|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-627 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1275.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 1 ENSYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGI 80
Cdd:PRK05644 5 AQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 81 QEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTDQ 160
Cdd:PRK05644 85 HPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 161 TGTITRFKPDPEIFqETTVYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKKE-FHYEGGIKSYVEHLNRSKQPIHEEP 239
Cdd:PRK05644 165 TGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEEtFHYEGGIKEYVEYLNRNKEPLHEEP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 240 VYVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLT 319
Cdd:PRK05644 244 IYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLT 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 320 AIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKSALEV 399
Cdd:PRK05644 324 AVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALES 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 400 SSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGG 479
Cdd:PRK05644 404 SSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGD 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 480 DFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKiQYAYNEKELEKILAELPA 559
Cdd:PRK05644 484 DFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAELKL 562
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 560 Q--PKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKY 627
Cdd:PRK05644 563 KgnPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKY 632
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
1-627 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1213.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 1 ENSYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGI 80
Cdd:COG0187 3 KSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 81 QEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTDQ 160
Cdd:COG0187 83 HPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDR 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 161 TGTITRFKPDPEIFqETTVYEFDTLATRMRELAFLNRNIKLTIEDKR-EHKQKKEFHYEGGIKSYVEHLNRSKQPIHEEP 239
Cdd:COG0187 163 TGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEReEEPKEETFHYEGGIKDFVEYLNEDKEPLHPEV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 240 VYVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLT 319
Cdd:COG0187 242 IYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 320 AIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKSALEV 399
Cdd:COG0187 322 AVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALES 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 400 SSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGG 479
Cdd:COG0187 402 SGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGD 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 480 DFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKIQYAYNEKELEKILAELPA 559
Cdd:COG0187 482 DFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKG 561
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190710595 560 QPKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKY 627
Cdd:COG0187 562 KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKF 629
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-626 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1081.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 1 ENSYDESQIQVLEGLEAVRKRPGMYIGSTS-GKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVG 79
Cdd:PRK14939 4 SNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 80 IQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTD 159
Cdd:PRK14939 84 IHPEEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETD 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 160 QTGTITRFKPDPEIFqETTVYEFDTLATRMRELAFLNRNIKLTIEDKReHKQKKEFHYEGGIKSYVEHLNRSKQPIHEEP 239
Cdd:PRK14939 164 KTGTEVRFWPSPEIF-ENTEFDYDILAKRLRELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNI 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 240 VYVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLT 319
Cdd:PRK14939 242 FYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 320 AIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKSALEV 399
Cdd:PRK14939 322 AVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 400 SSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIG- 478
Cdd:PRK14939 402 AGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGr 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 479 GDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKIQYAYNEKELEKILAEL- 557
Cdd:PRK14939 482 DEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELa 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 --------------------------------------------------------------------------------
Cdd:PRK14939 562 legatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsaeyrr 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 558 --------------PAQPKPG-------------------------IQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQD 598
Cdd:PRK14939 642 lvelaeklrglieeGAYLERGerkqpvssfeealdwllaearkglsIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIED 721
|
730 740
....*....|....*....|....*...
gi 190710595 599 AIEADETFEILMGDKVEPRRNFIQENAK 626
Cdd:PRK14939 722 AIAADEIFTTLMGDEVEPRREFIEENAL 749
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
4-627 |
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: 1060.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 4 YDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQEK 83
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 84 MGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTDQTGT 163
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 164 ITRFKPDPEIFqETTVYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKK-EFHYEGGIKSYVEHLNRSKQPIHEEPVYV 242
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKvTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 243 EGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLTAIV 322
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 323 SIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKSALEVSSL 402
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 403 PGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFD 482
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 483 IEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKIQYA------------------ 544
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIkddkekdlvgealedlka 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 545 ---YNEKELEKILAELPAQP---KPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRR 618
Cdd:TIGR01059 560 lyiYSDKEKEEAKTQIPVHLgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRR 639
|
....*....
gi 190710595 619 NFIQENAKY 627
Cdd:TIGR01059 640 EFIEANALD 648
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-626 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 919.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 1 ENSYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGI 80
Cdd:PRK05559 5 TNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 81 QEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDT-- 158
Cdd:PRK05559 85 HPEEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAgk 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 159 DQTGTITRFKPDPEIFqETTVYEFDTLATRMRELAFLNRNIKLTIEDKREhkqKKEFHYEGGIKSYVEHLNRSKQPIHEE 238
Cdd:PRK05559 165 RKTGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERE---RQTFHYENGLKDYLAELNEGKETLPEE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 239 PV-YVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKdADSNLTGEDVREG 317
Cdd:PRK05559 241 FVgSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 318 LTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKgtMAARARVAAKKARELTRRKSAL 397
Cdd:PRK05559 320 LAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEK--AIKAAQARLRAAKKVKRKKKTS 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 398 EvSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNI 477
Cdd:PRK05559 398 G-PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGP 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 478 GGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKIQYAYNEKELEKILAEL 557
Cdd:PRK05559 477 GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKL 556
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 558 -PAQPKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAK 626
Cdd:PRK05559 557 gKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGD 626
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
33-626 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 895.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 33 GLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGG 112
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 113 LHGVGASVVNALSTELEVFVHREGKIHYQKYER-GIPVADLKVIGDTDQTGTITRFKPDPEIFQETTVYEFDTLATRMRE 191
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 192 LAFLNRNIKLTIEDKREHKqKKEFHYEGGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVSLQYNEGYTNNIYSFTNN 271
Cdd:smart00433 161 LAFLNKGVKITLNDERSDE-EKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNN 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 272 IHTYEGGTHEVGFKTALTRVINDYGRKNSILKDAdsNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESV 351
Cdd:smart00433 240 IATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 352 FSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKsALEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSA 431
Cdd:smart00433 318 VSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 432 KQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTF 511
Cdd:smart00433 397 KSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 512 FYRYMRQIIEHGYIYIAQPPLFKVQQGKK---IQYAYNEKELEKILAELPAQPKPGIQRYKGLGEMNPTQLWETTMDPEV 588
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKkyvYSFYSLDEYEKWLEKTEGNKSKYEIQRYKGLGEMNADQLWETTMDPER 556
|
570 580 590
....*....|....*....|....*....|....*...
gi 190710595 589 RSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAK 626
Cdd:smart00433 557 RTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
2-627 |
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: 742.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 2 NSYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQ 81
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 82 EKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHREGKIHYQKYER-GIPVADLKVIGDTDQ 160
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 161 TGTITRFKPDPEIFQeTTVYEFDTLATRMRELAFLNRNIKLTIEDKReHKQKKEFHYEGGIKSYVEHLNRSKQpIHEEPV 240
Cdd:TIGR01058 163 TGTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKR-TNKTTVFFYENGLVDFVDYINETKE-TLSQVT 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 241 YVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLTA 320
Cdd:TIGR01058 240 YFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSA 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 321 IVSIKHP--NPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTR--RKSA 396
Cdd:TIGR01058 320 IISVRIPeeLIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKPK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 397 LEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTN 476
Cdd:TIGR01058 400 KEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTG 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 477 IGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQ--GKKIQYAYNEKELEKIL 554
Cdd:TIGR01058 480 IGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELESVK 559
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 190710595 555 AELPAQPkpgIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKY 627
Cdd:TIGR01058 560 KKLKNYT---LQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINF 629
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
2-625 |
6.59e-179 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 530.61 E-value: 6.59e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 2 NSYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQ 81
Cdd:PTZ00109 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 82 EKMGRPAVEVIMTVLH----------------------------------------AGGKFGGGGYKVSGGLHGVGASVV 121
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 122 NALSTELEVFVHREGKIHYQKYERGIPVADLKVIGD-TDQTGTITRFKPD-PEIFQETT-------------VYEFDTLA 186
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCpLKKRGTTIHFLPDyKHIFKTHHqhteteeeegcknGFNLDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 187 TRMRELAFLNRNIKLTIEDKREHKQKKEFHYE-----GGIKSYVEHLNRSKQPIHEEPVYV--EGSKDGIQVEVSLQYN- 258
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERIANENNFYPYEtikheGGTREFLEELIKDKTPLYKDINIIsiRGVIKNVNVEVSLSWSl 417
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 259 EGYTNNIYSFTNNIHTyEGGTHEVGFKTALTRVINDYGRKNSILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTK 338
Cdd:PTZ00109 418 ESYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTK 496
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 339 LGNSEARTITESVFSEAFEKFLLENPNVARKIVEKGTMAARARVAAKKARELTRRKSALEVSS-LPGKLADCSSKDPAIS 417
Cdd:PTZ00109 497 LGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDDIERN 576
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 418 EIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLD-KILSNDEVRTIITAIGTNIGGD---------------- 480
Cdd:PTZ00109 577 ELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtkaskd 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 481 ----------------FDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKV--------- 535
Cdd:PTZ00109 657 esvqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqfn 736
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 536 ---QQGKKIQYAYNEKELEKILAELPAQPKPG------------------------------------------------ 564
Cdd:PTZ00109 737 vstKNSKKYIYTWSDEELNVLIKLLNKDYSSKettrsveekgnapdldneyedekldnknmrennvdevelktelgtnva 816
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 565 ----------------------IQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQ 622
Cdd:PTZ00109 817 dteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIF 896
|
...
gi 190710595 623 ENA 625
Cdd:PTZ00109 897 ENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
3-623 |
3.60e-176 |
|
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: 514.08 E-value: 3.60e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 3 SYDESQIQVLEGLEAVRKRPGMYIGSTSgkgLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQE 82
Cdd:TIGR01055 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 83 KMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTDQ-- 160
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrl 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 161 TGTITRFKPDPEIFQETTvYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKKeFHYEGGIKSYVEHLNRSKQPIHEEPV 240
Cdd:TIGR01055 160 TGTSVHFTPDPEIFDSLH-FSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKAL-WNYPDGLKDYLSEAVNGDNTLPPKPF 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 241 YVEGSKDGIQVEVSLQY-NEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNSILKDAdSNLTGEDVREGLT 319
Cdd:TIGR01055 238 SGNFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 320 AIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEkgtMAARARVAAKKARELTRRKSALEV 399
Cdd:TIGR01055 317 YVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAE---HAISSAQRRKRAAKKVVRKKLTSG 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 400 SSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGG 479
Cdd:TIGR01055 394 PALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 480 DfDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQPPLFKVQQGKKIQYAYNEKELEKILAELP- 558
Cdd:TIGR01055 474 N-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKk 552
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 190710595 559 AQPKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDA--IEADETFEILMGDKV-EPRRNFIQE 623
Cdd:TIGR01055 553 KKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVqdQRVDKIMDMLLAKKRsEDRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
34-212 |
6.05e-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: 281.35 E-value: 6.05e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 34 LHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSIRVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGL 113
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 114 HGVGASVVNALSTELEVFVHREGKIHYQKYERGIPVADLKVIGDTDQTGTITRFKPDPEIFqETTVYEFDTLATRMRELA 193
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170
....*....|....*....
gi 190710595 194 FLNRNIKLTIEDKREHKQK 212
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEE 178
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
219-373 |
5.39e-85 |
|
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: 263.27 E-value: 5.39e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 219 GGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRK 298
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 190710595 299 NSILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEK 373
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
417-530 |
6.45e-82 |
|
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: 252.96 E-value: 6.45e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 417 SEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKARYHKVIIMTD 496
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 190710595 497 ADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQP 530
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
220-373 |
2.77e-73 |
|
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: 232.89 E-value: 2.77e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 220 GIKSYVEHLNRSKQPIHEEPVYVEG--SKDGIQVEVSLQYNEGYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGR 297
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGesPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190710595 298 KNSILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKIVEK 373
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
417-530 |
2.29e-68 |
|
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: 217.76 E-value: 2.29e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 417 SEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGG-DFDIEKARYHKVIIMT 495
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKdDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 190710595 496 DADVDGAHIRTLLLTFFYRYMRQIIEHGYIYIAQP 530
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
7-622 |
1.05e-46 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 174.17 E-value: 1.05e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 7 SQIQVLEGLEAVRKRPGMYIGSTS---------GK--------GLHHLVWEIVDNSIDEALAG---YCDEINVSIEeDNS 66
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAyeaherflfGKftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 67 IRVTDNGRGIPvgiQEKMGRPAVEVIMTVLHAGGKFG-----GGGYKVSGGLHGVGASVVNALSTeleVFVHREGKihyq 141
Cdd:PHA02569 81 VTVSDNGRGIP---QAMVTTPEGEEIPGPVAAWTRTKagsnfDDTNRVTGGMNGVGSSLTNFFSV---LFIGETCD---- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 142 kYERGIPV-----ADLKVIGD--TDQTGTITRFKPDPEIFQETTVYE--FDTLATRMRELAFLNRNIKLTIEDKRehkqk 212
Cdd:PHA02569 151 -GKNEVTVncsngAENISWSTkpGKGKGTSVTFIPDFSHFEVNGLDQqyLDIILDRLQTLAVVFPDIKFTFNGKK----- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 213 kefhYEGGIKSYVEHLNrskqpihEEPVYVEGSKDGIQVEVSlqyNEGYTNNiySFTNNIHTYEGGTHEVGFKTALT-RV 291
Cdd:PHA02569 225 ----VSGKFKKYAKQFG-------DDTIVQENDNVSIALAPS---PDGFRQL--SFVNGLHTKNGGHHVDCVMDDICeEL 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 292 INDYGRKNSIlkdadsNLTGEDVREGLTAIVSIKH-PNPQFEGQTKTKLGNS--EARTITESVFsEAFEKFLLENPNVAR 368
Cdd:PHA02569 289 IPMIKKKHKI------EVTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgEIRNHIDLDY-KKIAKQILKTEAIIM 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 369 KIVEkgtmAARARVAAKKARELTR-RKSALEV-------SSLPGKLADcsskdpaiSEIYIVEGDSAGGSAKQGRDRHFQ 440
Cdd:PHA02569 362 PIIE----AALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELH 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 441 AILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKarYHKVIIMTDADVDG-AHIRTLLLTFFYRYmRQI 519
Cdd:PHA02569 430 GGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENMN--YKNIAIMTDADVDGkGSIYPLLLAFFSRW-PEL 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 520 IEHGYIYIAQPPLFKVQQGKKIQYAYNEKELEKilaELPAQPKPGIQRYKGLGEMNptqlwettmDPEVRSLLQVSLQDA 599
Cdd:PHA02569 507 FEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEK---AKDSLKKWSIRYIKGLGSLR---------KSEYRRVINNPVYDV 574
|
650 660
....*....|....*....|....*..
gi 190710595 600 IEAD----ETFEILMGDKVEPRRNFIQ 622
Cdd:PHA02569 575 VVLPddwkELFEMLFGDDADLRKDWMS 601
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
15-623 |
2.69e-40 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 158.33 E-value: 2.69e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 15 LEAVRKRPGMYIGST-----------SGK----------GLHHLVWEIVDNSIDEALAG-YCDEINVSIE-EDNSIRVTD 71
Cdd:PLN03128 13 LEHILLRPDTYIGSTekhtqtlwvyeGGEmvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDvEQNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 72 NGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTE--LEVFVHREGKIHYQKYERGIPV 149
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEftVETADGNRGKKYKQVFTNNMSV 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 150 ADLKVIGDTDQTGTITR--FKPDPEIFQETTVYEfDT---LATRMRELA-FLNRNIKLTIEDKreHKQKKEFhyeggiKS 223
Cdd:PLN03128 173 KSEPKITSCKASENWTKitFKPDLAKFNMTRLDE-DVvalMSKRVYDIAgCLGKKLKVELNGK--KLPVKSF------QD 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 224 YVEHLNRSKQPIHEEPVYVEGSKDGIQVEVSLqyNEGYTNNIySFTNNIHTYEGGTHeVGFKTA--LTRVINDYGRKNSI 301
Cdd:PLN03128 244 YVGLYLGPNSREDPLPRIYEKVNDRWEVCVSL--SDGSFQQV-SFVNSIATIKGGTH-VDYVADqiVKHIQEKVKKKNKN 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 302 LKdadsNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKfLLENPNVARKIVEKGTMAARAR 381
Cdd:PLN03128 320 AT----HVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLK-KVEKCGVVENILSWAQFKQQKE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 382 VAAKKARELTRrksaleVSSLPgKLADCSSKDPAISE---IYIVEGDSA-----GGSAKQGRDRHfqAILPLKGKIINVE 453
Cdd:PLN03128 395 LKKKDGAKRQR------LTGIP-KLDDANDAGGKKSKdctLILTEGDSAkalamSGLSVVGRDHY--GVFPLRGKLLNVR 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 454 KARLDKILSNDEVRTIITAIGTNIGGDFDIEKA---RYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIE-HGYIYIAQ 529
Cdd:PLN03128 466 EASHKQIMKNAEITNIKQILGLQFGKTYDEENTkslRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKiPGFLVEFI 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 530 PPLFKVQQGKKIQYAYNEKELEKILAEL-PAQPKPGIQRYKGLGEMNPTQLWE--TTMDPEVRSLLQVSLQDAIEADETF 606
Cdd:PLN03128 546 TPIVKATKGGKSLSFYTMPEYEAWKESLeGETKGWTIKYYKGLGTSTSEEAKEyfSNLDIHKKEFLWQSDEDGDLIDMAF 625
|
650
....*....|....*..
gi 190710595 607 EilmGDKVEPRRNFIQE 623
Cdd:PLN03128 626 S---KKRVEDRKIWLNN 639
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
5-572 |
3.12e-40 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 158.29 E-value: 3.12e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 5 DESQIQVLEGLEAVRKRPGMYIGSTS-------------GK----------GLHHLVWEI----VDNSIDEALAGYCDEI 57
Cdd:PTZ00108 6 VEERYQKKTQIEHILLRPDTYIGSIEtqtedmwvydeekNRmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 58 NVSI-EEDNSIRVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFV--HR 134
Cdd:PTZ00108 86 KVTIdEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 135 EGKIHYQKYERGIPVADLKVIGDTDQTGTITR--FKPDPEIFQETTVYEfDTLATRMR---ELAFLNRNIKLTIEDKREh 209
Cdd:PTZ00108 166 SGKKFKMTWTDNMSKKSEPRITSYDGKKDYTKvtFYPDYAKFGMTEFDD-DMLRLLKKrvyDLAGCFGKLKVYLNGERI- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 210 kqkkefhyegGIKSYVEHLNRSKQPIHEE-PVYVEGSKDGIQ--VEVSLQYNEGyTNNIYSFTNNIHTYEGGTHeVGF-- 284
Cdd:PTZ00108 244 ----------AIKSFKDYVDLYLPDGEEGkKPPYPFVYTSVNgrWEVVVSLSDG-QFQQVSFVNSICTTKGGTH-VNYil 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 285 ---KTALTRVINDYGRKNsilKDADSNLtgedVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLL 361
Cdd:PTZ00108 312 dqlISKLQEKAKKKKKKG---KEIKPNQ----IKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVL 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 362 ENPNVARkIVEKGTMaararvaaKKARELTRRKSALEVSSLPG--KLADCSSKDPAISEI---YIVEGDSA-----GGSA 431
Cdd:PTZ00108 385 KSPILEN-IVEWAQA--------KLAAELNKKMKAGKKSRILGipKLDDANDAGGKNSEEctlILTEGDSAkalalAGLS 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 432 KQGRDRHfqAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDF-DIEKARYHKVIIMTDADVDGAHIRTLLLT 510
Cdd:PTZ00108 456 VVGRDYY--GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHIKGLLIN 533
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 190710595 511 FFYRYMRQIIEH-GYIYIAQPPLFKVQQ-GKKIQYAYNEKELEKILAELPaQPKPGIQRYKGLG 572
Cdd:PTZ00108 534 MIHHFWPSLLKNpGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQTVG-LKGWKIKYYKGLG 596
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
562-622 |
1.51e-39 |
|
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: 138.67 E-value: 1.51e-39
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190710595 562 KPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQ 622
Cdd:pfam00986 3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
15-572 |
6.99e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 113.80 E-value: 6.99e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 15 LEAVRKRPGMYIGS---------------------TSGKGLHHLVWEIVDNSIDEALAG-YCDEINVSIE-EDNSIRVTD 71
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRDpKMDSLRVVIDvEQNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 72 NGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTE--LEVFVHREGKIHYQKYERGIPV 149
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEfvIETADGKRQKKYKQVFSNNMGK 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 150 ADLKVIGDTDQTGTITR--FKPDPEIFQETTVyEFDTLATrMRELAF-----LNRNIKLTIEDKREHkqkkefhyeggIK 222
Cdd:PLN03237 198 KSEPVITKCKKSENWTKvtFKPDLAKFNMTHL-EDDVVAL-MKKRVVdiagcLGKTVKVELNGKRIP-----------VK 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 223 SYVEHLN-----RSKQPIHEEPVYVEGSKDGIQVEVSLqyNEGYTNNIySFTNNIHTYEGGTHeVGFKTA--LTRVINDY 295
Cdd:PLN03237 265 SFSDYVDlylesANKSRPENLPRIYEKVNDRWEVCVSL--SEGQFQQV-SFVNSIATIKGGTH-VDYVTNqiANHVMEAV 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 296 GRKNSilkdaDSNLTGEDVREGLTAIVSIKHPNPQFEGQTKtklgnsEARTITESVFS---EAFEKFL--LENPNVARKI 370
Cdd:PLN03237 341 NKKNK-----NANIKAHNVKNHLWVFVNALIDNPAFDSQTK------ETLTLRQSSFGskcELSEDFLkkVMKSGIVENL 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 371 VEKGTMAARARVAAKKARELTRrksaleVSSLPgKLADCSSKDPAISE---IYIVEGDSAGGSAKQGR---DRHFQAILP 444
Cdd:PLN03237 410 LSWADFKQSKELKKTDGAKTTR------VTGIP-KLEDANEAGGKNSEkctLILTEGDSAKALAVAGLsvvGRNYYGVFP 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 445 LKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKA-RYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIE-H 522
Cdd:PLN03237 483 LRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKvP 562
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 190710595 523 GYIYIAQPPLFKV-QQGKKIQYAYNEKELEKILAELPAQPKP-GIQRYKGLG 572
Cdd:PLN03237 563 SFLVEFITPIVKAtRRGKKVLSFYSMPEYEEWKESLGGNATGwSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
221-340 |
1.13e-22 |
|
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: 93.09 E-value: 1.13e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 221 IKSYVEHLNRSKqpIHEEPVYVEGSKDGIQVEVSLQYNE---GYTNNIYSFTNNIHTYEGGTHEVGFKTALTRVINdygr 297
Cdd:cd00329 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 190710595 298 knsilkdadsnltGEDVREGLTAIVSIKHPN--PQFE-GQTKTKLG 340
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
423-515 |
3.58e-19 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 83.50 E-value: 3.58e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 423 EGDSAGGSAKQGR---DRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDF--DIEKARYHKVIIMTDA 497
Cdd:cd03365 7 EGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMTDQ 86
|
90
....*....|....*...
gi 190710595 498 DVDGAHIRTLLLTFFYRY 515
Cdd:cd03365 87 DHDGSHIKGLLINFIHSF 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
418-530 |
2.08e-17 |
|
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: 77.40 E-value: 2.08e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 418 EIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNdevrtiitaigtniggdFDIEKARYHKVIIMTDA 497
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 190710595 498 DVDGAHIRTLLLTFfyrymRQIIEH--GYIYIAQP 530
Cdd:pfam01751 64 DREGEAIALKLLEL-----KELLENagGRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
32-173 |
1.21e-12 |
|
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: 64.70 E-value: 1.21e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 32 KGLHHLVWEIVDNSIDEAlaGYCDEINVSIEEDN--SIRVTDNGRGIPVGIQEKMGRPAVEVIMTvlhaggkfggggykv 109
Cdd:pfam02518 4 LRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLPRIFEPFSTADKR--------------- 66
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 190710595 110 SGGLHGVGASVVNALSTELevfvhrEGKIHYQkyergipvadlkvigDTDQTGTITRFKPDPEI 173
Cdd:pfam02518 67 GGGGTGLGLSIVRKLVELL------GGTITVE---------------SEPGGGTTVTLTLPLAQ 109
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
32-137 |
3.14e-11 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 60.36 E-value: 3.14e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 32 KGLHHLVWEIVDNSIDEALAGycDEINVSIEEDN---SIRVTDNGRGIPVGIQEKMGRPAVEVimtvlhaggkfggGGYK 108
Cdd:smart00387 4 DRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPEDLEKIFEPFFRT-------------DKRS 68
|
90 100
....*....|....*....|....*....
gi 190710595 109 VSGGLHGVGASVVNALSTELEVFVHREGK 137
Cdd:smart00387 69 RKIGGTGLGLSIVKKLVELHGGEISVESE 97
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
417-520 |
5.93e-07 |
|
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: 47.42 E-value: 5.93e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 417 SEIYIVEGDSAGGSAKQGRDrHFQAILPLKGKIINVEKARLDKILSndevrtiitaigtniggdfdiekaRYHKVIIMTD 496
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90 100
....*....|....*....|....
gi 190710595 497 ADVDGAHIRTLLLTFFYRYMRQII 520
Cdd:cd00188 56 ADREGEAIALRLLELLKSLGKKVR 79
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
34-87 |
4.88e-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: 42.59 E-value: 4.88e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 190710595 34 LHHLVWEIVDNSIDEALAGycDEINVSIEEDNS---IRVTDNGRGIPVGIQEKMGRP 87
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLERIFER 55
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
40-77 |
6.61e-05 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 45.98 E-value: 6.61e-05
10 20 30 40
....*....|....*....|....*....|....*....|
gi 190710595 40 EIVDNSIDealAGyCDEINVSIEED--NSIRVTDNGRGIP 77
Cdd:PRK00095 29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGIS 64
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
33-170 |
6.65e-05 |
|
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: 43.48 E-value: 6.65e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 33 GLHHLVWEIVDNSID-EALAGYCDEINVSI-EEDNSIRVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVS 110
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIdPENNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 190710595 111 GGLHGVGASVVNALSTELEV-FVHRE-GKIHYQKYERGIPVADLKVIGDTDQTGTITR--FKPD 170
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVeTADSEsKKKFKQTWTNNMGKASEPKITPYEKGKDYTKvtFKPD 147
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
40-77 |
9.80e-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: 43.58 E-value: 9.80e-05
10 20 30 40
....*....|....*....|....*....|....*....|
gi 190710595 40 EIVDNSIDealAGyCDEINVSIEED--NSIRVTDNGRGIP 77
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGIS 55
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
40-77 |
1.20e-04 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 45.03 E-value: 1.20e-04
10 20 30 40
....*....|....*....|....*....|....*....|
gi 190710595 40 EIVDNSIDealAGyCDEINVSIEED--NSIRVTDNGRGIP 77
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGgkSLIRVTDNGCGMS 65
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
219-339 |
5.49e-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: 40.73 E-value: 5.49e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190710595 219 GGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVSLQYNEGYTNNIySFTNNIHTYEGGTHeVGFKT-ALTRVINDYGR 297
Cdd:cd03481 1 KSFKDYVKLYLKDANKEDGPPPPVVYEPVNDRWEVAVALSDGQFQQV-SFVNSIATTKGGTH-VDYVAdQIVKKLDEVVK 78
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 190710595 298 KnsiLKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKL 339
Cdd:cd03481 79 K---KNKGGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL 117
|
|
| CitA |
COG3290 |
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ... |
41-84 |
9.48e-03 |
|
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms];
Pssm-ID: 442519 [Multi-domain] Cd Length: 389 Bit Score: 38.68 E-value: 9.48e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 190710595 41 IVDNSIDEALAGYCDE--INVSIEEDNS---IRVTDNGRGIPVGIQEKM 84
Cdd:COG3290 289 LLDNAIEAVEKLPEEErrVELSIRDDGDelvIEVEDSGPGIPEELLEKI 337
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