|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
44-714 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1257.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 44 KKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGI 123
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 124 PVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQGA 201
Cdd:PRK05644 81 PVDIHPKtGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTpLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 202 PTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERvtqdevvdevvsdvaeapksaseraaesta 281
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDER------------------------------ 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 282 PHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRS 361
Cdd:PRK05644 211 EGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKT 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 362 ALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTD 441
Cdd:PRK05644 291 ALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNV 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 442 SKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLR 521
Cdd:PRK05644 371 AKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLR 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 522 GKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVF 601
Cdd:PRK05644 451 GKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVY 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 602 LAQPPLYKLKWQRSdpEFAYSDRERDGLLEAGlkaGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAA 681
Cdd:PRK05644 531 IAQPPLYKIKKGGK--EYAYSDEELDEILAEL---KLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAA 605
|
650 660 670
....*....|....*....|....*....|...
gi 998490969 682 AADELFSILMGEDVDARRSFITRNAKDVRFLDV 714
Cdd:PRK05644 606 EADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
46-714 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1194.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 46 KAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPV 125
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 126 ATHA-SGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQGAPT 203
Cdd:COG0187 81 DIHPkEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGpLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 204 KKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERvtqdevvdevvsdvAEAPKSAseraaestaph 283
Cdd:COG0187 161 DRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDER--------------EEEPKEE----------- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 284 kvksrTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSAL 363
Cdd:COG0187 216 -----TFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTAL 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 364 TSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSK 443
Cdd:COG0187 291 TRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAK 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 444 VVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGK 523
Cdd:COG0187 371 KILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGK 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 524 IINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLA 603
Cdd:COG0187 451 ILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIA 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 604 QPPLYKLKWQRsDPEFAYSDRERDGLLEAgLKAGKKINkedgIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAA 683
Cdd:COG0187 531 QPPLYRIKKGK-KTYYAYSDAELDELLKE-LKGKKKVE----IQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEA 604
|
650 660 670
....*....|....*....|....*....|.
gi 998490969 684 DELFSILMGEDVDARRSFITRNAKDVRFLDV 714
Cdd:COG0187 605 DEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
51-714 |
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: 1097.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 51 YGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHAS 130
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 131 -GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQGAPTKKTGS 208
Cdd:TIGR01059 81 eGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGpLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 209 TVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTqdevvdevvsdvaeapksaseraaestaphKVKSR 288
Cdd:TIGR01059 161 TVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDG------------------------------KGKKV 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 289 TFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVN 368
Cdd:TIGR01059 211 TFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVIN 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 369 KYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNK 448
Cdd:TIGR01059 291 SYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEK 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 449 AVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVE 528
Cdd:TIGR01059 371 AILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVE 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 529 KARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLY 608
Cdd:TIGR01059 451 KARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLY 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 609 KLKWQRSDpEFAYSDRERDgLLEAGLKAGKKIN--------------------KEDGIQRYKGLGEMDAKELWETTMDPS 668
Cdd:TIGR01059 531 KVKKGKKE-RYIKDDKEKD-LVGEALEDLKALYiysdkekeeaktqipvhlgrKGIEIQRYKGLGEMNADQLWETTMDPE 608
|
650 660 670 680
....*....|....*....|....*....|....*....|....*.
gi 998490969 669 VRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV 714
Cdd:TIGR01059 609 SRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLDV 654
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
47-714 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 984.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 47 AQDEYGAASITILEGLEAVRKRPGMYIGSTGE-RGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPV 125
Cdd:PRK14939 3 MSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 126 ATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQGAPT 203
Cdd:PRK14939 83 DIHPEeGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVApLKVVGET 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 204 KKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERvtqdevvdevvsdvaeapksaseraaestaph 283
Cdd:PRK14939 163 DKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDER-------------------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 284 KVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSAL 363
Cdd:PRK14939 211 DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAAL 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 364 TSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSK 443
Cdd:PRK14939 291 TRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAK 370
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 444 VVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGK 523
Cdd:PRK14939 371 IIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGK 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 524 IINVEKARIDRVLKNTEVQAIITALGTGI-HDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFL 602
Cdd:PRK14939 451 ILNVEKARFDKMLSSQEIGTLITALGCGIgRDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYI 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 603 AQPPLYKLKWQRS------------------------------------------------------------------- 615
Cdd:PRK14939 531 AQPPLYKVKKGKQeqylkddealddylielalegatlhladgpaisgealeklvkeyravrkiidrlerrypravleali 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 616 -------------------DPEFAYS--------------DRERDG-----------------LLEAGLKAGKKinkedG 645
Cdd:PRK14939 611 yapaldlddladeaavaalDADFLTSaeyrrlvelaeklrGLIEEGaylergerkqpvssfeeALDWLLAEARK-----G 685
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 998490969 646 --IQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV 714
Cdd:PRK14939 686 lsIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
44-709 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 902.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 44 KKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGI 123
Cdd:PRK05559 1 AAMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 124 PVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQG- 200
Cdd:PRK05559 81 PVGIHPEeGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGpLEVVg 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 201 -APTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQdevvdevvsdvaeapksaseraaes 279
Cdd:PRK05559 161 tAGKRKTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ------------------------- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 280 taphkvksrTFHYPGGLVDFVKHINRTKNAIHSSIVD-FSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEG 358
Cdd:PRK05559 216 ---------TFHYENGLKDYLAELNEGKETLPEEFVGsFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENG 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 359 FRSALTSVVNKYAKDRKLLKdKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEAN 438
Cdd:PRK05559 287 FREGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQN 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 439 PTDSKVVVNKAVSSAQARIAARKarELVRRKSATdIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAIL 518
Cdd:PRK05559 366 PELAEKLAEKAIKAAQARLRAAK--KVKRKKKTS-GPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAIL 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 519 PLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENG 598
Cdd:PRK05559 443 PLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAG 522
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 599 HVFLAQPPLYKLKwQRSDPEFAYSDRERDGLLEAGLKAGKKINkedgIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLD 678
Cdd:PRK05559 523 HVYIALPPLYRVD-KGKKKIYALDEEEKEELLKKLGKKGGKPE----IQRFKGLGEMNPDQLWETTMDPETRRLVRVTID 597
|
650 660 670
....*....|....*....|....*....|.
gi 998490969 679 DAAAADELFSILMGEDVDARRSFITRNAKDV 709
Cdd:PRK05559 598 DAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
80-707 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 853.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 80 GLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHA-SGIPTVDVVMTQLHAGGKFDSDAYAISGG 158
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPkEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 159 LHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPL--GLKQGAPTKKTGSTVRFWADPAVFE-TTEYDFETVARRLQE 235
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKPlsEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 236 MAFLNKGLTINLTDERvtqdevvdevvsdvaeapksaseraaestaphKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIV 315
Cdd:smart00433 161 LAFLNKGVKITLNDER--------------------------------SDEEKTFLFEGGIKDYVELLNKNKELLSPEPT 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 316 DFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKdpNLTGDDIREGLAA 395
Cdd:smart00433 209 YIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK--NIKGEDVREGLTA 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 396 VISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVSSAQARIAARKARELvRRKSATDIG 475
Cdd:smart00433 287 FISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKAREL-TRKKKLSSI 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 476 GLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDE 555
Cdd:smart00433 366 SLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKD 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 556 FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWqRSDPEFAYSDRERDGLLEAGLK 635
Cdd:smart00433 446 FDIEKLRYGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTK-GKKKYVYSFYSLDEYEKWLEKT 524
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 998490969 636 AGKKINkeDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAK 707
Cdd:smart00433 525 EGNKSK--YEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
51-707 |
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: 715.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 51 YGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHAS 130
Cdd:TIGR01058 5 YNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQD 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 131 G-IPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPL--GLKQGAPTKKTG 207
Cdd:TIGR01058 85 GnISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENGGKIvqSLKKIGTTKKTG 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 208 STVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVvdevvsdvaeapksaseraaestaphkvks 287
Cdd:TIGR01058 165 TLVHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTTV------------------------------ 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 288 rtFHYPGGLVDFVKHINRTKNAIhSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVV 367
Cdd:TIGR01058 215 --FFYENGLVDFVDYINETKETL-SQVTYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVI 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 368 NKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEP--QFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVV 445
Cdd:TIGR01058 292 NSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLL 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 446 VNKAVSSAQARIAARKARELVR--RKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGK 523
Cdd:TIGR01058 372 IDKAIKARDAKEAAKKAREEKKsgKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGK 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 524 IINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLA 603
Cdd:TIGR01058 452 VLNVEKAKLADILKNEEINTIIFCIGTGIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIA 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 604 QPPLYKL-KWQRSDPEFAYSDRERDGLleaglkagKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAA 682
Cdd:TIGR01058 532 LPPLYKLsKKDGKKVKYAWSDLELESV--------KKKLKNYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLAR 603
|
650 660
....*....|....*....|....*
gi 998490969 683 ADELFSILMGEDVDARRSFITRNAK 707
Cdd:TIGR01058 604 AERQINTLMGDKVEPRKKWIEANIN 628
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
50-706 |
1.06e-174 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 522.90 E-value: 1.06e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 50 EYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATH- 128
Cdd:PTZ00109 99 EYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSe 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 129 ASGIPTVDVVMTQLHAGGKF----------------------------------------DSDAYAISGGLHGVGVSVVN 168
Cdd:PTZ00109 179 KTGKSGLETVLTVLHSGGKFqdtfpknsrsdksedkndtksskkgksshvkgpkeakekeSSQMYEYSSGLHGVGLSVVN 258
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 169 ALSTRLEVEIKRDGYEWSQVYEK---SEPLGLKQgAPTKKTGSTVRFWAD-PAVFETT--------------EYDFETVA 230
Cdd:PTZ00109 259 ALSSFLKVDVFKGGKIYSIELSKgkvTKPLSVFS-CPLKKRGTTIHFLPDyKHIFKTHhqhteteeeegcknGFNLDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 231 RRLQEMAFLNKGLTINLTDERVTQdevvdevvsdvaeapksaseraaESTAPHKvksRTFHYPGGLVDFVKHINRTKNAI 310
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERIAN-----------------------ENNFYPY---ETIKHEGGTREFLEELIKDKTPL 391
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 311 H--SSIVDFSGKGTGHEVEIAMQWNAG-YSESVHTFANTINThEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGD 387
Cdd:PTZ00109 392 YkdINIISIRGVIKNVNVEVSLSWSLEsYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGE 470
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 388 DIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVSSAQARIAARKARELVR 467
Cdd:PTZ00109 471 FIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIR 550
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 468 RKSATDIG-GLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARID-RVLKNTEVQAII 545
Cdd:PTZ00109 551 QKNNQYYStILPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLI 630
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 546 TALGTGIH-----------------DEF---------------DIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRP 593
Cdd:PTZ00109 631 TSIGLSVNpvtwrqydlshgtkaskDESvqnnnstltkkknslFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPS 710
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 594 LIENGHVFLAQPPLYKLKWQRSDPE-----------FAYSDRERDGLL-------------------------EAGLKAG 637
Cdd:PTZ00109 711 LYEHGRVYVACPPLYRITNNRMKQFnvstknskkyiYTWSDEELNVLIkllnkdysskettrsveekgnapdlDNEYEDE 790
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 638 KKINKEDG----------------------------------------IQRYKGLGEMDAKELWETTMDPSVRVLRQVTL 677
Cdd:PTZ00109 791 KLDNKNMRennvdevelktelgtnvadteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITV 870
|
810 820
....*....|....*....|....*....
gi 998490969 678 DDAAAADELFSILMGEDVDARRSFITRNA 706
Cdd:PTZ00109 871 SDAMRASELIFLLMGEDVQSRKQFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
51-702 |
6.65e-166 |
|
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: 490.97 E-value: 6.65e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 51 YGAASITILEGLEAVRKRPGMYIGSTGergLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHAS 130
Cdd:TIGR01055 4 YSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 131 -GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPT---KKT 206
Cdd:TIGR01055 81 eGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTcgkRLT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 207 GSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERvtqdevvdevvsdvaeapksaseraaestaphKVK 286
Cdd:TIGR01055 161 GTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEV--------------------------------NNT 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 287 SRTFHYPGGLVDFVKHINRTKNAIHSSIvdFSG--KGTGHEVEIAMQW-NAGYSESVHTFANTINTHEGGTHEEGFRSAL 363
Cdd:TIGR01055 209 KALWNYPDGLKDYLSEAVNGDNTLPPKP--FSGnfEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGL 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 364 TSVVNKYAKDRKLLKdKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSK 443
Cdd:TIGR01055 287 LDALREFCEMRNNLP-RGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAE 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 444 VVVNKAVSSAQARIaaRKARELVRrKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGK 523
Cdd:TIGR01055 366 HLAEHAISSAQRRK--RAAKKVVR-KKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGK 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 524 IINVEKARIDRVLKNTEVQAIITALGTGiHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLA 603
Cdd:TIGR01055 443 ILNTWEVSLDKVLNSQEIHDIEVALGID-PDSNDLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVA 521
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 604 QPPLYKLKwQRSDPEFAYSDRERDGLLEAGLKAGKKINkedgIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDA--A 681
Cdd:TIGR01055 522 KPPLYRID-LSKEVYYALDEEEKEKLLYKLKKKKGKPN----VQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVqdQ 596
|
650 660
....*....|....*....|..
gi 998490969 682 AADELFSILMGEDV-DARRSFI 702
Cdd:TIGR01055 597 RVDKIMDMLLAKKRsEDRFNWL 618
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
81-251 |
1.00e-101 |
|
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: 309.08 E-value: 1.00e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 81 LHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGL 159
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKtGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 160 HGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLG-LKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAF 238
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTpLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|...
gi 998490969 239 LNKGLTINLTDER 251
Cdd:cd16928 161 LNKGLKIVLEDER 173
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
294-465 |
1.09e-92 |
|
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: 285.61 E-value: 1.09e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 294 GGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKD 373
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 374 RKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVSSA 453
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAA 160
|
170
....*....|..
gi 998490969 454 QARIAARKAREL 465
Cdd:cd00822 161 KAREAARKAREL 172
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
295-465 |
1.18e-77 |
|
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: 246.37 E-value: 1.18e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 295 GLVDFVKHINRTKNAIHSSIVDFSGKGT--GHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAK 372
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGESPdnRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 373 DRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDSKVVVNKAVSS 452
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQA 160
|
170
....*....|...
gi 998490969 453 AQARIAARKAREL 465
Cdd:pfam00204 161 AKARLAARKAREA 173
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
492-605 |
7.57e-70 |
|
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: 223.30 E-value: 7.57e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 492 SELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMAD 571
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 998490969 572 ADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 605
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
492-605 |
6.00e-57 |
|
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: 188.87 E-value: 6.00e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 492 SELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIH-DEFDIGKLRYHKIVLMA 570
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 998490969 571 DADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQP 605
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
56-703 |
3.27e-42 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 162.23 E-value: 3.27e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 56 ITILEGLEAVRKRPGMYIGSTG----ER-------------GLHHLIWEVVDNAVDEAMAG---YATTVNVVLlEDGGVE 115
Cdd:PHA02569 4 FKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQVT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 116 VADDGRGIP---VAT-HASGIPTVDVVMTQLHAGGKFDsDAYAISGGLHGVGVSVVNALSTRLeVEIKRDGYEWSQV--- 188
Cdd:PHA02569 83 VSDNGRGIPqamVTTpEGEEIPGPVAAWTRTKAGSNFD-DTNRVTGGMNGVGSSLTNFFSVLF-IGETCDGKNEVTVncs 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 189 -------YEKSeplglkqgaPTKKTGSTVRFWADPAVFETTEYD---FETVARRLQEMAFLNKGLTINLTDERVtqdevv 258
Cdd:PHA02569 161 ngaenisWSTK---------PGKGKGTSVTFIPDFSHFEVNGLDqqyLDIILDRLQTLAVVFPDIKFTFNGKKV------ 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 259 devvsdvaeapksaseraaestaPHKVKSRTFHYpgGLVDFVKHINRTKNAIHSSIVDFSGKgtgheveiamqwnagyse 338
Cdd:PHA02569 226 -----------------------SGKFKKYAKQF--GDDTIVQENDNVSIALAPSPDGFRQL------------------ 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 339 svhTFANTINTHEGGTHEEGFRSALTSVVNKYAKdrkllKDKDPNLTGDDIREGLAAVISVK-VSEPQFEGQTKTKLGNT 417
Cdd:PHA02569 263 ---SFVNGLHTKNGGHHVDCVMDDICEELIPMIK-----KKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSP 334
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 418 --EVKSFVQ----KVCNEQLthwfeanptDSKVVVNKAVSSAQAR-IAARKARELVRRKSATDI-------GGLPGKLAD 483
Cdd:PHA02569 335 fgEIRNHIDldykKIAKQIL---------KTEAIIMPIIEAALARkLAAEKAAETKAAKKAKKAkvakhikANLIGKDAE 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 484 crstdprkSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITAlgTGIHDEFDIGKLRY 563
Cdd:PHA02569 406 --------TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAI--TGLVLGEKAENMNY 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 564 HKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLY------KLKWQRSDPEFaysDRERDGLleaglkAG 637
Cdd:PHA02569 476 KNIAIMTDADVDGKGSIYPLLLAFFSRWPELFEQGRIRFVKTPVIiaqvgkETKWFYSLDEF---EKAKDSL------KK 546
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 998490969 638 KKInkedgiqRY-KGLGEMDAKELWETTMDPsvrVLRQVTLDDaaAADELFSILMGEDVDARRSFIT 703
Cdd:PHA02569 547 WSI-------RYiKGLGSLRKSEYRRVINNP---VYDVVVLPD--DWKELFEMLFGDDADLRKDWMS 601
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
62-714 |
2.03e-38 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 153.71 E-value: 2.03e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 62 LEAVRKRPGMYIGSTGER---------------------GLHHLIWEVVDNAVDE-----AMAGYATTVNVvllEDGGVE 115
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHtqtlwvyeggemvnrevtyvpGLYKIFDEILVNAADNkqrdpSMDSLKVDIDV---EQNTIS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 116 VADDGRGIPVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIK--RDGYEWSQVY--- 189
Cdd:PLN03128 90 VYNNGKGIPVEIHKEeGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFtnn 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 190 --EKSEPLGLKQGAPTKKTgsTVRFWADPAVFETTEYDFETVA---RRLQEMA-FLNKGLTINLTDERVTqdevvdevvs 263
Cdd:PLN03128 170 msVKSEPKITSCKASENWT--KITFKPDLAKFNMTRLDEDVVAlmsKRVYDIAgCLGKKLKVELNGKKLP---------- 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 264 dvaeapksaseraaestaphkVKSrtFHYPGGLVDFVKHINRTKNAIHSSIVDfsgkgtghEVEIAMQWNAGYSESVhTF 343
Cdd:PLN03128 238 ---------------------VKS--FQDYVGLYLGPNSREDPLPRIYEKVND--------RWEVCVSLSDGSFQQV-SF 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 344 ANTINTHEGGTHEEgfrsALTSVVNKYAKDrkLLKDKDPNLTG---DDIREGLAAVISVKVSEPQFEGQTKTKLgNTEVK 420
Cdd:PLN03128 286 VNSIATIKGGTHVD----YVADQIVKHIQE--KVKKKNKNATHvkpFQIKNHLWVFVNCLIENPTFDSQTKETL-TTRPS 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 421 SFVQKvcneqlthwFEANPTDSKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPG--KLADCRSTDPRKSE---LY 495
Cdd:PLN03128 359 SFGSK---------CELSEEFLKKVEKCGVVENILSWAQFKQQKELKKKDGAKRQRLTGipKLDDANDAGGKKSKdctLI 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 496 VVEGDSAGGSAKSG-----RDsmFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALG---TGIHDEFDIGKLRYHKIV 567
Cdd:PLN03128 430 LTEGDSAKALAMSGlsvvgRD--HYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGlqfGKTYDEENTKSLRYGHLM 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 568 LMADADVDGQHIStLLLTLLFRFMRPLIENGHVFLAQ--PPLYKLKwQRSDPEFAYSDRERDGLLEAGLKAGKKINkedg 645
Cdd:PLN03128 508 IMTDQDHDGSHIK-GLIINFFHSFWPSLLKIPGFLVEfiTPIVKAT-KGGKSLSFYTMPEYEAWKESLEGETKGWT---- 581
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 998490969 646 IQRYKGLGEMDAKELWE--TTMDPSVRVLRQVTLDDAAAADELFSilmGEDVDARRSFITRNAKDVrFLDV 714
Cdd:PLN03128 582 IKYYKGLGTSTSEEAKEyfSNLDIHKKEFLWQSDEDGDLIDMAFS---KKRVEDRKIWLNNYEPGT-FLDQ 648
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
59-579 |
1.12e-37 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 151.74 E-value: 1.12e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 59 LEGLEAVRKRPGMYIGSTgER------------------------GLHHLIWEVVDNAVD----EAMAGYATTVNVVLLE 110
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEILVNAADnkarDKGGHRMTYIKVTIDE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 111 DGG-VEVADDGRGIPVATHASG---IPTVdvVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEI--KRDGYE 184
Cdd:PTZ00108 92 ENGeISVYNDGEGIPVQIHKEHkiyVPEM--IFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSKSGKK 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 185 WSQVY-----EKSEPL--GLKQGAPTKKtgstVRFWADPAVFETTEYDFETVA---RRLQEMAFLNKGLTINLTDERVtq 254
Cdd:PTZ00108 170 FKMTWtdnmsKKSEPRitSYDGKKDYTK----VTFYPDYAKFGMTEFDDDMLRllkKRVYDLAGCFGKLKVYLNGERI-- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 255 devvdevvsdvaeapksaseraaestaphkvKSRTFHypgglvDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAmqwnA 334
Cdd:PTZ00108 244 -------------------------------AIKSFK------DYVDLYLPDGEEGKKPPYPFVYTSVNGRWEVV----V 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 335 GYSESVHT---FANTINTHEGGTH----EEGFRSALTSVVNKYAKDRKLLKdkdPNLtgddIREGLAAVISVKVSEPQFE 407
Cdd:PTZ00108 283 SLSDGQFQqvsFVNSICTTKGGTHvnyiLDQLISKLQEKAKKKKKKGKEIK---PNQ----IKNHLWVFVNCLIVNPSFD 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 408 GQTKTKLgNTEVKSFVQKVcneQLTHWFEANPTDSKVVVNkAVSSAQARIAARKARELvRRKSATDIGGLPgKLADCRST 487
Cdd:PTZ00108 356 SQTKETL-TTKPSKFGSTC---ELSEKLIKYVLKSPILEN-IVEWAQAKLAAELNKKM-KAGKKSRILGIP-KLDDANDA 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 488 DPRKSE---LYVVEGDSAGGSAKSG-----RDSMfqAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEF-DI 558
Cdd:PTZ00108 429 GGKNSEectLILTEGDSAKALALAGlsvvgRDYY--GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDP 506
|
570 580
....*....|....*....|.
gi 998490969 559 GKLRYHKIVLMADADVDGQHI 579
Cdd:PTZ00108 507 KGLRYGSLMIMTDQDHDGSHI 527
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
637-702 |
1.83e-33 |
|
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: 122.49 E-value: 1.83e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 998490969 637 GKKINkedgIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFI 702
Cdd:pfam00986 1 KKKVE----IQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFI 62
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
62-579 |
9.98e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 113.80 E-value: 9.98e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 62 LEAVRKRPGMYIGS---------------------TGERGLHHLIWEVVDNAVDEAMAGYAT-TVNVVL-LEDGGVEVAD 118
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRDPKMdSLRVVIdVEQNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 119 DGRGIPVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKrDGY---EWSQVY----- 189
Cdd:PLN03237 118 NGDGVPVEIHQEeGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETA-DGKrqkKYKQVFsnnmg 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 190 EKSEPLGLKqgapTKKTG--STVRFWADPAVFETTEYDFETVA---RRLQEMA-FLNKGLTINLTDERVtqdevvdevvs 263
Cdd:PLN03237 197 KKSEPVITK----CKKSEnwTKVTFKPDLAKFNMTHLEDDVVAlmkKRVVDIAgCLGKTVKVELNGKRI----------- 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 264 dvaeapksaseraaestaphKVKSRTfhypgglvDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVhTF 343
Cdd:PLN03237 262 --------------------PVKSFS--------DYVDLYLESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SF 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 344 ANTINTHEGGTHEEGFRSALT----SVVNKyakdrkllKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLgNTEV 419
Cdd:PLN03237 313 VNSIATIKGGTHVDYVTNQIAnhvmEAVNK--------KNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL-TLRQ 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 420 KSFVQKVcneQLTHWFEANPTDSKVVVNkAVSSAQARiaarKARELVRR--KSATDIGGLPgKLADCRSTDPRKSE---L 494
Cdd:PLN03237 384 SSFGSKC---ELSEDFLKKVMKSGIVEN-LLSWADFK----QSKELKKTdgAKTTRVTGIP-KLEDANEAGGKNSEkctL 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 495 YVVEGDSAGGSAKSGRDSM---FQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGK-LRYHKIVLMA 570
Cdd:PLN03237 455 ILTEGDSAKALAVAGLSVVgrnYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKsLRYGHLMIMT 534
|
....*....
gi 998490969 571 DADVDGQHI 579
Cdd:PLN03237 535 DQDHDGSHI 543
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
296-415 |
9.75e-21 |
|
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.
Pssm-ID: 238202 [Multi-domain] Cd Length: 107 Bit Score: 87.70 E-value: 9.75e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 296 LVDFVKHINrtKNAIHSSIVDFSGKGTGHEVEIAMQWN---AGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNkyak 372
Cdd:cd00329 1 LKDRLAEIL--GDKVADKLIYVEGESDGFRVEGAISYPdsgRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 998490969 373 drkllkdkdpnltGDDIREGLAAVISVKV--SEPQFE-GQTKTKLG 415
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
494-579 |
5.36e-18 |
|
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: 80.42 E-value: 5.36e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 494 LYVVEGDSAGGSAKSG-----RDSMfqAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGI--HDEFDIGKLRYHKI 566
Cdd:cd03365 3 LILTEGDSAKALAVAGlsvvgRDYY--GVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHgkSDYESTKSLRYGRL 80
|
90
....*....|...
gi 998490969 567 VLMADADVDGQHI 579
Cdd:cd03365 81 MIMTDQDHDGSHI 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
78-182 |
7.84e-15 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 71.14 E-value: 7.84e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 78 ERGLHHLIWEVVDNAVDEAMAGyaTTVNVVLLEDGG---VEVADDGRGIPvathasgiptVDVVMTQLHAGGKFDSDAYA 154
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDhveITVEDNGPGIP----------PEDLEKIFEPFFRTDKRSRK 70
|
90 100
....*....|....*....|....*...
gi 998490969 155 ISGglHGVGVSVVNALSTRLEVEIKRDG 182
Cdd:smart00387 71 IGG--TGLGLSIVKKLVELHGGEISVES 96
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
78-213 |
3.72e-13 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 66.24 E-value: 3.72e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 78 ERGLHHLIWEVVDNAVDEAmaGYATTVNVVLLEDGG--VEVADDGRGIPVATHAsgiptvdvvmtqlHAGGKFdSDAYAI 155
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLP-------------RIFEPF-STADKR 66
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 998490969 156 SGGLHGVGVSVVNALSTRLEVEIKRDgyewsqvyekSEPLGlkqgaptkktGSTVRFW 213
Cdd:pfam02518 67 GGGGTGLGLSIVRKLVELLGGTITVE----------SEPGG----------GTTVTLT 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
493-605 |
3.89e-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: 65.46 E-value: 3.89e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 493 ELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKntevqaiitalgtgihdEFDIGKLRYHKIVLMADA 572
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK-----------------ALKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 998490969 573 DVDGQHIStllltLLFRFMRPLIEN--GHVFLAQP 605
Cdd:pfam01751 64 DREGEAIA-----LKLLELKELLENagGRVEFSEL 93
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
80-194 |
1.56e-05 |
|
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.
Pssm-ID: 340407 [Multi-domain] Cd Length: 147 Bit Score: 45.41 E-value: 1.56e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 80 GLHHLIWEVVDNAVD-EAMAGYATTVNVVLLEDGG-VEVADDGRGIPVATHAS-GIPTVDVVMTQLHAGGKFDSDAYAIS 156
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPENNeISVWNNGKGIPVVIHKEeKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 998490969 157 GGLHGVGVSVVNALSTRLEVEI--KRDGYEWSQVYE-----KSEP 194
Cdd:cd16930 84 GGRNGYGAKLCNIFSTEFTVETadSESKKKFKQTWTnnmgkASEP 128
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
81-188 |
1.14e-04 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 41.82 E-value: 1.14e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 81 LHHLIWEVVDNAVDEAMAGyaTTVNVVLLEDGG---VEVADDGRGIPVAthasgiptvdvvmTQLHAGGKFDSDAYAISG 157
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEE-------------DLERIFERFYRGDKSREG 65
|
90 100 110
....*....|....*....|....*....|...
gi 998490969 158 GLHGVGVSVVNALSTRL--EVEIKRDGYEWSQV 188
Cdd:cd00075 66 GGTGLGLAIVRRIVEAHggRITVESEPGGGTTF 98
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
492-579 |
2.58e-03 |
|
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: 37.41 E-value: 2.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 492 SELYVVEGDSAGGSAKSGRdSMFQAILPLRGKIINVEKARIDRVLKntevqaiitalgtgihdefdigklRYHKIVLMAD 571
Cdd:cd00188 1 KKLIIVEGPSDALALAQAG-GYGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
....*...
gi 998490969 572 ADVDGQHI 579
Cdd:cd00188 56 ADREGEAI 63
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
87-136 |
5.33e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 40.03 E-value: 5.33e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 998490969 87 EVVDNAVDeamAGyATTVNVVLlEDGGVE---VADDGRGIP-------VATHA-SGIPTVD 136
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEI-EEGGKSlirVTDNGCGMSpedlplaFERHAtSKIRSAE 85
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
343-425 |
9.01e-03 |
|
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: 37.27 E-value: 9.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998490969 343 FANTINTHEGGTHEEGFRSALTSVVNKYAKdrKLLKdKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLgNTEVKSF 422
Cdd:cd03481 49 FVNSIATTKGGTHVDYVADQIVKKLDEVVK--KKNK-GGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL-TTKPKSF 124
|
...
gi 998490969 423 VQK 425
Cdd:cd03481 125 GSK 127
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