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= psy7164
(2307 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1099
Score = 545 bits (1403), Expect = e-154, Method: Compositional matrix adjust.
Identities = 299/619 (48%), Positives = 387/619 (62%), Gaps = 103/619 (16%)
Query: 36 YQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNA 95
YQK SQLEHIL RPDTYIGSVE + W+ + ET+ M + +T VPGL+KIFDEILVNA
Sbjct: 6 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 65
Query: 96 CDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYN 155
DNK RDP M I + ++ E +TI V N+GKGIP+ H E +++P MIFGHLLTSSNY+
Sbjct: 66 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 125
Query: 156 DEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYK 215
D +E KVTGGRNGYGAKLCNIFS++F++ET+
Sbjct: 126 D-------------------------DEKKVTGGRNGYGAKLCNIFSTEFILETADLNVG 160
Query: 216 KSFKQVWKDNMSKVTSPEIKSGSKD-DFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDA 274
+ + Q W++NMS P+I S K +TK+TF PDLT+F M LD D++ ++ RR YD
Sbjct: 161 QKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDI 220
Query: 275 AASTKDVKVFLNGEKLPVKNFQDYVKLYTDRQDEDGDPVKIIYENVNPRWEVAIAPSDRG 334
S +D+ V+LNG+ L ++NF++YV+LY + P I+YE +N RWEVA A SD
Sbjct: 221 NGSVRDINVYLNGKSLKIRNFKNYVELYL----KSLIPT-ILYERINNRWEVAFAVSDIS 275
Query: 335 FQQVSFVNSIATTKGGRHVDAVVDAXXXXXXXXXXXXXXDLGCTIIMLFGXXXXXXXXXX 394
FQQ+SFVNSIATT GG HV+ + D
Sbjct: 276 FQQISFVNSIATTMGGTHVNYITD------------------------------------ 299
Query: 395 LQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTLQKGSFGSTC 454
Q+ K + +I + ++K FQ+KN+++IFINCLI NP F SQTKE +T + FGS C
Sbjct: 300 -QIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRC 358
Query: 455 ----------------------------VPKLEDANDAGTKNSIDCTLILTEGDSAKSLA 486
PKLEDAN AGTK CTL+LTEGDSA SLA
Sbjct: 359 EIPLEYINKIMKTDLATRMFEIASRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLA 418
Query: 487 VSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMK 546
V+GL VVGRD YG +PLRGK+LNVREA+ QIL+NAEI + KI+GLQ+ KKY ED K
Sbjct: 419 VAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKY---EDTK 475
Query: 547 TLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLP-FLEEFITPIIKAT---KARE 602
+LRYG LMIMTDQD DGSHIKGLIINF+ ++P LL + FL EFITPIIK + +
Sbjct: 476 SLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKN 535
Query: 603 ELSFYSLPEFEEWKEETTN 621
++FY++P++E+W+EE ++
Sbjct: 536 TIAFYNMPDYEKWREEESH 554
Score = 106 bits (265), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 47/96 (48%), Positives = 64/96 (66%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EPEWY+PI+PM+LVNGAEGIGTGW T IP NP EI+ NI+ ++ E+ M PW++ +
Sbjct: 771 VEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGW 830
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
G I+ R+ + G I + D+ LEITEL W
Sbjct: 831 TGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTW 866
Score = 54.7 bits (130), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 852 YDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDAL 901
Y+YLLGM WSLT ER +LLK++ +K TEL L K + D+W+ DL A
Sbjct: 1035 YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF 1084
>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
Length = 1103
Score = 543 bits (1399), Expect = e-154, Method: Compositional matrix adjust.
Identities = 300/626 (47%), Positives = 388/626 (61%), Gaps = 107/626 (17%)
Query: 36 YQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNA 95
YQK SQLEHIL RPDTYIGSVE + W+ + ET+ M + +T VPGL+KIFDEILVNA
Sbjct: 6 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 65
Query: 96 CDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYN 155
DNK RDP M I + ++ E +TI V N+GKGIP+ H E +++P MIFGHLLTSSNY+
Sbjct: 66 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 125
Query: 156 DEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYK 215
D +E KVTGGRNGYGAKLCNIFS++F++ET+
Sbjct: 126 D-------------------------DEKKVTGGRNGYGAKLCNIFSTEFILETADLNVG 160
Query: 216 KSFKQVWKDNMSKVTSPEIKSGSKD-DFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDA 274
+ + Q W++NMS P+I S K +TK+TF PDLT+F M LD D++ ++ RR YD
Sbjct: 161 QKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDI 220
Query: 275 AASTKDVKVFLNGEKLPVKNFQDYVKLYTDRQDEDGDPVKIIYENVNPRWEVAIAPSDRG 334
S +D+ V+LNG+ L ++NF++YV+LY + P I+YE +N RWEVA A SD
Sbjct: 221 NGSVRDINVYLNGKSLKIRNFKNYVELYL----KSLIPT-ILYERINNRWEVAFAVSDIS 275
Query: 335 FQQVSFVNSIATTKGGRHVDAVVDAXXXXXXXXXXXXXXDLGCTIIMLFGXXXXXXXXXX 394
FQQ+SFVNSIATT GG HV+ + D
Sbjct: 276 FQQISFVNSIATTMGGTHVNYITD------------------------------------ 299
Query: 395 LQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTLQKGSFGSTC 454
Q+ K + +I + ++K FQ+KN+++IFINCLI NP F SQTKE +T + FGS C
Sbjct: 300 -QIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTRVKDFGSRC 358
Query: 455 --------------------------------VPKLEDANDAGTKNSIDCTLILTEGDSA 482
PKLEDAN AGTK CTL+LTEGDSA
Sbjct: 359 EIPLEYINKIMKTDLATRMFEIADANESRITNYPKLEDANKAGTKEGYKCTLVLTEGDSA 418
Query: 483 KSLAVSGLGVVGRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTV 542
SLAV+GL VVGRD YG +PLRGK+LNVREA+ QIL+NAEI + KI+GLQ+ KKY
Sbjct: 419 LSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKY--- 475
Query: 543 EDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLP-FLEEFITPIIKAT--- 598
ED K+LRYG LMIMTDQD DGSHIKGLIINF+ ++P LL + FL EFITPIIK +
Sbjct: 476 EDTKSLRYGHLMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITK 535
Query: 599 KAREELSFYSLPEFEEWKEETTNWHT 624
+ ++FY++P++E+W+EE ++ T
Sbjct: 536 PTKNTIAFYNMPDYEKWREEESHKFT 561
Score = 106 bits (265), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 47/96 (48%), Positives = 64/96 (66%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EPEWY+PI+PM+LVNGAEGIGTGW T IP NP EI+ NI+ ++ E+ M PW++ +
Sbjct: 775 VEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGW 834
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
G I+ R+ + G I + D+ LEITEL W
Sbjct: 835 TGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTW 870
Score = 54.7 bits (130), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 852 YDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDAL 901
Y+YLLGM WSLT ER +LLK++ +K TEL L K + D+W+ DL A
Sbjct: 1039 YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF 1088
>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 = 489 bits (1259), Expect = e-138, Method: Compositional matrix adjust.
Identities = 250/448 (55%), Positives = 305/448 (68%), Gaps = 71/448 (15%)
Query: 31 SVEKIYQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDE 90
SVE+IYQKK+QLEHILLRPDTYIGSVE +T+ MW+ + + + RE+T+VPGLYKIFDE
Sbjct: 1 SVERIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVG-INYREVTFVPGLYKIFDE 59
Query: 91 ILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLT 150
ILVNA DNKQRDPKM+CI++T++ E N IS+WNNGKGIPVVEHK EKM+VP +IF
Sbjct: 60 ILVNAADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIF----- 114
Query: 151 SSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETS 210
G LLTSSNY+D+E KVTGGRNGYGAKLCNIFS+KF VET+
Sbjct: 115 --------------------GQLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTKFTVETA 154
Query: 211 CSEYKKSFKQVWKDNMSKVTSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRR 270
EYKK FKQ W DNM + E+K + +D+T ITF PDL+KFKM SLDKD+V L+ RR
Sbjct: 155 SREYKKMFKQTWMDNMGRAGEMELKPFNGEDYTCITFQPDLSKFKMQSLDKDIVALMVRR 214
Query: 271 AYDAAASTKDVKVFLNGEKLPVKNFQDYVKLY-TDRQDEDGDPVKIIYENVNPRWEVAIA 329
AYD A STKDVKVFLNG KLPVK F+ YV +Y D+ DE G+ +K+I+E VN RWEV +
Sbjct: 215 AYDIAGSTKDVKVFLNGNKLPVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLT 274
Query: 330 PSDRGFQQVSFVNSIATTKGGRHVDAVVDAXXXXXXXXXXXXXXDLGCTIIMLFGXXXXX 389
S++GFQQ+SFVNSIAT+KGGRHVD V D
Sbjct: 275 MSEKGFQQISFVNSIATSKGGRHVDYVAD------------------------------- 303
Query: 390 XXXXXLQMAKTLIDIGVR--LGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKENMTLQK 447
Q+ L+D+ + GG+A+K QVKNH+WIF+N LI NPTFDSQTKENMTLQ
Sbjct: 304 ------QIVTKLVDVVKKKNKGGVAVKAHQVKNHMWIFVNALIENPTFDSQTKENMTLQP 357
Query: 448 GSFGSTCVPKLEDANDAGTKNSIDCTLI 475
SFGSTC ++ K +I C ++
Sbjct: 358 KSFGSTC-----QLSEKFIKAAIGCGIV 380
>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 = 354 bits (908), Expect = 3e-97, Method: Compositional matrix adjust.
Identities = 198/440 (45%), Positives = 261/440 (59%), Gaps = 75/440 (17%)
Query: 36 YQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNA 95
YQK SQLEHIL RPDTYIGSVE + W+ + ET+ M + +T VPGL+KIFDEILVNA
Sbjct: 17 YQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIVPGLFKIFDEILVNA 76
Query: 96 CDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYN 155
DNK RDP M I + ++ E +TI V N+GKGIP+ H E +++P MIFGHLLTSSNY+
Sbjct: 77 ADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEMIFGHLLTSSNYD 136
Query: 156 DEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETSCSEYK 215
D +E KVTGGRNGYGAKLCNIFS++F++ET+
Sbjct: 137 D-------------------------DEKKVTGGRNGYGAKLCNIFSTEFILETADLNVG 171
Query: 216 KSFKQVWKDNMSKVTSPEIKSGSKD-DFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDA 274
+ + Q W++NMS P+I S K +TK+TF PDLT+F M LD D++ ++ RR YD
Sbjct: 172 QKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDI 231
Query: 275 AASTKDVKVFLNGEKLPVKNFQDYVKLY-----TDRQDEDG-------DPVKIIYENVNP 322
S +D+ V+LNG+ L ++NF++YV+LY RQ ++G D I+YE +N
Sbjct: 232 NGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINN 291
Query: 323 RWEVAIAPSDRGFQQVSFVNSIATTKGGRHVDAVVDAXXXXXXXXXXXXXXDLGCTIIML 382
RWEVA A SD FQQ+SFVNSIATT GG HV+ + D
Sbjct: 292 RWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITD------------------------ 327
Query: 383 FGXXXXXXXXXXLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFDSQTKEN 442
Q+ K + +I + ++K FQ+KN+++IFINCLI NP F SQTKE
Sbjct: 328 -------------QIVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQ 374
Query: 443 MTLQKGSFGSTCVPKLEDAN 462
+T + FGS C LE N
Sbjct: 375 LTTRVKDFGSRCEIPLEYIN 394
>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 = 339 bits (869), Expect = 1e-92, Method: Compositional matrix adjust.
Identities = 194/446 (43%), Positives = 256/446 (57%), Gaps = 75/446 (16%)
Query: 30 MSVEKIYQKKSQLEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFD 89
+S YQK SQLEHIL RPDTYIGSVE + W+ + ET+ + +T VPGL+KIFD
Sbjct: 11 VSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCXIEKNVTIVPGLFKIFD 70
Query: 90 EILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLL 149
EILVNA DNK RDP I + ++ E +TI V N+GKGIP+ H E +++P IFGHLL
Sbjct: 71 EILVNAADNKVRDPSXKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIPEXIFGHLL 130
Query: 150 TSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVET 209
TSSNY+D +E KVTGGRNGYGAKLCNIFS++F++ET
Sbjct: 131 TSSNYDD-------------------------DEKKVTGGRNGYGAKLCNIFSTEFILET 165
Query: 210 SCSEYKKSFKQVWKDNMSKVTSPEIKSGSKD-DFTKITFTPDLTKFKMTSLDKDMVDLIT 268
+ + + Q W++N S P+I S K +TK+TF PDLT+F LD D++ +
Sbjct: 166 ADLNVGQKYVQKWENNXSICHPPKITSYKKGPSYTKVTFKPDLTRFGXKELDNDILGVXR 225
Query: 269 RRAYDAAASTKDVKVFLNGEKLPVKNFQDYVKLY-----TDRQDEDG-------DPVKII 316
RR YD S +D+ V+LNG+ L ++NF++YV+LY RQ ++G D I+
Sbjct: 226 RRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTIL 285
Query: 317 YENVNPRWEVAIAPSDRGFQQVSFVNSIATTKGGRHVDAVVDAXXXXXXXXXXXXXXDLG 376
YE +N RWEVA A SD FQQ+SFVNSIATT GG HV+ + D
Sbjct: 286 YERINNRWEVAFAVSDISFQQISFVNSIATTXGGTHVNYITD------------------ 327
Query: 377 CTIIMLFGXXXXXXXXXXLQMAKTLIDIGVRLGGMALKPFQVKNHIWIFINCLIVNPTFD 436
Q+ K + +I + ++K FQ+KN+ +IFINCLI NP F
Sbjct: 328 -------------------QIVKKISEILKKKKKKSVKSFQIKNNXFIFINCLIENPAFT 368
Query: 437 SQTKENMTLQKGSFGSTCVPKLEDAN 462
SQTKE +T + FGS C LE N
Sbjct: 369 SQTKEQLTTRVKDFGSRCEIPLEYIN 394
>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 = 288 bits (736), Expect = 3e-77, Method: Compositional matrix adjust.
Identities = 128/167 (76%), Positives = 154/167 (92%)
Query: 455 VPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREAT 514
+PKL+DANDAG K+S++CTLILTEGDSAKSLAVSGLGV+GRD+YGVFPLRGK+LNVREA+
Sbjct: 36 IPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFPLRGKILNVREAS 95
Query: 515 HKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFI 574
HKQI+ENAEINN++KI+GLQY K Y E +KTLRYG++MIMTDQDQDGSHIKGL+INFI
Sbjct: 96 HKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGKIMIMTDQDQDGSHIKGLLINFI 155
Query: 575 HHNWPTLLRLPFLEEFITPIIKATKAREELSFYSLPEFEEWKEETTN 621
HHNWP+LL+ FLEEFITPI+KA+K ++ELSFYS+PEF+EWK+ N
Sbjct: 156 HHNWPSLLKHGFLEEFITPIVKASKNKQELSFYSIPEFDEWKKHIEN 202
Score = 139 bits (351), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 60/97 (61%), Positives = 77/97 (79%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKN 718
R+EPEWYIPIIPMVL+NGAEGIGTGW K+PN++ REIV+N++RM+ G DP PM P YKN
Sbjct: 433 RVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDPHPMLPNYKN 492
Query: 719 FKGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
FKG I G +++ V+GEI ++D + +EITEL V W
Sbjct: 493 FKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTW 529
Score = 67.8 bits (164), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 39/89 (43%), Positives = 57/89 (64%), Gaps = 7/89 (7%)
Query: 824 ERQERQAAEGE----DDEAGSQTQEEEDPDKDYDYLLGMTFWSLTMERKNELLKKRDDKM 879
E QE+ A E E D++ S + PD ++Y+L M+ WSLT E+ EL+K+RD K
Sbjct: 690 EAQEKAAEEDETQNQHDDSSSDSGTPSGPD--FNYILNMSLWSLTKEKVEELIKQRDAKG 747
Query: 880 TELNILKKKAPTDLWSDDLDALREK-DKI 907
E+N LK+K+P+DLW +DL A E+ DK+
Sbjct: 748 REVNDLKRKSPSDLWKEDLAAFVEELDKV 776
>pdb|4FM9|A Chain A, Human Topoisomerase Ii Alpha Bound To Dna
Length = 763
Score = 286 bits (731), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 129/167 (77%), Positives = 152/167 (91%)
Query: 455 VPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVREAT 514
+PKL+DANDAG +NS +CTLILTEGDSAK+LAVSGLGVVGRDKYGVFPLRGK+LNVREA+
Sbjct: 8 IPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFPLRGKILNVREAS 67
Query: 515 HKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFI 574
HKQI+ENAEINN++KI+GLQY K Y + +KTLRYG++MIMTDQDQDGSHIKGL+INFI
Sbjct: 68 HKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGKIMIMTDQDQDGSHIKGLLINFI 127
Query: 575 HHNWPTLLRLPFLEEFITPIIKATKAREELSFYSLPEFEEWKEETTN 621
HHNWP+LLR FLEEFITPI+K +K ++E++FYSLPEFEEWK T N
Sbjct: 128 HHNWPSLLRHRFLEEFITPIVKVSKNKQEMAFYSLPEFEEWKSSTPN 174
Score = 140 bits (353), Expect = 7e-33, Method: Compositional matrix adjust.
Identities = 61/97 (62%), Positives = 79/97 (81%)
Query: 659 RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKN 718
R+EPEWYIPIIPMVL+NGAEGIGTGW KIPN + REIV+NI+R++ GE+PLPM P YKN
Sbjct: 405 RVEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEEPLPMLPSYKN 464
Query: 719 FKGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
FKG I+ +++V++GE+AIL+ +EI+EL V W
Sbjct: 465 FKGTIEELAPNQYVISGEVAILNSTTIEISELPVRTW 501
Score = 57.0 bits (136), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 39/58 (67%)
Query: 847 DPDKDYDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDALREK 904
D ++YLL M W LT E+K+EL + R++K EL+ LK+K+P+DLW +DL E+
Sbjct: 690 DSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELDTLKRKSPSDLWKEDLATFIEE 747
>pdb|3GQC|A Chain A, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|B Chain B, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|C Chain C, Structure Of Human Rev1-Dna-Dntp Ternary Complex
pdb|3GQC|D Chain D, Structure Of Human Rev1-Dna-Dntp Ternary Complex
Length = 504
Score = 243 bits (619), Expect = 1e-63, Method: Compositional matrix adjust.
Identities = 120/246 (48%), Positives = 167/246 (67%), Gaps = 4/246 (1%)
Query: 1876 AYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAK 1935
AY+E+ + + +S + + AVSCDE VD +++L E LTP +FA+ +R I
Sbjct: 216 AYKEVAQTLYETL----ASYTHNIEAVSCDEALVDITEILAETKLTPDEFANAVRMEIKD 271
Query: 1936 ETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKL 1995
+T C S G GSN L AR+AT+KAKP+GQ+HL P+ + DF+ +++LPGVGHS+ KL
Sbjct: 272 QTKCAASVGIGSNILLARMATRKAKPDGQYHLKPEEVDDFIRGQLVTNLPGVGHSMESKL 331
Query: 1996 NSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGI 2055
SLG +TCGDLQ +++ +LQ E G K G LY+ CRG DD+ + E +RKSVSAE+NYGI
Sbjct: 332 ASLGIKTCGDLQYMTMAKLQKEFGPKTGQMLYRFCRGLDDRPVRTEKERKSVSAEINYGI 391
Query: 2056 RFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKLMVRSAEAPREASKFLGHGVCDYI 2115
RF +E E FL L+ E+++RLE MKGK +TLK+MVR AP E +KF GHG+CD I
Sbjct: 392 RFTQPKEAEAFLLSLSEEIQRRLEATGMKGKRLTLKIMVRKPGAPVETAKFGGHGICDNI 451
Query: 2116 TKSSSL 2121
++ +L
Sbjct: 452 ARTVTL 457
Score = 150 bits (378), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 86/230 (37%), Positives = 124/230 (53%), Gaps = 42/230 (18%)
Query: 1539 SNEDFLGEFYNKSRLHHLSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKT---SLGITE 1595
S+ +F+ FY+ SRLHH+S ++VN L+ + +G+F G E ++K KT +L +T+
Sbjct: 15 SDCNFISNFYSHSRLHHISMWKCELTEFVNTLQRQSNGIFPGREKLKKMKTGRSALVVTD 74
Query: 1596 DEDLEETFSDNPSPSEPEPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNS-SKVR 1654
D+ S SP + IMH+DMDCFFVSVGIR+ P+L+ +PVAV +G + +R
Sbjct: 75 TGDM----SVLNSPRH-QSCIMHVDMDCFFVSVGIRNRPDLKGKPVAVTSNRGTGRAPLR 129
Query: 1655 EGVDRQAEFDIYRQRTMNRMGLN---------------------------------TREY 1681
G + Q E+ Y+ + + + R+
Sbjct: 130 PGANPQLEWQYYQNKILKGKAADIPDSSLWENPDSAQANGIDSVLSRAEIASCSYEARQL 189
Query: 1682 GLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVS 1731
G+ NGMF GHA + CPNL+ VPYDF YKEV+ LY +AS T NIEAVS
Sbjct: 190 GIKNGMFFGHAKQLCPNLQAVPYDFHAYKEVAQTLYETLASYTHNIEAVS 239
Score = 32.7 bits (73), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 1193 SNEDFLGEFYNKSRLHHLSTMGSMFKQYVNQL 1224
S+ +F+ FY+ SRLHH+S ++VN L
Sbjct: 15 SDCNFISNFYSHSRLHHISMWKCELTEFVNTL 46
>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 = 214 bits (546), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 108/173 (62%), Positives = 134/173 (77%), Gaps = 7/173 (4%)
Query: 453 TCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVRE 512
T PKLEDAN AGTK CTL+LTEGDSA SLAV+GL VVGRD YG +PLRGK+LNVRE
Sbjct: 4 TNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVRE 63
Query: 513 ATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIIN 572
A+ QIL+NAEI + KI+GLQ+ KKY ED K+LRYG LMIMTDQD DGSHIKGLIIN
Sbjct: 64 ASADQILKNAEIQAIKKIMGLQHRKKY---EDTKSLRYGHLMIMTDQDHDGSHIKGLIIN 120
Query: 573 FIHHNWPTLLRLP-FLEEFITPIIKAT---KAREELSFYSLPEFEEWKEETTN 621
F+ ++P LL + FL EFITPIIK + + ++FY++P++E+W+EE ++
Sbjct: 121 FLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESH 173
Score = 106 bits (265), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 47/96 (48%), Positives = 64/96 (66%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EPEWY+PI+PM+LVNGAEGIGTGW T IP NP EI+ NI+ ++ E+ M PW++ +
Sbjct: 394 VEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGW 453
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
G I+ R+ + G I + D+ LEITEL W
Sbjct: 454 TGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTW 489
Score = 54.7 bits (130), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 852 YDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDAL 901
Y+YLLGM WSLT ER +LLK++ +K TEL L K + D+W+ DL A
Sbjct: 658 YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF 707
>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
Length = 759
Score = 211 bits (536), Expect = 5e-54, Method: Compositional matrix adjust.
Identities = 107/173 (61%), Positives = 133/173 (76%), Gaps = 7/173 (4%)
Query: 453 TCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVRE 512
T PKLEDAN AGTK CTL+LTEGDSA SLAV+GL VVGRD YG +PLRGK+LNVRE
Sbjct: 6 TNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVRE 65
Query: 513 ATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIIN 572
A+ QIL+NAEI + KI+GLQ+ KKY ED K+LRYG LMIMTDQD DGSHIKGLIIN
Sbjct: 66 ASADQILKNAEIQAIKKIMGLQHRKKY---EDTKSLRYGHLMIMTDQDHDGSHIKGLIIN 122
Query: 573 FIHHNWPTLLRLP-FLEEFITPIIKAT---KAREELSFYSLPEFEEWKEETTN 621
F+ ++ LL + FL EFITPIIK + + ++FY++P++E+W+EE ++
Sbjct: 123 FLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESH 175
Score = 106 bits (265), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 47/96 (48%), Positives = 64/96 (66%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EPEWY+PI+PM+LVNGAEGIGTGW T IP NP EI+ NI+ ++ E+ M PW++ +
Sbjct: 395 VEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGW 454
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
G I+ R+ + G I + D+ LEITEL W
Sbjct: 455 TGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTW 490
Score = 54.7 bits (130), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 852 YDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDAL 901
Y+YLLGM WSLT ER +LLK++ +K TEL L K + D+W+ DL A
Sbjct: 695 YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF 744
>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
Length = 793
Score = 211 bits (536), Expect = 6e-54, Method: Compositional matrix adjust.
Identities = 107/173 (61%), Positives = 133/173 (76%), Gaps = 7/173 (4%)
Query: 453 TCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKYGVFPLRGKLLNVRE 512
T PKLEDAN AGTK CTL+LTEGDSA SLAV+GL VVGRD YG +PLRGK+LNVRE
Sbjct: 16 TNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVRE 75
Query: 513 ATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIIN 572
A+ QIL+NAEI + KI+GLQ+ KKY ED K+LRYG LMIMTDQD DGSHIKGLIIN
Sbjct: 76 ASADQILKNAEIQAIKKIMGLQHRKKY---EDTKSLRYGHLMIMTDQDHDGSHIKGLIIN 132
Query: 573 FIHHNWPTLLRLP-FLEEFITPIIKAT---KAREELSFYSLPEFEEWKEETTN 621
F+ ++ LL + FL EFITPIIK + + ++FY++P++E+W+EE ++
Sbjct: 133 FLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWREEESH 185
Score = 106 bits (265), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 47/96 (48%), Positives = 64/96 (66%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EPEWY+PI+PM+LVNGAEGIGTGW T IP NP EI+ NI+ ++ E+ M PW++ +
Sbjct: 405 VEPEWYLPILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGW 464
Query: 720 KGEIDYCGDSRFVVNGEIAILDDDKLEITELQVGKW 755
G I+ R+ + G I + D+ LEITEL W
Sbjct: 465 TGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTW 500
Score = 54.7 bits (130), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/50 (52%), Positives = 34/50 (68%)
Query: 852 YDYLLGMTFWSLTMERKNELLKKRDDKMTELNILKKKAPTDLWSDDLDAL 901
Y+YLLGM WSLT ER +LLK++ +K TEL L K + D+W+ DL A
Sbjct: 705 YEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAF 754
>pdb|2AQ4|A Chain A, Ternary Complex Of The Catalytic Core Of Rev1 With Dna And
Dctp.
pdb|3BJY|A Chain A, Catalytic Core Of Rev1 In Complex With Dna (Modified
Template Guanine) And Incoming Nucleotide
pdb|3OSP|A Chain A, Structure Of Rev1
Length = 434
Score = 118 bits (295), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 82/229 (35%), Positives = 127/229 (55%), Gaps = 14/229 (6%)
Query: 1929 LRETIAKET-GCTCSTGFGSNKLQARLATKKAKPNG-QFHLTPQIISDFMLNIPLSDLPG 1986
+R+ I + T GCT S G + + ARLA K AKPNG + +F + L DLPG
Sbjct: 189 IRQEIFQGTNGCTVSIGCSDSLVLARLALKMAKPNGYNITFKSNLSEEFWSSFKLDDLPG 248
Query: 1987 VGHSLLFKLNSL--GAQTCGDL-QNISLKRLQNEVGNKNGLTLYKHCRGEDDKE---LTF 2040
VGHS L +L S + DL + +L L+ VG+K G+ ++ +G+DD+E + +
Sbjct: 249 VGHSTLSRLESTFDSPHSLNDLRKRYTLDALKASVGSKLGMKIHLALQGQDDEESLKILY 308
Query: 2041 E----HQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKLMVRS 2096
+ QRKS+S ++N+GIRF+N +++ F+++ + ++L E+ ITLKLM R
Sbjct: 309 DPKEVLQRKSLSIDINWGIRFKNITQVDLFIERGCQYLLEKLNEINKTTSQITLKLMRRC 368
Query: 2097 AEAPREASKFLGHGVCDYITKSSSL--PIYERPLIITYFLLLVRSAEAP 2143
+AP E K++G G CD ++SS L P E +I T L R+ P
Sbjct: 369 KDAPIEPPKYMGMGRCDSFSRSSRLGIPTNEFGIIATEMKSLYRTLGCP 417
Score = 66.2 bits (160), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 75/270 (27%), Positives = 107/270 (39%), Gaps = 91/270 (33%)
Query: 1542 DFLGEFYNKSRLHHLSTMGSMFKQYVNELREKHDGVFRGIEAIRKWKTSLGITEDEDLEE 1601
DFL ++ SRLHHLS WK +L +D+ L E
Sbjct: 10 DFLTSYFAHSRLHHLSA----------------------------WKANL---KDKFLNE 38
Query: 1602 TFSDNPSPSEPEP-VIMHIDMDCFFVSVGIRHHP------ELQDEPVAVAHGKGNSSKVR 1654
++ + +I HID DCFF +V + + +P+ V HG NS
Sbjct: 39 NIHKYTKITDKDTYIIFHIDFDCFFATVAYLCRSSSFSACDFKRDPIVVCHGTKNS---- 94
Query: 1655 EGVDRQAEFDIYRQRTMNRMGLNTREYGLGNGMFVGHALKKCPN-LKIV--PYDFEGYKE 1711
DI + N + R YG+ NGM+V A K PN +K++ PY FE ++
Sbjct: 95 ---------DI---ASCNYVA---RSYGIKNGMWVSQAEKMLPNGIKLISLPYTFEQFQL 139
Query: 1712 VSYCLY---------NLIASLTLNIEAVSLYT------NESFLNA-LPEDIRQEVLDDLS 1755
S Y NLI ++++ EAV + N + LNA L E+IRQE+
Sbjct: 140 KSEAFYSTLKRLNIFNLILPISID-EAVCVRIIPDNIHNTNTLNARLCEEIRQEIFQG-- 196
Query: 1756 RQQSVLSREQNTTEPLAQDIICADSHTLVR 1785
T I C+DS L R
Sbjct: 197 ------------TNGCTVSIGCSDSLVLAR 214
>pdb|2EBW|A Chain A, Solution Structure Of The Brct Domain From Human Dna Repair
Protein Rev1
Length = 97
Score = 116 bits (290), Expect = 2e-25, Method: Composition-based stats.
Identities = 60/98 (61%), Positives = 73/98 (74%), Gaps = 13/98 (13%)
Query: 1345 IFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYH-HYESSRTTHIIASNLP 1403
IF GVAI+VNGYT PSAEEL+ LMMLHGG YH +Y S+TTHIIA+NLP
Sbjct: 12 IFSGVAIYVNGYTD-----------PSAEELRKLMMLHGGQYHVYYSRSKTTHIIATNLP 60
Query: 1404 HTKIKKLKPGDKIIKPEWIVDSISAGKLLDHKKYLLYT 1441
+ KIK+LK G+K+I+PEWIV+SI AG+LL + Y LYT
Sbjct: 61 NAKIKELK-GEKVIRPEWIVESIKAGRLLSYIPYQLYT 97
>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 = 83.2 bits (204), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/165 (31%), Positives = 83/165 (50%), Gaps = 14/165 (8%)
Query: 463 DAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILE 520
D +K+ +C + L EGDSA G GRD + PLRGK+LNV +A +IL
Sbjct: 12 DCSSKSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKARLDRILN 66
Query: 521 NAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPT 580
N EI ++ G + D+ RY +++IMTD D DG+HI+ L++ F +
Sbjct: 67 NNEIRQMITAFGTGIGGDF----DLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 581 LLRLPFLEEFITPIIKATKAREELSFYSLPEFEEWKEE---TTNW 622
L+ ++ P+ K T+ +++ Y+ E ++ K E T W
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKW 167
Score = 37.0 bits (84), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 644 NLHKVTSDSISMFIG-RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
+++K T D I + G EP P +L NGA GI G T IP HN E+++ +
Sbjct: 373 DINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGV 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 = 83.2 bits (204), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/165 (31%), Positives = 83/165 (50%), Gaps = 14/165 (8%)
Query: 463 DAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILE 520
D +K+ +C + L EGDSA G GRD + PLRGK+LNV +A +IL
Sbjct: 12 DCSSKSPEECEIFLVEGDSA-----GGSTKSGRDSRTQAILPLRGKILNVEKARLDRILN 66
Query: 521 NAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPT 580
N EI ++ G + D+ RY +++IMTD D DG+HI+ L++ F +
Sbjct: 67 NNEIRQMITAFGTGIGGDF----DLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRP 122
Query: 581 LLRLPFLEEFITPIIKATKAREELSFYSLPEFEEWKEE---TTNW 622
L+ ++ P+ K T+ +++ Y+ E ++ K E T W
Sbjct: 123 LIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKW 167
Score = 37.0 bits (84), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 644 NLHKVTSDSISMFIG-RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
+++K T D I + G EP P +L NGA GI G T IP HN E+++ +
Sbjct: 373 DINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGV 430
>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 = 75.5 bits (184), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 51/161 (31%), Positives = 86/161 (53%), Gaps = 15/161 (9%)
Query: 464 AGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILEN 521
A +KN L L EGDSA G GRD+ + PLRGK++N +A IL+N
Sbjct: 40 AQSKNPAKNELYLVEGDSA-----GGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKN 94
Query: 522 AEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTL 581
EIN ++ +G ++ +ED Y +++IMTD D DG+HI+ L++ F + L
Sbjct: 95 EEINTMIYTIGAGVGADFS-IEDAN---YDKIIIMTDADTDGAHIQTLLLTFFYRYMRPL 150
Query: 582 LRLPFLEEFITPIIKATKA---REELSF-YSLPEFEEWKEE 618
+ + + P+ K +K +EE+++ ++ E EE +++
Sbjct: 151 VEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQ 191
>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 = 74.7 bits (182), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 46/137 (33%), Positives = 69/137 (50%), Gaps = 24/137 (17%)
Query: 463 DAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLLNVREATHKQILE 520
D +K+ +C + L EGDSA SG RD + PLRGK+LNV +A +IL
Sbjct: 12 DCSSKSPEECEIFLVEGDSAGGSTKSG-----RDSRTQAILPLRGKILNVEKARLDRILN 66
Query: 521 NAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPT 580
N EI ++ G + D+ RY +++IMTD D DG+HI+ L++ F +
Sbjct: 67 NNEIRQMITAFGTGIGGDF----DLAKARYHKIVIMTDADVDGAHIRTLLLTFFYR---- 118
Query: 581 LLRLPFLEEFITPIIKA 597
F+ P+I+A
Sbjct: 119 ---------FMRPLIEA 126
Score = 37.0 bits (84), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 644 NLHKVTSDSISMFIG-RIEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
+++K T D I + G EP P +L NGA GI G T IP HN E+++ +
Sbjct: 339 DINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGV 396
>pdb|4F4W|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4W|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4X|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #2
Length = 361
Score = 72.0 bits (175), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 43/169 (25%), Positives = 83/169 (49%), Gaps = 1/169 (0%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 99 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 158
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEV 2018
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 159 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKIT 218
Query: 2019 GNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFL 2067
G L L K + E ++ + RKS+ V +N +E++ +L
Sbjct: 219 GKAKALYLLKLAQDEYNEPIR-TRVRKSIGRIVTMKRNSRNLEEIKPYL 266
Score = 33.1 bits (74), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 33/151 (21%), Positives = 62/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V G + G A ++
Sbjct: 2 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKT--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 50 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 104
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 105 DEAYLDVTNKVEGNFENGIELARKIKQEILE 135
>pdb|1T94|A Chain A, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
pdb|1T94|B Chain B, Crystal Structure Of The Catalytic Core Of Human Dna
Polymerase Kappa
Length = 459
Score = 72.0 bits (175), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 86/168 (51%), Gaps = 8/168 (4%)
Query: 1929 LRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTP--QIISDFMLNIPLSDLPG 1986
+R I ++T T S G N + A++ + K KPNGQ+ + P Q + DF+ ++P+ + G
Sbjct: 230 IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSG 289
Query: 1987 VGHSLLFKLNSLGAQTCGDL--QNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQR 2044
+G L +LG TC +L Q L L +E L + G LT + +R
Sbjct: 290 IGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHI---SLGLGSTHLTRDGER 346
Query: 2045 KSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKL 2092
KS+S E + +E + ++L E+ + L++ ++KG+ +T+KL
Sbjct: 347 KSMSVERTFS-EINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKL 393
Score = 62.8 bits (151), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 40/125 (32%), Positives = 65/125 (52%), Gaps = 24/125 (19%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
I+HIDMD F+ +V +R +PEL+D+P+AV G+ S ++
Sbjct: 36 IVHIDMDAFYAAVEMRDNPELKDKPIAV----GSMS------------------MLSTSN 73
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
+ R +G+ M A + CP L IVP +F+ Y+ VS + ++A N A+SL +
Sbjct: 74 YHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSL--D 131
Query: 1736 ESFLN 1740
E++LN
Sbjct: 132 EAYLN 136
>pdb|3PZP|A Chain A, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
pdb|3PZP|B Chain B, Human Dna Polymerase Kappa Extending Opposite A Cis-Syn
Thymine Dimer
Length = 517
Score = 71.2 bits (173), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 46/167 (27%), Positives = 87/167 (52%), Gaps = 6/167 (3%)
Query: 1929 LRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTP--QIISDFMLNIPLSDLPG 1986
+R I ++T T S G N + A++ + K KPNGQ+ + P Q + DF+ ++P+ + G
Sbjct: 286 IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSG 345
Query: 1987 VGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCR-GEDDKELTFEHQRK 2045
+G L +LG TC +L + L + + ++ + H G LT + +RK
Sbjct: 346 IGKVTEKMLKALGIITCTEL--YQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERK 403
Query: 2046 SVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKL 2092
S+S E + +E + ++L E+ + L++ ++KG+ +T+KL
Sbjct: 404 SMSVERTFS-EINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKL 449
Score = 62.8 bits (151), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 49/173 (28%), Positives = 82/173 (47%), Gaps = 41/173 (23%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
I+HIDMD F+ +V +R +PEL+D+P+AV G+ S ++
Sbjct: 92 IVHIDMDAFYAAVEMRDNPELKDKPIAV----GSMS------------------MLSTSN 129
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
+ R +G+ M A + CP L IVP +F+ Y+ VS + ++A N A+SL +
Sbjct: 130 YHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSL--D 187
Query: 1736 ESFLNAL---------PEDIRQEVL--------DDLSRQQSVLSREQNTTEPL 1771
E++LN PED R+ + D+ ++ + LS + + PL
Sbjct: 188 EAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPL 240
>pdb|2OH2|A Chain A, Ternary Complex Of Human Dna Polymerase
pdb|2OH2|B Chain B, Ternary Complex Of Human Dna Polymerase
pdb|2W7O|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7O|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|A Chain A, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|2W7P|B Chain B, Structure And Activity Of Bypass Synthesis By Human Dna
Polymerase Kappa Opposite The 7,8-Dihydro-8-
Oxodeoxyguanosine Adduct
pdb|3IN5|A Chain A, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
pdb|3IN5|B Chain B, Structure Of Human Dna Polymerase Kappa Inserting Datp
Opposite An 8-Oxog Dna Lesion
Length = 508
Score = 71.2 bits (173), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 86/168 (51%), Gaps = 8/168 (4%)
Query: 1929 LRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTP--QIISDFMLNIPLSDLPG 1986
+R I ++T T S G N + A++ + K KPNGQ+ + P Q + DF+ ++P+ + G
Sbjct: 279 IRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSG 338
Query: 1987 VGHSLLFKLNSLGAQTCGDL--QNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQR 2044
+G L +LG TC +L Q L L +E L + G LT + +R
Sbjct: 339 IGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHI---SLGLGSTHLTRDGER 395
Query: 2045 KSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKL 2092
KS+S E + +E + ++L E+ + L++ ++KG+ +T+KL
Sbjct: 396 KSMSVERTFS-EINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKL 442
Score = 62.8 bits (151), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 40/125 (32%), Positives = 65/125 (52%), Gaps = 24/125 (19%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
I+HIDMD F+ +V +R +PEL+D+P+AV G+ S ++
Sbjct: 85 IVHIDMDAFYAAVEMRDNPELKDKPIAV----GSMS------------------MLSTSN 122
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
+ R +G+ M A + CP L IVP +F+ Y+ VS + ++A N A+SL +
Sbjct: 123 YHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSL--D 180
Query: 1736 ESFLN 1740
E++LN
Sbjct: 181 EAYLN 185
>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 = 70.1 bits (170), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 50/168 (29%), Positives = 78/168 (46%), Gaps = 10/168 (5%)
Query: 437 SQTKENMTLQKGSFGSTCVP-KLEDANDAGTKNSIDCTLILTEGDSAKSLAVSGLGVVGR 495
S T +KG+ +P KL D + ++ L L EGDSA A G R
Sbjct: 1 SNAAREXTRRKGALDLAGLPGKLADCQE---RDPALSELYLVEGDSAGGSAKQGRN---R 54
Query: 496 DKYGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMKTLRYGRLMI 555
+ PL+GK+LNV +A + L + E+ L+ LG + + LRY ++I
Sbjct: 55 KNQAILPLKGKILNVEKARFDKXLSSQEVATLITALGCGIGRDEYNPD---KLRYHSIII 111
Query: 556 MTDQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFITPIIKATKAREE 603
TD D DGSHI+ L++ F + P ++ + P+ K K ++E
Sbjct: 112 XTDADVDGSHIRTLLLTFFYRQXPEIVERGHVYIAQPPLYKVKKGKQE 159
>pdb|4F4Y|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
pdb|4F4Y|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
Length = 362
Score = 69.7 bits (169), Expect = 2e-11, Method: Composition-based stats.
Identities = 49/213 (23%), Positives = 101/213 (47%), Gaps = 5/213 (2%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 99 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 158
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEV 2018
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 159 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKIT 218
Query: 2019 GNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRL 2078
G L L K + E ++ + RKS+ + ++ + + +LK+ E ++
Sbjct: 219 GKAKALYLLKLAQDEYNEPIR-TRVRKSIGRYLTLPYNTRDVKVILPYLKKAINEAYNKV 277
Query: 2079 EEVKMKGKCITLKLMVRSAEAPREASKFLGHGV 2111
+ M+ IT+ ++ + + KF HG+
Sbjct: 278 NGIPMR---ITVIAIMEDLDILSKGKKF-KHGI 306
Score = 30.8 bits (68), Expect = 8.7, Method: Composition-based stats.
Identities = 33/151 (21%), Positives = 62/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V G + G A ++
Sbjct: 2 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKT--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 50 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 104
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 105 DEAYLDVTNKVEGNFENGIELARKIKQEILE 135
>pdb|3MR6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd
2bp Upstream Of The Active Site (Tt4)
pdb|3TQ1|A Chain A, Human Dna Polymerase Eta In Binary Complex With Dna
pdb|4EEY|A Chain A, Crystal Structure Of Human Dna Polymerase Eta In Ternary
Complex With A Cisplatin Dna Adduct
Length = 435
Score = 69.7 bits (169), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/153 (29%), Positives = 74/153 (48%), Gaps = 3/153 (1%)
Query: 1929 LRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVG 1988
+R I +ETG CS G NK+ A+LA KPN Q ++ + +P+ + +G
Sbjct: 203 MRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLG 262
Query: 1989 HSL-LFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSV 2047
L + LG + G+L + +LQ+ G KNG LY CRG + + K++
Sbjct: 263 GKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTI 322
Query: 2048 SAEVNY--GIRFQNNQEMETFLKQLAGEVEKRL 2078
N+ ++++ +L QLA E+E+RL
Sbjct: 323 GCSKNFPGKTALATREQVQWWLLQLAQELEERL 355
Score = 44.7 bits (104), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 17/85 (20%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
V+ +DMDCFFV V R +P L+++P AV ++ ++ + +
Sbjct: 11 VVALVDMDCFFVQVEQRQNPHLRNKPCAV-----------------VQYKSWKGGGIIAV 53
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNL 1699
R +G+ M+ A K CP+L
Sbjct: 54 SYEARAFGVTRSMWADDAKKLCPDL 78
>pdb|4DEZ|A Chain A, Structure Of Msdpo4
Length = 356
Score = 69.7 bits (169), Expect = 2e-11, Method: Composition-based stats.
Identities = 55/178 (30%), Positives = 86/178 (48%), Gaps = 5/178 (2%)
Query: 1922 PLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPL 1981
P++ A +R +A ETG +CS G NK +A++AT AKP G + LT M + P
Sbjct: 121 PVEVAERIRTVVAAETGLSCSVGISDNKQRAKVATGFAKPAGIYVLTEANWMTVMGDRPP 180
Query: 1982 SDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFE 2041
L GVG KL ++G T DL L G GL L +G D E++ E
Sbjct: 181 DALWGVGPKTTKKLAAMGITTVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSSE 240
Query: 2042 HQ-RKSVSAEVNYGIRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCIT-LKLMVRSA 2097
+S S V + +EM++ ++ LA + L E+ +G+ +T + + VR++
Sbjct: 241 PWVPRSRSHVVTFPQDLTERREMDSAVRDLALQT---LAEIVEQGRIVTRVAVTVRTS 295
Score = 55.5 bits (132), Expect = 4e-07, Method: Composition-based stats.
Identities = 37/131 (28%), Positives = 64/131 (48%), Gaps = 18/131 (13%)
Query: 1616 IMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRMG 1675
++H+D+D F SV +R P+L+ +PV V G G+ S+ R + +
Sbjct: 5 VLHVDLDQFLASVELRRRPDLRGQPVIVG-GSGDPSEPR--------------KVVTCAS 49
Query: 1676 LNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYTN 1735
RE+G+ GM + A ++CP+ +P D Y E S + L+ L +E +
Sbjct: 50 YEAREFGVHAGMPLRAAARRCPDATFLPSDPAAYDEASEQVMGLLRDLGHPLEVWGW--D 107
Query: 1736 ESFLNA-LPED 1745
E++L A LP++
Sbjct: 108 EAYLGADLPDE 118
>pdb|3MR2|A Chain A, Human Dna Polymerase Eta In Complex With Normal Dna And
Incoming Nucleotide (Nrm)
pdb|3MR3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The 3't
Of A Cpd In The Active Site (Tt1)
pdb|3MR5|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With A Cpd
1bp Upstream Of The Active Site (Tt3)
pdb|3SI8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex With The 5't
Of A Cpd In The Active Site (Tt2)
pdb|4DL2|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Cg
Template (Gg0a)
pdb|4DL3|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite Gg
Template (Gg0b).
pdb|4DL4|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The 3'g
Of Cisplatin Crosslinked Gs (Pt-Gg1).
pdb|4DL5|A Chain A, Human Dna Polymerase Eta Inserting Dcmpnpp Opposite The 5'g
Of Cisplatin Crosslinked Gs (Pt-Gg2).
pdb|4DL6|A Chain A, Human Dna Polymerase Eta Extending Primer Immediately After
Cisplatin Crosslink (Pt-Gg3).
pdb|4DL7|A Chain A, Human Dna Polymerase Eta Fails To Extend Primer 2 Nucleotide
After Cisplatin Crosslink (Pt-Gg4).
pdb|4ECQ|A Chain A, Human Dna Polymerase Eta- Dna Ternary Complex: At Crystal At
Ph6.8(K+ Mes) With 1 Ca2+ Ion
pdb|4ECR|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 40 Sec
pdb|4ECS|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 80 Sec
pdb|4ECT|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 140 Sec
pdb|4ECU|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 200 Sec
pdb|4ECV|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 230 Sec
pdb|4ECW|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 250 Sec
pdb|4ECX|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 7.0 For 300 Sec
pdb|4ECY|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ECZ|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.5 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED0|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 6.8 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED1|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.0 (Na+ Mes) With 1 Ca2+ Ion
pdb|4ED2|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.2 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED3|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: At Crystal
At Ph 7.5 (Na+ Hepes) With 1 Ca2+ Ion
pdb|4ED6|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The At Crystal At Ph 6.7 For 15 Hr, Sideway Translocation
pdb|4ED7|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Tg Crystal
At Ph 7.0 (K+ Mes) With 1 Ca2+ Ion
pdb|4ED8|A Chain A, Human Dna Polymerase Eta - Dna Ternary Complex: Reaction In
The Tg Crystal At Ph 7.0, Normal Translocation
Length = 435
Score = 69.7 bits (169), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 45/153 (29%), Positives = 74/153 (48%), Gaps = 3/153 (1%)
Query: 1929 LRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVG 1988
+R I +ETG CS G NK+ A+LA KPN Q ++ + +P+ + +G
Sbjct: 203 MRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLG 262
Query: 1989 HSL-LFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSV 2047
L + LG + G+L + +LQ+ G KNG LY CRG + + K++
Sbjct: 263 GKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTI 322
Query: 2048 SAEVNY--GIRFQNNQEMETFLKQLAGEVEKRL 2078
N+ ++++ +L QLA E+E+RL
Sbjct: 323 GCSKNFPGKTALATREQVQWWLLQLAQELEERL 355
Score = 44.7 bits (104), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 17/85 (20%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
V+ +DMDCFFV V R +P L+++P AV ++ ++ + +
Sbjct: 11 VVALVDMDCFFVQVEQRQNPHLRNKPCAV-----------------VQYKSWKGGGIIAV 53
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNL 1699
R +G+ M+ A K CP+L
Sbjct: 54 SYEARAFGVTRSMWADDAKKLCPDL 78
>pdb|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4
Length = 361
Score = 68.9 bits (167), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 35/130 (26%), Positives = 65/130 (50%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 99 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 158
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEV 2018
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 159 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKIT 218
Query: 2019 GNKNGLTLYK 2028
G L L K
Sbjct: 219 GKAKALYLLK 228
Score = 33.1 bits (74), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 33/151 (21%), Positives = 62/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V G + G A ++
Sbjct: 2 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKT--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 50 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 104
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 105 DEAYLDVTNKVEGNFENGIELARKIKQEILE 135
>pdb|4ID3|A Chain A, Crystal Structure Of The Brct Domain Of S. Cerevisiae Rev1
pdb|4ID3|B Chain B, Crystal Structure Of The Brct Domain Of S. Cerevisiae Rev1
Length = 92
Score = 67.4 bits (163), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 39/103 (37%), Positives = 56/103 (54%), Gaps = 14/103 (13%)
Query: 1339 SDSRGGIFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESSR--TTH 1396
S IF+ I++NGYTK P +L +++LHGG + HY SS+ TH
Sbjct: 1 SSQSSKIFKNCVIYINGYTK-----------PGRLQLHEMIVLHGGKFLHYLSSKKTVTH 49
Query: 1397 IIASNLPHTKIKKLKPGDKIIKPEWIVDSISAGKLLDHKKYLL 1439
I+ASNLP K + K++ P+WIVDS+ +LL + Y L
Sbjct: 50 IVASNLPLKKRIEF-ANYKVVSPDWIVDSVKEARLLPWQNYSL 91
>pdb|2M2I|A Chain A, Nmr Solution Structure Of Brct Domain Of Yeast Rev1
Length = 94
Score = 67.0 bits (162), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 39/103 (37%), Positives = 56/103 (54%), Gaps = 14/103 (13%)
Query: 1339 SDSRGGIFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESSR--TTH 1396
S IF+ I++NGYTK P +L +++LHGG + HY SS+ TH
Sbjct: 2 SSQSSKIFKNCVIYINGYTK-----------PGRLQLHEMIVLHGGKFLHYLSSKKTVTH 50
Query: 1397 IIASNLPHTKIKKLKPGDKIIKPEWIVDSISAGKLLDHKKYLL 1439
I+ASNLP K + K++ P+WIVDS+ +LL + Y L
Sbjct: 51 IVASNLPLKKRIEF-ANYKVVSPDWIVDSVKEARLLPWQNYSL 92
>pdb|3BQ0|A Chain A, Pre-insertion Binary Complex Of Dbh Dna Polymerase
pdb|3BQ1|A Chain A, Insertion Ternary Complex Of Dbh Dna Polymerase
pdb|3BQ2|A Chain A, Post-Insertion Binary Complex Of Dbh Dna Polymerase
pdb|4HYK|A Chain A, Dbh Ternary Complex (substrates Partially Disordered)
Length = 354
Score = 65.5 bits (158), Expect = 4e-10, Method: Composition-based stats.
Identities = 35/130 (26%), Positives = 65/130 (50%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 99 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 158
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEV 2018
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 159 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKIT 218
Query: 2019 GNKNGLTLYK 2028
G L L K
Sbjct: 219 GKAKALYLLK 228
Score = 30.8 bits (68), Expect = 9.6, Method: Composition-based stats.
Identities = 33/151 (21%), Positives = 62/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V G + G A ++
Sbjct: 2 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKT--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 50 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 104
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 105 DEAYLDVTNKVEGNFENGIELARKIKQEILE 135
>pdb|1K1Q|A Chain A, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1Q|B Chain B, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1S|A Chain A, Crystal Structure Of Dinb From Sulfolobus Solfataricus
Length = 354
Score = 65.1 bits (157), Expect = 5e-10, Method: Composition-based stats.
Identities = 35/130 (26%), Positives = 65/130 (50%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 99 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 158
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEV 2018
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 159 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKIT 218
Query: 2019 GNKNGLTLYK 2028
G L L K
Sbjct: 219 GKAKALYLLK 228
Score = 31.2 bits (69), Expect = 7.5, Method: Composition-based stats.
Identities = 33/151 (21%), Positives = 63/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V+ G + G A ++
Sbjct: 2 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVSVYSGRTKT--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 50 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 104
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 105 DEAYLDVTNKVEGNFENGIELARKIKQEILE 135
>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 = 63.5 bits (153), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 12/125 (9%)
Query: 474 LILTEGDSAKSLAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
L + EGDSA G RDK + P+RGK+LN E + ++L + E++++ +
Sbjct: 46 LFIVEGDSA-----GGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAI 100
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFI 591
G+ +D+ LRYG++ I+ D D DG HI L+ ++P L+ L +
Sbjct: 101 GVDPGS-----DDLSELRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAM 155
Query: 592 TPIIK 596
P+ +
Sbjct: 156 PPLFR 160
Score = 40.4 bits (93), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 640 LFKMNLHKVTSDSISMFIGRIEPEWYIPI-IPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
L L + TS+ F G ++ +P +P +L+NG GI G T IP HN RE+V
Sbjct: 399 LLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVK 458
Query: 699 NIKRMIR 705
+IR
Sbjct: 459 GTIALIR 465
>pdb|2XKJ|E Chain E, Crystal Structure Of Catalytic Core Of A. Baumannii Topo
Iv (Pare-Parc Fusion Truncate)
Length = 767
Score = 63.2 bits (152), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 37/125 (29%), Positives = 63/125 (50%), Gaps = 12/125 (9%)
Query: 474 LILTEGDSAKSLAVSGLGVVGRDK--YGVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
L + EGDSA G RDK + P+RGK+LN E + ++L + E++++ +
Sbjct: 46 LFIVEGDSA-----GGSAKQARDKNFQAIMPIRGKILNTWEVSSDEVLASQEVHDIAIAI 100
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHIKGLIINFIHHNWPTLLRLPFLEEFI 591
G+ +D+ LRYG++ I+ D D DG HI L+ ++P L+ L +
Sbjct: 101 GVDPGS-----DDLSELRYGKICILADADSDGLHIATLLCALFVKHFPALVEEGHLYVAM 155
Query: 592 TPIIK 596
P+ +
Sbjct: 156 PPLFR 160
Score = 40.4 bits (93), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 640 LFKMNLHKVTSDSISMFIGRIEPEWYIPI-IPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
L L + TS+ F G ++ +P +P +L+NG GI G T IP HN RE+V
Sbjct: 399 LLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVK 458
Query: 699 NIKRMIR 705
+IR
Sbjct: 459 GTIALIR 465
>pdb|1IM4|A Chain A, Crystal Structure Of A Dinb Homolog (Dbh) Lesion Bypass Dna
Polymerase Catalytic Fragment From Sulfolobus
Solfataricus
Length = 221
Score = 60.8 bits (146), Expect = 8e-09, Method: Composition-based stats.
Identities = 31/117 (26%), Positives = 61/117 (52%)
Query: 1899 VSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIAKETGCTCSTGFGSNKLQARLATKK 1958
+ S DE Y+D + ++ ++ A +++ I ++ T + G NK+ A++ K
Sbjct: 104 IEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADK 163
Query: 1959 AKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQ 2015
+KPNG + P + DF+ + + ++PG+G L +LN LG Q D+ + + L+
Sbjct: 164 SKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELE 220
Score = 30.8 bits (68), Expect = 9.7, Method: Composition-based stats.
Identities = 33/151 (21%), Positives = 62/151 (41%), Gaps = 30/151 (19%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D FF V +P+ + +P+ V G + G A ++
Sbjct: 7 IVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKT--SGAVATANYE---------- 54
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R+ G+ GM + A++ P+ VP Y+ S + NL+ IE S+
Sbjct: 55 ---ARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASI-- 109
Query: 1735 NESFLNA-------------LPEDIRQEVLD 1752
+E++L+ L I+QE+L+
Sbjct: 110 DEAYLDVTNKVEGNFENGIELARKIKQEILE 140
>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 = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/95 (36%), Positives = 53/95 (55%), Gaps = 11/95 (11%)
Query: 474 LILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
L + EGDSA A SG RD + PLRGK++NV +A ++L+N E+ ++ L
Sbjct: 14 LYVVEGDSAGGSAKSG-----RDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITAL 68
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHI 566
G ++ D+ LRY ++++M D D DG HI
Sbjct: 69 GTGIHDEF----DIGKLRYHKIVLMADADVDGQHI 99
>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 = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/95 (36%), Positives = 53/95 (55%), Gaps = 11/95 (11%)
Query: 474 LILTEGDSAKSLAVSGLGVVGRDKY--GVFPLRGKLLNVREATHKQILENAEINNLVKIL 531
L + EGDSA A SG RD + PLRGK++NV +A ++L+N E+ ++ L
Sbjct: 22 LYVVEGDSAGGSAKSG-----RDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITAL 76
Query: 532 GLQYSKKYTTVEDMKTLRYGRLMIMTDQDQDGSHI 566
G ++ D+ LRY ++++M D D DG HI
Sbjct: 77 GTGIHDEF----DIGKLRYHKIVLMADADVDGQHI 107
>pdb|3H40|A Chain A, Binary Complex Of Human Dna Polymerase Iota With Template UT
Length = 389
Score = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 63/128 (49%), Gaps = 1/128 (0%)
Query: 1924 QFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNI-PLS 1982
Q A+ +RE + + G T G SNKL A+L + KPN Q L P+ + ++ +
Sbjct: 153 QIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIK 212
Query: 1983 DLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEH 2042
++PG+G+ L +LG + DLQ S K L+ E+G + K GED+ +
Sbjct: 213 EIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSG 272
Query: 2043 QRKSVSAE 2050
+S S E
Sbjct: 273 PPQSFSEE 280
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 62/140 (44%), Gaps = 23/140 (16%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
VI+H+D+DCF+ V + +PEL+D+P+ V Y T N
Sbjct: 4 VIVHVDLDCFYAQVEMISNPELKDKPLGVQQK-------------------YLVVTCN-- 42
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTLNIEAVSLY 1733
R+ G+ M V A +KCP L +V D Y+E+SY + L+ + +E +
Sbjct: 43 -YEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFD 101
Query: 1734 TNESFLNALPEDIRQEVLDD 1753
N L + E Q++ D
Sbjct: 102 ENFVDLTEMVEKRLQQLQSD 121
>pdb|2DPI|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|2DPJ|A Chain A, Structure Of Hpoli With Dna And Dttp
pdb|2FLN|A Chain A, Binary Complex Of Catalytic Core Of Human Dna Polymerase
Iota With Dna (Template A)
pdb|2FLP|A Chain A, Binary Complex Of The Catalytic Core Of Human Dna Polymerase
Iota With Dna (Template G)
pdb|2FLL|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Dna And
Dttp
pdb|3EPG|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine
pdb|3EPI|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine And Incoming Ttp
pdb|3G6V|A Chain A, Dna Synthesis Across An Abasic Lesion By Human Dna
Polymerase-Iota
pdb|3G6X|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dgtp With An
Abasic Site At The Templating Position
pdb|3G6Y|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dttp With An
Abasic Site At The Templating Position
pdb|3GV7|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna And
Incoming Dttp
pdb|3GV8|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna And
Incoming Dgtp
pdb|3NGD|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3OSN|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3Q8P|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite
8-Oxo-Guanine
pdb|3Q8Q|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite
8-Oxo-Guanine
pdb|3Q8R|B Chain B, Human Dna Polymerase Iota Incorporating Dgtp Opposite
8-Oxo-Guanine
pdb|3Q8S|B Chain B, Human Dna Polymerase Iota Incorporating Dttp Opposite
8-Oxo-Guanine
pdb|4EBC|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBD|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBE|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4FS1|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dttp By
Human Polymerase Iota
pdb|4FS2|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dctp By
Human Polymerase Iota
pdb|4EYH|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
pdb|4EYI|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
Length = 420
Score = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 63/128 (49%), Gaps = 1/128 (0%)
Query: 1924 QFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNI-PLS 1982
Q A+ +RE + + G T G SNKL A+L + KPN Q L P+ + ++ +
Sbjct: 178 QIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIK 237
Query: 1983 DLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEH 2042
++PG+G+ L +LG + DLQ S K L+ E+G + K GED+ +
Sbjct: 238 EIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSG 297
Query: 2043 QRKSVSAE 2050
+S S E
Sbjct: 298 PPQSFSEE 305
Score = 53.5 bits (127), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 66/148 (44%), Gaps = 23/148 (15%)
Query: 1607 PSPSEPEPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIY 1666
P+P+ VI+H+D+DCF+ V + +PEL+D+P+ V Y
Sbjct: 21 PTPNASSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQK-------------------Y 61
Query: 1667 RQRTMNRMGLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTL 1725
T N R+ G+ M V A +KCP L +V D Y+E+SY + L+ +
Sbjct: 62 LVVTCN---YEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSP 118
Query: 1726 NIEAVSLYTNESFLNALPEDIRQEVLDD 1753
+E + N L + E Q++ D
Sbjct: 119 VVERLGFDENFVDLTEMVEKRLQQLQSD 146
>pdb|1T3N|A Chain A, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1T3N|B Chain B, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1ZET|A Chain A, X-Ray Data Do Not Support Hoogsteen Base-Pairing During
Replication By Human Polymerase Iota
Length = 388
Score = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 63/128 (49%), Gaps = 1/128 (0%)
Query: 1924 QFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNI-PLS 1982
Q A+ +RE + + G T G SNKL A+L + KPN Q L P+ + ++ +
Sbjct: 152 QIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIK 211
Query: 1983 DLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEH 2042
++PG+G+ L +LG + DLQ S K L+ E+G + K GED+ +
Sbjct: 212 EIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSG 271
Query: 2043 QRKSVSAE 2050
+S S E
Sbjct: 272 PPQSFSEE 279
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 62/140 (44%), Gaps = 23/140 (16%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
VI+H+D+DCF+ V + +PEL+D+P+ V Y T N
Sbjct: 3 VIVHVDLDCFYAQVEMISNPELKDKPLGVQQK-------------------YLVVTCN-- 41
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTLNIEAVSLY 1733
R+ G+ M V A +KCP L +V D Y+E+SY + L+ + +E +
Sbjct: 42 -YEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFD 100
Query: 1734 TNESFLNALPEDIRQEVLDD 1753
N L + E Q++ D
Sbjct: 101 ENFVDLTEMVEKRLQQLQSD 120
>pdb|2ALZ|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|3H4B|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Datp
pdb|3H4D|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Dgtp
Length = 390
Score = 60.5 bits (145), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 63/128 (49%), Gaps = 1/128 (0%)
Query: 1924 QFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNI-PLS 1982
Q A+ +RE + + G T G SNKL A+L + KPN Q L P+ + ++ +
Sbjct: 154 QIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIK 213
Query: 1983 DLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEH 2042
++PG+G+ L +LG + DLQ S K L+ E+G + K GED+ +
Sbjct: 214 EIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSG 273
Query: 2043 QRKSVSAE 2050
+S S E
Sbjct: 274 PPQSFSEE 281
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 39/140 (27%), Positives = 62/140 (44%), Gaps = 23/140 (16%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
VI+H+D+DCF+ V + +PEL+D+P+ V Y T N
Sbjct: 5 VIVHVDLDCFYAQVEMISNPELKDKPLGVQQK-------------------YLVVTCN-- 43
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTLNIEAVSLY 1733
R+ G+ M V A +KCP L +V D Y+E+SY + L+ + +E +
Sbjct: 44 -YEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFD 102
Query: 1734 TNESFLNALPEDIRQEVLDD 1753
N L + E Q++ D
Sbjct: 103 ENFVDLTEMVEKRLQQLQSD 122
>pdb|4F4Z|B Chain B, Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh
pdb|4F4Z|A Chain A, Y-family Dna Polymerase Chimera Dpo4-dpo4-dbh
Length = 361
Score = 58.2 bits (139), Expect = 6e-08, Method: Composition-based stats.
Identities = 51/237 (21%), Positives = 106/237 (44%), Gaps = 10/237 (4%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ +
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRYLTLP 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEEVKMKGKCITLKLMVRSAEAPREASKFLGHGV 2111
++ + + +LK+ E ++ + M+ IT+ ++ + + KF HG+
Sbjct: 253 YNTRDVKVILPYLKKAINEAYNKVNGIPMR---ITVIAIMEDLDILSKGKKF-KHGI 305
Score = 38.1 bits (87), Expect = 0.054, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|1JX4|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A Ternary
Complex With Dna Substrates And An Incoming Nucleotide
Length = 352
Score = 57.8 bits (138), Expect = 7e-08, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIXNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADXAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGXIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTXK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.4 bits (85), Expect = 0.090, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPXRKEVYQQVSSRIXNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|3GV5|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna And
Incoming Ddadp
pdb|3GV5|D Chain D, Human Dna Polymerase Iota In Complex With T Template Dna And
Incoming Ddadp
Length = 420
Score = 57.8 bits (138), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 40/128 (31%), Positives = 61/128 (47%), Gaps = 1/128 (0%)
Query: 1924 QFASYLRETIAKETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNI-PLS 1982
Q A+ RE + G T G SNKL A+L + KPN Q L P+ + ++ +
Sbjct: 178 QIAAEXREAXYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIK 237
Query: 1983 DLPGVGHSLLFKLNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEH 2042
++PG+G+ L +LG + DLQ S K L+ E+G + K GED+ +
Sbjct: 238 EIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSG 297
Query: 2043 QRKSVSAE 2050
+S S E
Sbjct: 298 PPQSFSEE 305
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 61/135 (45%), Gaps = 25/135 (18%)
Query: 1607 PSPSEPEPVIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIY 1666
P+P+ VI+H+D+DCF+ V +PEL+D+P+ V Y
Sbjct: 21 PTPNASSRVIVHVDLDCFYAQVEXISNPELKDKPLGVQQK-------------------Y 61
Query: 1667 RQRTMNRMGLNTREYGLGNGMFVGHALKKCPNLKIV-PYDFEGYKEVSYCLYNLIASLTL 1725
T N R+ G+ V A +KCP L +V D Y+E SY + L+ +
Sbjct: 62 LVVTCN---YEARKLGVKKLXNVRDAKEKCPQLVLVNGEDLTRYREXSYKVTELLEEFSP 118
Query: 1726 NIEAVSLYTNESFLN 1740
+E + +E+F++
Sbjct: 119 VVERLGF--DENFVD 131
>pdb|2AGO|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection
And Pyrophosphorolysis
pdb|2AGP|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection
And Pyrophosphorolysis
pdb|2AGP|B Chain B, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection
And Pyrophosphorolysis
pdb|2AGQ|A Chain A, Fidelity Of Dpo4: Effect Of Metal Ions, Nucleotide Selection
And Pyrophosphorolysis
pdb|3T5H|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Cxg-3' Vs
13-Mer) With Dpo4 And Incoming Ddgt
pdb|3T5J|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Txg-3' Vs
13-Mer) With Dpo4 And Incoming Ddtp
pdb|3T5K|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Txg-3' Vs
14-Mer) With Dpo4 And Incoming Ddtp
pdb|3T5L|A Chain A, Ternary Complex Of Hne Adduct Modified Dna (5'-Cxg-3' Vs
14-Mer) With Dpo4 And Incoming Ddgt
Length = 341
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.076, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|3PVX|A Chain A, Binary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv
pdb|3PW0|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv And Incoming Datp
pdb|3PW2|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-Fapy) With Dna Polymerase Iv And Incoming Dttp
pdb|3PW4|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Datp
pdb|3PW5|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dttp
pdb|3PW7|A Chain A, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dctp
pdb|3PW7|E Chain E, Ternary Complex Of Aflatoxin B1 Adduct Modified Dna
(Afb1-N7-Gua) With Dna Polymerase Iv And Incoming Dctp
Length = 347
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.076, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|3GII|A Chain A, Dpo4 Extension Ternary Complex With Disordered A Opposite An
Oxog In Anti Conformation
pdb|3GIJ|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Syn)-A(Anti) And
Oxog(Anti)- A(Syn) Pairs
pdb|3GIJ|B Chain B, Dpo4 Extension Ternary Complex With Oxog(Syn)-A(Anti) And
Oxog(Anti)- A(Syn) Pairs
pdb|3GIK|A Chain A, Dpo4 Extension Ternary Complex With The Oxog(Anti)-C(Anti)
Pair
pdb|3GIL|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Anti)-T(Anti) Pair
pdb|3GIL|B Chain B, Dpo4 Extension Ternary Complex With Oxog(Anti)-T(Anti) Pair
pdb|3GIM|A Chain A, Dpo4 Extension Ternary Complex With Oxog(Anti)-G(Syn) Pair
pdb|3KHG|A Chain A, Dpo4 Extension Ternary Complex With Misinserted A Opposite
The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHG|B Chain B, Dpo4 Extension Ternary Complex With Misinserted A Opposite
The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHH|A Chain A, Dpo4 Extension Ternary Complex With A C Base Opposite The 2-
Aminofluorene-Guanine [af]g Lesion
pdb|3KHH|B Chain B, Dpo4 Extension Ternary Complex With A C Base Opposite The 2-
Aminofluorene-Guanine [af]g Lesion
pdb|3KHL|A Chain A, Dpo4 Post-Extension Ternary Complex With Misinserted A
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHL|B Chain B, Dpo4 Post-Extension Ternary Complex With Misinserted A
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHR|A Chain A, Dpo4 Post-Extension Ternary Complex With The Correct C
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3KHR|B Chain B, Dpo4 Post-Extension Ternary Complex With The Correct C
Opposite The 2- Aminofluorene-Guanine [af]g Lesion
pdb|3RAQ|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 1-Methylguanine (Mg1) Lesion
pdb|3RAQ|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 1-Methylguanine (Mg1) Lesion
pdb|3RAX|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RAX|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB0|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB0|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB3|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 1-Methylguanine (M1g) Lesion
pdb|3RB4|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB4|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer G
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB6|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RB6|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer A
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBD|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBD|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer C
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBE|A Chain A, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 3-Methylcytosine (M3c) Lesion
pdb|3RBE|B Chain B, Dpo4 Extension Ternary Complex With 3'-Terminal Primer T
Base Opposite The 3-Methylcytosine (M3c) Lesion
Length = 341
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.076, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|2UVV|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
pdb|2UVW|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
Length = 358
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.076, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|2IMW|P Chain P, Mechanism Of Template-Independent Nucleotide Incorporation
Catalyzed By A Template-Dependent Dna Polymerase
Length = 348
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.076, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|3PR4|A Chain A, Dpo4 Y12a Mutant Incorporating Dadp Opposite Template Dt
pdb|3PR5|B Chain B, Dpo4 Y12a Mutant Incorporating Adp Opposite Template Dt
Length = 341
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 35.4 bits (80), Expect = 0.34, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 68/155 (43%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFAAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|3V6K|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6K|J Chain J, Replication Of N2,3-Ethenoguanine By Dna Polymerases
Length = 347
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 84 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 138
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 139 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 198
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 199 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 257
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 258 RNSRNLEEIKPYLFRAIEESYYKLDK 283
Score = 37.7 bits (86), Expect = 0.082, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 7 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 54
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 55 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 109
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 110 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 144
>pdb|2W9B|A Chain A, Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna
pdb|2W9C|A Chain A, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dttp
Length = 358
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKARYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.080, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|2RDI|A Chain A, Snapshots Of A Y-family Dna Polymerase In Replication: Dpo4
In Apo And Binary/ternary Complex Forms
Length = 342
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.082, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|3QZ7|A Chain A, T-3 Ternary Complex Of Dpo4
pdb|3QZ8|A Chain A, Tt-4 Ternary Complex Of Dpo4
Length = 360
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.075, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|2BQ3|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus
Dpo4. Analysis And Crystal Structures Of Multiple Base-
Pair Substitution And Frameshift Products With The Adduct
1,N2-Ethenoguanine
pdb|2BQR|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus
Dpo4. Analysis And Crystal Structures Of Multiple Base-
Pair Substitution And Frameshift Products With The Adduct
1,N2-Ethenoguanine
pdb|2BQU|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus
Dpo4. Analysis And Crystal Structures Of Multiple Base-
Pair Substitution And Frameshift Products With The Adduct
1,N2-Ethenoguanine
pdb|2BR0|A Chain A, Dna Adduct Bypass Polymerization By Sulfolobus Solfataricus
Dpo4. Analysis And Crystal Structures Of Multiple Base-
Pair Substitution And Frameshift Products With The Adduct
1,N2-Ethenoguanine
pdb|2C22|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C28|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2D|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2E|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2C2R|A Chain A, Efficient And High Fidelity Incorporation Of Dctp Opposite
7,8-Dihydro-8-Oxodeoxyguanosine By Sulfolobus
Solfataricus Dna Polymerase Dpo4
pdb|2J6S|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-Methylguanine Modified Dna, And Datp.
pdb|2J6T|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-Methylguanine Modified Dna, And Datp.
pdb|2J6U|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, O6-methylguanine Modified Dna, And Dgtp.
pdb|2JEF|A Chain A, The Molecular Basis Of Selectivity Of Nucleotide
Triphosphate Incorporation Opposite O6-benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-state
And Pre-steady-state And X-ray Crystallography Of Correct
And Incorrect Pairing
pdb|2JEG|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-Benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-State
And Pre-Steady-State Kinetics And X-Ray Crystallography
Of Correct And Incorrect Pairing
pdb|2JEI|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-state
And Pre-steady-state Kinetics And X-ray Crystallography
Of Correct And Incorrect Pairing
pdb|2JEJ|A Chain A, The Molecular Basis Of Selectivity Of Nucleoside
Triphosphate Incorporation Opposite O6-Benzylguanine By
Sulfolobus Solfataricus Dna Polymerase Iv: Steady-State
And Pre-Steady-State Kinetics And X-Ray Crystallography
Of Correct And Incorrect Pairing
pdb|2V9W|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2V9W|B Chain B, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA2|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA2|B Chain B, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2VA3|A Chain A, Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna
Duplex Containing A Hydrophobic Thymine Isostere 2,4-
Difluorotoluene Nucleotide In The Template Strand
pdb|2W8K|A Chain A, Y-Family Dna Polymerase Dpo4 Bypassing N2-Naphthyl-Guanine
Adduct In Syn Orientation
pdb|2W8L|A Chain A, Y-Family Dna Polymerase Dpo4 Bypassing N2-Naphthyl-Guanine
Adduct In Anti Orientation
pdb|2W9A|A Chain A, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dgtp
pdb|2W9B|B Chain B, Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna
pdb|2W9C|B Chain B, Ternary Complex Of Dpo4 Bound To N2,N2-Dimethyl-
Deoxyguanosine Modified Dna With Incoming Dttp
pdb|2V4Q|A Chain A, Post-Insertion Complex Of The Y-Family Dna Polymerase Dpo4
With M1dg Containing Template Dna
pdb|2V4R|A Chain A, Non-Productive Complex Of The Y-Family Dna Polymerase Dpo4
With Dgtp Skipping The M1dg Adduct To Pair With The Next
Template Cytosine
pdb|2XC9|A Chain A, Binary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase And 1,N2-Ethenoguanine Modified Dna, Magnesium
Form
pdb|2XCA|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dgtp - Magnesium Form
pdb|2XCP|A Chain A, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dctp - Magnesium Form
pdb|2XCP|B Chain B, Ternary Complex Of Sulfolobus Solfataricus Dpo4 Dna
Polymerase, 7,8-Dihydro-8-Oxodeoxyguanine Modified Dna
And Dctp - Magnesium Form
pdb|4GC6|A Chain A, Crystal Structure Of Dpo4 In Complex With N-mc-damp Opposite
Dt
Length = 358
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.079, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|1JXL|A Chain A, Crystal Structure Of A Y-Family Dna Polymerase In A Ternary
Complex With Dna Substrates And An Incoming Nucleotide
pdb|1N48|A Chain A, Y-Family Dna Polymerase Dpo4 In Complex With Dna Containing
Abasic Lesion
pdb|1N56|A Chain A, Y-Family Dna Polymerase Dpo4 In Complex With Dna Containing
Abasic Lesion
pdb|1N56|B Chain B, Y-Family Dna Polymerase Dpo4 In Complex With Dna Containing
Abasic Lesion
pdb|1RYR|A Chain A, Replication Of A Cis-Syn Thymine Dimer At Atomic Resolution
pdb|1RYS|A Chain A, Replication Of A Cis-Syn Thymine Dimer At Atomic Resolution
pdb|1RYS|B Chain B, Replication Of A Cis-Syn Thymine Dimer At Atomic Resolution
pdb|1S0M|A Chain A, Crystal Structure Of A Benzo[a]pyrene Diol Epoxide Adduct In
A Ternary Complex With A Dna Polymerase
pdb|1S0M|B Chain B, Crystal Structure Of A Benzo[a]pyrene Diol Epoxide Adduct In
A Ternary Complex With A Dna Polymerase
pdb|1S0N|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S0O|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S0O|B Chain B, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S10|A Chain A, Snapshots Of Replication Through An Abasic Lesion:
Structural Basis For Base Substitution And Frameshift
pdb|1S97|A Chain A, Dpo4 With Gt Mismatch
pdb|1S97|B Chain B, Dpo4 With Gt Mismatch
pdb|1S97|C Chain C, Dpo4 With Gt Mismatch
pdb|1S97|D Chain D, Dpo4 With Gt Mismatch
pdb|1S9F|A Chain A, Dpo With At Matched
pdb|1S9F|B Chain B, Dpo With At Matched
pdb|1S9F|C Chain C, Dpo With At Matched
pdb|1S9F|D Chain D, Dpo With At Matched
pdb|2IA6|A Chain A, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2IA6|B Chain B, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2IBK|A Chain A, Bypass Of Major Benzopyrene-Dg Adduct By Y-Family Dna
Polymerase With Unique Structural Gap
pdb|2RDJ|A Chain A, Snapshots Of A Y-family Dna Polymerase In Replication: Dpo4
In Apo And Binary/ternary Complex Forms
pdb|2RDJ|B Chain B, Snapshots Of A Y-family Dna Polymerase In Replication: Dpo4
In Apo And Binary/ternary Complex Forms
pdb|2R8G|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2-Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|2R8H|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2- Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|2R8I|A Chain A, Selectivity Of Nucleoside Triphosphate Incorporation
Opposite 1,N2-Propanodeoxyguanosine (Pdg) By The
Sulfolobus Solfataricus Dna Polymerase Dpo4 Polymerase
pdb|3FDS|A Chain A, Structural Insight Into Recruitment Of Translesion Dna
Polymerase Dpo4 To Sliding Clamp Pcna
pdb|3M9M|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing The
Major Cisplatin Lesion
pdb|3M9N|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing The
Major Cisplatin Lesion
pdb|3M9O|B Chain B, Crystal Structure Of Dpo4 In Complex With Dna Containing The
Major Cisplatin Lesion
Length = 352
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 79 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 133
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 134 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 193
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 194 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 252
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 253 RNSRNLEEIKPYLFRAIEESYYKLDK 278
Score = 37.7 bits (86), Expect = 0.079, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 2 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 49
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 50 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 104
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 105 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 139
>pdb|4GC7|A Chain A, Crystal Structure Of Dpo4 In Complex With S-mc-dadp Opposite
Dt
pdb|4GC7|B Chain B, Crystal Structure Of Dpo4 In Complex With S-mc-dadp Opposite
Dt
Length = 359
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 86 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 140
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 141 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 200
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 201 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 259
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 260 RNSRNLEEIKPYLFRAIEESYYKLDK 285
Score = 37.7 bits (86), Expect = 0.079, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 9 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 56
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 57 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 111
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 112 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 146
>pdb|3V6H|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6H|B Chain B, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6J|A Chain A, Replication Of N2,3-Ethenoguanine By Dna Polymerases
pdb|3V6J|J Chain J, Replication Of N2,3-Ethenoguanine By Dna Polymerases
Length = 348
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.083, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|2ASD|A Chain A, Oxog-Modified Insertion Ternary Complex
pdb|2ASD|B Chain B, Oxog-Modified Insertion Ternary Complex
pdb|2ASJ|A Chain A, Oxog-Modified Preinsertion Binary Complex
pdb|2ASJ|B Chain B, Oxog-Modified Preinsertion Binary Complex
pdb|2ASL|A Chain A, Oxog-Modified Postinsertion Binary Complex
pdb|2ASL|B Chain B, Oxog-Modified Postinsertion Binary Complex
pdb|2ATL|A Chain A, Unmodified Insertion Ternary Complex
pdb|2ATL|B Chain B, Unmodified Insertion Ternary Complex
pdb|2AU0|A Chain A, Unmodified Preinsertion Binary Complex
pdb|2AU0|B Chain B, Unmodified Preinsertion Binary Complex
Length = 360
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 87 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 141
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 142 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 201
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 202 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 260
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 261 RNSRNLEEIKPYLFRAIEESYYKLDK 286
Score = 37.7 bits (86), Expect = 0.079, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 10 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 57
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 58 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 112
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 113 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 147
>pdb|2UVR|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
pdb|2UVU|A Chain A, Crystal Structures Of Mutant Dpo4 Dna Polymerases With 8-
Oxog Containing Dna Template-Primer Constructs
Length = 358
Score = 57.0 bits (136), Expect = 1e-07, Method: Composition-based stats.
Identities = 47/206 (22%), Positives = 94/206 (45%), Gaps = 6/206 (2%)
Query: 1875 EAYQEMLSCVQSAMKHKPSSESKIVSAVSCDEMYVDCSQLLQELSLTPLQFASYLRETIA 1934
E YQ++ S + + ++ S+ + S DE Y+D S +++ ++ I
Sbjct: 85 EVYQQVSSRIMNLLREY----SEKIEIASIDEAYLDISDKVRDYR-EAYNLGLEIKNKIL 139
Query: 1935 KETGCTCSTGFGSNKLQARLATKKAKPNGQFHLTPQIISDFMLNIPLSDLPGVGHSLLFK 1994
++ T + G NK+ A++A AKPNG + + + + + ++D+PG+G+ K
Sbjct: 140 EKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEK 199
Query: 1995 LNSLGAQTCGDLQNISLKRLQNEVGNKNGLTLYKHCRGEDDKELTFEHQRKSVSAEVNYG 2054
L LG D +I +L+ +G L R E ++ + RKS+ V
Sbjct: 200 LKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIR-TRVRKSIGRIVTMK 258
Query: 2055 IRFQNNQEMETFLKQLAGEVEKRLEE 2080
+N +E++ +L + E +L++
Sbjct: 259 RNSRNLEEIKPYLFRAIEESYYKLDK 284
Score = 37.7 bits (86), Expect = 0.079, Method: Composition-based stats.
Identities = 37/155 (23%), Positives = 69/155 (44%), Gaps = 19/155 (12%)
Query: 1615 VIMHIDMDCFFVSVGIRHHPELQDEPVAVAHGKGNSSKVREGVDRQAEFDIYRQRTMNRM 1674
+++ +D D F+ V +P L+ +PV V G G A ++
Sbjct: 8 IVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFED--SGAVATANYE---------- 55
Query: 1675 GLNTREYGLGNGMFVGHALKKCPNLKIVPYDFEGYKEVSYCLYNLIASLTLNIEAVSLYT 1734
R++G+ G+ + A K PN +P E Y++VS + NL+ + IE S+
Sbjct: 56 ---ARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASI-- 110
Query: 1735 NESFLNALPE--DIRQEVLDDLSRQQSVLSREQNT 1767
+E++L+ + D R+ L + +L +E+ T
Sbjct: 111 DEAYLDISDKVRDYREAYNLGLEIKNKILEKEKIT 145
>pdb|3VU7|H Chain H, Crystal Structure Of Rev1-rev7-rev3 Ternary Complex
Length = 124
Score = 51.6 bits (122), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCE-SQPEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
L+ V +++T+LREW+ S P DI +Y ++L+EE+ L + +++++++R +
Sbjct: 32 LAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQ 91
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHKPSSESKI 1898
+ +VW A+ +L VQ ++ S K+
Sbjct: 92 QSVESVWNMAFDFILDNVQVVLQQTYGSTLKV 123
>pdb|2LSK|A Chain A, C-Terminal Domain Of Human Rev1 In Complex With
Dna-Polymerase H (Eta)
pdb|2LSY|A Chain A, Structure Of The C-Terminal Domain From Human Rev1
Length = 95
Score = 51.6 bits (122), Expect = 5e-06, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 52/92 (56%), Gaps = 1/92 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCE-SQPEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
L+ V +++T+LREW+ S P DI +Y ++L+EE+ L + +++++++R +
Sbjct: 3 LAGAVEFNDVKTLLREWITTISDPMEEDILQVVKYCTDLIEEKDLEKLDLVIKYMKRLMQ 62
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHKPSSESKI 1898
+ +VW A+ +L VQ ++ S K+
Sbjct: 63 QSVESVWNMAFDFILDNVQVVLQQTYGSTLKV 94
>pdb|2LSG|A Chain A, Solution Structure Of The Mouse Rev1 C-Terminal Domain
Length = 104
Score = 50.8 bits (120), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 51/92 (55%), Gaps = 1/92 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCE-SQPEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
L+ V +++T+L+EW+ S P DI Y ++L+EE+ L + +++++++R +
Sbjct: 12 LAGAVEFSDVKTLLKEWITTISDPMEEDILQVVRYCTDLIEEKDLEKLDLVIKYMKRLMQ 71
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHKPSSESKI 1898
+ +VW A+ +L VQ ++ S K+
Sbjct: 72 QSVESVWNMAFDFILDNVQVVLQQTYGSTLKV 103
>pdb|2LSJ|A Chain A, Solution Structure Of The Mouse Rev1 Ctd In Complex With The
Rev1- Interacting Region (Rir)of Pol Kappa
Length = 119
Score = 50.4 bits (119), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 51/92 (55%), Gaps = 1/92 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCE-SQPEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
L+ V +++T+L+EW+ S P DI Y ++L+EE+ L + +++++++R +
Sbjct: 27 LAGAVEFSDVKTLLKEWITTISDPMEEDILQVVRYCTDLIEEKDLEKLDLVIKYMKRLMQ 86
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHKPSSESKI 1898
+ +VW A+ +L VQ ++ S K+
Sbjct: 87 QSVESVWNMAFDFILDNVQVVLQQTYGSTLKV 118
>pdb|4FJO|A Chain A, Structure Of The Rev1 Ctd-Rev37-Pol Kappa Rir Complex
Length = 97
Score = 49.7 bits (117), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 51/92 (55%), Gaps = 1/92 (1%)
Query: 1808 LSSNVSLQEMRTMLREWMCE-SQPEPSDIEMFSEYLSNLVEERHLNPIVILLRFLRRHVG 1866
L+ V +++T+L+EW+ S P DI Y ++L+EE+ L + +++++++R +
Sbjct: 5 LAGAVEFSDVKTLLKEWITTISDPMEEDILQVVRYCTDLIEEKDLEKLDLVIKYMKRLMQ 64
Query: 1867 KKESTVWAEAYQEMLSCVQSAMKHKPSSESKI 1898
+ +VW A+ +L VQ ++ S K+
Sbjct: 65 QSVESVWNMAFDFILDNVQVVLQQTYGSTLKV 96
>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 = 47.8 bits (112), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 61/252 (24%), Positives = 98/252 (38%), Gaps = 63/252 (25%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNACDNKQR 101
LE + RP YIGS + GL+ + EI+ NA D +
Sbjct: 3 LEAVRKRPGMYIGSTDS-----------------------RGLHHLVYEIVDNAVD-EAL 38
Query: 102 DPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDEEDKV 161
N I +T+ Q+ N+I V ++G+G+P H +PT+
Sbjct: 39 SGYGNEINVTI-QKDNSICVADSGRGMPTGMHASG---IPTV------------------ 76
Query: 162 TGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVET--SCSEYKKSFK 219
+IF L + K +GG +G GA + N S V EY + F+
Sbjct: 77 -----EVIFTVLHAGGKFGQGGYKTSGGLHGVGASVVNALSKWLEVHIVRDGVEYMERFE 131
Query: 220 QVWK--DNMSKVTSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDAAAS 277
K + K+ + ++G T +TF PD T F T+ +++ R ++A
Sbjct: 132 DGGKPVGTLKKIGKTKKRNG-----TSVTFLPDDTIFSTTNFS---YEILAERLRESAFL 183
Query: 278 TKDVKVFLNGEK 289
K VK+ L E+
Sbjct: 184 LKGVKITLTDER 195
>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 = 46.6 bits (109), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 61/249 (24%), Positives = 104/249 (41%), Gaps = 64/249 (25%)
Query: 42 LEHILLRPDTYIGSVEPITETMWLMNRETNHMERREITYVPGLYKIFDEILVNACDNKQR 101
L+ + RP YIGS + GL+ + EI+ NA D +
Sbjct: 22 LDAVRKRPGMYIGSTDG-----------------------AGLHHLVWEIVDNAVD-EAL 57
Query: 102 DPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKMFVPTMIFGHLLTSSNYNDEEDKV 161
+ I +T+N++ +++V ++G+G+P H M +PT+
Sbjct: 58 SGFGDRIDVTINKD-GSLTVQDHGRGMPTGMHA---MGIPTV------------------ 95
Query: 162 TGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIFSSKFVVETS--CSEYKKSFK 219
+IF L + K +GG +G G+ + N SS VE + + YK+ F+
Sbjct: 96 -----EVIFTILHAGGKFGQGGYKTSGGLHGVGSSVVNALSSWLEVEITRDGAVYKQRFE 150
Query: 220 QVWK--DNMSKV-TSPEIKSGSKDDFTKITFTPDLTKFKMTSLDKDMVDLITRRAYDAAA 276
K + K+ T+ + K+G TK+TF PD T F T + I+ R ++A
Sbjct: 151 NGGKPVTTLKKIGTALKSKTG-----TKVTFMPDATIFSTTDFK---YNTISERLNESAF 202
Query: 277 STKDVKVFL 285
K+V + L
Sbjct: 203 LLKNVTLSL 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 = 43.9 bits (102), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 66/286 (23%), Positives = 122/286 (42%), Gaps = 53/286 (18%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 34 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 90
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 91 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 125
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKFKMT 257
S K +E K +Q+++ + + VT K+G T + F P L F T
Sbjct: 126 SQK--LELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF--T 176
Query: 258 SLDKDMVDLITRRAYDAAASTKDVKVFLNGEKLPVKNFQDY---VKLYTDRQDEDGDPV- 313
++ + +++ +R + + V + L ++ ++ Y +K + + +++ P+
Sbjct: 177 NVTEFEYEILAKRLRELSFLDSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIH 236
Query: 314 -KIIY---ENVNPRWEVAIAPSDRGFQQ--VSFVNSIATTKGGRHV 353
I Y E EVA+ +D GFQ+ F N+I GG H+
Sbjct: 237 PNIFYFSTEKDGIGVEVALQWND-GFQENIYCFTNNIPQRDGGTHL 281
>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 = 41.2 bits (95), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 40/177 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 22 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 78
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 79 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 113
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKF 254
S K E K +Q+++ + + VT K+G T + F P L F
Sbjct: 114 SQKL--ELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF 163
>pdb|3G7E|A Chain A, Crystal Structure Of E. Coli Gyrase B Co-Complexed With
Inhibitor
Length = 203
Score = 40.8 bits (94), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 40/177 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 21 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 77
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 78 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 112
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKF 254
S K E K +Q+++ + + VT K+G T + F P L F
Sbjct: 113 SQKL--ELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF 162
>pdb|1KZN|A Chain A, Crystal Structure Of E. Coli 24kda Domain In Complex With
Clorobiocin
Length = 205
Score = 40.8 bits (94), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 40/177 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 21 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 77
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 78 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 112
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKF 254
S K E K +Q+++ + + VT K+G T + F P L F
Sbjct: 113 SQKL--ELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF 162
>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 = 40.4 bits (93), Expect = 0.011, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 649 TSDSISMFIGRIEPEWYIPI-IPMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
T D I + GR++ +P P +L NG+ GI G T IP HN RE+ D +
Sbjct: 119 TVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAV 171
>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 = 40.4 bits (93), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 40/177 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 34 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 90
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 91 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 125
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKF 254
S K E K +Q+++ + + VT K+G T + F P L F
Sbjct: 126 SQKL--ELVIQHEGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF 175
>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 = 40.4 bits (93), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 72/177 (40%), Gaps = 40/177 (22%)
Query: 83 GLYKIFDEILVNACDNKQRDPKMNCIKITVN-QETNTISVWNNGKGIPVVEHKDEKMFVP 141
GL+ + E++ NA D +C +I V N++SV ++G+GIP H +E +
Sbjct: 35 GLHHMVFEVVDNAIDEALAG---HCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAA 91
Query: 142 TMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLCNIF 201
+I L ++D ++Y KV+GG +G G + N
Sbjct: 92 EVIMTVLHAGGKFDD--------------------NSY-----KVSGGLHGVGVSVVNAL 126
Query: 202 SSKFVVETSCSEYKKSFKQVWKDNMSK----VTSPEIKSGSKDDFTKITFTPDLTKF 254
S K E K +Q+++ + + VT K+G T + F P L F
Sbjct: 127 SQKL--ELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTG-----TMVRFWPSLETF 176
>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 = 40.4 bits (93), Expect = 0.012, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 649 TSDSISMFIGRIEPEWYIPI-IPMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
T D I + GR++ +P P +L NG+ GI G T IP HN RE+ D +
Sbjct: 149 TVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAV 201
>pdb|1ZVU|A Chain A, Structure Of The Full-Length E. Coli Parc Subunit
Length = 716
Score = 39.7 bits (91), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 640 LFKMNLHKVTSDSISMFIGRI-EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIV 697
L L + T+D + F G + EP+ +P +L+NG GI G T IP HN RE+
Sbjct: 105 LLLSELGQGTADWVPNFDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVA 163
>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 = 39.7 bits (91), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 24/44 (54%)
Query: 661 EPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMI 704
EP P +LVNG+ GI G+ T IP HN E++D MI
Sbjct: 151 EPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMI 194
>pdb|1AB4|A Chain A, 59kda Fragment Of Gyrase A From E. Coli
Length = 493
Score = 39.7 bits (91), Expect = 0.020, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 644 NLHKVTSDSISMFIGRIE-PEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKR 702
+L K T D + + G + P+ IP +LVNG+ GI G T IP HN E+++
Sbjct: 108 DLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLA 167
Query: 703 MIRGED 708
I ED
Sbjct: 168 YIDDED 173
>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 = 39.7 bits (91), Expect = 0.022, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 644 NLHKVTSDSISMFIGRIE-PEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKR 702
+L K T D + + G + P+ IP +LVNG+ GI G T IP HN E+++
Sbjct: 136 DLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLA 195
Query: 703 MIRGED 708
I ED
Sbjct: 196 YIDDED 201
>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 = 38.9 bits (89), Expect = 0.036, Method: Composition-based stats.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 644 NLHKVTSDSISMFIGRIE-PEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKR 702
+L K T D + + G + P+ IP +LVNG+ GI G T IP HN E+++
Sbjct: 137 DLEKETVDFVDNYDGTEKIPDVXPTKIPNLLVNGSSGIAVGXATNIPPHNLTEVINGCLA 196
Query: 703 MIRGED 708
I ED
Sbjct: 197 YIDDED 202
>pdb|3LNU|A Chain A, Crystal Structure Of Pare Subunit
pdb|3LPS|A Chain A, Crystal Structure Of Pare
Length = 408
Score = 38.5 bits (88), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 62/300 (20%), Positives = 115/300 (38%), Gaps = 65/300 (21%)
Query: 82 PGLY-------KIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHK 134
PG+Y + E++ N+ D I++T+ ++ + V ++G+G+PV H
Sbjct: 42 PGMYTDTARPNHLAQEVIDNSVDEALAG-HAKQIEVTLYKD-GSCEVSDDGRGMPVDIHP 99
Query: 135 DEKMFVPTMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYG 194
E+K+ GV +I L +N+ +GG +G G
Sbjct: 100 -----------------------EEKIPGV--ELILTRLHAGGKFNNRNYTFSGGLHGVG 134
Query: 195 AKLCNIFSSK--FVVETSCSEYKKSFKQVWKDNMSKVTSPEIKSGSKDDFTKITFTP--- 249
+ N S+K ++ SE++ F+ N + G K+ T++ F
Sbjct: 135 VSVVNALSTKVELFIKREGSEHRMEFRD---GNAASKLEVVGTVGKKNTGTRLRFWADPK 191
Query: 250 --DLTKFKMTSL------DKDMVDLITRRAYDAAASTKDVKVFLNGEKLPVKNFQDYVKL 301
D KF + +L + +T + +D A +D F NG +DY+K
Sbjct: 192 YFDTPKFNVRALRHLLRAKAVLCPGLTVKLHDEATGEQDSWYFENG-------LRDYLK- 243
Query: 302 YTDRQDEDGDPVKIIYENVNP-----RWEVAIAPSDRGFQQVSFVNSIATTKGGRHVDAV 356
+ + + P + ++ W P Q+ S+VN I T + G HV+ +
Sbjct: 244 -GEMAEHEMLPADLFVGSLKKDTEIVDWAAGWVPEGELVQE-SYVNLIPTAQHGTHVNGL 301
>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 = 38.1 bits (87), Expect = 0.064, Method: Composition-based stats.
Identities = 50/186 (26%), Positives = 75/186 (40%), Gaps = 36/186 (19%)
Query: 79 TYVPGLYKIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHKDEKM 138
T V G + +F EIL NA D I + +N E +++V +NG+GIPV
Sbjct: 28 TGVEGYHHLFKEILDNAVDEALAGYATE-ILVRLN-EDGSLTVEDNGRGIPV-------- 77
Query: 139 FVPTMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYGAKLC 198
+ EE K V I+ L + + KV+GG +G GA +
Sbjct: 78 --------------DLMPEEGKPAVEV---IYNTLHSGGKFEQGAYKVSGGLHGVGASVV 120
Query: 199 NIFSSKFVVET--SCSEYKKSFKQVWKDNMSKVT--SPEIKSGSKDDFTKITFTPDLTKF 254
N S VVE ++ +F + +V +P K+G T++TF PD F
Sbjct: 121 NALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTG-----TRVTFKPDPEIF 175
Query: 255 KMTSLD 260
D
Sbjct: 176 GNLRFD 181
>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 = 37.7 bits (86), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 19/31 (61%)
Query: 670 PMVLVNGAEGIGTGWMTKIPNHNPREIVDNI 700
P +LVNGA GI G T IP H EI+D +
Sbjct: 165 PNLLVNGAAGIAVGMATNIPPHQLGEIIDGV 195
>pdb|2INR|A Chain A, Crystal Structure Of A 59 Kda Fragment Of Topoisomerase Iv
Subunit A (Grla) From Staphylococcus Aureus
Length = 514
Score = 36.2 bits (82), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 660 IEPEWYIPIIPMVLVNGAEGIGTGWMTKIPNHNPREIVDNIKRMIRGEDPLPMKPWYKNF 719
+EP P +LVNG+ GI G+ T IP HN E++ + I D + + K
Sbjct: 174 LEPMVLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVIQATLKYIDNPD-ITVNQLMKYI 232
Query: 720 KG 721
KG
Sbjct: 233 KG 234
>pdb|3LPX|A Chain A, Crystal Structure Of Gyra
pdb|3LPX|B Chain B, Crystal Structure Of Gyra
Length = 500
Score = 35.0 bits (79), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 669 IPMVLVNGAEGIGTGWMTKIPNHNPREIVD 698
+P +LVNG GI G T IP HN E+++
Sbjct: 133 VPNLLVNGTSGIAVGMATNIPPHNLTEVIN 162
>pdb|3EF1|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 442
Score = 33.9 bits (76), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 1395 THIIASNLPHTKIKK-LKPGD-KIIKPEWIVDSISAGKLLDHKKYLLY 1440
TH+IA+ + K+KK + G+ K++K W+ +S+S K L YLLY
Sbjct: 395 THLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQWKRLPESDYLLY 442
>pdb|3EF0|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 372
Score = 33.9 bits (76), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 1395 THIIASNLPHTKIKK-LKPGD-KIIKPEWIVDSISAGKLLDHKKYLLY 1440
TH+IA+ + K+KK + G+ K++K W+ +S+S K L YLLY
Sbjct: 325 THLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQWKRLPESDYLLY 372
>pdb|2D8M|A Chain A, Solution Structure Of The First Brct Domain Of Dna-Repair
Protein Xrcc1
Length = 129
Score = 33.9 bits (76), Expect = 1.1, Method: Composition-based stats.
Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 14/105 (13%)
Query: 1337 ANSDSRGGIFQGVAIFVNGYTKHCMMLDAYYIVPSAEELKALMMLHGGIYHHYESSRTTH 1396
A + G I QGV + ++G+ P EL+ + G Y + +TH
Sbjct: 14 AGPEELGKILQGVVVVLSGFQN-----------PFRSELRDKALELGAKYRPDWTRDSTH 62
Query: 1397 IIAS--NLPHTKIKKLKPGDKIIKPEWIVDSISAGKLLDHKKYLL 1439
+I + N P + L G +I++ EW++D + L ++YL+
Sbjct: 63 LICAFANTPKYS-QVLGLGGRIVRKEWVLDCHRMRRRLPSQRYLM 106
>pdb|3SQD|A Chain A, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
pdb|3SQD|B Chain B, Crystal Structure Of Human Ptip Brct56-Gamma H2ax Complex
Length = 219
Score = 33.1 bits (74), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 1369 VPSAEELKALMMLHGGIYHHYESSRTTHIIASNLPHTK--IKKLKPGDKIIKPEWIVDSI 1426
V + +K L +L G + + + TH+IAS + T + + I+ PEW+ +
Sbjct: 27 VQVQQYIKKLYILGGEVAE--SAQKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECF 84
Query: 1427 SAGKLLDHKKYLL 1439
K +D + Y+L
Sbjct: 85 RCQKFIDEQNYIL 97
>pdb|2B5O|A Chain A, Ferredoxin-nadp Reductase
pdb|2B5O|B Chain B, Ferredoxin-nadp Reductase
Length = 402
Score = 32.7 bits (73), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 33/132 (25%), Positives = 59/132 (44%), Gaps = 5/132 (3%)
Query: 430 IVNP-TFDSQTKENMTLQKGSFGSTCVPKLEDANDAGTKNSIDCTLILTEGDSAKSLAVS 488
IV+P T D+ N+ K F C+ E ++ G+ T ++EGD + L
Sbjct: 102 IVHPKTTDTSVPVNIYRPKTPFLGKCIENYELVDEGGSGTVRHVTFDISEGD-LRYLEGQ 160
Query: 489 GLGVV--GRDKYGVFPLRGKLLNVREATHKQILENAEINNLVKILGLQYSKKYTTVEDMK 546
+G++ G DK G P + +L ++ H + +N ++ V+ L Q + TV +
Sbjct: 161 SIGIIPPGEDKNGK-PHKLRLYSIASTRHGDMEDNKTVSLCVRQLEYQDPESGETVYGVC 219
Query: 547 TLRYGRLMIMTD 558
+ L + TD
Sbjct: 220 STYLCNLPVGTD 231
>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 = 32.7 bits (73), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 70/289 (24%), Positives = 118/289 (40%), Gaps = 48/289 (16%)
Query: 82 PGLY-------KIFDEILVNACDNKQRDPKMNCIKITVNQETNTISVWNNGKGIPVVEHK 134
PG+Y + EI+ N+ D + + I IT+ E N+I V ++G+G+PV H
Sbjct: 22 PGMYTNIENPNHLIQEIIDNSVD-EVLAGFASKINITL-YEDNSIEVADDGRGMPVDIHP 79
Query: 135 DEKMFVPTMIFGHLLTSSNYNDEEDKVTGVVPTMIFGHLLTSSNYNDEEDKVTGGRNGYG 194
+ KM +I L + G ++ NY +GG +G G
Sbjct: 80 EHKMSGIELIMTKLHS--------------------GGKFSNKNYTH-----SGGLHGVG 114
Query: 195 AKLCNIFSSKFVVETSCSEYKKSFKQVWKDNMSKVTSPEI--KSGSKDDFTKITFTPDLT 252
+ N S++ +E + V++D K EI G K+ TKI F P+
Sbjct: 115 VSVVNALSTR--LEAEIKRDGNVYHIVFEDGF-KTKDLEIIDNVGKKNTGTKIRFWPNKK 171
Query: 253 KFKMTSLD-KDMVDLITRRAYDAAASTKDVKVFLNGEKLPVKNFQDYVKLYTDRQDED-- 309
F ++ K + +L+ +A A T + EKL +F+ +K Y D + E
Sbjct: 172 YFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKL-TWHFETGLKGYLDHKLEAET 230
Query: 310 --GDPVKII-YENVNPRWEVAIAPSDRGFQQV--SFVNSIATTKGGRHV 353
+P I + N + + + + + S+VN I T + G HV
Sbjct: 231 LPAEPFIIDNFSNGDSYLDAVFCWCEDPSESIKNSYVNLIPTPQDGTHV 279
>pdb|3II6|X Chain X, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv.
pdb|3II6|Y Chain Y, Structure Of Human Xrcc4 In Complex With The Tandem Brct
Domains Of Dna Ligaseiv
Length = 263
Score = 31.2 bits (69), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 44/100 (44%), Gaps = 17/100 (17%)
Query: 1356 YTKHCMMLDAYYIVPSAE--------ELKAL-MMLHGGIYHHYESSRTTHIIASNLPHTK 1406
+ +H + LD+Y ++ +KAL + HG + +H+I H++
Sbjct: 165 FRRHTVYLDSYAVINDLSTKNEGTRLAIKALELRFHGAKVVSCLAEGVSHVIIGE-DHSR 223
Query: 1407 I-------KKLKPGDKIIKPEWIVDSISAGKLLDHKKYLL 1439
+ + K KI+K W+ DSI +L + +YL+
Sbjct: 224 VADFKAFRRTFKRKFKILKESWVTDSIDKCELQEENQYLI 263
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 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 63,061,757
Number of Sequences: 62578
Number of extensions: 2561256
Number of successful extensions: 4831
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 81
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 4535
Number of HSP's gapped (non-prelim): 185
length of query: 2307
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2193
effective length of database: 7,839,445
effective search space: 17191902885
effective search space used: 17191902885
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 60 (27.7 bits)