|
Name |
Accession |
Description |
Interval |
E-value |
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
2-571 |
1.47e-164 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 481.90 E-value: 1.47e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLE-TMQPNFVIESSRKKIISQIKKEGKTA 80
Cdd:COG0550 1 KKLVIVESPAKAKTIAKYLG-----KDYVVTASVGHLRDLPKPE---LDVDVEnDFEPKYEVIPGKKKQVKELKKLAKKA 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 81 DLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQ 160
Cdd:COG0550 73 DEVILATDPDREGEAIAWHLLELLGDKKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLW 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 161 K--STGLmSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFvieskrAINLNLNKDKNNVLVNTEKTYYIDENQAKTIVDE 238
Cdd:COG0550 153 KkvKRGL-SAGRVQSPALRLIVEREREIEAFVPEEYWTIE------ATFKTGGGEFTAKLVKIDGKKILDEEEAEAILAA 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 239 L-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYIS 317
Cdd:COG0550 226 LkGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIE 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 318 KNYSSDLFKD-PIVGKKDQNSQEAHESIRPTNIWLTPEKASLEiednlLKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNN 396
Cdd:COG0550 306 ALYGKEYLPEkPRVYKTSKNAQEAHEAIRPTGVTRTPESLSGD-----EFKLYDLIWKRFLASQMPPAEYETTTVTIEVG 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 397 GYEFKQSWQEVKDLGYQAIKHSSSDENIEltDDGEEIVQ-SKNDKpeyqfnddfeisISKKFIKIESAKTNPPKMFNQAS 475
Cdd:COG0550 381 GEEFRASGKVIKFPGFLKVYGEGKDDEEE--EEEKRLPPlKEGEK------------LKLKKIEPEQHFTKPPPRYTEAS 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 476 LIKELKNLGIGRPSTYNPILTKLKDREYVEyPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDFDY 555
Cdd:COG0550 447 LVKAMEELGIGRPSTYASIIETLQDRGYVE-REGKRLVPTELGFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAEGKLDW 525
|
570
....*....|....*.
gi 499706891 556 VNWLKNIYNALNFKVK 571
Cdd:COG0550 526 KDVLEEFYKPFKELVE 541
|
|
| topA_bact |
TIGR01051 |
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ... |
4-615 |
7.86e-138 |
|
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: 416.01 E-value: 7.86e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 4 LVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLE-TMQPNFVIESSRKKIISQIKKEGKTADL 82
Cdd:TIGR01051 1 LVIVESPAKAKTIKKYLG-----DEYEVEASMGHIRDLPKSR---LGVDIEkDFEPEYVVSKGKKKVVKELKTLAKKADE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 83 IILASDPDREGEAIAYHLANLFKDHTN-IKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQK 161
Cdd:TIGR01051 73 VYLATDPDREGEAIAWHLAEVLKPKDPvYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 162 S-TGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKRAinlnLNKDKNNVLVNTEK---TYYIDENQAKTIVD 237
Cdd:TIGR01051 153 KvAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGE----ETFEALLTEVNGKKlkaGSDLDEAEATALKE 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 238 EL-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE--------LGYITYIRTDSVKYSSQF 308
Cdd:TIGR01051 229 QLkGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEgvstgdgtIGLITYMRTDSTRLSNQA 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 309 IGEVKDYISKNYSSDLFKDP--IVGKKDQNSQEAHESIRPTNIWLTPE--KASLEIEDnllKRVYNLIWWNSIKSLMKGP 384
Cdd:TIGR01051 309 VNEARNLIDKNYGKEYLGPKpkRYKSKEKNAQEAHEAIRPTSVFRTPEelKDYLKRDE---FRLYELIWKRFVASQMADA 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 385 SGFNHRWTFNN--NGYEFKQSWQEVKDLGYQAIKHSSSDENIELTDdgeeivqskNDKPEYQFNDdfeiSISKKFIKIES 462
Cdd:TIGR01051 386 RYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKD---------RILPPLKEGD----AVKLVEVKPNQ 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 463 AKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEME 542
Cdd:TIGR01051 453 HFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKK-ENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKME 531
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499706891 543 EKLDEITRGDFDYVNWLKNIYNALNFKVKKEIGE-----AKTEAICPRCGANLVYIKSRFNRGRGCSNFtiTKCGYRK 615
Cdd:TIGR01051 532 KDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMriivdFKTSQDCPLCGRPMVVKLGKYGPFLACSNF--PECKYTK 607
|
|
| PRK06599 |
PRK06599 |
DNA topoisomerase I; Validated |
1-615 |
8.56e-126 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235840 [Multi-domain] Cd Length: 675 Bit Score: 386.91 E-value: 8.56e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLET-MQPNFVIESSRKKIISQIKKEGKT 79
Cdd:PRK06599 2 AKKLVIVESPAKAKTIKKYLG-----KDYKVLASFGHVRDLPKKK---GGVDPDNdFAPKYEIIEGKEKVVDALKKAAKK 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 80 ADLIILASDPDREGEAIAYHLANLFK----DHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLV 155
Cdd:PRK06599 74 ADAVYLATDPDREGEAIAWHIAEVLKeaklKDKNVKRVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 156 SKSL-QKSTGLMSAGRVQTPALNILTTRDTLIKNFKEVLYkkiFVIESKRAINLNLNKDKNNVLVNTEK--TYYI-DENQ 231
Cdd:PRK06599 154 SPLLwKKVRRGLSAGRVQSVALRLICEREDEIEAFIPQEY---WTIEADLATSNGEPFTAKLVEVNGKKleKFSItNEEQ 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 232 AKTIVDEL-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE--------LGYITYIRTDSV 302
Cdd:PRK06599 231 AKALVKALeGQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEgidlgegtVGLITYMRTDSV 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 303 KYSSQFIGEVKDYISKNYSSD--LFKDPIVGKKDQNSQEAHESIRPTNIWLTPEkaslEIEDNLLK---RVYNLIWWNSI 377
Cdd:PRK06599 311 RLSNEALDEARKYITKKYGKEylPAKPRVYKKKSKNAQEAHEAIRPTSINRTPE----SLKPYLTPdqfKLYELIWKRTV 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 378 KSLMKgPSGFNH-RWTF--NNNGYEFKQSWQEVKDLGYQAIKHSSSDENIEltddgeeivQSKNDKPEYQFNDDF---EI 451
Cdd:PRK06599 387 ASQMA-PAILDQtSVDIasENGKYVFRATGSVILFPGFLKVYGESKDDEEE---------DDEKLLPPLKEGEKLkldEL 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 452 SISKKFikiesakTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKsKPIVVTNKGYSANEYLYDHYLD 531
Cdd:PRK06599 457 LPEQHF-------TEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVELEK-KRFIPTDLGRIVNDFLVEHFPK 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 532 FFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYNALNFKVKK--------EIGEAKTEAICPRCGANLVYIK-SRFNRGRG 602
Cdd:PRK06599 529 YVDYDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKveedvrteKVTQEETDETCPKCGGGPLVLKlGKNGKFLG 608
|
650
....*....|...
gi 499706891 603 CSNFtiTKCGYRK 615
Cdd:PRK06599 609 CSGY--PECKYTK 619
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
135-563 |
1.09e-86 |
|
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: 275.64 E-value: 1.09e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 135 MNLVNAQISRQILDKIIGY----LVSKSLQKSTGLmSAGRVQTPALNILTTRDTLIKNFKEvlykkifvieskrainlnl 210
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFnlsrLLTKKLRRKGVL-SAGRVQSPTLGLIVEREREIKAFVP------------------- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 211 nkdknnvlvnteKTYYidENQAKTIVDelgeiyrctdYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE 290
Cdd:cd00186 61 ------------EDYW--EIKEAVVVS----------VEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYE 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 291 LGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLFKD-----PIVGKKDQNSQEAHESIRPTNIwlTPEKASLEIEDNLL 365
Cdd:cd00186 117 AGLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPapllgRRNPKRGKKEQGAHEAIRPTKV--APTPELEANLSEDE 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 366 KRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAIKhsssdenieltddGEEIVQSKNDKPEYQF 445
Cdd:cd00186 195 FKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVY-------------PEEKDDEEEEPPPLKE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 446 NDDFEISIskkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKSKpIVVTNKGYSANEYL 525
Cdd:cd00186 262 GDELKLEE----VELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKK-LIPTELGFAVIELL 336
|
410 420 430
....*....|....*....|....*....|....*...
gi 499706891 526 YDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIY 563
Cdd:cd00186 337 EKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFY 374
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
132-560 |
2.77e-84 |
|
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: 270.27 E-value: 2.77e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 132 DIDMNLVNAQISRQILDKIIGYLVSKSLQKST---GLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIeskrainl 208
Cdd:pfam01131 1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgnKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEAT-------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 209 NLNKDKNNVLVNTEKTYYIDENQAKTIVDELGEI-YRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQK 287
Cdd:pfam01131 73 LKDGGGVFANAKWKRGRIFDKEEAEAILEKLKKGtAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 288 LYE-LGYITYIRTDSVKYSSQF-IGEVKDYISKNY------SSDLFKDPIVGKKDQNSQ-EAHESIRPTNIWLTPEKASL 358
Cdd:pfam01131 153 LYEkHGLITYPRTDSTYLSDDAtLKAILEYLTKNYgkylpyAPRLLKKTKGKLTVGNAKvTAHEAIRPTGDIPVLPELSD 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 359 EIednllKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAIKHSSSDEnieltdDGEEIvqskn 438
Cdd:pfam01131 233 DE-----RKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKE------DEEEL----- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 439 dkPEYQFNDDFEIsiskKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKG 518
Cdd:pfam01131 297 --PELKEGEELKV----TQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVER-KKKSLVPTELG 369
|
410 420 430 440
....*....|....*....|....*....|....*....|..
gi 499706891 519 YSANEyLYDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLK 560
Cdd:pfam01131 370 KALVE-ALEKFPDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
259-518 |
1.66e-53 |
|
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: 183.99 E-value: 1.66e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 259 KPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLFKDPIVGKKDQ--- 335
Cdd:smart00437 11 PPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLAVVLLKPRkpr 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 336 ---NSQEAHESIRPTNIWLTPEKASlEIEDNLLKrVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGY 412
Cdd:smart00437 91 kgkKAQGAHEAIRPTKPIFTPELEK-ELSEDEFK-LYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTLLFDGW 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 413 QAIKHSSSDE-NIELtddgeeivqskndkPEYQFNDDFEISIskkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTY 491
Cdd:smart00437 169 LKVYPEEKKEeEIEL--------------PTLKKGDELKVEE----VEVEEKETKPPARYTEASLIKLMEKRGIGRPSTY 230
|
250 260
....*....|....*....|....*..
gi 499706891 492 NPILTKLKDREYVEYpKSKPIVVTNKG 518
Cdd:smart00437 231 ASIIETLLDRGYVTK-KKKKLIPTELG 256
|
|
| zf-C4_Topoisom |
pfam01396 |
Topoisomerase DNA binding C4 zinc finger; |
582-619 |
7.44e-05 |
|
Topoisomerase DNA binding C4 zinc finger;
Pssm-ID: 307520 [Multi-domain] Cd Length: 39 Bit Score: 40.32 E-value: 7.44e-05
10 20 30
....*....|....*....|....*....|....*...
gi 499706891 582 ICPRCGANLVYIKSRFNRGRGCSNFtiTKCGYRKYEQP 619
Cdd:pfam01396 3 KCPKCGGDLVLKRGRFGKFVGCSNY--PECRFTRPLKK 38
|
|
| RPB9 |
COG1594 |
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ... |
578-626 |
2.18e-03 |
|
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 441202 [Multi-domain] Cd Length: 103 Bit Score: 38.01 E-value: 2.18e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 578 KTEAICPRCGANLVY-----IKS------RFnrgrgcsnFTITKCGYrkyeqpdgTWKEY 626
Cdd:COG1594 60 TTKVICPKCGNDEAYwwlkqTRSadepetRF--------FRCTKCGH--------TWREY 103
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
2-571 |
1.47e-164 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 481.90 E-value: 1.47e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLE-TMQPNFVIESSRKKIISQIKKEGKTA 80
Cdd:COG0550 1 KKLVIVESPAKAKTIAKYLG-----KDYVVTASVGHLRDLPKPE---LDVDVEnDFEPKYEVIPGKKKQVKELKKLAKKA 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 81 DLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQ 160
Cdd:COG0550 73 DEVILATDPDREGEAIAWHLLELLGDKKPVKRVVFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLW 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 161 K--STGLmSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFvieskrAINLNLNKDKNNVLVNTEKTYYIDENQAKTIVDE 238
Cdd:COG0550 153 KkvKRGL-SAGRVQSPALRLIVEREREIEAFVPEEYWTIE------ATFKTGGGEFTAKLVKIDGKKILDEEEAEAILAA 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 239 L-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYIS 317
Cdd:COG0550 226 LkGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIE 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 318 KNYSSDLFKD-PIVGKKDQNSQEAHESIRPTNIWLTPEKASLEiednlLKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNN 396
Cdd:COG0550 306 ALYGKEYLPEkPRVYKTSKNAQEAHEAIRPTGVTRTPESLSGD-----EFKLYDLIWKRFLASQMPPAEYETTTVTIEVG 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 397 GYEFKQSWQEVKDLGYQAIKHSSSDENIEltDDGEEIVQ-SKNDKpeyqfnddfeisISKKFIKIESAKTNPPKMFNQAS 475
Cdd:COG0550 381 GEEFRASGKVIKFPGFLKVYGEGKDDEEE--EEEKRLPPlKEGEK------------LKLKKIEPEQHFTKPPPRYTEAS 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 476 LIKELKNLGIGRPSTYNPILTKLKDREYVEyPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDFDY 555
Cdd:COG0550 447 LVKAMEELGIGRPSTYASIIETLQDRGYVE-REGKRLVPTELGFIVIDLLEEHFPDLVDYEFTAKMEEKLDEIAEGKLDW 525
|
570
....*....|....*.
gi 499706891 556 VNWLKNIYNALNFKVK 571
Cdd:COG0550 526 KDVLEEFYKPFKELVE 541
|
|
| topA_bact |
TIGR01051 |
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ... |
4-615 |
7.86e-138 |
|
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: 416.01 E-value: 7.86e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 4 LVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLE-TMQPNFVIESSRKKIISQIKKEGKTADL 82
Cdd:TIGR01051 1 LVIVESPAKAKTIKKYLG-----DEYEVEASMGHIRDLPKSR---LGVDIEkDFEPEYVVSKGKKKVVKELKTLAKKADE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 83 IILASDPDREGEAIAYHLANLFKDHTN-IKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQK 161
Cdd:TIGR01051 73 VYLATDPDREGEAIAWHLAEVLKPKDPvYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 162 S-TGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKRAinlnLNKDKNNVLVNTEK---TYYIDENQAKTIVD 237
Cdd:TIGR01051 153 KvAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGE----ETFEALLTEVNGKKlkaGSDLDEAEATALKE 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 238 EL-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE--------LGYITYIRTDSVKYSSQF 308
Cdd:TIGR01051 229 QLkGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEgvstgdgtIGLITYMRTDSTRLSNQA 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 309 IGEVKDYISKNYSSDLFKDP--IVGKKDQNSQEAHESIRPTNIWLTPE--KASLEIEDnllKRVYNLIWWNSIKSLMKGP 384
Cdd:TIGR01051 309 VNEARNLIDKNYGKEYLGPKpkRYKSKEKNAQEAHEAIRPTSVFRTPEelKDYLKRDE---FRLYELIWKRFVASQMADA 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 385 SGFNHRWTFNN--NGYEFKQSWQEVKDLGYQAIKHSSSDENIELTDdgeeivqskNDKPEYQFNDdfeiSISKKFIKIES 462
Cdd:TIGR01051 386 RYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKD---------RILPPLKEGD----AVKLVEVKPNQ 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 463 AKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEME 542
Cdd:TIGR01051 453 HFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKK-ENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKME 531
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499706891 543 EKLDEITRGDFDYVNWLKNIYNALNFKVKKEIGE-----AKTEAICPRCGANLVYIKSRFNRGRGCSNFtiTKCGYRK 615
Cdd:TIGR01051 532 KDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMriivdFKTSQDCPLCGRPMVVKLGKYGPFLACSNF--PECKYTK 607
|
|
| PRK06599 |
PRK06599 |
DNA topoisomerase I; Validated |
1-615 |
8.56e-126 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235840 [Multi-domain] Cd Length: 675 Bit Score: 386.91 E-value: 8.56e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGawgLGIDLET-MQPNFVIESSRKKIISQIKKEGKT 79
Cdd:PRK06599 2 AKKLVIVESPAKAKTIKKYLG-----KDYKVLASFGHVRDLPKKK---GGVDPDNdFAPKYEIIEGKEKVVDALKKAAKK 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 80 ADLIILASDPDREGEAIAYHLANLFK----DHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLV 155
Cdd:PRK06599 74 ADAVYLATDPDREGEAIAWHIAEVLKeaklKDKNVKRVVFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 156 SKSL-QKSTGLMSAGRVQTPALNILTTRDTLIKNFKEVLYkkiFVIESKRAINLNLNKDKNNVLVNTEK--TYYI-DENQ 231
Cdd:PRK06599 154 SPLLwKKVRRGLSAGRVQSVALRLICEREDEIEAFIPQEY---WTIEADLATSNGEPFTAKLVEVNGKKleKFSItNEEQ 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 232 AKTIVDEL-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE--------LGYITYIRTDSV 302
Cdd:PRK06599 231 AKALVKALeGQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEgidlgegtVGLITYMRTDSV 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 303 KYSSQFIGEVKDYISKNYSSD--LFKDPIVGKKDQNSQEAHESIRPTNIWLTPEkaslEIEDNLLK---RVYNLIWWNSI 377
Cdd:PRK06599 311 RLSNEALDEARKYITKKYGKEylPAKPRVYKKKSKNAQEAHEAIRPTSINRTPE----SLKPYLTPdqfKLYELIWKRTV 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 378 KSLMKgPSGFNH-RWTF--NNNGYEFKQSWQEVKDLGYQAIKHSSSDENIEltddgeeivQSKNDKPEYQFNDDF---EI 451
Cdd:PRK06599 387 ASQMA-PAILDQtSVDIasENGKYVFRATGSVILFPGFLKVYGESKDDEEE---------DDEKLLPPLKEGEKLkldEL 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 452 SISKKFikiesakTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKsKPIVVTNKGYSANEYLYDHYLD 531
Cdd:PRK06599 457 LPEQHF-------TEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVELEK-KRFIPTDLGRIVNDFLVEHFPK 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 532 FFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYNALNFKVKK--------EIGEAKTEAICPRCGANLVYIK-SRFNRGRG 602
Cdd:PRK06599 529 YVDYDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKveedvrteKVTQEETDETCPKCGGGPLVLKlGKNGKFLG 608
|
650
....*....|...
gi 499706891 603 CSNFtiTKCGYRK 615
Cdd:PRK06599 609 CSGY--PECKYTK 619
|
|
| PRK07561 |
PRK07561 |
DNA topoisomerase I subunit omega; Validated |
1-613 |
4.06e-115 |
|
DNA topoisomerase I subunit omega; Validated
Pssm-ID: 236048 [Multi-domain] Cd Length: 859 Bit Score: 364.50 E-value: 4.06e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHI----------NSIADKGAWG-LGIDLET-MQPNFVIESSRKK 68
Cdd:PRK07561 1 GKSLVIVESPAKAKTINKYLG-----SDYVVKASVGHIrdlptsassvPAKEKGALWArMGVDPDHdFEALYEVLPGKEK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 69 IISQIKKEGKTADLIILASDPDREGEAIAYHLANLFK-DHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQIL 147
Cdd:PRK07561 76 VVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGgDDVPVKRVVFNEITKNAIQEAFENPRELDINLVNAQQARRFL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 148 DKIIGYLVSKSLQK--STGLmSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFV-IESKRAINLNLNkdknnvLVN---- 220
Cdd:PRK07561 156 DRLVGYMVSPLLWKkiARGL-SAGRVQSVAVRLIVEREREIEAFVPEEYWDIHAdLTTPRGDAFEAR------LTHldgk 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 221 -TEKTYYIDENQAKTIVDELgeiyRCTDYKSTAYETRSFK-----PYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYI 294
Cdd:PRK07561 229 kFAPVDLLNEAQAEAAVAAL----EGARYSVASVEDKPTTrkpsaPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYI 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 295 TYIRTDSVKYSSQFIGEVKDYISKNYSSD-LFKDPIV-GKKDQNSQEAHESIRPTNIWLTPEKAS-LEIEDnllKRVYNL 371
Cdd:PRK07561 305 TYMRTDSTNLSQEAINAARGYIGDNYGKKyLPEKPRQySSKAKNAQEAHEAIRPSDVFRTPDQLKgLEGDA---QRLYEL 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 372 IWWNSIKSLMKgPSGFNH-RWTFNNNGYEFKQSWQEVKDLGYQAIKHSSSDENieltDDGEEI---VQSKNDKPEYQfnd 447
Cdd:PRK07561 382 IWKRFVASQMA-PARYDStTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDA----LDDEDRrlpALKVGDALTLE--- 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 448 dfEISISKKFikiesakTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVeYPKSKPIVVTNKGYSANEYLYD 527
Cdd:PRK07561 454 --KLDPTQHF-------TKPPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYV-RLENRRFYPEKMGRIVTDRLEE 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 528 HYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYnalnFKVKKEIGEAK---------------TEAICPRCGANL-- 590
Cdd:PRK07561 524 FFPRLVDYDFTARMEEELDDIANGEADWKPVLDDFY----KDFSQQLEKAEelreeggmrpnqmviTDRDCPTCGRGMgi 599
|
650 660 670
....*....|....*....|....*....|
gi 499706891 591 ------VYIksrfnrgrGCSNFTIT-KCGY 613
Cdd:PRK07561 600 rtgktgVFL--------GCSGYALKeRCKT 621
|
|
| PRK06319 |
PRK06319 |
DNA topoisomerase I/SWI domain fusion protein; Validated |
2-618 |
2.60e-91 |
|
DNA topoisomerase I/SWI domain fusion protein; Validated
Pssm-ID: 235778 [Multi-domain] Cd Length: 860 Bit Score: 301.36 E-value: 2.60e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEEsfpenEFVVLASGGHINSIADKGawgLGIDLET-MQPNFVIESSRKKIISQIKKEGKTA 80
Cdd:PRK06319 3 KSLIIVESPAKIKTLQKLLGE-----GFIFASSLGHIVDLPAKE---FGIDIENdFEPDYQILPDKEEVINKICKLAKKC 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 81 DLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGY----LVS 156
Cdd:PRK06319 75 DVVYLSPDPDREGEAIAWHIANQLPKNTKIQRISFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYkispILS 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 157 KSLQKSTGLmSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVI-----ESKR---AINLNLNKDKNNVLV--NTEKTYY 226
Cdd:PRK06319 155 RKLQRRSGV-SAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHlkdpkTQKTfwaHLYSVDGKKWEKEIPegKTEDEVL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 227 IDENQAKTivDELGEIYRCTDYKSTAYETRSFK-----PYSTAGLLQDGFTKLKLSTSQITLAAQKLYE---------LG 292
Cdd:PRK06319 234 LINSKEKA--DHIVELLESATYTVTRVESKEKRrnaypPFITSTLQQEASRHFRFSSSRTMNIAQTLYEgvdldsegaTG 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 293 YITYIRTDSVKYSSQFIGEVKDYISKNYSSD-LFKDPIVGKKDQNSQEAHESIRPTNIWLTPEKASLEIEDNLLKrVYNL 371
Cdd:PRK06319 312 LITYMRTDSVRTDPEALKQVRKYIEGTFGKEfLPSSPNVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYK-LYSL 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 372 IWWNSIKSLMKgPSGFNhrwTF-----NNNGYEFKQSWQEVKDLGYQAIKHSSSDenieltDDGEEivqsKNDKPEYQFN 446
Cdd:PRK06319 391 IWKRFVASQMI-PAIYD---TLairitTNKGIDLRATGSLLKFKGFLAVYEEKRD------DEGDE----EENIHLPKLH 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 447 DDFEisISKKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYV--EYPKSKPivvTNKGYSANEY 524
Cdd:PRK06319 457 EQDV--LTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTlkENQRLRP---TELGKIISQF 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 525 LYDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYNALNFKVKKEIGEA-----KTEAICPRC-GANLVYIKSRFN 598
Cdd:PRK06319 532 LETNFPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKEAfipriVTEIDCPKChKGKLVKIWAKNR 611
|
650 660
....*....|....*....|
gi 499706891 599 RGRGCSNFtiTKCGYRKYEQ 618
Cdd:PRK06319 612 YFYGCSEY--PECDYKTSEE 629
|
|
| PRK08780 |
PRK08780 |
DNA topoisomerase I; Provisional |
2-585 |
6.96e-89 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 181555 [Multi-domain] Cd Length: 780 Bit Score: 293.21 E-value: 6.96e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEEsfpenEFVVLASGGHINSIADK-GAwglgIDLE---TMQPNfVIESSRKKIiSQIKKEG 77
Cdd:PRK08780 3 KHLVIVESPAKAKTINKYLGK-----DFTVLASYGHVRDLVPKeGA----VDPEngfAMRYD-LIDKNEKHV-EAIAKAA 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 78 KTADLIILASDPDREGEAIAYHLANLFKDH-----TNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIG 152
Cdd:PRK08780 72 KSADDLYLATDPDREGEAISWHLAEILKERgllkdKPMQRVVFTEITPRAIKEAMAKPRDIASDLVDAQQARRALDYLVG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 153 YLVSKSLQK--STGLmSAGRVQTPALNILTTRDTLIKNFKEVLYkkiFVIESKRAINLNLNKDKNNVL--VNTEKTYYID 228
Cdd:PRK08780 152 FNLSPLLWRkiQRGL-SAGRVQSPALRMIVEREEEIEAFIAREY---WSIEADCAHPSQPFNAKLIKLdgQKFEQFTITD 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 229 ENQAKTIVDEL-----GEIyRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE---------LGYI 294
Cdd:PRK08780 228 GDTAEAARLRIqqaaqGTL-HVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEgvdlgdegsVGLI 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 295 TYIRTDSVKYSSQFIGEVKDYISKNYSSD-LFKDPIVGK-KDQNSQEAHESIRPTNIWLTPEKASLEIEDNLlKRVYNLI 372
Cdd:PRK08780 307 TYMRTDSVNLSQDALAEIRDVIARDYGTAsLPDQPNTYKtKSKNAQEAHEAVRPTSALRTPAQVARFLSDDQ-RRLYELI 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 373 WWNSIKSLMKgPSGFNhrwTFN-----NNGYEFKQSWQEVKDLGYQAIKHSSSDENIELTDDGEEIVqskndkPEYQFND 447
Cdd:PRK08780 386 WKRAVACQMI-PATLN---TVSvdlaaGSEHVFRATGSTVVVPGFLAVYEEGKDDKSAEDEDEGRKL------PPMKEGD 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 448 dfeiSISKKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKGYSANEYLYD 527
Cdd:PRK08780 456 ----NVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEM-EGRRFRPTDVGRAVNKFLTG 530
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*....
gi 499706891 528 HYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYNALNFKVK-KEIGEAKTEAICPR 585
Cdd:PRK08780 531 HFTRYVDYDFTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVEeKKDSVDRTEAGQVR 589
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
135-563 |
1.09e-86 |
|
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: 275.64 E-value: 1.09e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 135 MNLVNAQISRQILDKIIGY----LVSKSLQKSTGLmSAGRVQTPALNILTTRDTLIKNFKEvlykkifvieskrainlnl 210
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFnlsrLLTKKLRRKGVL-SAGRVQSPTLGLIVEREREIKAFVP------------------- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 211 nkdknnvlvnteKTYYidENQAKTIVDelgeiyrctdYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYE 290
Cdd:cd00186 61 ------------EDYW--EIKEAVVVS----------VEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYE 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 291 LGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLFKD-----PIVGKKDQNSQEAHESIRPTNIwlTPEKASLEIEDNLL 365
Cdd:cd00186 117 AGLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPapllgRRNPKRGKKEQGAHEAIRPTKV--APTPELEANLSEDE 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 366 KRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAIKhsssdenieltddGEEIVQSKNDKPEYQF 445
Cdd:cd00186 195 FKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVY-------------PEEKDDEEEEPPPLKE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 446 NDDFEISIskkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKSKpIVVTNKGYSANEYL 525
Cdd:cd00186 262 GDELKLEE----VELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKK-LIPTELGFAVIELL 336
|
410 420 430
....*....|....*....|....*....|....*...
gi 499706891 526 YDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIY 563
Cdd:cd00186 337 EKHFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFY 374
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
132-560 |
2.77e-84 |
|
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: 270.27 E-value: 2.77e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 132 DIDMNLVNAQISRQILDKIIGYLVSKSLQKST---GLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIeskrainl 208
Cdd:pfam01131 1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgnKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEAT-------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 209 NLNKDKNNVLVNTEKTYYIDENQAKTIVDELGEI-YRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQK 287
Cdd:pfam01131 73 LKDGGGVFANAKWKRGRIFDKEEAEAILEKLKKGtAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQK 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 288 LYE-LGYITYIRTDSVKYSSQF-IGEVKDYISKNY------SSDLFKDPIVGKKDQNSQ-EAHESIRPTNIWLTPEKASL 358
Cdd:pfam01131 153 LYEkHGLITYPRTDSTYLSDDAtLKAILEYLTKNYgkylpyAPRLLKKTKGKLTVGNAKvTAHEAIRPTGDIPVLPELSD 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 359 EIednllKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAIKHSSSDEnieltdDGEEIvqskn 438
Cdd:pfam01131 233 DE-----RKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKE------DEEEL----- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 439 dkPEYQFNDDFEIsiskKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKG 518
Cdd:pfam01131 297 --PELKEGEELKV----TQVEVEEKKTKPPPRYTEASLIKAMEKAGIGTPATRATIIETLLERGYVER-KKKSLVPTELG 369
|
410 420 430 440
....*....|....*....|....*....|....*....|..
gi 499706891 519 YSANEyLYDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLK 560
Cdd:pfam01131 370 KALVE-ALEKFPDLVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| TopG2 |
COG1110 |
Reverse gyrase [Replication, recombination and repair]; |
30-577 |
2.24e-71 |
|
Reverse gyrase [Replication, recombination and repair];
Pssm-ID: 440727 [Multi-domain] Cd Length: 1219 Bit Score: 251.05 E-value: 2.24e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 30 VVLASGGHI----NSIADKGAWGLGIDLETMQP-------------NFVIESSRKK------------IISQIKKEGKTA 80
Cdd:COG1110 672 LITASGGHVfdlvTEAYARGFYGVLVENGRFIPvydtikrcldcgeQFTDEVEVCPrcgspnivdsleIVEALRELATEV 751
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 81 DLIILASDPDREGEAIAYHLANLFKDHT-NIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSL 159
Cdd:COG1110 752 DEVLIGTDPDTEGEKIGWDVYNLLRPYAkNIKRIEFHEVTRKAILEALKNPREIDENLVEAQIVRRIEDRWIGFTLSQKL 831
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 160 QK--STGLMSAGRVQTPALNILTTRdtLIKNFKEVLYKKIFVIESKRainlnlnkdknnVLVNTEktyyiDENQAKTIVD 237
Cdd:COG1110 832 WKvfGNRNLSAGRVQTPVLGWIIER--YEESRKSKKYLIILTLENGR------------LELSIE-----DLKEAEEVRK 892
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 238 ELGEIYRCTDYKSTAYET--RSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDY 315
Cdd:COG1110 893 ALEKEVKVKVKKVEEEEEelNPLPPYTTDTLLRDASRRLGLSAEETMRLAQDLFESGLITYHRTDSTRVSDAGIAVAKEY 972
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 316 ISKNYSSDLFKDPIVGkkdqnSQEAHESIRPTNIwLTPEKASLEIEDNLLK----------RVYNLIWWNSIKSLMKgPS 385
Cdd:COG1110 973 ISERFGEEYFKPRRWG-----EGGAHEAIRPTRP-LDAEDLRRLIEEGVIElpipltrrhlRLYDLIFRRFMASQMR-PA 1045
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 386 gfnhrwtfnnngyefkqswqEVKdlgYQAIKHSSSDENIELTDDG-EEIVQSKNDKPEYQFNDDFEISISK-KFIKIESA 463
Cdd:COG1110 1046 --------------------KVE---KVKLRVSLELPGGEIEEERiVEIIEDGFLLIYPPIKVEPELKEGEyKVTEVKIR 1102
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 464 KTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYV-EYPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEME 542
Cdd:COG1110 1103 KVPKVPLYTQGDLVREMKERGIGRPSTYAKIVETLLRRGYVvESKKGKKLVPTKLGIEVYNYLSENFPDLVSEERTRELE 1182
|
570 580 590
....*....|....*....|....*....|....*
gi 499706891 543 EKLDEITRGDFDYVNWLKNIYNALNFKVKKEIGEA 577
Cdd:COG1110 1183 EKMDEIEEGEADYQDVLEELYNELRELVLSPESEL 1217
|
|
| rgy |
TIGR01054 |
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ... |
3-567 |
2.79e-65 |
|
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: 233.18 E-value: 2.79e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 3 VLVLLESPSKIEKIKHY--------------LEESFPENEFVVLASGGHI-NSIADKGAWGLGIDLETMQP--------- 58
Cdd:TIGR01054 603 ALLVVESPNKARTIARFfgkpsvrkiggsvvYEVPVGDLILMITASGGHVfDLVTDKGFHGVLVENGRYVPvytsikrcr 682
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 59 ----NFVIESSR------------KKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHT-NIKRITFNEITSE 121
Cdd:TIGR01054 683 dcgyQFTEDREScpkcgseniedsKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPYNpNVKRAEFHEVTRR 762
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 122 AITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQKSTG--LMSAGRVQTPALNilttrdtliknfkevlykkiFV 199
Cdd:TIGR01054 763 AILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNkrWLSAGRVQTPVLG--------------------WI 822
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 200 IESKRAINLNLNKDKNNVLVNTEKTYYIDENQAKtiVDELGEIYRCTDYKSTA---YETRSFKPYSTAGLLQDGFTKLKL 276
Cdd:TIGR01054 823 IDRYRESREKRGYLLIFALESDFRLGLEHDNRLE--AKEFEKDLTWLDVEDIAereEERNPLPPYTTDTMLEDANRKLGL 900
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 277 STSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLFKDPIVGKKDqnsqeAHESIRPTNIwLTPEKA 356
Cdd:TIGR01054 901 SVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLGGEYFYPREWGEGG-----AHECIRPTRP-LDVDDL 974
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 357 SLEIEDNLLK---------RVYNLIWWNSIKSLMKgpsgfnhrwTFNNNGYEFKqswqeVKDLGYQAIKHSSsdenIELT 427
Cdd:TIGR01054 975 QRLILEGVIElegltrehlRLYDLIFRRFMASQMR---------PAKVDTKEIT-----LKADGKEAEEEGI----VEIV 1036
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 428 DDGEEIVQSKNDKPEYQFNDDFeISISKKFIKIesaktnpPK--MFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVe 505
Cdd:TIGR01054 1037 ERGFELVYPLWRKNELEKGSTF-IVKDKELRSV-------PKvyPYTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYV- 1107
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499706891 506 YPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIYNALN 567
Cdd:TIGR01054 1108 VESKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVYREIK 1169
|
|
| PRK07219 |
PRK07219 |
DNA topoisomerase I; Validated |
52-606 |
8.87e-63 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235971 [Multi-domain] Cd Length: 822 Bit Score: 222.95 E-value: 8.87e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 52 DLETMQPNFVIESS------RKKIISQIKKEGKTADLIILASDPDREGEAI---AYHLANLFKDhTNIKRITFNEITSEA 122
Cdd:PRK07219 64 DWRDVDPAELIDADpvkkitKQNYINALKKLAKDADEIIIATDYDREGELIgkeAYHILREVCQ-VPVKRARFSSLTKKE 142
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 123 ITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQKS------TGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKK 196
Cdd:PRK07219 143 IRKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSvrqlgrWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWK 222
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 197 IFVIESKRAINLNLNKDKNnvlvnTEKTYYIDENQAKTIVDELGE--IYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKL 274
Cdd:PRK07219 223 IEALLDKEAQYFYRDLIGG-----HEAEKFWDEEEAEEIYEKLKGakEATVSSVKKRERTISPPAPFNTTEFLREASKIF 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 275 KLSTSQITLAAQKLYELGYITYIRTDSVKYSSQF-----------IGEVKDYISKNYSSDLFKdPIVGKKDQNsqeAHES 343
Cdd:PRK07219 298 GISPKRAMEIAEKLYTAGYISYPRTDNTVYPDDLdpkellkklskKKEYGPYAESILEQENIK-PTEGKKETT---DHPP 373
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 344 IRPTNiwltpEKASLEIEDNLLKrVYNLIWWNSIKSLMKgpsgfNHRWTFNN-----NGYEFKQSWQEVKDLGYQAI-KH 417
Cdd:PRK07219 374 IHPVD-----VPKREELSDDEWK-VYELIVRRFLATLAD-----PAEWEYLKveldvNGEIFKASGSRLVEEGWHEVyPY 442
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 418 SSSDENIeltddgeeivqskndKPEYQFNDdfEISISKkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTK 497
Cdd:PRK07219 443 EKFDEKE---------------LPDLEEGE--KLKVNK--IEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEK 503
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 498 LKDREYVeyPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRG--DFDYV-----NWLKNIYNALNFKv 570
Cdd:PRK07219 504 LYKRGYV--IEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEADMQAIEDGkkKKEDVteesrEMLKEILSELKEK- 580
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 499706891 571 KKEIGEAKTEAI------------CPRCGANLVYIKSR-FNRGRGCSNF 606
Cdd:PRK07219 581 RKEIGDHLAGSLkaenrslktigkCPECGGDLIIIRTDkGSRFVGCSGY 629
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
259-518 |
1.66e-53 |
|
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: 183.99 E-value: 1.66e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 259 KPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLFKDPIVGKKDQ--- 335
Cdd:smart00437 11 PPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLAVVLLKPRkpr 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 336 ---NSQEAHESIRPTNIWLTPEKASlEIEDNLLKrVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGY 412
Cdd:smart00437 91 kgkKAQGAHEAIRPTKPIFTPELEK-ELSEDEFK-LYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTLLFDGW 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 413 QAIKHSSSDE-NIELtddgeeivqskndkPEYQFNDDFEISIskkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTY 491
Cdd:smart00437 169 LKVYPEEKKEeEIEL--------------PTLKKGDELKVEE----VEVEEKETKPPARYTEASLIKLMEKRGIGRPSTY 230
|
250 260
....*....|....*....|....*..
gi 499706891 492 NPILTKLKDREYVEYpKSKPIVVTNKG 518
Cdd:smart00437 231 ASIIETLLDRGYVTK-KKKKLIPTELG 256
|
|
| TOPRIM_TopoIA_TopoI |
cd03363 |
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ... |
2-129 |
4.36e-51 |
|
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: 172.36 E-value: 4.36e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSIADKGAWGLGIDLEtMQPNFVIESSRKKIISQIKKEGKTAD 81
Cdd:cd03363 1 KKLVIVESPAKAKTIKKYLG-----KEYEVLASVGHIRDLPKKGLGVDGEDDG-FEPKYVVIPGKKKVVKELKKLAKKAD 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 499706891 82 LIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNN 129
Cdd:cd03363 75 EIYLATDPDREGEAIAWHLAEVLKLKKNVKRVVFNEITKEAIKEALKN 122
|
|
| PRK07220 |
PRK07220 |
DNA topoisomerase I; Validated |
5-606 |
1.21e-46 |
|
DNA topoisomerase I; Validated
Pssm-ID: 180892 [Multi-domain] Cd Length: 740 Bit Score: 176.10 E-value: 1.21e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 5 VLLESPSKIEKIK--HYLEESFPENEFVVLASGGHInsiadkgawgLGIDL-------------ETMQPNFVIESSRKKI 69
Cdd:PRK07220 18 ILAPKKPKKTRVSgvDVYRYEDNGDDTVVVGLSGHI----------VNIDFpkeynnwqkvdarDLIDAEIITTPTQKKI 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 70 ISQIKKEGKTADLIILASDPDREGEAI---AYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQI 146
Cdd:PRK07220 88 VTALKKLGKEADRVTIATDYDREGELIgveALNIIKKVNPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQV 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 147 LDKIIGYLVSKSLQKSTG-----LMSAGRVQTPALNILTTRDtliknfKEvlyKKIFVIESKRAINLNLNKDKNNVLVNT 221
Cdd:PRK07220 168 IDLVWGAALTRYISLAAGrlgkmFLSVGRVQSPTLALIVDRE------KE---REAFVPTPYWEIYATLENNGETFVAQH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 222 EKTYYIDENQAKTIVDELGEIYRCTDYKSTAYETRSFKPYSTAGLLQDGfTKLKLSTSQITLAAQKLYELGYITYIRTDS 301
Cdd:PRK07220 239 STRRFWEKEEADRVFEKLGKTAEVTEVEKGTKTDKPPTPFNTTEFISAA-NSIGFSAANAMRIAESLYTNGYISYPRTDN 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 302 VKYSS---------QFI-GEVKDYISKNYSSDLFKdPIVGKKDQNSqeaHESIRPTNIwltPEKASLEiEDNLlkRVYNL 371
Cdd:PRK07220 318 TVYPEsldlreqieIFAeGPFGEYAQKLLEKGELV-PTRGKKETTD---HPPIYPASL---AKKSELK-EDEW--KVYEL 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 372 IWWNSIKSLmKGPSGF-NHRWTFNNNGYEFKQSWQEVKDLGYQAIKHSSSDENIELtddgeeivqskndkPEYQFNDdfE 450
Cdd:PRK07220 388 VVRRFFATF-AGPAEWeTMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLL--------------PELSEGE--E 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 451 ISISKKfiKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEypkSKPIVVTNKGYSANEYLYDHYL 530
Cdd:PRK07220 451 LKVKKK--EMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH---GNPIQPTNTAFAVVDALEKYAP 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 531 DFFNLNYTAEMEEKLDEITRGDF--DYV-----NWLKNIYNALNfKVKKEIGEAKTEAI--------CPRCGANLVYIKS 595
Cdd:PRK07220 526 TITKPDMTSRLEEDMDKIAEGKIkeDAVleesrEMLEQVFDELD-KNREKIRESLREGLredkiigkCPLCGSDLMVRRS 604
|
650
....*....|..
gi 499706891 596 RFN-RGRGCSNF 606
Cdd:PRK07220 605 KRGsRFIGCEGY 616
|
|
| PTZ00407 |
PTZ00407 |
DNA topoisomerase IA; Provisional |
4-550 |
4.82e-43 |
|
DNA topoisomerase IA; Provisional
Pssm-ID: 173597 [Multi-domain] Cd Length: 805 Bit Score: 165.88 E-value: 4.82e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 4 LVLLESPSKIEKIKHYLEE-------SFPENEF----------VVLASGGHINSI--------ADKGAWGLGIDLETMQP 58
Cdd:PTZ00407 12 LVIVESPNKVIKVEGLLSDpkvipdwSFKQSHLrrigtgaekaVAMATTGHFMALkeitwspqASSPASVVGAGDEPFPS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 59 NFVIESSR--------KKIISQIKK--EGKTADL--IILASDPDREGEAIAYHLANLFKD-----HTNIKRITFNEITSE 121
Cdd:PTZ00407 92 NGTLAEYTlewellpgRRIQETLERyiEEKADNVteIILATDPDREGELIAVHALQTIKRlypklKVPFSRAYMHSITED 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 122 AITNAF--NNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQKSTGLM-SAGRVQTPALNILTTRDTLIKNFKEVlYKKIF 198
Cdd:PTZ00407 172 GIRKAMreRHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMrSIGRVQTPALILINEREDKIKAFLES-NKSTF 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 199 VIESKRAINLNLNKDKNNVL-----VNTEKTYYIDENQAKTIVdELGEIYRCTDY------KSTAYETRSFKPYSTAGLL 267
Cdd:PTZ00407 251 EVQAMCQFPSPHGTTFSQVVtitpdRKGGASHWATEAEARRCL-EQWKLNNCTGFsvplepKPQPSVVPPPQPFTMATAI 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 268 QDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVKYSSQFIGEVKDYISKNYSSDLF---KDPIVGKKDQ--------- 335
Cdd:PTZ00407 330 AKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLyrlEDRTVSAQEGkgskktgkk 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 336 --------------NSQEAHESIRPTNIWLTPEKASLEIEdnlLKRVYNLIWWNSIKSLM------------KGPSGfnh 389
Cdd:PTZ00407 410 rstkqkkgadtpvgNVEDAHEAIRPTNIDTTGESLSLSPP---TRAVYDLVRRNTLAVFMipmktekivatvKFTSG--- 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 390 rwtfNNNGYEFKQSWQEVKDLGYQAIKHSSS----------DENIELTDDGEEIVQSKNDKPEY---QFNDDFEISISKK 456
Cdd:PTZ00407 484 ----SGEKLEFELQGKRVVEPGWTRAFHKGDkgttgpaeetDEDITAVEEGAPVVPSLSQEEFKaimNLRSQLGSGVQKG 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 457 FIKIESA-----KTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKSKPIVVTNKGYSANEYLYDHYLD 531
Cdd:PTZ00407 560 FFELRSPqvrenRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLVETAKSTFPS 639
|
650
....*....|....*....
gi 499706891 532 FFNLNYTAEMEEKLDEITR 550
Cdd:PTZ00407 640 IVDIGFTAAFEKKLDRIAK 658
|
|
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
2-578 |
1.22e-39 |
|
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: 154.62 E-value: 1.22e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKI-----KHYLEESFPE--NEFVVLASGGHINSIADK-------GAWGLG-IDLETMQPNFVIESSR 66
Cdd:TIGR01056 1 MTLVLCEKPSQARDLatvlaKKKKGNGYLEigVGGFVTWAVGHLVELAEPeeydekyKNWRTYdLPLEPEDWQLVVSDKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 67 KKIISQIKK--EGKTADLIILASDPDREGEAIAYHLANL--FKDHTNIKRITFNEITSEAITNAFNNLRDID--MNLVNA 140
Cdd:TIGR01056 81 KKQFNVIKRilKENKVDEVVIATDPDREGELIAREILDYlkVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSetEGLYKS 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 141 QISRQILDKIIGYLVSKSLQKST------GLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIfvieskRAINLNLNKDK 214
Cdd:TIGR01056 161 GVARARADWLVGINLTRAFTKLGreagndGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEV------SATINKDEQEF 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 215 NNVLVN--TEKTYYIDENQAKTIVDEL-GEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYEL 291
Cdd:TIGR01056 235 TTEWQPykDEEERELHEFLAENVVTDLtQKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYET 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 292 G-YITYIRTDSVKYSSQFIGEVKDYIS--KNYSSDLFKDPIVGKKDQNSQ------EAHESIRPTNiwLTPEKASLEIED 362
Cdd:TIGR01056 315 HkLITYPRTDSRYLPEDEKEMLLEVLDalKVITPALLPIKKRDELTNNRLwndkkiEDHHAIIPTG--NDFNLSDLSEEE 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 363 nllKRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAI--KHSSSDENIELT----DDGEEI--- 433
Cdd:TIGR01056 393 ---RNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALlgKQEEDEETEDTTlpafQKGDELdve 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 434 ---VQSKNDKPEYQFNDDFEIsiskkfikieSAKTNPPKMFNQASLIKELK-NLGIGRPSTYNPILTKLKDREYVEYPKS 509
Cdd:TIGR01056 470 tleLLEKQTKPPARYTEGTLL----------SAMTNPAAFVQDKGLKKTLKeTKGLGTEATRADIIENLFKRGFIQKKKN 539
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499706891 510 KpIVVTNKGYSANEYLYDhylDFFNLNYTAEMEEKLDEITRGDFDYVNWLKNIynalNFKVKKEIGEAK 578
Cdd:TIGR01056 540 K-IYITKNGKLLCLLLPE---LLTKPDLTAQWEQYLNGISAGEKDDDDFINTI----NEMIKQTINEEK 600
|
|
| PRK05776 |
PRK05776 |
DNA topoisomerase I; Provisional |
1-628 |
4.15e-37 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 235602 [Multi-domain] Cd Length: 670 Bit Score: 147.06 E-value: 4.15e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKIKHYLEE----------SFPE-----NEFVVLASGGHINSIADKGAwGLGI-DLEtMQPNFVIES 64
Cdd:PRK05776 1 GYILVIAEKPKAARKIAEALSEkpircriygvPYWIvkrdgKKIVVAPAAGHLFGLHTKSK-GFPVfDYE-WKPLYEIDK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 65 SR---KKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQ 141
Cdd:PRK05776 79 GSkytKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLGDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMINAG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 142 ISRQILDKIIGYLVSKSLQKS----TG---LMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKrainlnlnkDK 214
Cdd:PRK05776 159 IARHELDWLWGINVSRALMSSvrdaSGkrvILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEK---------NG 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 215 NNVLVNTEKTYYIDENQAKTIVDELGEIYRCTDYKSTAYETRSFKPYS-TAGLLQD------GFTKLKlsTSQItlaAQK 287
Cdd:PRK05776 230 YEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPfNLGDLQVeaariyGFSPYK--TQSI---AED 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 288 LYELGYITYIRTDSVKYSS--------QFIGEVKDYisKNYSSDLFKD------PIVGKKDqnsQEAHESIRPTNIwlTP 353
Cdd:PRK05776 305 LYLDGLISYPRTNSQKLPPtlnirnilKGLSRSPQY--RPLVNLLLKEtkgvlkPVQGPKD---DPAHPAIYPTGE--PP 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 354 EKASLEIEdnllkRVYNLIWWNSIKSLMKGPSGFNHRWTFNNNG--YEFKQSWQEVKDLGYQAIK--HSSSDENIELTDD 429
Cdd:PRK05776 378 KNLSKDEF-----KLYDLIVRRFLASFAAPAVLSNTIVTLRVPGfpLVFSASGQRIEERGWLKYYpfHKFDEEELPLLKK 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 430 GEEIVQSKndkpeyqfnddfeisiskkfIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVeYPKS 509
Cdd:PRK05776 453 GERVKIVD--------------------VKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYL-TSNG 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 510 KPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDF---DYVNWLKNIYNAL--NFKVKKE---------IG 575
Cdd:PRK05776 512 KYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKAtreEVIEEAKETLNKLleEFKKNKDeigeelakaLG 591
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*....
gi 499706891 576 EAKTEAICPRCGANLV------YIKSRFNRGRGCSNFTITKCGYrkyeqpdgTWKEYIK 628
Cdd:PRK05776 592 LIKPVGKCKICGREAYkdglckYHYEAKKRLVKAYEEWKERTGY--------DHKEYLE 642
|
|
| PRK14973 |
PRK14973 |
DNA topoisomerase I; Provisional |
67-590 |
5.62e-35 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 184936 [Multi-domain] Cd Length: 936 Bit Score: 141.91 E-value: 5.62e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 67 KKIISQIKKEGKTADLIILASDPDREGEAI---AYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQIS 143
Cdd:PRK14973 84 KKIVGLIQKLAKKADRVTIATDFDTEGELIgkeAYELVRAVNPKVPIDRARFSAITKEEIVTAFAEPTDLDFALAAAGEA 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 144 RQILDKIIGYLVSK--SLQKSTG---LMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKRAInlnlnkdknNVL 218
Cdd:PRK14973 164 RQIIDLIWGASLTRfiSLAAHRGgdnILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATEKDGE---------GIE 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 219 VNTEKTYYIDENQAKTIVDELGEIYRCTDYKSTAYETRSFKPYSTAGLLQdGFTKLKLSTSQITLAAQKLYELGYITYIR 298
Cdd:PRK14973 235 ARHTHGRFTDSAAAEAAYDATKEPLVVTEVKEGHKVDRAPTPFDTTTFIV-AASRLGFSAANAMRIAEDLYMNGYISYPR 313
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 299 TDSVKY--------------SSQFIGEVkDYISKNYSSdlfkDPIVGKKdqnSQEAHESIRPTNIwLTPEkaslEIEDNL 364
Cdd:PRK14973 314 TDNTIYpksldlngvlatlaKGAFSKDV-AWVKDNRRP----VPTRGKK---SSTDHPPIHPTGV-ATRE----ELGDDR 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 365 LKrVYNLIWWNSIKSLMKGPSGFNHRWTFNNNGYEFKQSWQEVKDLGYQAI-KHSSSDENIeltddgeeivqskndKPEY 443
Cdd:PRK14973 381 WK-LYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVyPYSEAKENI---------------LPAF 444
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 444 QFNDDFEIsiskKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKSKPIVVtnkGYSANE 523
Cdd:PRK14973 445 ALGEKLPI----LAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIEGNPLRPTLV---GRAVTE 517
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 524 YLYDHYLDFFNLNYTAEMEEKLDEI-----TRGDF--DYVNWLKNIYNALNfKVKKEIG--------EAKTEAICPRCGA 588
Cdd:PRK14973 518 SLEEHAGTITEPDMTQTLEEHMQQIkerkrTRDDVvtESRKMLHRAFDELE-ANEAVIGrdimertaEELTIGPCPVCGK 596
|
..
gi 499706891 589 NL 590
Cdd:PRK14973 597 DL 598
|
|
| TOPRIM_TopoIA |
cd01028 |
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
2-130 |
1.80e-34 |
|
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: 127.73 E-value: 1.80e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYL-------EESFPENEFVVLASGGHINSIADKGAWGLGIDLETM-----QPNFVIESSRKKI 69
Cdd:cd01028 1 KVLIIAEKPSKAKTIAKILgkgskkkGFYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLelfpfEPKYVVIPDKKKQ 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499706891 70 ISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHT-NIKRITFNEITSEAITNAFNNL 130
Cdd:cd01028 81 LKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNkPVKRAWFSEITPKAIREAFKNL 142
|
|
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
66-615 |
2.44e-32 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 132.59 E-value: 2.44e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 66 RKKIISQ---IKKEGKTADLIILASDPDREGEAIA---YHLANLFKdhtNIKRITFNEITSEAITNAFNNLRD------- 132
Cdd:PRK07726 76 KKKTAKQfnvVKKLLKQATEIVIATDADREGELIAreiLDYCGVRK---PIKRLWISSLTDKAIKRAFANLKPgketipl 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 133 -------------IDMNLvnaqiSR--QILDKIIGYlvskslqksTGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKI 197
Cdd:PRK07726 153 yysalarsradwlVGINM-----TRayTLLGRKAGY---------NGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEV 218
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 198 FV----IESKRAINLNLNKDKNnvlvntEKTYYIDENQAKTIVDelgeiyRCTDYKS--TAYETRSFK-----PYSTAGL 266
Cdd:PRK07726 219 EAhltpGERFTAKWQPSEPYQD------EEGRLLDRPLAEQVVA------RIQGQPAkvTEVETKRKKeyaplLYDLSEL 286
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 267 LQDGFTKLKLSTSQiTL-AAQKLYE-LGYITYIRTDSvKY--SSQF--IGEVKDYISKNYSSDLFKDPIVgKKDQNSQ-- 338
Cdd:PRK07726 287 QIDANKRFGLSAKE-TLdIAQSLYEtHKLITYPRTDS-RYlpEDMVatLPEVLNAISKVDPYLLLAPPVL-DPSIRSRaw 363
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 339 -----EAHESIRPTNIWLTPEKASlEIEdnllKRVYNLIWWNSIKSLMkgPsgfNHRW-----TFNNNGYEFKQSWQEVK 408
Cdd:PRK07726 364 ndkkvTAHHAIIPTEQPPNLSKLS-EDE----RKVYDLIARRYLAQFL--P---PAEYdkttiELEIAGGTFIAKGKQVV 433
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 409 DLGYQAIKHSSSDEnieltDDGEEI--VQSKNDkpEYQFNDdfeisiskkfIKIESAKTNPPKMFNQASLI--------- 477
Cdd:PRK07726 434 EAGWKALLGKKEED-----EEKEQPlpVLAKGD--ELKVEK----------GEVKEGQTQPPKRFTEGTLLsameniarf 496
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 478 ---KELK-----NLGIGRPSTYNPILTKLKDREYVEyPKSKPIVVTNKG----YSANEYLYDHYLdffnlnyTAEMEEKL 545
Cdd:PRK07726 497 vqdKELKktlkeTDGLGTEATRAGIIEKLFKRGYLE-KKGKYIHATDKGkqliDALPEELTSPDM-------TAKWEQAL 568
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499706891 546 DEITRGDFDY-------VNWLKNIYNALNFKVKKEIGEAKTEAICPRCGANLVYIKSRFNRGRGCSNFTitkCGYRK 615
Cdd:PRK07726 569 DQISEGQLSYqdfmqplKQWLKQLVEQAKQSSEKYKFDNLTGPKCPDCGKPMLKVKGKNGKMLVCQDRE---CGKRK 642
|
|
| TOP1Bc |
smart00436 |
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ... |
110-194 |
7.74e-32 |
|
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: 118.45 E-value: 7.74e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 110 IKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQKS--TGLMSAGRVQTPALNILTTRDTLIK 187
Cdd:smart00436 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKlrNGVLSAGRVQTPTLGLIVEREREIK 80
|
....*..
gi 499706891 188 NFKEVLY 194
Cdd:smart00436 81 NFVPKPY 87
|
|
| YrdD |
COG0551 |
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ... |
1-615 |
2.56e-22 |
|
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];
Pssm-ID: 440317 [Multi-domain] Cd Length: 695 Bit Score: 101.87 E-value: 2.56e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKIKHYLEEsfpeNEFVVLASGGHINSIADKGAWGLGIDLETMQPNFVIESSRKKIISQIKKEGKTA 80
Cdd:COG0551 9 LAAAKEAVKLVKKKKKKKKEGK----KKGLAGALGLKKKLVDLLLKEKLKKLVENEKLIAELDIKDLKKLKKDKKKKAKA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 81 DLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQILDKIIGYLVSKSLQ 160
Cdd:COG0551 85 LAAALAAADDDAIEAAAAADEEEALKAAEALEAIRKAVVEEVKSRARKRAARAPADVAAAAAAAALARLLLLAAASRALR 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 161 KSTGLMSAGRVQTPALNILTTRDTLIKNFKEVLYKKIFVIESKRAINLNLNKDKNNVLVNTEKTYYIDENQAKTIVDELG 240
Cdd:COG0551 165 LLLLLAAGRLRLLSAVAAGLLELEELLKEFEEEEEEEAAEEEEEEEEAKKKKEEDKKKKKKKKKKDKEEETKAIKKKKKA 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 241 EIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYEL-------GYITYIRTDSVKYSSQFIGEVK 313
Cdd:COG0551 245 AEAVLAAKKAAKEAKAKKELPTTTTDALPEALATTSLTAAAAASALAAALLeeegellYTGGYIRYTRTPKSSEADALAA 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 314 DYISKNYSSDLFKDPIVGKKDQNSQEAHESIRPTNIWLTPEKASLEIEDNLLKRVYNLIWWNSIKSLMKGPSgfnhrwtf 393
Cdd:COG0551 325 LEALKKIAEEPPDERAKKKKKKAKKKKASEAKETTDHPPIPPTTAAALLELLEDRKLLLELLVRRRFAAAAD-------- 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 394 nnngyeFKQSWQEVKDLGYQAIKHSSSDENIELTDDGEEIVQSKNDKPEYQFNDDFEISISKKFIKIESAKTNPPKMFNQ 473
Cdd:COG0551 397 ------LAKVEELTKVEEADEEELVEAEGGLLEVLGEEEEDDEDEEEELLLPPLEEGEPLLLEELLLEKQTTTPPPRYTT 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 474 ASLIKELKNLGIGRPSTYNPILTKLKDREYVEYPKSKPIVVTNKGYSANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDF 553
Cdd:COG0551 471 ELLLKKLEEEGGGGRGTTATIIILILKRRYVVLEEKKTTPTELLVEVVLLLLLPFPKLEDTTETAEEEEALLDKEEGKED 550
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499706891 554 DYVNWLKNIY---------NALNFKVKKEIGEAKTEAICPRCGANLVYIKSRFNRGRGCSNFtiTKCGYRK 615
Cdd:COG0551 551 KVVEIREEEYpffkklleiAEEEGEEELSEEDEVLGEKCPKCGKPLVIKKGRYGKFLGCSNY--PECKYTK 619
|
|
| TOPRIM_TopoIA_TopoIII |
cd03362 |
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ... |
2-130 |
2.26e-18 |
|
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. 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: 173782 [Multi-domain] Cd Length: 151 Bit Score: 82.28 E-value: 2.26e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPS-------------KIEKIKHYLEESFPENEFVVLASGGHINSIADKGA-------WGLGIDLETMQPNFV 61
Cdd:cd03362 1 MVLIIAEKPSvakaiakilgggsKKKGKGRYYEFYGEGGGYVVTWASGHLLELDFPEEydpwdkvWPLEDPLFPAPFKLK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499706891 62 IESSRKKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHTN--IKRITFNEITSEAITNAFNNL 130
Cdd:cd03362 81 VDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCVKRkpVKRAWFSSLTPKAIRRAFKNL 151
|
|
| PRK08173 |
PRK08173 |
DNA topoisomerase III; Validated |
2-613 |
1.20e-17 |
|
DNA topoisomerase III; Validated
Pssm-ID: 236172 [Multi-domain] Cd Length: 862 Bit Score: 87.03 E-value: 1.20e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKI--------KHylEESFPENEFVVLASGGHINSIAD-------KGAWGLGiDLETMQPNFVI---- 62
Cdd:PRK08173 3 KALIIAEKPSVANDIaralggftKH--DEYFESDEYVLSSAVGHLLEIAApeeyevkRGKWSFA-HLPVIPPHFDLnpia 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 63 --ESSRKKIISQIKKegKTADLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLR-DIDM-NLV 138
Cdd:PRK08173 80 ktESRLKVLTKLIKR--KDVTRLINACDAGREGELIFRLIAQHAKAKKPVKRLWLQSMTPQAIRDGFANLRsDEDMqPLA 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 139 NAQISRQILDKIIGYLVSKSL----QKSTG--LMSAGRVQTPALNILTTRDTLIKNFKEVLYKKI---FVIESK----RA 205
Cdd:PRK08173 158 DAARCRSEADWLVGINGTRAMtafnSKGGGffLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVraeFVAAAGfyegRW 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 206 INLNLNKDKNNVLVNTEKTYyiDENQAKTIVDelgeiyRCTDYKSTAYETRsfKPyST--AGLLQD------------GF 271
Cdd:PRK08173 238 FDPKFKKDEFDPEKRASRLW--SEAAAEAIVA------ACRGKPGTVTEES--KP-STqlSPLLFDltslqreangrfGF 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 272 tklklsTSQITLA-AQKLYEL-GYITYIRTDSVKYSSQFIGEVKDYI-----SKNYSSdlFKDPIVGKK---------DQ 335
Cdd:PRK08173 307 ------SAKNTLGlAQALYEKhKVLTYPRTDSRALPEDYLGTVKQTLemlkeSNNYLP--HAKQILDKGwvkpnkrifDN 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 336 NSQEAHESIRPTNiwLTPEKASlEIEDNLlkrvYNLIwwnsIKSLMkgpSGFNHRWTFNNN-------GYEFKQSWQEVK 408
Cdd:PRK08173 379 SKISDHFAIIPTL--QAPKSLS-EPEQKL----YDLV----VKRFL---AVFFPAAEFLVTtritevaGHHFKTEGKVLV 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 409 DLGYQAIKHSssdeniELTDDGEEIVQSKNDKPeyqfnddfeisISKKFIKIESAKTNPPKMFNQASLI----------- 477
Cdd:PRK08173 445 NPGWLAVYGK------EAQGADANLVPVQKGEK-----------VKTDKIEAVALTTKPPARYNEATLLsamegagklve 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 478 -KELKNL----GIGRPSTYNPILTKLKDREYVEYpKSKPIVVTNKGYSANEYLydHYLDFFNL---NYTAEMEEKLDEIT 549
Cdd:PRK08173 508 dDELREAmaekGLGTPATRAAIIEGLLGEKYLVR-EGRELIPTAKAFQLMTLL--RGLGVEELtspELTGEWEYKLSQIE 584
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499706891 550 RGDFDYVNWLKNIY--------NALNFKVKKEIGEAKT-EAICPRCGAnlvYIKSRFNRgrgcsnFTITKCGY 613
Cdd:PRK08173 585 RGKLSRDAFMQEIAqmtqqivkRAKEYDSDTIPGDYATlQTPCPNCGG---VVKENYRR------FACTKCDF 648
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
3-118 |
9.26e-14 |
|
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: 67.38 E-value: 9.26e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 3 VLVLLESPSKIEKIKHYLEESFpeneFVVLASGGHInsiadkgawglgIDLETmqpnfvieSSRKKIISQIKKEGKTADL 82
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGF----QAVVAVLGHL------------LSLEK--------GPKKKALKALKELALKAKE 56
|
90 100 110
....*....|....*....|....*....|....*..
gi 499706891 83 IILASDPDREGEAIAYHLANLFK-DHTNIKRITFNEI 118
Cdd:pfam01751 57 VILATDPDREGEAIALKLLELKElLENAGGRVEFSEL 93
|
|
| PRK14724 |
PRK14724 |
DNA topoisomerase III; Provisional |
1-617 |
3.09e-13 |
|
DNA topoisomerase III; Provisional
Pssm-ID: 237803 [Multi-domain] Cd Length: 987 Bit Score: 73.07 E-value: 3.09e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 1 MKVLVLLESPSKIEKI------------KHylEESFPENEFVVLASGGHINSI-------ADKGAWGLGiDLETMQPNFV 61
Cdd:PRK14724 1 TKTLVIAEKPSVAQDIvraltpvagkfeKH--DEHFESDSYVVTSAVGHLVEIqapeefdVKRGKWSFA-NLPVIPPYFD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 62 IE--SSRKKIISQIKKEGKTADL--IILASDPDREGEAIaYHL----ANLFKDHTN--IKRITFNEITSEAITNAFNNLR 131
Cdd:PRK14724 78 LKpvDKTKTRLNAVVKLAKRKDVteLVNACDAGREGELI-FRLieqyAGGAKGGLGkpVKRLWLQSMTPQAIRDGFDNLR 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 132 -DIDM-NLVNAQISRQILDKIIGYLVSKSL----QKSTG--LMSAGRVQTPALNILTTRDTLIKNFKEVLYKKI---FVI 200
Cdd:PRK14724 157 sDAQMqGLASAARSRSEADWLVGINGTRAMtafnSRDGGffLTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIhagFHA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 201 ESKRAINLNLNKDKNNVLVNTE--KTYYIDENQAKTIVDELgeiyrctdYKSTAYETRSFKPYSTA-GLLQDgFTKLKLS 277
Cdd:PRK14724 237 EAGEYLGKWFDPQWKKASDDPEarADRVWSEREARAIADAV--------RGKAATVTEESKPTTQAsPLLFD-LTSLQRE 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 278 -------TSQITLA-AQKLYEL-GYITYIRTDSVKYSSQFIGEVKDY-------------------ISKNY---SSDLFk 326
Cdd:PRK14724 308 angkfgfSAKTTLAlAQSLYERhKALTYPRTDSRALPEDYLPVAKQTfemlatsgmrhlapfaqqaLDGNYvrpSKRIF- 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 327 dpivgkkDQNSQEAHESIRPTNiwLTPEKASlEIEdnllKRVYNLIwwnsIKSLMK--GPSGfNHRWTFNNN---GYEFK 401
Cdd:PRK14724 387 -------DNSKVSDHFAIIPTT--QAPSGLS-EAE----QKLYDLV----VRRFMAvfFPSA-EYQVTTRISqvvGHSFK 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 402 QSWQEVKDLGYQAI---KHSSSDENIELTDDGEEIVQSK-NDKPEYQFNDdfeisiskkfikIESAKTNPPKMFNQASLI 477
Cdd:PRK14724 448 TEGKVLVKPGWLAIygkEAANEVEDAKDGDKGQPLVPVKpGEMVRTEFAE------------AKGLKTKPPARYSEATLL 515
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 478 ------------KELKNL----GIGRPSTYNPILTKLKDREYVeYPKSKPIVVTNKGYSANEYLYDhyLDFFNL---NYT 538
Cdd:PRK14724 516 gamesagkqiddDELREAmqekGLGTPATRAAIIEGLLTEKYM-LREGRELIPTAKAFQLMTLLRG--LGVEELsraELT 592
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 539 AEMEEKLDEITRGDFDYVNWLKNIYNALNFKVKKEIG---------EAKTEAICPRCGAnlvYIKSRFNR---------G 600
Cdd:PRK14724 593 GEWEYKLAQMEKGQLSREAFMQQIAAMTEKLVKKAKEydrdtipgdYATLSTPCPNCGG---VVKENYRRyactgangaG 669
|
730
....*....|....*...
gi 499706891 601 RGCS-NFTITKCGyRKYE 617
Cdd:PRK14724 670 EGCGfSFTKSPAG-RTFE 686
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
2-107 |
9.89e-12 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 60.74 E-value: 9.89e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINSiadkgawglgidletmqpnfviessrKKIISQIKKEGKTAD 81
Cdd:smart00493 1 KVLIIVEGPADAIALEKAGG-----KRGNVVALGGHLLS--------------------------KEQIKLLKKLAKKAE 49
|
90 100
....*....|....*....|....*.
gi 499706891 82 lIILASDPDREGEAIAYHLANLFKDH 107
Cdd:smart00493 50 -VILATDPDREGEAIAWELAELLKPA 74
|
|
| TOPRIM_TopoIA_RevGyr |
cd03361 |
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ... |
3-129 |
1.10e-11 |
|
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: 63.49 E-value: 1.10e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 3 VLVLLESPSK---------------IEKIKHYlEESFPENEFVVLASGGHI-NSIADKGAWGLGIDLETMQP-------- 58
Cdd:cd03361 2 ALMIVESPNKartianffgrpsvrrLGGLVVY-EVSTGDGVLMITASGGHVyDLVTKEGGHGVVEDDGRYVPvydsikrc 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 59 -----NFVIESSR------------KKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHT-NIKRITFNEITS 120
Cdd:cd03361 81 rdcgyQFTEDSDKcprcgseniddkLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNkNIKRAEFHEVTR 160
|
....*....
gi 499706891 121 EAITNAFNN 129
Cdd:cd03361 161 RAILEALRN 169
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
2-115 |
2.37e-08 |
|
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: 51.66 E-value: 2.37e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIKHYLEesfpeNEFVVLASGGHINsiadkgawglgidletmqpnfviessrKKIISQIKKEGKTAD 81
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-----YGGAVVALGGHAL---------------------------NKTRELLKRLLGEAK 48
|
90 100 110
....*....|....*....|....*....|....*
gi 499706891 82 LIILASDPDREGEAIAYHLANLFKDHT-NIKRITF 115
Cdd:cd00188 49 EVIIATDADREGEAIALRLLELLKSLGkKVRRLLL 83
|
|
| COG1754 |
COG1754 |
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown]; |
67-553 |
2.57e-08 |
|
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
Pssm-ID: 441360 [Multi-domain] Cd Length: 892 Bit Score: 57.13 E-value: 2.57e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 67 KKIISQIKKEGKTADLIILASDPDREGEAIAYHLANLFKDHTNIKRITFNEITSEAITNAFNNLRDIDMNLVNAQISRQI 146
Cdd:COG1754 77 KKALALALAADDEDEELLAADDELEEEKVIKLLLLELAVERVARAAAVRAAAAEAARLAALLRRRLVLRRLVRRLLVRLL 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 147 LDKIIGYLVSKSLQKSTGLMSAGRVQTPALNILTTRDTLIKNFKEVLY---KKIFVIESKRAINLNLNKDKNNVLVNTEK 223
Cdd:COG1754 157 LLRLVLLLLRLLVARRAARRRRRRRRRRARRRELERRRERARAAEAEEaaaAAAAAADAGRAAAARDGKGGGKLAAGGAA 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 224 TYYIDENQAKTIVDELGEIYRCTDYKSTAYETRSFKPYSTAGLLQDGFTKLKLSTSQITLAAQKLYELGYITYIRTDSVK 303
Cdd:COG1754 237 AAAAAAAAAAAAAAALAEAAAAAAVREPPTPTTTTTAQAATTTTTRAAAARTTRSAQQAARRTRLGGEGTYTTTTTTTTT 316
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 304 YSS---QFIGEVKDYISKNYSSDLFKDPIVGKKDQNSQEAHESIRPTNIWLTPEKASLEieDNLLKRVYNLIWWNSIKSL 380
Cdd:COG1754 317 TSAaaaAAAAAAAALAAAAAAAYAPPPPYYYKKKAAAAAAAAAAAAAAAARRPPAARAA--LLSDDRLLLELLLLRRTAA 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 381 MkgpsgfnhrwtfnnngyefkQSWQEVKDLGYQAIKHSSSDENIELTDDGEEIVQSKNDKPEYQFNDD------------ 448
Cdd:COG1754 395 A--------------------AAAAAAATATTTAAAAAAGAGAVGTAAAGAVFFFGGFLLFAEEEDDDeeddddddlpal 454
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 449 -FEISISKKFIKIESAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVE------YPKSKPIVVT--NKGY 519
Cdd:COG1754 455 eEGLPLLKEGVLADQHFTQPPPRYTEAPLVKRMEELGIGRPSTYASILSTLADRIYVRldkrrlIPEDKGRLVTafLFSF 534
|
490 500 510
....*....|....*....|....*....|....
gi 499706891 520 SANEYLYDHYLDFFNLNYTAEMEEKLDEITRGDF 553
Cdd:COG1754 535 FRRYVEYDFTADLEEFLDDVSDGELDWKAVLRRF 568
|
|
| zf-C4_Topoisom |
pfam01396 |
Topoisomerase DNA binding C4 zinc finger; |
582-619 |
7.44e-05 |
|
Topoisomerase DNA binding C4 zinc finger;
Pssm-ID: 307520 [Multi-domain] Cd Length: 39 Bit Score: 40.32 E-value: 7.44e-05
10 20 30
....*....|....*....|....*....|....*...
gi 499706891 582 ICPRCGANLVYIKSRFNRGRGCSNFtiTKCGYRKYEQP 619
Cdd:pfam01396 3 KCPKCGGDLVLKRGRFGKFVGCSNY--PECRFTRPLKK 38
|
|
| RPB9 |
COG1594 |
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ... |
578-626 |
2.18e-03 |
|
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 441202 [Multi-domain] Cd Length: 103 Bit Score: 38.01 E-value: 2.18e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 578 KTEAICPRCGANLVY-----IKS------RFnrgrgcsnFTITKCGYrkyeqpdgTWKEY 626
Cdd:COG1594 60 TTKVICPKCGNDEAYwwlkqTRSadepetRF--------FRCTKCGH--------TWREY 103
|
|
| TOPRIM_recR |
cd01025 |
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
2-113 |
6.61e-03 |
|
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Pssm-ID: 173775 Cd Length: 112 Bit Score: 36.73 E-value: 6.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499706891 2 KVLVLLESPSKIEKIkhylEESfpeNEF----VVLasGGHINSIADKGAWGLGIDletmqpnfviessrkKIISQIKKEG 77
Cdd:cd01025 1 NKLCVVEEPRDVLAI----EES---GEYrglyHVL--GGLISPLDGIGPDDLNID---------------KLLERIAKGQ 56
|
90 100 110
....*....|....*....|....*....|....*..
gi 499706891 78 KTAdlIILASDPDREGEAIAYHLANLFKDHT-NIKRI 113
Cdd:cd01025 57 VKE--VILATNPTVEGEATALYIAKLLKDFGvKVTRL 91
|
|
| |
