|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-606 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1161.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:PRK05644 13 IQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDIHPKTGKPA 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEETGTSITFW 160
Cdd:PRK05644 93 VEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFK 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 161 ADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERpdhvNGEPHVVTYHYEGGISDFVKHINSKKEPVHSSVIDFEA 240
Cdd:PRK05644 173 PDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDER----EGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEG 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 241 EGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEgKDDNLTGDDIREGLTAIIS 320
Cdd:PRK05644 249 EKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKE-KDDNLTGEDVREGLTAVIS 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 321 VKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLLEaGSGL 400
Cdd:PRK05644 328 VKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALE-SSSL 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 401 PGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFD 480
Cdd:PRK05644 407 PGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFD 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 481 IQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRKGedasYAYSDRERDSIIQSGID 560
Cdd:PRK05644 487 ISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE----YAYSDEELDEILAELKL 562
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 559767649 561 AGRRDprqhDGVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:PRK05644 563 KGNPK----YGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 604
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-606 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1110.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:COG0187 11 IQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDIHPKEGKSA 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEETGTSITFW 160
Cdd:COG0187 91 LEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFK 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 161 ADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERPDhvngEPHVVTYHYEGGISDFVKHINSKKEPVHSSVIDFEA 240
Cdd:COG0187 171 PDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREE----EPKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEG 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 241 EGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEgKDDNLTGDDIREGLTAIIS 320
Cdd:COG0187 247 EKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVIS 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 321 VKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLLEaGSGL 400
Cdd:COG0187 326 VKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALE-SSGL 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 401 PGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFD 480
Cdd:COG0187 405 PGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFD 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 481 IQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWdrkGEDASYAYSDRERDSIIQSGId 560
Cdd:COG0187 485 LEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKK---GKKTYYAYSDAELDELLKELK- 560
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 559767649 561 agrrdPRQHDGVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:COG0187 561 -----GKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 601
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-606 |
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: 942.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:TIGR01059 6 IKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPEEGISA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEETGTSITFW 160
Cdd:TIGR01059 86 VEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFW 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 161 ADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERpdhvNGEPHVVTYHYEGGISDFVKHINSKKEPVHSSVIDFEA 240
Cdd:TIGR01059 166 PDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER----DGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 241 EGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEgKDDNLTGDDIREGLTAIIS 320
Cdd:TIGR01059 242 EKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKE-SKPNLTGEDIREGLTAVIS 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 321 VKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLLEAGsGL 400
Cdd:TIGR01059 321 VKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG-GL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 401 PGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFD 480
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 481 IQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRKGE------------------DA 542
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERyikddkekdlvgealedlKA 559
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 559767649 543 SYAYSDRERDSIIQSgidAGRRDPRQHDGVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:TIGR01059 560 LYIYSDKEKEEAKTQ---IPVHLGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDA 620
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-606 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 909.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGE-RGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRP 79
Cdd:PRK14939 12 IKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTDIHPEEGVS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 80 AVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEETGTSITF 159
Cdd:PRK14939 92 AAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRF 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 160 WADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERPDhvngepHVVTYHYEGGISDFVKHINSKKEPVHSSVIDFE 239
Cdd:PRK14939 172 WPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG------KEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFS 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 240 AEGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEGKdDNLTGDDIREGLTAII 319
Cdd:PRK14939 246 GEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAK-VSLTGDDAREGLTAVL 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 320 SVKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLLEaGSG 399
Cdd:PRK14939 325 SVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALD-IAG 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 400 LPGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGV-HAE 478
Cdd:PRK14939 404 LPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIgRDE 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 479 FDIQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrKGEDASYAYSDRERDS-IIQS 557
Cdd:PRK14939 484 FNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVK---KGKQEQYLKDDEALDDyLIEL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 558 GID------------AG---------------------RRDPR------------------------QHD---------- 570
Cdd:PRK14939 561 ALEgatlhladgpaiSGealeklvkeyravrkiidrleRRYPRavlealiyapaldlddladeaavaALDadfltsaeyr 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 571 ----------------------------------------------GVQRFKGLGEMNASQLWETTMNPATRVLLQVTLD 604
Cdd:PRK14939 641 rlvelaeklrglieegaylergerkqpvssfeealdwllaearkglSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIE 720
|
..
gi 559767649 605 DA 606
Cdd:PRK14939 721 DA 722
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-606 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 859.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:PRK05559 13 IEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGIHPEEGKSG 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGE--PTEETGTSIT 158
Cdd:PRK05559 93 VEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGtaGKRKTGTRVR 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 159 FWADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERPDHvngephvvTYHYEGGISDFVKHINSKKEPVH-SSVID 237
Cdd:PRK05559 173 FWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ--------TFHYENGLKDYLAELNEGKETLPeEFVGS 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 238 FEAEGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKegKDDNLTGDDIREGLTA 317
Cdd:PRK05559 245 FEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP--KGKKLEGEDVREGLAA 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 318 IISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARdlTRRKslLEAG 397
Cdd:PRK05559 323 VLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKK--KTSG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 398 SGLPGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHA 477
Cdd:PRK05559 399 PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGD 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 478 EFDIQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIkwdRKGEDASYAYSDRERDSIIQS 557
Cdd:PRK05559 479 SFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRV---DKGKKKIYALDEEEKEELLKK 555
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 559767649 558 GIDAGRRDPrqhdgVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:PRK05559 556 LGKKGGKPE-----IQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDA 599
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
25-606 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 804.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 25 GLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPAVEVVLTVLHAGGKFDSKSYAVSGG 104
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 105 LHGVGVSVVNALSTRLEVEIKTDGHHWRQSY-VESKPTGPLVKGEPTEETGTSITFWADGTIFETTT-WNFETLSRRLQE 182
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTdDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 183 MAFLNKGLSIVLRDERpdhvngEPHVVTYHYEGGISDFVKHINSKKEPVHSSVIDFEAEGDGISVEIAMQWNASYSESVY 262
Cdd:smart00433 161 LAFLNKGVKITLNDER------SDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 263 TFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEgkdDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLGNTEAK 342
Cdd:smart00433 235 SFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKE---KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVR 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 343 SFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLlEAGSgLPGKLADCQWTEPEKCELYIVEG 422
Cdd:smart00433 312 FGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKL-SSIS-LPGKLADASSAGPKKCELFLVEG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 423 DSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFDIQKLRYHKLILMADADVDGQHI 502
Cdd:smart00433 390 DSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHI 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 503 TTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRKGEDASYAYSDRERDSIIQSGIDAGRrdprqhDGVQRFKGLGEMN 582
Cdd:smart00433 470 KGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFYSLDEYEKWLEKTEGNKSK------YEIQRYKGLGEMN 543
|
570 580
....*....|....*....|....
gi 559767649 583 ASQLWETTMNPATRVLLQVTLDDA 606
Cdd:smart00433 544 ADQLWETTMDPERRTLLFVTLDDA 567
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
1-606 |
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: 663.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:TIGR01058 10 IKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQDGNIST 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVE-SKPTGPLVKGEPTEETGTSITF 159
Cdd:TIGR01058 90 VETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKKTGTLVHF 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 160 WADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDERPDhvngepHVVTYHYEGGISDFVKHINSKKEpVHSSVIDFE 239
Cdd:TIGR01058 170 HPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTN------KTTVFFYENGLVDFVDYINETKE-TLSQVTYFE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 240 AEGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEgKDDNLTGDDIREGLTAII 319
Cdd:TIGR01058 243 GEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKE-KDKNLEGSDIREGLSAII 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 320 SVKLADP--QFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRR-KSLLEA 396
Cdd:TIGR01058 322 SVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSgKKPKKE 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 397 GSGLPGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVH 476
Cdd:TIGR01058 402 KGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGIG 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 477 AEFDIQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwDRKGEDASYAYSDRERDSIiq 556
Cdd:TIGR01058 482 ADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLS-KKDGKKVKYAWSDLELESV-- 558
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 559767649 557 sgidagrRDPRQHDGVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:TIGR01058 559 -------KKKLKNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDL 601
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
1-606 |
3.20e-167 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 499.79 E-value: 3.20e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:PTZ00109 105 IVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEKTGKSG 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKF-----------------DSKS-----------------------YAVSGGLHGVGVSVVNALSTRL 120
Cdd:PTZ00109 185 LETVLTVLHSGGKFqdtfpknsrsdksedknDTKSskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVVNALSSFL 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 121 EVEIKTDGHHWRQSYVESKPTGPL-VKGEPTEETGTSITFWADG-TIFETTT--------------WNFETLSRRLQEMA 184
Cdd:PTZ00109 265 KVDVFKGGKIYSIELSKGKVTKPLsVFSCPLKKRGTTIHFLPDYkHIFKTHHqhteteeeegckngFNLDLIKNRIHELS 344
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 185 FLNKGLSIVLRDERPDHVNGEPHVVTYHYEGGISDFVKHINSKKEPVH--SSVIDFEAEGDGISVEIAMQWNA-SYSESV 261
Cdd:PTZ00109 345 YLNPGLTFYLVDERIANENNFYPYETIKHEGGTREFLEELIKDKTPLYkdINIISIRGVIKNVNVEVSLSWSLeSYTALI 424
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 262 YTFANTINTAeGGTHEEGFRAALTTIVNRYAREQKFLKeGKDDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLGNTEA 341
Cdd:PTZ00109 425 KSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFK-GNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLL 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 342 KSFVQKACNDSIRDWFERNPGEAKEILSKSLQASRARIAARQARDLTRRKSLLEAGSGLPGKLADCQWTEPEKCELYIVE 421
Cdd:PTZ00109 503 KTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDIERNELFIVE 582
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 422 GDSAGGSAKGGRDPKFQAILPIRGKILNVEKARID-RVLKNNEVQALITALGTGVHAE---------------------- 478
Cdd:PTZ00109 583 GESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtkaskdesvqnn 662
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 479 ----------FDIQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRKGEDAS----- 543
Cdd:PTZ00109 663 nstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFNVstkns 742
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 544 ----YAYSDRERDSII----------------QSGIDAGRRDPRQHDG-------------------------------- 571
Cdd:PTZ00109 743 kkyiYTWSDEELNVLIkllnkdysskettrsvEEKGNAPDLDNEYEDEkldnknmrennvdevelktelgtnvadteqtd 822
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|.
gi 559767649 572 ----------------VQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:PTZ00109 823 eldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDA 873
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
1-605 |
1.44e-162 |
|
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: 478.64 E-value: 1.44e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTGergLHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPA 80
Cdd:TIGR01055 9 IEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPKEGVSA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEE--TGTSIT 158
Cdd:TIGR01055 86 VEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlTGTSVH 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 159 FWADGTIFETTTWNFETLSRRLQEMAFLNKGLSIVLRDErpdhVNGEPHVvtYHYEGGISDFVKHINSKKEPVHSSVIDF 238
Cdd:TIGR01055 166 FTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDE----VNNTKAL--WNYPDGLKDYLSEAVNGDNTLPPKPFSG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 239 EAEGDGISVEIAMQWNASYSESVY-TFANTINTAEGGTHEEGFRAALTTIVNRYAREQKFLKEGKddNLTGDDIREGLTA 317
Cdd:TIGR01055 240 NFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGV--KLTAEDIWDRCSY 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 318 IISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSLqaSRARIAARQARDLTRRKslLEAG 397
Cdd:TIGR01055 318 VLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVRKK--LTSG 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 398 SGLPGKLADCQWTEPEKCELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHA 477
Cdd:TIGR01055 394 PALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 478 EfDIQKLRYHKLILMADADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrKGEDASYAYSDRERDSIIQS 557
Cdd:TIGR01055 474 N-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRID---LSKEVYYALDEEEKEKLLYK 549
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 559767649 558 gidagRRDPRQHDGVQRFKGLGEMNASQLWETTMNPATRVLLQVTLDD 605
Cdd:TIGR01055 550 -----LKKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDD 592
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
26-198 |
5.25e-103 |
|
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: 309.47 E-value: 5.25e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 26 LHHLVQEVVDNSVDEALAGHADHIEVTLLADNGVRVVDNGRGIPVGIVPGEQRPAVEVVLTVLHAGGKFDSKSYAVSGGL 105
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 106 HGVGVSVVNALSTRLEVEIKTDGHHWRQSYVESKPTGPLVKGEPTEETGTSITFWADGTIFETTTWNFETLSRRLQEMAF 185
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|...
gi 559767649 186 LNKGLSIVLRDER 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 ... |
215-372 |
1.23e-78 |
|
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: 246.32 E-value: 1.23e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 215 GGISDFVKHINSKKEPVHSSVIDFEAEGDGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYARE 294
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 559767649 295 QKFLKEgKDDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSL 372
Cdd:cd00822 81 NNLLKK-KDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAI 157
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
415-528 |
1.55e-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: 1.55e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 415 CELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFDIQKLRYHKLILMAD 494
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 559767649 495 ADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQP 528
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
216-372 |
1.86e-69 |
|
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: 222.11 E-value: 1.86e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 216 GISDFVKHINSKKEPVHSSVIDFEAEG--DGISVEIAMQWNASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNRYAR 293
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 559767649 294 EQKFLKEgKDDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDSIRDWFERNPGEAKEILSKSL 372
Cdd:pfam00204 81 KKGLLKK-KDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
415-528 |
1.28e-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: 188.87 E-value: 1.28e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 415 CELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVH-AEFDIQKLRYHKLILMA 493
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 559767649 494 DADVDGQHITTLLLTLLFRFMRPLIEAGHVYLSQP 528
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
1-605 |
9.96e-45 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 168.01 E-value: 9.96e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 1 ITVLEGLEAVRKRPGMYIGSTG----ER-------------GLHHLVQEVVDNSVDEALAG---HADHIEVTlLADNGVR 60
Cdd:PHA02569 4 FKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVT-IKNNQVT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 61 VVDNGRGIPVGIV---PGEQRPAVEVVLTVLHAGGKFDSKSyAVSGGLHGVGVSVVNALSTRL---------EVEIK-TD 127
Cdd:PHA02569 83 VSDNGRGIPQAMVttpEGEEIPGPVAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFigetcdgknEVTVNcSN 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 128 GHHwRQSYvESKPTGplvkgepteETGTSITFWADGTIFETTTWNFETL---SRRLQemaflnkGLSIVLrderPD---H 201
Cdd:PHA02569 162 GAE-NISW-STKPGK---------GKGTSVTFIPDFSHFEVNGLDQQYLdiiLDRLQ-------TLAVVF----PDikfT 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 202 VNGEPHvvtyhyEGGISDFVKHINSKkepvhsSVIdfeAEGDGISVEIAMqwnasySESVY---TFANTINTAEGGTHEE 278
Cdd:PHA02569 220 FNGKKV------SGKFKKYAKQFGDD------TIV---QENDNVSIALAP------SPDGFrqlSFVNGLHTKNGGHHVD 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 279 GFRAALTT-IVNRYAREQKFlkegkddNLTGDDIREGLTAIISVK-LADPQFEGQTKTKLGNT--EAKSFVQ---KACND 351
Cdd:PHA02569 279 CVMDDICEeLIPMIKKKHKI-------EVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHIDldyKKIAK 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 352 SIRDwferNPGEAKEILSKSLQASRARIAARqardLTR-RKSLLEAG------SGLPGKLADCQwtepekceLYIVEGDS 424
Cdd:PHA02569 352 QILK----TEAIIMPIIEAALARKLAAEKAA----ETKaAKKAKKAKvakhikANLIGKDAETT--------LFLTEGDS 415
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 425 AGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKNNEVqALITALgTGVHAEFDIQKLRYHKLILMADADVDGQHITT 504
Cdd:PHA02569 416 AIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKEL-FDICAI-TGLVLGEKAENMNYKNIAIMTDADVDGKGSIY 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 505 LLLTLLFRFMRPLIEAGHVYLSQPPLYkIKWDRKGEDASYAYSDRERDsiiqsgidagRRDPRQHDgVQRFKGLGEMNAS 584
Cdd:PHA02569 494 PLLLAFFSRWPELFEQGRIRFVKTPVI-IAQVGKETKWFYSLDEFEKA----------KDSLKKWS-IRYIKGLGSLRKS 561
|
650 660
....*....|....*....|.
gi 559767649 585 QLWETTMNPatrVLLQVTLDD 605
Cdd:PHA02569 562 EYRRVINNP---VYDVVVLPD 579
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
7-502 |
1.39e-40 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 158.72 E-value: 1.39e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 7 LEAVRKRPGMYIGSTGER---------------------GLHHLVQEVVDNSVDEALAG-HADHIEVTLLADNG-VRVVD 63
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHtqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEQNtISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 64 NGRGIPVGIVPGEQRPAVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIkTDGH---HWRQSYVE--S 138
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVET-ADGNrgkKYKQVFTNnmS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 139 KPTGPLVKGEPTEETGTSITFWADGTIFETTTWNFET---LSRRLQEMA-FLNKGLSIVLrderpdhvNGEPHVVtyhye 214
Cdd:PLN03128 172 VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVEL--------NGKKLPV----- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 215 GGISDFV---KHINSKKEPVHSSvidFEAEGDGISVEIAMQwNASYSEsvYTFANTINTAEGGTHEEgfraALTTIVNRY 291
Cdd:PLN03128 239 KSFQDYVglyLGPNSREDPLPRI---YEKVNDRWEVCVSLS-DGSFQQ--VSFVNSIATIKGGTHVD----YVADQIVKH 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 292 AREQKFLKEGKDDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQK-ACNDSIRDWFErNPGEAKEILSK 370
Cdd:PLN03128 309 IQEKVKKKNKNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL-TTRPSSFGSKcELSEEFLKKVE-KCGVVENILSW 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 371 SlqaSRARIAARQARDLTRRKSLLeagsGLPgKLADCQW---TEPEKCELYIVEGDSAGGSAKGG-----RDpkFQAILP 442
Cdd:PLN03128 387 A---QFKQQKELKKKDGAKRQRLT----GIP-KLDDANDaggKKSKDCTLILTEGDSAKALAMSGlsvvgRD--HYGVFP 456
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 559767649 443 IRGKILNVEKARIDRVLKNNEVQALITALG---TGVHAEFDIQKLRYHKLILMADADVDGQHI 502
Cdd:PLN03128 457 LRGKLLNVREASHKQIMKNAEITNIKQILGlqfGKTYDEENTKSLRYGHLMIMTDQDHDGSHI 519
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
4-502 |
6.33e-39 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 153.66 E-value: 6.33e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 4 LEGLEAVRKRPGMYIGSTgER------------------------GLHHLVQEV----VDNSVDEALAGHADHIEVTLLA 55
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKVTIDE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 56 DNG-VRVVDNGRGIPVGI-------VPgeqrpavEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEIKTD 127
Cdd:PTZ00108 92 ENGeISVYNDGEGIPVQIhkehkiyVP-------EMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDS 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 128 --GHHWRQSYVE--SKPTGPLVKGEPTEETGTSITFWADGTIFETTTWNFETLS---RRLQEMAFLNKGLSIVLRDERPd 200
Cdd:PTZ00108 165 ksGKKFKMTWTDnmSKKSEPRITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERI- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 201 hvngephvvtyhyegGISDFVKHIN--SKKEPVHSSVID-FEAEGDGISVEIAmqwnASYSESVYT---FANTINTAEGG 274
Cdd:PTZ00108 244 ---------------AIKSFKDYVDlyLPDGEEGKKPPYpFVYTSVNGRWEVV----VSLSDGQFQqvsFVNSICTTKGG 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 275 THeegFRAALTTIVNRYAREQKFLKEGKDDnLTGDDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQK-ACNDSI 353
Cdd:PTZ00108 305 TH---VNYILDQLISKLQEKAKKKKKKGKE-IKPNQIKNHLWVFVNCLIVNPSFDSQTKETL-TTKPSKFGSTcELSEKL 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 354 RDWFERNPgeakeILSKSLQASRARIAARQARDL-TRRKSLLeagSGLPgKLADCQWTEP---EKCELYIVEGDSAGGSA 429
Cdd:PTZ00108 380 IKYVLKSP-----ILENIVEWAQAKLAAELNKKMkAGKKSRI---LGIP-KLDDANDAGGknsEECTLILTEGDSAKALA 450
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 559767649 430 KGG-----RDpKFqAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEF-DIQKLRYHKLILMADADVDGQHI 502
Cdd:PTZ00108 451 LAGlsvvgRD-YY-GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHI 527
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
572-606 |
7.32e-23 |
|
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: 92.06 E-value: 7.32e-23
10 20 30
....*....|....*....|....*....|....*
gi 559767649 572 VQRFKGLGEMNASQLWETTMNPATRVLLQVTLDDA 606
Cdd:pfam00986 6 IQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDA 40
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
7-502 |
1.01e-22 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 103.40 E-value: 1.01e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 7 LEAVRKRPGMYIGS------------TGER---------GLHHLVQEVVDNSVDEALAG-HADHIEVTLLADNG-VRVVD 63
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyeTDKMvqrsvtyvpGLYKIFDEILVNAADNKQRDpKMDSLRVVIDVEQNlISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 64 NGRGIPVGIVPGEQRPAVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTRLEVEiKTDGHH---WRQSYVES-- 138
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIE-TADGKRqkkYKQVFSNNmg 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 139 KPTGPLVKGEPTEETGTSITFWADGTIFETTTWNFET---LSRRLQEMA-FLNKGLSIVLrderpdhvNGEPHVVTyhye 214
Cdd:PLN03237 197 KKSEPVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVvalMKKRVVDIAgCLGKTVKVEL--------NGKRIPVK---- 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 215 gGISDFVK-HINSKKEPVHSSVIDF-EAEGDgisveiamQWN--ASYSESVY---TFANTINTAEGGTHEEgfraALTTI 287
Cdd:PLN03237 265 -SFSDYVDlYLESANKSRPENLPRIyEKVND--------RWEvcVSLSEGQFqqvSFVNSIATIKGGTHVD----YVTNQ 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 288 VNRYAREqKFLKEGKDDNLTGDDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQKaCNDSIrDWFER--NPGEAK 365
Cdd:PLN03237 332 IANHVME-AVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL-TLRQSSFGSK-CELSE-DFLKKvmKSGIVE 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 366 EILSKSlqaSRARIAARQARDLTRRKSLleagSGLPgKLADCQWT---EPEKCELYIVEGDSA-----GGSAKGGRDpkF 437
Cdd:PLN03237 408 NLLSWA---DFKQSKELKKTDGAKTTRV----TGIP-KLEDANEAggkNSEKCTLILTEGDSAkalavAGLSVVGRN--Y 477
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 559767649 438 QAILPIRGKILNVEKARIDRVLKNNEVQALITALGTGVHAEFD-IQKLRYHKLILMADADVDGQHI 502
Cdd:PLN03237 478 YGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYEsVKSLRYGHLMIMTDQDHDGSHI 543
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
217-337 |
1.03e-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: 87.32 E-value: 1.03e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 217 ISDFVKHINSKKepVHSSVIDFEAEGDGISVEIAMQWN---ASYSESVYTFANTINTAEGGTHEEGFRAALTTIVNryar 293
Cdd:cd00329 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPdsgRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 559767649 294 eqkflkegkddnltGDDIREGLTAIISVKL--ADPQFE-GQTKTKLG 337
Cdd:cd00329 75 --------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
415-502 |
8.58e-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: 8.58e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 415 CELYIVEGDSAGGSAKGGR---DPKFQAILPIRGKILNVEKARIDRVLKNNEVQALITALGT--GVHAEFDIQKLRYHKL 489
Cdd:cd03365 1 CTLILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLqhGKSDYESTKSLRYGRL 80
|
90
....*....|...
gi 559767649 490 ILMADADVDGQHI 502
Cdd:cd03365 81 MIMTDQDHDGSHI 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
23-160 |
4.36e-16 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 74.22 E-value: 4.36e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 23 ERGLHHLVQEVVDNSVDEALAGhaDHIEVTLLADNG---VRVVDNGRGIPvgivpgeqrpaVEVVLTVLHAGGKFDSKSY 99
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDhveITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRSR 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 559767649 100 AVSGglHGVGVSVVNALSTRLEVEIKtdghhwrqsyVESKPTGplvkgepteetGTSITFW 160
Cdd:smart00387 70 KIGG--TGLGLSIVKKLVELHGGEIS----------VESEPGG-----------GTTFTIT 107
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
416-502 |
9.25e-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: 70.08 E-value: 9.25e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 416 ELYIVEGDSAGGSAKGGRDPKFQAILPIRGKILNVEKARIDRVLKnnevqalitalgtgvhaEFDIQKLRYHKLILMADA 495
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
....*..
gi 559767649 496 DVDGQHI 502
Cdd:pfam01751 64 DREGEAI 70
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
23-160 |
1.21e-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: 70.09 E-value: 1.21e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 23 ERGLHHLVQEVVDNSVDEAlaGHADHIEVTLLADNG--VRVVDNGRGIPVGIVPgeqrpavevvltvlHAGGKFDSKSyA 100
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLP--------------RIFEPFSTAD-K 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 101 VSGGLHGVGVSVVNALSTRLEVEIktdghhwrqsYVESKPTGplvkgepteetGTSITFW 160
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELLGGTI----------TVESEPGG-----------GTTVTLT 104
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
25-162 |
2.41e-07 |
|
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: 50.41 E-value: 2.41e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 25 GLHHLVQEVVDNSVD-EALAGHADHIEVTLLADNG-VRVVDNGRGIPVGIVPGEQRPAVEVVLTVLHAGGKFDSKSYAVS 102
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPENNeISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 559767649 103 GGLHGVGVSVVNALSTRLEVEI--KTDGHHWRQSYVE--SKPTGPLVKGEPTEETGTSITFWAD 162
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVETadSESKKKFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
26-160 |
8.48e-06 |
|
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: 44.90 E-value: 8.48e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 26 LHHLVQEVVDNSVDEALAGhaDHIEVTLLADNG---VRVVDNGRGIPVgivpgEQRPavevvltvlHAGGKFDSKSYAVS 102
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPE-----EDLE---------RIFERFYRGDKSRE 64
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 559767649 103 GGLHGVGVSVVNALSTRLEVEIktdghhwrqsYVESKPTGplvkgepteetGTSITFW 160
Cdd:cd00075 65 GGGTGLGLAIVRRIVEAHGGRI----------TVESEPGG-----------GTTFTVT 101
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
415-502 |
1.36e-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: 1.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 415 CELYIVEGDSAGGSAKGGRDpKFQAILPIRGKILNVEKARIDRVLKnnevqalitalgtgvhaefdiqklRYHKLILMAD 494
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
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....*...
gi 559767649 495 ADVDGQHI 502
Cdd:cd00188 56 ADREGEAI 63
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| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
30-69 |
1.76e-03 |
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DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 41.18 E-value: 1.76e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 559767649 30 VQEVVDNSVDealAGhADHIEVTLlADNGV---RVVDNGRGIP 69
Cdd:COG0323 28 VKELVENAID---AG-ATRIEVEI-EEGGKsliRVTDNGCGMS 65
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| HATPase_TopVIB-like |
cd16933 |
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ... |
8-126 |
4.52e-03 |
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Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends.
Pssm-ID: 340410 [Multi-domain] Cd Length: 203 Bit Score: 38.87 E-value: 4.52e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767649 8 EAVRKRPGMYIGSTGERGLHHLVQEVVDNSVDEA-LAGHADHIEVTL-LADNG---VRVVDNGRGIPVGIVPgeqrpavE 82
Cdd:cd16933 2 EFFRKNKEMLGFDNPIRSLYTTVRELVENSLDATeEAGILPDIKVEIeEIGKDhykVIVEDNGPGIPEEQIP-------K 74
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90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 559767649 83 VVLTVLhAGGKFDSKSyavSGGLHGVGVSVV---NALSTRLEVEIKT 126
Cdd:cd16933 75 VFGKVL-YGSKYHNKQ---SRGQQGLGISAAvlySQMTTGKPVEIIS 117
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| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
30-69 |
7.70e-03 |
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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: 37.80 E-value: 7.70e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767649 30 VQEVVDNSVDealAGhADHIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEI--EEGglklIRVTDNGSGIS 55
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| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
30-69 |
9.65e-03 |
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DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 39.04 E-value: 9.65e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767649 30 VQEVVDNSVDealAGhADHIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:PRK00095 27 VKELVENALD---AG-ATRIDIEI--EEGglklIRVRDNGCGIS 64
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