|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-631 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1237.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 1 MSNYDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDL 80
Cdd:PRK05644 5 AQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIPVDI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 81 HPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSDH 160
Cdd:PRK05644 85 HPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 161 TGTIVTFKSDHLVFtETTVYEYEILRNRIQQLAFLNKGIKITIIDARGAVAIENSYHYEGGIVEYVSFLNQGKGKINHDV 240
Cdd:PRK05644 165 TGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 241 LYIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLK-KDESFLGEDVKEGLT 319
Cdd:PRK05644 244 IYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKeKDDNLTGEDVREGLT 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 320 VIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRKSPLDA 399
Cdd:PRK05644 324 AVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALES 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 400 LGFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGD 479
Cdd:PRK05644 404 SSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGD 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 480 EFDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGKRvEYVYSDEQLTKILAEIGG 559
Cdd:PRK05644 484 DFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILAELKL 562
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088626583 560 ----RPNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQENAIYADNIDA 631
Cdd:PRK05644 563 kgnpKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
2-631 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1197.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 2 SNYDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLH 81
Cdd:COG0187 4 SNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDIH 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 82 PKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSDHT 161
Cdd:COG0187 84 PKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRT 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 162 GTIVTFKSDHLVFtETTVYEYEILRNRIQQLAFLNKGIKITIIDARGAVAIENSYHYEGGIVEYVSFLNQGKGKINHDVL 241
Cdd:COG0187 164 GTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKDFVEYLNEDKEPLHPEVI 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 242 YIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLK-KDESFLGEDVKEGLTV 320
Cdd:COG0187 243 YFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKeKDKNLTGDDVREGLTA 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 321 IVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRKSPLDAL 400
Cdd:COG0187 323 VISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESS 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 401 GFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDE 480
Cdd:COG0187 403 GLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDD 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 481 FDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGKRVEYVYSDEQLTKILAEIGGR 560
Cdd:COG0187 483 FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKGK 562
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088626583 561 --PNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQENAIYADNIDA 631
Cdd:COG0187 563 kkVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-630 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1033.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 1 MSNYDASNIQILEGLEAVRKRPGMYIGSTG-SRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVD 79
Cdd:PRK14939 4 SNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 80 LHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSD 159
Cdd:PRK14939 84 IHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETD 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 160 HTGTIVTFKSDHLVFTeTTVYEYEILRNRIQQLAFLNKGIKITIIDARGAvaIENSYHYEGGIVEYVSFLNQGKGKINHD 239
Cdd:PRK14939 164 KTGTEVRFWPSPEIFE-NTEFDYDILAKRLRELAFLNSGVRIRLKDERDG--KEEEFHYEGGIKAFVEYLNRNKTPLHPN 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 240 VLYIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLKKD-ESFLGEDVKEGL 318
Cdd:PRK14939 241 IFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAkVSLTGDDAREGL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 319 TVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRKSPLD 398
Cdd:PRK14939 321 TAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 399 ALGFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIG 478
Cdd:PRK14939 401 IAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 479 -DEFDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGKRVEYVYSDEQLTKILAEI 557
Cdd:PRK14939 481 rDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIEL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 558 G----------GRP------------------------------------------------------------------ 561
Cdd:PRK14939 561 AlegatlhladGPAisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsaeyr 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 562 ----------------------------------------------NIQRYKGLGEMNPEQLWETTMDPENRILLQVSLK 595
Cdd:PRK14939 641 rlvelaeklrglieegaylergerkqpvssfeealdwllaearkglSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIE 720
|
730 740 750
....*....|....*....|....*....|....*
gi 1088626583 596 DAMDADQVFSMLMGEEVEPRKAFIQENAIYADNID 630
Cdd:PRK14939 721 DAIAADEIFTTLMGDEVEPRREFIEENALNVANLD 755
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
4-630 |
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: 1019.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 4 YDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLHPK 83
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 84 TNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSDHTGT 163
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 164 IVTFKSDHLVFtETTVYEYEILRNRIQQLAFLNKGIKITIIDARGAVAIENSYHYEGGIVEYVSFLNQGKGKINHDVLYI 243
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 244 DKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLKK-DESFLGEDVKEGLTVIV 322
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKEsKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 323 SIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRKSPLDALGF 402
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 403 ASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDEFD 482
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 483 GEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGK---------------------RV 541
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKkeryikddkekdlvgealedlKA 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 542 EYVYSDEQLTKILAEI---GGR--PNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRK 616
Cdd:TIGR01059 560 LYIYSDKEKEEAKTQIpvhLGRkgIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRR 639
|
650
....*....|....
gi 1088626583 617 AFIQENAIYADNID 630
Cdd:TIGR01059 640 EFIEANALDVKNLD 653
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-628 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 909.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 1 MSNYDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDL 80
Cdd:PRK05559 5 TNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 81 HPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGT--S 158
Cdd:PRK05559 85 HPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTagK 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 159 DHTGTIVTFKSDHLVFtETTVYEYEILRNRIQQLAFLNKGIKITIIDARGavaiENSYHYEGGIVEYVSFLNQGKGKI-N 237
Cdd:PRK05559 165 RKTGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERE----RQTFHYENGLKDYLAELNEGKETLpE 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 238 HDVLYIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLKKDESFLGEDVKEG 317
Cdd:PRK05559 240 EFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKKLEGEDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 318 LTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKaREATRRKSPL 397
Cdd:PRK05559 320 LAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAK-KVKRKKKTSG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 398 DALgfASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGI 477
Cdd:PRK05559 399 PAL--PGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGP 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 478 GDEFDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGKRVEYVYSDEQLTKILAEI 557
Cdd:PRK05559 477 GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKL 556
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088626583 558 ---GGRPNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQENAIYADN 628
Cdd:PRK05559 557 gkkGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFAEE 630
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
33-623 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 864.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 33 GLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGG 112
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 113 LHGVGMSVVNALSENFLVEIMRNGNIYQQKYER-GIPVTDVIINGTSDHTGTIVTFKSDHLVFTETTVYEYEILRNRIQQ 191
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 192 LAFLNKGIKITIIDARGAvaIENSYHYEGGIVEYVSFLNQGKGKINHDVLYIDKEVDGITIDIALQYNDSYATNLYSFAN 271
Cdd:smart00433 161 LAFLNKGVKITLNDERSD--EEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVN 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 272 NIPTHEGGMHEDGFKMALTRVLNKYATEQGMLKKDeSFLGEDVKEGLTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQI 351
Cdd:smart00433 239 NIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK-NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 352 VGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRKSpLDALGFASKLADCRSKDPVISEIYIVEGDSAGGSA 431
Cdd:smart00433 318 VSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 432 KQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDEFDGEKARYHKVVIMTDADIDGAHIRTLLLTF 511
Cdd:smart00433 397 KSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 512 FFRYMKQLIDLGYVYIAQPPLYKVQLGKRVEYVYS---DEQLTKILAEIGGR--PNIQRYKGLGEMNPEQLWETTMDPEN 586
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYSFyslDEYEKWLEKTEGNKskYEIQRYKGLGEMNADQLWETTMDPER 556
|
570 580 590
....*....|....*....|....*....|....*..
gi 1088626583 587 RILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQENA 623
Cdd:smart00433 557 RTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
2-622 |
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: 737.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 2 SNYDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLH 81
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 82 PKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYER-GIPVTDVIINGTSDH 160
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 161 TGTIVTFKSDHLVFTeTTVYEYEILRNRIQQLAFLNKGIKITIIDARGAVAIEnsYHYEGGIVEYVSFLNQGKgKINHDV 240
Cdd:TIGR01058 163 TGTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTV--FFYENGLVDFVDYINETK-ETLSQV 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 241 LYIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLK-KDESFLGEDVKEGLT 319
Cdd:TIGR01058 239 TYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKeKDKNLEGSDIREGLS 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 320 VIVSIKHP--NPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRR-KSP 396
Cdd:TIGR01058 319 AIISVRIPeeLIQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKSgKKP 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 397 LDALGFAS-KLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGT 475
Cdd:TIGR01058 399 KKEKGILSgKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGT 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 476 GIGDEFDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQL--GKRVEYVYSDEQLTKI 553
Cdd:TIGR01058 479 GIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELESV 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088626583 554 LAEIGGRpNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQEN 622
Cdd:TIGR01058 559 KKKLKNY-TLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEAN 626
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
2-621 |
6.03e-179 |
|
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: 521.40 E-value: 6.03e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 2 SNYDASNIQILEGLEAVRKRPGMYIGSTGsrgLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLH 81
Cdd:TIGR01055 2 TNYSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIH 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 82 PKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSDH- 160
Cdd:TIGR01055 79 PKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKr 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 161 -TGTIVTFKSDHLVFTE---TTVYEYEILRNRiqqlAFLNKGIKITIIDargavAIENS---YHYEGGIVEYVSflnqgk 233
Cdd:TIGR01055 159 lTGTSVHFTPDPEIFDSlhfSVSRLYHILRAK----AVLCRGVEIEFED-----EVNNTkalWNYPDGLKDYLS------ 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 234 GKINHDVLYIDK------EVDGITIDIALQY-NDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATEQGMLKKD 306
Cdd:TIGR01055 224 EAVNGDNTLPPKpfsgnfEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 307 ESFLGEDVKEGLTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARiaaKK 386
Cdd:TIGR01055 304 VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRR---KR 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 387 AREATRRKSPLDALGFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEI 466
Cdd:TIGR01055 381 AAKKVVRKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEI 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 467 LSLIQAFGTGiGDEFDGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKVQLGKRVEYVYS 546
Cdd:TIGR01055 461 HDIEVALGID-PDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALD 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 547 DEQLTKILAEIG---GRPNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMD--ADQVFSMLMGEEV-EPRKAFIQ 620
Cdd:TIGR01055 540 EEEKEKLLYKLKkkkGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDqrVDKIMDMLLAKKRsEDRFNWLQ 619
|
.
gi 1088626583 621 E 621
Cdd:TIGR01055 620 E 620
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
2-623 |
4.65e-171 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 510.58 E-value: 4.65e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 2 SNYDASNIQILEGLEAVRKRPGMYIGSTGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLH 81
Cdd:PTZ00109 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 82 PKTNRPAVETILTSLHSGGKF-----------------DGKS-----------------------YKVSGGLHGVGMSVV 121
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHSGGKFqdtfpknsrsdksedknDTKSskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 122 NALSENFLVEIMRNGNIYQQKYERGIPVTDV-IINGTSDHTGTIVTFKSD-------HLVFTETTVYE-------YEILR 186
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLsVFSCPLKKRGTTIHFLPDykhifktHHQHTETEEEEgckngfnLDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 187 NRIQQLAFLNKGIKITIIDARgAVAIENSYHYE-----GGIVEYVSFLNQGKGKINHDVLYIDKE--VDGITIDIALQYN 259
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDER-IANENNFYPYEtikheGGTREFLEELIKDKTPLYKDINIISIRgvIKNVNVEVSLSWS 416
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 260 -DSYATNLYSFANNIPThEGGMHEDGFKMALTRVLNKYATEQGMLKKD-ESFLGEDVKEGLTVIVSIKHPNPQFEGQTKT 337
Cdd:PTZ00109 417 lESYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNfVNIPGEFIREGMTAIISVKLNGAEFDGQTKT 495
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 338 KLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMASRARIAAKKAREATRRK-SPLDALGFASKLADCRSKDPVI 416
Cdd:PTZ00109 496 KLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKnNQYYSTILPGKLVDCISDDIER 575
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 417 SEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLD-KILSNKEILSLIQAFGTGIG----------------- 478
Cdd:PTZ00109 576 NELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNpvtwrqydlshgtkask 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 479 DEF---------------DGEKARYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQPPLYKV-------- 535
Cdd:PTZ00109 656 DESvqnnnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqf 735
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 536 ----QLGKRVEYVYSDEQLTKILAEIGG----------------------------------RPN--------------- 562
Cdd:PTZ00109 736 nvstKNSKKYIYTWSDEELNVLIKLLNKdysskettrsveekgnapdldneyedekldnknmRENnvdevelktelgtnv 815
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 563 -----------------------IQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFI 619
Cdd:PTZ00109 816 adteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFI 895
|
....
gi 1088626583 620 QENA 623
Cdd:PTZ00109 896 FENS 899
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
34-207 |
7.11e-93 |
|
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: 284.04 E-value: 7.11e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 34 LHHLVWEIVDNSIDEALGGYATNILLELLPGEIVRVTDDGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGL 113
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 114 HGVGMSVVNALSENFLVEIMRNGNIYQQKYERGIPVTDVIINGTSDHTGTIVTFKSDHLVFtETTVYEYEILRNRIQQLA 193
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170
....*....|....
gi 1088626583 194 FLNKGIKITIIDAR 207
Cdd:cd16928 160 FLNKGLKIVLEDER 173
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
220-389 |
1.84e-82 |
|
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: 256.72 E-value: 1.84e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 220 GGIVEYVSFLNQGKGKINHDVLYIDKEVDGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYATE 299
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 300 QGMLKK-DESFLGEDVKEGLTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMAS 378
Cdd:cd00822 81 NNLLKKkDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAA 160
|
170
....*....|.
gi 1088626583 379 RARIAAKKARE 389
Cdd:cd00822 161 KAREAARKARE 171
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
417-530 |
8.62e-76 |
|
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: 237.17 E-value: 8.62e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 417 SEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDEFDGEKARYHKVVIMTD 496
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 1088626583 497 ADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQP 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 ... |
221-390 |
1.39e-74 |
|
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: 236.36 E-value: 1.39e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 221 GIVEYVSFLNQGKGKINHDVLYIDKEV--DGITIDIALQYNDSYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNKYAT 298
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 299 EQGMLKK-DESFLGEDVKEGLTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENPSDARAIVEKCQMA 377
Cdd:pfam00204 81 KKGLLKKkDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160
|
170
....*....|...
gi 1088626583 378 SRARIAAKKAREA 390
Cdd:pfam00204 161 AKARLAARKAREA 173
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
417-530 |
1.85e-63 |
|
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: 205.05 E-value: 1.85e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 417 SEIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIG-DEFDGEKARYHKVVIMT 495
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 1088626583 496 DADIDGAHIRTLLLTFFFRYMKQLIDLGYVYIAQP 530
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
7-620 |
2.70e-59 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 208.84 E-value: 2.70e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 7 SNIQILEGLEAVRKRPGMYIGSTGSR-----------------GLHHLVWEIVDNSIDEALGG---YATNILLELlPGEI 66
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAYEaherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 67 VRVTDDGRGIPVDL--HPKTNR-PAVETILTSLHSGGKFDGKSyKVSGGLHGVGMSVVNALSENFLVE--------IMRN 135
Cdd:PHA02569 81 VTVSDNGRGIPQAMvtTPEGEEiPGPVAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLFIGEtcdgknevTVNC 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 136 GNIYQQKYERGIPvtdviingtSDHTGTIVTFKSDHLVFTETTVYE--YEILRNRIQQLAFLNKGIKITIidargavaie 213
Cdd:PHA02569 160 SNGAENISWSTKP---------GKGKGTSVTFIPDFSHFEVNGLDQqyLDIILDRLQTLAVVFPDIKFTF---------- 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 214 NSYHYEGGIVEYVSFLNQGKgkinhdvlyIDKEVDGITIDIAlQYNDSYATNlySFANNIPTHEGGMHEDGfkmaltrVL 293
Cdd:PHA02569 221 NGKKVSGKFKKYAKQFGDDT---------IVQENDNVSIALA-PSPDGFRQL--SFVNGLHTKNGGHHVDC-------VM 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 294 NKYATE-QGMLKKDESF--LGEDVKEGLTVIVSIKH-PNPQFEGQTKTKLGNP--EVRQiTSQIVGEGLEKYLMENPSDA 367
Cdd:PHA02569 282 DDICEElIPMIKKKHKIevTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgEIRN-HIDLDYKKIAKQILKTEAII 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 368 RAIVEKC---QMASRARIAAKKAREATRRKspldalgFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGRESEYQAILP 444
Cdd:PHA02569 361 MPIIEAAlarKLAAEKAAETKAAKKAKKAK-------VAKHIKANLIGKDAETTLFLTEGDSAIGYLIEVRDEELHGGYP 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 445 LRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDefDGEKARYHKVVIMTDADIDG-AHIRTLLLTFFFRYMKqLIDLG 523
Cdd:PHA02569 434 LRGKVLNTWGMSYADILKNKELFDICAITGLVLGE--KAENMNYKNIAIMTDADVDGkGSIYPLLLAFFSRWPE-LFEQG 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 524 YVYIAQPPLYKVQLGKRVEYVYSDEQLTKILAEIGGRpNIQRYKGLGEMNPEQLWETTMDPenrILLQVSLKDamDADQV 603
Cdd:PHA02569 511 RIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSLKKW-SIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPD--DWKEL 584
|
650
....*....|....*..
gi 1088626583 604 FSMLMGEEVEPRKAFIQ 620
Cdd:PHA02569 585 FEMLFGDDADLRKDWMS 601
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
15-621 |
4.30e-44 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 169.89 E-value: 4.30e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 15 LEAVRKRPGMYIGSTGSRGLHHLVWE---IVDNSI----------DEALGGYATNIL----LELLPGEI------VRVTD 71
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHTQTLWVYEggeMVNREVtyvpglykifDEILVNAADNKQrdpsMDSLKVDIdveqntISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 72 DGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIM--RNGNIYQQKYERGIPV 149
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFTNNMSV 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 150 TD--VIINGTSDHTGTIVTFKSDHLVFTETTVYE--YEILRNRIQQLA-FLNKGIKITIIDARGAVaiensyhyeGGIVE 224
Cdd:PLN03128 173 KSepKITSCKASENWTKITFKPDLAKFNMTRLDEdvVALMSKRVYDIAgCLGKKLKVELNGKKLPV---------KSFQD 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 225 YVS-FLNQGKGKINHDVLYiDKEVDGITIDIALQyNDSYatNLYSFANNIPTHEGGMHEDgfkmALTRVLNKYATEqgML 303
Cdd:PLN03128 244 YVGlYLGPNSREDPLPRIY-EKVNDRWEVCVSLS-DGSF--QQVSFVNSIATIKGGTHVD----YVADQIVKHIQE--KV 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 304 KKDESFLGE----DVKEGLTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLEKYLMENpsdarAIVEKC-QMA- 377
Cdd:PLN03128 314 KKKNKNATHvkpfQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKVEKC-----GVVENIlSWAq 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 378 SRARIAAKKAREATRRKspldALGFAsKLADC------RSKDpviSEIYIVEGDSAGGSAKQGRE---SEYQAILPLRGK 448
Cdd:PLN03128 389 FKQQKELKKKDGAKRQR----LTGIP-KLDDAndaggkKSKD---CTLILTEGDSAKALAMSGLSvvgRDHYGVFPLRGK 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 449 VLNVEKARLDKILSNKEILSLIQAFGTGIGDEFDGEKA---RYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDL-GY 524
Cdd:PLN03128 461 LLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENTkslRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIpGF 540
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 525 VYIAQPPLYKVQLGKRVEYVYSDEQLTKILAEIGG---RPNIQRYKGLGEMNPEQLWE--TTMDPENRILLQVSLKDAMD 599
Cdd:PLN03128 541 LVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEGetkGWTIKYYKGLGTSTSEEAKEyfSNLDIHKKEFLWQSDEDGDL 620
|
650 660
....*....|....*....|..
gi 1088626583 600 ADQVFSmlmGEEVEPRKAFIQE 621
Cdd:PLN03128 621 IDMAFS---KKRVEDRKIWLNN 639
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
5-621 |
1.82e-42 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 165.22 E-value: 1.82e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 5 DASNIQILEGLEAVRKRPGMYIGST-------------GSR----------GLHHLVWEI----VDNSIDEALGGYATNI 57
Cdd:PTZ00108 6 VEERYQKKTQIEHILLRPDTYIGSIetqtedmwvydeeKNRmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 58 LLELLP--GEIvRVTDDGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIM-- 133
Cdd:PTZ00108 86 KVTIDEenGEI-SVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVds 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 134 RNGNIYQQKY-----ERGIP-VTDViiNGTSDHTgtIVTFKSDHLVF--TETTVYEYEILRNRIQQLAFLNKGIKITIID 205
Cdd:PTZ00108 165 KSGKKFKMTWtdnmsKKSEPrITSY--DGKKDYT--KVTFYPDYAKFgmTEFDDDMLRLLKKRVYDLAGCFGKLKVYLNG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 206 ARGAVAIENSY---HYEGGIVEYVSFLNQGKGKINHDVlyidkevdgitiDIALQYNDSyATNLYSFANNIPTHEGGMHE 282
Cdd:PTZ00108 241 ERIAIKSFKDYvdlYLPDGEEGKKPPYPFVYTSVNGRW------------EVVVSLSDG-QFQQVSFVNSICTTKGGTHV 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 283 DgfkmALTRVLNKYATEQGMLKKDEsflGEDVKEG-----LTVIVSIKHPNPQFEGQTKTKLGNPEVRQITSQIVGEGLE 357
Cdd:PTZ00108 308 N----YILDQLISKLQEKAKKKKKK---GKEIKPNqiknhLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLI 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 358 KYLMENPsdaraIVEKCQMASRARIAAKKARE-ATRRKSPLdaLGFaSKLADCRSKDPVISEI---YIVEGDSAGGSAKQ 433
Cdd:PTZ00108 381 KYVLKSP-----ILENIVEWAQAKLAAELNKKmKAGKKSRI--LGI-PKLDDANDAGGKNSEEctlILTEGDSAKALALA 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 434 GRESE---YQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDEFDGEKA-RYHKVVIMTDADIDGAHIRTLLL 509
Cdd:PTZ00108 453 GLSVVgrdYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGlRYGSLMIMTDQDHDGSHIKGLLI 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 510 TFFFRYMKQLIDL-GYVYIAQPPLYKVQL-GKRVEYVYSDEQLTKILAEIGGRP-NIQRYKGLGEMNPEQLWE--TTMDp 584
Cdd:PTZ00108 533 NMIHHFWPSLLKNpGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQTVGLKGwKIKYYKGLGTSTDKEGKEyfSNID- 611
|
650 660 670
....*....|....*....|....*....|....*...
gi 1088626583 585 ENRILLQVSLKDAMDA-DQVFSmlmGEEVEPRKAFIQE 621
Cdd:PTZ00108 612 KHRIRFVYVDDSDDDSiDLAFS---KKRVEDRKEWITN 646
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
558-620 |
2.75e-41 |
|
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: 143.67 E-value: 2.75e-41
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088626583 558 GGRPNIQRYKGLGEMNPEQLWETTMDPENRILLQVSLKDAMDADQVFSMLMGEEVEPRKAFIQ 620
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
15-570 |
6.82e-29 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 123.05 E-value: 6.82e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 15 LEAVRKRPGMYIGS---------------------TGSRGLHHLVWEIVDNSIDEALGGYATNILLELLPGE--IVRVTD 71
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRDPKMDSLRVVIDVEqnLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 72 DGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIM--RNGNIYQQKYER--GI 147
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETAdgKRQKKYKQVFSNnmGK 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 148 PVTDVIINGTSDHTGTIVTFKSDHLVFTETTVYE--YEILRNRIQQLA-FLNKGIKITIIDARGAVAiensyhyegGIVE 224
Cdd:PLN03237 198 KSEPVITKCKKSENWTKVTFKPDLAKFNMTHLEDdvVALMKKRVVDIAgCLGKTVKVELNGKRIPVK---------SFSD 268
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 225 YVSFLNQGKGKINHDVLYIDKEVDGITIDIALQYNDSYATNLySFANNIPTHEGGMHEDgfkMALTRVLNKYATEQGMLK 304
Cdd:PLN03237 269 YVDLYLESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHVD---YVTNQIANHVMEAVNKKN 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 305 KDESFLGEDVKEGLTVIVSIKHPNPQFEGQTKTKLgnpEVRQITSQIVGEGLEKYL--MENPSdaraIVEkcQMASRARI 382
Cdd:PLN03237 345 KNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL---TLRQSSFGSKCELSEDFLkkVMKSG----IVE--NLLSWADF 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 383 AAKKAREAT--RRKSPLDALGFASKLADCRSKDPVISEIYIVEGDSAGGSAKQGR---ESEYQAILPLRGKVLNVEKARL 457
Cdd:PLN03237 416 KQSKELKKTdgAKTTRVTGIPKLEDANEAGGKNSEKCTLILTEGDSAKALAVAGLsvvGRNYYGVFPLRGKLLNVREASH 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 458 DKILSNKEILSLIQAFGTGIGDEFDGEKA-RYHKVVIMTDADIDGAHIRTLLLTFFFRYMKQLIDLG--YVYIAQPPLYK 534
Cdd:PLN03237 496 KQIMNNAEIENIKQILGLQHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVPsfLVEFITPIVKA 575
|
570 580 590
....*....|....*....|....*....|....*....
gi 1088626583 535 VQLGKRVEYVYS---DEQLTKILAEIGGRPNIQRYKGLG 570
Cdd:PLN03237 576 TRRGKKVLSFYSmpeYEEWKESLGGNATGWSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
222-340 |
4.10e-21 |
|
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: 88.47 E-value: 4.10e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 222 IVEYVSFLNqgKGKINHDVLYIDKEVDGITIDIALQYND---SYATNLYSFANNIPTHEGGMHEDGFKMALTRVLNkyat 298
Cdd:cd00329 1 LKDRLAEIL--GDKVADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1088626583 299 eqgmlkkdesflGEDVKEGLTVIVSIKHPN--PQFE-GQTKTKLG 340
Cdd:cd00329 75 ------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
423-512 |
9.19e-21 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 88.13 E-value: 9.19e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 423 EGDSAGGSAKQGRES---EYQAILPLRGKVLNVEKARLDKILSNKEILSLIQAFGTGIGDEF--DGEKARYHKVVIMTDA 497
Cdd:cd03365 7 EGDSAKALAVAGLSVvgrDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMTDQ 86
|
90
....*....|....*
gi 1088626583 498 DIDGAHIRTLLLTFF 512
Cdd:cd03365 87 DHDGSHIKGLLINFI 101
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
418-530 |
1.39e-15 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 72.39 E-value: 1.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 418 EIYIVEGDSAGGSAKQGRESEYQAILPLRGKVLNVEKARLDKILsnkeilsliqafgtgigDEFDGEKARYHKVVIMTDA 497
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKAL-----------------KALKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|...
gi 1088626583 498 DIDGAHIRTLLLTfFFRYMKQLIdlGYVYIAQP 530
Cdd:pfam01751 64 DREGEAIALKLLE-LKELLENAG--GRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
31-128 |
1.73e-13 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 67.01 E-value: 1.73e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 31 SRGLHHLVWEIVDNSIDEAlgGYATNILLELLPGE--IVRVTDDGRGIPVDLHPktnrpavetiltslHSGGKFDGKSyK 108
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLP--------------RIFEPFSTAD-K 65
|
90 100
....*....|....*....|
gi 1088626583 109 VSGGLHGVGMSVVNALSENF 128
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELL 85
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
32-137 |
9.37e-13 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 64.98 E-value: 9.37e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 32 RGLHHLVWEIVDNSIDEALGGyaTNILLELLPGE---IVRVTDDGRGIPVDLHPKtnrpavetiltSLHSGGKFDGKSYK 108
Cdd:smart00387 4 DRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPEDLEK-----------IFEPFFRTDKRSRK 70
|
90 100
....*....|....*....|....*....
gi 1088626583 109 VSGglHGVGMSVVNALSENFLVEIMRNGN 137
Cdd:smart00387 71 IGG--TGLGLSIVKKLVELHGGEISVESE 97
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
67-170 |
7.72e-09 |
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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: 54.65 E-value: 7.72e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 67 VRVTDDGRGIPVDLHPKTNRPAVETILTSLHSGGKFDGKSYKVSGGLHGVGMSVVNALSENFLVEIM--RNGNIYQQKYE 144
Cdd:cd16930 40 ISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFTVETAdsESKKKFKQTWT 119
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90 100
....*....|....*....|....*...
gi 1088626583 145 RGIPVTD--VIINGTSDHTGTIVTFKSD 170
Cdd:cd16930 120 NNMGKASepKITPYEKGKDYTKVTFKPD 147
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| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
417-515 |
3.72e-06 |
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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: 45.11 E-value: 3.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 417 SEIYIVEGDSAGGSAKQGRESEYqAILPLRGKVLNVEKARLDKILSnkeilsliqafgtgigdefdgekaRYHKVVIMTD 496
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGGYGG-AVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
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90
....*....|....*....
gi 1088626583 497 ADIDGAHIRTLLLTFFFRY 515
Cdd:cd00188 56 ADREGEAIALRLLELLKSL 74
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| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
34-128 |
7.95e-04 |
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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: 39.12 E-value: 7.95e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088626583 34 LHHLVWEIVDNSIDEALGGYATNILLELLPGEI-VRVTDDGRGIPVDLHPKtnrpavetILTSLHSGGKfdgksyKVSGG 112
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPGGTIEISLRQEGDGVvLEVEDNGPGIPEEDLER--------IFERFYRGDK------SREGG 66
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90
....*....|....*.
gi 1088626583 113 LHGVGMSVVNALSENF 128
Cdd:cd00075 67 GTGLGLAIVRRIVEAH 82
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| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
40-79 |
4.95e-03 |
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Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.
Pssm-ID: 340403 [Multi-domain] Cd Length: 188 Bit Score: 38.57 E-value: 4.95e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1088626583 40 EIVDNSIDEAlggyATNILLELLPGEI--VRVTDDGRGIPVD 79
Cdd:cd16926 20 ELVENSIDAG----ATRIDVEIEEGGLklIRVTDNGSGISRE 57
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