|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07561 |
PRK07561 |
DNA topoisomerase I subunit omega; Validated |
3-781 |
0e+00 |
|
DNA topoisomerase I subunit omega; Validated
Pssm-ID: 236048 [Multi-domain] Cd Length: 859 Bit Score: 918.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDL-----------KKKEFS---IDIEKNFKPKYEIPEEKQELVDKLK 68
Cdd:PRK07561 2 KSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLptsassvpakeKGALWArmgVDPDHDFEALYEVLPGKEKVVSELK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 69 EEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGF 148
Cdd:PRK07561 82 KAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGY 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 149 ELSPVLWKKVKPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDADG---KLVEMKAE-LAR-RLKTKKEA 223
Cdd:PRK07561 162 MVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAfeaRLTHLDGKkFAPvDLLNEAQA 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 224 QKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEG 303
Cdd:PRK07561 242 EAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINA 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 304 SKAAIAQMMGEQYVH--PRHFATKTKGAQEAHEAIRPTYME---NQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTA 378
Cdd:PRK07561 322 ARGYIGDNYGKKYLPekPRQYSSKAKNAQEAHEAIRPSDVFrtpDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTV 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 379 TigISSGSDKFTATGEVIKFDGFLRVYKESYDDdnEQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKL 458
Cdd:PRK07561 402 T--IAAGDAELRATGRVLRFDGFLKVYVEGRDD--ALDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKEL 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 459 EELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFP 538
Cdd:PRK07561 478 EKLGIGRPSTYASIISTIQDRGYVRL-------------------------------ENRRFYPEKMGRIVTDRLEEFFP 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 539 NILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFH---------------------------PSVETTLATKT----- 586
Cdd:PRK07561 527 RLVDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSqqlekaeelreeggmrpnqmvitdrdcPTCGRGMGIRTgktgv 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 587 ------------------------------EHKVGERILGEEPKTGKTVSVKIGRFGPVVQigtADDTDKPRFAQMKKGQ 636
Cdd:PRK07561 607 flgcsgyalkerckttrnltpeeetlnvleGEDAETRALGADPECGTAMVLRSGRFGPYVQ---EGEGDKPRRLSLPKGN 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 637 SMETITLEEALDLFKLPRKVGEFEE--KTVTIGTGRFGPYVYHDSKYVSLPKTYDPLEVTLDEAIELI----LGKREAEA 710
Cdd:PRK07561 684 NPECVGLEIALGLLSLPRPVGEHPEcgSEIQAKIGRFGPYVKCGGTYASLKNTRKVLTIGLNRAVELLaepkRPKEDPVP 763
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1501682078 711 KKHIKKFDEDPEMEILNGRYGPYITYKGSNYKIPKDVVPADLnykTCLEIIKLQSEKAESAPKRGRYAKKK 781
Cdd:PRK07561 764 LPELGCPKSGAPFVLRDGRYGPYVKHGKANATLPKGRETRAP---TVEEALELLAEKPEKLRYLADAPAKD 831
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-579 |
0e+00 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 820.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLASD 82
Cdd:COG0550 1 KKLVIVESPAKAKTIAKYLGKDYVVTASVGHLRDLPKPELDVDVENDFEPKYEVIPGKKKQVKELKKLAKKADEVILATD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 83 EDREGEAISWHLYEVLKlKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPAL 162
Cdd:COG0550 81 PDREGEAIAWHLLELLG-DKKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 163 SAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDA--DGKLVEMKAElarRLKTKKEAQKFLESCKAATFSIEDI 240
Cdd:COG0550 160 SAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGefTAKLVKIDGK---KILDEEEAEAILAALKGKTFTVTSV 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 241 VTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYV--H 318
Cdd:COG0550 237 EKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLpeK 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 319 PRHFATKtKGAQEAHEAIRPTYMENQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKF 398
Cdd:COG0550 317 PRVYKTS-KNAQEAHEAIRPTGVTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEV--GGEEFRASGKVIKF 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 399 DGFLRVYKESYDDDNEQEDEshLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQ 478
Cdd:COG0550 394 PGFLKVYGEGKDDEEEEEEK--RLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGRPSTYASIIETLQD 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 479 REYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAE 558
Cdd:COG0550 472 RGYVER-------------------------------EGKRLVPTELGFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAE 520
|
570 580
....*....|....*....|.
gi 1501682078 559 GDKKWTSIMKDFYKEFHPSVE 579
Cdd:COG0550 521 GKLDWKDVLEEFYKPFKELVE 541
|
|
| topA_bact |
TIGR01051 |
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ... |
5-629 |
0e+00 |
|
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273416 [Multi-domain] Cd Length: 610 Bit Score: 692.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLASDED 84
Cdd:TIGR01051 1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGVDIEKDFEPEYVVSKGKKKVVKELKTLAKKADEVYLATDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 85 REGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPALSA 164
Cdd:TIGR01051 81 REGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 165 GRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLV--PDADGKLVEMKAE--LARRLKTKKEAQKFLESCKAATFSIEDI 240
Cdd:TIGR01051 161 GRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKgeETFEALLTEVNGKklKAGSDLDEAEATALKEQLKGEELVVEEI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 241 VTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYE--------SGLITYMRTDSVNLSEYATEGSKAAIAQMM 312
Cdd:TIGR01051 241 EKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEgvstgdgtIGLITYMRTDSTRLSNQAVNEARNLIDKNY 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 313 GEQYV--HPRHFATKTKGAQEAHEAIRPTY---MENQTVEG-SAQERKLYDLIWKRTIASQMADAELEKTTATIGISSGS 386
Cdd:TIGR01051 321 GKEYLgpKPKRYKSKEKNAQEAHEAIRPTSvfrTPEELKDYlKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 387 DKFTATGEVIKFDGFLRVYKEsyDDDNEQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRP 466
Cdd:TIGR01051 401 YVFKATGRKLIFDGYYKVYVE--GSDDPLEEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEELGIGRP 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 467 STYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFT 546
Cdd:TIGR01051 479 STYASIISTIQDRGYVKK-------------------------------ENKRLYPTELGFAVTDLLEKHFGDVVDYDFT 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 547 ANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETtlATKTEHKVGERILGEEPKTGKTVSVKIGRFGPVVQIGTADDTDK 626
Cdd:TIGR01051 528 AKMEKDLDEIAEGKAEWKPVLKNFYTGFSSKVKK--LRNMRIIVDFKTSQDCPLCGRPMVVKLGKYGPFLACSNFPECKY 605
|
...
gi 1501682078 627 PRF 629
Cdd:TIGR01051 606 TKS 608
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
127-568 |
1.20e-145 |
|
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Pssm-ID: 426069 [Multi-domain] Cd Length: 410 Bit Score: 433.21 E-value: 1.20e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 127 DIDINLVNAQQARRILDRIVGFELSPVLWKKVK--PALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVpdaDG 204
Cdd:pfam01131 1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKgnKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKD---GG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 205 KLVEMKAELARRLKTKKEAQKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYE-S 283
Cdd:pfam01131 78 GVFANAKWKRGRIFDKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEkH 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 284 GLITYMRTDSVNLSEYATegsKAAIAQMMGEQY-----------VHPRHFATKTKGAQEAHEAIRPTYMENQTVEGSAQE 352
Cdd:pfam01131 158 GLITYPRTDSTYLSDDAT---LKAILEYLTKNYgkylpyaprllKKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDE 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 353 RKLYDLIWKRTIASQMADAELEKTTATIgiSSGSDKFTATGEVIKFDGFLRVYKESYDDDNEQedeshlLPPLKKGQILE 432
Cdd:pfam01131 235 RKLYELIVRRFLASQMPPAVYETTTVVL--EVGGEEFRASGKVILEDGWLKVYPYEKKEDEEE------LPELKEGEELK 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 433 HQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtev 512
Cdd:pfam01131 307 VTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVER---------------------------- 358
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1501682078 513 vgaEKSKLLPTDIGTVVNDFLtEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMK 568
Cdd:pfam01131 359 ---KKKSLVPTELGKALVEAL-EKFPDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
130-575 |
6.37e-136 |
|
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Pssm-ID: 238110 [Multi-domain] Cd Length: 381 Bit Score: 407.38 E-value: 6.37e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 130 INLVNAQQARRILDRIVGFELSPVLWKKV--KPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVtavflvpdadgklv 207
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLrrKGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI-------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 208 emkaelarrlktkKEAQkflesckaatfsIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLIT 287
Cdd:cd00186 67 -------------KEAV------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLIT 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 288 YMRTDSVNLSEYATEGSKAAIAQMMGEQYVHP-----RHFATKTKGAQEAHEAIRPT---YMENQTVEGSAQERKLYDLI 359
Cdd:cd00186 122 YPRTDSTRLSEEAILEAREYIQAIYGKEYLYPapllgRRNPKRGKKEQGAHEAIRPTkvaPTPELEANLSEDEFKLYELI 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 360 WKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKFDGFLRVYKEsydddnEQEDESHLLPPLKKGQILEHQGIVAT 439
Cdd:cd00186 202 WRRFLASQMADAKYEETTVTLEI--GGEKFKASGKVLLEDGWLEVYPE------EKDDEEEEPPPLKEGDELKLEEVELE 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 440 ERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSK 519
Cdd:cd00186 274 EKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEK-------------------------------EKKK 322
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1501682078 520 LLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFH 575
Cdd:cd00186 323 LIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFK 378
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
243-484 |
2.39e-86 |
|
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Pssm-ID: 214663 [Multi-domain] Cd Length: 259 Bit Score: 273.74 E-value: 2.39e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 243 RPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYVHP--- 319
Cdd:smart00437 3 KEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLavv 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 320 ---RHFATKTKGAQEAHEAIRPT---YMENQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATG 393
Cdd:smart00437 83 llkPRKPRKGKKAQGAHEAIRPTkpiFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKI--GGEKFKAKG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 394 EVIKFDGFLRVYKESYDDDNEQedeshlLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTI 473
Cdd:smart00437 161 KTLLFDGWLKVYPEEKKEEEIE------LPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASII 234
|
250
....*....|.
gi 1501682078 474 STIQQREYVEK 484
Cdd:smart00437 235 ETLLDRGYVTK 245
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07561 |
PRK07561 |
DNA topoisomerase I subunit omega; Validated |
3-781 |
0e+00 |
|
DNA topoisomerase I subunit omega; Validated
Pssm-ID: 236048 [Multi-domain] Cd Length: 859 Bit Score: 918.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDL-----------KKKEFS---IDIEKNFKPKYEIPEEKQELVDKLK 68
Cdd:PRK07561 2 KSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLptsassvpakeKGALWArmgVDPDHDFEALYEVLPGKEKVVSELK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 69 EEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGF 148
Cdd:PRK07561 82 KAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGY 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 149 ELSPVLWKKVKPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDADG---KLVEMKAE-LAR-RLKTKKEA 223
Cdd:PRK07561 162 MVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAfeaRLTHLDGKkFAPvDLLNEAQA 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 224 QKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEG 303
Cdd:PRK07561 242 EAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINA 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 304 SKAAIAQMMGEQYVH--PRHFATKTKGAQEAHEAIRPTYME---NQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTA 378
Cdd:PRK07561 322 ARGYIGDNYGKKYLPekPRQYSSKAKNAQEAHEAIRPSDVFrtpDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTV 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 379 TigISSGSDKFTATGEVIKFDGFLRVYKESYDDdnEQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKL 458
Cdd:PRK07561 402 T--IAAGDAELRATGRVLRFDGFLKVYVEGRDD--ALDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKEL 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 459 EELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFP 538
Cdd:PRK07561 478 EKLGIGRPSTYASIISTIQDRGYVRL-------------------------------ENRRFYPEKMGRIVTDRLEEFFP 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 539 NILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFH---------------------------PSVETTLATKT----- 586
Cdd:PRK07561 527 RLVDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSqqlekaeelreeggmrpnqmvitdrdcPTCGRGMGIRTgktgv 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 587 ------------------------------EHKVGERILGEEPKTGKTVSVKIGRFGPVVQigtADDTDKPRFAQMKKGQ 636
Cdd:PRK07561 607 flgcsgyalkerckttrnltpeeetlnvleGEDAETRALGADPECGTAMVLRSGRFGPYVQ---EGEGDKPRRLSLPKGN 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 637 SMETITLEEALDLFKLPRKVGEFEE--KTVTIGTGRFGPYVYHDSKYVSLPKTYDPLEVTLDEAIELI----LGKREAEA 710
Cdd:PRK07561 684 NPECVGLEIALGLLSLPRPVGEHPEcgSEIQAKIGRFGPYVKCGGTYASLKNTRKVLTIGLNRAVELLaepkRPKEDPVP 763
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1501682078 711 KKHIKKFDEDPEMEILNGRYGPYITYKGSNYKIPKDVVPADLnykTCLEIIKLQSEKAESAPKRGRYAKKK 781
Cdd:PRK07561 764 LPELGCPKSGAPFVLRDGRYGPYVKHGKANATLPKGRETRAP---TVEEALELLAEKPEKLRYLADAPAKD 831
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-579 |
0e+00 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 820.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLASD 82
Cdd:COG0550 1 KKLVIVESPAKAKTIAKYLGKDYVVTASVGHLRDLPKPELDVDVENDFEPKYEVIPGKKKQVKELKKLAKKADEVILATD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 83 EDREGEAISWHLYEVLKlKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPAL 162
Cdd:COG0550 81 PDREGEAIAWHLLELLG-DKKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 163 SAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDA--DGKLVEMKAElarRLKTKKEAQKFLESCKAATFSIEDI 240
Cdd:COG0550 160 SAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGefTAKLVKIDGK---KILDEEEAEAILAALKGKTFTVTSV 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 241 VTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYV--H 318
Cdd:COG0550 237 EKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLpeK 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 319 PRHFATKtKGAQEAHEAIRPTYMENQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKF 398
Cdd:COG0550 317 PRVYKTS-KNAQEAHEAIRPTGVTRTPESLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEV--GGEEFRASGKVIKF 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 399 DGFLRVYKESYDDDNEQEDEshLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQ 478
Cdd:COG0550 394 PGFLKVYGEGKDDEEEEEEK--RLPPLKEGEKLKLKKIEPEQHFTKPPPRYTEASLVKAMEELGIGRPSTYASIIETLQD 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 479 REYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAE 558
Cdd:COG0550 472 RGYVER-------------------------------EGKRLVPTELGFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAE 520
|
570 580
....*....|....*....|.
gi 1501682078 559 GDKKWTSIMKDFYKEFHPSVE 579
Cdd:COG0550 521 GKLDWKDVLEEFYKPFKELVE 541
|
|
| PRK08780 |
PRK08780 |
DNA topoisomerase I; Provisional |
1-781 |
0e+00 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 181555 [Multi-domain] Cd Length: 780 Bit Score: 797.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 1 MQKNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLA 80
Cdd:PRK08780 1 MSKHLVIVESPAKAKTINKYLGKDFTVLASYGHVRDLVPKEGAVDPENGFAMRYDLIDKNEKHVEAIAKAAKSADDLYLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 81 SDEDREGEAISWHLYEVLK----LKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWK 156
Cdd:PRK08780 81 TDPDREGEAISWHLAEILKerglLKDKPMQRVVFTEITPRAIKEAMAKPRDIASDLVDAQQARRALDYLVGFNLSPLLWR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 157 KVKPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDA--DGKLVEMKAELARRL-----KTKKEAQKFLES 229
Cdd:PRK08780 161 KIQRGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPSQpfNAKLIKLDGQKFEQFtitdgDTAEAARLRIQQ 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 230 CKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYES---------GLITYMRTDSVNLSEYA 300
Cdd:PRK08780 241 AAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQDA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 301 TEGSKAAIAQMMGEQYV--HPRHFATKTKGAQEAHEAIRPT--YMENQTVEG--SAQERKLYDLIWKRTIASQMADAELE 374
Cdd:PRK08780 321 LAEIRDVIARDYGTASLpdQPNTYKTKSKNAQEAHEAVRPTsaLRTPAQVARflSDDQRRLYELIWKRAVACQMIPATLN 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 375 ktTATIGISSGSDK-FTATGEVIKFDGFLRVYKESYDDDN-EQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEA 452
Cdd:PRK08780 401 --TVSVDLAAGSEHvFRATGSTVVVPGFLAVYEEGKDDKSaEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEA 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 453 SLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgEERSFdiltlkddqitdvkhtevvgaeksklLPTDIGTVVNDF 532
Cdd:PRK08780 479 SLVKALEEYGIGRPSTYASIISTLQFRKYVEM-----EGRRF--------------------------RPTDVGRAVNKF 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 533 LTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETTLATKT-EHKVGERILGEEPKTGKTVSVKIGR 611
Cdd:PRK08780 528 LTGHFTRYVDYDFTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKDSVDrTEAGQVRELGTDPKSGKPVSVRIGR 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 612 FGPVVQIGTADDTDKPRFAQMKKGQSMETITLEEALDLFKLPRKVGEFEE-KTVTIGTGRFGPYVYHDSKYVSLPKTYDP 690
Cdd:PRK08780 608 FGPMVQIGTKDDEEKPRFASLRPGQSIDSITLEEALELFKLPRALGETDEgEDVSVGIGRFGPFVKRGSKYASLKKEDDP 687
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 691 LEVTLDEAIELILGKREAEAKKHIKKFDEDpEMEILNGRYGPYITYKGSNYKIPKDVVPADLNYKTCLEIIklqsekAES 770
Cdd:PRK08780 688 YTIDLARALFLIEEKEEIARNRVIKDFEGS-GIQVLNGRYGPYITDGKLNGKIPKDREPASLTLEEVQQLL------ADA 760
|
810
....*....|.
gi 1501682078 771 APKRGRYAKKK 781
Cdd:PRK08780 761 PVRKGFRAKKA 771
|
|
| PRK06599 |
PRK06599 |
DNA topoisomerase I; Validated |
1-613 |
0e+00 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235840 [Multi-domain] Cd Length: 675 Bit Score: 781.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 1 MQKNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLA 80
Cdd:PRK06599 1 MAKKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDPDNDFAPKYEIIEGKEKVVDALKKAAKKADAVYLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 81 SDEDREGEAISWHLYEVLK---LKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKK 157
Cdd:PRK06599 81 TDPDREGEAIAWHIAEVLKeakLKDKNVKRVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 158 VKPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDADG---KLVEM---KAElARRLKTKKEAQKFLESCK 231
Cdd:PRK06599 161 VRRGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPftaKLVEVngkKLE-KFSITNEEQAKALVKALE 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 232 AATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYES--------GLITYMRTDSVNLSEYATEG 303
Cdd:PRK06599 240 GQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEGidlgegtvGLITYMRTDSVRLSNEALDE 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 304 SKAAIAQMMGEQYV--HPRHFATKTKGAQEAHEAIRPTYMeNQTVEG-----SAQERKLYDLIWKRTIASQMADAELEKT 376
Cdd:PRK06599 320 ARKYITKKYGKEYLpaKPRVYKKKSKNAQEAHEAIRPTSI-NRTPESlkpylTPDQFKLYELIWKRTVASQMAPAILDQT 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 377 TATIGISSGSDKFTATGEVIKFDGFLRVYKESYDDDNEQEDEshLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVR 456
Cdd:PRK06599 399 SVDIASENGKYVFRATGSVILFPGFLKVYGESKDDEEEDDEK--LLPPLKEGEKLKLDELLPEQHFTEPPPRYSEASLVK 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 457 KLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEY 536
Cdd:PRK06599 477 KLEEYGIGRPSTYASIISTLQDREYVEL-------------------------------EKKRFIPTDLGRIVNDFLVEH 525
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1501682078 537 FPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETTLATKTEHKVGERILGEE-PK-TGKTVSVKIGRFG 613
Cdd:PRK06599 526 FPKYVDYDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKVEEDVRTEKVTQEETDETcPKcGGGPLVLKLGKNG 604
|
|
| topA_bact |
TIGR01051 |
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ... |
5-629 |
0e+00 |
|
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273416 [Multi-domain] Cd Length: 610 Bit Score: 692.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLASDED 84
Cdd:TIGR01051 1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKSRLGVDIEKDFEPEYVVSKGKKKVVKELKTLAKKADEVYLATDPD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 85 REGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPALSA 164
Cdd:TIGR01051 81 REGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 165 GRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLV--PDADGKLVEMKAE--LARRLKTKKEAQKFLESCKAATFSIEDI 240
Cdd:TIGR01051 161 GRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKgeETFEALLTEVNGKklKAGSDLDEAEATALKEQLKGEELVVEEI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 241 VTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYE--------SGLITYMRTDSVNLSEYATEGSKAAIAQMM 312
Cdd:TIGR01051 241 EKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEgvstgdgtIGLITYMRTDSTRLSNQAVNEARNLIDKNY 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 313 GEQYV--HPRHFATKTKGAQEAHEAIRPTY---MENQTVEG-SAQERKLYDLIWKRTIASQMADAELEKTTATIGISSGS 386
Cdd:TIGR01051 321 GKEYLgpKPKRYKSKEKNAQEAHEAIRPTSvfrTPEELKDYlKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 387 DKFTATGEVIKFDGFLRVYKEsyDDDNEQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRP 466
Cdd:TIGR01051 401 YVFKATGRKLIFDGYYKVYVE--GSDDPLEEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEELGIGRP 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 467 STYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFT 546
Cdd:TIGR01051 479 STYASIISTIQDRGYVKK-------------------------------ENKRLYPTELGFAVTDLLEKHFGDVVDYDFT 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 547 ANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETtlATKTEHKVGERILGEEPKTGKTVSVKIGRFGPVVQIGTADDTDK 626
Cdd:TIGR01051 528 AKMEKDLDEIAEGKAEWKPVLKNFYTGFSSKVKK--LRNMRIIVDFKTSQDCPLCGRPMVVKLGKYGPFLACSNFPECKY 605
|
...
gi 1501682078 627 PRF 629
Cdd:TIGR01051 606 TKS 608
|
|
| PRK06319 |
PRK06319 |
DNA topoisomerase I/SWI domain fusion protein; Validated |
1-607 |
5.44e-169 |
|
DNA topoisomerase I/SWI domain fusion protein; Validated
Pssm-ID: 235778 [Multi-domain] Cd Length: 860 Bit Score: 509.36 E-value: 5.44e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 1 MQKNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLA 80
Cdd:PRK06319 1 MKKSLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKEFGIDIENDFEPDYQILPDKEEVINKICKLAKKCDVVYLS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 81 SDEDREGEAISWHLYEVLklkPENT--KRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKV 158
Cdd:PRK06319 81 PDPDREGEAIAWHIANQL---PKNTkiQRISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 159 K--PALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVP-----------DADGK-----LVEMKAELARRLKTK 220
Cdd:PRK06319 158 QrrSGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPktqktfwahlySVDGKkwekeIPEGKTEDEVLLINS 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 221 KE-AQKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYE---------SGLITYMR 290
Cdd:PRK06319 238 KEkADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEgvdldsegaTGLITYMR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 291 TDSVNLSEYATEGSKAAIAQMMGEQYV--HPRHFATKtKGAQEAHEAIRPTYMEN--QTVEG--SAQERKLYDLIWKRTI 364
Cdd:PRK06319 318 TDSVRTDPEALKQVRKYIEGTFGKEFLpsSPNVYTTK-KMAQDAHEAIRPTDITLtpEKLRSklTEDQYKLYSLIWKRFV 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 365 ASQMADAELEKTTATIGISSGSDkFTATGEVIKFDGFLRVYKESYDDDnEQEDESHLLPPLKKGQILEHQGIVATERFTQ 444
Cdd:PRK06319 397 ASQMIPAIYDTLAIRITTNKGID-LRATGSLLKFKGFLAVYEEKRDDE-GDEEENIHLPKLHEQDVLTKEELSAEQAFTK 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 445 RPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYvekgdktgeersfdilTLKDDQitdvkhtevvgaeksKLLPTD 524
Cdd:PRK06319 475 PLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREY----------------TLKENQ---------------RLRPTE 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 525 IGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETTLATKTEHKVGERILGEEPKTGKT 604
Cdd:PRK06319 524 LGKIISQFLETNFPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKEAFIPRIVTEIDCPKCHKGKL 603
|
...
gi 1501682078 605 VSV 607
Cdd:PRK06319 604 VKI 606
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
127-568 |
1.20e-145 |
|
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Pssm-ID: 426069 [Multi-domain] Cd Length: 410 Bit Score: 433.21 E-value: 1.20e-145
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 127 DIDINLVNAQQARRILDRIVGFELSPVLWKKVK--PALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVpdaDG 204
Cdd:pfam01131 1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLKgnKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKD---GG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 205 KLVEMKAELARRLKTKKEAQKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYE-S 283
Cdd:pfam01131 78 GVFANAKWKRGRIFDKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEkH 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 284 GLITYMRTDSVNLSEYATegsKAAIAQMMGEQY-----------VHPRHFATKTKGAQEAHEAIRPTYMENQTVEGSAQE 352
Cdd:pfam01131 158 GLITYPRTDSTYLSDDAT---LKAILEYLTKNYgkylpyaprllKKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDE 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 353 RKLYDLIWKRTIASQMADAELEKTTATIgiSSGSDKFTATGEVIKFDGFLRVYKESYDDDNEQedeshlLPPLKKGQILE 432
Cdd:pfam01131 235 RKLYELIVRRFLASQMPPAVYETTTVVL--EVGGEEFRASGKVILEDGWLKVYPYEKKEDEEE------LPELKEGEELK 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 433 HQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtev 512
Cdd:pfam01131 307 VTQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVER---------------------------- 358
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1501682078 513 vgaEKSKLLPTDIGTVVNDFLtEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMK 568
Cdd:pfam01131 359 ---KKKSLVPTELGKALVEAL-EKFPDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
130-575 |
6.37e-136 |
|
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Pssm-ID: 238110 [Multi-domain] Cd Length: 381 Bit Score: 407.38 E-value: 6.37e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 130 INLVNAQQARRILDRIVGFELSPVLWKKV--KPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVtavflvpdadgklv 207
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLrrKGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI-------------- 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 208 emkaelarrlktkKEAQkflesckaatfsIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLIT 287
Cdd:cd00186 67 -------------KEAV------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLIT 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 288 YMRTDSVNLSEYATEGSKAAIAQMMGEQYVHP-----RHFATKTKGAQEAHEAIRPT---YMENQTVEGSAQERKLYDLI 359
Cdd:cd00186 122 YPRTDSTRLSEEAILEAREYIQAIYGKEYLYPapllgRRNPKRGKKEQGAHEAIRPTkvaPTPELEANLSEDEFKLYELI 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 360 WKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKFDGFLRVYKEsydddnEQEDESHLLPPLKKGQILEHQGIVAT 439
Cdd:cd00186 202 WRRFLASQMADAKYEETTVTLEI--GGEKFKASGKVLLEDGWLEVYPE------EKDDEEEEPPPLKEGDELKLEEVELE 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 440 ERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSK 519
Cdd:cd00186 274 EKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEK-------------------------------EKKK 322
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 1501682078 520 LLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFH 575
Cdd:cd00186 323 LIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFK 378
|
|
| COG1754 |
COG1754 |
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown]; |
6-781 |
1.20e-121 |
|
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
Pssm-ID: 441360 [Multi-domain] Cd Length: 892 Bit Score: 386.86 E-value: 1.20e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 6 VIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIEKNFKPKYEIPEEKQELVDKLKEEASKAETVWLASDEDR 85
Cdd:COG1754 21 KVLPKYAKKKKGVKAVLKKADVAKADDKVVDDDDKKDDVDDDKKKKKKLLKAAAKKKKALALALAADDEDEELLAADDEL 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 86 EGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPALSAG 165
Cdd:COG1754 101 EEEKVIKLLLLELAVERVARAAAVRAAAAEAARLAALLRRRLVLRRLVRRLLVRLLLLRLVLLLLRLLVARRAARRRRRR 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 166 RVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDADGKLVEMKAELARRLKTKKEAQKFLESCKAATFSIEDIVTRPV 245
Cdd:COG1754 181 RRRRARRRELERRRERARAAEAEEAAAAAAAAADAGRAAAARDGKGGGKLAAGGAAAAAAAAAAAAAAAAALAEAAAAAA 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 246 KKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGL--------ITYMRTDSVNLSEYATEGSKAAIAQMMGEQYV 317
Cdd:COG1754 261 VREPPTPTTTTTAQAATTTTTRAAAARTTRSAQQAARRTRlggegtytTTTTTTTTTSAAAAAAAAAAAALAAAAAAAYA 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 318 HPRHFATKTKGAQEAHEAIRPTYMENQTVE------GSAQERKLYDLIWKRTIASQMADAELEKTTATIGISS--GSDKF 389
Cdd:COG1754 341 PPPPYYYKKKAAAAAAAAAAAAAAAARRPPaaraalLSDDRLLLELLLLRRTAAAAAAAAAATATTTAAAAAAgaGAVGT 420
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 390 TATGEVIKFDGFLRVYKESYDDDneQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTY 469
Cdd:COG1754 421 AAAGAVFFFGGFLLFAEEEDDDE--EDDDDDDLPALEEGLPLLKEGVLADQHFTQPPPRYTEAPLVKRMEELGIGRPSTY 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 470 APTISTIQQREYVEKgdktgeersfdiltlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANV 549
Cdd:COG1754 499 ASILSTLADRIYVRL-------------------------------DKRRLIPEDKGRLVTAFLFSFFRRYVEYDFTADL 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 550 EKQFDEIAEGDKKWTSIMKDFYKEFHPSVETTLATKTEHKV--------------------------------------- 590
Cdd:COG1754 548 EEFLDDVSDGELDWKAVLRRFWRDFSAAYDETGDLRISEVLdaledlgeidpreinscplgtgglslrvgrygpfiecsn 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 591 -------------------------------GERILGEEPKTGKTVSVKIGRFGPVVQIGTA--DDTDKPRFAQMKKGQS 637
Cdd:COG1754 628 yeprrasipeclapdeltpekaeelleapadGPRVLGTDPETGKPIVLKDGRFGPYVQLGEPekEDKPKPKRASLPKGMS 707
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 638 METITLEEALDLFKLPRKVGEFEE--KTVTIGTGRFGPYVYHDSKYVSLPKTYDPLEVTLDEAIELI---LGKREAEAKK 712
Cdd:COG1754 708 PETVTLEDALKLLSLPRVVGEHPEtgEEITAQNGRFGPYLKHGKDYRSLKSEDDVFTITLNRALELLaqpKARGRRAAAP 787
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1501682078 713 HIKKFDEDPE----MEILNGRYGPYITYKGSNYKIPKDVVPADLNYKTCLEIIklqSEKAESAPKRGRYAKKK 781
Cdd:COG1754 788 PLKELGEHPVsgkpVVVKDGRYGPYVTDGKTNATLPKDDDPESLTLERALELL---AEKRAKGPAKKKKAAKK 857
|
|
| TopG2 |
COG1110 |
Reverse gyrase [Replication, recombination and repair]; |
5-573 |
6.85e-101 |
|
Reverse gyrase [Replication, recombination and repair];
Pssm-ID: 440727 [Multi-domain] Cd Length: 1219 Bit Score: 338.10 E-value: 6.85e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFK-------------------VLSSYGHIRDLKKKEFSIDI------EKNFKPKY----- 54
Cdd:COG1110 632 LVIVESPNKARTIASFFGKPSRrrigglrvyevsigdylllITASGGHVFDLVTEAYARGFygvlveNGRFIPVYdtikr 711
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 55 --------------------EIPEEKQELVDKLKEEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEIT 114
Cdd:COG1110 712 cldcgeqftdevevcprcgsPNIVDSLEIVEALRELATEVDEVLIGTDPDTEGEKIGWDVYNLLRPYAKNIKRIEFHEVT 791
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 115 KTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKV-KPALSAGRVQSVAVRLIVEREREiqaFKSEASYRV 193
Cdd:COG1110 792 RKAILEALKNPREIDENLVEAQIVRRIEDRWIGFTLSQKLWKVFgNRNLSAGRVQTPVLGWIIERYEE---SRKSKKYLI 868
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 194 TAVFlvpdaDGKLVEMkaelarRLKTKKEAQKFLESCKAATFSIEDIVTRPVK-KSPAAPFTTSTLQQEAARKLGFTVAQ 272
Cdd:COG1110 869 ILTL-----ENGRLEL------SIEDLKEAEEVRKALEKEVKVKVKKVEEEEEeLNPLPPYTTDTLLRDASRRLGLSAEE 937
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 273 TMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYVHPRHFatktkGAQEAHEAIRPTY------MENQTV 346
Cdd:COG1110 938 TMRLAQDLFESGLITYHRTDSTRVSDAGIAVAKEYISERFGEEYFKPRRW-----GEGGAHEAIRPTRpldaedLRRLIE 1012
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 347 EGSAQ------ER--KLYDLIWKRTIASQMADAELEKTTATIGISSGSDKFTATGEV-IKFDGFLRVYkesydddneqed 417
Cdd:COG1110 1013 EGVIElpipltRRhlRLYDLIFRRFMASQMRPAKVEKVKLRVSLELPGGEIEEERIVeIIEDGFLLIY------------ 1080
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 418 eshllPPLKKGQILEHQGIVATERFTQRPSR---YTEASLVRKLEELGIGRPSTYAPTISTIQQREYVekgdktgeersf 494
Cdd:COG1110 1081 -----PPIKVEPELKEGEYKVTEVKIRKVPKvplYTQGDLVREMKERGIGRPSTYAKIVETLLRRGYV------------ 1143
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1501682078 495 diltlkddqitdvkhteVVGAEKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKE 573
Cdd:COG1110 1144 -----------------VESKKGKKLVPTKLGIEVYNYLSENFPDLVSEERTRELEEKMDEIEEGEADYQDVLEELYNE 1205
|
|
| rgy |
TIGR01054 |
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ... |
5-573 |
2.81e-92 |
|
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273418 [Multi-domain] Cd Length: 1171 Bit Score: 313.31 E-value: 2.81e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFK-------------------VLSSYGHIRDL-KKKEFSIDIEKN--FKPKY-------- 54
Cdd:TIGR01054 604 LLVVESPNKARTIARFFGKPSVrkiggsvvyevpvgdlilmITASGGHVFDLvTDKGFHGVLVENgrYVPVYtsikrcrd 683
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 55 -----------------EIPEEKQELVDKLKEEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEITKTA 117
Cdd:TIGR01054 684 cgyqftedrescpkcgsENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPYNPNVKRAEFHEVTRRA 763
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 118 ILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKV-KPALSAGRVQSVAVRLIVEREREiqafkseasYRVTAV 196
Cdd:TIGR01054 764 ILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFnKRWLSAGRVQTPVLGWIIDRYRE---------SREKRG 834
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 197 FLVPDAdgklVEMKAELARRLKTKKEAQKFLESCKAAtfSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMV 276
Cdd:TIGR01054 835 YLLIFA----LESDFRLGLEHDNRLEAKEFEKDLTWL--DVEDIAEREEERNPLPPYTTDTMLEDANRKLGLSVKETMQI 908
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 277 AQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYVHPRHFatktkGAQEAHEAIRPTY------MENQTVEGSA 350
Cdd:TIGR01054 909 AQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLGGEYFYPREW-----GEGGAHECIRPTRpldvddLQRLILEGVI 983
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 351 Q-------ERKLYDLIWKRTIASQMADAELEKTTATIGiSSGSDKFTATGEVIKFDGFLRVYKesydddneqedeSHLLP 423
Cdd:TIGR01054 984 ElegltreHLRLYDLIFRRFMASQMRPAKVDTKEITLK-ADGKEAEEEGIVEIVERGFELVYP------------LWRKN 1050
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 424 PLKKGQIlehqGIVATERFTQRP--SRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdiltlkd 501
Cdd:TIGR01054 1051 ELEKGST----FIVKDKELRSVPkvYPYTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYVVE----------------- 1109
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1501682078 502 dqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKE 573
Cdd:TIGR01054 1110 --------------SKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVYRE 1167
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
243-484 |
2.39e-86 |
|
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Pssm-ID: 214663 [Multi-domain] Cd Length: 259 Bit Score: 273.74 E-value: 2.39e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 243 RPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYVHP--- 319
Cdd:smart00437 3 KEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLavv 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 320 ---RHFATKTKGAQEAHEAIRPT---YMENQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATG 393
Cdd:smart00437 83 llkPRKPRKGKKAQGAHEAIRPTkpiFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKI--GGEKFKAKG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 394 EVIKFDGFLRVYKESYDDDNEQedeshlLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTI 473
Cdd:smart00437 161 KTLLFDGWLKVYPEEKKEEEIE------LPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASII 234
|
250
....*....|.
gi 1501682078 474 STIQQREYVEK 484
Cdd:smart00437 235 ETLLDRGYVTK 245
|
|
| PRK07219 |
PRK07219 |
DNA topoisomerase I; Validated |
4-607 |
9.28e-69 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235971 [Multi-domain] Cd Length: 822 Bit Score: 242.60 E-value: 9.28e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 4 NLVIVESPAKAKTIEKFL---------------------GKDFKVLSSYGHIrdlkkkeFSIDIEKNFK--PKYEI---- 56
Cdd:PRK07219 2 ELIIAEKNNAARRIADILsggkakkkrvngvpyyeferkGEKWIVIGLSGHI-------VTVDFPEEYGdwRDVDPaeli 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 57 ---PEEK---QELVDKLKEEASKAETVWLASDEDREGEAISWHLYEVLK-LKPENTKRIVFHEITKTAILKAIEQPRDID 129
Cdd:PRK07219 75 dadPVKKitkQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILReVCQVPVKRARFSSLTKKEIRKAFENPDEID 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 130 INLVNAQQARRILDRIVGFELSPVLWKKVKPA-----LSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDADG 204
Cdd:PRK07219 155 FNLADAGEARQIIDLYWGAALTRFLSLSVRQLgrwdfLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKEAQYF 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 205 KLVEMKAELARRLKTKKEAQKF---LESCKAATfsIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLY 281
Cdd:PRK07219 235 YRDLIGGHEAEKFWDEEEAEEIyekLKGAKEAT--VSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLY 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 282 ESGLITYMRTDS----------------VNLSEYategsKAAIAQMMGEQYVHPrhfatkTKGAQE--AHEAIRPTYMEN 343
Cdd:PRK07219 313 TAGYISYPRTDNtvypddldpkellkklSKKKEY-----GPYAESILEQENIKP------TEGKKEttDHPPIHPVDVPK 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 344 QTvEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKFDGFLRVYKESYDDDNEqedeshlLP 423
Cdd:PRK07219 382 RE-ELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDV--NGEIFKASGSRLVEEGWHEVYPYEKFDEKE-------LP 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 424 PLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKGDktgeersfdilTLKddq 503
Cdd:PRK07219 452 DLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYVIEGD-----------PPR--- 517
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 504 itdvkhtevvgaekskllPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKW-------TSIMKDFYKEFHP 576
Cdd:PRK07219 518 ------------------PTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGKKKKedvteesREMLKEILSELKE 579
|
650 660 670
....*....|....*....|....*....|....*
gi 1501682078 577 S---VETTLATK-TEHKVGERILGEEPKTGKTVSV 607
Cdd:PRK07219 580 KrkeIGDHLAGSlKAENRSLKTIGKCPECGGDLII 614
|
|
| PRK05776 |
PRK05776 |
DNA topoisomerase I; Provisional |
2-562 |
5.94e-63 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 235602 [Multi-domain] Cd Length: 670 Bit Score: 223.33 E-value: 5.94e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 2 QKNLVIVESPAKAKTIEKFL--------------------GKDFKVLSSYGHIRDL--KKKEFSI-DIEknFKPKYEIPE 58
Cdd:PRK05776 1 GYILVIAEKPKAARKIAEALsekpircriygvpywivkrdGKKIVVAPAAGHLFGLhtKSKGFPVfDYE--WKPLYEIDK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 59 EK---QELVDKLKEEASKAETVWLASDEDREGEAISwhlYEVLKL--KPENTKRIVFHEITKTAILKAIEQPRDIDINLV 133
Cdd:PRK05776 79 GSkytKKYYELLSSLSKYADEFINACDYDIEGSVIG---YLIIKYlgDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMI 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 134 NAQQARRILDRIVGFELSPVLWKKVKPA------LSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLvpdadGKLV 207
Cdd:PRK05776 156 NAGIARHELDWLWGINVSRALMSSVRDAsgkrviLSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIE-----KNGY 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 208 EMKAELA-RRLKTKKEAQKFLESCKAATF-SIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYESGL 285
Cdd:PRK05776 231 EFTLKYEnKKFETKEEAKEILEEIKKTGYlKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGL 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 286 ITYMRTDS----VNLSEYATEGSKAAIAQMMGeqYVHPRHFATKTK-----GAQE--AHEAIRPTymENQTVEGSAQERK 354
Cdd:PRK05776 311 ISYPRTNSqklpPTLNIRNILKGLSRSPQYRP--LVNLLLKETKGVlkpvqGPKDdpAHPAIYPT--GEPPKNLSKDEFK 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 355 LYDLIWKRTIASQMADAELEKTTATIGISSGSDKFTATGEVIKFDGFLRVYKESydddNEQEDEshlLPPLKKGQILEHQ 434
Cdd:PRK05776 387 LYDLIVRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFH----KFDEEE---LPLLKKGERVKIV 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 435 GIVATERFTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKGdktgeersfdiltlkddqitdvkhtevvg 514
Cdd:PRK05776 460 DVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTSN----------------------------- 510
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 1501682078 515 aeKSKLLPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKK 562
Cdd:PRK05776 511 --GKYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKAT 556
|
|
| TOPRIM_TopoIA_TopoI |
cd03363 |
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ... |
3-125 |
4.62e-60 |
|
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173783 [Multi-domain] Cd Length: 123 Bit Score: 198.55 E-value: 4.62e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDLKKKEFSIDIE-KNFKPKYEIPEEKQELVDKLKEEASKAETVWLAS 81
Cdd:cd03363 1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEdDGFEPKYVVIPGKKKVVKELKKLAKKADEIYLAT 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1501682078 82 DEDREGEAISWHLYEVLKLKpENTKRIVFHEITKTAILKAIEQP 125
Cdd:cd03363 81 DPDREGEAIAWHLAEVLKLK-KNVKRVVFNEITKEAIKEALKNP 123
|
|
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
73-488 |
3.05e-58 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 210.02 E-value: 3.05e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 73 KAETVWLASDEDREGEAISWHLYEVLKLKpENTKRIVFHEITKTAILKAIEQPRDID--INLVNAQQARRILDRIVGFEL 150
Cdd:PRK07726 92 QATEIVIATDADREGELIAREILDYCGVR-KPIKRLWISSLTDKAIKRAFANLKPGKetIPLYYSALARSRADWLVGINM 170
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 151 SPVLWKKVKPA-----LSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDA-DGKLV--EMKAELARRLKTKKE 222
Cdd:PRK07726 171 TRAYTLLGRKAgyngvLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGERfTAKWQpsEPYQDEEGRLLDRPL 250
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 223 AQKFLESCKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYES-GLITYMRTDSVNLSEYAT 301
Cdd:PRK07726 251 AEQVVARIQGQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYEThKLITYPRTDSRYLPEDMV 330
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 302 EGSKA---AIAQMMGE-QYVHPRHFATKTKGAQ-----EAHEAIRPTyMENQTVEG-SAQERKLYDLIWKRTIASQMADA 371
Cdd:PRK07726 331 ATLPEvlnAISKVDPYlLLAPPVLDPSIRSRAWndkkvTAHHAIIPT-EQPPNLSKlSEDERKVYDLIARRYLAQFLPPA 409
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 372 ELEKTTATIGIssGSDKFTATGEVIKFDGflrvYKESYDDDNEQEDESHLLPPLKKGQILEHQGIVATERFTQRPSRYTE 451
Cdd:PRK07726 410 EYDKTTIELEI--AGGTFIAKGKQVVEAG----WKALLGKKEEDEEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTE 483
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 1501682078 452 ASLVRKLE---------EL--------GIGRPSTYAPTISTIQQREYVEKGDKT 488
Cdd:PRK07726 484 GTLLSAMEniarfvqdkELkktlketdGLGTEATRAGIIEKLFKRGYLEKKGKY 537
|
|
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
3-569 |
3.15e-57 |
|
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273419 [Multi-domain] Cd Length: 660 Bit Score: 207.39 E-value: 3.15e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFK------------VLSSYGHIRDLKKKEFSIDIEKNFKpKYEIPEEKQELVDKLKEE 70
Cdd:TIGR01056 1 MTLVLCEKPSQARDLATVLAKKKKgngyleigvggfVTWAVGHLVELAEPEEYDEKYKNWR-TYDLPLEPEDWQLVVSDK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 71 ASK-------------AETVWLASDEDREGEAISWHLYEVLKLKPENT-KRIVFHEITKTAILKAIEQ--PRDIDINLVN 134
Cdd:TIGR01056 80 TKKqfnvikrilkenkVDEVVIATDPDREGELIAREILDYLKVTDKVTiKRLWISSLVDSSIRKAFKNlrPKSETEGLYK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 135 AQQARRILDRIVGFELSPVLWKKVKPA-----LSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLVPDadgklVEM 209
Cdd:TIGR01056 160 SGVARARADWLVGINLTRAFTKLGREAgndgvLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDE-----QEF 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 210 KAELA-RRLKTKKEAQKFLES-----CKAATFSIEDIVTRPVKKSPAAPFTTSTLQQEAARKLGFTVAQTMMVAQKLYES 283
Cdd:TIGR01056 235 TTEWQpYKDEEERELHEFLAEnvvtdLTQKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYET 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 284 G-LITYMRTDSVNLSEYATEGSKAAIAQMMG---EQYVHPRHFATKTKG-----AQEAHEAIRPTYMENQTVEGSAQERK 354
Cdd:TIGR01056 315 HkLITYPRTDSRYLPEDEKEMLLEVLDALKVitpALLPIKKRDELTNNRlwndkKIEDHHAIIPTGNDFNLSDLSEEERN 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 355 LYDLIWKRTIASQMADAELEKTTATIGIssGSDKFTATGEVIKFDGFLRVYKESYDDDneqEDESHLLPPLKKGQILEHQ 434
Cdd:TIGR01056 395 VYKLIAQNYLMQFMPKEEYETTTIEIAI--GKLMFEAKGKILQDNGWKALLGKQEEDE---ETEDTTLPAFQKGDELDVE 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 435 GIVATERFTQRPSRYTEASLVRKL-----------------EELGIGRPSTYAPTISTIQQREYVEKgdktgeersfdil 497
Cdd:TIGR01056 470 TLELLEKQTKPPARYTEGTLLSAMtnpaafvqdkglkktlkETKGLGTEATRADIIENLFKRGFIQK------------- 536
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1501682078 498 tlkddqitdvkhtevvgaEKSKLLPTDIGTVVNDFLTEYFPNIldyNFTANVEKQFDEIAEGDKKWTSIMKD 569
Cdd:TIGR01056 537 ------------------KKNKIYITKNGKLLCLLLPELLTKP---DLTAQWEQYLNGISAGEKDDDDFINT 587
|
|
| PRK14973 |
PRK14973 |
DNA topoisomerase I; Provisional |
57-608 |
1.32e-54 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 184936 [Multi-domain] Cd Length: 936 Bit Score: 203.54 E-value: 1.32e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 57 PEEKQ--ELVDKLkeeASKAETVWLASDEDREGEAISWHLYEVLKLKPENTK--RIVFHEITKTAILKAIEQPRDIDINL 132
Cdd:PRK14973 81 PTEKKivGLIQKL---AKKADRVTIATDFDTEGELIGKEAYELVRAVNPKVPidRARFSAITKEEIVTAFAEPTDLDFAL 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 133 VNAQQARRILDRIVGFELSPVLWKKVKPA----LSAGRVQSVAVRLIVEREREIQAFKSEASYRVTavfLVPDADGKLVE 208
Cdd:PRK14973 158 AAAGEARQIIDLIWGASLTRFISLAAHRGgdniLSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLS---LATEKDGEGIE 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 209 MKaELARRLKTKKEAQKFLESCKAATFSIEDIVTRPVKKSPAaPFTTSTLQQEAARkLGFTVAQTMMVAQKLYESGLITY 288
Cdd:PRK14973 235 AR-HTHGRFTDSAAAEAAYDATKEPLVVTEVKEGHKVDRAPT-PFDTTTFIVAASR-LGFSAANAMRIAEDLYMNGYISY 311
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 289 MRTD------SVNLSEYATEGSKAAIAQMMGEQYVHPRHFATKTKGAQEAHEAIRPTYMENQtvEGSAQER-KLYDLIWK 361
Cdd:PRK14973 312 PRTDntiypkSLDLNGVLATLAKGAFSKDVAWVKDNRRPVPTRGKKSSTDHPPIHPTGVATR--EELGDDRwKLYELVVR 389
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 362 RTIASQMADAELEktTATIGISSGSDKFTATGEVIKFDGFLRVYKESydddneqEDESHLLPPLKKGQILEHQGIVATER 441
Cdd:PRK14973 390 RFLATLSPDAEWA--TMKVNFDAGGEPYTATGGRLLEAGWRTVYPYS-------EAKENILPAFALGEKLPILAVNLEEK 460
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 442 FTQRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVekgdktgeersfdiltlkddqitdvkhtevvgaEKSKLL 521
Cdd:PRK14973 461 ETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYI---------------------------------EGNPLR 507
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 522 PTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSIMKDFYKEFHPSVETTLATKT-------EHKVGERI 594
Cdd:PRK14973 508 PTLVGRAVTESLEEHAGTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAvigrdimERTAEELT 587
|
570
....*....|....
gi 1501682078 595 LGEEPKTGKTVSVK 608
Cdd:PRK14973 588 IGPCPVCGKDLRIK 601
|
|
| PRK07220 |
PRK07220 |
DNA topoisomerase I; Validated |
63-613 |
2.31e-52 |
|
DNA topoisomerase I; Validated
Pssm-ID: 180892 [Multi-domain] Cd Length: 740 Bit Score: 194.59 E-value: 2.31e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 63 LVDKLKEEASKAETVWLASDEDREGEAISWHLYEVLK-LKPE-NTKRIVFHEITKTAILKAIEQPRDIDINLVNAQQARR 140
Cdd:PRK07220 87 IVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKkVNPDiKFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQ 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 141 ILDRIVGFELSPVLWKKV----KPALSAGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFlvpDADGKLVEMKAElARR 216
Cdd:PRK07220 167 VIDLVWGAALTRYISLAAgrlgKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATL---ENNGETFVAQHS-TRR 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 217 LKTKKEAQKFLES-CKAATFSieDIVTRPVKKSPAAPFTTSTLQQeAARKLGFTVAQTMMVAQKLYESGLITYMRTD--- 292
Cdd:PRK07220 243 FWEKEEADRVFEKlGKTAEVT--EVEKGTKTDKPPTPFNTTEFIS-AANSIGFSAANAMRIAESLYTNGYISYPRTDntv 319
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 293 ---SVNLSE----YATEGSKAAIAQMMGEQYVHPrhfatkTKGAQEA--HEAIRPTYMENQTvEGSAQERKLYDLIWKRT 363
Cdd:PRK07220 320 ypeSLDLREqieiFAEGPFGEYAQKLLEKGELVP------TRGKKETtdHPPIYPASLAKKS-ELKEDEWKVYELVVRRF 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 364 IASQMADAELEKTTATIGIssGSDKFTATGEVIKFDGFLRVYkeSYdddNEQEDEshLLPPLKKGQILEHQGIVATERFT 443
Cdd:PRK07220 393 FATFAGPAEWETMKLRFDI--GGEEFRANGSRLTEPGWRWYY--PY---NAPEDR--LLPELSEGEELKVKKKEMLDKET 463
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 444 QRPSRYTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEkGDktgeersfdiltlkddqitdvkhtevvgaeksKLLPT 523
Cdd:PRK07220 464 QPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH-GN--------------------------------PIQPT 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 524 DIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAEGDKKWTSI-------MKDFYKEFHPSVETTLATKTEHKVGERILG 596
Cdd:PRK07220 511 NTAFAVVDALEKYAPTITKPDMTSRLEEDMDKIAEGKIKEDAVleesremLEQVFDELDKNREKIRESLREGLREDKIIG 590
|
570
....*....|....*..
gi 1501682078 597 EEPKTGKTVSVKIGRFG 613
Cdd:PRK07220 591 KCPLCGSDLMVRRSKRG 607
|
|
| TOP1Bc |
smart00436 |
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ... |
106-191 |
7.46e-42 |
|
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Pssm-ID: 214662 [Multi-domain] Cd Length: 89 Bit Score: 147.34 E-value: 7.46e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 106 KRIVFHEITKTAILKAIEQPRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPA-LSAGRVQSVAVRLIVEREREIQA 184
Cdd:smart00436 2 KRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNGvLSAGRVQTPTLGLIVEREREIKN 81
|
....*..
gi 1501682078 185 FKSEASY 191
Cdd:smart00436 82 FVPKPYW 88
|
|
| TOPRIM_TopoIA |
cd01028 |
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
3-125 |
2.86e-41 |
|
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173778 [Multi-domain] Cd Length: 142 Bit Score: 147.37 E-value: 2.86e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGK------------DFKVLSSYGHIRDLKKKEFSIDIEKN-------FKPKYEIPEEKQEL 63
Cdd:cd01028 1 KVLIIAEKPSKAKTIAKILGKgskkkgfygeggGYVVTASVGHLLELPFPEEYVDWDKDwplelfpFEPKYVVIPDKKKQ 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1501682078 64 VDKLKEEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEITKTAILKAIEQP 125
Cdd:cd01028 81 LKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSEITPKAIREAFKNL 142
|
|
| PTZ00407 |
PTZ00407 |
DNA topoisomerase IA; Provisional |
5-558 |
3.44e-41 |
|
DNA topoisomerase IA; Provisional
Pssm-ID: 173597 [Multi-domain] Cd Length: 805 Bit Score: 162.03 E-value: 3.44e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLgKDFKV-----------------------LSSYGHIRDLKKKEFSIDI----------EKNFK 51
Cdd:PTZ00407 12 LVIVESPNKVIKVEGLL-SDPKVipdwsfkqshlrrigtgaekavaMATTGHFMALKEITWSPQAsspasvvgagDEPFP 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 52 PK---------YE-IPEEK-QELVDK-LKEEASKAETVWLASDEDREGEAISWHLYEVL-----KLKPENTkRIVFHEIT 114
Cdd:PTZ00407 91 SNgtlaeytleWElLPGRRiQETLERyIEEKADNVTEIILATDPDREGELIAVHALQTIkrlypKLKVPFS-RAYMHSIT 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 115 KTAILKAIEQ--PRDIDINLVNAQQARRILDRIVGFELSPVLWKKVKPALSAGRVQSVAVRLIVEREREIQAF--KSEAS 190
Cdd:PTZ00407 170 EDGIRKAMRErhVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKAFleSNKST 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 191 YRVTAVFLVPDADG----KLVEMKAEL---ARRLKTKKEAQKFLE-----SCKAATFSIEDIVTrPVKKSPAAPFTTSTL 258
Cdd:PTZ00407 250 FEVQAMCQFPSPHGttfsQVVTITPDRkggASHWATEAEARRCLEqwklnNCTGFSVPLEPKPQ-PSVVPPPQPFTMATA 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 259 QQEAARKLGFTVAQTMMVAQKLYESGLITYMRTDSVNLSEYATEGSKAAIAQMMGEQYVHP------------------- 319
Cdd:PTZ00407 329 IAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLYRledrtvsaqegkgskktgk 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 320 RHFATKTKGA-------QEAHEAIRPT--YMENQTVEGSAQERKLYDLIWKRTIASQMADAELEKTTATIGISSGSD--- 387
Cdd:PTZ00407 409 KRSTKQKKGAdtpvgnvEDAHEAIRPTniDTTGESLSLSPPTRAVYDLVRRNTLAVFMIPMKTEKIVATVKFTSGSGekl 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 388 KFTATGEVIKFDGFLRVYK-----------ESYDDDNEQEDESHLLPPLKKGQI------------LEHQGIVATERFTQ 444
Cdd:PTZ00407 489 EFELQGKRVVEPGWTRAFHkgdkgttgpaeETDEDITAVEEGAPVVPSLSQEEFkaimnlrsqlgsGVQKGFFELRSPQV 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 445 RPSR------YTEASLVRKLEELGIGRPSTYAPTISTIQQREYVEKGDKTGEErsfdiltlkddqitdvkhtevvgaeks 518
Cdd:PTZ00407 569 RENRpvpplpHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCE--------------------------- 621
|
650 660 670 680
....*....|....*....|....*....|....*....|
gi 1501682078 519 kllPTDIGTVVNDFLTEYFPNILDYNFTANVEKQFDEIAE 558
Cdd:PTZ00407 622 ---TTPVGRMLVETAKSTFPSIVDIGFTAAFEKKLDRIAK 658
|
|
| PRK08173 |
PRK08173 |
DNA topoisomerase III; Validated |
1-499 |
8.19e-29 |
|
DNA topoisomerase III; Validated
Pssm-ID: 236172 [Multi-domain] Cd Length: 862 Bit Score: 123.62 E-value: 8.19e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 1 MQKNLVIVESPAKAKTIEKFLGK----------DFKVLSS-YGHI--------RDLKKKEFSIDIEKNFKPKYEI-PEEK 60
Cdd:PRK08173 1 MSKALIIAEKPSVANDIARALGGftkhdeyfesDEYVLSSaVGHLleiaapeeYEVKRGKWSFAHLPVIPPHFDLnPIAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 61 QELVDKLKEEASKAETVWL---ASDEDREGEAISWHLYEVLKLKpENTKRIVFHEITKTAILKAIEQPRDID--INLVNA 135
Cdd:PRK08173 81 TESRLKVLTKLIKRKDVTRlinACDAGREGELIFRLIAQHAKAK-KPVKRLWLQSMTPQAIRDGFANLRSDEdmQPLADA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 136 QQARRILDRIVG----------------FELSPVlwkkvkpalsaGRVQSVAVRLIVEREREIQAFKSEASYRVTAVFLV 199
Cdd:PRK08173 160 ARCRSEADWLVGingtramtafnskgggFFLTTV-----------GRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVA 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 200 P---------DADGKLVEMKAEL-ARRLKTKKEAQKFLESCKAATFSIEDiVTRPVKKSPAAPFTTSTLQQEAARKLGFT 269
Cdd:PRK08173 229 AagfyegrwfDPKFKKDEFDPEKrASRLWSEAAAEAIVAACRGKPGTVTE-ESKPSTQLSPLLFDLTSLQREANGRFGFS 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 270 VAQTMMVAQKLYES-GLITYMRTDSVNLSE-Y-----------ATEGSKAAIA-QMMGEQYVHP--RHFATKTKgaqEAH 333
Cdd:PRK08173 308 AKNTLGLAQALYEKhKVLTYPRTDSRALPEdYlgtvkqtlemlKESNNYLPHAkQILDKGWVKPnkRIFDNSKI---SDH 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 334 EAIRPTymeNQTVEG-SAQERKLYDLIWKRTIASQMADAELEKTTaTIGISSGsDKFTATGEVIKFDGFLRVY-KESYDD 411
Cdd:PRK08173 385 FAIIPT---LQAPKSlSEPEQKLYDLVVKRFLAVFFPAAEFLVTT-RITEVAG-HHFKTEGKVLVNPGWLAVYgKEAQGA 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 412 DNEqedeshlLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLE----------------ELGIGRPSTYAPTIST 475
Cdd:PRK08173 460 DAN-------LVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklveddelreamaEKGLGTPATRAAIIEG 532
|
570 580
....*....|....*....|....*....
gi 1501682078 476 IQQREYVEkgdKTGEE-----RSFDILTL 499
Cdd:PRK08173 533 LLGEKYLV---REGREliptaKAFQLMTL 558
|
|
| PRK14724 |
PRK14724 |
DNA topoisomerase III; Provisional |
3-499 |
3.13e-28 |
|
DNA topoisomerase III; Provisional
Pssm-ID: 237803 [Multi-domain] Cd Length: 987 Bit Score: 121.99 E-value: 3.13e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTI---------------EKFLGKDFKVLSSYGHIRDLKK-KEFSIDIEK-NFKPKYEIPEE-KQELV 64
Cdd:PRK14724 2 KTLVIAEKPSVAQDIvraltpvagkfekhdEHFESDSYVVTSAVGHLVEIQApEEFDVKRGKwSFANLPVIPPYfDLKPV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 65 DKLK-------EEASKAETVWL--ASDEDREGEAIsWHLYEVLK-------LKPenTKRIVFHEITKTAILKAIEQPRDI 128
Cdd:PRK14724 82 DKTKtrlnavvKLAKRKDVTELvnACDAGREGELI-FRLIEQYAggakgglGKP--VKRLWLQSMTPQAIRDGFDNLRSD 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 129 D--INLVNAQQARRILDRIVG----------------FELSPVlwkkvkpalsaGRVQSVAVRLIVEREREIQAFKSEAS 190
Cdd:PRK14724 159 AqmQGLASAARSRSEADWLVGingtramtafnsrdggFFLTTV-----------GRVQTPTLSLVVEREEKIRKFVSRDY 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 191 YRVTAVFLVP---------DADGKLVEMKAEL-ARRLKTKKEAQKFLESC--KAATFSIEdivTRPVKKSPAAPFTTSTL 258
Cdd:PRK14724 228 WEIHAGFHAEageylgkwfDPQWKKASDDPEArADRVWSEREARAIADAVrgKAATVTEE---SKPTTQASPLLFDLTSL 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 259 QQEAARKLGFTVAQTMMVAQKLYES-GLITYMRTDSVNLSE------------YATEGSK---AAIAQMMGEQYVHP--R 320
Cdd:PRK14724 305 QREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEdylpvakqtfemLATSGMRhlaPFAQQALDGNYVRPskR 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 321 HFatkTKGAQEAHEAIRPTymeNQTVEG-SAQERKLYDLIWKRTIASQMADAELEKTTaTIGISSGSdKFTATGEVIKFD 399
Cdd:PRK14724 385 IF---DNSKVSDHFAIIPT---TQAPSGlSEAEQKLYDLVVRRFMAVFFPSAEYQVTT-RISQVVGH-SFKTEGKVLVKP 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 400 GFLRVY-KESYDDDNEQE--DESHLLPPLKKGQILEHQGIVATERFTQRPSRYTEASLVRKLE----------------E 460
Cdd:PRK14724 457 GWLAIYgKEAANEVEDAKdgDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsagkqidddelreamqE 536
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 1501682078 461 LGIGRPSTYAPTISTIQQREYV--EKGDKTGEERSFDILTL 499
Cdd:PRK14724 537 KGLGTPATRAAIIEGLLTEKYMlrEGRELIPTAKAFQLMTL 577
|
|
| TOPRIM_TopoIA_RevGyr |
cd03361 |
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ... |
5-125 |
9.84e-23 |
|
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173781 [Multi-domain] Cd Length: 170 Bit Score: 95.84 E-value: 9.84e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFK-------------------VLSSYGHIRDLKKKEFSIDIEKN---FKPKY-------- 54
Cdd:cd03361 3 LMIVESPNKARTIANFFGRPSVrrlgglvvyevstgdgvlmITASGGHVYDLVTKEGGHGVVEDdgrYVPVYdsikrcrd 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 55 -----------------EIPEEKQELVDKLKEEASKAETVWLASDEDREGEAISWHLYEVLKLKPENTKRIVFHEITKTA 117
Cdd:cd03361 83 cgyqftedsdkcprcgsENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNIKRAEFHEVTRRA 162
|
....*...
gi 1501682078 118 ILKAIEQP 125
Cdd:cd03361 163 ILEALRNP 170
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
5-113 |
7.83e-19 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 82.02 E-value: 7.83e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFK-VLSSYGHIRDLKKKEfsidieknfkpkyeipeeKQELVDKLKEEASKAETVWLASDE 83
Cdd:pfam01751 2 LIIVEGPSDAIALEKALGGGFQaVVAVLGHLLSLEKGP------------------KKKALKALKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|
gi 1501682078 84 DREGEAISWHLYEVLKLKPENTKRIVFHEI 113
Cdd:pfam01751 64 DREGEAIALKLLELKELLENAGGRVEFSEL 93
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
3-99 |
6.86e-15 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 69.98 E-value: 6.86e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 3 KNLVIVESPAKAKTIEKFLGKDFKVLSSYGHIRdlkkkefsidieknfkpkyeipeeKQELVDKLKEEASKAEtVWLASD 82
Cdd:smart00493 1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLL------------------------SKEQIKLLKKLAKKAE-VILATD 55
|
90
....*....|....*..
gi 1501682078 83 EDREGEAISWHLYEVLK 99
Cdd:smart00493 56 PDREGEAIAWELAELLK 72
|
|
| Toprim_C_rpt |
pfam13368 |
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the ... |
660-706 |
6.52e-14 |
|
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.
Pssm-ID: 433151 [Multi-domain] Cd Length: 51 Bit Score: 66.31 E-value: 6.52e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1501682078 660 EEKTVTIGTGRFGPYVYHDSKYVSLPKTYDPLEVTLDEAIELILGKR 706
Cdd:pfam13368 4 TGEPIVVKDGRYGPYVKHGKTNASLPKGDDPETITLEEALELLAEKR 50
|
|
| Toprim_C_rpt |
pfam13368 |
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the ... |
599-655 |
8.17e-13 |
|
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.
Pssm-ID: 433151 [Multi-domain] Cd Length: 51 Bit Score: 63.23 E-value: 8.17e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1501682078 599 PKTGKTVSVKIGRFGPVVQIGtaddtdkPRFAQMKKGQSMETITLEEALDLFKLPRK 655
Cdd:pfam13368 2 PETGEPIVVKDGRYGPYVKHG-------KTNASLPKGDDPETITLEEALELLAEKRA 51
|
|
| Toprim_C_rpt |
pfam13368 |
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the ... |
717-764 |
1.03e-11 |
|
Topoisomerase C-terminal repeat; This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.
Pssm-ID: 433151 [Multi-domain] Cd Length: 51 Bit Score: 60.15 E-value: 1.03e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1501682078 717 FDEDPEMEILNGRYGPYITYKGSNYKIPKDVVPADLNYKTCLEIIKLQ 764
Cdd:pfam13368 2 PETGEPIVVKDGRYGPYVKHGKTNASLPKGDDPETITLEEALELLAEK 49
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
5-110 |
8.22e-11 |
|
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 58.59 E-value: 8.22e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1501682078 5 LVIVESPAKAKTIEKFLGKDFKVLSSYGHIRDlkkkefsidieknfkpkyeipeekqELVDKLKEEASKAETVWLASDED 84
Cdd:cd00188 3 LIIVEGPSDALALAQAGGYGGAVVALGGHALN-------------------------KTRELLKRLLGEAKEVIIATDAD 57
|
90 100
....*....|....*....|....*.
gi 1501682078 85 REGEAISWHLYEVLKLKPENTKRIVF 110
Cdd:cd00188 58 REGEAIALRLLELLKSLGKKVRRLLL 83
|
|
| |
