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= 002260
(946 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 = 479 bits (1234), Expect = e-135, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 342/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 42 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 101
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 102 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 161
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 162 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSP 221
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 222 P-PGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 279
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 280 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 339
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 340 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 399
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 400 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 459
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 460 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 514
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N+LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 515 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQ 574
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 575 REKFAWAIDMADEDYEF 591
>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 = 479 bits (1234), Expect = e-135, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 342/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 15 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 74
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 75 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 134
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 135 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 193
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 194 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 252
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 253 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 312
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 313 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 372
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 373 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 432
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 433 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 487
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N+LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 488 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQ 547
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 548 REKFAWAIDMADEDYEF 564
>pdb|1R49|A Chain A, Human Topoisomerase I (Topo70) Double Mutant K532rY723F
Length = 592
Score = 479 bits (1232), Expect = e-135, Method: Compositional matrix adjust.
Identities = 263/557 (47%), Positives = 342/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 43 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 102
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 103 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 162
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 163 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSP 222
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 223 P-PGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 280
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 281 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 340
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLG+DSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 341 LHPELDGQEYVVEFDFLGRDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 400
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 401 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 460
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 461 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 515
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N+LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 516 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQ 575
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 576 REKFAWAIDMADEDYEF 592
>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 = 478 bits (1230), Expect = e-135, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 43 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 102
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 103 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 162
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 163 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSP 222
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 223 P-PGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 280
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 281 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 340
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 341 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 400
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 401 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 460
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 461 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 515
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 516 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAWCKKWGVPIEKIYNKTQ 575
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 576 REKFAWAIDMADEDYEF 592
>pdb|1A31|A Chain A, Human Reconstituted Dna Topoisomerase I In Covalent
Complex With A 22 Base Pair Dna Duplex
Length = 591
Score = 478 bits (1230), Expect = e-135, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 42 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 101
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 102 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 161
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 162 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSP 221
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 222 P-PGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 279
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 280 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 339
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 340 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 399
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 400 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 459
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 460 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 514
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 515 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAWCKKWGVPIEKIYNKTQ 574
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 575 REKFAWAIDMADEDYEF 591
>pdb|1NH3|A Chain A, Human Topoisomerase I Ara-C Complex
Length = 563
Score = 477 bits (1228), Expect = e-134, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 14 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 73
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 74 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 133
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 134 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 192
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 193 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 251
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 252 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 311
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 312 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 371
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 372 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 431
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 432 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 486
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 487 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNXLDPRITVAWCKKWGVPIEKIYNKTQ 546
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 547 REKFAWAIDMADEDYEF 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 = 476 bits (1225), Expect = e-134, Method: Compositional matrix adjust.
Identities = 263/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 43 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 102
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 103 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 162
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 163 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 221
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 222 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 280
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 281 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 340
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 341 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 400
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 401 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 460
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 461 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 515
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK++ LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 516 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLSXLDPRITVAWCKKWGVPIEKIYNKTQ 575
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 576 REKFAWAIDMADEDYEF 592
>pdb|1RRJ|A Chain A, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 476 bits (1224), Expect = e-134, Method: Compositional matrix adjust.
Identities = 263/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 16 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 75
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 76 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 135
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 136 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 194
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 195 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 253
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 254 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 313
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 314 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 373
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 374 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 433
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
R KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 434 RAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 488
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK++ LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 489 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLSXLDPRITVAWCKKWGVPIEKIYNKTQ 548
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 549 REKFAWAIDMADEDYEF 565
>pdb|1EJ9|A Chain A, Crystal Structure Of Human Topoisomerase I Dna Complex
Length = 563
Score = 475 bits (1223), Expect = e-134, Method: Compositional matrix adjust.
Identities = 263/557 (47%), Positives = 341/557 (61%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 14 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 73
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 74 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 133
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGLFRGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 134 KEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 192
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 193 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 251
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 252 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 311
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 312 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 371
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 372 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 431
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
KT M L KI+ K L D R DL A K +MKD+ K+ E+ +
Sbjct: 432 IAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKK----VVESKK 486
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
+ + + ++ K+E +E+ K +ALGTSK+N+LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 487 KAVQRLEEQLMKLEVQATDREENKQIALGTSKLNFLDPRITVAWCKKWGVPIEKIYNKTQ 546
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 547 REKFAWAIDMADEDYEF 563
>pdb|1RR8|C Chain C, Structural Mechanisms Of Camptothecin Resistance By
Mutations In Human Topoisomerase I
Length = 565
Score = 472 bits (1215), Expect = e-133, Method: Compositional matrix adjust.
Identities = 264/557 (47%), Positives = 339/557 (60%), Gaps = 19/557 (3%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW L H G +F PPY LP VK Y GK + L+P+ EEVAT FA MLD +Y K FR
Sbjct: 16 KWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFR 75
Query: 460 ENFWNDWRKLLG--KNHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
+NF+ DWRK + + ++I NL CDF + +
Sbjct: 76 KNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLL 135
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + I+D KE++ NF++EPPGL RGRG HPKMG LK+RI P DI IN KD +P
Sbjct: 136 KEYGFCIMDNHKERIANFKIEPPGLSRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVP-S 194
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P PG WKEV+HDN VTWL W + I KY+ L SS +KG+ D +KYE AR+LK
Sbjct: 195 PPPGHKWKEVRHDNKVTWLVSWTENIQG-SIKYIMLNPSSRIKGEKDWQKYETARRLKKC 253
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDE-ADTVGCCTLKVGNVE 696
+ IR Y +D+ S++ RQ AVA Y IDKLALRAGNEK++ E ADTVGCC+L+V ++
Sbjct: 254 VDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHIN 313
Query: 697 CIPP-----NKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKL 751
P ++FDFLGKDSI+Y N V VE V+K + F K+ DDLFD+L+T L
Sbjct: 314 LHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL 373
Query: 752 NAHLKELMPGLTAKVFRTYNASITLDGMLNKGTG-DGDVAVKIDVYQRANKEVAIICNHQ 810
N HL++LM GLTAKVFRTYNASITL L + T D ++ KI Y RAN+ VAI+CNHQ
Sbjct: 374 NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQ 433
Query: 811 RTVSKTHSAQMSRLTEKIEDLKGVLKDLRVDLDRAKKGKPPLMKDSDGKRKRNLAPEALE 870
+ KT M L KI+ K L D R DL A K +MKD+ K+ +A++
Sbjct: 434 QAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSA-KADAKVMKDAKTKKVVESKKKAVQ 492
Query: 871 RKMAQTNAKIEKMERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSL 930
R Q + K+E +E+ K +ALGTSK+N LDPRITVAWCK+ VPIEKI+NK+
Sbjct: 493 RLEEQ----LMKLEVQATDREENKQIALGTSKLNXLDPRITVAWCKKWGVPIEKIYNKTQ 548
Query: 931 LAKFAWAMDV-DPEFRF 946
KFAWA+D+ D ++ F
Sbjct: 549 REKFAWAIDMADEDYEF 565
>pdb|2B9S|A Chain A, Crystal Structure Of Heterodimeric L. Donovani
Topoisomerase I-Vanadate-Dna Complex
Length = 432
Score = 439 bits (1128), Expect = e-123, Method: Compositional matrix adjust.
Identities = 218/417 (52%), Positives = 275/417 (65%), Gaps = 5/417 (1%)
Query: 399 GQKKWTTLVHNGVIFPPPYLPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKF 458
G+++W TL HNGV+FPP Y PHG+ + Y G+E +TPE+EEVATMFAVM + DY + F
Sbjct: 18 GERRWETLAHNGVLFPPEYEPHGIPIFYDGREFKMTPEEEEVATMFAVMKEHDYYRMEVF 77
Query: 459 RENFWNDWRKLLGK-NHVIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXXXXXX 517
R NF+ WR++L K H I+ LE CDF+PIY WH
Sbjct: 78 RRNFFESWREILDKRQHPIRRLELCDFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEA 137
Query: 518 XXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVPIPEC 577
Y + + DG +E+V NFRVEPPGLFRGRG+HP MGKLK R+QP DITINIG+ +P
Sbjct: 138 EPYRYCVWDGRREQVANFRVEPPGLFRGRGKHPLMGKLKVRVQPEDITINIGETAEVP-V 196
Query: 578 PIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAASSSLKGQSDREKYEKARKLKDY 637
P G W V+HD+TVTWLA W D + KYV LA SSS+KGQSD K+EKARKLKD
Sbjct: 197 PPAGHKWAAVQHDHTVTWLAMWRDSV-AGNMKYVMLAPSSSVKGQSDMVKFEKARKLKDK 255
Query: 638 IHSIRAAYTKDFVSRDGTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVEC 697
+ IRA+Y +DF S D Q AVA Y ID+LALR GNEK +DEADTVGCC+L+V +++
Sbjct: 256 VDDIRASYMEDFKSNDLHVAQRAVAMYFIDRLALRVGNEKGEDEADTVGCCSLRVEHIQL 315
Query: 698 IPPNKLKFDFLGKDSIQYVNTVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKE 757
+P N ++FDFLGKDSI+Y N V V VY + +F K D+FD+L+ +LN HLK
Sbjct: 316 MPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTRRKSPGMDIFDQLNPTQLNDHLKS 375
Query: 758 LMPGLTAKVFRTYNASITLDGMLNKGTGD--GDVAVKIDVYQRANKEVAIICNHQRT 812
M GL+AKVFRTYNASITLD + D A K+ + +AN EVAI+CNHQ++
Sbjct: 376 FMDGLSAKVFRTYNASITLDRWFKEKPVDPKWSTADKLAYFNKANTEVAILCNHQKS 432
>pdb|1OIS|A Chain A, Yeast Dna Topoisomerase I, N-Terminal Fragment
Length = 223
Score = 193 bits (491), Expect = 3e-49, Method: Compositional matrix adjust.
Identities = 98/222 (44%), Positives = 132/222 (59%), Gaps = 10/222 (4%)
Query: 402 KWTTLVHNGVIFPPPY--LPHGVKMLYKGKEVNLTPEQEEVATMFAVMLDTDYMQKPKFR 459
KW TL HNGVIFPPPY LP +K+ Y GK V+L P+ EEVA FA +L++D+ + P F+
Sbjct: 4 KWVTLKHNGVIFPPPYQPLPSHIKLYYDGKPVDLPPQAEEVAGFFAALLESDHAKNPVFQ 63
Query: 460 ENFWNDWRKLLGKNH------VIQNLEGCDFKPIYDWHXXXXXXXXXXXXXXXXXXXXXX 513
+NF+ND+ ++L ++ I+ CDF ++D+
Sbjct: 64 KNFFNDFLQVLKESGGPLNGIEIKEFSRCDFTKMFDYFQLQKEQKKQLTSQEKKQIRLER 123
Query: 514 XXXXXXYMWAIVDGVKEKVGNFRVEPPGLFRGRGEHPKMGKLKKRIQPSDITINIGKDVP 573
Y + +DG +E+VGNF+VEPP LFRGRG HPK GKLK+R+ P DI +N+ KD P
Sbjct: 124 EKFEEDYKFCELDGRREQVGNFKVEPPDLFRGRGAHPKTGKLKRRVNPEDIVLNLSKDAP 183
Query: 574 IPECPIPGESWKEVKHDNTVTWLAFWNDPINPKEFKYVFLAA 615
+P P G W E++HDNTV WLA W + I FKYV LAA
Sbjct: 184 VPPAP-EGHKWGEIRHDNTVQWLAMWRENIF-NSFKYVRLAA 223
>pdb|2B9S|B Chain B, Crystal Structure Of Heterodimeric L. Donovani
Topoisomerase I-Vanadate-Dna Complex
Length = 62
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 42/58 (72%)
Query: 884 ERDMKTKEDLKTVALGTSKINYLDPRITVAWCKRHEVPIEKIFNKSLLAKFAWAMDVD 941
E ++ K+D K V+LGTSKINY+DPRI +W K +VPI KIF+ ++ KF WAM+ +
Sbjct: 1 ENIIRIKDDNKAVSLGTSKINYIDPRIICSWAKAQDVPINKIFSATIQKKFPWAMNAE 58
>pdb|2H7F|X Chain X, Structure Of Variola Topoisomerase Covalently Bound To Dna
Length = 314
Score = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 3/119 (2%)
Query: 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVN 717
Q+AV + +R G K E +TVG TLK ++E I P+K+ F+GKD + +
Sbjct: 116 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIE-ISPDKIVIKFVGKDKVSHEF 174
Query: 718 TVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITL 776
V +YK + + + LF+KL K+ +K+ G+ K RTY + T
Sbjct: 175 VVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQF--GIRIKDLRTYGVNYTF 231
>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 = 50.4 bits (119), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 3/119 (2%)
Query: 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVN 717
Q+AV + +R G K E +TVG TLK ++E I P+K+ F+GKD + +
Sbjct: 116 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIE-ISPDKIVIKFVGKDKVSHEF 174
Query: 718 TVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITL 776
V +YK + + + LF+KL K+ +K+ G+ K RTY + T
Sbjct: 175 VVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYESIKQF--GIRIKDLRTYGVNYTF 231
>pdb|1A41|A Chain A, Type 1-Topoisomerase Catalytic Fragment From Vaccinia
Virus
Length = 234
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 35/119 (29%), Positives = 57/119 (47%), Gaps = 3/119 (2%)
Query: 658 QIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSIQYVN 717
Q+AV + +R G K E +TVG TLK ++E I P+++ F+GKD + +
Sbjct: 36 QLAVFMLMETMFFIRFGKMKYLKENETVGLLTLKNKHIE-ISPDEIVIKFVGKDKVSHEF 94
Query: 718 TVEVELPVYKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAKVFRTYNASITL 776
V +YK + + + LF+KL K+ +K+ G+ K RTY + T
Sbjct: 95 VVHKSNRLYKPLLKLTDDSSPEEFLFNKLSERKVYECIKQF--GIRIKDLRTYGVNYTF 151
>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 = 37.7 bits (86), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 45/189 (23%), Positives = 87/189 (46%), Gaps = 20/189 (10%)
Query: 597 AFWNDPINPKEFKYV--FLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDF-VSRD 653
AF D +++Y F+ A + +K+++ + + +++ A T D S
Sbjct: 66 AFGRDAAGRLQYRYHPDFVQAGAL-------KKWQRLTRFAGALPTLKVATTADLRASGL 118
Query: 654 GTRRQIAVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSI 713
R+ +A+ T L+ R G++ + T G TL+ +V + N + F F GK +
Sbjct: 119 PPRKVMALMTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHV-VVDGNTVTFRFKGKHGV 177
Query: 714 -QYVNTVEVELP--VYKAIGQ-----FQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAK 765
Q+ T + L + K + FQT + ++ + +LNA+L+E++ TAK
Sbjct: 178 SQHKATSDRTLAANMQKLLDLPGPWLFQTVDAGGGER-RRIHSTELNAYLREVIGPFTAK 236
Query: 766 VFRTYNASI 774
FRT+ ++
Sbjct: 237 DFRTWGGTL 245
>pdb|2F4Q|A Chain A, Crystal Structure Of Deinococcus Radiodurans Topoisomerase
Ib
Length = 346
Score = 36.6 bits (83), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 43/189 (22%), Positives = 84/189 (44%), Gaps = 20/189 (10%)
Query: 597 AFWNDPINPKEFKYV--FLAASSSLKGQSDREKYEKARKLKDYIHSIRAAYTKDFVSRDG 654
AF D +++Y F+ A + +K+++ + + +++ A T D +
Sbjct: 66 AFGRDAAGRLQYRYHPDFVQAGAL-------KKWQRLTRFAGALPTLKVATTADLRASGL 118
Query: 655 TRRQI-AVATYLIDKLALRAGNEKDDDEADTVGCCTLKVGNVECIPPNKLKFDFLGKDSI 713
R++ A+ T L+ R G++ + T G TL+ +V + N + F F GK +
Sbjct: 119 PPRKVXALXTRLLHVARFRVGSDIYARQHKTYGLSTLRQRHV-VVDGNTVTFRFKGKHGV 177
Query: 714 -QYVNTVEVELPV-------YKAIGQFQTGKKQNDDLFDKLDTAKLNAHLKELMPGLTAK 765
Q+ T + L FQT + ++ + +LNA+L+E++ TAK
Sbjct: 178 SQHKATSDRTLAANXQKLLDLPGPWLFQTVDAGGGER-RRIHSTELNAYLREVIGPFTAK 236
Query: 766 VFRTYNASI 774
FRT+ ++
Sbjct: 237 DFRTWGGTL 245
>pdb|3ZQJ|A Chain A, Mycobacterium Tuberculosis Uvra
pdb|3ZQJ|B Chain B, Mycobacterium Tuberculosis Uvra
pdb|3ZQJ|C Chain C, Mycobacterium Tuberculosis Uvra
pdb|3ZQJ|D Chain D, Mycobacterium Tuberculosis Uvra
pdb|3ZQJ|E Chain E, Mycobacterium Tuberculosis Uvra
pdb|3ZQJ|F Chain F, Mycobacterium Tuberculosis Uvra
Length = 993
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 40/155 (25%), Positives = 65/155 (41%), Gaps = 29/155 (18%)
Query: 742 LFDKLDT---AKLNAHLKELMPGLTAKVFRTYNASITLDGMLNKGTGDGDVAVKI----D 794
+FDK+ T A A ++ PG ++N G TGDG + +++ D
Sbjct: 741 VFDKIRTLFAATTEAKVRGYQPGRF-----SFNVK---GGRCEACTGDGTIKIEMNFLPD 792
Query: 795 VY--------QRANKEVAIICNHQRTVSKTHSAQMSRLTEKIEDLKGVLKDLR----VDL 842
VY R N+E + +TVS+ + E E + GV + LR V L
Sbjct: 793 VYVPCEVCQGARYNRETLEVHYKGKTVSEVLDMSIEEAAEFFEPIAGVHRYLRTLVDVGL 852
Query: 843 DRAKKGKP-PLMKDSDGKRKRNLAPEALERKMAQT 876
+ G+P P + + +R + LA E +R +T
Sbjct: 853 GYVRLGQPAPTLSGGEAQRVK-LASELQKRSTGRT 886
>pdb|2JVC|A Chain A, Nmr Solution Structure Of Ubiquitin Like Protein
Length = 82
Score = 30.8 bits (68), Expect = 3.5, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 678 DDDEADTVGCCTLKVGNVECIPPNKLKFDFLGK 710
D D ADTVG K+ + E IPP++ + F GK
Sbjct: 21 DVDHADTVGAVKAKIYDKEGIPPDQQRLIFGGK 53
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
0.314 0.131 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,421,186
Number of Sequences: 62578
Number of extensions: 1015465
Number of successful extensions: 1968
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1856
Number of HSP's gapped (non-prelim): 32
length of query: 946
length of database: 14,973,337
effective HSP length: 108
effective length of query: 838
effective length of database: 8,214,913
effective search space: 6884097094
effective search space used: 6884097094
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (26.2 bits)