|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-611 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1162.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:PRK05644 13 IQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDIHPKTGKPA 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDETGTSITFW 160
Cdd:PRK05644 93 VEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFK 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 161 ADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERPGHsagedgedgPVEVTYHYEGGLSDFVKHLNSKKDAAHVSV 240
Cdd:PRK05644 173 PDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGE---------EKEETFHYEGGIKEYVEYLNRNKEPLHEEP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 241 IDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGL 320
Cdd:PRK05644 244 IYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKE-KDDNLTGEDVREGL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 321 TAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLLE 400
Cdd:PRK05644 323 TAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALE 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 401 aGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGV 480
Cdd:PRK05644 403 -SSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 481 HDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGedasYAYSDPERDAII 560
Cdd:PRK05644 482 GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE----YAYSDEELDEIL 557
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|.
gi 559767655 561 EEGIGRGRRDprlhDGIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:PRK05644 558 AELKLKGNPK----YGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 604
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-611 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1116.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:COG0187 11 IQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDIHPKEGKSA 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDETGTSITFW 160
Cdd:COG0187 91 LEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFK 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 161 ADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERpghsagedgEDGPVEVTYHYEGGLSDFVKHLNSKKDAAHVSV 240
Cdd:COG0187 171 PDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDER---------EEEPKEETFHYEGGIKDFVEYLNEDKEPLHPEV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 241 IDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGL 320
Cdd:COG0187 242 IYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 321 TAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLLE 400
Cdd:COG0187 321 TAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 401 aGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGV 480
Cdd:COG0187 401 -SSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 481 HDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWdrrGEDASYAYSDPERDAII 560
Cdd:COG0187 480 GDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKK---GKKTYYAYSDAELDELL 556
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|.
gi 559767655 561 EEGIGRGRrdprlhDGIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:COG0187 557 KELKGKKK------VEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 601
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-611 |
0e+00 |
|
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273421 [Multi-domain] Cd Length: 654 Bit Score: 946.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:TIGR01059 6 IKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPEEGISA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDETGTSITFW 160
Cdd:TIGR01059 86 VEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFW 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 161 ADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERpghsagedgEDGPVEVTYHYEGGLSDFVKHLNSKKDAAHVSV 240
Cdd:TIGR01059 166 PDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER---------DGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEI 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 241 IDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGL 320
Cdd:TIGR01059 237 IYIKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKE-SKPNLTGEDIREGL 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 321 TAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLLE 400
Cdd:TIGR01059 316 TAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALD 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 401 AGsGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGV 480
Cdd:TIGR01059 396 SG-GLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 481 HDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGE--------------- 545
Cdd:TIGR01059 475 GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERyikddkekdlvgeal 554
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 559767655 546 ---DASYAYSDPERD---AIIEEGIGRGRrdprlhDGIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:TIGR01059 555 edlKALYIYSDKEKEeakTQIPVHLGRKG------IEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDA 620
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-611 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 912.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRP 79
Cdd:PRK14939 12 IKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTDIHPEEGVS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 80 AVEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDETGTSITF 159
Cdd:PRK14939 92 AAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRF 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 160 WADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERPGhsagedgedgpVEVTYHYEGGLSDFVKHLNSKKDAAHVS 239
Cdd:PRK14939 172 WPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG-----------KEEEFHYEGGIKAFVEYLNRNKTPLHPN 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 240 VIDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEGKdDNLTGEDIREG 319
Cdd:PRK14939 241 IFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAK-VSLTGDDAREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 320 LTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLL 399
Cdd:PRK14939 320 LTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 400 EaGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTG 479
Cdd:PRK14939 400 D-IAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 480 V-HDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrRGEDASYAYSDPERDA 558
Cdd:PRK14939 479 IgRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVK---KGKQEQYLKDDEALDD 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 --------------------------------------------------------------------------------
Cdd:PRK14939 556 ylielalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadflt 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 559 ----------------IIEEG--IGRGRRDPRLHD----------------GIQRFKGLGEMNAGQLWDTTMNPETRVLR 604
Cdd:PRK14939 636 saeyrrlvelaeklrgLIEEGayLERGERKQPVSSfeealdwllaearkglSIQRYKGLGEMNPEQLWETTMDPENRRLL 715
|
....*..
gi 559767655 605 LVTLDDA 611
Cdd:PRK14939 716 QVTIEDA 722
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-611 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 861.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:PRK05559 13 IEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGIHPEEGKSG 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGE--PTDETGTSIT 158
Cdd:PRK05559 93 VEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGtaGKRKTGTRVR 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 159 FWADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERPghsagedgedgpvEVTYHYEGGLSDFVKHLNSKKDAAH- 237
Cdd:PRK05559 173 FWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERE-------------RQTFHYENGLKDYLAELNEGKETLPe 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 238 VSVIDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKegKDDNLTGEDIR 317
Cdd:PRK05559 240 EFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP--KGKKLEGEDVR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 318 EGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLqaSRARLAARQARDLTRRKs 397
Cdd:PRK05559 318 EGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAI--KAAQARLRAAKKVKRKK- 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 398 lLEAGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMG 477
Cdd:PRK05559 395 -KTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIG 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 478 TGVHDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIkwdRRGEDASYAYSDPERD 557
Cdd:PRK05559 474 IGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRV---DKGKKKIYALDEEEKE 550
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 559767655 558 AIIEEGIGRGRRDPrlhdgIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:PRK05559 551 ELLKKLGKKGGKPE-----IQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDA 599
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
25-611 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 814.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 25 GLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGG 104
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 105 LHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADT-RPTHPLAKGEPTDETGTSITFWADPTIFETTT-WNFETLSRRFQE 182
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNgKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTdDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 183 MAFLNKGLTISLRDERPGhsagedgedgpVEVTYHYEGGLSDFVKHLNSKKDAAHVSVIDFEESGEGISVEIAMQWNNSY 262
Cdd:smart00433 161 LAFLNKGVKITLNDERSD-----------EEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGY 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 263 SESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgkdDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLG 342
Cdd:smart00433 230 SENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKE---KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 343 NTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLlEAGSgLPGKLADCQWSDPEKCEL 422
Cdd:smart00433 307 TSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKL-SSIS-LPGKLADASSAGPKKCEL 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 423 FIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGVHDEFDIAKLRYHKLILMADADV 502
Cdd:smart00433 385 FLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADV 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 503 DGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGEDASYaYSDPERDAIIEEGIGRgrrdpRLHDGIQRFKG 582
Cdd:smart00433 465 DGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSF-YSLDEYEKWLEKTEGN-----KSKYEIQRYKG 538
|
570 580
....*....|....*....|....*....
gi 559767655 583 LGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:smart00433 539 LGEMNADQLWETTMDPERRTLLFVTLDDA 567
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
1-611 |
0e+00 |
|
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130130 [Multi-domain] Cd Length: 637 Bit Score: 665.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:TIGR01058 10 IKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQDGNIST 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSY-ADTRPTHPLAKGEPTDETGTSITF 159
Cdd:TIGR01058 90 VETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFeNGGKIVQSLKKIGTTKKTGTLVHF 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 160 WADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDERPGHSagedgedgpveVTYHYEGGLSDFVKHLNSKKDAAHvS 239
Cdd:TIGR01058 170 HPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKT-----------TVFFYENGLVDFVDYINETKETLS-Q 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 240 VIDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREG 319
Cdd:TIGR01058 238 VTYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKE-KDKNLEGSDIREG 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 320 LTAIISVKLADP--QFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRR-K 396
Cdd:TIGR01058 317 LSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSgK 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 397 SLLEAGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAM 476
Cdd:TIGR01058 397 KPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCI 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 477 GTGVHDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwDRRGEDASYAYSDPER 556
Cdd:TIGR01058 477 GTGIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLS-KKDGKKVKYAWSDLEL 555
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 559767655 557 DAIIEEGIGRgrrdprlhdGIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:TIGR01058 556 ESVKKKLKNY---------TLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDL 601
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
1-611 |
1.80e-170 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 508.27 E-value: 1.80e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:PTZ00109 105 IVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEKTGKSG 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKF-----------------DGKS-----------------------YAVSGGLHGVGVSVVNALSNRL 120
Cdd:PTZ00109 185 LETVLTVLHSGGKFqdtfpknsrsdksedknDTKSskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVVNALSSFL 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 121 EVEIRTDGHYWRQSYADTRPTHPLA-KGEPTDETGTSITFWAD-PTIFETTT--------------WNFETLSRRFQEMA 184
Cdd:PTZ00109 265 KVDVFKGGKIYSIELSKGKVTKPLSvFSCPLKKRGTTIHFLPDyKHIFKTHHqhteteeeegckngFNLDLIKNRIHELS 344
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 185 FLNKGLTISLRDERpghSAGEDGEdgPVEVTYHYEGGLSDFVKHLNSKKDAAH--VSVIDFEESGEGISVEIAMQWN-NS 261
Cdd:PTZ00109 345 YLNPGLTFYLVDER---IANENNF--YPYETIKHEGGTREFLEELIKDKTPLYkdINIISIRGVIKNVNVEVSLSWSlES 419
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 262 YSESVYTFANTINTAeGGTHEEGFRAALTSIVNRYAREQKFLKeGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKL 341
Cdd:PTZ00109 420 YTALIKSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFK-GNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKL 497
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 342 GNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLQASRARLAARQARDLTRRKSLLEAGSGLPGKLADCQWSDPEKCE 421
Cdd:PTZ00109 498 GNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDIERNE 577
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 422 LFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARID-KVLKNTEVQALITAMGTGVH-----------------DE 483
Cdd:PTZ00109 578 LFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNpvtwrqydlshgtkaskDE 657
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 484 F---------------DIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGEDAS 548
Cdd:PTZ00109 658 SvqnnnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFNV 737
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 549 ---------YAYSDPERDAII----------EEGIGRGRRDPRLHDG--------------------------------- 576
Cdd:PTZ00109 738 stknskkyiYTWSDEELNVLIkllnkdysskETTRSVEEKGNAPDLDneyedekldnknmrennvdevelktelgtnvad 817
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*.
gi 559767655 577 ---------------------IQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:PTZ00109 818 teqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDA 873
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
1-610 |
3.62e-164 |
|
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130127 [Multi-domain] Cd Length: 625 Bit Score: 482.88 E-value: 3.62e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTGergLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPA 80
Cdd:TIGR01055 9 IEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPKEGVSA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 81 VEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDE--TGTSIT 158
Cdd:TIGR01055 86 VEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlTGTSVH 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 159 FWADPTIFETTTWNFETLSRRFQEMAFLNKGLTISLRDErpghsagedgedgpVEVT---YHYEGGLSDFVKHLNSKKDA 235
Cdd:TIGR01055 166 FTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDE--------------VNNTkalWNYPDGLKDYLSEAVNGDNT 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 236 AHVSVIDFEESGEGISVEIAMQWNNSYSESVY-TFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEGKddNLTGE 314
Cdd:TIGR01055 232 LPPKPFSGNFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGV--KLTAE 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 315 DIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSLqaSRARLAARQARDLTR 394
Cdd:TIGR01055 310 DIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVR 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 395 RKslLEAGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALIT 474
Cdd:TIGR01055 388 KK--LTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEV 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 475 AMGTGvHDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrRGEDASYAYSDP 554
Cdd:TIGR01055 466 ALGID-PDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRID---LSKEVYYALDEE 541
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 559767655 555 ERDAIIEEgIGRGRRDPRlhdgIQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDD 610
Cdd:TIGR01055 542 EKEKLLYK-LKKKKGKPN----VQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDD 592
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
26-198 |
2.58e-104 |
|
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.
Pssm-ID: 340405 [Multi-domain] Cd Length: 180 Bit Score: 312.93 E-value: 2.58e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 26 LHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGGL 105
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 106 HGVGVSVVNALSNRLEVEIRTDGHYWRQSYADTRPTHPLAKGEPTDETGTSITFWADPTIFETTTWNFETLSRRFQEMAF 185
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|...
gi 559767655 186 LNKGLTISLRDER 198
Cdd:cd16928 161 LNKGLKIVLEDER 173
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
220-377 |
1.01e-77 |
|
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Pssm-ID: 238419 [Multi-domain] Cd Length: 172 Bit Score: 244.01 E-value: 1.01e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 220 GGLSDFVKHLNSKKDAAHVSVIDFEESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYARE 299
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 559767655 300 QKFLKEgKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSL 377
Cdd:cd00822 81 NNLLKK-KDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAI 157
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
221-377 |
6.45e-70 |
|
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.
Pssm-ID: 425522 [Multi-domain] Cd Length: 173 Bit Score: 223.65 E-value: 6.45e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 221 GLSDFVKHLNSKKDAAHVSVIDF--EESGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAR 298
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFegESPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 559767655 299 EQKFLKEgKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDIINKSL 377
Cdd:pfam00204 81 KKGLLKK-KDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
420-533 |
2.13e-69 |
|
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173786 [Multi-domain] Cd Length: 114 Bit Score: 220.22 E-value: 2.13e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 420 CELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGVHDEFDIAKLRYHKLILMAD 499
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 559767655 500 ADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQP 533
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
420-533 |
6.22e-57 |
|
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173780 [Multi-domain] Cd Length: 115 Bit Score: 187.33 E-value: 6.22e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 420 CELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGVH-DEFDIAKLRYHKLILMA 498
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 559767655 499 DADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQP 533
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
7-507 |
8.76e-40 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 156.41 E-value: 8.76e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 7 LEAVRKRPGMYIGSTGERGLHHLVYE---VVDNSV----------DEALAGHAD---------RIEVTLLADNG-VRVVD 63
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHTQTLWVYEggeMVNREVtyvpglykifDEILVNAADnkqrdpsmdSLKVDIDVEQNtISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 64 NGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIrTDGH---YWRQSYAD--T 138
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVET-ADGNrgkKYKQVFTNnmS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 139 RPTHPLAKGEPTDETGTSITFWADPTIFETTTWNFET---LSRRFQEMA-FLNKGLTISLrderpghsageDGEDGPVev 214
Cdd:PLN03128 172 VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVEL-----------NGKKLPV-- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 215 tyhyeGGLSDFVK-HLNSKKDAAHVSVIdFEESGEGISVEIamqwnnSYSESVY---TFANTINTAEGGTHEEgfraALT 290
Cdd:PLN03128 239 -----KSFQDYVGlYLGPNSREDPLPRI-YEKVNDRWEVCV------SLSDGSFqqvSFVNSIATIKGGTHVD----YVA 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 291 SIVNRYAREQKFLKEGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQKAcndHLRDWFER---NPG 367
Cdd:PLN03128 303 DQIVKHIQEKVKKKNKNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL-TTRPSSFGSKC---ELSEEFLKkveKCG 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 368 EAKDIINKSlqaSRARLAARQARDLTRRKSLLeagsGLPgKLADCQWS---DPEKCELFIVEGDSAGGSAKGG-----RD 439
Cdd:PLN03128 379 VVENILSWA---QFKQQKELKKKDGAKRQRLT----GIP-KLDDANDAggkKSKDCTLILTEGDSAKALAMSGlsvvgRD 450
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 559767655 440 srFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMG---TGVHDEFDIAKLRYHKLILMADADVDGQHI 507
Cdd:PLN03128 451 --HYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGlqfGKTYDEENTKSLRYGHLMIMTDQDHDGSHI 519
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
1-610 |
1.81e-39 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 152.99 E-value: 1.81e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 1 ITVLEGLEAVRKRPGMYIGSTG----ER-------------GLHHLVYEVVDNSVDEALAG---HADRIEVTlLADNGVR 60
Cdd:PHA02569 4 FKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVT-IKNNQVT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 61 VVDNGRGIPVGMhpVEKRPAVEVVL-----TVLHAGGKFDGKSyAVSGGLHGVGVSVVNALSNRL---------EVEIR- 125
Cdd:PHA02569 83 VSDNGRGIPQAM--VTTPEGEEIPGpvaawTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFigetcdgknEVTVNc 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 126 TDGH---YWRQSyadtrpthplakgePTDETGTSITFWADPTIFETTTWN----------FETLSRRFQEMAFLNKGLTI 192
Cdd:PHA02569 160 SNGAeniSWSTK--------------PGKGKGTSVTFIPDFSHFEVNGLDqqyldiildrLQTLAVVFPDIKFTFNGKKV 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 193 SLRDERPGHSAGEdgedgpvevtyhyegglsDFVKHLNSKkdaahVSVIdFEESGEGIsveiamqwnnsyseSVYTFANT 272
Cdd:PHA02569 226 SGKFKKYAKQFGD------------------DTIVQENDN-----VSIA-LAPSPDGF--------------RQLSFVNG 267
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 273 INTAEGGTHEEGFRAALTS-IVNRYAREQKFlkegkddNLTGEDIREGLTAIISVK-LADPQFEGQTKTKLGNTEAKsfv 350
Cdd:PHA02569 268 LHTKNGGHHVDCVMDDICEeLIPMIKKKHKI-------EVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPFGE--- 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 351 qkaCNDHLRDWFERnpgEAKDIINKS------LQASRARLAARQARDLTR-RKSLLEAG------SGLPGKLADCQwsdp 417
Cdd:PHA02569 338 ---IRNHIDLDYKK---IAKQILKTEaiimpiIEAALARKLAAEKAAETKaAKKAKKAKvakhikANLIGKDAETT---- 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 418 ekceLFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKNTEVqALITAMgTGVHDEFDIAKLRYHKLILM 497
Cdd:PHA02569 408 ----LFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKEL-FDICAI-TGLVLGEKAENMNYKNIAIM 481
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 498 ADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYkIKWDRRGEDASYAYSDPERDaiieegigrgRRDPRLHDgI 577
Cdd:PHA02569 482 TDADVDGKGSIYPLLLAFFSRWPELFEQGRIRFVKTPVI-IAQVGKETKWFYSLDEFEKA----------KDSLKKWS-I 549
|
650 660 670
....*....|....*....|....*....|...
gi 559767655 578 QRFKGLGEMNAGQLWDTTMNPetrVLRLVTLDD 610
Cdd:PHA02569 550 RYIKGLGSLRKSEYRRVINNP---VYDVVVLPD 579
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
4-507 |
3.71e-39 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 154.43 E-value: 3.71e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 4 LEGLEAVRKRPGMYIGSTgER------------------------GLHHLVYEV----VDNSVDEALAGHADRIEVTLLA 55
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKVTIDE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 56 DNG-VRVVDNGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIRTD--GHYWR 132
Cdd:PTZ00108 92 ENGeISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSksGKKFK 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 133 QSYAD--TRPTHPLAKGEPTDETGTSITFWADPTIFETTTWNFETLS---RRFQEMAFLNKGLTISLRDERPGHSAgedg 207
Cdd:PTZ00108 172 MTWTDnmSKKSEPRITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERIAIKS---- 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 208 edgpvevtyhyeggLSDFVKhLNSKKDAAHVSVIDfEESGEGIS--VEIAMqwnnSYSESVYT---FANTINTAEGGTHe 282
Cdd:PTZ00108 248 --------------FKDYVD-LYLPDGEEGKKPPY-PFVYTSVNgrWEVVV----SLSDGQFQqvsFVNSICTTKGGTH- 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 283 egFRAALTSIVNRYAREQKFLKEGKDDnLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQK-ACNDHLRDW 361
Cdd:PTZ00108 307 --VNYILDQLISKLQEKAKKKKKKGKE-IKPNQIKNHLWVFVNCLIVNPSFDSQTKETL-TTKPSKFGSTcELSEKLIKY 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 362 FERNPgeakdIINKSLQASRARLAARQARDL-TRRKSLLeagSGLPgKLADCQWSDP---EKCELFIVEGDSAGGSAKGG 437
Cdd:PTZ00108 383 VLKSP-----ILENIVEWAQAKLAAELNKKMkAGKKSRI---LGIP-KLDDANDAGGknsEECTLILTEGDSAKALALAG 453
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 559767655 438 -----RDsRFqAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGVHDEF-DIAKLRYHKLILMADADVDGQHI 507
Cdd:PTZ00108 454 lsvvgRD-YY-GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHI 527
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
7-507 |
7.95e-25 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 110.34 E-value: 7.95e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 7 LEAVRKRPGMYIGSTGERGLHHLVYE---VVDNSV----------DEALAGHADR---------IEVTLLADNG-VRVVD 63
Cdd:PLN03237 38 LEHILLRPDTYIGSIEKHTQTLWVYEtdkMVQRSVtyvpglykifDEILVNAADNkqrdpkmdsLRVVIDVEQNlISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 64 NGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGGLHGVGVSVVNALSNRLEVEIrTDGHYWRQsYADTRPTHP 143
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIET-ADGKRQKK-YKQVFSNNM 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 144 LAKGEPT------DETGTSITFWADPTIFETTTWNFET---LSRRFQEMA-FLNKGLTISLrderpghsageDGEDGPVE 213
Cdd:PLN03237 196 GKKSEPVitkckkSENWTKVTFKPDLAKFNMTHLEDDVvalMKKRVVDIAgCLGKTVKVEL-----------NGKRIPVK 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 214 vtyhyegGLSDFVK-HLNSK-KDAAHVSVIDFEESGEGISVEIAMQWNNSYSESvytFANTINTAEGGTHEEgfraALTS 291
Cdd:PLN03237 265 -------SFSDYVDlYLESAnKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQVS---FVNSIATIKGGTHVD----YVTN 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 292 IVNRYAREqKFLKEGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQKAcndHLRDWFERNPGEAkD 371
Cdd:PLN03237 331 QIANHVME-AVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL-TLRQSSFGSKC---ELSEDFLKKVMKS-G 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 372 IINKSLQ-ASRARLAARQARDLTRRKSLleagSGLPgKLADCQWS---DPEKCELFIVEGDSA-----GGSAKGGRDsrF 442
Cdd:PLN03237 405 IVENLLSwADFKQSKELKKTDGAKTTRV----TGIP-KLEDANEAggkNSEKCTLILTEGDSAkalavAGLSVVGRN--Y 477
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 559767655 443 QAILPIRGKILNVEKARIDKVLKNTEVQALITAMGTGVHDEFDIAK-LRYHKLILMADADVDGQHI 507
Cdd:PLN03237 478 YGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKsLRYGHLMIMTDQDHDGSHI 543
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
222-342 |
2.34e-20 |
|
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.
Pssm-ID: 238202 [Multi-domain] Cd Length: 107 Bit Score: 86.55 E-value: 2.34e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 222 LSDFVKHLNSKKDAAHVsvIDFEESGEGISVEIAMQWNN---SYSESVYTFANTINTAEGGTHEEGFRAALTSIVNryar 298
Cdd:cd00329 1 LKDRLAEILGDKVADKL--IYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 559767655 299 eqkflkegkddnltGEDIREGLTAIISVKL--ADPQFE-GQTKTKLG 342
Cdd:cd00329 75 --------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
577-611 |
5.65e-20 |
|
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,.
Pssm-ID: 460016 [Multi-domain] Cd Length: 63 Bit Score: 83.58 E-value: 5.65e-20
10 20 30
....*....|....*....|....*....|....*
gi 559767655 577 IQRFKGLGEMNAGQLWDTTMNPETRVLRLVTLDDA 611
Cdd:pfam00986 6 IQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDA 40
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
420-507 |
8.83e-19 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 82.35 E-value: 8.83e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 420 CELFIVEGDSAGGSAKGGR---DSRFQAILPIRGKILNVEKARIDKVLKNTEVQALITAMGT--GVHDEFDIAKLRYHKL 494
Cdd:cd03365 1 CTLILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLqhGKSDYESTKSLRYGRL 80
|
90
....*....|...
gi 559767655 495 ILMADADVDGQHI 507
Cdd:cd03365 81 MIMTDQDHDGSHI 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
23-125 |
1.62e-15 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 72.68 E-value: 1.62e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 23 ERGLHHLVYEVVDNSVDEALAGhaDRIEVTLLADNG---VRVVDNGRGIPvgmhpvekrpaVEVVLTVLHAGGKFDGKSY 99
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDhveITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRSR 69
|
90 100
....*....|....*....|....*.
gi 559767655 100 AVSGglHGVGVSVVNALSNRLEVEIR 125
Cdd:smart00387 70 KIGG--TGLGLSIVKKLVELHGGEIS 93
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
421-533 |
5.25e-15 |
|
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: 70.85 E-value: 5.25e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 421 ELFIVEGDSAGGSAKGGRDSRFQAILPIRGKILNVEKARIDKVLKntevqalitamgtgvhdEFDIAKLRYHKLILMADA 500
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 559767655 501 DVDGQHINtllltLLFRFMRPLIEA--GHVYLSQP 533
Cdd:pfam01751 64 DREGEAIA-----LKLLELKELLENagGRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
23-165 |
8.53e-14 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 67.78 E-value: 8.53e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 23 ERGLHHLVYEVVDNSVDEAlaGHADRIEVTLLADNG--VRVVDNGRGIPVGMHPvekrpavevvltvlHAGGKFDGKSyA 100
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLP--------------RIFEPFSTAD-K 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 559767655 101 VSGGLHGVGVSVVNALSNRLEVEIRTdghywrqsyadtrpthplakgEPTDETGTSITFWADPTI 165
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELLGGTITV---------------------ESEPGGGTTVTLTLPLAQ 109
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
38-162 |
7.91e-10 |
|
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.
Pssm-ID: 340407 [Multi-domain] Cd Length: 147 Bit Score: 57.73 E-value: 7.91e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 38 VDEALAGHAD---------RIEVTLLADNG-VRVVDNGRGIPVGMHPVEKRPAVEVVLTVLHAGGKFDGKSYAVSGGLHG 107
Cdd:cd16930 9 FDEILVNAADnkqrdksmtCIKVTIDPENNeISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNG 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 559767655 108 VGVSVVNALSNRLEVEIRTD--GHYWRQSYAD--TRPTHPLAKGEPTDETGTSITFWAD 162
Cdd:cd16930 89 YGAKLCNIFSTEFTVETADSesKKKFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
26-125 |
6.48e-05 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 42.20 E-value: 6.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 26 LHHLVYEVVDNSVDEALAGhaDRIEVTLLADNG---VRVVDNGRGIPVGMHPvekrpavevvltvlHAGGKFDGKSYAVS 102
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE--------------RIFERFYRGDKSRE 64
|
90 100
....*....|....*....|...
gi 559767655 103 GGLHGVGVSVVNALSNRLEVEIR 125
Cdd:cd00075 65 GGGTGLGLAIVRRIVEAHGGRIT 87
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
420-507 |
1.44e-03 |
|
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: 37.79 E-value: 1.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767655 420 CELFIVEGDSAGGSAKGGRdSRFQAILPIRGKILNVEKARIDKVLKntevqalitamgtgvhdefdiaklRYHKLILMAD 499
Cdd:cd00188 1 KKLIIVEGPSDALALAQAG-GYGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
....*...
gi 559767655 500 ADVDGQHI 507
Cdd:cd00188 56 ADREGEAI 63
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
32-69 |
1.51e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 41.57 E-value: 1.51e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 559767655 32 EVVDNSVDealAGhADRIEVTLlADNGV---RVVDNGRGIP 69
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEI-EEGGKsliRVTDNGCGMS 65
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
30-69 |
2.68e-03 |
|
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.
Pssm-ID: 340403 [Multi-domain] Cd Length: 188 Bit Score: 39.34 E-value: 2.68e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767655 30 VYEVVDNSVDealAGhADRIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEI--EEGglklIRVTDNGSGIS 55
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
30-69 |
6.86e-03 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 39.43 E-value: 6.86e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767655 30 VYEVVDNSVDealAGhADRIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:PRK00095 27 VKELVENALD---AG-ATRIDIEI--EEGglklIRVRDNGCGIS 64
|
|
| |
