|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
4-640 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1290.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 4 KQMQENAYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGI 83
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 84 PVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIG 163
Cdd:PRK05644 81 PVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 164 DTDKTGTITRFKPDPEIFkETTEYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKKE-FHYEGGIKSYVEHLNRSKQPI 242
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEEtFHYEGGIKEYVEYLNRNKEPL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 243 HEEPVYVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVR 322
Cdd:PRK05644 240 HEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 323 EGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKS 402
Cdd:PRK05644 320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 403 ALEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGT 482
Cdd:PRK05644 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGT 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 483 NIGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKiQYAYNDKELEKILA 562
Cdd:PRK05644 480 GIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILA 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 563 ELPAQ--PKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKYVKNLDI 640
Cdd:PRK05644 559 ELKLKgnPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
7-640 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1227.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 7 QENAYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVG 86
Cdd:COG0187 2 KKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 87 IQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGDTD 166
Cdd:COG0187 82 IHPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 167 KTGTITRFKPDPEIFkETTEYEFDTLATRMRELAFLNRNIKLTIEDKR-EHKQKKEFHYEGGIKSYVEHLNRSKQPIHEE 245
Cdd:COG0187 162 RTGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEReEEPKEETFHYEGGIKDFVEYLNEDKEPLHPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 246 PVYVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVREGL 325
Cdd:COG0187 241 VIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 326 TAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKSALE 405
Cdd:COG0187 321 TAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 406 VSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIG 485
Cdd:COG0187 401 SSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 486 GDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKIQYAYNDKELEKILAELP 565
Cdd:COG0187 481 DDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELK 560
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446358125 566 AQPKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKYVKNLDI 640
Cdd:COG0187 561 GKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
5-640 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1099.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 5 QMQENAYDESQIQVLEGLEAVRKRPGMYIGSTS-GKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGI 83
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 84 PVGIQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIG 163
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 164 DTDKTGTITRFKPDPEIFkETTEYEFDTLATRMRELAFLNRNIKLTIEDKReHKQKKEFHYEGGIKSYVEHLNRSKQPIH 243
Cdd:PRK14939 161 ETDKTGTEVRFWPSPEIF-ENTEFDYDILAKRLRELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 244 EEPVYVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVRE 323
Cdd:PRK14939 239 PNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDARE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 324 GLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKSA 403
Cdd:PRK14939 319 GLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 404 LEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTN 483
Cdd:PRK14939 399 LDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 484 IG-GDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKIQYAYNDKELEKILA 562
Cdd:PRK14939 479 IGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLI 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 563 EL------------------------------------------------------------------------------ 564
Cdd:PRK14939 559 ELalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsae 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 565 -----------------PAQPKPG-------------------------IQRYKGLGEMNPTQLWETTMDPEVRSLLQVS 602
Cdd:PRK14939 639 yrrlvelaeklrglieeGAYLERGerkqpvssfeealdwllaearkglsIQRYKGLGEMNPEQLWETTMDPENRRLLQVT 718
|
730 740 750
....*....|....*....|....*....|....*...
gi 446358125 603 LQDAIEADETFEILMGDKVEPRRNFIQENAKYVKNLDI 640
Cdd:PRK14939 719 IEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
11-640 |
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: 1077.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 11 YDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQEK 90
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 91 MGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGDTDKTGT 170
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 171 ITRFKPDPEIFkETTEYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKK-EFHYEGGIKSYVEHLNRSKQPIHEEPVYV 249
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKvTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 250 EGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVREGLTAIV 329
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 330 SIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKSALEVSSL 409
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 410 PGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFD 489
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 490 IEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKIQYA------------------ 551
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIkddkekdlvgealedlka 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 552 ---YNDKELEKILAELPAQP---KPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRR 625
Cdd:TIGR01059 560 lyiYSDKEKEEAKTQIPVHLgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRR 639
|
650
....*....|....*
gi 446358125 626 NFIQENAKYVKNLDI 640
Cdd:TIGR01059 640 EFIEANALDVKNLDV 654
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
6-635 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 922.96 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 6 MQENAYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPV 85
Cdd:PRK05559 3 MMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 86 GIQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGDT 165
Cdd:PRK05559 83 GIHPEEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 166 --DKTGTITRFKPDPEIFKeTTEYEFDTLATRMRELAFLNRNIKLTIEDKREhkqKKEFHYEGGIKSYVEHLNRSKQPIH 243
Cdd:PRK05559 163 gkRKTGTRVRFWPDPKIFD-SPKFSPERLKERLRSKAFLLPGLTITLNDERE---RQTFHYENGLKDYLAELNEGKETLP 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 244 EEPV-YVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKdADSNLTGEDVR 322
Cdd:PRK05559 239 EEFVgSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 323 EGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKgtMAARARVAAKKARELTRRKS 402
Cdd:PRK05559 318 EGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEK--AIKAAQARLRAAKKVKRKKK 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 403 ALEvSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGT 482
Cdd:PRK05559 396 TSG-PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGI 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 483 NIGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKIQYAYNDKELEKILA 562
Cdd:PRK05559 475 GPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLK 554
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446358125 563 ELPAQ-PKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKYV 635
Cdd:PRK05559 555 KLGKKgGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
40-633 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 899.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 40 GLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGG 119
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 120 LHGVGASVVNALSTELEVFVHRDGKIHYQKYER-GIPVADLKVIGDTDKTGTITRFKPDPEIFKETTEYEFDTLATRMRE 198
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 199 LAFLNRNIKLTIEDKREHKqKKEFHYEGGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVALQYNEGYTNHIYSFTNN 278
Cdd:smart00433 161 LAFLNKGVKITLNDERSDE-EKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNN 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 279 IHTYEGGTHEVGFKTALTRVINDYGRKNNILKDAdsNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESV 358
Cdd:smart00433 240 IATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 359 FSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKsALEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSA 438
Cdd:smart00433 318 VSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 439 KQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTF 518
Cdd:smart00433 397 KSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 519 FYRYMRQIIECGYIYIAQPPLFKVQQGKKiQYAYNDKELEKILAELPAQP----KPGIQRYKGLGEMNPTQLWETTMDPE 594
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKK-KYVYSFYSLDEYEKWLEKTEgnksKYEIQRYKGLGEMNADQLWETTMDPE 555
|
570 580 590
....*....|....*....|....*....|....*....
gi 446358125 595 VRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAK 633
Cdd:smart00433 556 RRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
9-634 |
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: 746.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 9 NAYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQ 88
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 89 EKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHRDGKIHYQKYER-GIPVADLKVIGDTDK 167
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 168 TGTITRFKPDPEIFKeTTEYEFDTLATRMRELAFLNRNIKLTIEDKReHKQKKEFHYEGGIKSYVEHLNRSKQpIHEEPV 247
Cdd:TIGR01058 163 TGTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKR-TNKTTVFFYENGLVDFVDYINETKE-TLSQVT 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 248 YVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVREGLTA 327
Cdd:TIGR01058 240 YFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSA 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 328 IVSIKHP--NPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTR--RKSA 403
Cdd:TIGR01058 320 IISVRIPeeLIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKPK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 404 LEVSSLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTN 483
Cdd:TIGR01058 400 KEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTG 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 484 IGGDFDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQ--GKKIQYAYNDKELEKIL 561
Cdd:TIGR01058 480 IGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELESVK 559
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446358125 562 AELPAQPkpgIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQENAKY 634
Cdd:TIGR01058 560 KKLKNYT---LQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINF 629
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
9-632 |
1.32e-178 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 530.22 E-value: 1.32e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 9 NAYDESQIQVLEGLEAVRKRPGMYIGSTSGKGLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQ 88
Cdd:PTZ00109 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 89 EKMGRPAVEVIMTVLH----------------------------------------AGGKFGGGGYKVSGGLHGVGASVV 128
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 129 NALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGD-TDKTGTITRFKPD-PEIFKETTEYEF-------------DTLA 193
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCpLKKRGTTIHFLPDyKHIFKTHHQHTEteeeegckngfnlDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 194 TRMRELAFLNRNIKLTIEDKREHKQKKEFHYE-----GGIKSYVEHLNRSKQPIHEEPVYV--EGSKDGIQVEVALQYN- 265
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERIANENNFYPYEtikheGGTREFLEELIKDKTPLYKDINIIsiRGVIKNVNVEVSLSWSl 417
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 266 EGYTNHIYSFTNNIHTyEGGTHEVGFKTALTRVINDYGRKNNILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTK 345
Cdd:PTZ00109 418 ESYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTK 496
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 346 LGNSEARTITESVFSEAFEKFLLENPNVARKVVDKGTMAARARVAAKKARELTRRKSALEVSS-LPGKLADCSSKDPAIS 424
Cdd:PTZ00109 497 LGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDDIERN 576
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 425 EIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLD-KILSNDEVRTIITAIGTNIGGD---------------- 487
Cdd:PTZ00109 577 ELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtkaskd 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 488 ----------------FDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKV--------- 542
Cdd:PTZ00109 657 esvqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqfn 736
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 543 ---QQGKKIQYAYNDKELEKILAELPAQPKPG------------------------------------------------ 571
Cdd:PTZ00109 737 vstKNSKKYIYTWSDEELNVLIKLLNKDYSSKettrsveekgnapdldneyedekldnknmrennvdevelktelgtnva 816
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 572 ----------------------IQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQ 629
Cdd:PTZ00109 817 dteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIF 896
|
...
gi 446358125 630 ENA 632
Cdd:PTZ00109 897 ENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
11-630 |
2.27e-175 |
|
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: 512.54 E-value: 2.27e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 11 YDESQIQVLEGLEAVRKRPGMYIGSTSgkgLHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQEK 90
Cdd:TIGR01055 4 YSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 91 MGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGDTDK--T 168
Cdd:TIGR01055 81 EGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 169 GTITRFKPDPEIFKEtTEYEFDTLATRMRELAFLNRNIKLTIEDKREHKQKKeFHYEGGIKSYVEHLNRSKQPIHEEPVY 248
Cdd:TIGR01055 161 GTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKAL-WNYPDGLKDYLSEAVNGDNTLPPKPFS 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 249 VEGSKDGIQVEVALQY-NEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRKNNILKDAdSNLTGEDVREGLTA 327
Cdd:TIGR01055 239 GNFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSY 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 328 IVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDkgtMAARARVAAKKARELTRRKSALEVS 407
Cdd:TIGR01055 318 VLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAE---HAISSAQRRKRAAKKVVRKKLTSGP 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 408 SLPGKLADCSSKDPAISEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGD 487
Cdd:TIGR01055 395 ALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDSN 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 488 fDIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQPPLFKVQQGKKIQYAYNDKELEKILAELP-A 566
Cdd:TIGR01055 475 -DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKkK 553
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446358125 567 QPKPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDA--IEADETFEILMGDKV-EPRRNFIQE 630
Cdd:TIGR01055 554 KGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVqdQRVDKIMDMLLAKKRsEDRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
41-219 |
7.25e-94 |
|
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: 286.74 E-value: 7.25e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 41 LHHLVWEIVDNSIDEALAGYCDEINVSIEEDNSILVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGL 120
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 121 HGVGASVVNALSTELEVFVHRDGKIHYQKYERGIPVADLKVIGDTDKTGTITRFKPDPEIFkETTEYEFDTLATRMRELA 200
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170
....*....|....*....
gi 446358125 201 FLNRNIKLTIEDKREHKQK 219
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 ... |
226-380 |
1.28e-84 |
|
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: 262.50 E-value: 1.28e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 226 GGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGRK 305
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446358125 306 NNILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDK 380
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
424-537 |
1.84e-81 |
|
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: 252.19 E-value: 1.84e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 424 SEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKARYHKVIIMTD 503
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 446358125 504 ADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQP 537
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 ... |
227-380 |
3.11e-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: 3.11e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 227 GIKSYVEHLNRSKQPIHEEPVYVEG--SKDGIQVEVALQYNEGYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINDYGR 304
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGesPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446358125 305 KNNILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNVARKVVDK 380
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
424-537 |
3.79e-67 |
|
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173780 [Multi-domain] Cd Length: 115 Bit Score: 214.68 E-value: 3.79e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 424 SEIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGG-DFDIEKARYHKVIIMT 502
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKdDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 446358125 503 DADVDGAHIRTLLLTFFYRYMRQIIECGYIYIAQP 537
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
14-629 |
7.01e-44 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 166.08 E-value: 7.01e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 14 SQIQVLEGLEAVRKRPGMYIGSTS---------GK--------GLHHLVWEIVDNSIDEALAG---YCDEINVSIEeDNS 73
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAyeaherflfGKftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 74 ILVTDNGRGIPvgiQEKMGRPAVEVIMTVLHAGGKFG-----GGGYKVSGGLHGVGASVVNALSTeleVFVHR--DGKih 146
Cdd:PHA02569 81 VTVSDNGRGIP---QAMVTTPEGEEIPGPVAAWTRTKagsnfDDTNRVTGGMNGVGSSLTNFFSV---LFIGEtcDGK-- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 147 yqkyeRGIPVA---DLKVIGDTDK----TGTITRFKPDPEIFKETT---EYEfDTLATRMRELAFLNRNIKLTIEDKReh 216
Cdd:PHA02569 153 -----NEVTVNcsnGAENISWSTKpgkgKGTSVTFIPDFSHFEVNGldqQYL-DIILDRLQTLAVVFPDIKFTFNGKK-- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 217 kqkkefhYEGGIKSYVEHLNrskqpihEEPVYVEGSKDGIQVEVAlqyNEGYTNhiYSFTNNIHTYEGGTHEVGFKTALT 296
Cdd:PHA02569 225 -------VSGKFKKYAKQFG-------DDTIVQENDNVSIALAPS---PDGFRQ--LSFVNGLHTKNGGHHVDCVMDDIC 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 297 -RVINDYGRKNNIlkdadsNLTGEDVREGLTAIVSIKH-PNPQFEGQTKTKLGNS--EARTITESVFsEAFEKFLLENPN 372
Cdd:PHA02569 286 eELIPMIKKKHKI------EVTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgEIRNHIDLDY-KKIAKQILKTEA 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 373 V---------ARK-VVDKGTMAARARVAakkarelTRRKSALEV-SSLPGKLADcsskdpaiSEIYIVEGDSAGGSAKQG 441
Cdd:PHA02569 359 IimpiieaalARKlAAEKAAETKAAKKA-------KKAKVAKHIkANLIGKDAE--------TTLFLTEGDSAIGYLIEV 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 442 RDRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKarYHKVIIMTDADVDG-AHIRTLLLTFFY 520
Cdd:PHA02569 424 RDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENMN--YKNIAIMTDADVDGkGSIYPLLLAFFS 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 521 RYmRQIIECGYIYIAQPPLFKVQQGKKIQYAYNDKELEKilaELPAQPKPGIQRYKGLGEMNptqlwettmDPEVRSLLQ 600
Cdd:PHA02569 502 RW-PELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEK---AKDSLKKWSIRYIKGLGSLR---------KSEYRRVIN 568
|
650 660 670
....*....|....*....|....*....|...
gi 446358125 601 VSLQDAIEAD----ETFEILMGDKVEPRRNFIQ 629
Cdd:PHA02569 569 NPVYDVVVLPddwkELFEMLFGDDADLRKDWMS 601
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
12-579 |
3.96e-41 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 160.98 E-value: 3.96e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 12 DESQIQVLEGLEAVRKRPGMYIGSTS-------------GK----------GLHHLVWEI----VDNSIDEALAGYCDEI 64
Cdd:PTZ00108 6 VEERYQKKTQIEHILLRPDTYIGSIEtqtedmwvydeekNRmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 65 NVSI-EEDNSILVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELEVFV--HR 141
Cdd:PTZ00108 86 KVTIdEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 142 DGKIHYQKYERGIPVADLKVIGDTDKTGTITR--FKPDPEIFKeTTEYEFDTLATRMR---ELAFLNRNIKLTIEDKREh 216
Cdd:PTZ00108 166 SGKKFKMTWTDNMSKKSEPRITSYDGKKDYTKvtFYPDYAKFG-MTEFDDDMLRLLKKrvyDLAGCFGKLKVYLNGERI- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 217 kqkkefhyegGIKSYVEHLNRSKQPIHEE-PVYVEGSKDGIQ--VEVALQYNEGYTNHIySFTNNIHTYEGGTHeVGFkt 293
Cdd:PTZ00108 244 ----------AIKSFKDYVDLYLPDGEEGkKPPYPFVYTSVNgrWEVVVSLSDGQFQQV-SFVNSICTTKGGTH-VNY-- 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 294 ALTRVINDYGRKNNILKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKFLLENPNV 373
Cdd:PTZ00108 310 ILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSPIL 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 374 ARKVvdkgtmaarARVAAKKARELTRRKSALEVSSLPG--KLADCSSKDPAISEI---YIVEGDSA-----GGSAKQGRD 443
Cdd:PTZ00108 390 ENIV---------EWAQAKLAAELNKKMKAGKKSRILGipKLDDANDAGGKNSEEctlILTEGDSAkalalAGLSVVGRD 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 444 RHfqAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDF-DIEKARYHKVIIMTDADVDGAHIRTLLLTFFYRY 522
Cdd:PTZ00108 461 YY--GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHF 538
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*....
gi 446358125 523 MRQIIEC-GYIYIAQPPLFKVQQ-GKKIQYAYNDKELEKILAELPaQPKPGIQRYKGLG 579
Cdd:PTZ00108 539 WPSLLKNpGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQTVG-LKGWKIKYYKGLG 596
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
569-629 |
2.34e-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: 138.28 E-value: 2.34e-39
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446358125 569 KPGIQRYKGLGEMNPTQLWETTMDPEVRSLLQVSLQDAIEADETFEILMGDKVEPRRNFIQ 629
Cdd:pfam00986 3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
22-630 |
5.03e-39 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 154.48 E-value: 5.03e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 22 LEAVRKRPGMYIGST-----------SGK----------GLHHLVWEIVDNSIDEALAG-YCDEINVSIE-EDNSILVTD 78
Cdd:PLN03128 13 LEHILLRPDTYIGSTekhtqtlwvyeGGEmvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSLKVDIDvEQNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 79 NGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTE--LEVFVHRDGKIHYQKYERGIPV 156
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEftVETADGNRGKKYKQVFTNNMSV 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 157 ADLKVIGDTDKTGTITR--FKPDPEIFKETT--EYEFDTLATRMRELA-FLNRNIKLTIEDKreHKQKKEFhyeggiKSY 231
Cdd:PLN03128 173 KSEPKITSCKASENWTKitFKPDLAKFNMTRldEDVVALMSKRVYDIAgCLGKKLKVELNGK--KLPVKSF------QDY 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 232 VEHLNRSKQPIHEEPVYVEGSKDGIQVEVALqyNEGYTNHIySFTNNIHTYEGGTHeVGFKTA--LTRVINDYGRKNNIL 309
Cdd:PLN03128 245 VGLYLGPNSREDPLPRIYEKVNDRWEVCVSL--SDGSFQQV-SFVNSIATIKGGTH-VDYVADqiVKHIQEKVKKKNKNA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 310 KdadsNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKLGNSEARTITESVFSEAFEKfLLENPNVARKVVDKGTMAARARV 389
Cdd:PLN03128 321 T----HVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLK-KVEKCGVVENILSWAQFKQQKEL 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 390 AAKKARELTRrksaleVSSLPgKLADCSSKDPAISE---IYIVEGDSA-----GGSAKQGRDRHfqAILPLKGKIINVEK 461
Cdd:PLN03128 396 KKKDGAKRQR------LTGIP-KLDDANDAGGKKSKdctLILTEGDSAkalamSGLSVVGRDHY--GVFPLRGKLLNVRE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 462 ARLDKILSNDEVRTIITAIGTNIGGDFDIEKA---RYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEC-GYIYIAQP 537
Cdd:PLN03128 467 ASHKQIMKNAEITNIKQILGLQFGKTYDEENTkslRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIpGFLVEFIT 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 538 PLFKVQQGKKIQYAYNDKELEKILAEL-PAQPKPGIQRYKGLGEMNPTQLWE--TTMDPEVRSLLQVSLQDAIEADETFE 614
Cdd:PLN03128 547 PIVKATKGGKSLSFYTMPEYEAWKESLeGETKGWTIKYYKGLGTSTSEEAKEyfSNLDIHKKEFLWQSDEDGDLIDMAFS 626
|
650
....*....|....*.
gi 446358125 615 ilmGDKVEPRRNFIQE 630
Cdd:PLN03128 627 ---KKRVEDRKIWLNN 639
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
22-579 |
3.23e-25 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 111.88 E-value: 3.23e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 22 LEAVRKRPGMYIGS---------------------TSGKGLHHLVWEIVDNSIDEALAG-YCDEINVSIE-EDNSILVTD 78
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRDpKMDSLRVVIDvEQNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 79 NGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSTELeVFVHRDG---KIHYQKYERGIP 155
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEF-VIETADGkrqKKYKQVFSNNMG 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 156 VADLKVIGDTDKTGTITR--FKPDPEIFKeTTEYEFDTLATrMRELAF-----LNRNIKLTIEDKREHkqkkefhyeggI 228
Cdd:PLN03237 197 KKSEPVITKCKKSENWTKvtFKPDLAKFN-MTHLEDDVVAL-MKKRVVdiagcLGKTVKVELNGKRIP-----------V 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 229 KSYVEHLN---RSKQPIHEEPVYVEGSKDGIQVEVALQYNEGYTNHIySFTNNIHTYEGGTHeVGFKTA--LTRVINDYG 303
Cdd:PLN03237 264 KSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTH-VDYVTNqiANHVMEAVN 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 304 RKNNilkdaDSNLTGEDVREGLTAIVSIKHPNPQFEGQTKtklgnsEARTITESVFS---EAFEKFLlenpnvaRKVVDK 380
Cdd:PLN03237 342 KKNK-----NANIKAHNVKNHLWVFVNALIDNPAFDSQTK------ETLTLRQSSFGskcELSEDFL-------KKVMKS 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 381 GTMAARAR-VAAKKAREL--TRRKSALEVSSLPgKLADCSSKDPAISE---IYIVEGDSAGGSAKQGR---DRHFQAILP 451
Cdd:PLN03237 404 GIVENLLSwADFKQSKELkkTDGAKTTRVTGIP-KLEDANEAGGKNSEkctLILTEGDSAKALAVAGLsvvGRNYYGVFP 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 452 LKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDFDIEKA-RYHKVIIMTDADVDGAHIRTLLLTFFYRYMRQIIEC- 529
Cdd:PLN03237 483 LRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVp 562
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 446358125 530 GYIYIAQPPLFKV-QQGKKIQYAYNDKELEKILAELPAQPKP-GIQRYKGLG 579
Cdd:PLN03237 563 SFLVEFITPIVKAtRRGKKVLSFYSMPEYEEWKESLGGNATGwSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
228-347 |
1.34e-23 |
|
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: 95.79 E-value: 1.34e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 228 IKSYVEHLNRSKqpIHEEPVYVEGSKDGIQVEVALQYNE---GYTNHIYSFTNNIHTYEGGTHEVGFKTALTRVINdygr 304
Cdd:cd00329 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 446358125 305 knnilkdadsnltGEDVREGLTAIVSIKHPN--PQFE-GQTKTKLG 347
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
430-522 |
3.74e-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: 3.74e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 430 EGDSAGGSAKQGR---DRHFQAILPLKGKIINVEKARLDKILSNDEVRTIITAIGTNIGGDF--DIEKARYHKVIIMTDA 504
Cdd:cd03365 7 EGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMTDQ 86
|
90
....*....|....*...
gi 446358125 505 DVDGAHIRTLLLTFFYRY 522
Cdd:cd03365 87 DHDGSHIKGLLINFIHSF 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
425-537 |
3.33e-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: 77.01 E-value: 3.33e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 425 EIYIVEGDSAGGSAKQGRDRHFQAILPLKGKIINVEKARLDKILSNdevrtiitaigtniggdFDIEKARYHKVIIMTDA 504
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|...
gi 446358125 505 DVDGAHIRTLLLTfFYRYMRQIIecGYIYIAQP 537
Cdd:pfam01751 64 DREGEAIALKLLE-LKELLENAG--GRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
39-180 |
3.90e-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: 63.16 E-value: 3.90e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 39 KGLHHLVWEIVDNSIDEAlaGYCDEINVSIEEDN--SILVTDNGRGIPVGIQEKMGRPAVEVIMTvlhaggkfggggykv 116
Cdd:pfam02518 4 LRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLPRIFEPFSTADKR--------------- 66
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446358125 117 SGGLHGVGASVVNALSTELevfvhrDGKIHYQkyergipvadlkvigDTDKTGTITRFKPDPEI 180
Cdd:pfam02518 67 GGGGTGLGLSIVRKLVELL------GGTITVE---------------SEPGGGTTVTLTLPLAQ 109
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
39-144 |
3.61e-10 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 57.66 E-value: 3.61e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 39 KGLHHLVWEIVDNSIDEALAGycDEINVSIEEDN---SILVTDNGRGIPVGIQEKMGRPAVEVimtvlhaggkfggGGYK 115
Cdd:smart00387 4 DRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPEDLEKIFEPFFRT-------------DKRS 68
|
90 100
....*....|....*....|....*....
gi 446358125 116 VSGGLHGVGASVVNALSTELEVFVHRDGK 144
Cdd:smart00387 69 RKIGGTGLGLSIVKKLVELHGGEISVESE 97
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
424-527 |
6.49e-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: 6.49e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 424 SEIYIVEGDSAGGSAKQGRDrHFQAILPLKGKIINVEKARLDKILSndevrtiitaigtniggdfdiekaRYHKVIIMTD 503
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90 100
....*....|....*....|....
gi 446358125 504 ADVDGAHIRTLLLTFFYRYMRQII 527
Cdd:cd00188 56 ADREGEAIALRLLELLKSLGKKVR 79
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
226-346 |
8.33e-05 |
|
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: 43.04 E-value: 8.33e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 226 GGIKSYVEHLNRSKQPIHEEPVYVEGSKDGIQVEVALQYNEGYTNHIySFTNNIHTYEGGTHeVGFKT-ALTRVINDYGR 304
Cdd:cd03481 1 KSFKDYVKLYLKDANKEDGPPPPVVYEPVNDRWEVAVALSDGQFQQV-SFVNSIATTKGGTH-VDYVAdQIVKKLDEVVK 78
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 446358125 305 KnniLKDADSNLTGEDVREGLTAIVSIKHPNPQFEGQTKTKL 346
Cdd:cd03481 79 K---KNKGGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL 117
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
40-177 |
1.43e-04 |
|
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: 42.33 E-value: 1.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446358125 40 GLHHLVWEIVDNSID-EALAGYCDEINVSI-EEDNSILVTDNGRGIPVGIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVS 117
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIdPENNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446358125 118 GGLHGVGASVVNALSTELEV-FVHRD-GKIHYQKYERGIPVADLKVIGDTDKTGTITR--FKPD 177
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVeTADSEsKKKFKQTWTNNMGKASEPKITPYEKGKDYTKvtFKPD 147
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
41-94 |
2.05e-04 |
|
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: 41.05 E-value: 2.05e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 446358125 41 LHHLVWEIVDNSIDEALAGycDEINVSIEEDNS---ILVTDNGRGIPVGIQEKMGRP 94
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLERIFER 55
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
47-84 |
7.51e-04 |
|
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.
Pssm-ID: 340403 [Multi-domain] Cd Length: 188 Bit Score: 40.88 E-value: 7.51e-04
10 20 30 40
....*....|....*....|....*....|....*....|
gi 446358125 47 EIVDNSIDealAGyCDEINVSIEED--NSILVTDNGRGIP 84
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGIS 55
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
47-84 |
8.88e-04 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 42.51 E-value: 8.88e-04
10 20 30 40
....*....|....*....|....*....|....*....|
gi 446358125 47 EIVDNSIDealAGyCDEINVSIEED--NSILVTDNGRGIP 84
Cdd:PRK00095 29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGIS 64
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
47-84 |
1.51e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 41.57 E-value: 1.51e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 446358125 47 EIVDNSIDealAGyCDEINVSIEED--NSILVTDNGRGIP 84
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGgkSLIRVTDNGCGMS 65
|
|
| |
