLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQ 466
Query: 509 QGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQDHDGSHIKGL 568
+Y + KSLRYGHLMIMTDQ DHDGSHIKGL
Sbjct: 467 HRKKYEDTKSLRYGHLMIMTDQ----------------------------DHDGSHIKGL 498
Query: 569 LINFIHSFWPSLLKIPSFLVEFITPIVKA--TNKNGKVLSFYSMPDYEAWKESLGGNASS 626
+INF+ S +P LL I FL+EFITPI+K T ++FY+MPDYE W+E + +
Sbjct: 499 IINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREE-ESHKFT 557
Query: 627 WSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQ 686
W KYY TS ++E +EYF N+ H K F D + I+LAFSKKK + RK+WL Q
Sbjct: 558 WKQKYY----TSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQ 613
Query: 687 FEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFI 746
+EPG LD K I SDF+NKELILFS+AD RSIP+++DG KPGQRK+L+ FK+N
Sbjct: 614 YEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLK 673
Query: 747 KEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKD 806
E KVAQ + YVSE +AYHHGEQSLA TI+G+AQ+FVGSNNI LL PNG FGTR GGKD
Sbjct: 674 SELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKD 733
Query: 807 AASAR-YIFTRLSPITRFLFPXXXXXXXXYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGT 865
AA+AR YI+T L+ +TR +F Y+ ED + +EP WY+PI+P +LVNG+EGIGT
Sbjct: 734 AAAARXYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGT 793
Query: 866 GWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIE 925
GWS+YIP +NP +I+ N+R L+N E +E MHPW+RG+ GTIE+ + Y + G IE
Sbjct: 794 GWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEP----LRYRMYGRIE 849
Query: 926 EVNETTLRIKELPIRRWTQDYREFLESIIDQNDS---FIRGFRQYSDDTTVDFEVFLSEE 982
++ + L I ELP R WT +E+L + ND +I+ + DD + F + LS E
Sbjct: 850 QIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDD-NIKFIITLSPE 908
Query: 983 SMMRTKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKK 1042
M +T++ G ++FKL + IS NM FD G IKKY++ +IL EF+++RLE+Y+KRK
Sbjct: 909 EMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKD 968
Query: 1043 VQXXXXXXXXXXXXXXVRFILGVVNGEIVVNNRKRTDLLLELRQKGFTPFPKNSKSIEAV 1102
V+FI ++ E+ V N+ R ++ EL GF F K K
Sbjct: 969 HMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKP---- 1024
Query: 1103 VAGATDXXXXXXXXXXVVNGVQSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLR 1162
G+ + Y+YLL M I +LT E+ Q LL + + E+++L
Sbjct: 1025 YYGSEELYGT---------------YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLL 1069
Query: 1163 KATPESLWVKDLDALDMQLDELDKSDARA 1191
K + + +W DL A ++ E + DA A
Sbjct: 1070 KLSAKDIWNTDLKAFEVGYQEFLQRDAEA 1098
>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 = 713 bits (1841), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 385/796 (48%), Positives = 514/796 (64%), Gaps = 58/796 (7%)
Query: 419 DGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLR 478
D K ++GI KL+DAN AGG++S +CTLILTEGDSAK+LA++GL V+GRDR+GVFPLR
Sbjct: 26 DSVKYSKIKGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLR 85
Query: 479 GKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNN---VKSLRYGHLMIMTDQVLLAP 535
GK+LNVREAS Q++ N+EI NI KI+GL+ Y++ +K+LRYG +MIMTDQ
Sbjct: 86 GKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQ----- 140
Query: 536 LSFLLWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIV 595
D DGSHIKGLLINFIH WPSLLK FL EFITPIV
Sbjct: 141 -----------------------DQDGSHIKGLLINFIHHNWPSLLK-HGFLEEFITPIV 176
Query: 596 KATNKNGKVLSFYSMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKK 655
KA+ KN + LSFYS+P+++ WK+ + N +W IKYYKGLGTST+KE KEYF ++ H+
Sbjct: 177 KAS-KNKQELSFYSIPEFDEWKKHIE-NQKAWKIKYYKGLGTSTAKEAKEYFADMERHRI 234
Query: 656 DFVWEDDQDGEAIELAFSKKKIEARKKWLLQFE-----------PGNHL-DQKEKYIKYS 703
F + +D AI LAFSKKKI+ RK+WL F P L K++ Y+
Sbjct: 235 LFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQFLYGTATKHLTYN 294
Query: 704 DFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSA 763
DF+NKELILFS +D +RSIPS+VDG KPGQRK+LF FKRN +E KVAQ +G V+E SA
Sbjct: 295 DFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSA 354
Query: 764 YHHGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRF 823
YHHGEQ+L TI+ +AQ+FVGSNNINLLQP GQFGTR GGKDAAS RYIFT LS + R
Sbjct: 355 YHHGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLSTLARL 414
Query: 824 LFPXXXXXXXXYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANV 883
LFP +L +D Q++EP WY+PIIP VL+NG+EGIGTGW+ +PNY+ R+IV NV
Sbjct: 415 LFPAVDDNLLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNV 474
Query: 884 RRLLNGEMMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWT 943
RR+L+G PM P Y+ F GTI++ + Y V+G I V+ T+ I ELP+R WT
Sbjct: 475 RRMLDGLDPHPMLPNYKNFKGTIQELGQNQ----YAVSGEIFVVDRNTVEITELPVRTWT 530
Query: 944 QDYRE-FLESII---DQNDSFIRGFRQYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLT 999
Q Y+E LE ++ D+ + I +++Y DTTV F V ++EE + + + GL K FKL
Sbjct: 531 QVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGLHKVFKLQ 590
Query: 1000 TTISTSNMHLFDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKKVQXXXXXXXXXXXXXXV 1059
TT++ ++M LFD G +KKY+T + IL+EFF +RL +Y RK+
Sbjct: 591 TTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKEWLVGMLGAESTKLNNQA 650
Query: 1060 RFILGVVNGEIVVNNRKRTDLLLELRQKGFTPFPKNSKSIEAVVAGATDXXXXXXXXXXV 1119
RFIL + G+I + NR + DL+ L Q+G+ P + A D
Sbjct: 651 RFILEKIQGKITIENRSKKDLIQMLVQRGYESDPVKAWKEAQEKAAEEDETQNQHDDSSS 710
Query: 1120 VNGVQS-IDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALD 1178
+G S D++Y+L+M++ +LT EKV+ L+ RD EV+DL++ +P LW +DL A
Sbjct: 711 DSGTPSGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLKRKSPSDLWKEDLAAF- 769
Query: 1179 MQLDELDKSDARAEEE 1194
++ELDK +++ E+
Sbjct: 770 --VEELDKVESQERED 783
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 692 bits (1787), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 373/799 (46%), Positives = 501/799 (62%), Gaps = 56/799 (7%)
Query: 415 LKKNDGTKTEDVRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGV 474
LKK+DGT+ + KLEDAN AG + +CTL+LTEGDSA +LA+AGL+VVGRD +G
Sbjct: 4 LKKSDGTRKSRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGC 63
Query: 475 FPLRGKLLNVREASSNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLA 534
+PLRGK+LNVREAS++Q+L N+EI IKKI+GL+ +Y + KSLRYGHLMIMTD
Sbjct: 64 YPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTD----- 118
Query: 535 PLSFLLWFILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPI 594
QDHDGSHIKGL+INF+ S + LL I FL+EFITPI
Sbjct: 119 -----------------------QDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPI 155
Query: 595 VKA--TNKNGKVLSFYSMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITL 652
+K T ++FY+MPDYE W+E + +W KYYKGLGTS ++E +EYF N+
Sbjct: 156 IKVSITKPTKNTIAFYNMPDYEKWREE-ESHKFTWKQKYYKGLGTSLAQEVREYFSNLDR 214
Query: 653 HKKDFVWEDDQDGEAIELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELIL 712
H K F D + I+LAFSKKK + RK+WL Q+EPG LD K I SDF+NKELIL
Sbjct: 215 HLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELIL 274
Query: 713 FSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQSLA 772
FS+AD RSIP+++DG KPGQRK+L+ FK+N E KVAQ + YVSE +AYHHGEQSLA
Sbjct: 275 FSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLA 334
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXX 832
TI+G+AQ+FVGSNNI LL PNG FGTR GGKDAA+ARYI+T L+ +TR +F
Sbjct: 335 QTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPL 394
Query: 833 XXYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMM 892
Y+ ED + +EP WY+PI+P +LVNG+EGIGTGWS+YIP +NP +I+ N+R L+N E +
Sbjct: 395 YKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEEL 454
Query: 893 EPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYREFLES 952
E MHPW+RG+ GTIE+ + Y + G IE++ + L I ELP R WT +E+L
Sbjct: 455 EQMHPWFRGWTGTIEEIEP----LRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLL 510
Query: 953 IIDQNDS---FIRGFRQYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSNMHL 1009
+ ND +I+ + DD + F + LS E M +T++ G ++FKL + IS NM
Sbjct: 511 GLSGNDKIKPWIKDMEEQHDD-NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVA 569
Query: 1010 FDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKKVQXXXXXXXXXXXXXXVRFILGVVNGE 1069
FD G IKKY++ +IL EF+++RLE+Y+KRK V+FI ++ E
Sbjct: 570 FDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKE 629
Query: 1070 IVVNNRKRTDLLLELRQKGFTPFPK---------NSKSIEAV--VAGAT----DXXXXXX 1114
+ V N+ R ++ EL GF F K N + E + V GAT D
Sbjct: 630 LTVTNKPRNAIIQELENLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHE 689
Query: 1115 XXXXVVNGVQSI--DYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVK 1172
V+NG + + Y+YLL M I +LT E+ Q LL + + E+++L K + + +W
Sbjct: 690 DTENVINGPEELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNT 749
Query: 1173 DLDALDMQLDELDKSDARA 1191
DL A ++ E + DA A
Sbjct: 750 DLKAFEVGYQEFLQRDAEA 768
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 690 bits (1781), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 372/791 (47%), Positives = 506/791 (63%), Gaps = 58/791 (7%)
Query: 426 VRGISKLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVR 485
++GI KL+DAN AGGRNS +CTLILTEGDSAK LA++GL VVGRD++GVFPLRGK+LNVR
Sbjct: 5 IKGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFPLRGKILNVR 64
Query: 486 EASSNQVLNNSEIGNIKKILGLKQGVEY---NNVKSLRYGHLMIMTDQVLLAPLSFLLWF 542
EAS Q++ N+EI NI KI+GL+ Y +++K+LRYG +MIMTDQ
Sbjct: 65 EASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGKIMIMTDQ------------ 112
Query: 543 ILIFAWITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNG 602
D DGSHIKGLLINFIH WPSLL+ FL EFITPIVK + KN
Sbjct: 113 ----------------DQDGSHIKGLLINFIHHNWPSLLR-HRFLEEFITPIVKVS-KNK 154
Query: 603 KVLSFYSMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDD 662
+ ++FYS+P++E WK S N W +KYYKGLGTSTSKE KEYF ++ H+ F +
Sbjct: 155 QEMAFYSLPEFEEWKSS-TPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHRIQFKYSGP 213
Query: 663 QDGEAIELAFSKKKIEARKKWLLQFE-----------PGNHL-DQKEKYIKYSDFVNKEL 710
+D AI LAFSKK+I+ RK+WL F P ++L Q Y+ Y+DF+NKEL
Sbjct: 214 EDDAAISLAFSKKQIDDRKEWLTNFMEDRRQRKLLGLPEDYLYGQTTTYLTYNDFINKEL 273
Query: 711 ILFSMADLQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQS 770
ILFS +D +RSIPSMVDGLKPGQRK+LF FKRN +E KVAQ +G V+E S+YHHGE S
Sbjct: 274 ILFSNSDNERSIPSMVDGLKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSSYHHGEMS 333
Query: 771 LASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXX 830
L TI+ +AQ+FVGSNN+NLLQP GQFGTR GGKD+AS RYIFT LS + R LFP
Sbjct: 334 LMMTIINLAQNFVGSNNLNLLQPIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDD 393
Query: 831 XXXXYLNEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGE 890
+L +D Q++EP WY+PIIP VL+NG+EGIGTGWS IPN++ R+IV N+RRL++GE
Sbjct: 394 HTLKFLYDDNQRVEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGE 453
Query: 891 MMEPMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYRE-F 949
PM P Y+ F GTIE+ A + Y ++G + +N TT+ I ELP+R WTQ Y+E
Sbjct: 454 EPLPMLPSYKNFKGTIEELAPNQ----YVISGEVAILNSTTIEISELPVRTWTQTYKEQV 509
Query: 950 LESII---DQNDSFIRGFRQYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSN 1006
LE ++ ++ I +R+Y DTTV F V ++EE + ++ GL K FKL T+++ ++
Sbjct: 510 LEPMLNGTEKTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVGLHKVFKLQTSLTCNS 569
Query: 1007 MHLFDSKGVIKKYDTPEQILEEFFHIRLEFYEKRKKVQXXXXXXXXXXXXXXVRFILGVV 1066
M LFD G +KKYDT IL +FF +RL++Y RK+ RFIL +
Sbjct: 570 MVLFDHVGCLKKYDTVLDILRDFFELRLKYYGLRKEWLLGMLGAESAKLNNQARFILEKI 629
Query: 1067 NGEIVVNNRKRTDLLLELRQKGFTPFPKNS--KSIEAVVAGATDXXXXXXXXXXVVNGV- 1123
+G+I++ N+ + +L+ L Q+G+ P + ++ + V + + V
Sbjct: 630 DGKIIIENKPKKELIKVLIQRGYDSDPVKAWKEAQQKVPDEEENEESDNEKETEKSDSVT 689
Query: 1124 -QSIDYDYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLD 1182
++YLL M + LT EK L R++ +E+D L++ +P LW +DL +L+
Sbjct: 690 DSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELDTLKRKSPSDLWKEDLATFIEELE 749
Query: 1183 ELDKSDARAEE 1193
++ + + E+
Sbjct: 750 AVEAKEKQDEQ 760
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 682 bits (1759), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 366/783 (46%), Positives = 489/783 (62%), Gaps = 56/783 (7%)
Query: 431 KLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVREASSN 490
KLEDAN AG + +CTL+LTEGDSA +LA+AGL+VVGRD +G +PLRGK+LNVREAS++
Sbjct: 10 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASAD 69
Query: 491 QVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWIT 550
Q+L N+EI IKKI+GL+ +Y + KSLRYGHLMIMTD
Sbjct: 70 QILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTD--------------------- 108
Query: 551 TFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKA--TNKNGKVLSFY 608
QDHDGSHIKGL+INF+ S + LL I FL+EFITPI+K T ++FY
Sbjct: 109 -------QDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFY 161
Query: 609 SMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAI 668
+MPDYE W+E + +W KYYKGLGTS ++E +EYF N+ H K F D + I
Sbjct: 162 NMPDYEKWREE-ESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYI 220
Query: 669 ELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDG 728
+LAFSKKK + RK+WL Q+EPG LD K I SDF+NKELILFS+AD RSIP+++DG
Sbjct: 221 DLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDG 280
Query: 729 LKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNI 788
KPGQRK+L+ FK+N E KVAQ + YVSE +AYHHGEQSLA TI+G+AQ+FVGSNNI
Sbjct: 281 FKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNI 340
Query: 789 NLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXYLNEDGQQIEPTWY 848
LL PNG FGTR GGKDAA+ARYI+T L+ +TR +F Y+ ED + +EP WY
Sbjct: 341 YLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWY 400
Query: 849 MPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIEK 908
+PI+P +LVNG+EGIGTGWS+YIP +NP +I+ N+R L+N E +E MHPW+RG+ GTIE+
Sbjct: 401 LPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEE 460
Query: 909 TASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYREFLESIIDQNDS---FIRGFR 965
+ Y + G IE++ + L I ELP R WT +E+L + ND +I+
Sbjct: 461 IEP----LRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDME 516
Query: 966 QYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQI 1025
+ DD + F + LS E M +T++ G ++FKL + IS NM FD G IKKY++ +I
Sbjct: 517 EQHDD-NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEI 575
Query: 1026 LEEFFHIRLEFYEKRKKVQXXXXXXXXXXXXXXVRFILGVVNGEIVVNNRKRTDLLLELR 1085
L EF+++RLE+Y+KRK V+FI ++ E+ V N+ R ++ EL
Sbjct: 576 LSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELE 635
Query: 1086 QKGFTPFPKNSKSIEAV-----------VAGAT----DXXXXXXXXXXVVNGVQSI--DY 1128
GF F K K V GAT D V+NG + + Y
Sbjct: 636 NLGFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTY 695
Query: 1129 DYLLSMAIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSD 1188
+YLL M I +LT E+ Q LL + + E+++L K + + +W DL A ++ E + D
Sbjct: 696 EYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRD 755
Query: 1189 ARA 1191
A A
Sbjct: 756 AEA 758
>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 = 676 bits (1743), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 360/767 (46%), Positives = 482/767 (62%), Gaps = 59/767 (7%)
Query: 431 KLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVREASSN 490
KLEDAN AG + +CTL+LTEGDSA +LA+AGL+VVGRD +G +PLRGK+LNVREAS++
Sbjct: 8 KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASAD 67
Query: 491 QVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWIT 550
Q+L N+EI IKKI+GL+ +Y + KSLRYGHLMIMTDQ
Sbjct: 68 QILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQ-------------------- 107
Query: 551 TFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKA--TNKNGKVLSFY 608
DHDGSHIKGL+INF+ S +P LL I FL+EFITPI+K T ++FY
Sbjct: 108 --------DHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFY 159
Query: 609 SMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEAI 668
+MPDYE W+E + +W KYYKGLGTS ++E +EYF N+ H K F D + I
Sbjct: 160 NMPDYEKWREE-ESHKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYI 218
Query: 669 ELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIPSMVDG 728
+LAFSKKK + RK+WL Q+EPG LD K I SDF+NKELILFS+AD RSIP+++DG
Sbjct: 219 DLAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIPNVLDG 278
Query: 729 LKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNI 788
KPGQRK+L+ FK+N E KVAQ + YVSE +AYHHGEQSLA TI+G+AQ+FVGSNNI
Sbjct: 279 FKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNI 338
Query: 789 NLLQPNGQFGTRNQGGKDAASAR-YIFTRLSPITRFLFPXXXXXXXXYLNEDGQQIEPTW 847
LL PNG FGTR GGKDAA+AR YI+T L+ +TR +F Y+ ED + +EP W
Sbjct: 339 YLLLPNGAFGTRATGGKDAAAARXYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEW 398
Query: 848 YMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNGEMMEPMHPWYRGFGGTIE 907
Y+PI+P +LVNG+EGIGTGWS+YIP +NP +I+ N+R L+N E +E MHPW+RG+ GTIE
Sbjct: 399 YLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIE 458
Query: 908 KTASKEAGVTYTVTGIIEEVNETTLRIKELPIRRWTQDYREFLESIIDQNDS---FIRGF 964
+ + Y + G IE++ + L I ELP R WT +E+L + ND +I+
Sbjct: 459 EIEP----LRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDM 514
Query: 965 RQYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTPEQ 1024
+ DD + F + LS E M +T++ G ++FKL + IS NM FD G IKKY++ +
Sbjct: 515 EEQHDD-NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNE 573
Query: 1025 ILEEFFHIRLEFYEKRKKVQXXXXXXXXXXXXXXVRFILGVVNGEIVVNNRKRTDLLLEL 1084
IL EF+++RLE+Y+KRK V+FI ++ E+ V N+ R ++ EL
Sbjct: 574 ILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQEL 633
Query: 1085 RQKGFTPFPKNSKSIEAVVAGATDXXXXXXXXXXVVNGVQSIDYDYLLSMAIGTLTLEKV 1144
GF F K K G+ + Y+YLL M I +LT E+
Sbjct: 634 ENLGFPRFNKEGKP----YYGSEELYGT---------------YEYLLGMRIWSLTKERY 674
Query: 1145 QGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSDARA 1191
Q LL + + E+++L K + + +W DL A ++ E + DA A
Sbjct: 675 QKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEA 721
>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 = 432 bits (1111), Expect = e-121, Method: Compositional matrix adjust.
Identities = 218/401 (54%), Positives = 282/401 (70%), Gaps = 13/401 (3%)
Query: 26 TIEEMYQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDE 85
++E +YQKK+QLEHILLRPDTYIGS+E TQ +W+Y+E+ + +R +++VPGLYKIFDE
Sbjct: 1 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDV-GINYREVTFVPGLYKIFDE 59
Query: 86 ILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLT 145
ILVNAADNKQRDPKM ++V ID E++LIS+ N+G G+PV H+ E +YVP LIFG LLT
Sbjct: 60 ILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLT 119
Query: 146 SSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNIS 205
SSNYDD+ KK TGGRNGYGAKL NIFST+F +ETA + K +KQ + +NMG+ E +
Sbjct: 120 SSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMEL- 178
Query: 206 KCKEGDNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVK 265
K G+++T ++F+PDL+KF M L+ D+VALM +R D+AG K VKV LNG+++PVK
Sbjct: 179 KPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGST-KDVKVFLNGNKLPVK 237
Query: 266 SFAEYVDMYPK--------SVTRFHERVNERWEICVTLSEGQFQQVSFVNGIATIKGGTH 317
F YVDMY K S+ HE+VN RWE+C+T+SE FQQ+SFVN IAT KGG H
Sbjct: 238 GFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQISFVNSIATSKGGRH 297
Query: 318 VDYVANQXXXXXXXXXXXXXX-XXXXXXXXXXXXLWVFVNALIDNPAFDSQTKETLTLRQ 376
VDYVA+Q +W+FVNALI+NP FDSQTKE +TL+
Sbjct: 298 VDYVADQIVTKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQP 357
Query: 377 SSFGSKCELSEEFLKKVTAKSGIVETLLSWANFKQSKDLKK 417
SFGS C+LSE+F+K GIVE++L+W FK L K
Sbjct: 358 KSFGSTCQLSEKFIKAAIG-CGIVESILNWVKFKAQVQLNK 397
>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 = 383 bits (983), Expect = e-106, Method: Compositional matrix adjust.
Identities = 192/405 (47%), Positives = 258/405 (63%), Gaps = 22/405 (5%)
Query: 31 YQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNA 90
YQK SQLEHIL RPDTYIGS+E Q WIY+EE+ MI + ++ VPGL+KIFDEILVNA
Sbjct: 17 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 76
Query: 91 ADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYD 150
ADNK RDP M + V I E I V N G G+P+EIH +E +Y+PE+IFGHLLTSSNYD
Sbjct: 77 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 136
Query: 151 DNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEG 210
D+ KK TGGRNGYGAKL NIFSTEFI+ETAD +KY Q + NNM P I+ K+G
Sbjct: 137 DDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNMSICHPPKITSYKKG 196
Query: 211 DNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVKSFAEY 270
++TKV+FKPDL +F M L++D++ +M++RV D+ G + + + V LNG + +++F Y
Sbjct: 197 PSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSV-RDINVYLNGKSLKIRNFKNY 255
Query: 271 VDMYPKSV-------------------TRFHERVNERWEICVTLSEGQFQQVSFVNGIAT 311
V++Y KS+ T +ER+N RWE+ +S+ FQQ+SFVN IAT
Sbjct: 256 VELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIAT 315
Query: 312 IKGGTHVDYVANQXXXXXXXXXXXXXXXXXXXXXXXXXXLWVFVNALIDNPAFDSQTKET 371
GGTHV+Y+ +Q +++F+N LI+NPAF SQTKE
Sbjct: 316 TMGGTHVNYITDQ-IVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQ 374
Query: 372 LTLRQSSFGSKCELSEEFLKKVTAKSGIVETLLSWANFKQSKDLK 416
LT R FGS+CE+ E++ K+ K+ + + A+ + LK
Sbjct: 375 LTTRVKDFGSRCEIPLEYINKI-MKTDLATRMFEIADANEENALK 418
>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 = 365 bits (937), Expect = e-100, Method: Compositional matrix adjust.
Identities = 184/382 (48%), Positives = 243/382 (63%), Gaps = 21/382 (5%)
Query: 31 YQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNA 90
YQK SQLEHIL RPDTYIGS+E Q WIY+EE+ I + ++ VPGL+KIFDEILVNA
Sbjct: 17 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCXIEKNVTIVPGLFKIFDEILVNA 76
Query: 91 ADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYD 150
ADNK RDP + V I E I V N G G+P+EIH +E +Y+PE IFGHLLTSSNYD
Sbjct: 77 ADNKVRDPSXKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEXIFGHLLTSSNYD 136
Query: 151 DNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEG 210
D+ KK TGGRNGYGAKL NIFSTEFI+ETAD +KY Q + NN P I+ K+G
Sbjct: 137 DDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNXSICHPPKITSYKKG 196
Query: 211 DNWTKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHRVPVKSFAEY 270
++TKV+FKPDL +F L++D++ + ++RV D+ G + + + V LNG + +++F Y
Sbjct: 197 PSYTKVTFKPDLTRFGXKELDNDILGVXRRRVYDINGSV-RDINVYLNGKSLKIRNFKNY 255
Query: 271 VDMYPKSV-------------------TRFHERVNERWEICVTLSEGQFQQVSFVNGIAT 311
V++Y KS+ T +ER+N RWE+ +S+ FQQ+SFVN IAT
Sbjct: 256 VELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDISFQQISFVNSIAT 315
Query: 312 IKGGTHVDYVANQXXXXXXXXXXXXXXXXXXXXXXXXXXLWVFVNALIDNPAFDSQTKET 371
GGTHV+Y+ +Q ++F+N LI+NPAF SQTKE
Sbjct: 316 TXGGTHVNYITDQIVKKISEILKKKKKKSVKSFQIKNNX-FIFINCLIENPAFTSQTKEQ 374
Query: 372 LTLRQSSFGSKCELSEEFLKKV 393
LT R FGS+CE+ E++ K+
Sbjct: 375 LTTRVKDFGSRCEIPLEYINKI 396
>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 = 133 bits (335), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 133/484 (27%), Positives = 212/484 (43%), Gaps = 93/484 (19%)
Query: 431 KLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREAS 488
KL D + ++ E+C + L EGDSA G + GRD + PLRGK+LNV +A
Sbjct: 9 KLADCS---SKSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 489 SNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAW 548
+++LNN+EI + G G +++ K+ RY ++IMTD
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGDFDLAKA-RYHKIVIMTDA------------------ 101
Query: 549 ITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFY 608
D DG+HI+ LL+ F + F L++ ++ P+ K T K +Y
Sbjct: 102 ----------DVDGAHIRTLLLTFFYRFMRPLIE-AGYVYIAQPPLYKLTQGKQK---YY 147
Query: 609 SMPDYEAWKESLGGNAS-SWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEA 667
D E K N + WSI YKGLG + D +WE + E
Sbjct: 148 VYNDRELDKLKSELNPTPKWSIARYKGLGEMNA---------------DQLWETTMNPEH 192
Query: 668 IELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIK----YS--DF-------VNKELILFS 714
L K + + G+ ++ + ++I+ Y+ DF +N+ I
Sbjct: 193 RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSE 252
Query: 715 MAD----------LQRSIPSMVDGLKPGQRKILFCSFKRNFIKEA---KVAQFSGYVSEH 761
M + + R++P + DGLKP R+IL+ ++ + K A+ G V
Sbjct: 253 MRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDV--M 310
Query: 762 SAYH-HGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPI 820
YH HG+ S+ ++ MAQDF S L+ G FG+ + G AA+ RY R++ I
Sbjct: 311 GKYHPHGDSSIYEAMVRMAQDF--SYRYPLVDGQGNFGSMD--GDGAAAMRYTEARMTKI 366
Query: 821 TRFLFPXXXXXXXXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDI 879
T L ++ N DG + EP+ P +L NG+ GI G ++ IP +N ++
Sbjct: 367 TLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTEL 426
Query: 880 VANV 883
+ V
Sbjct: 427 INGV 430
>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 = 132 bits (331), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 132/484 (27%), Positives = 212/484 (43%), Gaps = 93/484 (19%)
Query: 431 KLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREAS 488
KL D + ++ E+C + L EGDSA G + GRD + PLRGK+LNV +A
Sbjct: 9 KLADCS---SKSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 489 SNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAW 548
+++LNN+EI + G G +++ K+ RY ++IMTD
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGDFDLAKA-RYHKIVIMTDA------------------ 101
Query: 549 ITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFY 608
D DG+HI+ LL+ F + F L++ ++ P+ K T K +Y
Sbjct: 102 ----------DVDGAHIRTLLLTFFYRFMRPLIE-AGYVYIAQPPLYKLTQGKQK---YY 147
Query: 609 SMPDYEAWKESLGGNAS-SWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEA 667
D E K N + WSI YKGLG + D +WE + E
Sbjct: 148 VYNDRELDKLKSELNPTPKWSIARYKGLGEMNA---------------DQLWETTMNPEH 192
Query: 668 IELAFSKKKIEARKKWLLQFEPGNHLDQKEKYIK----YS--DF-------VNKELILFS 714
L K + + G+ ++ + ++I+ Y+ DF +N+ I
Sbjct: 193 RALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSE 252
Query: 715 MAD----------LQRSIPSMVDGLKPGQRKILFCSFKRNFIKEA---KVAQFSGYVSEH 761
M + + R++P + DGLKP R+IL+ ++ + K A+ G V
Sbjct: 253 MRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDV--M 310
Query: 762 SAYH-HGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPI 820
YH HG+ S+ ++ MAQDF S L+ G FG+ + G AA+ R+ R++ I
Sbjct: 311 GKYHPHGDSSIYEAMVRMAQDF--SYRYPLVDGQGNFGSMD--GDGAAAMRFTEARMTKI 366
Query: 821 TRFLFPXXXXXXXXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDI 879
T L ++ N DG + EP+ P +L NG+ GI G ++ IP +N ++
Sbjct: 367 TLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTEL 426
Query: 880 VANV 883
+ V
Sbjct: 427 INGV 430
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 115 bits (287), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 119/465 (25%), Positives = 205/465 (44%), Gaps = 69/465 (14%)
Query: 440 GRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSE 497
G+ E+ L + EGDSA G + RD+ + P+RGK+LN E SS++VL + E
Sbjct: 38 GQTREESELFIVEGDSA-----GGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQE 92
Query: 498 IGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLA 557
+ +I +G+ G +++ LRYG + I+ D
Sbjct: 93 VHDIAIAIGVDPG--SDDLSELRYGKICILADA--------------------------- 123
Query: 558 QDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFYSMPD--YEA 615
D DG HI LL +P+L++ L + P+ + GK + Y++ D E
Sbjct: 124 -DSDGLHIATLLCALFVKHFPALVE-EGHLYVAMPPLFRI--DIGKDV-HYALDDEELET 178
Query: 616 WKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEA--IELAFS 673
+++ GN + I +KGLG + + +E + + + DD A ++ +
Sbjct: 179 ILKNVKGNKNP-QITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLA 237
Query: 674 KKKIEARKKWLLQFEPGNHLD--------------QKEKYIKYSDFVNKELILFSM-ADL 718
KK+ RK+WL Q GN D + ++F + + ++M +
Sbjct: 238 KKRAADRKQWLEQ--KGNLADITVEDKLTMTSLAHHATENRSVAEFTEQAYLNYAMYVIM 295
Query: 719 QRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSE-HSAYH-HGEQSLASTIL 776
R++P + DGLKP QR+I++ + K + + V + YH HG+ + ++
Sbjct: 296 DRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMV 355
Query: 777 GMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXYL 836
MAQ F S L++ G +G+ + K A+ RY +LS + L +
Sbjct: 356 LMAQPF--SYRYPLIEGQGNWGSPDDP-KSFAAMRYTEAKLSAYSELLLSELGQGTSEWQ 412
Query: 837 -NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
N DG EP +P +L+NG+ GI G ++ IP +N R++V
Sbjct: 413 DNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVV 457
>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 = 113 bits (282), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 121/465 (26%), Positives = 204/465 (43%), Gaps = 89/465 (19%)
Query: 431 KLEDANLAGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREAS 488
KL D + ++ E+C + L EGDSA G + GRD + PLRGK+LNV +A
Sbjct: 9 KLADCS---SKSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 489 SNQVLNNSEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAW 548
+++LNN+EI + G G +++ K+ RY ++IMTD
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGDFDLAKA-RYHKIVIMTDA------------------ 101
Query: 549 ITTFCFMLAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFY 608
D DG+HI+ LL+ F + F L I + V P T G
Sbjct: 102 ----------DVDGAHIRTLLLTFFYRFMRPL--IEAGYVYIAQP---PTGYKG----LG 142
Query: 609 SMPDYEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQ----NITLHKKDFVWEDDQD 664
M + W+ ++ N ++ K + E + F+ ++ +++ F+ ED+
Sbjct: 143 EMNADQLWETTM--NPEHRALLQVK---LEDAIEADQTFEMLMGDVVENRRQFI-EDNAV 196
Query: 665 GEAIELA-FSKKKIEARKKWLLQFEPGNHLDQKEKYIKYSDFVNKELILFSMADLQRSIP 723
++ A + +I R + +E ++ Y+ V + R++P
Sbjct: 197 YANLDFAELPQSRINERNITS---------EMRESFLDYAMSVI----------VARALP 237
Query: 724 SMVDGLKPGQRKILFCSFKRNFIKEA---KVAQFSGYVSEHSAYH-HGEQSLASTILGMA 779
+ DGLKP R+IL+ ++ + K A+ G V YH HG+ S+ ++ MA
Sbjct: 238 DVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDV--MGKYHPHGDSSIYEAMVRMA 295
Query: 780 QDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXYL-NE 838
QDF S L+ G FG+ + G AA+ R+ R++ IT L ++ N
Sbjct: 296 QDF--SYRYPLVDGQGNFGSMD--GDGAAAMRFTEARMTKITLELLRDINKDTIDFIDNY 351
Query: 839 DGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANV 883
DG + EP+ P +L NG+ GI G ++ IP +N +++ V
Sbjct: 352 DGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGV 396
>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 = 112 bits (279), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 118/465 (25%), Positives = 204/465 (43%), Gaps = 69/465 (14%)
Query: 440 GRNSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSE 497
G+ E+ L + EGDSA G + RD+ + P+RGK+LN E SS++VL + E
Sbjct: 38 GQTREESELFIVEGDSA-----GGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQE 92
Query: 498 IGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLA 557
+ +I +G+ G +++ LRYG + I+ D
Sbjct: 93 VHDIAIAIGVDPG--SDDLSELRYGKICILADA--------------------------- 123
Query: 558 QDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGKVLSFYSMPD--YEA 615
D DG HI LL +P+L++ L + P+ + GK + Y++ D E
Sbjct: 124 -DSDGLHIATLLCALFVKHFPALVE-EGHLYVAMPPLFRI--DIGKDV-HYALDDEELET 178
Query: 616 WKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNITLHKKDFVWEDDQDGEA--IELAFS 673
+++ GN + I +KGLG + + +E + + + DD A ++ +
Sbjct: 179 ILKNVKGNKNP-QITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLA 237
Query: 674 KKKIEARKKWLLQFEPGNHLD--------------QKEKYIKYSDFVNKELILFSM-ADL 718
KK+ RK+WL Q GN D + ++F + + ++M +
Sbjct: 238 KKRAADRKQWLEQ--KGNLADITVEDKLTMTSLAHHATENRSVAEFTEQAYLNYAMYVIM 295
Query: 719 QRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSE-HSAYH-HGEQSLASTIL 776
R++P + DGLKP QR+I++ + K + + V + YH HG+ + ++
Sbjct: 296 DRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDSACYEAMV 355
Query: 777 GMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXYL 836
MAQ F S L++ G +G+ + K A+ R +LS + L +
Sbjct: 356 LMAQPF--SYRYPLIEGQGNWGSPDDP-KSFAAMRXTEAKLSAYSELLLSELGQGTSEWQ 412
Query: 837 -NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
N DG EP +P +L+NG+ GI G ++ IP +N R++V
Sbjct: 413 DNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVV 457
>pdb|3IFZ|A Chain A, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
pdb|3IFZ|B Chain B, Crystal Structure Of The First Part Of The Mycobacterium
Tuberculosis Dna Gyrase Reaction Core: The Breakage And
Reunion Domain At 2.7 A Resolution
Length = 508
Score = 82.8 bits (203), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 87/353 (24%), Positives = 154/353 (43%), Gaps = 36/353 (10%)
Query: 687 FEPGNHLDQKEKYIKYSDFVNKELILFSMADL-QRSIPSMVDGLKPGQRKILFCSFKRNF 745
P + LD+ E + + + I ++M+ + R++P + DGLKP R++L+ F F
Sbjct: 6 LPPDDSLDRIEP-VDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGF 64
Query: 746 IKEAKVAQFSGYVSEHSA-YH-HGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQG 803
+ A+ + V+E YH HG+ S+ +++ MAQ + S L+ G FG+ G
Sbjct: 65 RPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMAQPW--SLRYPLVDGQGNFGS--PG 120
Query: 804 GKDAASARYIFTRLSPITRFLFPXXXXXXXXYL-NEDGQQIEPTWYMPIIPTVLVNGSEG 862
A+ RY RL+P+ + ++ N DG+ EPT P +L NGS G
Sbjct: 121 NDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGG 180
Query: 863 IGTGWSSYIPNYNPRDIV-----------ANVRRLLNGEMMEPMHPWYRGFGGTIEKTAS 911
I G ++ IP +N R++ A+ L M P + G + +
Sbjct: 181 IAVGMATNIPPHNLRELADAVFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGT 240
Query: 912 KEAGVT----YTVTGIIE----EVNETTLRIKELPIRRWTQDYREFLESIIDQ-NDSFIR 962
+A T + G++E T+L I ELP + ++ F+ SI +Q D +
Sbjct: 241 ADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELP---YQVNHDNFITSIAEQVRDGKLA 297
Query: 963 GFR----QYSDDTTVDFEVFLSEESMMRTKQEGLLKKFKLTTTISTSNMHLFD 1011
G Q SD + + + +++ + L K +L T+ + + + D
Sbjct: 298 GISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVD 350
>pdb|3ILW|A Chain A, Structure Of Dna Gyrase Subunit A N-Terminal Domain
pdb|3ILW|B Chain B, Structure Of Dna Gyrase Subunit A N-Terminal Domain
Length = 470
Score = 79.0 bits (193), Expect = 2e-14, Method: Composition-based stats.
Identities = 81/319 (25%), Positives = 139/319 (43%), Gaps = 34/319 (10%)
Query: 720 RSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEHSA-YH-HGEQSLASTILG 777
R++P + DGLKP R++L+ F F + A+ + V+E YH HG+ S+ +++
Sbjct: 9 RALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVR 68
Query: 778 MAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXYL- 836
MAQ + S L+ G FG+ G A+ RY RL+P+ + ++
Sbjct: 69 MAQPW--SLRYPLVDGQGNFGS--PGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIP 124
Query: 837 NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV-----------ANVRR 885
N DG+ EPT P +L NGS GI G ++ IP +N R++ A+
Sbjct: 125 NYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEEE 184
Query: 886 LLNGEMMEPMHPWYRGFGGTIEKTASKEAGVT----YTVTGIIE----EVNETTLRIKEL 937
L M P + G + + +A T + G++E T+L I EL
Sbjct: 185 TLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITEL 244
Query: 938 PIRRWTQDYREFLESIIDQ-NDSFIRGFR----QYSDDTTVDFEVFLSEESMMRTKQEGL 992
P + ++ F+ SI +Q D + G Q SD + + + +++ + L
Sbjct: 245 P---YQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNL 301
Query: 993 LKKFKLTTTISTSNMHLFD 1011
K +L T+ + + + D
Sbjct: 302 YKHTQLQTSFGANMLAIVD 320
>pdb|4DDQ|A Chain A, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|B Chain B, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|C Chain C, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|D Chain D, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|E Chain E, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
pdb|4DDQ|F Chain F, Structural Plasticity Of The Bacillus Subtilis Gyra
Homodimer
Length = 502
Score = 78.2 bits (191), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 87/335 (25%), Positives = 141/335 (42%), Gaps = 32/335 (9%)
Query: 718 LQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSEH-SAYH-HGEQSLASTI 775
+ R++P + DGLKP R+IL+ + + + V E YH HG+ ++ ++
Sbjct: 31 VSRALPDVRDGLKPVHRRILYAMNDLGMTSDKPYKKSARIVGEVIGKYHPHGDSAVYESM 90
Query: 776 LGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXY 835
+ MAQDF + L+ +G FG+ + G AA+ RY R+S I+ + Y
Sbjct: 91 VRMAQDF--NYRYMLVDGHGNFGSVD--GDSAAAMRYTEARMSKISMEILRDITKDTIDY 146
Query: 836 L-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLNG----- 889
N DG + EP P +LVNG+ GI G ++ IP + +I+ V +
Sbjct: 147 QDNYDGSEREPVVMPSRFPNLLVNGAAGIAVGMATNIPPHQLGEIIDGVLAVSENPDITI 206
Query: 890 -EMME-------PMHPWYRGFGGTIEKTASKEAGVTYTVTGIIEEVNETTLRI--KELPI 939
E+ME P G G + S +T IE+ + RI ELP
Sbjct: 207 PELMEVIPGPDFPTAGQILGRSGIRKAYESGRGSITIRAKAEIEQTSSGKERIIVTELP- 265
Query: 940 RRWTQDYREFLESIIDQ-NDSFIRG---FRQYSDDTTVDFEVFLSEESMMRTKQEGLLKK 995
+ + + +E I D D I G R SD T + + + ++ L K+
Sbjct: 266 --YQVNKAKLIEKIADLVRDKKIEGITDLRDESDRTGMRIVIEIRRDANANVILNNLYKQ 323
Query: 996 FKLTTTISTSNMHLFDSKGVIKKYDTPEQILEEFF 1030
L T+ + + L D + K T +Q LE +
Sbjct: 324 TALQTSFGINLLALVDGQ---PKVLTLKQCLEHYL 355
>pdb|2NOV|A Chain A, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|B Chain B, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|C Chain C, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|2NOV|D Chain D, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
Structure Of A Gram-Positive Quinolone Target
pdb|3FOE|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOE|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3FOF|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
Of Type Iia Topoisomerases
pdb|3K9F|A Chain A, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3K9F|B Chain B, Detailed Structural Insight Into The Quinolone-Dna
Cleavage Complex Of Type Iia Topoisomerases
pdb|3KSA|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSA|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Cleaved Form)
pdb|3KSB|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3KSB|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
Of Type Iia Topoisomerases (Re-Sealed Form)
pdb|3LTN|A Chain A, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3LTN|B Chain B, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
(S. Pneumoniae)
pdb|3RAF|A Chain A, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAF|B Chain B, Quinazolinedione-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|A Chain A, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAD|B Chain B, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|A Chain A, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
pdb|3RAE|B Chain B, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
Topoisomerase From S. Pneumoniae
Length = 496
Score = 75.5 bits (184), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 55/192 (28%), Positives = 97/192 (50%), Gaps = 27/192 (14%)
Query: 697 EKYIKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFC------SFKRNFIKEAK 750
E++ +YS ++ ++ R++P + DGLKP QR+IL+ +F +++ K AK
Sbjct: 15 ERFGRYSKYIIQD----------RALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAK 64
Query: 751 -VAQFSGYVSEHSAYHHGEQSLASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAAS 809
V G + + HG+ S+ ++ M+Q++ N L++ +G G+ + G A+
Sbjct: 65 SVGNIMG-----NFHPHGDSSIYDAMVRMSQNW--KNREILVEMHGNNGSMD--GDPPAA 115
Query: 810 ARYIFTRLSPITRFLFPXXXXXXXXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWS 868
RY RLS I +L + N D + EPT P +LVNGS GI G++
Sbjct: 116 MRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYA 175
Query: 869 SYIPNYNPRDIV 880
+ IP +N +++
Sbjct: 176 TDIPPHNLAEVI 187
>pdb|2Y3P|A Chain A, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
pdb|2Y3P|B Chain B, Crystal Structure Of N-Terminal Domain Of Gyra With The
Antibiotic Simocyclinone D8
Length = 522
Score = 74.3 bits (181), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 55/169 (32%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 720 RSIPSMVDGLKPGQRKILFC------SFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP R++L+ + + + K A+V G V YH HG+ ++
Sbjct: 31 RALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVV---GDVI--GKYHPHGDSAVY 85
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXX 832
TI+ MAQ F S L+ G FG+ + G AA+ RY RL+ I L
Sbjct: 86 DTIVRMAQPF--SLRYMLVDGQGNFGSID--GDSAAAMRYTEIRLAKIAHELMADLEKET 141
Query: 833 XXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
++ N DG + P IP +LVNGS GI G ++ IP +N +++
Sbjct: 142 VDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVI 190
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 73.9 bits (180), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 55/169 (32%), Positives = 84/169 (49%), Gaps = 17/169 (10%)
Query: 720 RSIPSMVDGLKPGQRKILFC------SFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP R++L+ + + + K A+V G V YH HG+ ++
Sbjct: 3 RALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVV---GDVI--GKYHPHGDSAVY 57
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXX 832
TI+ MAQ F S L+ G FG+ + G AA+ RY RL+ I L
Sbjct: 58 DTIVRMAQPF--SLRYMLVDGQGNFGSID--GDSAAAMRYTEIRLAKIAHELMADLEKET 113
Query: 833 XXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
++ N DG + P IP +LVNGS GI G ++ IP +N +++
Sbjct: 114 VDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVI 162
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 73.9 bits (180), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 54/177 (30%), Positives = 87/177 (49%), Gaps = 17/177 (9%)
Query: 720 RSIPSMVDGLKPGQRKILFC------SFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP R++LF + + + K A+V G V YH HG+ ++
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVV---GDVI--GKYHPHGDTAVY 56
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXX 832
TI+ MAQ F S L+ G FG+ + G AA+ RY R+S I +
Sbjct: 57 DTIVRMAQPF--SLRYMLVDGQGNFGSVD--GDSAAAMRYTEIRMSKIAHSILADLDKET 112
Query: 833 XXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIVANVRRLLN 888
++ N DG + P +P +LVNG+ GI G ++ IP +N +++ L++
Sbjct: 113 VDFVPNYDGTEHIPAVMPTRVPNLLVNGTSGIAVGMATNIPPHNLTEVINACLALID 169
>pdb|3NUH|A Chain A, A Domain Insertion In E. Coli Gyrb Adopts A Novel Fold
That Plays A Critical Role In Gyrase Function
Length = 525
Score = 70.9 bits (172), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 54/169 (31%), Positives = 83/169 (49%), Gaps = 17/169 (10%)
Query: 720 RSIPSMVDGLKPGQRKILFC------SFKRNFIKEAKVAQFSGYVSEHSAYH-HGEQSLA 772
R++P + DGLKP R++L+ + + + K A+V G V YH HG+ ++
Sbjct: 32 RALPDVRDGLKPVHRRVLYAXNVLGNDWNKAYKKSARVV---GDVI--GKYHPHGDSAVY 86
Query: 773 STILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXX 832
TI+ AQ F S L+ G FG+ + G AA+ RY RL+ I L
Sbjct: 87 DTIVRXAQPF--SLRYXLVDGQGNFGSID--GDSAAAXRYTEIRLAKIAHELXADLEKET 142
Query: 833 XXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
++ N DG + P IP +LVNGS GI G ++ IP +N +++
Sbjct: 143 VDFVDNYDGTEKIPDVXPTKIPNLLVNGSSGIAVGXATNIPPHNLTEVI 191
>pdb|1ZVU|A Chain A, Structure Of The Full-Length E. Coli Parc Subunit
Length = 716
Score = 68.6 bits (166), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 49/166 (29%), Positives = 81/166 (48%), Gaps = 6/166 (3%)
Query: 718 LQRSIPSMVDGLKPGQRKILFCSFKRNFIKEAKVAQFSGYVSE-HSAYH-HGEQSLASTI 775
+ R++P + DGLKP QR+I++ + AK + + V + YH HG+ + +
Sbjct: 1 MDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAM 60
Query: 776 LGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXXXXXXY 835
+ MAQ F S L+ G +G + K A+ RY +RLS + L +
Sbjct: 61 VLMAQPF--SYRYPLVDGQGNWGAPDDP-KSFAAMRYTESRLSKYSELLLSELGQGTADW 117
Query: 836 L-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
+ N DG EP +P +L+NG+ GI G ++ IP +N R++
Sbjct: 118 VPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVA 163
>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
Subunit A (Grla) From Staphylococcus Aureus
Length = 514
Score = 68.2 bits (165), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 50/171 (29%), Positives = 85/171 (49%), Gaps = 19/171 (11%)
Query: 719 QRSIPSMVDGLKPGQRKILFCSFK------RNFIKEAK-VAQFSGYVSEHSAYH-HGEQS 770
+R++P + DGLKP QR+IL+ + +NF K AK V G YH HG+ S
Sbjct: 51 ERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTVGDVIG------QYHPHGDSS 104
Query: 771 LASTILGMAQDFVGSNNINLLQPNGQFGTRNQGGKDAASARYIFTRLSPITRFLFPXXXX 830
+ ++ ++QD+ + L++ +G G+ + A+ RY +LS + L
Sbjct: 105 VYEAMVRLSQDWKLRHV--LIEMHGNNGSIDNDP--PAAMRYTEAKLSLLAEELLRDINK 160
Query: 831 XXXXYL-NEDGQQIEPTWYMPIIPTVLVNGSEGIGTGWSSYIPNYNPRDIV 880
++ N D +EP P +LVNGS GI G+++ IP +N +++
Sbjct: 161 ETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVI 211
>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 = 67.0 bits (162), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 77/302 (25%), Positives = 126/302 (41%), Gaps = 55/302 (18%)
Query: 37 LEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNAADNKQR 96
L+ + RP YIG + T GL+ + E++ NA D
Sbjct: 15 LDAVRKRPGMYIGDTDDGT----------------------GLHHMVFEVVDNAIDEALA 52
Query: 97 DPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKT 156
+ + + + +SV + G G+P IH EEGV E+I L +DDN K
Sbjct: 53 GHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKV 110
Query: 157 TGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEGDNWT 214
+GG +G G + N S E +I+ + K ++Q++ + G P + T
Sbjct: 111 SGGLHGVGVSVVNALSQKLELVIQ----REGKIHRQIYEH--GVPQAPLAVTGETEKTGT 164
Query: 215 KVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR----------VP 263
V F P L F N+T E +++A KR+ +L+ L V + L R
Sbjct: 165 MVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLDSGVSIRLRDKRDGKEDHFHYEGG 220
Query: 264 VKSFAEYVD-----MYPKSVTRFHERVNERWEICVTLSEGQFQQ--VSFVNGIATIKGGT 316
+K+F EY++ ++P E+ E+ + ++G FQ+ F N I GGT
Sbjct: 221 IKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDG-FQENIYCFTNNIPQRDGGT 279
Query: 317 HV 318
H+
Sbjct: 280 HL 281
>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 = 65.1 bits (157), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 66/255 (25%), Positives = 108/255 (42%), Gaps = 48/255 (18%)
Query: 438 AGGRNSEQCTLILTEGDSAKALAMAGLSVVGRDR--FGVFPLRGKLLNVREASSNQVLNN 495
A +N + L L EGDSA G + GRDR + PLRGK++N +A +L N
Sbjct: 40 AQSKNPAKNELYLVEGDSA-----GGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKN 94
Query: 496 SEIGNIKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFM 555
EI + +G G +++ ++ Y ++IMTD
Sbjct: 95 EEINTMIYTIGAGVGADFS-IEDANYDKIIIMTDA------------------------- 128
Query: 556 LAQDHDGSHIKGLLINFIHSFWPSLLKIPSFLVEFITPIVKATNKNGK---VLSFYSMPD 612
D DG+HI+ LL+ F + + L++ + + P+ K + GK V ++ +
Sbjct: 129 ---DTDGAHIQTLLLTFFYRYMRPLVEAGHVYIA-LPPLYKMSKGKGKKEEVAYAWTDGE 184
Query: 613 YEAWKESLGGNASSWSIKYYKGLGTSTSKEGKEYFQNI---TLHKKDFVWEDDQDGEAIE 669
E ++ G A +++ YKGLG + + E N TL + ED E
Sbjct: 185 LEELRKQFGKGA---TLQRYKGLGEMNADQLWETTMNPETRTLIR--VTIEDLARAERRV 239
Query: 670 LAFSKKKIEARKKWL 684
K+E R+KW+
Sbjct: 240 NVLMGDKVEPRRKWI 254
>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 = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 79/328 (24%), Positives = 134/328 (40%), Gaps = 33/328 (10%)
Query: 70 HRTISY-----VPGLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVP 124
HR Y V G + +F EIL NA D + + V ++++ L +V ++G G+P
Sbjct: 19 HRPAMYIGGTGVEGYHHLFKEILDNAVDEALAGYATE-ILVRLNEDGSL-TVEDNGRGIP 76
Query: 125 VEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKR 184
V++ EEG E+I+ L + ++ K +GG +G GA + N S ++E +
Sbjct: 77 VDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVVNALSEWTVVEVF--RE 134
Query: 185 LKKYKQVFTNNMGKKSEP--NISKCKEGDNWTKVSFKPDLAKFNMTHLEDDVVALMKKRV 242
K ++ F+ G+ +EP + + G T+V+FKPD F + + + V
Sbjct: 135 GKHHRIAFSR--GEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRFDPSKIRARLREV 192
Query: 243 VDLAGCL---------GK-SVKVELNGHRVPVKSFAEYVDMY---PKSVTRFHERVNERW 289
L L GK V ++ G K+ AE D+ P + H V
Sbjct: 193 AYLVAGLKLVFQDRQHGKEEVFLDKGGVASFAKALAEGEDLLYEKPFLIRGTHGEVE--V 250
Query: 290 EICVTLSEGQFQQV-SFVNGIATIKGGTHVDYVANQXXXXXXXXXXXXXXXXXXXXXXXX 348
E+ ++G ++ ++ N I T GGTH+ +
Sbjct: 251 EVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKAGLNKEKGPQPTG 310
Query: 349 ----XXLWVFVNALIDNPAFDSQTKETL 372
L+ V+ + NP F+ QTK L
Sbjct: 311 DDLLEGLYAVVSVKLPNPQFEGQTKGKL 338
>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 = 60.1 bits (144), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 86/187 (45%), Gaps = 15/187 (8%)
Query: 78 GLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPE 137
GL+ + E++ NA D + + + + +SV + G G+P IH EEGV E
Sbjct: 22 GLHHMVFEVVDNAIDEALAGHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAE 79
Query: 138 LIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNN 195
+I L +DDN K +GG +G G + N S E +I+ + K ++Q++ +
Sbjct: 80 VIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ----REGKIHRQIYEH- 134
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVK 254
G P + T V F P L F N+T E +++A KR+ +L+ L V
Sbjct: 135 -GVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVS 189
Query: 255 VELNGHR 261
+ L R
Sbjct: 190 IRLRDKR 196
>pdb|3G7E|A Chain A, Crystal Structure Of E. Coli Gyrase B Co-Complexed With
Inhibitor
Length = 203
Score = 59.7 bits (143), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 86/187 (45%), Gaps = 15/187 (8%)
Query: 78 GLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPE 137
GL+ + E++ NA D + + + + +SV + G G+P IH EEGV E
Sbjct: 21 GLHHMVFEVVDNAIDEALAGHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAE 78
Query: 138 LIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNN 195
+I L +DDN K +GG +G G + N S E +I+ + K ++Q++ +
Sbjct: 79 VIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ----REGKIHRQIYEH- 133
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVK 254
G P + T V F P L F N+T E +++A KR+ +L+ L V
Sbjct: 134 -GVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVS 188
Query: 255 VELNGHR 261
+ L R
Sbjct: 189 IRLRDKR 195
>pdb|1KZN|A Chain A, Crystal Structure Of E. Coli 24kda Domain In Complex With
Clorobiocin
Length = 205
Score = 59.7 bits (143), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 86/187 (45%), Gaps = 15/187 (8%)
Query: 78 GLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPE 137
GL+ + E++ NA D + + + + +SV + G G+P IH EEGV E
Sbjct: 21 GLHHMVFEVVDNAIDEALAGHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAE 78
Query: 138 LIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNN 195
+I L +DDN K +GG +G G + N S E +I+ + K ++Q++ +
Sbjct: 79 VIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ----REGKIHRQIYEH- 133
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVK 254
G P + T V F P L F N+T E +++A KR+ +L+ L V
Sbjct: 134 -GVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVS 188
Query: 255 VELNGHR 261
+ L R
Sbjct: 189 IRLRDKR 195
>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 = 59.7 bits (143), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 86/187 (45%), Gaps = 15/187 (8%)
Query: 78 GLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPE 137
GL+ + E++ NA D + + + + +SV + G G+P IH EEGV E
Sbjct: 35 GLHHMVFEVVDNAIDEALAGHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAE 92
Query: 138 LIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNN 195
+I L +DDN K +GG +G G + N S E +I+ + K ++Q++ +
Sbjct: 93 VIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ----REGKIHRQIYEH- 147
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVK 254
G P + T V F P L F N+T E +++A KR+ +L+ L V
Sbjct: 148 -GVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVS 202
Query: 255 VELNGHR 261
+ L R
Sbjct: 203 IRLRDKR 209
>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 = 58.5 bits (140), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 53/187 (28%), Positives = 85/187 (45%), Gaps = 15/187 (8%)
Query: 78 GLYKIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPE 137
GL+ + E++ NA D + + + + +SV + G G+P IH EEGV E
Sbjct: 34 GLHHMVFEVVDNAIDEALAGHCKEIIVTI--HADNSVSVQDDGRGIPTGIHPEEGVSAAE 91
Query: 138 LIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST--EFIIETADGKRLKKYKQVFTNN 195
+I L +DDN K +GG +G G + N S E +I+ K ++Q++ +
Sbjct: 92 VIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQ----HEGKIHRQIYEH- 146
Query: 196 MGKKSEPNISKCKEGDNWTKVSFKPDLAKF-NMTHLEDDVVALMKKRVVDLAGCLGKSVK 254
G P + T V F P L F N+T E +++A KR+ +L+ L V
Sbjct: 147 -GVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILA---KRLRELS-FLNSGVS 201
Query: 255 VELNGHR 261
+ L R
Sbjct: 202 IRLRDKR 208
>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 = 57.8 bits (138), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 41/142 (28%), Positives = 62/142 (43%), Gaps = 31/142 (21%)
Query: 441 RNSEQCTLILTEGDSAKALAMAGLSVVGRDRFGVFPLRGKLLNVREASSNQVLNNSEIGN 500
R+ L L EGDSA A G + R + PL+GK+LNV +A ++ L++ E+
Sbjct: 29 RDPALSELYLVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKXLSSQEVAT 85
Query: 501 IKKILGLKQGVEYNNVKSLRYGHLMIMTDQVLLAPLSFLLWFILIFAWITTFCFMLAQDH 560
+ LG G + N LRY ++I TD D
Sbjct: 86 LITALGCGIGRDEYNPDKLRYHSIIIXTD----------------------------ADV 117
Query: 561 DGSHIKGLLINFIHSFWPSLLK 582
DGSHI+ LL+ F + P +++
Sbjct: 118 DGSHIRTLLLTFFYRQXPEIVE 139
>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 = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 78/329 (23%), Positives = 128/329 (38%), Gaps = 35/329 (10%)
Query: 77 PGLY-------KIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQ 129
PG+Y + E++ N+ D V V++ + L V + G G+PV+IH
Sbjct: 23 PGMYTDTTRPNHLGQEVIDNSVDEALAG-HAKRVDVILHADQSL-EVIDDGRGMPVDIHP 80
Query: 130 EEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYK 189
EEGV ELI L + + + +GG +G G + N S +E + + Y
Sbjct: 81 EEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKR--VEVNVRRDGQVYN 138
Query: 190 QVFTNNMGKKSEPNISKCKEGDNWTKVSFKPDLAKFNMTHLE-DDVVALMKKRVVDLAGC 248
F N + + C + + T V F PD F+ + ++K + V G
Sbjct: 139 IAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPG- 197
Query: 249 LGKSVKVELNG--HRVPVKS-----FAEYVDMYPKS-----VTRFH---ERVNERWEICV 293
+ + K E+N R + AE V+ P + F E V+ W +
Sbjct: 198 VEITFKDEINNTEQRWCYQDGLNDYLAEAVNGLPTLPEKPFIGNFAGDTEAVD--WALLW 255
Query: 294 TLSEGQFQQVSFVNGIATIKGGTHVDYVANQXXXXXXXXXXXXXXXXXXXXXXXXXXLW- 352
G+ S+VN I T++GGTHV+ + Q +W
Sbjct: 256 LPEGGELLTESYVNLIPTMQGGTHVNGL-RQGLLDAMREFCEYRNILPRGVKLSAEDIWD 314
Query: 353 ---VFVNALIDNPAFDSQTKETLTLRQSS 378
++ + +P F QTKE L+ RQ +
Sbjct: 315 RCAYVLSVKMQDPQFAGQTKERLSSRQCA 343
>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 = 52.8 bits (125), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 57/212 (26%), Positives = 91/212 (42%), Gaps = 33/212 (15%)
Query: 28 EEMYQKKSQLEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEIL 87
++ Q L+ + RP YIGS + GL+ + EI+
Sbjct: 13 DDAIQVLEGLDAVRKRPGMYIGSTDG-----------------------AGLHHLVWEIV 49
Query: 88 VNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSS 147
NA D + D + V I+++ L +V + G G+P +H G+ E+IF L
Sbjct: 50 DNAVD-EALSGFGDRIDVTINKDGSL-TVQDHGRGMPTGMHAM-GIPTVEVIFTILHAGG 106
Query: 148 NYDDNVKKTTGGRNGYGAKLTNIFSTEFIIE-TADGKRLKKYKQVFTNNMGK--KSEPNI 204
+ KT+GG +G G+ + N S+ +E T DG YKQ F N GK + I
Sbjct: 107 KFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAV---YKQRFENG-GKPVTTLKKI 162
Query: 205 SKCKEGDNWTKVSFKPDLAKFNMTHLEDDVVA 236
+ TKV+F PD F+ T + + ++
Sbjct: 163 GTALKSKTGTKVTFMPDATIFSTTDFKYNTIS 194
>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 = 50.8 bits (120), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 65/228 (28%), Positives = 100/228 (43%), Gaps = 38/228 (16%)
Query: 37 LEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNAADNKQR 96
LE + RP YIGS + GL+ + EI+ NA D +
Sbjct: 3 LEAVRKRPGMYIGSTDSR-----------------------GLHHLVYEIVDNAVD-EAL 38
Query: 97 DPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKT 156
+ + V I Q+ + I V +SG G+P +H G+ E+IF L + KT
Sbjct: 39 SGYGNEINVTI-QKDNSICVADSGRGMPTGMHAS-GIPTVEVIFTVLHAGGKFGQGGYKT 96
Query: 157 TGGRNGYGAKLTNIFSTEFIIETA-DGKRLKKYKQVFTNNMGK--KSEPNISKCKEGDNW 213
+GG +G GA + N S + DG +Y + F + GK + I K K+ N
Sbjct: 97 SGGLHGVGASVVNALSKWLEVHIVRDG---VEYMERFEDG-GKPVGTLKKIGKTKK-RNG 151
Query: 214 TKVSFKPDLAKFNMTHLEDDVVALMKKRVVDLAGCLGKSVKVELNGHR 261
T V+F PD F+ T+ +++A +R+ + A L K VK+ L R
Sbjct: 152 TSVTFLPDDTIFSTTNFSYEILA---ERLRESAFLL-KGVKITLTDER 195
>pdb|3LNU|A Chain A, Crystal Structure Of Pare Subunit
pdb|3LPS|A Chain A, Crystal Structure Of Pare
Length = 408
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 78/295 (26%), Positives = 120/295 (40%), Gaps = 51/295 (17%)
Query: 116 VHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFST-- 173
V + G G+PV+IH EE + ELI L +++ +GG +G G + N ST
Sbjct: 86 VSDDGRGMPVDIHPEEKIPGVELILTRLHAGGKFNNRNYTFSGGLHGVGVSVVNALSTKV 145
Query: 174 ---------EFIIETADGKRLKKYKQVFTNNMGKKSEPNISKCKEGDNWTKVSFKPDLAK 224
E +E DG K + V T +GKK+ + W + D K
Sbjct: 146 ELFIKREGSEHRMEFRDGNAASKLEVVGT--VGKKNTGTRLRF-----WADPKYF-DTPK 197
Query: 225 FNMTHLEDDVVALMKKRVVDLAGCLGKSVKVE------------LNGHRVPVKS-FAEY- 270
FN+ L L++ + V C G +VK+ NG R +K AE+
Sbjct: 198 FNVRALRH----LLRAKAVL---CPGLTVKLHDEATGEQDSWYFENGLRDYLKGEMAEHE 250
Query: 271 ---VDMYPKSVTRFHERVNERWEICVTLSEGQFQQVSFVNGIATIKGGTHVDYVANQXXX 327
D++ S+ + E V+ W + EG+ Q S+VN I T + GTHV+ +
Sbjct: 251 MLPADLFVGSLKKDTEIVD--W-AAGWVPEGELVQESYVNLIPTAQHGTHVNGL-RSGLT 306
Query: 328 XXXXXXXXXXXXXXXXXXXXXXXLW---VFVNAL-IDNPAFDSQTKETLTLRQSS 378
+W FV +L + +P F QTKE L+ RQ++
Sbjct: 307 DALREFCDFRNLLPRGVKLAPEDVWDRVTFVLSLKMTDPQFSGQTKERLSSRQAA 361
>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 = 49.7 bits (117), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 8/90 (8%)
Query: 442 NSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSEIG 499
+ + L + EGDSA G + GRD + PLRGK++NV +A ++VL N+E+
Sbjct: 8 DPRKSELYVVEGDSA-----GGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQ 62
Query: 500 NIKKILGLKQGVEYNNVKSLRYGHLMIMTD 529
I LG E+ ++ LRY +++M D
Sbjct: 63 AIITALGTGIHDEF-DIGKLRYHKIVLMAD 91
>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 = 49.3 bits (116), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 49/90 (54%), Gaps = 8/90 (8%)
Query: 442 NSEQCTLILTEGDSAKALAMAGLSVVGRDRF--GVFPLRGKLLNVREASSNQVLNNSEIG 499
+ + L + EGDSA G + GRD + PLRGK++NV +A ++VL N+E+
Sbjct: 16 DPRKSELYVVEGDSA-----GGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQ 70
Query: 500 NIKKILGLKQGVEYNNVKSLRYGHLMIMTD 529
I LG E+ ++ LRY +++M D
Sbjct: 71 AIITALGTGIHDEF-DIGKLRYHKIVLMAD 99
>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 = 48.5 bits (114), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 66/157 (42%), Gaps = 11/157 (7%)
Query: 77 PGLY-------KIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQ 129
PG+Y + E++ N+ D V V++ + L V + G G+PV+IH
Sbjct: 12 PGMYTDTTRPNHLGQEVIDNSVDEALAG-HAKRVDVILHADQSL-EVIDDGRGMPVDIHP 69
Query: 130 EEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYK 189
EEGV ELI L + + + +GG +G G + N S +E + + Y
Sbjct: 70 EEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKR--VEVNVRRDGQVYN 127
Query: 190 QVFTNNMGKKSEPNISKCKEGDNWTKVSFKPDLAKFN 226
F N + + C + + T V F PD F+
Sbjct: 128 IAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFD 164
>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 = 48.1 bits (113), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 41/157 (26%), Positives = 66/157 (42%), Gaps = 11/157 (7%)
Query: 77 PGLY-------KIFDEILVNAADNKQRDPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQ 129
PG+Y + E++ N+ D V V++ + L V + G G+PV+IH
Sbjct: 9 PGMYTDTTRPNHLGQEVIDNSVDEALAG-HAKRVDVILHADQSL-EVIDDGRGMPVDIHP 66
Query: 130 EEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTNIFSTEFIIETADGKRLKKYK 189
EEGV ELI L + + + +GG +G G + N S +E + + Y
Sbjct: 67 EEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKR--VEVNVRRDGQVYN 124
Query: 190 QVFTNNMGKKSEPNISKCKEGDNWTKVSFKPDLAKFN 226
F N + + C + + T V F PD F+
Sbjct: 125 IAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFD 161
>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 = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 51/118 (43%), Gaps = 4/118 (3%)
Query: 110 EHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKTTGGRNGYGAKLTN 169
E + I V + G G+PV+IH E + ELI L + + + +GG +G G + N
Sbjct: 60 EDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSNKNYTHSGGLHGVGVSVVN 119
Query: 170 IFSTEFIIETA-DGKRLKKYKQVFTNNMGKKSEPNISKCKEGDNWTKVSFKPDLAKFN 226
ST E DG Y VF + K I + + TK+ F P+ F+
Sbjct: 120 ALSTRLEAEIKRDGNV---YHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFD 174
>pdb|1M0S|A Chain A, Northeast Structural Genomics Consortium (Nesg Id Ir21)
pdb|1M0S|B Chain B, Northeast Structural Genomics Consortium (Nesg Id Ir21)
Length = 219
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 45/83 (54%), Gaps = 8/83 (9%)
Query: 1135 AIGTLTLEKVQGLLADRDKLNEEVDDLRKATPESLWVKDLDALDMQLDELDKSDARAEEE 1194
A+GT+ +K+QG +A K +EE+ LRK E D+ +LD+ +D D+ + +
Sbjct: 38 ALGTIK-DKIQGAVA-ASKESEEL--LRKQGIEVFNANDVSSLDIYVDGADEIN----PQ 89
Query: 1195 RMKIKGNGNGDAGPKIVAKRAPK 1217
+M IKG G KIVA A K
Sbjct: 90 KMMIKGGGAALTREKIVAALAKK 112
>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 = 31.2 bits (69), Expect = 4.3, Method: Composition-based stats.
Identities = 39/148 (26%), Positives = 61/148 (41%), Gaps = 26/148 (17%)
Query: 37 LEHILLRPDTYIGSIEKHTQALWIYEEESKTMIHRTISYVPGLYKIFDEILVNAADNKQR 96
LE + RP YIGS GL+ + EI+ N+ D
Sbjct: 2 LEAVRKRPGMYIGSTSGE-----------------------GLHHLVWEIVDNSIDEALA 38
Query: 97 DPKMDAVKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIFGHLLTSSNYDDNVKKT 156
+++V+I+ + D I+V + G G+PV I + G E +F L + K
Sbjct: 39 G-FAKSIQVIIEPD-DSITVIDDGRGIPVGIQAKTGRPAVETVFTVLHAGGKFGGGGYKV 96
Query: 157 TGGRNGYGAKLTNIFSTEFIIET-ADGK 183
+GG +G G+ + N ST + DGK
Sbjct: 97 SGGLHGVGSSVVNALSTSLDVRVYKDGK 124
>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 = 31.2 bits (69), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 37/176 (21%), Positives = 76/176 (43%), Gaps = 24/176 (13%)
Query: 10 TTSNNANVVGPTAPNKTIEEMYQKKSQLEHILLRPDTYIGSIE-KHTQALWIYEEESKTM 68
+ + N + +G PN + + Q + +L Y+ S E K TQ + ++
Sbjct: 166 SQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCD-QYYLSSPELKLTQVNGKFPDQP--- 221
Query: 69 IHRTISYVPG-----LYKIFDEILVNAADNKQRDPKMDAVKV--VIDQEHDLISVHNSGD 121
IH I YVP L+++F + ++++ P + ++V V+ +E I + + G
Sbjct: 222 IH--IVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGG 279
Query: 122 GVPVEIHQEEGVYVPELIFGHLLTSSNYD--DNVKKTTGGRNGYGAKLTNIFSTEF 175
GVP+ I +F + +++ DN + GYG ++ +++ F
Sbjct: 280 GVPLRIIDR--------LFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYF 327
>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 = 30.8 bits (68), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 37/176 (21%), Positives = 76/176 (43%), Gaps = 24/176 (13%)
Query: 10 TTSNNANVVGPTAPNKTIEEMYQKKSQLEHILLRPDTYIGSIE-KHTQALWIYEEESKTM 68
+ + N + +G PN + + Q + +L Y+ S E K TQ + ++
Sbjct: 166 SQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCD-QYYLSSPELKLTQVNGKFPDQP--- 221
Query: 69 IHRTISYVPG-----LYKIFDEILVNAADNKQRDPKMDAVKV--VIDQEHDLISVHNSGD 121
IH I YVP L+++F + ++++ P + ++V V+ +E I + + G
Sbjct: 222 IH--IVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGG 279
Query: 122 GVPVEIHQEEGVYVPELIFGHLLTSSNYD--DNVKKTTGGRNGYGAKLTNIFSTEF 175
GVP+ I +F + +++ DN + GYG ++ +++ F
Sbjct: 280 GVPLRIIDR--------LFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYF 327
>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 = 30.8 bits (68), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 103 VKVVIDQEHDLISVHNSGDGVPVEIHQEEGVYVPELIF 140
V V++ + L V + G G+PV+IH EEGV ELI
Sbjct: 55 VDVILHADQSL-EVIDDGRGMPVDIHPEEGVPAVELIL 91
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
0.315 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 39,392,276
Number of Sequences: 62578
Number of extensions: 1603900
Number of successful extensions: 3946
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 3766
Number of HSP's gapped (non-prelim): 80
length of query: 1484
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1373
effective length of database: 8,027,179
effective search space: 11021316767
effective search space used: 11021316767
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)