|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
26-662 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1189.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 26 EQEYDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGI 105
Cdd:PRK05644 5 AQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 106 QPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPTEE 185
Cdd:PRK05644 85 HPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 186 KGTSVAFKADAAIFEeTTEYDYDTLLRRLREQAFLNAGVYIVLRDQRGTEPVEEHLHYEGGIRSFVEHIHKSKgvEPIHD 265
Cdd:PRK05644 165 TGTTVTFKPDPEIFE-TTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNK--EPLHE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 266 EIIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKD-DEKFSGEDVLEG 344
Cdd:PRK05644 242 EPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEkDDNLTGEDVREG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 345 LTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVARRKSAL 424
Cdd:PRK05644 322 LTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSAL 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 425 ETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGI 504
Cdd:PRK05644 402 ESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 505 GDEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQvRYAFSDEERDQYIREL 584
Cdd:PRK05644 482 GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAEL 560
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 493928418 585 CPDGSGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIEQNAKYVQNLDI 662
Cdd:PRK05644 561 KLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
25-662 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1167.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 25 DEQEYDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVG 104
Cdd:COG0187 2 KKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 105 IQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPTE 184
Cdd:COG0187 82 IHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 185 EKGTSVAFKADAAIFEeTTEYDYDTLLRRLREQAFLNAGVYIVLRDQRGTEPVEEHLHYEGGIRSFVEHIHKSKgvEPIH 264
Cdd:COG0187 162 RTGTTVRFKPDPEIFE-TTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKDFVEYLNEDK--EPLH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 265 DEIIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKD-DEKFSGEDVLE 343
Cdd:COG0187 239 PEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEkDKNLTGDDVRE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 344 GLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVARRKSA 423
Cdd:COG0187 319 GLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 424 LETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTG 503
Cdd:COG0187 399 LESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 504 IGDEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQYIRE 583
Cdd:COG0187 479 IGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKE 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493928418 584 LcpDGSGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIEQNAKYVQNLDI 662
Cdd:COG0187 559 L--KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
24-662 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 996.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 24 PDEQEYDGSQIQVLEGLEAVRKRPGMYIGSTG-PRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIP 102
Cdd:PRK14939 2 MMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 103 VGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGP 182
Cdd:PRK14939 82 TDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 183 TEEKGTSVAFKADAAIFeETTEYDYDTLLRRLREQAFLNAGVYIVLRDQRgtEPVEEHLHYEGGIRSFVEHIHKSKgvEP 262
Cdd:PRK14939 162 TDKTGTEVRFWPSPEIF-ENTEFDYDILAKRLRELAFLNSGVRIRLKDER--DGKEEEFHYEGGIKAFVEYLNRNK--TP 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 263 IHDEIIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLK-DDEKFSGEDV 341
Cdd:PRK14939 237 LHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKkAKVSLTGDDA 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 342 LEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVARRK 421
Cdd:PRK14939 317 REGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRK 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 422 SALETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALG 501
Cdd:PRK14939 397 GALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALG 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 502 TGIG-DEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQY 580
Cdd:PRK14939 477 CGIGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDY 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 --------------------------------------------------------------------------------
Cdd:PRK14939 557 lielalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadflts 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 581 ------------IRELCPDGS------------------------GK--ADVQRYKGLGEMDPEQLWETTMDPRNRTMLR 622
Cdd:PRK14939 637 aeyrrlvelaekLRGLIEEGAylergerkqpvssfeealdwllaeARkgLSIQRYKGLGEMNPEQLWETTMDPENRRLLQ 716
|
730 740 750 760
....*....|....*....|....*....|....*....|
gi 493928418 623 VEMADAIRADEIFTVLMGDKVAPRKDFIEQNAKYVQNLDI 662
Cdd:PRK14939 717 VTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
29-662 |
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: 996.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 29 YDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQPK 108
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 109 LGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPTEEKGT 188
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 189 SVAFKADAAIFEeTTEYDYDTLLRRLREQAFLNAGVYIVLRDQRGTEPVEEHLHYEGGIRSFVEHIHKSKgvEPIHDEII 268
Cdd:TIGR01059 161 TVRFWPDPEIFE-TTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKVTFHYEGGIKSFVKYLNRNK--EPLHEEII 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 269 YLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKD-DEKFSGEDVLEGLTA 347
Cdd:TIGR01059 238 YIKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKEsKPNLTGEDIREGLTA 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 348 IVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVARRKSALETA 427
Cdd:TIGR01059 318 VISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSG 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 428 SLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDE 507
Cdd:TIGR01059 398 GLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 508 FDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQYIREL--- 584
Cdd:TIGR01059 478 FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKDLVGEALedl 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 585 -------------------CPDGSGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAP 645
Cdd:TIGR01059 558 kalyiysdkekeeaktqipVHLGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEP 637
|
650
....*....|....*..
gi 493928418 646 RKDFIEQNAKYVQNLDI 662
Cdd:TIGR01059 638 RREFIEANALDVKNLDV 654
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
24-657 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 917.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 24 PDEQEYDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPV 103
Cdd:PRK05559 3 MMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 104 GIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPT 183
Cdd:PRK05559 83 GIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 184 EEK--GTSVAFKADAAIFEeTTEYDYDTLLRRLREQAFLNAGVYIVLRDqrgtEPVEEHLHYEGGIRSFVEHihKSKGVE 261
Cdd:PRK05559 163 GKRktGTRVRFWPDPKIFD-SPKFSPERLKERLRSKAFLLPGLTITLND----ERERQTFHYENGLKDYLAE--LNEGKE 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 262 PIHDE-IIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKDDEKFSGED 340
Cdd:PRK05559 236 TLPEEfVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKKLEGED 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 341 VLEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVarr 420
Cdd:PRK05559 316 VREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVKR--- 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 421 KSALETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITAL 500
Cdd:PRK05559 393 KKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAI 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 501 GTGIGDEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQY 580
Cdd:PRK05559 473 GIGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEEL 552
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 493928418 581 IRELCPDGsGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIEQNAKYV 657
Cdd:PRK05559 553 LKKLGKKG-GKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
58-655 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 852.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 58 GLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGG 137
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 138 LHGVGASVVNALSEWLEVEVCDGSARYYQRFER-GVAVEPLKNTGPTEEKGTSVAFKADAAIFEETTEYDYDTLLRRLRE 216
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 217 QAFLNAGVYIVLRDQRGTEPVEehLHYEGGIRSFVEHIHKSKgvEPIHDEIIYLAARDGDNTAEVAMQYNDSYTDLILSF 296
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEKT--FLFEGGIKDYVELLNKNK--ELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSF 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 297 ANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKDDeKFSGEDVLEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVS 376
Cdd:smart00433 237 VNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK-NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 377 SLVYEKLTTYYEENPAVAKAIIEKsINASRAREAARRARDVARRKSALETASLPGKLADCSQRGRDGTEIYIVEGDSAGG 456
Cdd:smart00433 316 KIVSECLLSFLEENPVEASKIVEK-VLLAAKARAAAKKARELTRKKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGG 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 457 SAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEFDIEKLRYGKVIIMADADVDGSHIRTLLL 536
Cdd:smart00433 395 SAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLL 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 537 TFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQvRYAFSDEERDQYIRELCPDGSGKA--DVQRYKGLGEMDPEQLWETTMD 614
Cdd:smart00433 475 TFFYRYMPPLIEAGFVYIAIPPLYKVTKGKK-KYVYSFYSLDEYEKWLEKTEGNKSkyEIQRYKGLGEMNADQLWETTMD 553
|
570 580 590 600
....*....|....*....|....*....|....*....|.
gi 493928418 615 PRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIEQNAK 655
Cdd:smart00433 554 PERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
27-656 |
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: 705.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 27 QEYDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQ 106
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 107 PKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFER-GVAVEPLKNTGPTEE 185
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 186 KGTSVAFKADAAIFeETTEYDYDTLLRRLREQAFLNAGVYIVLRDQRGTEPVEehLHYEGGIRSFVEHIHKSKgvePIHD 265
Cdd:TIGR01058 163 TGTLVHFHPDPTIF-KTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTV--FFYENGLVDFVDYINETK---ETLS 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 266 EIIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKD-DEKFSGEDVLEG 344
Cdd:TIGR01058 237 QVTYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEkDKNLEGSDIREG 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 345 LTAIVSVKLTDA--QFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRA--RDVARR 420
Cdd:TIGR01058 317 LSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAreEKKSGK 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 421 KSALETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITAL 500
Cdd:TIGR01058 397 KPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCI 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 501 GTGIGDEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSR--GKQVRYAFSDEERD 578
Cdd:TIGR01058 477 GTGIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELE 556
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 493928418 579 QYIRELcpdgsGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIEQNAKY 656
Cdd:TIGR01058 557 SVKKKL-----KNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINF 629
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
13-654 |
5.41e-180 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 534.85 E-value: 5.41e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 13 GDQNELNPGIVPDEQEYDGSQIQVLEGLEAVRKRPGMYIGSTGPRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIV 92
Cdd:PTZ00109 84 VEQQKERVPQLQRCSEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSV 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 93 KVSDNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKF---------GGSG-------------------------------Y 132
Cdd:PTZ00109 164 EISDNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFqdtfpknsrSDKSedkndtksskkgksshvkgpkeakekessqmY 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 133 KVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTG-PTEEKGTSVAFKADAA-IFEETTE------ 204
Cdd:PTZ00109 244 EYSSGLHGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFScPLKKRGTTIHFLPDYKhIFKTHHQhtetee 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 205 -------YDYDTLLRRLREQAFLNAGVYIVLRDQRGT----EPVEEHLHYEGGIRSFVEHIHKSKgvEPIHDEIIYLAAR 273
Cdd:PTZ00109 324 eegckngFNLDLIKNRIHELSYLNPGLTFYLVDERIAnennFYPYETIKHEGGTREFLEELIKDK--TPLYKDINIISIR 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 274 DGDNTAEVAMQYN---DSYTDLILSFANNIHTTdGGTHESGFKTALTRTMNDYAHKYKLLKDDEK-FSGEDVLEGLTAIV 349
Cdd:PTZ00109 402 GVIKNVNVEVSLSwslESYTALIKSFANNVSTT-AGTHIDGFKYAITRCVNGNIKKNGYFKGNFVnIPGEFIREGMTAII 480
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 350 SVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINASRAREAARRARDVARRKSA-LETAS 428
Cdd:PTZ00109 481 SVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNqYYSTI 560
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 429 LPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLD-KVYGNDKLMPVITALGTGIG-- 505
Cdd:PTZ00109 561 LPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNpv 640
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 506 ---------------DEF---------------DIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIA 555
Cdd:PTZ00109 641 twrqydlshgtkaskDESvqnnnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVA 720
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 556 QPPLFKVS--RGKQVR----------YAFSDEERDQYIRELCPDGSGKAD------------------------------ 593
Cdd:PTZ00109 721 CPPLYRITnnRMKQFNvstknskkyiYTWSDEELNVLIKLLNKDYSSKETtrsveekgnapdldneyedekldnknmren 800
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 594 --------------------------------------VQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIF 635
Cdd:PTZ00109 801 nvdevelktelgtnvadteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELI 880
|
810
....*....|....*....
gi 493928418 636 TVLMGDKVAPRKDFIEQNA 654
Cdd:PTZ00109 881 FLLMGEDVQSRKQFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
27-652 |
1.55e-171 |
|
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: 503.68 E-value: 1.55e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 27 QEYDGSQIQVLEGLEAVRKRPGMYIGSTGPrglHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQ 106
Cdd:TIGR01055 2 TNYSAKDIEVLDGLEPVRKRPGMYTDTTRP---NHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIH 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 107 PKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPTEEK 186
Cdd:TIGR01055 79 PKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 187 --GTSVAFKADAAIFEEtTEYDYDTLLRRLREQAFLNAGVYIVLRDQrgTEPVEEHLHYEGGIRSFVehIHKSKGVEPIH 264
Cdd:TIGR01055 159 ltGTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKALWNYPDGLKDYL--SEAVNGDNTLP 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 265 DEiIYLAARDGDNTA-EVAMQYNDSYTDLIL-SFANNIHTTDGGTHESGFKTALTRTMNDYAHKYKLLKDDEKFSGEDVL 342
Cdd:TIGR01055 234 PK-PFSGNFEGDDEAvEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGVKLTAEDIW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 343 EGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSINasrAREAARRARDVARRKS 422
Cdd:TIGR01055 313 DRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAIS---SAQRRKRAAKKVVRKK 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 423 ALETASLPGKLADCSQRGRDGTEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGT 502
Cdd:TIGR01055 390 LTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGI 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 503 GiGDEFDIEKLRYGKVIIMADADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQYIR 582
Cdd:TIGR01055 470 D-PDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLY 548
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493928418 583 ELcPDGSGKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRV--EMADAIRADEIFTVLMGDKVAP-RKDFIEQ 652
Cdd:TIGR01055 549 KL-KKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLtlDDVQDQRVDKIMDMLLAKKRSEdRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
59-238 |
1.68e-97 |
|
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: 296.76 E-value: 1.68e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 59 LHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGL 138
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 139 HGVGASVVNALSEWLEVEVCDGSARYYQRFERGVAVEPLKNTGPTEEKGTSVAFKADAAIFEEtTEYDYDTLLRRLREQA 218
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEK-TEFDFDTLKRRLRELA 159
|
170 180
....*....|....*....|
gi 493928418 219 FLNAGVYIVLRDQRGTEPVE 238
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEEV 179
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
444-557 |
1.03e-77 |
|
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: 242.95 E-value: 1.03e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 444 TEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEFDIEKLRYGKVIIMAD 523
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 493928418 524 ADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQP 557
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
245-403 |
9.17e-75 |
|
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: 237.46 E-value: 9.17e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 245 GGIRSFVEHIHKSKgvEPIHDEIIYLAARDGDNTAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDYA 324
Cdd:cd00822 1 GGLKDFVEELNKDK--EPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 325 HKYKLLKD-DEKFSGEDVLEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSIN 403
Cdd:cd00822 79 KKNNLLKKkDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
444-557 |
2.28e-67 |
|
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: 215.83 E-value: 2.28e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 444 TEIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIG-DEFDIEKLRYGKVIIMA 522
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 493928418 523 DADVDGSHIRTLLLTFFFRFMRPLIEHGHVCIAQP 557
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
246-403 |
9.16e-66 |
|
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: 213.63 E-value: 9.16e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 246 GIRSFVEHIhkSKGVEPIHDEIIYLAARDGDN--TAEVAMQYNDSYTDLILSFANNIHTTDGGTHESGFKTALTRTMNDY 323
Cdd:pfam00204 1 GLKDFVEEL--NKDKKPLHKEIIYFEGESPDNriEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEY 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 324 AHKYKLLKD-DEKFSGEDVLEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYYEENPAVAKAIIEKSI 402
Cdd:pfam00204 79 AKKKGLLKKkDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
.
gi 493928418 403 N 403
Cdd:pfam00204 159 Q 159
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
32-652 |
3.08e-56 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 201.14 E-value: 3.08e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 32 SQIQVLEGLEAVRKRPGMYIGSTGPR-----------------GLHHLVYEIVDNSIDEALAG---HCTKIEVDLlPGNI 91
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAYEaherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 92 VKVSDNGRGIP---VGIQPKLGIPAVTVVFTVLHAGGKFGGSGyKVSGGLHGVGASVVNALSEWLEVEVCDGSARYYQRF 168
Cdd:PHA02569 81 VTVSDNGRGIPqamVTTPEGEEIPGPVAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNC 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 169 ERGvAVEPLKNTGPTEEKGTSVAFKADAAIFEETT--EYDYDTLLRRLREQAflnagvyIVLRDQRGTEPVEEHlhyEGG 246
Cdd:PHA02569 160 SNG-AENISWSTKPGKGKGTSVTFIPDFSHFEVNGldQQYLDIILDRLQTLA-------VVFPDIKFTFNGKKV---SGK 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 247 IRSFVehihKSKGVEPIHDEiiylaardGDNTAEVAMQYNDSYTDLilSFANNIHTTDGGTHESGFktaltrtMND-YAH 325
Cdd:PHA02569 229 FKKYA----KQFGDDTIVQE--------NDNVSIALAPSPDGFRQL--SFVNGLHTKNGGHHVDCV-------MDDiCEE 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 326 KYKLLKDDEKF--SGEDVLEGLTAIVSVK-LTDAQFEGQTKARLGNTQmrAMVSS---LVYEKLTTYYEENPAVAKAIIE 399
Cdd:PHA02569 288 LIPMIKKKHKIevTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPF--GEIRNhidLDYKKIAKQILKTEAIIMPIIE 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 400 KSInasRAREAARRARDVARRKSALET-------ASLPGKLADcsqrgrdgTEIYIVEGDSAGGSAKMGRDRRFQAILPL 472
Cdd:PHA02569 366 AAL---ARKLAAEKAAETKAAKKAKKAkvakhikANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELHGGYPL 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 473 WGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDefDIEKLRYGKVIIMADADVDG-SHIRTLLLTFFFRFMRpLIEHGH 551
Cdd:PHA02569 435 RGKVLNTWGMSYADILKNKELFDICAITGLVLGE--KAENMNYKNIAIMTDADVDGkGSIYPLLLAFFSRWPE-LFEQGR 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 552 VCIAQPPLFKVSRGKQVRYAFSDEERDQYirelcPDGSGKADVQRYKGLGEMDPEQLwettmdprnRTMLRVEMADAIRA 631
Cdd:PHA02569 512 IRFVKTPVIIAQVGKETKWFYSLDEFEKA-----KDSLKKWSIRYIKGLGSLRKSEY---------RRVINNPVYDVVVL 577
|
650 660
....*....|....*....|....*
gi 493928418 632 D----EIFTVLMGDKVAPRKDFIEQ 652
Cdd:PHA02569 578 PddwkELFEMLFGDDADLRKDWMSQ 602
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
32-662 |
9.04e-43 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 166.38 E-value: 9.04e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 32 SQIQVLEGLEAVRKRPGMYIGSTGPR-----------------------GLHHLVYEI----VDNSIDEALAGHCTKIEV 84
Cdd:PTZ00108 8 ERYQKKTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 85 DLLPG-NIVKVSDNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGSAR 163
Cdd:PTZ00108 88 TIDEEnGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVDSKSG 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 164 --YYQRFERGVavepLKNTGP--TEEKG----TSVAFKADAAIFEeTTEYDYDT---LLRRLREQAFLNAGVYIVLRDQR 232
Cdd:PTZ00108 168 kkFKMTWTDNM----SKKSEPriTSYDGkkdyTKVTFYPDYAKFG-MTEFDDDMlrlLKKRVYDLAGCFGKLKVYLNGER 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 233 GtepveehlhyegGIRSFVEHIhkskGVEPIHDEIIYLAARDGDNTA-----EVAMQYNDSyTDLILSFANNIHTTDGGT 307
Cdd:PTZ00108 243 I------------AIKSFKDYV----DLYLPDGEEGKKPPYPFVYTSvngrwEVVVSLSDG-QFQQVSFVNSICTTKGGT 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 308 HESGFKTALTRTMNDYAHKYKllKDDEKFSGEDVLEGLTAIVSVKLTDAQFEGQTKARLGNTQMRAMVSSLVYEKLTTYY 387
Cdd:PTZ00108 306 HVNYILDQLISKLQEKAKKKK--KKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYV 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 388 EENPavakaIIEKSINASRAREAARRARDVARRKSALETaSLPgKLADCSQRGRDGTEI---YIVEGDSAGGSAKMG--- 461
Cdd:PTZ00108 384 LKSP-----ILENIVEWAQAKLAAELNKKMKAGKKSRIL-GIP-KLDDANDAGGKNSEEctlILTEGDSAKALALAGlsv 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 462 RDRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEF-DIEKLRYGKVIIMADADVDGSHIRTLLLTFFF 540
Cdd:PTZ00108 457 VGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIH 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 541 RFMRPLIEH-GHVCIAQPPLFKVS-RGKQVRYAFSDEERDQYIRELcpdGSGKADVQRYKGLGEMDPEQLWE--TTMDpR 616
Cdd:PTZ00108 537 HFWPSLLKNpGFLKEFITPIVKATkKGNQVISFFTIPDFEKWKQTV---GLKGWKIKYYKGLGTSTDKEGKEyfSNID-K 612
|
650 660 670 680
....*....|....*....|....*....|....*....|....*..
gi 493928418 617 NRTMLR-VEMADAIRADEIFTvlmGDKVAPRKDFIeqnAKYVQNLDI 662
Cdd:PTZ00108 613 HRIRFVyVDDSDDDSIDLAFS---KKRVEDRKEWI---TNYKGGTYV 653
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
40-651 |
2.32e-41 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 162.19 E-value: 2.32e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 40 LEAVRKRPGMYIGSTGPR---------------------GLHHLVYEIVDNSIDEALAG-HCTKIEVDLLPG-NIVKVSD 96
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHtqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEqNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 97 NGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGS--ARYYQRFERGVAV 174
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETADGNrgKKYKQVFTNNMSV 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 175 --EPLKNTGPTEEKGTSVAFKADAAIF--EETTEYDYDTLLRRLREQA-FLNAGVYIVLRDQRGTepveehlhyeggIRS 249
Cdd:PLN03128 173 ksEPKITSCKASENWTKITFKPDLAKFnmTRLDEDVVALMSKRVYDIAgCLGKKLKVELNGKKLP------------VKS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 250 FVEHIHKSKGVEPIHDEI--IYLAARDGdntAEVAMQYNDSYTDLIlSFANNIHTTDGGTHESGFKTALTRTMNDYAHKY 327
Cdd:PLN03128 241 FQDYVGLYLGPNSREDPLprIYEKVNDR---WEVCVSLSDGSFQQV-SFVNSIATIKGGTHVDYVADQIVKHIQEKVKKK 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 328 KllKDDEKFSGEDVLEGLTAIVSVKLTDAQFEGQTKarlgntqmramvsslvyEKLTT-------YYEENPAVAK----- 395
Cdd:PLN03128 317 N--KNATHVKPFQIKNHLWVFVNCLIENPTFDSQTK-----------------ETLTTrpssfgsKCELSEEFLKkvekc 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 396 AIIEKSINASRAREAARRARDVARRKSALetASLPgKLADC----SQRGRDGTEIyIVEGDSA-----GGSAKMGRDrrF 466
Cdd:PLN03128 378 GVVENILSWAQFKQQKELKKKDGAKRQRL--TGIP-KLDDAndagGKKSKDCTLI-LTEGDSAkalamSGLSVVGRD--H 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 467 QAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEFDIE---KLRYGKVIIMADADVDGSHIRTLLLTFFFRFM 543
Cdd:PLN03128 452 YGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEEntkSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFW 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 544 RPLIE-HGHVCIAQPPLFKVSRGKQVRYAFSDEERDQYIRELCPDGSGkADVQRYKGLGEMDPEQ--------------- 607
Cdd:PLN03128 532 PSLLKiPGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEGETKG-WTIKYYKGLGTSTSEEakeyfsnldihkkef 610
|
650 660 670 680
....*....|....*....|....*....|....*....|....
gi 493928418 608 LWETTMDPRnrtmlRVEMAdairadeiFTvlmGDKVAPRKDFIE 651
Cdd:PLN03128 611 LWQSDEDGD-----LIDMA--------FS---KKRVEDRKIWLN 638
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
590-651 |
2.09e-38 |
|
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: 135.97 E-value: 2.09e-38
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493928418 590 GKADVQRYKGLGEMDPEQLWETTMDPRNRTMLRVEMADAIRADEIFTVLMGDKVAPRKDFIE 651
Cdd:pfam00986 2 KKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
40-601 |
2.19e-27 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 118.81 E-value: 2.19e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 40 LEAVRKRPGMYIGS---------------------TGPRGLHHLVYEIVDNSIDEAL---AGHCTKIEVDLlPGNIVKVS 95
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQrdpKMDSLRVVIDV-EQNLISVY 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 96 DNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVSGGLHGVGASVVNALSEWLEVEVCDGS--ARYYQRFER--G 171
Cdd:PLN03237 117 NNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETADGKrqKKYKQVFSNnmG 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 172 VAVEPLKNTGPTEEKGTSVAFKADAAIFEET-TEYDYDTLLR-RLREQA-FLNAGVYIVLRDQRgtEPVeehlhyeggiR 248
Cdd:PLN03237 197 KKSEPVITKCKKSENWTKVTFKPDLAKFNMThLEDDVVALMKkRVVDIAgCLGKTVKVELNGKR--IPV----------K 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 249 SFVEHIHkskgvepihdeiIYLAARD---GDNTAEVAMQYNDSYTDLI---------LSFANNIHTTDGGTHESGFKTAL 316
Cdd:PLN03237 265 SFSDYVD------------LYLESANksrPENLPRIYEKVNDRWEVCVslsegqfqqVSFVNSIATIKGGTHVDYVTNQI 332
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 317 T-RTMNDYAHKYKllkdDEKFSGEDVLEGLTAIVSVKLTDAQFEGQTKARLGNTQ-------------MRAMVSSLVYEK 382
Cdd:PLN03237 333 AnHVMEAVNKKNK----NANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLTLRQssfgskcelsedfLKKVMKSGIVEN 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 383 LTTY--YEENPAVAKAIIEKsinasrareaarrardvarrksaleTASLPG--KLADCSQRGRDGTE---IYIVEGDSA- 454
Cdd:PLN03237 409 LLSWadFKQSKELKKTDGAK-------------------------TTRVTGipKLEDANEAGGKNSEkctLILTEGDSAk 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 455 ----GGSAKMGRDrrFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEFD-IEKLRYGKVIIMADADVDGS 529
Cdd:PLN03237 464 alavAGLSVVGRN--YYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYEsVKSLRYGHLMIMTDQDHDGS 541
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493928418 530 HIRTLLLTFFFRFMRPL--IEHGHVCIAQPPLFKVSRGKQVRYAFSDEERDQYIRELCPDGSGkADVQRYKGLG 601
Cdd:PLN03237 542 HIKGLLINFIHSFWPSLlkVPSFLVEFITPIVKATRRGKKVLSFYSMPEYEEWKESLGGNATG-WSIKYYKGLG 614
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
448-549 |
1.01e-20 |
|
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: 88.13 E-value: 1.01e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 448 IVEGDSAGGSAKMGR---DRRFQAILPLWGKMLNVEKARLDKVYGNDKLMPVITALGTGIGDEF--DIEKLRYGKVIIMA 522
Cdd:cd03365 5 LTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMT 84
|
90 100
....*....|....*....|....*..
gi 493928418 523 DADVDGSHIRTLLLTFFFRFMRPLIEH 549
Cdd:cd03365 85 DQDHDGSHIKGLLINFIHSFWPSLLKI 111
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
247-367 |
2.62e-17 |
|
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: 77.69 E-value: 2.62e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 247 IRSFVEHIHKSKgvepIHDEIIYLAARDGDNTAEVAMQYND---SYTDLILSFANNIHTTDGGTHESGFKTALTRTMNdy 323
Cdd:cd00329 1 LKDRLAEILGDK----VADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN-- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 493928418 324 ahkykllkddekfsGEDVLEGLTAIVSVKLTDA--QFE-GQTKARLG 367
Cdd:cd00329 75 --------------GDDVRRYPVAVLSLKIPPSlvDVNvHPTKEEVR 107
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
445-539 |
7.26e-16 |
|
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: 73.16 E-value: 7.26e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 445 EIYIVEGDSAGGSAKMGRDRRFQAILPLWGKMLNVEKARLDKVYGndklmpvitalgtgigdEFDIEKLRYGKVIIMADA 524
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
90
....*....|....*
gi 493928418 525 DVDGSHIRTLLLTFF 539
Cdd:pfam01751 64 DREGEAIALKLLELK 78
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
56-175 |
7.96e-15 |
|
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: 70.86 E-value: 7.96e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 56 PRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNIVKVSDNGRGIPVGIQPKLgipavtvvftvlhaGGKFgGSGYKVS 135
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHAAKAGEITVTLSEGGELTLTVEDNGIGIPPEDLPRI--------------FEPF-STADKRG 67
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 493928418 136 GGLHGVGASVVNALSEWLevevcDGSARYYQRFERGVAVE 175
Cdd:pfam02518 68 GGGTGLGLSIVRKLVELL-----GGTITVESEPGGGTTVT 102
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
56-157 |
1.31e-14 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 70.37 E-value: 1.31e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 56 PRGLHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNI-VKVSDNGRGIPVGIQPKLgipavtvvftvLHAGGKFGGSGYKV 134
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGDHVeITVEDNGPGIPPEDLEKI-----------FEPFFRTDKRSRKI 71
|
90 100
....*....|....*....|...
gi 493928418 135 SGglHGVGASVVNALSEWLEVEV 157
Cdd:smart00387 72 GG--TGLGLSIVKKLVELHGGEI 92
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
58-195 |
5.90e-10 |
|
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.
Pssm-ID: 340407 [Multi-domain] Cd Length: 147 Bit Score: 58.12 E-value: 5.90e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 58 GLHHLVYEIVDNSID-EALAGHCTKIEVDLLP-GNIVKVSDNGRGIPVGIQPKLGIPAVTVVFTVLHAGGKFGGSGYKVS 135
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPeNNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493928418 136 GGLHGVGASVVNALSEWLEVEVCDGSAR--YYQRFER--GVAVEPLKNTGPTEEKGTSVAFKAD 195
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVETADSESKkkFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| top6b |
TIGR01052 |
DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type ... |
41-237 |
5.10e-06 |
|
DNA topoisomerase VI, B subunit; This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273417 [Multi-domain] Cd Length: 488 Bit Score: 49.43 E-value: 5.10e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 41 EAVRKRPGMyIGSTGP-RGLHHLVYEIVDNSIDEA-LAGHCTKIEVDLL----PGNIVKVSDNGRGIPVGIQPKlgipav 114
Cdd:TIGR01052 11 EFFRKNKHM-LGYSGKiRSLTTVIHELVTNSLDACeEAGILPDIKVEIEkigkDHYKVTVEDNGPGIPEEYIPK------ 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 115 tvVFTVLHAGGKFggSGYKVSGGLHGVGASVVNALSEWLE---VEVCDGSARYYQRFERGVAVEPLKNTGPTEEK----- 186
Cdd:TIGR01052 84 --VFGKMLAGSKF--HRIIQSRGQQGIGISGAVLYSQMTTgkpVKVISSTGGEIYVYKMKLKIDVQKNEGEIVEKgewnk 159
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 493928418 187 ----GTSV--AFKADAAIFEETTEYDYdtllrrLREQAFLNAGVYIVLRDQRGTEPV 237
Cdd:TIGR01052 160 pgwrGTRIelEFKGVSYRRSKQGVYEY------LRRTAVANPHAKIVLVDPDGEIYV 210
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
59-151 |
3.72e-05 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 42.98 E-value: 3.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 59 LHHLVYEIVDNSIDEALAGhcTKIEVDLLPGN---IVKVSDNGRGIPVGIQPKLGIPavtvvftvlhaggkFGGSGYKVS 135
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGdgvVLEVEDNGPGIPEEDLERIFER--------------FYRGDKSRE 64
|
90
....*....|....*.
gi 493928418 136 GGLHGVGASVVNALSE 151
Cdd:cd00075 65 GGGTGLGLAIVRRIVE 80
|
|
| HATPase_TopVIB-like |
cd16933 |
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ... |
41-146 |
2.55e-04 |
|
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: 42.72 E-value: 2.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 41 EAVRKRPGMyIGSTGP-RGLHHLVYEIVDNSIDEA-LAGHCTKIEVDLLPGN----IVKVSDNGRGIPVGIQPKlgipav 114
Cdd:cd16933 2 EFFRKNKEM-LGFDNPiRSLYTTVRELVENSLDATeEAGILPDIKVEIEEIGkdhyKVIVEDNGPGIPEEQIPK------ 74
|
90 100 110
....*....|....*....|....*....|..
gi 493928418 115 tvVFTVLHAGGKFGGsgyKVSGGLHGVGASVV 146
Cdd:cd16933 75 --VFGKVLYGSKYHN---KQSRGQQGLGISAA 101
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
63-102 |
2.84e-04 |
|
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: 42.42 E-value: 2.84e-04
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 493928418 63 VYEIVDNSIDealAGhCTKIEVDLLPGNI--VKVSDNGRGIP 102
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEIEEGGLklIRVTDNGSGIS 55
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
63-102 |
2.08e-03 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 41.36 E-value: 2.08e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 493928418 63 VYEIVDNSIDealAGhCTKIEVDLLPG--NIVKVSDNGRGIP 102
Cdd:PRK00095 27 VKELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGIS 64
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
445-542 |
4.47e-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: 36.64 E-value: 4.47e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 445 EIYIVEGDSAGGSAKMGRDRRfQAILPLWGKMLNVEKARLDKVYGNDKlmpvitalgtgigdefdieklrygKVIIMADA 524
Cdd:cd00188 2 KLIIVEGPSDALALAQAGGYG-GAVVALGGHALNKTRELLKRLLGEAK------------------------EVIIATDA 56
|
90
....*....|....*...
gi 493928418 525 DVDGSHIRTLLLTFFFRF 542
Cdd:cd00188 57 DREGEAIALRLLELLKSL 74
|
|
| COG1389 |
COG1389 |
DNA topoisomerase VI, subunit B [Replication, recombination and repair]; |
56-144 |
7.24e-03 |
|
DNA topoisomerase VI, subunit B [Replication, recombination and repair];
Pssm-ID: 440999 [Multi-domain] Cd Length: 530 Bit Score: 39.43 E-value: 7.24e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493928418 56 PRGLHHLVYEIVDNSIDEALAGHC---TKIEVDLLPGN---IVKVSDNGRGIPVGIQPKlgipavtvVFTVLHAGGKFGg 129
Cdd:COG1389 33 ARALYTTVKEAVDNSLDACEEAGIlpdIKVSIERVDGKdiyRVTVEDNGPGIPPEQIPK--------VFGKLLYGSKFH- 103
|
90
....*....|....*
gi 493928418 130 sGYKVSGGLHGVGAS 144
Cdd:COG1389 104 -VLRQSRGQQGIGIS 117
|
|
| KdpD |
COG2205 |
K+-sensing histidine kinase KdpD [Signal transduction mechanisms]; |
59-131 |
8.58e-03 |
|
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
Pssm-ID: 441807 [Multi-domain] Cd Length: 239 Bit Score: 38.35 E-value: 8.58e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493928418 59 LHHLVYEIVDNSIDEALAGHCTKIEVDLLPGNI-VKVSDNGRGIPVGIQPKLGIPavtvvFTVLHAGGKFGGSG 131
Cdd:COG2205 133 LEQVLANLLDNAIKYSPPGGTITISARREGDGVrISVSDNGPGIPEEELERIFER-----FYRGDNSRGEGGTG 201
|
|
| |
