|
Name |
Accession |
Description |
Interval |
E-value |
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
13-652 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 946.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 13 AASTNYTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIP 92
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADG-SVTVEDNGRGIP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 93 VDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSEVVKGEP 172
Cdd:COG0187 80 VDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 173 ARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGT--QVEYRHDGGVADFLNEIHRRRNdvKV 250
Cdd:COG0187 160 TDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEEpkEETFHYEGGIKDFVEYLNEDKE--PL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 251 APTVFVLERDdpREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLK-KGMEIKGED 329
Cdd:COG0187 238 HPEVIYFEGE--KDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKeKDKNLTGDD 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 330 IREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQARR 409
Cdd:COG0187 316 VREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRR 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 410 KSpVVGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSA 489
Cdd:COG0187 396 KS-ALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITA 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 490 LGCGMDDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDTYWAADEAAKAA 569
Cdd:COG0187 475 LGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 570 ILAKLPKNAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVpdEDRHYVDSTITDLMGKDPEPRFRFIMEEAYNARD 649
Cdd:COG0187 555 LLKELKGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTI--EDAAEADEIFSLLMGDKVEPRREFIEENAKFVRN 632
|
...
gi 503331464 650 IDI 652
Cdd:COG0187 633 LDI 635
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
12-644 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 840.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 12 SAASTNYTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGRtLSVSDNGRGI 91
Cdd:PRK05559 2 AMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGS-VSVRDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 92 PVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTS--EVVK 169
Cdd:PRK05559 81 PVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGplEVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 170 GEPARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKagTQVEYRHDGGVADFLNEIHrrrNDVK 249
Cdd:PRK05559 161 TAGKRKTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER--ERQTFHYENGLKDYLAELN---EGKE 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 250 VAPTVFVLERDDPREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKGMEIKGED 329
Cdd:PRK05559 236 TLPEEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKKLEGED 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 330 IREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAaaNQARR 409
Cdd:PRK05559 316 VREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAK--KVKRK 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 410 KspVVGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSA 489
Cdd:PRK05559 394 K--KTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVA 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 490 LGCGMDDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDT-YWAADEAAKA 568
Cdd:PRK05559 472 IGIGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKiYALDEEEKEE 551
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503331464 569 AILAKLPKNAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVPDEDRhyVDSTITDLMGKDPEPRFRFIMEEA 644
Cdd:PRK05559 552 LLKKLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEE--TEKLVDMLMGKKAEPRREWIEENG 625
|
|
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
12-652 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 833.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 12 SAASTNYTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGI 91
Cdd:PRK05644 2 EEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDG-SITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 92 PVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSEVVKGE 171
Cdd:PRK05644 81 PVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 172 PARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGT--QVEYRHDGGVADFLNEIHRRRNdvK 249
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEekEETFHYEGGIKEYVEYLNRNKE--P 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 250 VAPTVFVLERDdpREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKGME-IKGE 328
Cdd:PRK05644 239 LHEEPIYFEGE--KDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDnLTGE 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 329 DIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQAR 408
Cdd:PRK05644 317 DVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTR 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 409 RKSPVvGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVS 488
Cdd:PRK05644 397 RKSAL-ESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALIT 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 489 ALGCGMDDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDTY-WAADEAAK 567
Cdd:PRK05644 476 ALGTGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKEYaYSDEELDE 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 568 AAILAKLPKNAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVpdEDRHYVDSTITDLMGKDPEPRFRFIMEEAYNA 647
Cdd:PRK05644 556 ILAELKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTI--EDAAEADEIFSILMGDDVEPRREFIEENAKYV 633
|
....*
gi 503331464 648 RDIDI 652
Cdd:PRK05644 634 RNLDI 638
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
18-652 |
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: 739.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 18 YTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIPVDLHA 97
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDG-SVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 98 KTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSEVVKGEPARGTG 177
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 178 TTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGT--QVEYRHDGGVADFLNEIHRRRNDVKVAPTVF 255
Cdd:TIGR01059 160 TTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKgkKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 256 VLERDdpreGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKGME-IKGEDIREGL 334
Cdd:TIGR01059 240 KGEKE----GIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPnLTGEDIREGL 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 335 TAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQARRKSPVv 414
Cdd:TIGR01059 316 TAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSAL- 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 415 GRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGM 494
Cdd:TIGR01059 395 DSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 495 DDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDTYWAADEAAKAAILAKL 574
Cdd:TIGR01059 475 GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKDLVGEAL 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 575 PKNA------------------------KITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVpdEDRHYVDSTITDLMG 630
Cdd:TIGR01059 555 EDLKalyiysdkekeeaktqipvhlgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTI--EDAVEADRIFSTLMG 632
|
650 660
....*....|....*....|..
gi 503331464 631 KDPEPRFRFIMEEAYNARDIDI 652
Cdd:TIGR01059 633 DEVEPRREFIEANALDVKNLDV 654
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
12-652 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 701.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 12 SAASTNYTSESITVLEGLEPVRKRPGMYIGGL-DKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRG 90
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTdDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADG-SVSVSDNGRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 91 IPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSEVVKG 170
Cdd:PRK14939 80 IPTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 171 EPARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGTQVEYRHDGGVADF---LNeihrrRND 247
Cdd:PRK14939 160 GETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDGKEEEFHYEGGIKAFveyLN-----RNK 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 248 VKVAPTVFVLERDdpREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKG-MEIK 326
Cdd:PRK14939 235 TPLHPNIFYFSGE--KDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAkVSLT 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 327 GEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWrareasraaanQ 406
Cdd:PRK14939 313 GDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAA-----------R 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 407 AR-----------RKSpVVGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRA 475
Cdd:PRK14939 382 AReaarkareltrRKG-ALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFD 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 476 KVLDNKELSDIVSALGCGM-DDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITH 554
Cdd:PRK14939 461 KMLSSQEIGTLITALGCGIgRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKK 540
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 555 G-QDTY-------------------------------------------------------------------------- 559
Cdd:PRK14939 541 GkQEQYlkddealddylielalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddl 620
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 560 -------------------------------WAADEAAKAAILAKLP------------KNAK--ITMTRFKGLGEMPAK 594
Cdd:PRK14939 621 adeaavaaldadfltsaeyrrlvelaeklrgLIEEGAYLERGERKQPvssfeealdwllAEARkgLSIQRYKGLGEMNPE 700
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*...
gi 503331464 595 LLFETTLDPARRRLLKVVVPDEDRhyVDSTITDLMGKDPEPRFRFIMEEAYNARDIDI 652
Cdd:PRK14939 701 QLWETTMDPENRRLLQVTIEDAIA--ADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
47-644 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 700.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 47 GLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAG 126
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDN-SISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 127 GLHGVGASVVNALSERLEVKVKRDGFHFSQTYQR-GKPTSEVVKGEPARGTGTTVRFTPDREIFH-DQVFDPVLIGERLD 204
Cdd:smart00433 80 GLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 205 IKAYLNKGLSIQFVDRKAGTQVEYRHDGGVADFLNEIHRRRNDVKVAPTVFVLERDdpreGLRLHLALAWTEATDEHVLS 284
Cdd:smart00433 160 ELAFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKD----NIRVEVAFQYTDGYSENIVS 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 285 FVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKgMEIKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALV 364
Cdd:smart00433 236 FVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKE-KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGV 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 365 ESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQARRKSpvVGRLTLPGKLHDCDSSKVEESELFLVEGDSA 444
Cdd:smart00433 315 EKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK--LSSISLPGKLADASSAGPKKCELFLVEGDSA 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 445 GGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDQYDPSRLRYGKIILLTDADSDGHHIATL 524
Cdd:smart00433 393 GGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGL 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 525 LLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDT-----YWAADEAAKAAILAKlpKNAKITMTRFKGLGEMPAKLLFET 599
Cdd:smart00433 473 LLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKyvysfYSLDEYEKWLEKTEG--NKSKYEIQRYKGLGEMNADQLWET 550
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 503331464 600 TLDPARRRLLKVVVPDEDRhyVDSTITDLMGKDPEPRFRFIMEEA 644
Cdd:smart00433 551 TMDPERRTLLFVTLDDADE--ADLIFSALMGDKVEPRKEWIEENA 593
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
15-640 |
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: 582.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 15 STNYTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIPVD 94
Cdd:TIGR01058 2 ASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDN-SITVQDDGRGIPTG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 95 LHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQR-GKPTSEVVKGEPA 173
Cdd:TIGR01058 81 IHQDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 174 RGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGTQVEYRHDGGVADFLNEIHrrrNDVKVAPT 253
Cdd:TIGR01058 161 KKTGTLVHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTVFFYENGLVDFVDYIN---ETKETLSQ 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 254 VFVLERDDprEGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLK-KGMEIKGEDIRE 332
Cdd:TIGR01058 238 VTYFEGEK--NGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKeKDKNLEGSDIRE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 333 GLTAVLSVNIAEP--QFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQARR- 409
Cdd:TIGR01058 316 GLSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSg 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 410 KSPVVGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSA 489
Cdd:TIGR01058 396 KKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFC 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 490 LGCGMDDQYDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQD-TYWAADEAAKA 568
Cdd:TIGR01058 476 IGTGIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDGkKVKYAWSDLEL 555
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503331464 569 AILAKLPKNAkiTMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVPDEDRhyVDSTITDLMGKDPEPRFRFI 640
Cdd:TIGR01058 556 ESVKKKLKNY--TLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLAR--AERQINTLMGDKVEPRKKWI 623
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
15-643 |
0e+00 |
|
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: 569.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 15 STNYTSESITVLEGLEPVRKRPGMYIgglDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADgRTLSVSDNGRGIPVD 94
Cdd:TIGR01055 1 TTNYSAKDIEVLDGLEPVRKRPGMYT---DTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQD-QSIEVFDNGRGMPVD 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 95 LHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSE--VVKGEP 172
Cdd:TIGR01055 77 IHPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDliSAGTCG 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 173 ARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKAYLNKGLSIQFVDRKAGTQVEYRHDGGVADFLNEIHRRRNDVKVAP 252
Cdd:TIGR01055 157 KRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLSEAVNGDNTLPPKP 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 253 TVFVLERDDpregLRLHLALAW-TEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDLLKKGMEIKGEDIR 331
Cdd:TIGR01055 237 FSGNFEGDD----EAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRGVKLTAEDIW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 332 EGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIqaWRAREASRAAANQARRKs 411
Cdd:TIGR01055 313 DRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVRKK- 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 412 pVVGRLTLPGKLHDCDSSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALG 491
Cdd:TIGR01055 390 -LTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALG 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 492 CGMDDQyDPSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITHGQDTYWA-ADEAAKAAI 570
Cdd:TIGR01055 469 IDPDSN-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYAlDEEEKEKLL 547
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503331464 571 LAKLPKNAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVPDEDRHYVDSTITDLMG-KDPEPRFRFIMEE 643
Cdd:TIGR01055 548 YKLKKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDQRVDKIMDMLLAkKRSEDRFNWLQEK 621
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
17-644 |
5.60e-157 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 475.14 E-value: 5.60e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 17 NYTSESITVLEGLEPVRKRPGMYIGGLDKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIPVDLH 96
Cdd:PTZ00109 99 EYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDG-SVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 97 AKTGKSALEVIFTTLHAGGKFDN----------------------------------------NAYKVAGGLHGVGASVV 136
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHSGGKFQDtfpknsrsdksedkndtksskkgksshvkgpkeakekessQMYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 137 NALSERLEVKVKRDGFHFSQTYQRGKPTSEV-VKGEPARGTGTTVRFTPD-REIF---HDQVFDPV-----------LIG 200
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLsVFSCPLKKRGTTIHFLPDyKHIFkthHQHTETEEeegckngfnldLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 201 ERLDIKAYLNKGLSIQFVDRKAGTQVE------YRHDGGVADFLNEIhrRRNDVKVAPTVFVLERDDPREGLRLHLALAW 274
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERIANENNfypyetIKHEGGTREFLEEL--IKDKTPLYKDINIISIRGVIKNVNVEVSLSW 415
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 275 T-EATDEHVLSFVNTIPTrDGGTHEQGMREAVSKAVrkffaDHDLLKKGM------EIKGEDIREGLTAVLSVNIAEPQF 347
Cdd:PTZ00109 416 SlESYTALIKSFANNVST-TAGTHIDGFKYAITRCV-----NGNIKKNGYfkgnfvNIPGEFIREGMTAIISVKLNGAEF 489
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 348 QGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVIQAWRAREASRAAANQARRKSPVVGRLTLPGKLHDCD 427
Cdd:PTZ00109 490 DGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTILPGKLVDCI 569
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 428 SSKVEESELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQ-AGRAKVLDNKELSDIVSALG--------------- 491
Cdd:PTZ00109 570 SDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKiKNNKKVFENSEIKLLITSIGlsvnpvtwrqydlsh 649
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 492 ---CGMDDQYD--------------PSRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACPPLYKITH 554
Cdd:PTZ00109 650 gtkASKDESVQnnnstltkkknslfDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITN 729
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 555 GQ-------------------------------DTYWAADEAAKAAILAKLPK--------------------------- 576
Cdd:PTZ00109 730 NRmkqfnvstknskkyiytwsdeelnvlikllnKDYSSKETTRSVEEKGNAPDldneyedekldnknmrennvdevelkt 809
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 577 ------------------------NAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVPDEDRhyVDSTITDLMGKD 632
Cdd:PTZ00109 810 elgtnvadteqtdeldinkaffkfSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMR--ASELIFLLMGED 887
|
810
....*....|..
gi 503331464 633 PEPRFRFIMEEA 644
Cdd:PTZ00109 888 VQSRKQFIFENS 899
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
48-228 |
2.66e-92 |
|
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: 283.27 E-value: 2.66e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 48 LHHLCWEIVDNAIDEVMNGHASRIVVELEADGrTLSVSDNGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGG 127
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDN-SITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 128 LHGVGASVVNALSERLEVKVKRDGFHFSQTYQRGKPTSEVVKGEPARGTGTTVRFTPDREIFHDQVFDPVLIGERLDIKA 207
Cdd:cd16928 80 LHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELA 159
|
170 180
....*....|....*....|.
gi 503331464 208 YLNKGLSIQFVDRKAGTQVEY 228
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEEVF 180
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
434-547 |
1.64e-60 |
|
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: 197.49 E-value: 1.64e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 434 SELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDQYDPSRLRYGKIILLTD 513
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 503331464 514 ADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACP 547
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 ... |
232-392 |
6.55e-58 |
|
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: 192.78 E-value: 6.55e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 232 GGVADFLNEIHRrrNDVKVAPTVFVLERDdpREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRK 311
Cdd:cd00822 1 GGLKDFVEELNK--DKEPLHEEPIYIEGE--KDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAIND 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 312 FFADHDLLKKGME-IKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERV 390
Cdd:cd00822 77 YAKKNNLLKKKDVkLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKA 156
|
..
gi 503331464 391 IQ 392
Cdd:cd00822 157 IL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
434-547 |
3.91e-54 |
|
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: 180.39 E-value: 3.91e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 434 SELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDQY-DPSRLRYGKIILLT 512
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDfDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 503331464 513 DADSDGHHIATLLLTFFYRHLPGLLNEGRVFLACP 547
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
20-636 |
2.19e-52 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 190.35 E-value: 2.19e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 20 SESITVLEGLEPVRKRPGMYIGGLDK-----------------AGLHHLCWEIVDNAIDEVMNG---HASRIVVELeaDG 79
Cdd:PHA02569 1 KDEFKVLSDREHILKRPGMYIGSVAYeaherflfgkftqveyvPGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI--KN 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 80 RTLSVSDNGRGIPVDL-HAKTGKSAL--EVIFTTLHAGGKFDnNAYKVAGGLHGVGASVVNALSERLeVKVKRDGFHFSq 156
Cdd:PHA02569 79 NQVTVSDNGRGIPQAMvTTPEGEEIPgpVAAWTRTKAGSNFD-DTNRVTGGMNGVGSSLTNFFSVLF-IGETCDGKNEV- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 157 TYQRGKPTSEV-VKGEPARGTGTTVRFTPDREIFHDQVFDPV---LIGERLdikaylnKGLSIQFVDRKAGTQVEyRHDG 232
Cdd:PHA02569 156 TVNCSNGAENIsWSTKPGKGKGTSVTFIPDFSHFEVNGLDQQyldIILDRL-------QTLAVVFPDIKFTFNGK-KVSG 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 233 GVADFlneihrrrndVKVAPTVFVLERDDpreglRLHLALAWTEATDEHvLSFVNTIPTRDGGTHEQGMREAVS----KA 308
Cdd:PHA02569 228 KFKKY----------AKQFGDDTIVQEND-----NVSIALAPSPDGFRQ-LSFVNGLHTKNGGHHVDCVMDDICeeliPM 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 309 VRKffadhdllKKGMEIKGEDIREGLTAVLSV-NIAEPQFQGQTKGRLNNP--EVR--------------ALVESAIRPR 371
Cdd:PHA02569 292 IKK--------KHKIEVTKARVKECLTIVLFVrNMSNPRFDSQTKERLTSPfgEIRnhidldykkiakqiLKTEAIIMPI 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 372 LEDFFHKnKSVGEAVAERVIQawrareasraaanQARRKSPVVGRLtlpgKLHDCDSSKveESELFLVEGDSAGGSAKQG 451
Cdd:PHA02569 364 IEAALAR-KLAAEKAAETKAA-------------KKAKKAKVAKHI----KANLIGKDA--ETTLFLTEGDSAIGYLIEV 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 452 RDRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDqyDPSRLRYGKIILLTDADSDGH-HIATLLLTFFY 530
Cdd:PHA02569 424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGE--KAENMNYKNIAIMTDADVDGKgSIYPLLLAFFS 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 531 RhLPGLLNEGRVFLACPPLYKITHGQDTYWAADEAAKAAILAKLPKNakiTMTRFKGLGEMPAKLLFETTLDParrrLLK 610
Cdd:PHA02569 502 R-WPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSLKKW---SIRYIKGLGSLRKSEYRRVINNP----VYD 573
|
650 660
....*....|....*....|....*.
gi 503331464 611 VVVPDEDrhyVDSTITDLMGKDPEPR 636
Cdd:PHA02569 574 VVVLPDD---WKELFEMLFGDDADLR 596
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
233-392 |
1.51e-51 |
|
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: 175.88 E-value: 1.51e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 233 GVADFLNEIHRrrNDVKVAPTVFVLERDDPREGLRLHLALAWTEATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAVRKF 312
Cdd:pfam00204 1 GLKDFVEELNK--DKKPLHKEIIYFEGESPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEY 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 313 FADHDLLKKG-MEIKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLEDFFHKNKSVGEAVAERVI 391
Cdd:pfam00204 79 AKKKGLLKKKdEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
.
gi 503331464 392 Q 392
Cdd:pfam00204 159 Q 159
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
29-558 |
6.10e-47 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 178.75 E-value: 6.10e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 29 LEPVRKRPGMYIGGLDKA---------------------GLHHLCWEIVDNAID-EVMNGHASRIVVELEADGRTLSVSD 86
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHtqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADnKQRDPSMDSLKVDIDVEQNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 87 NGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVK--RDGFHFSQTYQRG-KP 163
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFTNNmSV 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 164 TSE-VVKGEPARGTGTTVRFTPDREIFHDQVFDP---VLIGER-LDIKAYLNKGLSIQFvdrkAGTQVEYrhdGGVADFL 238
Cdd:PLN03128 173 KSEpKITSCKASENWTKITFKPDLAKFNMTRLDEdvvALMSKRvYDIAGCLGKKLKVEL----NGKKLPV---KSFQDYV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 239 NEIHRRRNDVKVAPTVFVLERDdpreglRLHLALAWTEATDEHVlSFVNTIPTRDGGTHEQGMREAVSKAVRKFFADHDl 318
Cdd:PLN03128 246 GLYLGPNSREDPLPRIYEKVND------RWEVCVSLSDGSFQQV-SFVNSIATIKGGTHVDYVADQIVKHIQEKVKKKN- 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 319 lKKGMEIKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEvralveSAIRPR--LEDFFHKnKSVGEAVAERVIQAWRA 396
Cdd:PLN03128 318 -KNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRP------SSFGSKceLSEEFLK-KVEKCGVVENILSWAQF 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 397 REASRAAANQARRKSpvvgRLTLPGKLHDCDSSKVEESE---LFLVEGDSA-----GGSAKQGRDRriQAILPLKGKVLN 468
Cdd:PLN03128 390 KQQKELKKKDGAKRQ----RLTGIPKLDDANDAGGKKSKdctLILTEGDSAkalamSGLSVVGRDH--YGVFPLRGKLLN 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 469 AEQAGRAKVLDNKELSDIVSALGCGMDDQYDP---SRLRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLLnEGRVFLA 545
Cdd:PLN03128 464 VREASHKQIMKNAEITNIKQILGLQFGKTYDEentKSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLL-KIPGFLV 542
|
570
....*....|....*
gi 503331464 546 --CPPLYKITHGQDT 558
Cdd:PLN03128 543 efITPIVKATKGGKS 557
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
26-538 |
1.52e-44 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 171.77 E-value: 1.52e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 26 LEGLEPVRKRPGMYIGGLDKA-----------------------GLHHLCWEIVDNAID----EVMNGHASRIVVELEAD 78
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEILVNAADnkarDKGGHRMTYIKVTIDEE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 79 GRTLSVSDNGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKV--KRDGFHFSQ 156
Cdd:PTZ00108 93 NGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSKSGKKFKM 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 157 TY-----QRGKPTSEVVKGEPARgtgTTVRFTPDREIFHDQVFDP---VLIGERL--------DIKAYLNkGLSIQFVDR 220
Cdd:PTZ00108 173 TWtdnmsKKSEPRITSYDGKKDY---TKVTFYPDYAKFGMTEFDDdmlRLLKKRVydlagcfgKLKVYLN-GERIAIKSF 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 221 KAGTQVEYRHDG-GVADFLNEIHRRRND-VKVAPTVfvlerddpreglrlhlalawTEATDEHVlSFVNTIPTRDGGTH- 297
Cdd:PTZ00108 249 KDYVDLYLPDGEeGKKPPYPFVYTSVNGrWEVVVSL--------------------SDGQFQQV-SFVNSICTTKGGTHv 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 298 ----EQGMREAVSKAVRKffadhdlLKKGMEIKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNNPEVRALVESAIRPRLE 373
Cdd:PTZ00108 308 nyilDQLISKLQEKAKKK-------KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLI 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 374 DFFHKNKSVgeavaERVIQAWRAreasraaaNQARR-----KSPVVGRLTLPGKLHDCDSSKVEESE---LFLVEGDSA- 444
Cdd:PTZ00108 381 KYVLKSPIL-----ENIVEWAQA--------KLAAElnkkmKAGKKSRILGIPKLDDANDAGGKNSEectLILTEGDSAk 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 445 ----GGSAKQGRDRriQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDQY-DPSRLRYGKIILLTDADSDGH 519
Cdd:PTZ00108 448 alalAGLSVVGRDY--YGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGS 525
|
570
....*....|....*....
gi 503331464 520 HIATLLLTFFYRHLPGLLN 538
Cdd:PTZ00108 526 HIKGLLINMIHHFWPSLLK 544
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
29-537 |
7.64e-36 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 145.01 E-value: 7.64e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 29 LEPVRKRPGMYIGGLDK---------------------AGLHHLCWEIVDNAID-EVMNGHASRIVVELEADGRTLSVSD 86
Cdd:PLN03237 38 LEHILLRPDTYIGSIEKhtqtlwvyetdkmvqrsvtyvPGLYKIFDEILVNAADnKQRDPKMDSLRVVIDVEQNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 87 NGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVAGGLHGVGASVVNALSERLEVKVKrDGFH---FSQTYQR--G 161
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETA-DGKRqkkYKQVFSNnmG 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 162 KPTSEVVKGEPARGTGTTVRFTPDREIFH------DQVfdpVLIGERL-DIKAYLNKGLSIQFvdrkAGTQVEYRhdgGV 234
Cdd:PLN03237 197 KKSEPVITKCKKSENWTKVTFKPDLAKFNmthledDVV---ALMKKRVvDIAGCLGKTVKVEL----NGKRIPVK---SF 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 235 ADFLNEIHRRRNDVKVAPTVFVLErddpREGLRLHLALAWTEATDEHVlSFVNTIPTRDGGTH-EQGMREAVSKAVRKFF 313
Cdd:PLN03237 267 SDYVDLYLESANKSRPENLPRIYE----KVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHvDYVTNQIANHVMEAVN 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 314 ADHdllkKGMEIKGEDIREGLTAVLSVNIAEPQFQGQTKGRLNnpevraLVESAIRPRLE---DFFHKNKSVGeaVAERV 390
Cdd:PLN03237 342 KKN----KNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLT------LRQSSFGSKCElseDFLKKVMKSG--IVENL 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 391 IQAWRAREASRAAANQARRKspvvGRLTLPGKLHDCDSSKVEESE---LFLVEGDSA-----GGSAKQGRDRriQAILPL 462
Cdd:PLN03237 410 LSWADFKQSKELKKTDGAKT----TRVTGIPKLEDANEAGGKNSEkctLILTEGDSAkalavAGLSVVGRNY--YGVFPL 483
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503331464 463 KGKVLNAEQAGRAKVLDNKELSDIVSALGCGMDDQYDPSR-LRYGKIILLTDADSDGHHIATLLLTFFYRHLPGLL 537
Cdd:PLN03237 484 RGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKsLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLL 559
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
577-641 |
5.32e-25 |
|
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: 98.22 E-value: 5.32e-25
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503331464 577 NAKITMTRFKGLGEMPAKLLFETTLDPARRRLLKVVVPDEDrhYVDSTITDLMGKDPEPRFRFIM 641
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAA--EADEIFSTLMGDKVEPRREFIE 63
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
436-537 |
5.49e-23 |
|
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: 94.29 E-value: 5.49e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 436 LFLVEGDSAGGSAKQGR---DRRIQAILPLKGKVLNAEQAGRAKVLDNKELSDIVSALGC--GMDDQYDPSRLRYGKIIL 510
Cdd:cd03365 3 LILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLqhGKSDYESTKSLRYGRLMI 82
|
90 100
....*....|....*....|....*..
gi 503331464 511 LTDADSDGHHIATLLLTFFYRHLPGLL 537
Cdd:cd03365 83 MTDQDHDGSHIKGLLINFIHSFWPSLL 109
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
44-187 |
1.73e-17 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 78.46 E-value: 1.73e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 44 DKAGLHHLCWEIVDNAIDEVMNGHASRIVVELEADGRTLSVSDNGRGIPVDLhaktgksaLEVIFttlHAGGKFDNNAYK 123
Cdd:smart00387 2 DPDRLRQVLSNLLDNAIKYTPEGGRITVTLERDGDHVEITVEDNGPGIPPED--------LEKIF---EPFFRTDKRSRK 70
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503331464 124 VAGglHGVGASVVNALSERLEVKVKrdgfhfsqtyqrgkptsevVKGEParGTGTTVRFTPDRE 187
Cdd:smart00387 71 IGG--TGLGLSIVKKLVELHGGEIS-------------------VESEP--GGGTTFTITLPLE 111
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
44-188 |
1.18e-16 |
|
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: 75.87 E-value: 1.18e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 44 DKAGLHHLCWEIVDNAIDEvmNGHASRIVVELEADGR-TLSVSDNGRGIPVDLHAKtgksalevIFttlhagGKFDnNAY 122
Cdd:pfam02518 2 DELRLRQVLSNLLDNALKH--AAKAGEITVTLSEGGElTLTVEDNGIGIPPEDLPR--------IF------EPFS-TAD 64
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503331464 123 KVAGGLHGVGASVVNALSERLEVKVKRdgfhfsqtyqrgkptsevvkgEPARGTGTTVRFTPDREI 188
Cdd:pfam02518 65 KRGGGGTGLGLSIVRKLVELLGGTITV---------------------ESEPGGGTTVTLTLPLAQ 109
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
234-355 |
1.52e-14 |
|
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: 69.98 E-value: 1.52e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 234 VADFLNEIHRRrndvKVAPTVFVLERDDprEGLRLHLALAWTE---ATDEHVLSFVNTIPTRDGGTHEQGMREAVSKAvr 310
Cdd:cd00329 1 LKDRLAEILGD----KVADKLIYVEGES--DGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRA-- 72
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 503331464 311 kffadhdllkkgmeIKGEDIREGLTAVLSVNI--AEPQF-QGQTKGRL 355
Cdd:cd00329 73 --------------LNGDDVRRYPVAVLSLKIppSLVDVnVHPTKEEV 106
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
435-529 |
3.13e-14 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 68.54 E-value: 3.13e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 435 ELFLVEGDSAGGSAKQGRDRRIQAILPLKGKVLNAEQAGRAKVLDNkelsdivsalgcgmddqYDPSRLRYGKIILLTDA 514
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90
....*....|....*
gi 503331464 515 DSDGHHIATLLLTFF 529
Cdd:pfam01751 64 DREGEAIALKLLELK 78
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
47-185 |
4.20e-13 |
|
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: 66.98 E-value: 4.20e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 47 GLHHLCWEIVDNAID-EVMNGHASRIVVELEADGRTLSVSDNGRGIPVDLHAKTGKSALEVIFTTLHAGGKFDNNAYKVA 125
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPENNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503331464 126 GGLHGVGASVVNALSERLEVKV--KRDGFHFSQTYQR--GKPTSEVVKGEPARGTGTTVRFTPD 185
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVETadSESKKKFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
48-143 |
1.99e-06 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 46.44 E-value: 1.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 48 LHHLCWEIVDNAIDEVMNGHASRIVVELEADGRTLSVSDNGRGIPvdlhaktgKSALEVIFTTLHAGGKfdnnayKVAGG 127
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPGGTIEISLRQEGDGVVLEVEDNGPGIP--------EEDLERIFERFYRGDK------SREGG 66
|
90
....*....|....*.
gi 503331464 128 LHGVGASVVNALSERL 143
Cdd:cd00075 67 GTGLGLAIVRRIVEAH 82
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
54-94 |
5.67e-06 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 49.27 E-value: 5.67e-06
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 503331464 54 EIVDNAIDevmnGHASRIVVELEADGRTL-SVSDNGRGIPVD 94
Cdd:COG0323 30 ELVENAID----AGATRIEVEIEEGGKSLiRVTDNGCGMSPE 67
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
54-94 |
1.35e-05 |
|
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: 46.28 E-value: 1.35e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 503331464 54 EIVDNAIDevmnGHASRIVVELEADGRTL-SVSDNGRGIPVD 94
Cdd:cd16926 20 ELVENSID----AGATRIDVEIEEGGLKLiRVTDNGSGISRE 57
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
54-94 |
4.42e-05 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 46.75 E-value: 4.42e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 503331464 54 EIVDNAIDevmnGHASRIVVELEADGRTL-SVSDNGRGIPVD 94
Cdd:PRK00095 29 ELVENALD----AGATRIDIEIEEGGLKLiRVRDNGCGISKE 66
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
434-532 |
1.80e-04 |
|
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: 40.49 E-value: 1.80e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 434 SELFLVEGDSAGGSAKQGRDRRIqAILPLKGKVLNAEqagRAKVLDNKELSDivsalgcgmddqydpsrlrygKIILLTD 513
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGGYGG-AVVALGGHALNKT---RELLKRLLGEAK---------------------EVIIATD 55
|
90
....*....|....*....
gi 503331464 514 ADSDGHHIATLLLTFFYRH 532
Cdd:cd00188 56 ADREGEAIALRLLELLKSL 74
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
267-355 |
4.01e-04 |
|
TopoIIA_Trans_ScTopoIIA: 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 Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. 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. 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.
Pssm-ID: 239563 [Multi-domain] Cd Length: 153 Bit Score: 41.12 E-value: 4.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503331464 267 RLHLALAWTEATDEHVlSFVNTIPTRDGGTH----EQGMREAVSKAVRKffadhdLLKKGMEIKGEDIREGLTAVLSVNI 342
Cdd:cd03481 32 RWEVAVALSDGQFQQV-SFVNSIATTKGGTHvdyvADQIVKKLDEVVKK------KNKGGINVKPFQVKNHLWIFVNCLI 104
|
90
....*....|...
gi 503331464 343 AEPQFQGQTKGRL 355
Cdd:cd03481 105 ENPSFDSQTKETL 117
|
|
| COG4191 |
COG4191 |
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ... |
55-98 |
6.10e-04 |
|
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms];
Pssm-ID: 443345 [Multi-domain] Cd Length: 361 Bit Score: 42.48 E-value: 6.10e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 503331464 55 IVDNAIDEVMNGHASRIVVELEADGR--TLSVSDNGRGIPVDLHAK 98
Cdd:COG4191 264 LLINAIDAMEEGEGGRITISTRREGDyvVISVRDNGPGIPPEVLER 309
|
|
| CitA |
COG3290 |
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ... |
55-98 |
2.12e-03 |
|
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms];
Pssm-ID: 442519 [Multi-domain] Cd Length: 389 Bit Score: 40.99 E-value: 2.12e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 503331464 55 IVDNAIDEVMNGHAS--RIVVELEADGRTL--SVSDNGRGIPVDLHAK 98
Cdd:COG3290 289 LLDNAIEAVEKLPEEerRVELSIRDDGDELviEVEDSGPGIPEELLEK 336
|
|
| |
