|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-676 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1190.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 1 MANENDYDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIP 80
Cdd:PRK05644 2 EEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 81 VDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGT 160
Cdd:PRK05644 82 VDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 161 SDSTGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDERESTPHVEEFCYEGGIIDFVKFLNEGKDVpeA 240
Cdd:PRK05644 162 TDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNKEP--L 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 241 FKEPIYIEGKSDPdapvakmGEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKDAN 320
Cdd:PRK05644 240 HEEPIYFEGEKDG-------IEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDN 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 321 LTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKAR 400
Cdd:PRK05644 313 LTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKAR 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 401 EATRRKSLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQS 480
Cdd:PRK05644 393 ELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRA 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 481 LITAIGCGVttsagdGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKvRNKIH 560
Cdd:PRK05644 473 LITALGTGI------GDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIK-KGGKE 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 561 YVYpngrqpEDEILRDTIQSLGlnpddndedgkakdgkiTKKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIE 640
Cdd:PRK05644 546 YAY------SDEELDEILAELK-----------------LKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIE 602
|
650 660 670
....*....|....*....|....*....|....*.
gi 1801528178 641 DAVVADRAVRELMGSEVGYRREYIEKHAHDARFLDA 676
Cdd:PRK05644 603 DAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
2-676 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1170.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 2 ANENDYDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPV 81
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 82 DEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGTS 161
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 162 DSTGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDERESTPHVEEFCYEGGIIDFVKFLNEGKDVpeAF 241
Cdd:COG0187 161 DRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKDFVEYLNEDKEP--LH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 242 KEPIYIEGKSDPdapvakmGEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKDANL 321
Cdd:COG0187 239 PEVIYFEGEKDG-------IEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNL 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 322 TGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKARE 401
Cdd:COG0187 312 TGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARE 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 402 ATRRKSLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSL 481
Cdd:COG0187 392 LVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDL 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 482 ITAIGCGVttsagdGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKVRNKIHY 561
Cdd:COG0187 472 ITALGTGI------GDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYY 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 562 VYpngrqpedeilrdtiqslglnpDDNDEDGKAKDGkitKKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIED 641
Cdd:COG0187 546 AY----------------------SDAELDELLKEL---KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIED 600
|
650 660 670
....*....|....*....|....*....|....*
gi 1801528178 642 AVVADRAVRELMGSEVGYRREYIEKHAHDARFLDA 676
Cdd:COG0187 601 AAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
1-675 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1004.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 1 MANENDYDGGEIKILEGLEAVRKRPGMYIGSTS-ASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGI 79
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 80 PVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVG 159
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 160 TSDSTGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDEResTPHVEEFCYEGGIIDFVKFLNEGKDVpe 239
Cdd:PRK14939 161 ETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDER--DGKEEEFHYEGGIKAFVEYLNRNKTP-- 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 240 AFKEPIYIEGKSDpdapvakmG-EVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKD 318
Cdd:PRK14939 237 LHPNIFYFSGEKD--------GiGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAK 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 319 ANLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARK 398
Cdd:PRK14939 309 VSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARK 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 399 AREATRRKSLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTI 478
Cdd:PRK14939 389 ARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEI 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 479 QSLITAIGCGVTTsagdgGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIK---- 554
Cdd:PRK14939 469 GTLITALGCGIGR-----DEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKkgkq 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 555 ----------------------------------------------VRN---KIHYVYPNgrqpedEILRDTIQSLGLNP 585
Cdd:PRK14939 544 eqylkddealddylielalegatlhladgpaisgealeklvkeyraVRKiidRLERRYPR------AVLEALIYAPALDL 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 586 DDND---------------------------------EDGKAKDGKITKK---------------RKGYTVQRYKGLGEM 617
Cdd:PRK14939 618 DDLAdeaavaaldadfltsaeyrrlvelaeklrglieEGAYLERGERKQPvssfeealdwllaeaRKGLSIQRYKGLGEM 697
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*...
gi 1801528178 618 DPKQLASTTMDPKTRILQRVSIEDAVVADRAVRELMGSEVGYRREYIEKHAHDARFLD 675
Cdd:PRK14939 698 NPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLD 755
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
7-675 |
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: 969.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 7 YDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEHPV 86
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 87 KKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGTSDSTGT 166
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 167 TVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDERESTPHVEEFCYEGGIIDFVKFLNEGKDVpeAFKEPIY 246
Cdd:TIGR01059 161 TVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKVTFHYEGGIKSFVKYLNRNKEP--LHEEIIY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 247 IEGKSDPDapvakmgEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKDANLTGDDV 326
Cdd:TIGR01059 239 IKGEKEGI-------EVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDI 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 327 REGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKAREATRRK 406
Cdd:TIGR01059 312 REGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRK 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 407 SLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIG 486
Cdd:TIGR01059 392 SALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALG 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 487 CGVttsagdGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKVRNKIHYVYPN- 565
Cdd:TIGR01059 472 CGI------GKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDk 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 566 GRQPEDEILRDTIQSLGLNPDDNDEDGKAKDGKITkkRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIEDAVVA 645
Cdd:TIGR01059 546 EKDLVGEALEDLKALYIYSDKEKEEAKTQIPVHLG--RKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEA 623
|
650 660 670
....*....|....*....|....*....|
gi 1801528178 646 DRAVRELMGSEVGYRREYIEKHAHDARFLD 675
Cdd:TIGR01059 624 DRIFSTLMGDEVEPRREFIEANALDVKNLD 653
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-671 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 914.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 1 MANENDYDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIP 80
Cdd:PRK05559 2 AMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 81 VDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGT 160
Cdd:PRK05559 82 VGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 161 SDS--TGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDEREStphvEEFCYEGGIIDFVKFLNEGKD-V 237
Cdd:PRK05559 162 AGKrkTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERER----QTFHYENGLKDYLAELNEGKEtL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 238 PEAFkePIYIEGKsdpdapvAKMGEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKeK 317
Cdd:PRK05559 238 PEEF--VGSFEGE-------AEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-K 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 318 DANLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAAR 397
Cdd:PRK05559 308 GKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAA 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 398 KarEATRRKsLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDT 477
Cdd:PRK05559 388 K--KVKRKK-KTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEE 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 478 IQSLITAIGCGVttsagdGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKVRN 557
Cdd:PRK05559 465 IHDIIVAIGIGP------GDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGK 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 558 KIHYVYpngrqpedeilrdtiqslglnpDDNDEDGKAKdgKITKKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRV 637
Cdd:PRK05559 539 KKIYAL----------------------DEEEKEELLK--KLGKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRV 594
|
650 660 670
....*....|....*....|....*....|....
gi 1801528178 638 SIEDAVVADRAVRELMGSEVGYRREYIEKHAHDA 671
Cdd:PRK05559 595 TIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
36-668 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 830.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 36 GLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGG 115
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 116 LHGVGISVVNALSKRVVVQVRRDGNTYEMEFSR-GKTVKKMEVVGTSDSTGTTVTFWPDDEIFE-TCIYDFDTLHNRLQE 193
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 194 TAFLNKNLKIVLTDERESTPhvEEFCYEGGIIDFVKFLNEGKDVPeaFKEPIYIEGKSDPDapvakmgEVEVSLQWNSGY 273
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEE--KTFLFEGGIKDYVELLNKNKELL--SPEPTYIEGEKDNI-------RVEVAFQYTDGY 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 274 GENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKdaNLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGS 353
Cdd:smart00433 230 SENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGT 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 354 SYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKAREATRRKSlLETASLPGKLADCSVRDAELTELFI 433
Cdd:smart00433 308 SEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFL 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 434 VEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCGVttsagdGGDFDITKARYHKIIIMT 513
Cdd:smart00433 387 VEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGI------GKDFDIEKLRYGKIIIMT 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 514 DADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKVRNKIHYVYpngrqpedeilrdtiqslglnpDDNDEDGK 593
Cdd:smart00433 461 DADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYS----------------------FYSLDEYE 518
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1801528178 594 AKDGKITKKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIEDAVVADRAVRELMGSEVGYRREYIEKHA 668
Cdd:smart00433 519 KWLEKTEGNKSKYEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
5-667 |
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 1801528178 5 NDYDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEH 84
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 85 PVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSR-GKTVKKMEVVGTSDS 163
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 164 TGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDEResTPHVEEFCYEGGIIDFVKFLNEGKDVpeaFKE 243
Cdd:TIGR01058 163 TGTLVHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKR--TNKTTVFFYENGLVDFVDYINETKET---LSQ 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 244 PIYIEGKSDPDapvakmgEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLKEKDANLTG 323
Cdd:TIGR01058 238 VTYFEGEKNGI-------EVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEG 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 324 DDVREGLSAVISVKLPDP--QFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKARE 401
Cdd:TIGR01058 311 SDIREGLSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKARE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 402 ATR--RKSLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQ 479
Cdd:TIGR01058 391 EKKsgKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEIN 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 480 SLITAIGCGVttsagdGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGI--KVRN 557
Cdd:TIGR01058 471 TIIFCIGTGI------GADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLskKDGK 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 558 KIHYVYPNGRQpedeilrdtiqslglnpddndedgkakdGKITKKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRV 637
Cdd:TIGR01058 545 KVKYAWSDLEL----------------------------ESVKKKLKNYTLQRYKGLGEMNADQLWETTMNPETRTLVRV 596
|
650 660 670
....*....|....*....|....*....|
gi 1801528178 638 SIEDAVVADRAVRELMGSEVGYRREYIEKH 667
Cdd:TIGR01058 597 KIDDLARAERQINTLMGDKVEPRKKWIEAN 626
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
5-668 |
0e+00 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 568.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 5 NDYDGGEIKILEGLEAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEH 84
Cdd:PTZ00109 98 SEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 85 PVKKIPTLEVVMTILHAGGKFDNSA----------------------------------------YKVSGGLHGVGISVV 124
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHSGGKFQDTFpknsrsdksedkndtksskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 125 NALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGTSDS-TGTTVTFWPD-DEIFET------------CIYDF--DTLH 188
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLKkRGTTIHFLPDyKHIFKThhqhteteeeegCKNGFnlDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 189 NRLQETAFLNKNLKIVLTDER----ESTPHVEEFCYEGGIIDFVKFLNegKDVPEAFKEPIYIEGKSdpdapVAKMGEVE 264
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERianeNNFYPYETIKHEGGTREFLEELI--KDKTPLYKDINIISIRG-----VIKNVNVE 410
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 265 VSLQWNSG-YGENVMSFANDIYTpEGGMHLEGFRTALTRVINDYARKQNLLKEKDANLTGDDVREGLSAVISVKLPDPQF 343
Cdd:PTZ00109 411 VSLSWSLEsYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEF 489
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 344 EGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARNAARKAREATRRK-SLLETASLPGKLADCS 422
Cdd:PTZ00109 490 DGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKnNQYYSTILPGKLVDCI 569
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 423 VRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDH-RAFSSDTIQSLITAIGCGV------------ 489
Cdd:PTZ00109 570 SDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVnpvtwrqydlsh 649
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 490 --------------TTSAGDGGDFDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPI----- 550
Cdd:PTZ00109 650 gtkaskdesvqnnnSTLTKKKNSLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLyritn 729
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 551 -----FGIKVRNKIHYVY----------------------PNGRQPEDEILRDTIQSLGLNPDDNDEDGKAKDGKITKK- 602
Cdd:PTZ00109 730 nrmkqFNVSTKNSKKYIYtwsdeelnvlikllnkdysskeTTRSVEEKGNAPDLDNEYEDEKLDNKNMRENNVDEVELKt 809
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 603 ------------------------RKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIEDAVVADRAVRELMGSEVG 658
Cdd:PTZ00109 810 elgtnvadteqtdeldinkaffkfSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQ 889
|
810
....*....|
gi 1801528178 659 YRREYIEKHA 668
Cdd:PTZ00109 890 SRKQFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
6-661 |
1.83e-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: 524.48 E-value: 1.83e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 6 DYDGGEIKILEGLEAVRKRPGMYIGSTSasgLHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEHP 85
Cdd:TIGR01055 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 86 VKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGTSD--S 163
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGkrL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 164 TGTTVTFWPDDEIFETCIYDFDTLHNRLQETAFLNKNLKIVLTDERESTPHVeeFCYEGGIIDFV-KFLNEGKDVPEafk 242
Cdd:TIGR01055 160 TGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKAL--WNYPDGLKDYLsEAVNGDNTLPP--- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 243 EPIYIEGKSDPDApvakmgeVEVSLQWNSGYGENVM-SFANDIYTPEGGMHLEGFRTALTRVINDYARKQNLLkEKDANL 321
Cdd:TIGR01055 235 KPFSGNFEGDDEA-------VEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNL-PRGVKL 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 322 TGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREIVKKAQQACKARnaaRKARE 401
Cdd:TIGR01055 307 TAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRR---KRAAK 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 402 ATRRKSLLETASLPGKLADCSVRDAELTELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSL 481
Cdd:TIGR01055 384 KVVRKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDI 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 482 ITAIGCGVTTSagdggdfDITKARYHKIIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACPPIFGIKVRNKIHY 561
Cdd:TIGR01055 464 EVALGIDPDSN-------DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYY 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 562 VYpngrqpedeilrdtiqslglnpddnDEDGKAKDGKITKKRKGY-TVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIE 640
Cdd:TIGR01055 537 AL-------------------------DEEEKEKLLYKLKKKKGKpNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLD 591
|
650 660
....*....|....*....|.
gi 1801528178 641 DavVADRAVRELMGSEVGYRR 661
Cdd:TIGR01055 592 D--VQDQRVDKIMDMLLAKKR 610
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
37-210 |
5.44e-109 |
|
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: 326.80 E-value: 5.44e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 37 LHHLVWEIVDNSVDEAMAGFCTEIQVTVHADNSITVVDNGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGL 116
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 117 HGVGISVVNALSKRVVVQVRRDGNTYEMEFSRGKTVKKMEVVGTSDSTGTTVTFWPDDEIFETCIYDFDTLHNRLQETAF 196
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|....
gi 1801528178 197 LNKNLKIVLTDERE 210
Cdd:cd16928 161 LNKGLKIVLEDERT 174
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
222-401 |
2.16e-81 |
|
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: 255.18 E-value: 2.16e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 222 GGIIDFVKFLNEGKDVPeaFKEPIYIEGKSDPdapvakmGEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALT 301
Cdd:cd00822 1 GGLKDFVEELNKDKEPL--HEEPIYIEGEKDG-------VEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALT 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 302 RVINDYARKQNLLKEKDANLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPARE 381
Cdd:cd00822 72 RAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKK 151
|
170 180
....*....|....*....|
gi 1801528178 382 IVKKAQQACKARNAARKARE 401
Cdd:cd00822 152 ILEKAILAAKAREAARKARE 171
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
223-402 |
3.31e-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: 233.66 E-value: 3.31e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 223 GIIDFVKFLNEGKDVPeaFKEPIYIEGKSdpdapVAKMGEVEVSLQWNSGYGENVMSFANDIYTPEGGMHLEGFRTALTR 302
Cdd:pfam00204 1 GLKDFVEELNKDKKPL--HKEIIYFEGES-----PDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 303 VINDYARKQNLLKEKDANLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPAREI 382
Cdd:pfam00204 74 TINEYAKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKI 153
|
170 180
....*....|....*....|
gi 1801528178 383 VKKAQQACKARNAARKAREA 402
Cdd:pfam00204 154 LEKALQAAKARLAARKAREA 173
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
429-548 |
2.36e-68 |
|
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: 218.68 E-value: 2.36e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 429 TELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCGVttsagdGGDFDITKARYHK 508
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGI------GEDFDLEKLRYHK 74
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1801528178 509 IIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACP 548
Cdd:cd03366 75 IIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
429-548 |
1.80e-56 |
|
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: 187.33 E-value: 1.80e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 429 TELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCGVttsagDGGDFDITKARYHK 508
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGI-----GKDDFDLDKLRYGK 75
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 1801528178 509 IIIMTDADVDGAHIRILLLTFFYKYMRPLIDAGYVYVACP 548
Cdd:cd01030 76 IIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
11-635 |
2.61e-55 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 198.82 E-value: 2.61e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 11 EIKILEGLEAVRKRPGMYIGSTS-----------------ASGLHHLVWEIVDNSVDEAMAG---FCTEIQVTVHaDNSI 70
Cdd:PHA02569 3 EFKVLSDREHILKRPGMYIGSVAyeaherflfgkftqveyVPGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NNQV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 71 TVVDNGRGIP---VDEHPVKKIPTLEVVMTILHAGGKFDnSAYKVSGGLHGVGISVVNALSKRVVVQVRRDGNTYEMEFS 147
Cdd:PHA02569 82 TVSDNGRGIPqamVTTPEGEEIPGPVAAWTRTKAGSNFD-DTNRVTGGMNGVGSSLTNFFSVLFIGETCDGKNEVTVNCS 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 148 RGktvkkMEVVGTSDS----TGTTVTFWPDDEIFETCIYD---FDTLHNRLQetaflnkNLKIVLTDerestphveefcy 220
Cdd:PHA02569 161 NG-----AENISWSTKpgkgKGTSVTFIPDFSHFEVNGLDqqyLDIILDRLQ-------TLAVVFPD------------- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 221 eggiidfVKFLNEGKDVPEAFKEpiyiegksdpdapVAKM-GEVEVSLQWN--------SGYGENVMSFANDIYTPEGGM 291
Cdd:PHA02569 216 -------IKFTFNGKKVSGKFKK-------------YAKQfGDDTIVQENDnvsialapSPDGFRQLSFVNGLHTKNGGH 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 292 HLEGfrtaltrVIND-YARKQNLLKEKDA-NLTGDDVREGLSAVISVK-LPDPQFEGQTKAKLGSSY----------MRA 358
Cdd:PHA02569 276 HVDC-------VMDDiCEELIPMIKKKHKiEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPFgeirnhidldYKK 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 359 LTLKIV-TDGLVDYLEEhPKPAREIVKKAQQACKARNAARKAREATRRKslletASLPGKLADcsvrdaelTELFIVEGD 437
Cdd:PHA02569 349 IAKQILkTEAIIMPIIE-AALARKLAAEKAAETKAAKKAKKAKVAKHIK-----ANLIGKDAE--------TTLFLTEGD 414
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 438 SAGGSAKDGRRRDIQAILPLRGKILNVERVGDHRAFSSDTIQSLitaigCGVTTSagDGGDFDITKArYHKIIIMTDADV 517
Cdd:PHA02569 415 SAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDI-----CAITGL--VLGEKAENMN-YKNIAIMTDADV 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 518 DG-AHIRILLLTFFYKYmrplidagyvyvacPPIFGIKvrnKIHYVypngRQPEdeilrdTIQSLGLNPD---DNDEDGK 593
Cdd:PHA02569 487 DGkGSIYPLLLAFFSRW--------------PELFEQG---RIRFV----KTPV------IIAQVGKETKwfySLDEFEK 539
|
650 660 670 680
....*....|....*....|....*....|....*....|..
gi 1801528178 594 AKDgkitkKRKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQ 635
Cdd:PHA02569 540 AKD-----SLKKWSIRYIKGLGSLRKSEYRRVINNPVYDVVV 576
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
15-615 |
6.42e-42 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 164.06 E-value: 6.42e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 15 LEGLEAVRKRPGMYIGSTSAS-----------------------GLHHLVWEI----VDNSVDEAMAGFCTEIQVTV-HA 66
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKVTIdEE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 67 DNSITVVDNGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVR--RDGNTYEM 144
Cdd:PTZ00108 93 NGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVdsKSGKKFKM 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 145 EFSRGKTVKKMEVVGTSDSTG--TTVTFWPDDEIFETCIYDFDT---LHNRLQETAFLNKNLKIVLTDEREstphveefc 219
Cdd:PTZ00108 173 TWTDNMSKKSEPRITSYDGKKdyTKVTFYPDYAKFGMTEFDDDMlrlLKKRVYDLAGCFGKLKVYLNGERI--------- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 220 yegGIIDFVKFLnegkDVPEAFKEPIYIegKSDPDAPVAKMGEVEVSLQWNSGyGENVMSFANDIYTPEGGMHLEGFRTA 299
Cdd:PTZ00108 244 ---AIKSFKDYV----DLYLPDGEEGKK--PPYPFVYTSVNGRWEVVVSLSDG-QFQQVSFVNSICTTKGGTHVNYILDQ 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 300 LTRVINDYARKqnlLKEKDANLTGDDVREGLSAVISVKLPDPQFEGQTKAKLGSSYMRALTLKIVTDGLVDYLEEHPKPA 379
Cdd:PTZ00108 314 LISKLQEKAKK---KKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSPILE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 380 ReIVKKAQQacKARNAARKAREATRRKSL-----LETASLPGKladcsvRDAELTELFIVEGDSAGGSAKDG---RRRDI 451
Cdd:PTZ00108 391 N-IVEWAQA--KLAAELNKKMKAGKKSRIlgipkLDDANDAGG------KNSEECTLILTEGDSAKALALAGlsvVGRDY 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 452 QAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCGVTTSAGDggdfdITKARYHKIIIMTDADVDGAHIRILLLTFFY 531
Cdd:PTZ00108 462 YGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYED-----PKGLRYGSLMIMTDQDHDGSHIKGLLINMIH 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 532 KYMRPLIDA-GYVYVACPPIfgIKVRNKihyvypnGRQpedEILRDTIQSLglnpddndedgkaKDGKITKKRKGYTVQR 610
Cdd:PTZ00108 537 HFWPSLLKNpGFLKEFITPI--VKATKK-------GNQ---VISFFTIPDF-------------EKWKQTVGLKGWKIKY 591
|
....*
gi 1801528178 611 YKGLG 615
Cdd:PTZ00108 592 YKGLG 596
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
18-615 |
1.27e-38 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 153.71 E-value: 1.27e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 18 LEAVRKRPGMYIGSTS---------------------ASGLHHLVWEIVDNSVDEAMAG-FCTEIQVTVHAD-NSITVVD 74
Cdd:PLN03128 13 LEHILLRPDTYIGSTEkhtqtlwvyeggemvnrevtyVPGLYKIFDEILVNAADNKQRDpSMDSLKVDIDVEqNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 75 NGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVrRDGN---TYEMEFSRGKT 151
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVET-ADGNrgkKYKQVFTNNMS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 152 VKKMEVVGT--SDSTGTTVTFWPDDEIFETCIYDFDT---LHNRLQETA-FLNKNLKIVLTDEREStphveefcyeggII 225
Cdd:PLN03128 172 VKSEPKITSckASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKKLP------------VK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 226 DFVKFLNegkdvpeafkepIYIEGKSDPDaPVAKMGEvEVSLQWNSGYGE-----NVMSFANDIYTPEGGMHLEGFRTAL 300
Cdd:PLN03128 240 SFQDYVG------------LYLGPNSRED-PLPRIYE-KVNDRWEVCVSLsdgsfQQVSFVNSIATIKGGTHVDYVADQI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 301 TRVINDYARKQNllkEKDANLTGDDVREGLSAVISVKLPDPQFEGQTKAKL-------GSSYM--RALTLKIVTDGLVDy 371
Cdd:PLN03128 306 VKHIQEKVKKKN---KNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLttrpssfGSKCElsEEFLKKVEKCGVVE- 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 372 leehpkparEIVK----KAQQACKARNAARKAREATRRKslLETASLPGKladcsvRDAELTELFIVEGDSAGGSAKDGR 447
Cdd:PLN03128 382 ---------NILSwaqfKQQKELKKKDGAKRQRLTGIPK--LDDANDAGG------KKSKDCTLILTEGDSAKALAMSGL 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 448 R---RDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGcgvtTSAGDGGDFDITKA-RYHKIIIMTDADVDGAHIR 523
Cdd:PLN03128 445 SvvgRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILG----LQFGKTYDEENTKSlRYGHLMIMTDQDHDGSHIK 520
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 524 ILLLTFFYKYMRPLID-AGYVYVACPPIFGIKVRNKIHYVYPNgrqPEDEILRDTiqslgLNPDDndedgkakdgkitkk 602
Cdd:PLN03128 521 GLIINFFHSFWPSLLKiPGFLVEFITPIVKATKGGKSLSFYTM---PEYEAWKES-----LEGET--------------- 577
|
650
....*....|...
gi 1801528178 603 rKGYTVQRYKGLG 615
Cdd:PLN03128 578 -KGWTIKYYKGLG 589
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
603-665 |
2.51e-30 |
|
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: 113.24 E-value: 2.51e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1801528178 603 RKGYTVQRYKGLGEMDPKQLASTTMDPKTRILQRVSIEDAVVADRAVRELMGSEVGYRREYIE 665
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
18-615 |
3.25e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 115.34 E-value: 3.25e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 18 LEAVRKRPGMYIGS---------------------TSASGLHHLVWEIV----DNSV-DEAMAGFCTEIQVtvhADNSIT 71
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILvnaaDNKQrDPKMDSLRVVIDV---EQNLIS 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 72 VVDNGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSAYKVSGGLHGVGISVVNALSKRVVVQVrRDG---NTYEMEFSR 148
Cdd:PLN03237 115 VYNNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIET-ADGkrqKKYKQVFSN 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 149 GKTvKKMEVVGTSDSTG---TTVTFWPDDEIFETCIYDFDT---LHNRLQETA-FLNKNLKIVLTDEREStphVEEFCye 221
Cdd:PLN03237 194 NMG-KKSEPVITKCKKSenwTKVTFKPDLAKFNMTHLEDDVvalMKKRVVDIAgCLGKTVKVELNGKRIP---VKSFS-- 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 222 ggiiDFVKFLNEGKDVPEAFKEPIYIEGKSDpdapvakMGEVEVSLqwNSGYGENVmSFANDIYTPEGGMHLEGFRTALT 301
Cdd:PLN03237 268 ----DYVDLYLESANKSRPENLPRIYEKVND-------RWEVCVSL--SEGQFQQV-SFVNSIATIKGGTHVDYVTNQIA 333
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 302 RVINDYARKqnllKEKDANLTGDDVREGLSAVISVKLPDPQFEGQTKAKL-------GSSY--MRALTLKIVTDGLVDYL 372
Cdd:PLN03237 334 NHVMEAVNK----KNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETLtlrqssfGSKCelSEDFLKKVMKSGIVENL 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 373 EEHPKpareivKKAQQACKARNAARKAREATRRKslLETAslpgklADCSVRDAELTELFIVEGDSAGGSAKDGRR---R 449
Cdd:PLN03237 410 LSWAD------FKQSKELKKTDGAKTTRVTGIPK--LEDA------NEAGGKNSEKCTLILTEGDSAKALAVAGLSvvgR 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 450 DIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCgvttsaGDGGDFDITKA-RYHKIIIMTDADVDGAHIRILLLT 528
Cdd:PLN03237 476 NYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGL------QHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLIN 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 529 FFYKYMRPLIDA-GYVYVACPPIFGIKVRNKIHYVYPNgrQPEDEILRdtiQSLGLNPddndedgkakdgkitkkrKGYT 607
Cdd:PLN03237 550 FIHSFWPSLLKVpSFLVEFITPIVKATRRGKKVLSFYS--MPEYEEWK---ESLGGNA------------------TGWS 606
|
....*...
gi 1801528178 608 VQRYKGLG 615
Cdd:PLN03237 607 IKYYKGLG 614
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
34-175 |
1.62e-17 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 78.46 E-value: 1.62e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 34 ASGLHHLVWEIVDNSVDEAMAGfcTEIQVTVHADN---SITVVDNGRGIPVdehpvkkiptlEVVMTILHAGGKFDNSAY 110
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPP-----------EDLEKIFEPFFRTDKRSR 69
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1801528178 111 KVSGglHGVGISVVNALSKRVVVQVRrdgntyemefsrgktvkkmevVGTSDSTGTTVTFWPDDE 175
Cdd:smart00387 70 KIGG--TGLGLSIVKKLVELHGGEIS---------------------VESEPGGGTTFTITLPLE 111
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
34-176 |
9.50e-17 |
|
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: 76.25 E-value: 9.50e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 34 ASGLHHLVWEIVDNSVDEAmaGFCTEIQVTVHADN--SITVVDNGRGIPVDEHPvkkiptlevvmtilHAGGKFDnSAYK 111
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLP--------------RIFEPFS-TADK 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1801528178 112 VSGGLHGVGISVVNALSKRVVVQVRrdgntyemefsrgktvkkmevVGTSDSTGTTVTFWPDDEI 176
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELLGGTIT---------------------VESEPGGGTTVTLTLPLAQ 109
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
431-533 |
1.70e-16 |
|
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: 75.80 E-value: 1.70e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 431 LFIVEGDSAGGSAKDGRR---RDIQAILPLRGKILNVERVGDHRAFSSDTIQSLITAIGCGVttsaGDGGDFDITKARYH 507
Cdd:cd03365 3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQH----GKSDYESTKSLRYG 78
|
90 100
....*....|....*....|....*.
gi 1801528178 508 KIIIMTDADVDGAHIRILLLTFFYKY 533
Cdd:cd03365 79 RLMIMTDQDHDGSHIKGLLINFIHSF 104
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
36-173 |
1.90e-14 |
|
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: 70.83 E-value: 1.90e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 36 GLHHLVWEIV----DNSV-DEAMagfcTEIQVTVHAD-NSITVVDNGRGIPVDEHPVKKIPTLEVVMTILHAGGKFDNSA 109
Cdd:cd16930 4 GLYKIFDEILvnaaDNKQrDKSM----TCIKVTIDPEnNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDE 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1801528178 110 YKVSGGLHGVGISVVNALSKRVVVQV--RRDGNTYEMEFSRGKTvKKMEVVGTSDSTG---TTVTFWPD 173
Cdd:cd16930 80 KKVTGGRNGYGAKLCNIFSTEFTVETadSESKKKFKQTWTNNMG-KASEPKITPYEKGkdyTKVTFKPD 147
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
430-546 |
1.22e-13 |
|
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: 67.00 E-value: 1.22e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 430 ELFIVEGDSAGGSAKDGRRRDIQAILPLRGKILNVErvgdhrafsSDTIQSLITAIgcgvttsagdggdfDITKARYHKI 509
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLE---------KGPKKKALKAL--------------KELALKAKEV 57
|
90 100 110
....*....|....*....|....*....|....*..
gi 1801528178 510 IIMTDADVDGAHIRILLLTfFYKYMRPLIdaGYVYVA 546
Cdd:pfam01751 58 ILATDPDREGEAIALKLLE-LKELLENAG--GRVEFS 91
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
37-130 |
4.97e-06 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 45.67 E-value: 4.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 37 LHHLVWEIVDNSVDEAMAGfcTEIQVTVHADNS---ITVVDNGRGIPVDEHPvkkiptlevvmtilHAGGKFDNSAYKVS 113
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE--------------RIFERFYRGDKSRE 64
|
90
....*....|....*..
gi 1801528178 114 GGLHGVGISVVNALSKR 130
Cdd:cd00075 65 GGGTGLGLAIVRRIVEA 81
|
|
| COG1389 |
COG1389 |
DNA topoisomerase VI, subunit B [Replication, recombination and repair]; |
43-207 |
1.33e-04 |
|
DNA topoisomerase VI, subunit B [Replication, recombination and repair];
Pssm-ID: 440999 [Multi-domain] Cd Length: 530 Bit Score: 45.20 E-value: 1.33e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 43 EIVDNSVDEA-MAGFCTEIQVTVHADNS-----ITVVDNGRGIPVDehpvkKIPtlEVVMTILhAGGKFdnSAYKVSGGL 116
Cdd:COG1389 42 EAVDNSLDACeEAGILPDIKVSIERVDGkdiyrVTVEDNGPGIPPE-----QIP--KVFGKLL-YGSKF--HVLRQSRGQ 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 117 HGVGISVVNALSK-------RVVVQVRRDGNTYEMEFS------RGKtVKKMEVVGTSDSTGTTVTF-----WP--DDEI 176
Cdd:COG1389 112 QGIGISAAVLYAQmttgkpvEVISKTGGSEPAYYFELKidtkknEPV-ILEKEEVDWDRWHGTRVELelegdYVrgKQSI 190
|
170 180 190
....*....|....*....|....*....|.
gi 1801528178 177 FEtciYdfdtlhnrLQETAFLNKNLKIVLTD 207
Cdd:COG1389 191 YE---Y--------LKRTAIVNPHARITFID 210
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
430-533 |
1.57e-04 |
|
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 40.87 E-value: 1.57e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 430 ELFIVEGDSAGGSAKDGRRRDIqAILPLRGKILNvervgdhrafssDTIQSLITAIGcgvttsagdggdfditkaRYHKI 509
Cdd:cd00188 2 KLIIVEGPSDALALAQAGGYGG-AVVALGGHALN------------KTRELLKRLLG------------------EAKEV 50
|
90 100
....*....|....*....|....
gi 1801528178 510 IIMTDADVDGAHIRILLLTFFYKY 533
Cdd:cd00188 51 IIATDADREGEAIALRLLELLKSL 74
|
|
| HATPase_TopVIB-like |
cd16933 |
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ... |
19-129 |
8.12e-04 |
|
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends.
Pssm-ID: 340410 [Multi-domain] Cd Length: 203 Bit Score: 41.18 E-value: 8.12e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 19 EAVRKRPGMYIGSTSASGLHHLVWEIVDNSVDEA-MAGFCTEIQVTVH---ADN-SITVVDNGRGIPVDEhpvkkIPtlE 93
Cdd:cd16933 2 EFFRKNKEMLGFDNPIRSLYTTVRELVENSLDATeEAGILPDIKVEIEeigKDHyKVIVEDNGPGIPEEQ-----IP--K 74
|
90 100 110
....*....|....*....|....*....|....*.
gi 1801528178 94 VVMTILhAGGKFDNsayKVSGGLHGVGISVVNALSK 129
Cdd:cd16933 75 VFGKVL-YGSKYHN---KQSRGQQGLGISAAVLYSQ 106
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
43-83 |
4.73e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 40.03 E-value: 4.73e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1801528178 43 EIVDNSVDeamAGfCTEIQVTVHAD--NSITVVDNGRGIPVDE 83
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGgkSLIRVTDNGCGMSPED 68
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
43-169 |
9.69e-03 |
|
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: 37.80 E-value: 9.69e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1801528178 43 EIVDNSVDeamAGfCTEIQVTVHAD--NSITVVDNGRGIPVDE-------HPVKKIPTLEVVMTILHAGgkFDNSAykvs 113
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGISREDlelaferHATSKISSFEDLFSITTLG--FRGEA---- 89
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1801528178 114 ggLHgvGISvvnALSkRVVVQVRRDGN--TYEMEFSRGKTVKKMEVVGTsdSTGTTVT 169
Cdd:cd16926 90 --LA--SIA---SVS-RLTITTRTADDdvGTRLVVDGGGIIEEVKPAAA--PVGTTVT 137
|
|
| |
