|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
4-640 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1315.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 4 EQKIEHTYDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGI 83
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 84 PVDIQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIG 163
Cdd:PRK05644 81 PVDIHPKTGKPAVEVVLTVLHAggkfggggykvsggLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 164 ETDRTGTTVRFKPDPEIFtETTEFDYETLATRLRELAFLNRGLKITLEDKRVEN-RKNEYHYEGGIKSYVKHLNRTREVL 242
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEeKEETFHYEGGIKEYVEYLNRNKEPL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 243 HEEPIYIIGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVR 322
Cdd:PRK05644 240 HEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 323 EGLTAIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKS 402
Cdd:PRK05644 320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 403 ALEISNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGT 482
Cdd:PRK05644 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGT 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 483 GIGEDFDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQvKYAYNDRQLEKILA 562
Cdd:PRK05644 480 GIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILA 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 563 ELPE--NPKPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEENARYVKNLDI 640
Cdd:PRK05644 559 ELKLkgNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
8-640 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1256.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 8 EHTYDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDI 87
Cdd:COG0187 3 KSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPVDI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 88 QEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGETDR 167
Cdd:COG0187 83 HPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDR 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 168 TGTTVRFKPDPEIFtETTEFDYETLATRLRELAFLNRGLKITLEDKRVE-NRKNEYHYEGGIKSYVKHLNRTREVLHEEP 246
Cdd:COG0187 163 TGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEePKEETFHYEGGIKDFVEYLNEDKEPLHPEV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 247 IYIIGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVREGLT 326
Cdd:COG0187 242 IYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 327 AIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKSALEI 406
Cdd:COG0187 322 AVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALES 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 407 SNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGE 486
Cdd:COG0187 402 SGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGD 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 487 DFDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAELPE 566
Cdd:COG0187 482 DFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKELKG 561
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1329726007 567 NPKPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEENARYVKNLDI 640
Cdd:COG0187 562 KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
11-640 |
0e+00 |
|
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273421 [Multi-domain] Cd Length: 654 Bit Score: 1103.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 11 YDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQEK 90
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 91 MGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGETDRTGT 170
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 171 TVRFKPDPEIFtETTEFDYETLATRLRELAFLNRGLKITLEDKRVEN-RKNEYHYEGGIKSYVKHLNRTREVLHEEPIYI 249
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKgKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 250 IGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVREGLTAIV 329
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 330 SIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKSALEISNL 409
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 410 PGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFD 489
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 490 ITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQVKYA------------------ 551
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIkddkekdlvgealedlka 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 552 ---YNDRQLEKILAELPENP---KPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRR 625
Cdd:TIGR01059 560 lyiYSDKEKEEAKTQIPVHLgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRR 639
|
650
....*....|....*
gi 1329726007 626 QFIEENARYVKNLDI 640
Cdd:TIGR01059 640 EFIEANALDVKNLDV 654
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
8-640 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1097.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 8 EHTYDASQIQVLEGLEAVRKRPGMYIGSTG-PKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVD 86
Cdd:PRK14939 4 SNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 87 IQEKMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGETD 166
Cdd:PRK14939 84 IHPEEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETD 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 167 RTGTTVRFKPDPEIFTeTTEFDYETLATRLRELAFLNRGLKITLEDKRvENRKNEYHYEGGIKSYVKHLNRTREVLHEEP 246
Cdd:PRK14939 164 KTGTEVRFWPSPEIFE-NTEFDYDILAKRLRELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNI 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 247 IYIIGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVREGLT 326
Cdd:PRK14939 242 FYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 327 AIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKSALEI 406
Cdd:PRK14939 322 AVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 407 SNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIG- 485
Cdd:PRK14939 402 AGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGr 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 486 EDFDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAEL- 564
Cdd:PRK14939 482 DEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELa 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 565 -------PENPKP------------------------------------------------------------------- 570
Cdd:PRK14939 562 legatlhLADGPAisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsaeyrr 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 571 ---------------------------------------------TIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQD 605
Cdd:PRK14939 642 lvelaeklrglieegaylergerkqpvssfeealdwllaearkglSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIED 721
|
730 740 750
....*....|....*....|....*....|....*
gi 1329726007 606 AIEADETFEILMGDKVEPRRQFIEENARYVKNLDI 640
Cdd:PRK14939 722 AIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
10-635 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 942.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 10 TYDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQE 89
Cdd:PRK05559 7 NYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVGIHP 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 90 KMGRPAVEVIMTVLHAggkfggggykvsggLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGET--DR 167
Cdd:PRK05559 87 EEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAgkRK 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 168 TGTTVRFKPDPEIFtETTEFDYETLATRLRELAFLNRGLKITLEDKRVENrknEYHYEGGIKSYVKHLNRTREVLHEEPI 247
Cdd:PRK05559 167 TGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ---TFHYENGLKDYLAELNEGKETLPEEFV 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 248 -YIIGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKdNDPNLTGEDVREGLT 326
Cdd:PRK05559 243 gSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLA 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 327 AIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKgmMAARARLAAKKARELTRRKSALEi 406
Cdd:PRK05559 322 AVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEK--AIKAAQARLRAAKKVKRKKKTSG- 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 407 SNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGE 486
Cdd:PRK05559 399 PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGD 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 487 DFDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAEL-P 565
Cdd:PRK05559 479 SFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELLKKLgK 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 566 ENPKPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEENARYV 635
Cdd:PRK05559 559 KGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
40-633 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 926.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 40 GLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGG 119
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 120 LHGVGASVVNALSEELEVYVHRDGKIHYQKYQR-GVPCTDLEVIGETDRTGTTVRFKPDPEIFTETTEFDYETLATRLRE 198
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 199 LAFLNRGLKITLEDKRvENRKNEYHYEGGIKSYVKHLNRTREVLHEEPIYIIGERDGIYVEIALQYNDSYSSNIYSFVNN 278
Cdd:smart00433 161 LAFLNKGVKITLNDER-SDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNN 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 279 IHTHEGGTHESGFKTALTRIINDYARKHQILKDndPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLGNSDARAVTDAI 358
Cdd:smart00433 240 IATTEGGTHENGFKDALTRVINEYAKKKKKLKE--KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 359 FSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKsALEISNLPGKLADCSSKDPSISELYVVEGDSAGGSA 438
Cdd:smart00433 318 VSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 439 KQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFDITKARYHKIIIMTDADVDGAHIRTLLLTF 518
Cdd:smart00433 397 KSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTF 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 519 FYRYMREFIERGYVYIAQPPLYKIEQGKQvKYAYNDRQLEKILAELPE----NPKPTIQRYKGLGEMNPEQLWETTMNPE 594
Cdd:smart00433 477 FYRYMPPLIEAGFVYIAIPPLYKVTKGKK-KYVYSFYSLDEYEKWLEKtegnKSKYEIQRYKGLGEMNADQLWETTMDPE 555
|
570 580 590
....*....|....*....|....*....|....*....
gi 1329726007 595 TRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEENAR 633
Cdd:smart00433 556 RRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
11-634 |
0e+00 |
|
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130130 [Multi-domain] Cd Length: 637 Bit Score: 771.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 11 YDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQEK 90
Cdd:TIGR01058 5 YNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQD 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 91 MGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRG-VPCTDLEVIGETDRTG 169
Cdd:TIGR01058 85 GNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENGgKIVQSLKKIGTTKKTG 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 170 TTVRFKPDPEIFTeTTEFDYETLATRLRELAFLNRGLKITLEDKRvENRKNEYHYEGGIKSYVKHLNRTREVLHEEpIYI 249
Cdd:TIGR01058 165 TLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKR-TNKTTVFFYENGLVDFVDYINETKETLSQV-TYF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 250 IGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVREGLTAIV 329
Cdd:TIGR01058 242 EGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSAII 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 330 SIKHPSP--QFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTR--RKSALE 405
Cdd:TIGR01058 322 SVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKPKKE 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 406 ISNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIG 485
Cdd:TIGR01058 402 KGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGIG 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 486 EDFDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQ--GKQVKYAYNDRQLEKILAE 563
Cdd:TIGR01058 482 ADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELESVKKK 561
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1329726007 564 LPENpkpTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEENARY 634
Cdd:TIGR01058 562 LKNY---TLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINF 629
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
11-632 |
0e+00 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 550.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 11 YDASQIQVLEGLEAVRKRPGMYIGSTGPKGLHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQEK 90
Cdd:PTZ00109 100 YDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEK 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 91 MGRPAVEVIMTVLH----------------------------------------AGGKFGGGGYKVSGGLHGVGASVVNA 130
Cdd:PTZ00109 180 TGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSVVNA 259
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 131 LSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGE-TDRTGTTVRFKPD-PEIF------TETTE-------FDYETLATR 195
Cdd:PTZ00109 260 LSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCpLKKRGTTIHFLPDyKHIFkthhqhTETEEeegckngFNLDLIKNR 339
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 196 LRELAFLNRGLKITLEDKRVENRKNEYHYE-----GGIKSYVKHLNRTREVLHEEP--IYIIGERDGIYVEIALQYN-DS 267
Cdd:PTZ00109 340 IHELSYLNPGLTFYLVDERIANENNFYPYEtikheGGTREFLEELIKDKTPLYKDIniISIRGVIKNVNVEVSLSWSlES 419
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 268 YSSNIYSFVNNIHThEGGTHESGFKTALTRIINDYARKHQILKDNDPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLG 347
Cdd:PTZ00109 420 YTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLG 498
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 348 NSDARAVTDAIFSEQFETFLLENPTIARKIVEKGMMAARARLAAKKARELTRRKSALEISN-LPGKLADCSSKDPSISEL 426
Cdd:PTZ00109 499 NHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDDIERNEL 578
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 427 YVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLD-KILSNNEVRAIITALGTGIGED------------------ 487
Cdd:PTZ00109 579 FIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtkaskdes 658
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 488 --------------FDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKI----------- 542
Cdd:PTZ00109 659 vqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqfnvs 738
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 543 -EQGKQVKYAYNDRQLEKILAELPENPKP--------------------------------------------------- 570
Cdd:PTZ00109 739 tKNSKKYIYTWSDEELNVLIKLLNKDYSSkettrsveekgnapdldneyedekldnknmrennvdevelktelgtnvadt 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 571 -------------------TIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIEEN 631
Cdd:PTZ00109 819 eqtdeldinkaffkfskhyEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFEN 898
|
.
gi 1329726007 632 A 632
Cdd:PTZ00109 899 S 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
10-630 |
0e+00 |
|
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130127 [Multi-domain] Cd Length: 625 Bit Score: 533.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 10 TYDASQIQVLEGLEAVRKRPGMYIGSTGPkglHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQE 89
Cdd:TIGR01055 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTRP---NHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 90 KMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGETDR-- 167
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrl 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 168 TGTTVRFKPDPEIFTEtTEFDYETLATRLRELAFLNRGLKITLEDKrVENRKNEYHYEGGIKSYVKHLNRTREVLHEEPI 247
Cdd:TIGR01055 160 TGTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDE-VNNTKALWNYPDGLKDYLSEAVNGDNTLPPKPF 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 248 YIIGERDGIYVEIALQY-NDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYArKHQILKDNDPNLTGEDVREGLT 326
Cdd:TIGR01055 238 SGNFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFC-EMRNNLPRGVKLTAEDIWDRCS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 327 AIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEkgmMAARARLAAKKARELTRRKSALEI 406
Cdd:TIGR01055 317 YVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAE---HAISSAQRRKRAAKKVVRKKLTSG 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 407 SNLPGKLADCSSKDPSISELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGE 486
Cdd:TIGR01055 394 PALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDS 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 487 DfDITKARYHKIIIMTDADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAELPE 566
Cdd:TIGR01055 474 N-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKLKK 552
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1329726007 567 NP-KPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDA--IEADETFEILMGDKV-EPRRQFIEE 630
Cdd:TIGR01055 553 KKgKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVqdQRVDKIMDMLLAKKRsEDRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
41-220 |
4.61e-99 |
|
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: 300.22 E-value: 4.61e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 41 LHHLVWEIVDNSIDEALAGYCTEINVTIEKDNIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGL 120
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 121 HGVGASVVNALSEELEVYVHRDGKIHYQKYQRGVPCTDLEVIGETDRTGTTVRFKPDPEIFtETTEFDYETLATRLRELA 200
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170 180
....*....|....*....|
gi 1329726007 201 FLNRGLKITLEDKRVENRKN 220
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEEV 179
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
226-380 |
5.99e-87 |
|
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: 268.66 E-value: 5.99e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 226 GGIKSYVKHLNRTREVLHEEPIYIIGERDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARK 305
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1329726007 306 HQILKDNDPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEK 380
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
424-537 |
7.69e-84 |
|
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: 258.35 E-value: 7.69e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 424 SELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFDITKARYHKIIIMTD 503
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 1329726007 504 ADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQP 537
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
227-380 |
9.09e-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: 234.43 E-value: 9.09e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 227 GIKSYVKHLNRTREVLHEEPIYIIGE--RDGIYVEIALQYNDSYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYAR 304
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1329726007 305 KHQILKDNDPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFSEQFETFLLENPTIARKIVEK 380
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
424-537 |
5.51e-69 |
|
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: 219.68 E-value: 5.51e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 424 SELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIG-EDFDITKARYHKIIIMT 502
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 1329726007 503 DADVDGAHIRTLLLTFFYRYMREFIERGYVYIAQP 537
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
14-628 |
2.81e-58 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 206.53 E-value: 2.81e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 14 SQIQVLEGLEAVRKRPGMYIGSTGPK-----------------GLHHLVWEIVDNSIDEALAG---YCTEINVTIeKDNI 73
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAYEaherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 74 IAITDNGRGIPvdiQEKMGRPAVEVIMTVLHAGGKFG-----GGGYKVSGGLHGVGASVVNALSEELeVYVHRDGKIHYQ 148
Cdd:PHA02569 81 VTVSDNGRGIP---QAMVTTPEGEEIPGPVAAWTRTKagsnfDDTNRVTGGMNGVGSSLTNFFSVLF-IGETCDGKNEVT 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 149 kyqrgVPCTD-LEVIGETDR----TGTTVRFKPDPEIFtETTEFDYETL---ATRLRELAFLNRGLKITLEDKRVENRkn 220
Cdd:PHA02569 157 -----VNCSNgAENISWSTKpgkgKGTSVTFIPDFSHF-EVNGLDQQYLdiiLDRLQTLAVVFPDIKFTFNGKKVSGK-- 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 221 eyhyeggIKSYVKHLNrtrevlhEEPIyiIGERDGIYVEIAlQYNDSYSSNiySFVNNIHTHEGGTHESGFKTALT-RII 299
Cdd:PHA02569 229 -------FKKYAKQFG-------DDTI--VQENDNVSIALA-PSPDGFRQL--SFVNGLHTKNGGHHVDCVMDDICeELI 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 300 NDYARKHQIlkdndpNLTGEDVREGLTAIVSIKH-PSPQFEGQTKTKLGNS----------DARAVTDAIfseqfetflL 368
Cdd:PHA02569 290 PMIKKKHKI------EVTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgeirnhidlDYKKIAKQI---------L 354
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 369 ENPTIARKIVEKGM---MAARARLAAKKARELTRRKSALEI-SNLPGKLADcsskdpsiSELYVVEGDSAGGSAKQGRDR 444
Cdd:PHA02569 355 KTEAIIMPIIEAALarkLAAEKAAETKAAKKAKKAKVAKHIkANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDE 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 445 HFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFDITKarYHKIIIMTDADVDG-AHIRTLLLTFFYRYm 523
Cdd:PHA02569 427 ELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENMN--YKNIAIMTDADVDGkGSIYPLLLAFFSRW- 503
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 524 REFIERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAELpenPKPTIQRYKGLGEMNPEQLWETTMNPetrTLLQVSL 603
Cdd:PHA02569 504 PELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSL---KKWSIRYIKGLGSLRKSEYRRVINNP---VYDVVVL 577
|
650 660
....*....|....*....|....*
gi 1329726007 604 QDaiEADETFEILMGDKVEPRRQFI 628
Cdd:PHA02569 578 PD--DWKELFEMLFGDDADLRKDWM 600
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
2-579 |
7.64e-43 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 166.38 E-value: 7.64e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 2 TMEQKIEHTYdasqiQVLEGLEAVRKRPGMYIGSTGPK-----------------------GLHHLVWEI----VDNSID 54
Cdd:PTZ00108 1 KKNKTVEERY-----QKKTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKAR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 55 EALAGYCTEINVTI-EKDNIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSE 133
Cdd:PTZ00108 76 DKGGHRMTYIKVTIdEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFST 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 134 ELEVYV--HRDGKIHYQKYQRGVPCTDLEVIGETDRTG--TTVRFKPDPEIFtETTEFDYETLAT---RLRELAFLNRGL 206
Cdd:PTZ00108 156 KFTVECvdSKSGKKFKMTWTDNMSKKSEPRITSYDGKKdyTKVTFYPDYAKF-GMTEFDDDMLRLlkkRVYDLAGCFGKL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 207 KITLEDKRVENRKneyhyeggIKSYVKHlnrtreVLHEEPIYIIGERDGIY------VEIALQYNDSySSNIYSFVNNIH 280
Cdd:PTZ00108 235 KVYLNGERIAIKS--------FKDYVDL------YLPDGEEGKKPPYPFVYtsvngrWEVVVSLSDG-QFQQVSFVNSIC 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 281 THEGGTHESGFKTALTRIINDYARKhqiLKDNDPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLGNSDARAVTDAIFS 360
Cdd:PTZ00108 300 TTKGGTHVNYILDQLISKLQEKAKK---KKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELS 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 361 EQFETFLLENPTIARkIVEkgMMAARARLAAKKARELTRRKSALEISnlpgKLADCSSKDPSISE---LYVVEGDSA--- 434
Cdd:PTZ00108 377 EKLIKYVLKSPILEN-IVE--WAQAKLAAELNKKMKAGKKSRILGIP----KLDDANDAGGKNSEectLILTEGDSAkal 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 435 --GGSAKQGRDRHfqAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFDITKA-RYHKIIIMTDADVDGAHI 511
Cdd:PTZ00108 450 alAGLSVVGRDYY--GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGlRYGSLMIMTDQDHDGSHI 527
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 512 RTLLLTFFYRYMREFIE-RGYVYIAQPPLYKIEQ-GKQVKYAYNDRQLEKILAELPeNPKPTIQRYKGLG 579
Cdd:PTZ00108 528 KGLLINMIHHFWPSLLKnPGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQTVG-LKGWKIKYYKGLG 596
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
567-629 |
1.09e-42 |
|
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: 147.52 E-value: 1.09e-42
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1329726007 567 NPKPTIQRYKGLGEMNPEQLWETTMNPETRTLLQVSLQDAIEADETFEILMGDKVEPRRQFIE 629
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
7-630 |
3.77e-40 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 157.95 E-value: 3.77e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 7 IEHTYdasqiQVLEGLEAVRKRPGMYIGSTGPK---------------------GLHHLVWEIVDNSIDEALAG-YCTEI 64
Cdd:PLN03128 3 IEETY-----QKKTQLEHILLRPDTYIGSTEKHtqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADNKQRDpSMDSL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 65 NVTIEKD-NIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSEE--LEVYVHR 141
Cdd:PLN03128 78 KVDIDVEqNTISVYNNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEftVETADGN 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 142 DGKIHYQKYQRGVPCTDLEVIG--ETDRTGTTVRFKPDPEIFTETT--EFDYETLATRLRELA-FLNRGLKITLEDKRVE 216
Cdd:PLN03128 158 RGKKYKQVFTNNMSVKSEPKITscKASENWTKITFKPDLAKFNMTRldEDVVALMSKRVYDIAgCLGKKLKVELNGKKLP 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 217 NrkneyhyeGGIKSYVK-HLNRTREvlhEEPIYIIGERDGIYVEIALQYNDSySSNIYSFVNNIHTHEGGTHESGFKTAL 295
Cdd:PLN03128 238 V--------KSFQDYVGlYLGPNSR---EDPLPRIYEKVNDRWEVCVSLSDG-SFQQVSFVNSIATIKGGTHVDYVADQI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 296 TRIINDYARKhqilKDNDP-NLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLgNSDARAvtdaiFSEQFETflleNPTIA 374
Cdd:PLN03128 306 VKHIQEKVKK----KNKNAtHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL-TTRPSS-----FGSKCEL----SEEFL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 375 RKIVEKGMMAARARLAAKKARELTRRKSALEISNLPG--KLADCS---SKDPSISELYVVEGDSA-----GGSAKQGRDR 444
Cdd:PLN03128 372 KKVEKCGVVENILSWAQFKQQKELKKKDGAKRQRLTGipKLDDANdagGKKSKDCTLILTEGDSAkalamSGLSVVGRDH 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 445 HfqAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFD---ITKARYHKIIIMTDADVDGAHIRTLLLTFFYR 521
Cdd:PLN03128 452 Y--GVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDeenTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHS 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 522 ----------YMREFIErgyvyiaqpPLYKIEQGKQVKYAYNDRQLEKILAEL-PENPKPTIQRYKGLGEMNPEQLWE-- 588
Cdd:PLN03128 530 fwpsllkipgFLVEFIT---------PIVKATKGGKSLSFYTMPEYEAWKESLeGETKGWTIKYYKGLGTSTSEEAKEyf 600
|
650 660 670 680
....*....|....*....|....*....|....*....|..
gi 1329726007 589 TTMNPETRTLLQVSLQDAIEADETFEilmGDKVEPRRQFIEE 630
Cdd:PLN03128 601 SNLDIHKKEFLWQSDEDGDLIDMAFS---KKRVEDRKIWLNN 639
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
1-579 |
7.28e-25 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 110.72 E-value: 7.28e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 1 MTMEQKIEHTYdasqiQVLEGLEAVRKRPGMYIGS---------------------TGPKGLHHLVWEIVDNSIDEALAG 59
Cdd:PLN03237 22 SSGGKTIEEMY-----QKKSQLEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRD 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 60 -YCTEINVTIEKD-NIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVSGGLHGVGASVVNALSEELeV 137
Cdd:PLN03237 97 pKMDSLRVVIDVEqNLISVYNNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEF-V 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 138 YVHRDGKiHYQKYQR------GVPCTDLEVIGETDRTGTTVRFKPDPEIFTeTTEFDYETLA---TRLRELA-FLNRGLK 207
Cdd:PLN03237 176 IETADGK-RQKKYKQvfsnnmGKKSEPVITKCKKSENWTKVTFKPDLAKFN-MTHLEDDVVAlmkKRVVDIAgCLGKTVK 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 208 ITLEDKRVENRkneyhyegGIKSYVKHLNRTREVLHEEPIYIIGERDGIYVEIALQYNDSYSSNIySFVNNIHTHEGGTH 287
Cdd:PLN03237 254 VELNGKRIPVK--------SFSDYVDLYLESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTH 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 288 ESGFKTALTRIINDYARKhqilKDNDPNLTGEDVREGLTAIVSIKHPSPQFEGQTKTKLgnsDARAVTDAIFSEQFETFL 367
Cdd:PLN03237 325 VDYVTNQIANHVMEAVNK----KNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL---TLRQSSFGSKCELSEDFL 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 368 lenptiaRKIVEKGMMAARARLAAKKARELTRRKSALEISNLPG--KLADCSSKDPSISE---LYVVEGDSAGGSAKQGR 442
Cdd:PLN03237 398 -------KKVMKSGIVENLLSWADFKQSKELKKTDGAKTTRVTGipKLEDANEAGGKNSEkctLILTEGDSAKALAVAGL 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 443 ---DRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDFDITKA-RYHKIIIMTDADVDGAHIRTLLLTF 518
Cdd:PLN03237 471 svvGRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLINF 550
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1329726007 519 FYRYMREF--IERGYVYIAQPPLYKIEQGKQVKYAYNDRQLEKILAELPENPKP-TIQRYKGLG 579
Cdd:PLN03237 551 IHSFWPSLlkVPSFLVEFITPIVKATRRGKKVLSFYSMPEYEEWKESLGGNATGwSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
228-347 |
9.84e-24 |
|
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: 96.18 E-value: 9.84e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 228 IKSYVKHLNRTREvlHEEPIYIIGERDGIYVEIALQYND---SYSSNIYSFVNNIHTHEGGTHESGFKTALTRIINdyar 304
Cdd:cd00329 1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1329726007 305 khqilkdndpnltGEDVREGLTAIVSIKHP--SPQFE-GQTKTKLG 347
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPpsLVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
426-522 |
1.84e-20 |
|
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: 87.36 E-value: 1.84e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 426 LYVVEGDSAGGSAKQGR---DRHFQAILPLRGKIINVEKARLDKILSNNEVRAIITALGTGIGEDF--DITKARYHKIII 500
Cdd:cd03365 3 LILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMI 82
|
90 100
....*....|....*....|..
gi 1329726007 501 MTDADVDGAHIRTLLLTFFYRY 522
Cdd:cd03365 83 MTDQDHDGSHIKGLLINFIHSF 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
425-537 |
5.11e-17 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 76.63 E-value: 5.11e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 425 ELYVVEGDSAGGSAKQGRDRHFQAILPLRGKIINVEKARLDKILSNnevraiitalgtgigedFDITKARYHKIIIMTDA 504
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|...
gi 1329726007 505 DVDGAHIRTLLLTfFYRYMREFIerGYVYIAQP 537
Cdd:pfam01751 64 DREGEAIALKLLE-LKELLENAG--GRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
38-180 |
2.74e-15 |
|
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: 72.02 E-value: 2.74e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 38 PKGLHHLVWEIVDNSIDEAlaGYCTEINVTIEKDN--IIAITDNGRGIPVDIQEKMGRPAVEVIMTvlhaggkfggggyk 115
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLPRIFEPFSTADKR-------------- 66
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1329726007 116 vSGGLHGVGASVVNALSEELevyvhrDGKIHYQkyqrgvpctdlevigETDRTGTTVRFKPDPEI 180
Cdd:pfam02518 67 -GGGGTGLGLSIVRKLVELL------GGTITVE---------------SEPGGGTTVTLTLPLAQ 109
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
38-179 |
1.36e-13 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 67.29 E-value: 1.36e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 38 PKGLHHLVWEIVDNSIDEALAGycTEINVTIEKDN---IIAITDNGRGIPVDIQEKMGRPAVEVimtvlhaggkfggGGY 114
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPEDLEKIFEPFFRT-------------DKR 67
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1329726007 115 KVSGGLHGVGASVVNALSEELEVYVHRDGKihyqkyqrgvpctdlevigetDRTGTTVRFKPDPE 179
Cdd:smart00387 68 SRKIGGTGLGLSIVKKLVELHGGEISVESE---------------------PGGGTTFTITLPLE 111
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
424-522 |
2.08e-06 |
|
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: 45.88 E-value: 2.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 424 SELYVVEGDSAGGSAKQGRDrHFQAILPLRGKIINVEKARLDKILSnnevraiitalgtgigedfditkaRYHKIIIMTD 503
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90
....*....|....*....
gi 1329726007 504 ADVDGAHIRTLLLTFFYRY 522
Cdd:cd00188 56 ADREGEAIALRLLELLKSL 74
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
41-94 |
2.12e-05 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 43.75 E-value: 2.12e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1329726007 41 LHHLVWEIVDNSIDEALAGycTEINVTIEKDN---IIAITDNGRGIPVDIQEKMGRP 94
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGdgvVLEVEDNGPGIPEEDLERIFER 55
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
40-177 |
1.61e-04 |
|
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.
Pssm-ID: 340407 [Multi-domain] Cd Length: 147 Bit Score: 42.33 E-value: 1.61e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 40 GLHHLVWEIVDNSID-EALAGYCTEINVTIEKD-NIIAITDNGRGIPVDIQEKMGRPAVEVIMTVLHAGGKFGGGGYKVS 117
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPEnNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1329726007 118 GGLHGVGASVVNALSEELEV-YVHRD-GKIHYQKYQRGV-PCTDLEVIGETDRTG-TTVRFKPD 177
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVeTADSEsKKKFKQTWTNNMgKASEPKITPYEKGKDyTKVTFKPD 147
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
226-346 |
2.12e-04 |
|
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Pssm-ID: 239563 [Multi-domain] Cd Length: 153 Bit Score: 41.89 E-value: 2.12e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 226 GGIKSYVKHLNRTREVLHEEPIYIIGERDGIYVEIALQYNDSySSNIYSFVNNIHTHEGGTHESGFKTALTRIINDYARK 305
Cdd:cd03481 1 KSFKDYVKLYLKDANKEDGPPPPVVYEPVNDRWEVAVALSDG-QFQQVSFVNSIATTKGGTHVDYVADQIVKKLDEVVKK 79
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1329726007 306 hqiLKDNDPNLTGEDVREGLTAIVS--IKHPSpqFEGQTKTKL 346
Cdd:cd03481 80 ---KNKGGINVKPFQVKNHLWIFVNclIENPS--FDSQTKETL 117
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
47-86 |
9.85e-04 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 42.13 E-value: 9.85e-04
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1329726007 47 EIVDNSIDealAGyCTEINVTIEKD--NIIAITDNGRGIPVD 86
Cdd:PRK00095 29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGISKE 66
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
47-86 |
2.99e-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: 39.34 E-value: 2.99e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1329726007 47 EIVDNSIDealAGyCTEINVTIEKDNI--IAITDNGRGIPVD 86
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGGLklIRVTDNGSGISRE 57
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
47-86 |
4.64e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 40.03 E-value: 4.64e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1329726007 47 EIVDNSIDealAGyCTEINVTIEKDNI--IAITDNGRGIPVD 86
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGGKslIRVTDNGCGMSPE 67
|
|
| HATPase_TopVIB-like |
cd16933 |
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ... |
23-86 |
8.51e-03 |
|
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: 38.10 E-value: 8.51e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1329726007 23 EAVRKRPGMyIGSTGP-KGLHHLVWEIVDNSIDEA-LAGYCTEINVTIEKDN----IIAITDNGRGIPVD 86
Cdd:cd16933 2 EFFRKNKEM-LGFDNPiRSLYTTVRELVENSLDATeEAGILPDIKVEIEEIGkdhyKVIVEDNGPGIPEE 70
|
|
| KdpD |
COG2205 |
K+-sensing histidine kinase KdpD [Signal transduction mechanisms]; |
41-94 |
8.61e-03 |
|
K+-sensing histidine kinase KdpD [Signal transduction mechanisms];
Pssm-ID: 441807 [Multi-domain] Cd Length: 239 Bit Score: 38.35 E-value: 8.61e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1329726007 41 LHHLVWEIVDNSIDEALAGycTEINVTIEKDN---IIAITDNGRGIPVDIQEKMGRP 94
Cdd:COG2205 133 LEQVLANLLDNAIKYSPPG--GTITISARREGdgvRISVSDNGPGIPEEELERIFER 187
|
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| |
