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= 001100
(1158 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt
pdb|1CY2|A Chain A, Complex Of E.Coli Dna Topoisomerase I With Tptptp3'
pdb|1CY6|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3' Thymidine
Monophosphate
pdb|1CY7|A Chain A, Complex Of E.coli Dna Topoisomerase I With 5'-thymidine
Monophosphate
pdb|1CY8|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'-Thymidine
Monophosphate And 3'-Thymidine Monophosphate
pdb|1CY0|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 3'-5'-Adenosine
Diphosphate
pdb|1CY4|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptptp3'
Length = 599
Score = 346 bits (887), Expect = 5e-95, Method: Compositional matrix adjust.
Identities = 221/604 (36%), Positives = 317/604 (52%), Gaps = 71/604 (11%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSV----------------RPDDDFSMVWEVPSAA 407
I YLG Y V S GH+RDL SGS + D+ ++V +
Sbjct: 19 INKYLGSDYVVKSSVGHIRDLPT-SGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDP 77
Query: 408 WTHLKSIKVALSGAENLI--------------LASDPDREGEAIAWHIVEMLQQQDALHE 453
W + ++ L G E ++ LA+D DREGEAIAWH+ E++ DA +
Sbjct: 78 WHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY- 136
Query: 454 NITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGC 513
+RVVF+EIT+ +I+ A E++ + V A ARR +D ++G+ +SPLLW+K+
Sbjct: 137 ----SRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG 192
Query: 514 QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKR 573
SAGRVQS A+ L+ +RE EI F P+E+W V+A +L +TH K
Sbjct: 193 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKP 247
Query: 574 LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSAT 633
++ A + +K A + V++ + K P+ITSTLQQ A+ +L F
Sbjct: 248 FRPVNKEQTQAAVSLLEK---ARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 304
Query: 634 YTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 693
TM +AQ+LYE AG ITYMRTD ++S +A +R I + +G + P E P
Sbjct: 305 KTMMMAQRLYE---------AGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESP 354
Query: 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753
+Y K +N+QEAHEAIRP+D+ + L ++ D KLY LIW + +ACQM PA
Sbjct: 355 NQYASK-ENSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDS 412
Query: 754 IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKT 813
+ +G D + R R F G+ + G + DR IL ++
Sbjct: 413 TTLTVGAGDFRLKARGRILR--FDGWTKVMPALRKG--------DEDR-----ILPAVNK 457
Query: 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR 873
GD L L E+ QH T+PPAR+SE SLVK+LE+ GIGRPSTYAS + +QDR YV V++R
Sbjct: 458 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR 517
Query: 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYC 933
Y E G +V+ L F E+ +Y FTA ME LD V+ EWK +L ++S F+
Sbjct: 518 RFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQL 577
Query: 934 TCAQ 937
A+
Sbjct: 578 DKAE 581
>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna
Topoisomerase I (Residues 2-590 Of Mature Protein)
Cloning Artifact Adds Two Residues To The Amino-Terminus
Which Were Not Observed In The Experimental Electron
Density (Gly-2, Ser-1)
Length = 597
Score = 345 bits (884), Expect = 1e-94, Method: Compositional matrix adjust.
Identities = 221/604 (36%), Positives = 316/604 (52%), Gaps = 71/604 (11%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSV----------------RPDDDFSMVWEVPSAA 407
I YLG Y V S GH+RDL SGS + D+ ++V +
Sbjct: 17 INKYLGSDYVVKSSVGHIRDLPT-SGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDP 75
Query: 408 WTHLKSIKVALSGAENLI--------------LASDPDREGEAIAWHIVEMLQQQDALHE 453
W + ++ L G E ++ LA+D DREGEAIAWH+ E++ DA +
Sbjct: 76 WHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY- 134
Query: 454 NITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGC 513
+RVVF+EIT+ +I+ A E++ + V A ARR +D ++G+ +SPLLW+K+
Sbjct: 135 ----SRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG 190
Query: 514 QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKR 573
SAGRVQS A+ L+ +RE EI F P+E+W V+A +L +TH K
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKP 245
Query: 574 LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSAT 633
++ A + +K A + V++ + K P+ITSTLQQ A+ +L F
Sbjct: 246 FRPVNKEQTQAAVSLLEK---ARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 302
Query: 634 YTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 693
TM +AQ+LYE AG ITYMRTD ++S +A +R I + +G + P E P
Sbjct: 303 KTMMMAQRLYE---------AGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESP 352
Query: 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753
+Y K N+QEAHEAIRP+D+ + L ++ D KLY LIW + +ACQM PA
Sbjct: 353 NQYASK-GNSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDS 410
Query: 754 IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKT 813
+ +G D + R R F G+ + G + DR IL ++
Sbjct: 411 TTLTVGAGDFRLKARGRILR--FDGWTKVMPALRKG--------DEDR-----ILPAVNK 455
Query: 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR 873
GD L L E+ QH T+PPAR+SE SLVK+LE+ GIGRPSTYAS + +QDR YV V++R
Sbjct: 456 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR 515
Query: 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYC 933
Y E G +V+ L F E+ +Y FTA ME LD V+ EWK +L ++S F+
Sbjct: 516 RFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQL 575
Query: 934 TCAQ 937
A+
Sbjct: 576 DKAE 579
>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia
Length = 596
Score = 344 bits (882), Expect = 2e-94, Method: Compositional matrix adjust.
Identities = 220/604 (36%), Positives = 317/604 (52%), Gaps = 71/604 (11%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSV----------------RPDDDFSMVWEVPSAA 407
I YLG Y V S GH+RDL SGS + D+ ++V +
Sbjct: 17 INKYLGSDYVVKSSVGHIRDLPT-SGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDP 75
Query: 408 WTHLKSIKVALSGAENLI--------------LASDPDREGEAIAWHIVEMLQQQDALHE 453
W + ++ L G E ++ LA++ DREGEAIAWH+ E++ DA +
Sbjct: 76 WHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARY- 134
Query: 454 NITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGC 513
+RVVF+EIT+ +I+ A E++ + V A ARR +D ++G+ +SPLLW+K+
Sbjct: 135 ----SRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG 190
Query: 514 QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKR 573
SAGRVQS A+ L+ +RE EI F P+E+W V+A +L +TH K
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKP 245
Query: 574 LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSAT 633
++ A + +K A + V++ + K P+ITSTLQQ A+ +L F
Sbjct: 246 FRPVNKEQTQAAVSLLEK---ARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 302
Query: 634 YTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 693
TM +AQ+LYE AG ITYMRTD ++S +A +R I + +G + P E P
Sbjct: 303 KTMMMAQRLYE---------AGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESP 352
Query: 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753
+Y K +N+QEAHEAIRP+D+ + L ++ D KLY LIW + +ACQM PA
Sbjct: 353 NQYASK-ENSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDS 410
Query: 754 IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKT 813
+ +G D + R R F G+ + G + DR IL ++
Sbjct: 411 TTLTVGAGDFRLKARGRILR--FDGWTKVMPALRKG--------DEDR-----ILPAVNK 455
Query: 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR 873
GD L L E+ QH T+PPAR+SE SLVK+LE+ GIGRPSTYAS + +QDR YV V++R
Sbjct: 456 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR 515
Query: 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYC 933
Y E G +V+ L F E+ +Y FTA ME LD V+ EWK +L ++S F+
Sbjct: 516 RFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQL 575
Query: 934 TCAQ 937
A+
Sbjct: 576 DKAE 579
>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67
Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I
And 5'-Acttcgggatg-3'
pdb|1MW9|X Chain X, Crystal Structure Of H365r Mutant Of 67 Kda N-Terminal
Fragment Of E. Coli Dna Topoisomerase I
Length = 592
Score = 343 bits (879), Expect = 4e-94, Method: Compositional matrix adjust.
Identities = 220/604 (36%), Positives = 316/604 (52%), Gaps = 71/604 (11%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSV----------------RPDDDFSMVWEVPSAA 407
I YLG Y V S GH+RDL SGS + D+ ++V +
Sbjct: 17 INKYLGSDYVVKSSVGHIRDLPT-SGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDP 75
Query: 408 WTHLKSIKVALSGAENLI--------------LASDPDREGEAIAWHIVEMLQQQDALHE 453
W + ++ L G E ++ LA+D DREGEAIAWH+ E++ DA +
Sbjct: 76 WHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY- 134
Query: 454 NITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGC 513
+RVVF+EIT+ +I+ A E++ + V A ARR +D ++G+ +SPLLW+K+
Sbjct: 135 ----SRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG 190
Query: 514 QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKR 573
SAGRVQS A+ L+ +RE EI F P+E+W V+A +L +TH K
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKP 245
Query: 574 LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSAT 633
++ A + +K A + V++ + K P+ITSTLQQ A+ +L F
Sbjct: 246 FRPVNKEQTQAAVSLLEK---ARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 302
Query: 634 YTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 693
TM +AQ+LYE AG ITYMRTD ++S +A +R I + +G + P E P
Sbjct: 303 KTMMMAQRLYE---------AGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESP 352
Query: 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753
+Y K +N+QEA EAIRP+D+ + L ++ D KLY LIW + +ACQM PA
Sbjct: 353 NQYASK-ENSQEAREAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDS 410
Query: 754 IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKT 813
+ +G D + R R F G+ + G + DR IL ++
Sbjct: 411 TTLTVGAGDFRLKARGRILR--FDGWTKVMPALRKG--------DEDR-----ILPAVNK 455
Query: 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR 873
GD L L E+ QH T+PPAR+SE SLVK+LE+ GIGRPSTYAS + +QDR YV V++R
Sbjct: 456 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR 515
Query: 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYC 933
Y E G +V+ L F E+ +Y FTA ME LD V+ EWK +L ++S F+
Sbjct: 516 RFYAEKMGEIVTDRLEENFRELMNYDFTAQMENNLDQVANHEAEWKAVLDHFFSDFTQQL 575
Query: 934 TCAQ 937
A+
Sbjct: 576 DKAE 579
>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a
With Substrate
Length = 595
Score = 341 bits (875), Expect = 1e-93, Method: Compositional matrix adjust.
Identities = 219/604 (36%), Positives = 316/604 (52%), Gaps = 71/604 (11%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSV----------------RPDDDFSMVWEVPSAA 407
I YLG Y V S GH+RDL SGS + D+ ++V +
Sbjct: 17 INKYLGSDYVVKSSVGHIRDLPT-SGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDP 75
Query: 408 WTHLKSIKVALSGAENLI--------------LASDPDREGEAIAWHIVEMLQQQDALHE 453
W + ++ L G E ++ LA++ DREGEAIAWH+ E++ DA +
Sbjct: 76 WHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARY- 134
Query: 454 NITVARVVFHEITEASIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGC 513
+RVVF+EIT+ +I+ A E++ + V A ARR +D ++G+ +SPLLW+K+
Sbjct: 135 ----SRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG 190
Query: 514 QSAGRVQSAALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKR 573
SAGRVQS A+ L+ +RE EI F P+E+W V+A +L +TH K
Sbjct: 191 LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKP 245
Query: 574 LNQLSIGSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSAT 633
++ A + +K A + V++ + K P+ITSTLQQ A+ +L F
Sbjct: 246 FRPVNKEQTQAAVSLLEK---ARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVK 302
Query: 634 YTMKLAQKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGP 693
TM +AQ+LYE AG IT MRTD ++S +A +R I + +G + P E P
Sbjct: 303 KTMMMAQRLYE---------AGYITXMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESP 352
Query: 694 RKYFKKVKNAQEAHEAIRPTDIRRLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQ 753
+Y K +N+QEAHEAIRP+D+ + L ++ D KLY LIW + +ACQM PA
Sbjct: 353 NQYASK-ENSQEAHEAIRPSDVNVMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDS 410
Query: 754 IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKT 813
+ +G D + R R F G+ + G + DR IL ++
Sbjct: 411 TTLTVGAGDFRLKARGRILR--FDGWTKVMPALRKG--------DEDR-----ILPAVNK 455
Query: 814 GDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSR 873
GD L L E+ QH T+PPAR+SE SLVK+LE+ GIGRPSTYAS + +QDR YV V++R
Sbjct: 456 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR 515
Query: 874 ILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSYC 933
Y E G +V+ L F E+ +Y FTA ME LD V+ EWK +L ++S F+
Sbjct: 516 RFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQL 575
Query: 934 TCAQ 937
A+
Sbjct: 576 DKAE 579
>pdb|2GAI|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAI|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Triclinic Crystal Form
pdb|2GAJ|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
pdb|2GAJ|B Chain B, Structure Of Full Length Topoisomerase I From Thermotoga
Maritima In Monoclinic Crystal Form
Length = 633
Score = 339 bits (869), Expect = 6e-93, Method: Compositional matrix adjust.
Identities = 218/602 (36%), Positives = 317/602 (52%), Gaps = 78/602 (12%)
Query: 364 IQGYLGDMYEVLPSYGHVRDLAARSGSVRPDDDFSMVWEVPSAAWTHLKSIKVALSGAEN 423
I+ LG+ YEV S GH+ DL V + DF + V ++ +K L+
Sbjct: 20 IKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLK-DLAKKGE 78
Query: 424 LILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREIDAN 483
L++ASD DREGEAIAWHI + + R+VF EIT I+ A++ REID
Sbjct: 79 LLIASDMDREGEAIAWHIARVTNTLGRKN------RIVFSEITPRVIREAVKNPREIDMK 132
Query: 484 LVQAYLARRALDYLIGFNISPLLWRKLPGCQSAGRVQSAALSLICDREMEIDEFKPQEYW 543
V+A LARR LD ++G+++SP+LWR SAGRVQSA L L+CDRE EI F P++Y
Sbjct: 133 KVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYH 192
Query: 544 TVE-------AVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSAN 596
+ A +D KE D L QS +++L + E+K++
Sbjct: 193 RITVNFDGLTAEIDVKEKKFFDA----ETLKEIQS--IDELVVE--------EKKVSVKK 238
Query: 597 FQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGL 656
F P P+ TSTLQQ+A +KL FS + TM +AQ+LYEGV+ DG A
Sbjct: 239 FA------------PPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIA-F 285
Query: 657 ITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 716
ITYMRTD +SD A +E R+LI E +G + + R+ K Q+AHEAIRPT++
Sbjct: 286 ITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKRERR--KSNAKIQDAHEAIRPTNVF 343
Query: 717 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEF 776
P L+ D KLY LIW R +A QM+P+ + + + D F+ + + F
Sbjct: 344 MTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIF 403
Query: 777 LGFQAAYE-DVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARY 835
G++ ++ + + G ++E E S+K P+ V++++ T+P RY
Sbjct: 404 DGYEKVWKTERNTGEFPFEEGE------------SVK---PVV---VKIEEQETKPKPRY 445
Query: 836 SEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV 895
+EGSLVK++E LGIGRPSTYAST+K+L +R Y+ LYP G +V +L +S+V
Sbjct: 446 TEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDV 505
Query: 896 TDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSSY----------------CTCAQSL 939
SFTA+ME +LD V G K +L +++ FSS C+C + +
Sbjct: 506 VSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEM 565
Query: 940 HI 941
+
Sbjct: 566 RL 567
>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
Length = 1054
Score = 159 bits (401), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 155/535 (28%), Positives = 235/535 (43%), Gaps = 105/535 (19%)
Query: 409 THLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEA 468
+ +++++ AE +I+ +DPD EGE IAW + +L A V R FHE+T
Sbjct: 611 SRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGA------VKRAEFHEVTRR 664
Query: 469 SIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQ-SAGRVQSAALSLI 527
+I AL++ R++D NLV+A + RR D IGF +S LW + SAGR Q+ L I
Sbjct: 665 AILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWI 724
Query: 528 CDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 587
DR E +E + V D F L H E D
Sbjct: 725 IDRFQE-----SRERRKIAIVRD-----------FDLVLEH-------------DEEEFD 755
Query: 588 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQ 647
+ K+ +R +R PY T T+ DA L FS TM++AQ+L+E
Sbjct: 756 LTIKLVE---------EREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFEN-- 804
Query: 648 LPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAH 707
GLITY RTD +SD + + + + + E G AH
Sbjct: 805 -------GLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESG-------------AH 844
Query: 708 EAIRPT------DIRRLPAMLSGLLDEDCLK-----LYSLIWSRTMACQMQPATVGQIQV 756
E IRPT D++RL + G+L + L+ LY LI+ R MA Q +P V
Sbjct: 845 ECIRPTRPLTRDDVQRL--IQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKV----- 897
Query: 757 DIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDP 816
+V + S +EF G A E + +R E + + A + N L TG
Sbjct: 898 --------VVKKYS---IEFDGKTAEEERI----VR-AEGRAYELYRAVWVKNELPTGT- 940
Query: 817 LYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKSRILY 876
+ + E+K P +++ +++ ++E GIGRPSTYA+ + L RNYV K +
Sbjct: 941 -FRVKAEVKSVPKVLP--FTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYGRMI 997
Query: 877 PEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 931
P G V FL +++ T D+E+ +D + G ++ L D ++ S
Sbjct: 998 PTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDMYAEIKS 1052
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 158 bits (400), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 154/539 (28%), Positives = 232/539 (43%), Gaps = 113/539 (20%)
Query: 409 THLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEA 468
+ +++++ AE +I+ +DPD EGE IAW + +L A V R FHE+T
Sbjct: 611 SRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGA------VKRAEFHEVTRR 664
Query: 469 SIKVALQAAREIDANLVQAYLARRALDYLIGFNISPLLWRKLPGCQ-SAGRVQSAALSLI 527
+I AL++ R++D NLV+A + RR D IGF +S LW + SAGR Q+ L I
Sbjct: 665 AILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWI 724
Query: 528 CDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKD 587
DR E +E + V D F L H E D
Sbjct: 725 IDRFQE-----SRERRKIAIVRD-----------FDLVLEH-------------DEEEFD 755
Query: 588 IEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQ 647
+ K+ +R +R PY T T+ DA L FS TM++AQ+L+E
Sbjct: 756 LTIKLVE---------EREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFEN-- 804
Query: 648 LPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAH 707
GLITY RTD +SD + + + + + E G AH
Sbjct: 805 -------GLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESG-------------AH 844
Query: 708 EAIRPT------DIRRLPAMLSGLLDEDCLK-----LYSLIWSRTMACQMQPATVG---- 752
E IRPT D++RL + G+L + L+ LY LI+ R MA Q +P V
Sbjct: 845 ECIRPTRPLTRDDVQRL--IQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKY 902
Query: 753 QIQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLK 812
I+ D A+E + R+ AYE + A + N L
Sbjct: 903 SIEFDGKTAEEERIVRAEGR---------AYE----------------LYRAVWVKNELP 937
Query: 813 TGDPLYLGEVELKQHHTQPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTVKS 872
TG + + E+K P +++ +++ ++E GIGRPSTYA+ + L RNYV K
Sbjct: 938 TGT--FRVKAEVKSVPKVLP--FTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKY 993
Query: 873 RILYPEFRGRMVSAFLSHYFSEVTDYSFTADMETELDNVSAGLTEWKGLLVDYWSRFSS 931
+ P G V FL +++ T D+E+ +D + G ++ L D ++ S
Sbjct: 994 GRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIERGELDYLKALEDMYAEIKS 1052
>pdb|1CY9|A Chain A, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Monoclinic Form
pdb|1CY9|B Chain B, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Monoclinic Form
pdb|1CYY|A Chain A, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Hexagonal Form
pdb|1CYY|B Chain B, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna
Topoisomerase I. Hexagonal Form
Length = 264
Score = 146 bits (369), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 100/299 (33%), Positives = 146/299 (48%), Gaps = 35/299 (11%)
Query: 537 FKPQEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSAN 596
F P+E+W V+A +L +TH K ++ A + +K A
Sbjct: 1 FVPEEFWEVDASTTTPSGEAL-----ALQVTHQNDKPFRPVNKEQTQAAVSLLEK---AR 52
Query: 597 FQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGL 656
+ V++ + K P+ITSTLQQ A+ +L F TM +AQ+LYE AG
Sbjct: 53 YSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE---------AGY 103
Query: 657 ITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPTDIR 716
ITYMRTD ++S +A +R I + +G + P E P +Y K +N+QEAHEAIRP+D+
Sbjct: 104 ITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLP-ESPNQYASK-ENSQEAHEAIRPSDVN 161
Query: 717 RLPAMLSGLLDEDCLKLYSLIWSRTMACQMQPATVGQIQVDIGNADESIVFRSSCSRVEF 776
+ L ++ D KLY LIW + +ACQM PA + +G D + R R F
Sbjct: 162 VMAESLKD-MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILR--F 218
Query: 777 LGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHTQPPARY 835
G+ + G + DR IL ++ GD L L E+ QH T+PPAR+
Sbjct: 219 DGWTKVMPALRKG--------DEDR-----ILPAVNKGDALTLVELTPAQHFTKPPARF 264
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered Orthorhombic
Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 130 bits (328), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 138/514 (26%), Positives = 215/514 (41%), Gaps = 95/514 (18%)
Query: 421 AENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEASIKVALQAAREI 480
A+ +++A+DPD EGE I+W + + L L ++ R+ HEIT K A ++ R +
Sbjct: 660 ADEILVATDPDVEGEKISWDVTQYL-----LPSTRSLRRIEMHEITRYGFKKARESVRFV 714
Query: 481 DANLVQAYLARRALDYLIGFNISPLLWRKLPGCQ-SAGRVQSAALSLICDREMEIDEFKP 539
D NLV+A + RR D IGF +S L ++ SAGRVQS L I +RE +E+K
Sbjct: 715 DFNLVKAQIVRRVQDRWIGFELSGKLQKRFGRSNLSAGRVQSTVLGWIVERE---EEYKK 771
Query: 540 QEYWTVEAVLDKKESHSLDTFSFPAHLTHFQSKRLNQLSIGSHTEAKDIEQKINSANFQV 599
E VL+ + E K + + Q
Sbjct: 772 SEKDFTLLVLEN--------------------------GVNLEVEGKIADDVVTVVELQE 805
Query: 600 IKNSKRSMVRKNPT-PYITSTLQQDAANKLNFSATYTMKLAQKLYEGVQLPDGTAAGLIT 658
+ KNP PY TS+ + + KL M + Q L+E G IT
Sbjct: 806 AEEE------KNPLPPYTTSSALSEISQKLRLGVQEVMDILQDLFE---------KGFIT 850
Query: 659 YMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFKKVKNAQEAHEAIRPT---DI 715
Y RTD IS E R+ + + G + + + + AHEAIRP D
Sbjct: 851 YHRTDSTRISLEGQNVARTYL-RKIGKEDI-------FMGRSWSTEGAHEAIRPVKPIDA 902
Query: 716 RRLPAML-SGL---LDEDCLKLYSLIWSRTMACQMQPATVGQ--IQVDIGNADESIVFRS 769
R L M+ GL L + L++Y LI++R +A Q V + + VD+
Sbjct: 903 RELEEMIEEGLIADLTKKHLRVYELIFNRFLASQSAAVKVKKQIVTVDVDGKR------- 955
Query: 770 SCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAILNSLKTGDPLYLGEVELKQHHT 829
+G + E + G + + R E K + HT
Sbjct: 956 -------MGIEQIVEILRDGWNLFVPLTVSPRFEHRTYKIKEKK----------FYKKHT 998
Query: 830 QPPARYSEGSLVKKLEELGIGRPSTYASTLKVLQDRNYVTV-KSRILYPEFRGRMVSAFL 888
P +++ S+V+++++ GIGRPSTYA ++VL R YV K + + P G MV ++L
Sbjct: 999 VPL--FTQASIVEEMKKRGIGRPSTYAKIVEVLFRRGYVYEDKYKRVRPTRFGVMVYSYL 1056
Query: 889 SHYFSEVTDYSFTADMETELDNVSAGLTEWKGLL 922
+ + T +E +D V G +++ L
Sbjct: 1057 KERYEKYVTEETTRRLEEIMDKVERGEEDYQATL 1090
>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 5.5
pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol At Ph 7.0
pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glycerol Ph 8.0
pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 5.5
pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
8- Base Single Stranded Oligonucleotide. Frozen In
Glucose Ph 7.0
Length = 659
Score = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 135/542 (24%), Positives = 230/542 (42%), Gaps = 82/542 (15%)
Query: 410 HLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEAS 469
L IK L A ++ A DPDREG+ + +++ LQ A + V R + +++ +
Sbjct: 84 QLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQL--APEKRQQVQRCLINDLNPQA 141
Query: 470 IKVALQAAREID--ANLVQAYLARRALDYLIGFNIS---PLLWRK--LPGCQSAGRVQSA 522
++ A+ R L + LAR D+L G N++ +L R G S GRVQ+
Sbjct: 142 VERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTP 201
Query: 523 ALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTH-FQSK--RLNQLSI 579
L L+ R+ EI+ F ++++ V+A + P+ +Q + RL +
Sbjct: 202 VLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPL 261
Query: 580 GSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 639
H + +I+ V + + P P+ S LQ +AA + SA + +
Sbjct: 262 AEH-----VVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDIC 316
Query: 640 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFK- 698
QKLYE LITY R+D ++ +E +++ S HAP+ P+
Sbjct: 317 QKLYE--------THKLITYPRSDCRYLPEEHFAGRHAVM--NAISVHAPDLLPQPVVDP 366
Query: 699 KVKN------AQEAHEAIRPTDIRRLPAMLSGL-LDEDCLKLYSLIWSRTMACQMQPATV 751
++N +AH AI PT A S + L E+ K+Y+LI +R Q P V
Sbjct: 367 DIRNRCWDDKKVDAHHAIIPT------ARSSAINLTENEAKVYNLI-ARQYLMQFCPDAV 419
Query: 752 GQ---IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAIL 808
+ I++DI ++ FL +AG ++E D L
Sbjct: 420 FRKCVIELDIAKG-------KFVAKARFLA--------EAGWRTLLGSKERDEENDGTPL 464
Query: 809 NSLKTGDPLYLGEVELKQHHTQPPARYSEGSLV------------KKLEEL-----GIGR 851
+ GD L + E+ + TQPP +++ +L+ K L+++ G+G
Sbjct: 465 PVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGT 524
Query: 852 PSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV-TDYSFTADMETELDN 910
+T A +++L R ++T K R ++ G+ L H E+ T TA E+ L
Sbjct: 525 EATRAGIIELLFKRGFLTKKGRYIHSTDAGKA----LFHSLPEMATRPDMTAHWESVLTQ 580
Query: 911 VS 912
+S
Sbjct: 581 IS 582
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 100 bits (250), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 135/542 (24%), Positives = 230/542 (42%), Gaps = 82/542 (15%)
Query: 410 HLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEAS 469
L IK L A ++ A DPDREG+ + +++ LQ A + V R + +++ +
Sbjct: 84 QLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQL--APEKRQQVQRCLINDLNPQA 141
Query: 470 IKVALQAAREID--ANLVQAYLARRALDYLIGFNIS---PLLWRK--LPGCQSAGRVQSA 522
++ A+ R L + LAR D+L G N++ +L R G S GRVQ+
Sbjct: 142 VERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTP 201
Query: 523 ALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTH-FQSK--RLNQLSI 579
L L+ R+ EI+ F ++++ V+A + P+ +Q + RL +
Sbjct: 202 VLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPL 261
Query: 580 GSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 639
H + +I+ V + + P P+ S LQ +AA + SA + +
Sbjct: 262 AEH-----VVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDIC 316
Query: 640 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFK- 698
QKLYE LITY R+D ++ +E +++ S HAP+ P+
Sbjct: 317 QKLYE--------THKLITYPRSDCRYLPEEHFAGRHAVM--NAISVHAPDLLPQPVVDP 366
Query: 699 KVKN------AQEAHEAIRPTDIRRLPAMLSGL-LDEDCLKLYSLIWSRTMACQMQPATV 751
++N +AH AI PT A S + L E+ K+Y+LI +R Q P V
Sbjct: 367 DIRNRCWDDKKVDAHHAIIPT------ARSSAINLTENEAKVYNLI-ARQYLMQFCPDAV 419
Query: 752 GQ---IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAIL 808
+ I++DI ++ FL +AG ++E D L
Sbjct: 420 FRKCVIELDIAKG-------KFVAKARFLA--------EAGWRTLLGSKERDEENDGTPL 464
Query: 809 NSLKTGDPLYLGEVELKQHHTQPPARYSEGSLV------------KKLEEL-----GIGR 851
+ GD L + E+ + TQPP +++ +L+ K L+++ G+G
Sbjct: 465 PVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGT 524
Query: 852 PSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV-TDYSFTADMETELDN 910
+T A +++L R ++T K R ++ G+ L H E+ T TA E+ L
Sbjct: 525 EATRAGIIELLFKRGFLTKKGRYIHSTDAGKA----LFHSLPEMATRPDMTAHWESVLTQ 580
Query: 911 VS 912
+S
Sbjct: 581 IS 582
>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
An 8-Base Single-Stranded Dna Oligonucleotide
Length = 659
Score = 99.8 bits (247), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 134/542 (24%), Positives = 230/542 (42%), Gaps = 82/542 (15%)
Query: 410 HLKSIKVALSGAENLILASDPDREGEAIAWHIVEMLQQQDALHENITVARVVFHEITEAS 469
L IK L A ++ A DPDREG+ + +++ LQ A + V R + +++ +
Sbjct: 84 QLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQL--APEKRQQVQRCLINDLNPQA 141
Query: 470 IKVALQAAREID--ANLVQAYLARRALDYLIGFNIS---PLLWRK--LPGCQSAGRVQSA 522
++ A+ R L + LAR D+L G N++ +L R G S GRVQ+
Sbjct: 142 VERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTP 201
Query: 523 ALSLICDREMEIDEFKPQEYWTVEAVLDKKESHSLDTFSFPAHLTH-FQSK--RLNQLSI 579
L L+ R+ EI+ F ++++ V+A + P+ +Q + RL +
Sbjct: 202 VLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPL 261
Query: 580 GSHTEAKDIEQKINSANFQVIKNSKRSMVRKNPTPYITSTLQQDAANKLNFSATYTMKLA 639
H + +I+ V + + P P+ S LQ +AA + SA + +
Sbjct: 262 AEH-----VVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDIC 316
Query: 640 QKLYEGVQLPDGTAAGLITYMRTDGLHISDEAAKEIRSLIFERYGSHHAPEEGPRKYFK- 698
QKLYE LIT+ R+D ++ +E +++ S HAP+ P+
Sbjct: 317 QKLYE--------THKLITFPRSDCRYLPEEHFAGRHAVM--NAISVHAPDLLPQPVVDP 366
Query: 699 KVKN------AQEAHEAIRPTDIRRLPAMLSGL-LDEDCLKLYSLIWSRTMACQMQPATV 751
++N +AH AI PT A S + L E+ K+Y+LI +R Q P V
Sbjct: 367 DIRNRCWDDKKVDAHHAIIPT------ARSSAINLTENEAKVYNLI-ARQYLMQFCPDAV 419
Query: 752 GQ---IQVDIGNADESIVFRSSCSRVEFLGFQAAYEDVDAGAIRYKENEENDRHEAFAIL 808
+ I++DI ++ FL +AG ++E D L
Sbjct: 420 FRKCVIELDIAKG-------KFVAKARFLA--------EAGWRTLLGSKERDEENDGTPL 464
Query: 809 NSLKTGDPLYLGEVELKQHHTQPPARYSEGSLV------------KKLEEL-----GIGR 851
+ GD L + E+ + TQPP +++ +L+ K L+++ G+G
Sbjct: 465 PVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGT 524
Query: 852 PSTYASTLKVLQDRNYVTVKSRILYPEFRGRMVSAFLSHYFSEV-TDYSFTADMETELDN 910
+T A +++L R ++T K R ++ G+ L H E+ T TA E+ L
Sbjct: 525 EATRAGIIELLFKRGFLTKKGRYIHSTDAGKA----LFHSLPEMATRPDMTAHWESVLTQ 580
Query: 911 VS 912
+S
Sbjct: 581 IS 582
>pdb|3JRO|C Chain C, Nup84-Nup145c-Sec13 Edge Element Of The Npc Lattice
Length = 426
Score = 30.0 bits (66), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 393 PDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEML 445
P D F+++ E SAA ++ +A SG E+ +++S D E EA WH+VE+L
Sbjct: 34 PIDPFNIIREFRSAAGQ--LALDLANSGDESNVISS-KDWELEARFWHLVELL 83
>pdb|3IKO|C Chain C, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|F Chain F, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
pdb|3IKO|I Chain I, Crystal Structure Of The Heterotrimeric
Sec13-Nup145c-Nup84 Nucleoporin Complex
Length = 460
Score = 30.0 bits (66), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 393 PDDDFSMVWEVPSAAWTHLKSIKVALSGAENLILASDPDREGEAIAWHIVEML 445
P D F+++ E SAA ++ +A SG E+ +++S D E EA WH+VE+L
Sbjct: 32 PIDPFNIIREFRSAAGQ--LALDLANSGDESNVISS-KDWELEARFWHLVELL 81
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
0.316 0.132 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,229,674
Number of Sequences: 62578
Number of extensions: 1247209
Number of successful extensions: 2876
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 2792
Number of HSP's gapped (non-prelim): 48
length of query: 1158
length of database: 14,973,337
effective HSP length: 109
effective length of query: 1049
effective length of database: 8,152,335
effective search space: 8551799415
effective search space used: 8551799415
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: 57 (26.6 bits)