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= 046997
(807 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 121 bits (304), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 139/525 (26%), Positives = 221/525 (42%), Gaps = 60/525 (11%)
Query: 97 VPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSAL 156
V + K+ + + L++ A++ + L+ D DREGE IA+ + R N R FS +
Sbjct: 59 VIKGKEKVVEKLKDLAKKGELLIAS-DMDREGEAIAWHI---ARVTNTLGRKNRIVFSEI 114
Query: 157 IDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLV 216
R I +AV+N + + A AR+ +D +G S + +L +NF +
Sbjct: 115 TPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLS---PVLWRNFKSN--------- 162
Query: 217 LSYGPCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVI 276
LS G Q TL V +R EI +++ I + TA FD +
Sbjct: 163 LSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDG--LTAEIDVKEKKFFDAETLKE 220
Query: 277 IY---EMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLY 333
I E+ V+E +V K PP P T L++ A S TM +A+ LY
Sbjct: 221 IQSIDELVVEEKKVSVKKF-------APPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLY 273
Query: 334 QA--------GFISYPRTETDSFS--SGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWR 383
+ FI+Y RT++ S + ++ E G G +R R
Sbjct: 274 EGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKRER---------R 324
Query: 384 NPGSGGHDDKAHPPIHPTK-FSSGESR---WSQDHYKLYELVVRHFLACVSQPAVGAETI 439
+ D AH I PT F + E + D KLYEL+ + FLA +P+ ET
Sbjct: 325 KSNAKIQD--AHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETR 382
Query: 440 VEINIAGEVFSTSGRVI--LAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTR 497
+ + G V+ + Y V++ E G + G+ P + ++ T+
Sbjct: 383 FVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEF--PFEEGESVKPVVVKIEEQETK 440
Query: 498 PPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557
P P +E L+ M++ GIG +T IK LL+R Y IK PT +G ++VM Y
Sbjct: 441 PKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGY-IKKIRGYLYPTIVG-SVVMDYL 498
Query: 558 DMGY-ELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACF 601
+ Y ++ + + ME D+ EV G K+ VL + + F
Sbjct: 499 EKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVF 543
>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 = 121 bits (303), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 124/502 (24%), Positives = 206/502 (41%), Gaps = 58/502 (11%)
Query: 101 KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160
K+ + L++ A + + L D DREGE IA+ + EV + R F+ +
Sbjct: 89 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY--SRVVFNEITKNA 146
Query: 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220
I QA + N +A AR+ +D +G + +L K LS G
Sbjct: 147 IRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS---PLLWKKIARG---------LSAG 194
Query: 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEM 280
Q + VVER EI+A EEFW ++ S + G A + H D + E
Sbjct: 195 RVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA-LALQVTHQNDKPFRPVNKEQ 253
Query: 281 C------VQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQ 334
+++ +V + + P P T L++ AS + TM +A+ LY+
Sbjct: 254 TQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 335 AGFISYPRTETDSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392
AG+I+Y RT++ + S N+ G + + G ++ L + + S G+
Sbjct: 314 AGYITYMRTDSTNLSQDAVNMVRGYISDNFG--------KKYLPESPNQY---ASKGNSQ 362
Query: 393 KAHPPIHPTK---FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVF 449
+AH I P+ + D KLY+L+ R F+AC PA T + +
Sbjct: 363 EAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRL 422
Query: 450 STSGRVILAKNYLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRP 498
GR++ RF+ W + ++P G LT T+P
Sbjct: 423 KARGRIL---------RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKP 473
Query: 499 PPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDD 558
P SEA L+ ++K GIG +T I + DR Y ++ N RF +GE + ++
Sbjct: 474 PARFSEASLVKELEKRGIGRPSTYASIISTIQDRGY-VRVENRRFYAEKMGEIVTDRLEE 532
Query: 559 MGYELWKPNLRSMMESDMKEVS 580
EL + + ME+ + +V+
Sbjct: 533 NFRELMNYDFTAQMENSLDQVA 554
>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 = 117 bits (294), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 123/502 (24%), Positives = 205/502 (40%), Gaps = 58/502 (11%)
Query: 101 KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160
K+ + L++ A + + L D DREGE IA+ + EV + R F+ +
Sbjct: 91 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY--SRVVFNEITKNA 148
Query: 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220
I QA + N +A AR+ +D +G + +L K LS G
Sbjct: 149 IRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS---PLLWKKIARG---------LSAG 196
Query: 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEM 280
Q + VVER EI+A EEFW ++ S + G A + H D + E
Sbjct: 197 RVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA-LALQVTHQNDKPFRPVNKEQ 255
Query: 281 C------VQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQ 334
+++ +V + + P P T L++ AS + TM +A+ LY+
Sbjct: 256 TQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 315
Query: 335 AGFISYPRTETDSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392
AG+I+Y RT++ + S N+ G + + G ++ L + + S +
Sbjct: 316 AGYITYMRTDSTNLSQDAVNMVRGYISDNFG--------KKYLPESPNQY---ASKENSQ 364
Query: 393 KAHPPIHPTK---FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVF 449
+AH I P+ + D KLY+L+ R F+AC PA T + +
Sbjct: 365 EAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRL 424
Query: 450 STSGRVILAKNYLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRP 498
GR++ RF+ W + ++P G LT T+P
Sbjct: 425 KARGRIL---------RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKP 475
Query: 499 PPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDD 558
P SEA L+ ++K GIG +T I + DR Y ++ N RF +GE + ++
Sbjct: 476 PARFSEASLVKELEKRGIGRPSTYASIISTIQDRGY-VRVENRRFYAEKMGEIVTDRLEE 534
Query: 559 MGYELWKPNLRSMMESDMKEVS 580
EL + + ME+ + +V+
Sbjct: 535 NFRELMNYDFTAQMENSLDQVA 556
>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 = 115 bits (289), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 120/499 (24%), Positives = 203/499 (40%), Gaps = 52/499 (10%)
Query: 101 KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160
K+ + L++ A + + L D DREGE IA+ + EV + R F+ +
Sbjct: 89 KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARY--SRVVFNEITKNA 146
Query: 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220
I QA + N +A AR+ +D +G + +L K LS G
Sbjct: 147 IRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS---PLLWKKIARG---------LSAG 194
Query: 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEM 280
Q + VVER EI+A EEFW ++ S + G A + H D + E
Sbjct: 195 RVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA-LALQVTHQNDKPFRPVNKEQ 253
Query: 281 C------VQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQ 334
+++ +V + + P P T L++ AS + TM +A+ LY+
Sbjct: 254 TQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 335 AGFISYPRTETDSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392
AG+I+Y RT++ + S N+ G + + G ++ L + + + +
Sbjct: 314 AGYITYMRTDSTNLSQDAVNMVRGYISDNFG--------KKYLPESPNQYASKENSQEAR 365
Query: 393 KAHPPIHPTKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTS 452
+A P + D KLY+L+ R F+AC PA T + +
Sbjct: 366 EAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKAR 425
Query: 453 GRVILAKNYLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRPPPL 501
GR++ RF+ W + ++P G LT T+PP
Sbjct: 426 GRIL---------RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPAR 476
Query: 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGY 561
SEA L+ ++K GIG +T I + DR Y ++ N RF +GE + ++
Sbjct: 477 FSEASLVKELEKRGIGRPSTYASIISTIQDRGY-VRVENRRFYAEKMGEIVTDRLEENFR 535
Query: 562 ELWKPNLRSMMESDMKEVS 580
EL + + ME+++ +V+
Sbjct: 536 ELMNYDFTAQMENNLDQVA 554
>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia
Length = 596
Score = 115 bits (289), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 122/502 (24%), Positives = 205/502 (40%), Gaps = 58/502 (11%)
Query: 101 KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160
K+ + L++ A + + L + DREGE IA+ + EV + R F+ +
Sbjct: 89 KEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARY--SRVVFNEITKNA 146
Query: 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220
I QA + N +A AR+ +D +G + +L K LS G
Sbjct: 147 IRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS---PLLWKKIARG---------LSAG 194
Query: 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEM 280
Q + VVER EI+A EEFW ++ S + G A + H D + E
Sbjct: 195 RVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA-LALQVTHQNDKPFRPVNKEQ 253
Query: 281 C------VQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQ 334
+++ +V + + P P T L++ AS + TM +A+ LY+
Sbjct: 254 TQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 335 AGFISYPRTETDSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392
AG+I+Y RT++ + S N+ G + + G ++ L + + S +
Sbjct: 314 AGYITYMRTDSTNLSQDAVNMVRGYISDNFG--------KKYLPESPNQY---ASKENSQ 362
Query: 393 KAHPPIHPTK---FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVF 449
+AH I P+ + D KLY+L+ R F+AC PA T + +
Sbjct: 363 EAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRL 422
Query: 450 STSGRVILAKNYLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRP 498
GR++ RF+ W + ++P G LT T+P
Sbjct: 423 KARGRIL---------RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKP 473
Query: 499 PPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDD 558
P SEA L+ ++K GIG +T I + DR Y ++ N RF +GE + ++
Sbjct: 474 PARFSEASLVKELEKRGIGRPSTYASIISTIQDRGY-VRVENRRFYAEKMGEIVTDRLEE 532
Query: 559 MGYELWKPNLRSMMESDMKEVS 580
EL + + ME+ + +V+
Sbjct: 533 NFRELMNYDFTAQMENSLDQVA 554
>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a
With Substrate
Length = 595
Score = 112 bits (281), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 121/502 (24%), Positives = 204/502 (40%), Gaps = 58/502 (11%)
Query: 101 KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160
K+ + L++ A + + L + DREGE IA+ + EV + R F+ +
Sbjct: 89 KEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARY--SRVVFNEITKNA 146
Query: 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220
I QA + N +A AR+ +D +G + +L K LS G
Sbjct: 147 IRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVS---PLLWKKIARG---------LSAG 194
Query: 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEM 280
Q + VVER EI+A EEFW ++ S + G A + H D + E
Sbjct: 195 RVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA-LALQVTHQNDKPFRPVNKEQ 253
Query: 281 C------VQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQ 334
+++ +V + + P P T L++ AS + TM +A+ LY+
Sbjct: 254 TQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 335 AGFISYPRTETDSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392
AG+I+ RT++ + S N+ G + + G ++ L + + S +
Sbjct: 314 AGYITXMRTDSTNLSQDAVNMVRGYISDNFG--------KKYLPESPNQY---ASKENSQ 362
Query: 393 KAHPPIHPTK---FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVF 449
+AH I P+ + D KLY+L+ R F+AC PA T + +
Sbjct: 363 EAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRL 422
Query: 450 STSGRVILAKNYLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRP 498
GR++ RF+ W + ++P G LT T+P
Sbjct: 423 KARGRIL---------RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKP 473
Query: 499 PPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDD 558
P SEA L+ ++K GIG +T I + DR Y ++ N RF +GE + ++
Sbjct: 474 PARFSEASLVKELEKRGIGRPSTYASIISTIQDRGY-VRVENRRFYAEKMGEIVTDRLEE 532
Query: 559 MGYELWKPNLRSMMESDMKEVS 580
EL + + ME+ + +V+
Sbjct: 533 NFRELMNYDFTAQMENSLDQVA 554
>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 = 108 bits (270), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 153/621 (24%), Positives = 253/621 (40%), Gaps = 92/621 (14%)
Query: 11 LNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLME 70
L +AEKPS+A+++A +L K R+G F GQ ++T GHL+E
Sbjct: 3 LFIAEKPSLARAIADVLPKPH----RKGDG-------FIECGNGQ----VVTWCIGHLLE 47
Query: 71 LD----FDERYRKWHSCD----PADLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWL 122
+D RY +W+ D P P R V + IK+ L E + +V
Sbjct: 48 QAQPDAYDSRYARWNLADLPIVPEKWQLQP-RPSVTKQLNVIKRFLHEASE----IVHAG 102
Query: 123 DCDREGENIAFEVIEVCR-AVNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDA 181
D DREG+ + EV++ + A ++R + L + + +A+ L +++ V A
Sbjct: 103 DPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSA 162
Query: 182 --RQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQA 239
R D G + TR T+L +N V LS G Q P LG VV R EI+
Sbjct: 163 LARARADWLYGINMTRAYTILGRNAGYQGV-------LSVGRVQTPVLGLVVRRDEEIEN 215
Query: 240 HESEEFWTINCSH------------KSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTA 287
+++F+ + + E + G L A + +P A
Sbjct: 216 FVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQP-A 274
Query: 288 TVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQA-GFISYPRTETD 346
VT + + + P P S L+ A++ F +S+++ + + + LY+ I+YPR++
Sbjct: 275 IVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCR 334
Query: 347 SFSSG--TNLHGIVQEQIGH-PDWGPYAQRLLDHAAGLWRNPGSGGHDDK---AHPPIHP 400
H ++ H PD P D W DDK AH I P
Sbjct: 335 YLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCW--------DDKKVDAHHAIIP 386
Query: 401 TKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKN 460
T SS + +++ K+Y L+ R +L AV + ++E++IA F R +
Sbjct: 387 TARSSAIN-LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAG 445
Query: 461 YLDVY----RFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCM----- 511
+ + R E G +P G + + + T+PP ++A LLS M
Sbjct: 446 WRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIAR 505
Query: 512 ---DK---------AGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDM 559
DK G+GT+AT I+ L R + K T+ G+AL +M
Sbjct: 506 FVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRY-IHSTDAGKALFHSLPEM 564
Query: 560 GYELWKPNLRSMMESDMKEVS 580
+P++ + ES + ++S
Sbjct: 565 AT---RPDMTAHWESVLTQIS 582
>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
Length = 653
Score = 108 bits (270), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 153/621 (24%), Positives = 253/621 (40%), Gaps = 92/621 (14%)
Query: 11 LNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLME 70
L +AEKPS+A+++A +L K R+G F GQ ++T GHL+E
Sbjct: 3 LFIAEKPSLARAIADVLPKPH----RKGDG-------FIECGNGQ----VVTWCIGHLLE 47
Query: 71 LD----FDERYRKWHSCD----PADLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWL 122
+D RY +W+ D P P R V + IK+ L E + +V
Sbjct: 48 QAQPDAYDSRYARWNLADLPIVPEKWQLQP-RPSVTKQLNVIKRFLHEASE----IVHAG 102
Query: 123 DCDREGENIAFEVIEVCR-AVNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDA 181
D DREG+ + EV++ + A ++R + L + + +A+ L +++ V A
Sbjct: 103 DPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSA 162
Query: 182 --RQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQA 239
R D G + TR T+L +N V LS G Q P LG VV R EI+
Sbjct: 163 LARARADWLYGINMTRAYTILGRNAGYQGV-------LSVGRVQTPVLGLVVRRDEEIEN 215
Query: 240 HESEEFWTINCSH------------KSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTA 287
+++F+ + + E + G L A + +P A
Sbjct: 216 FVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQP-A 274
Query: 288 TVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQA-GFISYPRTETD 346
VT + + + P P S L+ A++ F +S+++ + + + LY+ I+YPR++
Sbjct: 275 IVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCR 334
Query: 347 SFSSG--TNLHGIVQEQIGH-PDWGPYAQRLLDHAAGLWRNPGSGGHDDK---AHPPIHP 400
H ++ H PD P D W DDK AH I P
Sbjct: 335 YLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCW--------DDKKVDAHHAIIP 386
Query: 401 TKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKN 460
T SS + +++ K+Y L+ R +L AV + ++E++IA F R +
Sbjct: 387 TARSSAIN-LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAG 445
Query: 461 YLDVY----RFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCM----- 511
+ + R E G +P G + + + T+PP ++A LLS M
Sbjct: 446 WRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIAR 505
Query: 512 ---DK---------AGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDM 559
DK G+GT+AT I+ L R + K T+ G+AL +M
Sbjct: 506 FVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRY-IHSTDAGKALFHSLPEM 564
Query: 560 GYELWKPNLRSMMESDMKEVS 580
+P++ + ES + ++S
Sbjct: 565 AT---RPDMTAHWESVLTQIS 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 = 107 bits (266), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 152/621 (24%), Positives = 253/621 (40%), Gaps = 92/621 (14%)
Query: 11 LNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLME 70
L +AEKPS+A+++A +L K R+G F GQ ++T GHL+E
Sbjct: 3 LFIAEKPSLARAIADVLPKPH----RKGDG-------FIECGNGQ----VVTWCIGHLLE 47
Query: 71 LD----FDERYRKWHSCD----PADLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWL 122
+D RY +W+ D P P R V + IK+ L E + +V
Sbjct: 48 QAQPDAYDSRYARWNLADLPIVPEKWQLQP-RPSVTKQLNVIKRFLHEASE----IVHAG 102
Query: 123 DCDREGENIAFEVIEVCR-AVNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDA 181
D DREG+ + EV++ + A ++R + L + + +A+ L +++ V A
Sbjct: 103 DPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSA 162
Query: 182 --RQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQA 239
R D G + TR T+L +N V LS G Q P LG VV R EI+
Sbjct: 163 LARARADWLYGINMTRAYTILGRNAGYQGV-------LSVGRVQTPVLGLVVRRDEEIEN 215
Query: 240 HESEEFWTINCSH------------KSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTA 287
+++F+ + + E + G L A + +P A
Sbjct: 216 FVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQP-A 274
Query: 288 TVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQA-GFISYPRTETD 346
VT + + + P P S L+ A++ F +S+++ + + + LY+ I++PR++
Sbjct: 275 IVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITFPRSDCR 334
Query: 347 SFSSG--TNLHGIVQEQIGH-PDWGPYAQRLLDHAAGLWRNPGSGGHDDK---AHPPIHP 400
H ++ H PD P D W DDK AH I P
Sbjct: 335 YLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCW--------DDKKVDAHHAIIP 386
Query: 401 TKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKN 460
T SS + +++ K+Y L+ R +L AV + ++E++IA F R +
Sbjct: 387 TARSSAIN-LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAG 445
Query: 461 YLDVY----RFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCM----- 511
+ + R E G +P G + + + T+PP ++A LLS M
Sbjct: 446 WRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIAR 505
Query: 512 ---DK---------AGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDM 559
DK G+GT+AT I+ L R + K T+ G+AL +M
Sbjct: 506 FVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRY-IHSTDAGKALFHSLPEM 564
Query: 560 GYELWKPNLRSMMESDMKEVS 580
+P++ + ES + ++S
Sbjct: 565 AT---RPDMTAHWESVLTQIS 582
>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 = 84.0 bits (206), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 107/462 (23%), Positives = 195/462 (42%), Gaps = 91/462 (19%)
Query: 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAV 165
+ L + A +++++ D D EGE IA+++ + ++RA F + R I +A+
Sbjct: 614 EALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGA---VKRAEFHEVTRRAILEAL 670
Query: 166 QNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFP 225
++L D ++ A R+ D IG ++ L + F ++RNL S G Q
Sbjct: 671 ESLRDVDENLVKAQVVRRIEDRWIGFVLSQ---KLWERF------NNRNL--SAGRAQTL 719
Query: 226 TLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEP 285
LG++++R+ ES E I FD ++ E +E
Sbjct: 720 VLGWIIDRF-----QESRERRKIAIVRD---------------FD-----LVLEHDEEEF 754
Query: 286 TATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTET 345
T+ V ++E+L+ P P +T + A+R + S + TM++A++L++ G I+Y RT++
Sbjct: 755 DLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFENGLITYHRTDS 814
Query: 346 DSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSS 405
S I +E +G D W G AH I PT+ +
Sbjct: 815 TRVSDVG--QRIAKEYLGD-----------DFVGREWGESG-------AHECIRPTRPLT 854
Query: 406 GES---------------RWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFS 450
+ RW +H+ LY+L+ R F+A +P I G+ +
Sbjct: 855 RDDVQRLIQEGVLVVEGLRW--EHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKT-A 911
Query: 451 TSGRVILAK-NYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLL--SEADL 507
R++ A+ ++YR W +PT T + + V P +L +++++
Sbjct: 912 EEERIVRAEGRAYELYR-AVWVKNELPT---------GTFRVKAEVKSVPKVLPFTQSEI 961
Query: 508 LSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIG 549
+ M + GIG +T + +L R Y ++ R PT +G
Sbjct: 962 IQMMKERGIGRPSTYATIVDRLFMRNYVVEKYG-RMIPTKLG 1002
>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
Length = 1054
Score = 84.0 bits (206), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 107/462 (23%), Positives = 195/462 (42%), Gaps = 91/462 (19%)
Query: 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAV 165
+ L + A +++++ D D EGE IA+++ + ++RA F + R I +A+
Sbjct: 614 EALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLSGCGA---VKRAEFHEVTRRAILEAL 670
Query: 166 QNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFP 225
++L D ++ A R+ D IG ++ L + F ++RNL S G Q
Sbjct: 671 ESLRDVDENLVKAQVVRRIEDRWIGFVLSQ---KLWERF------NNRNL--SAGRAQTL 719
Query: 226 TLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEP 285
LG++++R+ ES E I FD ++ E +E
Sbjct: 720 VLGWIIDRF-----QESRERRKIAIVRD---------------FD-----LVLEHDEEEF 754
Query: 286 TATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTET 345
T+ V ++E+L+ P P +T + A+R + S + TM++A++L++ G I+Y RT++
Sbjct: 755 DLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQELFENGLITYHRTDS 814
Query: 346 DSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSS 405
S I +E +G D W G AH I PT+ +
Sbjct: 815 TRVSDVG--QRIAKEYLGD-----------DFVGREWGESG-------AHECIRPTRPLT 854
Query: 406 GES---------------RWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFS 450
+ RW +H+ LY+L+ R F+A +P I G+ +
Sbjct: 855 RDDVQRLIQEGVLVVEGLRW--EHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKT-A 911
Query: 451 TSGRVILAK-NYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLL--SEADL 507
R++ A+ ++YR W +PT T + + V P +L +++++
Sbjct: 912 EEERIVRAEGRAYELYR-AVWVKNELPT---------GTFRVKAEVKSVPKVLPFTQSEI 961
Query: 508 LSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIG 549
+ M + GIG +T + +L R Y ++ R PT +G
Sbjct: 962 IQMMKERGIGRPSTYATIVDRLFMRNYVVEKYG-RMIPTKLG 1002
>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 = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 115/525 (21%), Positives = 200/525 (38%), Gaps = 89/525 (16%)
Query: 99 EDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALID 158
+DK + + L E + +++ D D EGE I+++V + + LRR +
Sbjct: 644 DDKTETLRALREISLEADEILVATDPDVEGEKISWDVTQYL--LPSTRSLRRIEMHEITR 701
Query: 159 REIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQT--MLLKNFHIDSVTDDRNLV 216
+A +++ F D + +I R+ + F+ L K F +
Sbjct: 702 YGFKKARESV-----RFVDFNLVKAQIVRRVQDRWIGFELSGKLQKRFGRSN-------- 748
Query: 217 LSYGPCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVI 276
LS G Q LG++VER EE+ KSE+ G +
Sbjct: 749 LSAGRVQSTVLGWIVER--------EEEY------KKSEKDFTLLVLENGVNLEV----- 789
Query: 277 IYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAG 336
E + + TV ++++ E+ K P P +T S+ R+ + M + +DL++ G
Sbjct: 790 --EGKIADDVVTVVELQEAEEEKNPLPPYTTSSALSEISQKLRLGVQEVMDILQDLFEKG 847
Query: 337 FISYPRTETDSFS-SGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAH 395
FI+Y RT++ S G N+ +IG D W G AH
Sbjct: 848 FITYHRTDSTRISLEGQNVARTYLRKIGKEDI---------FMGRSWSTEG-------AH 891
Query: 396 PPIHPTKFSSGE-----------SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINI 444
I P K + ++ H ++YEL+ FLA S + IV +++
Sbjct: 892 EAIRPVKPIDARELEEMIEEGLIADLTKKHLRVYELIFNRFLASQSAAVKVKKQIVTVDV 951
Query: 445 AGEVFSTSGRVILAKNYLDVY-------RFESWGGLVIPTYVHGQQFIPTTLTLDSGVTR 497
G+ V + ++ +++ RFE TY ++ T+
Sbjct: 952 DGKRMGIEQIVEILRDGWNLFVPLTVSPRFEH------RTYKIKEKKFYKKHTV------ 999
Query: 498 PPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557
PL ++A ++ M K GIG +T ++ L R Y +D R PT G +V Y
Sbjct: 1000 --PLFTQASIVEEMKKRGIGRPSTYAKIVEVLFRRGYVYEDKYKRVRPTRFG-VMVYSYL 1056
Query: 558 DMGYELW-KPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACF 601
YE + +E M +V G + L +++K+
Sbjct: 1057 KERYEKYVTEETTRRLEEIMDKVERGEEDYQATLRLLYEEIKSLM 1101
>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 = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 64/290 (22%), Positives = 114/290 (39%), Gaps = 48/290 (16%)
Query: 229 FVVERYWEIQAHE---SEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEP 285
FV E +WE+ A S E + +H++++ R + T A + +++
Sbjct: 1 FVPEEFWEVDASTTTPSGEALALQVTHQNDKP------FRPVNKEQTQAAV---SLLEKA 51
Query: 286 TATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTET 345
+V + + P P T L++ AS + TM +A+ LY+AG+I+Y RT++
Sbjct: 52 RYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS 111
Query: 346 DSFS-SGTNL-HGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTK- 402
+ S N+ G + + G ++ L + + S + +AH I P+
Sbjct: 112 TNLSQDAVNMVRGYISDNFG--------KKYLPESPNQY---ASKENSQEAHEAIRPSDV 160
Query: 403 --FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKN 460
+ D KLY+L+ R F+AC PA T + + GR++
Sbjct: 161 NVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRIL---- 216
Query: 461 YLDVYRFESWGGL-----------VIPTYVHGQQFIPTTLTLDSGVTRPP 499
RF+ W + ++P G LT T+PP
Sbjct: 217 -----RFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPP 261
>pdb|2R5V|A Chain A, Hydroxymandelate Synthase Crystal Structure
pdb|2R5V|B Chain B, Hydroxymandelate Synthase Crystal Structure
Length = 357
Score = 33.1 bits (74), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 21/43 (48%)
Query: 669 AVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFN 711
AV PG SEAAVTT T LIQ E+PPGF
Sbjct: 99 AVRAPGQHSEAAVTTATIGGFGDVVHTLIQRDGTSAELPPGFT 141
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 762 CIYCQQMGHSSSDCPSQFSGSRNARAN 788
C YC++ GH + DCP + G R R
Sbjct: 13 CAYCKEKGHWAKDCPKKPRGPRGPRPQ 39
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 762 CIYCQQMGHSSSDCPSQFSGSRNAR 786
C YC++ GH + DCP + G R R
Sbjct: 26 CAYCKEKGHWAKDCPKKPRGPRGPR 50
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
0.320 0.135 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,095,771
Number of Sequences: 62578
Number of extensions: 1057739
Number of successful extensions: 2148
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2089
Number of HSP's gapped (non-prelim): 22
length of query: 807
length of database: 14,973,337
effective HSP length: 107
effective length of query: 700
effective length of database: 8,277,491
effective search space: 5794243700
effective search space used: 5794243700
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)