|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-607 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1166.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:PRK05644 13 IQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDIHPKTGKPA 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEETGTSITFW 160
Cdd:PRK05644 93 VEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFK 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 161 ADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERpdhivNGEPAEVVYHYEGGLSDFVQHLNSKKEAAHVSVIDFE 240
Cdd:PRK05644 173 PDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDER-----EGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFE 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 241 EHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGLTAII 320
Cdd:PRK05644 248 GEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKE-KDDNLTGEDVREGLTAVI 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 321 SVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLLESgSG 400
Cdd:PRK05644 327 SVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALES-SS 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 401 LPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEF 480
Cdd:PRK05644 406 LPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDF 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 481 DIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGedasYAYSDRERDAIIEdgm 560
Cdd:PRK05644 486 DISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE----YAYSDEELDEILA--- 558
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 559767659 561 sRGKRDPRLHDGIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:PRK05644 559 -ELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 604
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-607 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1119.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:COG0187 11 IQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDIHPKEGKSA 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEETGTSITFW 160
Cdd:COG0187 91 LEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFK 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 161 ADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERPDhivngEPAEVVYHYEGGLSDFVQHLNSKKEAAHVSVIDFE 240
Cdd:COG0187 171 PDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREE-----EPKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 241 EHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGLTAII 320
Cdd:COG0187 246 GEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVI 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 321 SVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLLESgSG 400
Cdd:COG0187 325 SVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALES-SG 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 401 LPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEF 480
Cdd:COG0187 404 LPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDF 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 481 DIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWdrrGEDASYAYSDRERDAIIEDGM 560
Cdd:COG0187 484 DLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKK---GKKTYYAYSDAELDELLKELK 560
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 559767659 561 SRGKrdprlhDGIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:COG0187 561 GKKK------VEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDA 601
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
1-607 |
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: 949.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:TIGR01059 6 IKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPEEGISA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEETGTSITFW 160
Cdd:TIGR01059 86 VEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFW 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 161 ADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERpdhivNGEPAEVVYHYEGGLSDFVQHLNSKKEAAHVSVIDFE 240
Cdd:TIGR01059 166 PDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER-----DGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 241 EHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGLTAII 320
Cdd:TIGR01059 241 GEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKE-SKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 321 SVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLLESGsG 400
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG-G 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 401 LPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEF 480
Cdd:TIGR01059 399 LPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDF 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 481 DIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGE------------------D 542
Cdd:TIGR01059 479 DLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERyikddkekdlvgealedlK 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 559767659 543 ASYAYSDRERDAIIEdgmSRGKRDPRLHDGIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:TIGR01059 559 ALYIYSDKEKEEAKT---QIPVHLGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDA 620
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-607 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 928.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRP 79
Cdd:PRK14939 12 IKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTDIHPEEGVS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 80 AVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEETGTSITF 159
Cdd:PRK14939 92 AAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRF 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 160 WADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERPDhivngepAEVVYHYEGGLSDFVQHLNSKKEAAHVSVIDF 239
Cdd:PRK14939 172 WPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG-------KEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYF 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 240 EEHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEGKdDNLTGEDIREGLTAI 319
Cdd:PRK14939 245 SGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAK-VSLTGDDAREGLTAV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 320 ISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLLEsGS 399
Cdd:PRK14939 324 LSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALD-IA 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 400 GLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGV-HD 478
Cdd:PRK14939 403 GLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIgRD 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 479 EFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrRGEDASYAYSDRERDA---- 554
Cdd:PRK14939 483 EFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVK---KGKQEQYLKDDEALDDylie 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 --------------------------------------------------------------------------------
Cdd:PRK14939 560 lalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsaey 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 555 ------------IIEDG--MSRGKRDPRLHD----------------GIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTL 604
Cdd:PRK14939 640 rrlvelaeklrgLIEEGayLERGERKQPVSSfeealdwllaearkglSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTI 719
|
...
gi 559767659 605 DDA 607
Cdd:PRK14939 720 EDA 722
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-607 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 864.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:PRK05559 13 IEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGIHPEEGKSG 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGE--PTEETGTSIT 158
Cdd:PRK05559 93 VEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGtaGKRKTGTRVR 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 159 FWADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERpdhivngepAEVVYHYEGGLSDFVQHLNSKKEAAH-VSVI 237
Cdd:PRK05559 173 FWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER---------ERQTFHYENGLKDYLAELNEGKETLPeEFVG 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 238 DFEEHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKegKDDNLTGEDIREGLT 317
Cdd:PRK05559 244 SFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP--KGKKLEGEDVREGLA 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 318 AIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARdlTRRKslLES 397
Cdd:PRK05559 322 AVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKK--KTS 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 398 GSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVH 477
Cdd:PRK05559 398 GPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPG 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 478 DEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIkwdRRGEDASYAYSDRERDAIIE 557
Cdd:PRK05559 478 DSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRV---DKGKKKIYALDEEEKEELLK 554
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 559767659 558 DGMSRGKRDPrlhdgIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:PRK05559 555 KLGKKGGKPE-----IQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDA 599
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
25-607 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 813.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 25 GLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGG 104
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 105 LHGVGVSVVNALSTALEVEIRTDGHHWRQSYS-HSKPTAPLAKGEPTEETGTSITFWADDTIFETTT-WNFETLSRRFQE 182
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTdDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 183 MAFLNKGLTITLRDERpdhivngEPAEVVYHYEGGLSDFVQHLNSKKEAAHVSVIDFEEHGEGISVEIAMQWNNSYSESV 262
Cdd:smart00433 161 LAFLNKGVKITLNDER-------SDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 263 YTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgkdDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTEA 342
Cdd:smart00433 234 VSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKE---KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEV 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 343 KSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLleSGSGLPGKLADCQWSDPEKCELFIVE 422
Cdd:smart00433 311 RFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKL--SSISLPGKLADASSAGPKKCELFLVE 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 423 GDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEFDIAKLRYHKLILMADADVDGQH 502
Cdd:smart00433 389 GDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSH 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 503 INTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGEDASYaYSDRERDAIIEDgmsrgKRDPRLHDGIQRFKGLGEM 582
Cdd:smart00433 469 IKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSF-YSLDEYEKWLEK-----TEGNKSKYEIQRYKGLGEM 542
|
570 580
....*....|....*....|....*
gi 559767659 583 NAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:smart00433 543 NADQLWETTMDPERRTLLFVTLDDA 567
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
1-607 |
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 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:TIGR01058 10 IKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQDGNIST 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSH-SKPTAPLAKGEPTEETGTSITF 159
Cdd:TIGR01058 90 VETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKKTGTLVHF 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 160 WADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERPDHivngepaEVVYHYEGGLSDFVQHLNSKKEAAHvSVIDF 239
Cdd:TIGR01058 170 HPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNK-------TTVFFYENGLVDFVDYINETKETLS-QVTYF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 240 EEHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEgKDDNLTGEDIREGLTAI 319
Cdd:TIGR01058 242 EGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKE-KDKNLEGSDIREGLSAI 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 320 ISVKLADP--QFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRR-KSLLE 396
Cdd:TIGR01058 321 ISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSgKKPKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 397 SGSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGV 476
Cdd:TIGR01058 401 EKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 477 HDEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwDRRGEDASYAYSDRERDAIi 556
Cdd:TIGR01058 481 GADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLS-KKDGKKVKYAWSDLELESV- 558
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|.
gi 559767659 557 edgmsrgkRDPRLHDGIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:TIGR01058 559 --------KKKLKNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDL 601
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
1-607 |
2.76e-173 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 515.59 E-value: 2.76e-173
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:PTZ00109 105 IVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEKTGKSG 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKF-----------------DSKS-----------------------YAVSGGLHGVGVSVVNALSTAL 120
Cdd:PTZ00109 185 LETVLTVLHSGGKFqdtfpknsrsdksedknDTKSskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVVNALSSFL 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 121 EVEIRTDGHHWRQSYSHSKPTAPLA-KGEPTEETGTSITFWAD-DTIFETTT--------------WNFETLSRRFQEMA 184
Cdd:PTZ00109 265 KVDVFKGGKIYSIELSKGKVTKPLSvFSCPLKKRGTTIHFLPDyKHIFKTHHqhteteeeegckngFNLDLIKNRIHELS 344
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 185 FLNKGLTITLRDERPDHiVNGEPAEVVYHYEGGLSDFVQHLNSKKEAAH--VSVIDFEEHGEGISVEIAMQWN-NSYSES 261
Cdd:PTZ00109 345 YLNPGLTFYLVDERIAN-ENNFYPYETIKHEGGTREFLEELIKDKTPLYkdINIISIRGVIKNVNVEVSLSWSlESYTAL 423
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 262 VYTFANTINTAeGGTHEEGFRAALTSIVNRYAREQKFLKeGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTE 341
Cdd:PTZ00109 424 IKSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFK-GNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHL 501
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 342 AKSFVQKACNDHLRDWFERNPGEAKDVINKSLQASRARIAARQARDLTRRKSLLESGSGLPGKLADCQWSDPEKCELFIV 421
Cdd:PTZ00109 502 LKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCISDDIERNELFIV 581
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 422 EGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARID-KVLKNAEVQALITAMGTGVH-----------------DEF--- 480
Cdd:PTZ00109 582 EGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNpvtwrqydlshgtkaskDESvqn 661
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 481 ------------DIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKWDRRGEDAS---- 544
Cdd:PTZ00109 662 nnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFNVstkn 741
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 545 -----YAYSDRERDAII------------EDGMSRGKRDPRLHDG----------------------------------- 572
Cdd:PTZ00109 742 skkyiYTWSDEELNVLIkllnkdyssketTRSVEEKGNAPDLDNEyedekldnknmrennvdevelktelgtnvadteqt 821
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|..
gi 559767659 573 -----------------IQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:PTZ00109 822 deldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDA 873
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
1-606 |
2.32e-165 |
|
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: 485.96 E-value: 2.32e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTGergLHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPA 80
Cdd:TIGR01055 9 IEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPKEGVSA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 81 VEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEE--TGTSIT 158
Cdd:TIGR01055 86 VEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlTGTSVH 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 159 FWADDTIFETTTWNFETLSRRFQEMAFLNKGLTITLRDERpdhivngEPAEVVYHYEGGLSDFVQHLNSKKEAAHVSVID 238
Cdd:TIGR01055 166 FTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEV-------NNTKALWNYPDGLKDYLSEAVNGDNTLPPKPFS 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 239 FEEHGEGISVEIAMQWNNSYSESVY-TFANTINTAEGGTHEEGFRAALTSIVNRYAREQKFLKEGKddNLTGEDIREGLT 317
Cdd:TIGR01055 239 GNFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGV--KLTAEDIWDRCS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 318 AIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSLqaSRARIAARQARDLTRRKslLES 397
Cdd:TIGR01055 317 YVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVRKK--LTS 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 398 GSGLPGKLADCQWSDPEKCELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGvH 477
Cdd:TIGR01055 393 GPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID-P 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 478 DEFDIAKLRYHKLILMADADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQPPLYKIKwdrRGEDASYAYSDRERDAIIE 557
Cdd:TIGR01055 472 DSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRID---LSKEVYYALDEEEKEKLLY 548
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 559767659 558 DgMSRGKRDPRlhdgIQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDD 606
Cdd:TIGR01055 549 K-LKKKKGKPN----VQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDD 592
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
26-198 |
1.12e-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: 311.01 E-value: 1.12e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 26 LHHLVYEVVDNSVDEALAGHADRIEVTLLADNGVRVVDNGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGGL 105
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 106 HGVGVSVVNALSTALEVEIRTDGHHWRQSYSHSKPTAPLAKGEPTEETGTSITFWADDTIFETTTWNFETLSRRFQEMAF 185
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|...
gi 559767659 186 LNKGLTITLRDER 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 ... |
216-373 |
3.87e-76 |
|
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: 239.77 E-value: 3.87e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 216 GGLSDFVQHLNSKKEAAHVSVIDFEEHGEGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYARE 295
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 559767659 296 QKFLKEgKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSL 373
Cdd:cd00822 81 NNLLKK-KDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAI 157
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
416-529 |
2.66e-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: 219.83 E-value: 2.66e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 416 CELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEFDIAKLRYHKLILMAD 495
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 559767659 496 ADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQP 529
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 ... |
217-373 |
5.02e-68 |
|
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: 218.64 E-value: 5.02e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 217 GLSDFVQHLNSKKEAAHVSVIDFEEHG--EGISVEIAMQWNNSYSESVYTFANTINTAEGGTHEEGFRAALTSIVNRYAR 294
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 559767659 295 EQKFLKEgKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLGNTEAKSFVQKACNDHLRDWFERNPGEAKDVINKSL 373
Cdd:pfam00204 81 KKGLLKK-KDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
416-529 |
2.79e-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: 188.10 E-value: 2.79e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 416 CELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVH-DEFDIAKLRYHKLILMA 494
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 559767659 495 DADVDGQHINTLLLTLLFRFMRPLIEAGHVYLSQP 529
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
1-606 |
1.01e-42 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 162.23 E-value: 1.01e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 1 ITVLEGLEAVRKRPGMYIGSTG----ER-------------GLHHLVYEVVDNSVDEALAG---HADRIEVTlLADNGVR 60
Cdd:PHA02569 4 FKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVT-IKNNQVT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 61 VVDNGRGIPVGIV---EAEGRPAVEVVLTVLHAGGKFDSKSyAVSGGLHGVGVSVVNALSTAL---------EVEIR-TD 127
Cdd:PHA02569 83 VSDNGRGIPQAMVttpEGEEIPGPVAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFigetcdgknEVTVNcSN 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 128 GHHwRQSYSHSkptaplakgePTEETGTSITFWADDTIFETTTWNFETL---SRRFQEMAFLNKGLTITLrderpdhivN 204
Cdd:PHA02569 162 GAE-NISWSTK----------PGKGKGTSVTFIPDFSHFEVNGLDQQYLdiiLDRLQTLAVVFPDIKFTF---------N 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 205 GEPAevvyhyEGGLSDFVQHLNSKKeaahvsvIDFEEhgEGISVEIAMqwnnsySESVY---TFANTINTAEGGTHEEGF 281
Cdd:PHA02569 222 GKKV------SGKFKKYAKQFGDDT-------IVQEN--DNVSIALAP------SPDGFrqlSFVNGLHTKNGGHHVDCV 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 282 RAALTS-IVNRYAREQKFlkegkddNLTGEDIREGLTAIISVK-LADPQFEGQTKTKLGNTEAKsfvqkaCNDHLRDWFE 359
Cdd:PHA02569 281 MDDICEeLIPMIKKKHKI-------EVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPFGE------IRNHIDLDYK 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 360 RnpgEAKDVINKS------LQASRARIAARQARDLTRRKSllesgSGLPGKLAD----CQWSDPEKCELFIVEGDSAGGS 429
Cdd:PHA02569 348 K---IAKQILKTEaiimpiIEAALARKLAAEKAAETKAAK-----KAKKAKVAKhikaNLIGKDAETTLFLTEGDSAIGY 419
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 430 AKGGRDSKFQAILPIRGKILNVEKARIDKVLKNAEVqALITAMgTGVHDEFDIAKLRYHKLILMADADVDGQHINTLLLT 509
Cdd:PHA02569 420 LIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKEL-FDICAI-TGLVLGEKAENMNYKNIAIMTDADVDGKGSIYPLLL 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 510 LLFRFMRPLIEAGHVYLSQPPLYkIKWDRRGEDASYAYSDRERDaiiedgmsrgKRDPRLHDgIQRFKGLGEMNAGQLWD 589
Cdd:PHA02569 498 AFFSRWPELFEQGRIRFVKTPVI-IAQVGKETKWFYSLDEFEKA----------KDSLKKWS-IRYIKGLGSLRKSEYRR 565
|
650
....*....|....*..
gi 559767659 590 TTMNPetrVLLQVTLDD 606
Cdd:PHA02569 566 VINNP---VYDVVVLPD 579
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
7-503 |
1.67e-42 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 164.50 E-value: 1.67e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 7 LEAVRKRPGMYIGSTGERGLHHLVYE---VVDNSV----------DEALAGHAD---------RIEVTLLADNG-VRVVD 63
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHTQTLWVYEggeMVNREVtyvpglykifDEILVNAADnkqrdpsmdSLKVDIDVEQNtISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 64 NGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIrTDGH---HWRQSYSH--S 138
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVET-ADGNrgkKYKQVFTNnmS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 139 KPTAPLAKGEPTEETGTSITFWADDTIFETTTWNFET---LSRRFQEMA-FLNKGLTITLrderpdhivNGEPAEVvyhy 214
Cdd:PLN03128 172 VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVEL---------NGKKLPV---- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 215 eGGLSDFVQ-HLNSKKEAAHVSVIdFEEHGEGISVEIamqwnnSYSESVY---TFANTINTAEGGTHEEgfraALTSIVN 290
Cdd:PLN03128 239 -KSFQDYVGlYLGPNSREDPLPRI-YEKVNDRWEVCV------SLSDGSFqqvSFVNSIATIKGGTHVD----YVADQIV 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 291 RYAREQKFLKEGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQKAcndHLRDWFER---NPGEAKD 367
Cdd:PLN03128 307 KHIQEKVKKKNKNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL-TTRPSSFGSKC---ELSEEFLKkveKCGVVEN 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 368 VINKSlqaSRARIAARQARDLTRRKSLLesgsGLPgKLADCQWS---DPEKCELFIVEGDSAGGSAKGG-----RDskFQ 439
Cdd:PLN03128 383 ILSWA---QFKQQKELKKKDGAKRQRLT----GIP-KLDDANDAggkKSKDCTLILTEGDSAKALAMSGlsvvgRD--HY 452
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 559767659 440 AILPIRGKILNVEKARIDKVLKNAEVQALITAMG---TGVHDEFDIAKLRYHKLILMADADVDGQHI 503
Cdd:PLN03128 453 GVFPLRGKLLNVREASHKQIMKNAEITNIKQILGlqfGKTYDEENTKSLRYGHLMIMTDQDHDGSHI 519
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
4-503 |
9.15e-39 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 153.28 E-value: 9.15e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 4 LEGLEAVRKRPGMYIGSTgER------------------------GLHHLVYEV----VDNSVDEALAGHADRIEVTLLA 55
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKVTIDE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 56 DNG-VRVVDNGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIRTD--GHHWR 132
Cdd:PTZ00108 92 ENGeISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSksGKKFK 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 133 QSYSH--SKPTAPLAKGEPTEETGTSITFWADDTIFETTTWNFETLS---RRFQEMAFLNKGLTITLRDERPdhivngep 207
Cdd:PTZ00108 172 MTWTDnmSKKSEPRITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERI-------- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 208 aevvyhyegGLSDFVQH--LNSKKEAAHVSVIDFEEHGE-GISVEIAMqwnnSYSESVYT---FANTINTAEGGTHeegF 281
Cdd:PTZ00108 244 ---------AIKSFKDYvdLYLPDGEEGKKPPYPFVYTSvNGRWEVVV----SLSDGQFQqvsFVNSICTTKGGTH---V 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 282 RAALTSIVNRYAREQKFLKEGKDDnLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQK-ACNDHLRDWFER 360
Cdd:PTZ00108 308 NYILDQLISKLQEKAKKKKKKGKE-IKPNQIKNHLWVFVNCLIVNPSFDSQTKETL-TTKPSKFGSTcELSEKLIKYVLK 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 361 NP----------GEAKDVINKSLQasrariaarqardlTRRKSLLesgSGLPgKLADCQWSDP---EKCELFIVEGDSAG 427
Cdd:PTZ00108 386 SPilenivewaqAKLAAELNKKMK--------------AGKKSRI---LGIP-KLDDANDAGGknsEECTLILTEGDSAK 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 428 GSAKGGRDS---KFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEF-DIAKLRYHKLILMADADVDGQHI 503
Cdd:PTZ00108 448 ALALAGLSVvgrDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHI 527
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
7-503 |
4.86e-27 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 117.27 E-value: 4.86e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 7 LEAVRKRPGMYIGSTGERGLHHLVYE---VVDNSV----------DEALAGHADR---------IEVTLLADNG-VRVVD 63
Cdd:PLN03237 38 LEHILLRPDTYIGSIEKHTQTLWVYEtdkMVQRSVtyvpglykifDEILVNAADNkqrdpkmdsLRVVIDVEQNlISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 64 NGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGGLHGVGVSVVNALSTALEVEIrTDGHH---WRQSYSHS-- 138
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIET-ADGKRqkkYKQVFSNNmg 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 139 KPTAPLAKGEPTEETGTSITFWADDTIFETTTWNFET---LSRRFQEMA-FLNKGLTITLrderpdhivNGEPAEVvyhy 214
Cdd:PLN03237 197 KKSEPVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVvalMKKRVVDIAgCLGKTVKVEL---------NGKRIPV---- 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 215 eGGLSDFVQ-HLNSKKEaahvsviDFEEHGEGISVEIAMQWN--NSYSESVY---TFANTINTAEGGTHEEgfraALTSI 288
Cdd:PLN03237 264 -KSFSDYVDlYLESANK-------SRPENLPRIYEKVNDRWEvcVSLSEGQFqqvSFVNSIATIKGGTHVD----YVTNQ 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 289 VNRYAREqKFLKEGKDDNLTGEDIREGLTAIISVKLADPQFEGQTKTKLgNTEAKSFVQKAcndhlrdwfernpgEAKDV 368
Cdd:PLN03237 332 IANHVME-AVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL-TLRQSSFGSKC--------------ELSED 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 369 INKSLQASRARIAARQARDLTRRKSLLESG-------SGLPgKLADCQWS---DPEKCELFIVEGDSA-----GGSAKGG 433
Cdd:PLN03237 396 FLKKVMKSGIVENLLSWADFKQSKELKKTDgakttrvTGIP-KLEDANEAggkNSEKCTLILTEGDSAkalavAGLSVVG 474
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 559767659 434 RDskFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGTGVHDEFDIAK-LRYHKLILMADADVDGQHI 503
Cdd:PLN03237 475 RN--YYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKsLRYGHLMIMTDQDHDGSHI 543
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
573-607 |
1.59e-22 |
|
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: 90.90 E-value: 1.59e-22
10 20 30
....*....|....*....|....*....|....*
gi 559767659 573 IQRFKGLGEMNAGQLWDTTMNPETRVLLQVTLDDA 607
Cdd:pfam00986 6 IQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDA 40
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
416-503 |
1.31e-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: 84.66 E-value: 1.31e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 416 CELFIVEGDSAGGSAKGGR---DSKFQAILPIRGKILNVEKARIDKVLKNAEVQALITAMGT--GVHDEFDIAKLRYHKL 490
Cdd:cd03365 1 CTLILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLqhGKSDYESTKSLRYGRL 80
|
90
....*....|...
gi 559767659 491 ILMADADVDGQHI 503
Cdd:cd03365 81 MIMTDQDHDGSHI 93
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
218-338 |
1.39e-19 |
|
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: 84.23 E-value: 1.39e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 218 LSDFVQHLNSKKEAAHVsvIDFEEHGEGISVEIAMQWNN---SYSESVYTFANTINTAEGGTHEEGFRAALTSIVNryar 294
Cdd:cd00329 1 LKDRLAEILGDKVADKL--IYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 559767659 295 eqkflkegkddnltGEDIREGLTAIISVKL--ADPQFE-GQTKTKLG 338
Cdd:cd00329 75 --------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
417-529 |
3.17e-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: 71.23 E-value: 3.17e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 417 ELFIVEGDSAGGSAKGGRDSKFQAILPIRGKILNVEKARIDKVLKnaevqalitamgtgvhdEFDIAKLRYHKLILMADA 496
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 559767659 497 DVDGQHINtllltLLFRFMRPLIEA--GHVYLSQP 529
Cdd:pfam01751 64 DREGEAIA-----LKLLELKELLENagGRVEFSEL 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
23-125 |
3.33e-15 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 71.91 E-value: 3.33e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 23 ERGLHHLVYEVVDNSVDEALAGhaDRIEVTLLADNG---VRVVDNGRGIPvgiveaegrpaVEVVLTVLHAGGKFDSKSY 99
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDhveITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRSR 69
|
90 100
....*....|....*....|....*.
gi 559767659 100 AVSGglHGVGVSVVNALSTALEVEIR 125
Cdd:smart00387 70 KIGG--TGLGLSIVKKLVELHGGEIS 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
23-165 |
8.47e-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: 8.47e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 23 ERGLHHLVYEVVDNSVDEAlaGHADRIEVTLLADNG--VRVVDNGRGIPVGIVEaegrpavevvltvlHAGGKFDSKSyA 100
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLP--------------RIFEPFSTAD-K 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 559767659 101 VSGGLHGVGVSVVNALSTALEVEIRTdghhwrqsyshskptaplakgEPTEETGTSITFWADDTI 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 |
6.42e-08 |
|
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: 51.96 E-value: 6.42e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 38 VDEALAGHAD---------RIEVTLLADNG-VRVVDNGRGIPVGIVEAEGRPAVEVVLTVLHAGGKFDSKSYAVSGGLHG 107
Cdd:cd16930 9 FDEILVNAADnkqrdksmtCIKVTIDPENNeISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNG 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 559767659 108 VGVSVVNALSTALEVEIRTD--GHHWRQSYSH--SKPTAPLAKGEPTEETGTSITFWAD 162
Cdd:cd16930 89 YGAKLCNIFSTEFTVETADSesKKKFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
26-125 |
1.48e-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: 44.13 E-value: 1.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 26 LHHLVYEVVDNSVDEALAGhaDRIEVTLLADNG---VRVVDNGRGIPVGIVEaegrpavevvltvlHAGGKFDSKSYAVS 102
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE--------------RIFERFYRGDKSRE 64
|
90 100
....*....|....*....|...
gi 559767659 103 GGLHGVGVSVVNALSTALEVEIR 125
Cdd:cd00075 65 GGGTGLGLAIVRRIVEAHGGRIT 87
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
32-69 |
1.56e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 41.18 E-value: 1.56e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 559767659 32 EVVDNSVDealAGhADRIEVTLlADNGV---RVVDNGRGIP 69
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEI-EEGGKsliRVTDNGCGMS 65
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
416-503 |
1.62e-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: 1.62e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 559767659 416 CELFIVEGDSAGGSAKGGRdSKFQAILPIRGKILNVEKARIDKVLKnaevqalitamgtgvhdefdiaklRYHKLILMAD 495
Cdd:cd00188 1 KKLIIVEGPSDALALAQAG-GYGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
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....*...
gi 559767659 496 ADVDGQHI 503
Cdd:cd00188 56 ADREGEAI 63
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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 |
2.95e-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: 38.96 E-value: 2.95e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767659 30 VYEVVDNSVDealAGhADRIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEI--EEGglklIRVTDNGSGIS 55
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| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
30-69 |
7.16e-03 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 39.43 E-value: 7.16e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 559767659 30 VYEVVDNSVDealAGhADRIEVTLlaDNG----VRVVDNGRGIP 69
Cdd:PRK00095 27 VKELVENALD---AG-ATRIDIEI--EEGglklIRVRDNGCGIS 64
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