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= psy17743
(618 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1A35|A Chain A, Human Topoisomerase IDNA COMPLEX
pdb|1A36|A Chain A, Topoisomerase IDNA COMPLEX
Length = 591
Score = 686 bits (1769), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 328/493 (66%), Positives = 383/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 70 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 129
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 130 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 189
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 190 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 249
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 250 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 309
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 310 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 369
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 370 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 429
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 430 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 489
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN+
Sbjct: 490 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNF 549
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 550 LDPRITVAWCKKW 562
Score = 188 bits (477), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 236 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 295
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 296 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 345
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 568 KIYNKTQREKFAWAIDMADEDYEF 591
>pdb|1R49|A Chain A, Human Topoisomerase I (Topo70) Double Mutant K532rY723F
Length = 592
Score = 684 bits (1766), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 327/493 (66%), Positives = 383/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 71 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 130
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 131 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 190
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 191 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 250
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 251 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 310
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLG+DSIRYYN+VPV
Sbjct: 311 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGRDSIRYYNKVPV 370
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 371 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 430
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 431 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 490
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN+
Sbjct: 491 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNF 550
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 551 LDPRITVAWCKKW 563
Score = 188 bits (477), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 237 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 296
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 297 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 346
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 569 KIYNKTQREKFAWAIDMADEDYEF 592
>pdb|1LPQ|A Chain A, Human Dna Topoisomerase I (70 Kda) In Non-Covalent Complex
With A 22 Base Pair Dna Duplex Containing An 8-Oxog
Lesion
Length = 564
Score = 684 bits (1765), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 328/493 (66%), Positives = 383/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 43 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 102
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 103 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 162
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 163 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 222
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 223 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 282
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 283 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 342
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 343 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 402
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 403 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 462
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN+
Sbjct: 463 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNF 522
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 523 LDPRITVAWCKKW 535
Score = 187 bits (475), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 209 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 268
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 269 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 318
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 541 KIYNKTQREKFAWAIDMADEDYEF 564
>pdb|1K4S|A Chain A, Human Dna Topoisomerase I In Covalent Complex With A 22
Base Pair Dna Duplex
pdb|1K4T|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Poison Topotecan And Covalent Complex With A 22 Base
Pair Dna Duplex
pdb|1SC7|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indenoisoquinoline Mj-Ii-38 And Covalent Complex With A
22 Base Pair Dna Duplex
pdb|1T8I|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Poison Camptothecin And Covalent Complex With A 22 Base
Pair Dna Duplex
pdb|1TL8|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indenoisoquinoline Ai-Iii-52 And Covalent Complex With A
22 Base Pair Dna Duplex
Length = 592
Score = 683 bits (1763), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 328/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 71 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 130
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 131 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 190
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 191 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 250
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 251 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 310
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 311 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 370
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 371 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 430
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 431 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 490
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN
Sbjct: 491 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNX 550
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 551 LDPRITVAWCKKW 563
Score = 187 bits (476), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 237 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 296
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 297 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 346
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 569 KIYNKTQREKFAWAIDMADEDYEF 592
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 591
Score = 683 bits (1763), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 328/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 70 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 129
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 130 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 189
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 190 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 249
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 250 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 309
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 310 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 369
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 370 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 429
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 430 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 489
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN
Sbjct: 490 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNX 549
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 550 LDPRITVAWCKKW 562
Score = 187 bits (476), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 236 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 295
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 296 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 345
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 568 KIYNKTQREKFAWAIDMADEDYEF 591
>pdb|1NH3|A Chain A, Human Topoisomerase I Ara-C Complex
Length = 563
Score = 682 bits (1761), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 328/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 42 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 101
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 102 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 161
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 162 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 221
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 222 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 281
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 282 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 341
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 342 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 401
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 402 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 461
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN
Sbjct: 462 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNX 521
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 522 LDPRITVAWCKKW 534
Score = 187 bits (475), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 208 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 267
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 268 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 317
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 540 KIYNKTQREKFAWAIDMADEDYEF 563
>pdb|1SEU|A Chain A, Human Dna Topoisomerase I (70 Kda) In Complex With The
Indolocarbazole Sa315f And Covalent Complex With A 22
Base Pair Dna Duplex
Length = 592
Score = 681 bits (1758), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 327/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 71 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 130
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 131 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 190
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 191 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 250
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 251 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 310
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 311 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 370
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 371 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 430
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 431 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 490
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKL+
Sbjct: 491 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLSX 550
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 551 LDPRITVAWCKKW 563
Score = 188 bits (477), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 237 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 296
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 297 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 346
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 569 KIYNKTQREKFAWAIDMADEDYEF 592
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 681 bits (1758), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 327/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 42 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 101
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 102 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 161
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 162 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 221
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 222 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 281
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 282 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 341
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 342 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 401
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQ + PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 402 ELTAPDENIPAKILSYNRANRAVAILCNHQIAPPKTFEKSMMNLQTKIDAKKEQLADARR 461
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN+
Sbjct: 462 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNF 521
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 522 LDPRITVAWCKKW 534
Score = 187 bits (475), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 208 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 267
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 268 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 317
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 540 KIYNKTQREKFAWAIDMADEDYEF 563
>pdb|1RRJ|A Chain A, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 681 bits (1756), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 327/493 (66%), Positives = 382/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 44 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 103
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGLFRG
Sbjct: 104 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRG 163
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 164 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 223
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 224 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 283
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 284 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 343
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 344 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 403
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQR+ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 404 ELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARR 463
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKL+
Sbjct: 464 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLSX 523
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 524 LDPRITVAWCKKW 536
Score = 187 bits (475), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 210 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 269
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 270 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 319
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 542 KIYNKTQREKFAWAIDMADEDYEF 565
>pdb|1RR8|C Chain C, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 677 bits (1748), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 326/493 (66%), Positives = 381/493 (77%), Gaps = 7/493 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK MKLS AEE+ATF+A+M++HEYTTKE F NF KDWRK MT +E+ +IT+LSKCDF
Sbjct: 44 GKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFT 103
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
+M YF ++ + KEYG C +D HKE+I NF+IEPPGL RG
Sbjct: 104 QMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLSRG 163
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG HPKMG LKRR+ EDIIINCSKD+KVP PPPGHKWKEVRHDN+VTWL SWTEN+QG
Sbjct: 164 RGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGS 223
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKEM++RQRAVALYFID
Sbjct: 224 IKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFID 283
Query: 245 KLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPV 303
KLALRAGNEK+E + ADTVGCCSLRVEHI LH E DG+ YVV FDFLGKDSIRYYN+VPV
Sbjct: 284 KLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPV 343
Query: 304 EKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLN 363
EKRVFKNLQLF+ENK+ DDLFDRLNT +LNKHL +LMEGLTAKVFRTYNASITLQQQL
Sbjct: 344 EKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLK 403
Query: 364 ELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAER 423
EL PD + KIL+YNRANRAVA+LCNHQ++ PK+ +KSM NL+ KI K++Q+ DA R
Sbjct: 404 ELTAPDENIPAKILSYNRANRAVAILCNHQQAPPKTFEKSMMNLQTKIDAKKEQLADARR 463
Query: 424 ALKDAK------KAGESKAMTDKKKTALGRXXXXXXXXXXXXTDKEENKTIALGTSKLNY 477
LK AK K ++K + + KK A+ R TD+EENK IALGTSKLN
Sbjct: 464 DLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNX 523
Query: 478 LDPRISVTWLASW 490
LDPRI+V W W
Sbjct: 524 LDPRITVAWCKKW 536
Score = 187 bits (475), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 86/110 (78%), Positives = 98/110 (89%), Gaps = 1/110 (0%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWL SWTEN+QG +KYIMLNPSS++KGEKDWQKYETAR+L K ++KIR Y+ DWKSKE
Sbjct: 210 VTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKE 269
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDE-DQADTVGCCSLRVEHIQLHEEKD 592
M++RQRAVALYFIDKLALRAGNEK+E + ADTVGCCSLRVEHI LH E D
Sbjct: 270 MKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELD 319
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/24 (75%), Positives = 19/24 (79%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KIYNKTQR KF WAIDMA D+ F
Sbjct: 542 KIYNKTQREKFAWAIDMADEDYEF 565
>pdb|2B9S|A Chain A, Crystal Structure Of Heterodimeric L. Donovani
Topoisomerase I-Vanadate-Dna Complex
Length = 432
Score = 398 bits (1023), Expect = e-111, Method: Compositional matrix adjust.
Identities = 196/392 (50%), Positives = 259/392 (66%), Gaps = 7/392 (1%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
G+E K++ + EE+AT +A M EH+Y E F NF + WR+ + +K + I L CDF
Sbjct: 47 GREFKMTPEEEEVATMFAVMKEHDYYRMEVFRRNFFESWRE-ILDKRQHPIRRLELCDFE 105
Query: 65 KMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
++ + + + A + Y C DG +E++ NFR+EPPGLFRG
Sbjct: 106 PIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYRYCVWDGRREQVANFRVEPPGLFRG 165
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RG+HP MGKLK RVQ EDI IN + ++VP PP GHKW V+HD+ VTWLA W ++V G
Sbjct: 166 RGKHPLMGKLKVRVQPEDITINIGETAEVPVPPAGHKWAAVQHDHTVTWLAMWRDSVAGN 225
Query: 185 VKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFID 244
+KY+ML PSS +KG+ D K+E ARKL ++ IR +Y D+KS ++ + QRAVA+YFID
Sbjct: 226 MKYVMLAPSSSVKGQSDMVKFEKARKLKDKVDDIRASYMEDFKSNDLHVAQRAVAMYFID 285
Query: 245 KLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVE 304
+LALR GNEK ED+ADTVGCCSLRVEHIQL + +V FDFLGKDSIRY N+V V
Sbjct: 286 RLALRVGNEKGEDEADTVGCCSLRVEHIQLMPDN-----IVRFDFLGKDSIRYQNDVAVL 340
Query: 305 KRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLNE 364
V+ LQ F K D+FD+LN + LN HL M+GL+AKVFRTYNASITL + E
Sbjct: 341 PEVYALLQRFTRRKSPGMDIFDQLNPTQLNDHLKSFMDGLSAKVFRTYNASITLDRWFKE 400
Query: 365 -LMDPDFSEAEKILAYNRANRAVAVLCNHQRS 395
+DP +S A+K+ +N+AN VA+LCNHQ+S
Sbjct: 401 KPVDPKWSTADKLAYFNKANTEVAILCNHQKS 432
Score = 144 bits (362), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 65/105 (61%), Positives = 83/105 (79%)
Query: 483 SVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSK 542
+VTWLA W ++V G +KY+ML PSS +KG+ D K+E ARKL ++ IR +Y D+KS
Sbjct: 211 TVTWLAMWRDSVAGNMKYVMLAPSSSVKGQSDMVKFEKARKLKDKVDDIRASYMEDFKSN 270
Query: 543 EMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL 587
++ + QRAVA+YFID+LALR GNEK ED+ADTVGCCSLRVEHIQL
Sbjct: 271 DLHVAQRAVAMYFIDRLALRVGNEKGEDEADTVGCCSLRVEHIQL 315
>pdb|1OIS|A Chain A, Yeast Dna Topoisomerase I, N-Terminal Fragment
Length = 223
Score = 176 bits (445), Expect = 4e-44, Method: Compositional matrix adjust.
Identities = 81/190 (42%), Positives = 109/190 (57%), Gaps = 4/190 (2%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAV----ITDLSK 60
GK + L AEE+A F+A ++E ++ F NF D+ + + E + I + S+
Sbjct: 32 GKPVDLPPQAEEVAGFFAALLESDHAKNPVFQKNFFNDFLQVLKESGGPLNGIEIKEFSR 91
Query: 61 CDFRKMHAYFVQKSXXXXXXXXXXXXXXXXXXXAITKEYGVCTIDGHKEKIGNFRIEPPG 120
CDF KM YF + ++Y C +DG +E++GNF++EPP
Sbjct: 92 CDFTKMFDYFQLQKEQKKQLTSQEKKQIRLEREKFEEDYKFCELDGRREQVGNFKVEPPD 151
Query: 121 LFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTEN 180
LFRGRG HPK GKLKRRV EDI++N SKD+ VPP P GHKW E+RHDN V WLA W EN
Sbjct: 152 LFRGRGAHPKTGKLKRRVNPEDIVLNLSKDAPVPPAPEGHKWGEIRHDNTVQWLAMWREN 211
Query: 181 VQGQVKYIML 190
+ KY+ L
Sbjct: 212 IFNSFKYVRL 221
>pdb|2B9S|B Chain B, Crystal Structure Of Heterodimeric L. Donovani
Topoisomerase I-Vanadate-Dna Complex
Length = 62
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 22/25 (88%)
Query: 462 KEENKTIALGTSKLNYLDPRISVTW 486
K++NK ++LGTSK+NY+DPRI +W
Sbjct: 7 KDDNKAVSLGTSKINYIDPRIICSW 31
>pdb|3M4A|A Chain A, Crystal Structure Of A Bacterial Topoisomerase Ib In
Complex With Dna Reveals A Secondary Dna Binding Site
Length = 346
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 47/218 (21%), Positives = 93/218 (42%), Gaps = 22/218 (10%)
Query: 157 PPGHKWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSIN 216
PP ++ V D + L ++ + G+++Y + K WQ+ + A ++
Sbjct: 48 PPAYQDVYVSPDAE-NELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLT---RFAGALP 103
Query: 217 KIRENYQADWKSKEMRIRQ-RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLH 275
++ AD ++ + R+ A+ + R G++ Q T G +LR H+ +
Sbjct: 104 TLKVATTADLRASGLPPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVV- 162
Query: 276 EEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQ---------LFVENKKGSDDLFD 326
DG V F F GK + + ++ + N+Q LF G +
Sbjct: 163 ---DGN--TVTFRFKGKHGVSQHKAT-SDRTLAANMQKLLDLPGPWLFQTVDAGGGER-R 215
Query: 327 RLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLNE 364
R++++ LN +L E++ TAK FRT+ ++ + L +
Sbjct: 216 RIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQ 253
>pdb|2F4Q|A Chain A, Crystal Structure Of Deinococcus Radiodurans Topoisomerase
Ib
Length = 346
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 47/218 (21%), Positives = 92/218 (42%), Gaps = 22/218 (10%)
Query: 157 PPGHKWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSIN 216
PP ++ V D + L ++ + G+++Y + K WQ+ + A ++
Sbjct: 48 PPAYQDVYVSPDAE-NELQAFGRDAAGRLQYRYHPDFVQAGALKKWQRLT---RFAGALP 103
Query: 217 KIRENYQADWKSKEMRIRQ-RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLH 275
++ AD ++ + R+ A+ + R G++ Q T G +LR H+ +
Sbjct: 104 TLKVATTADLRASGLPPRKVXALXTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHVVV- 162
Query: 276 EEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQ---------LFVENKKGSDDLFD 326
DG V F F GK + + ++ + N Q LF G +
Sbjct: 163 ---DGN--TVTFRFKGKHGVSQHKAT-SDRTLAANXQKLLDLPGPWLFQTVDAGGGER-R 215
Query: 327 RLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLNE 364
R++++ LN +L E++ TAK FRT+ ++ + L +
Sbjct: 216 RIHSTELNAYLREVIGPFTAKDFRTWGGTLLAAEYLAQ 253
>pdb|2H7G|X Chain X, Structure Of Variola Topoisomerase Non-Covalently Bound To
Dna
pdb|3IGC|A Chain A, Smallpox Virus Topoisomerase-Dna Transition State
Length = 314
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 58/124 (46%), Gaps = 8/124 (6%)
Query: 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDS 294
Q AV + +R G K + +TVG +L+ +HI++ +K + F+GKD
Sbjct: 116 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDK------IVIKFVGKDK 169
Query: 295 IRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNA 354
+ + V R++K L ++ + LF++L+ + + + + G+ K RTY
Sbjct: 170 VSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQF--GIRIKDLRTYGV 227
Query: 355 SITL 358
+ T
Sbjct: 228 NYTF 231
>pdb|2H7F|X Chain X, Structure Of Variola Topoisomerase Covalently Bound To Dna
Length = 314
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 30/124 (24%), Positives = 58/124 (46%), Gaps = 8/124 (6%)
Query: 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDS 294
Q AV + +R G K + +TVG +L+ +HI++ +K + F+GKD
Sbjct: 116 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDK------IVIKFVGKDK 169
Query: 295 IRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNA 354
+ + V R++K L ++ + LF++L+ + + + + G+ K RTY
Sbjct: 170 VSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQF--GIRIKDLRTYGV 227
Query: 355 SITL 358
+ T
Sbjct: 228 NYTF 231
>pdb|1A41|A Chain A, Type 1-Topoisomerase Catalytic Fragment From Vaccinia
Virus
Length = 234
Score = 36.2 bits (82), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 29/124 (23%), Positives = 58/124 (46%), Gaps = 8/124 (6%)
Query: 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDS 294
Q AV + +R G K + +TVG +L+ +HI++ ++ + F+GKD
Sbjct: 36 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIEISPDE------IVIKFVGKDK 89
Query: 295 IRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNA 354
+ + V R++K L ++ + LF++L+ + + + + G+ K RTY
Sbjct: 90 VSHEFVVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYECIKQF--GIRIKDLRTYGV 147
Query: 355 SITL 358
+ T
Sbjct: 148 NYTF 151
>pdb|1NO4|A Chain A, Crystal Structure Of The Pre-Assembly Scaffolding Protein
Gp7 From The Double-Stranded Dna Bacteriophage Phi29
pdb|1NO4|B Chain B, Crystal Structure Of The Pre-Assembly Scaffolding Protein
Gp7 From The Double-Stranded Dna Bacteriophage Phi29
pdb|1NO4|C Chain C, Crystal Structure Of The Pre-Assembly Scaffolding Protein
Gp7 From The Double-Stranded Dna Bacteriophage Phi29
pdb|1NO4|D Chain D, Crystal Structure Of The Pre-Assembly Scaffolding Protein
Gp7 From The Double-Stranded Dna Bacteriophage Phi29
pdb|1NOH|A Chain A, The Structure Of Bacteriophage Phi29 Scaffolding Protein
Gp7 After Prohead Assembly
pdb|1NOH|B Chain B, The Structure Of Bacteriophage Phi29 Scaffolding Protein
Gp7 After Prohead Assembly
pdb|1NOH|C Chain C, The Structure Of Bacteriophage Phi29 Scaffolding Protein
Gp7 After Prohead Assembly
pdb|1NOH|D Chain D, The Structure Of Bacteriophage Phi29 Scaffolding Protein
Gp7 After Prohead Assembly
Length = 97
Score = 28.9 bits (63), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 362 LNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKI-SNKR--KQV 418
LN+L+DP+ +++E+ A + + + KSH+K + I SN + +Q+
Sbjct: 11 LNKLLDPELAQSERTEALQQLRVNYGSFVSEYNDLTKSHEKLAAEKDDLIVSNSKLFRQI 70
Query: 419 KDAERALKDAKKAGESKAMT 438
E+ +D KKA S+ +T
Sbjct: 71 GLTEKQEEDHKKADISETIT 90
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 0.130 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,561,740
Number of Sequences: 62578
Number of extensions: 692796
Number of successful extensions: 1768
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1671
Number of HSP's gapped (non-prelim): 51
length of query: 618
length of database: 14,973,337
effective HSP length: 105
effective length of query: 513
effective length of database: 8,402,647
effective search space: 4310557911
effective search space used: 4310557911
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)