|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
5-691 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1138.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 5 QENAPHYDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIP 84
Cdd:PRK05644 2 EEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGIP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 85 VAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEE 164
Cdd:PRK05644 82 VDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 165 TTETGTSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRpvedpvdddlpdldnldqdvdendgindaar 244
Cdd:PRK05644 162 TDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDER------------------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 245 pteagadtaeKPKTKSVTFLYEQGLEDFVKYINKQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTI 324
Cdd:PRK05644 211 ----------EGEEKEETFHYEGGIKEYVEYLNRNK--EPLHEEPIYFEGEKDG--IEVEVAMQYNDGYSENILSFANNI 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 325 NTHEGGTHEEGFRSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVM 404
Cdd:PRK05644 277 NTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVV 356
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 405 TDKLADWASAHPNEMKTIVTKAQSAAAAREAARKARDATRRKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAV 484
Cdd:PRK05644 357 SEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAK 436
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 485 SGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLTLL 564
Cdd:PRK05644 437 QGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFF 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 565 FRYMRPLIELGHVFIAMPPLYRLKWTNapHEYVFSDAERDRKLEEGraaGKRIPKDNGIQRYKGLGEMDWRELQTTTMDR 644
Cdd:PRK05644 517 YRYMRPLIEAGYVYIAQPPLYKIKKGG--KEYAYSDEELDEILAEL---KLKGNPKYGIQRYKGLGEMNPEQLWETTMDP 591
|
650 660 670 680
....*....|....*....|....*....|....*....|....*..
gi 514222659 645 DLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAKDVRFLDI 691
Cdd:PRK05644 592 ETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
6-691 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1100.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 6 ENAPHYDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPV 85
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 86 AMHPTEKKPAVELVLTVLHAggkfggggyavsggLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEET 165
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 166 TETGTSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRPVEdpvdddlpdldnldqdvdendgindaarp 245
Cdd:COG0187 161 DRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEE----------------------------- 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 246 teagadtaekpkTKSVTFLYEQGLEDFVKYINKQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTIN 325
Cdd:COG0187 212 ------------PKEETFHYEGGIKDFVEYLNEDK--EPLHPEVIYFEGEKDG--IEVEVALQWNDGYSENIHSFVNNIN 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 326 THEGGTHEEGFRSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMT 405
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVS 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 406 DKLADWASAHPNEMKTIVTKAQSAAAAREAARKARDATRRKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAVS 485
Cdd:COG0187 356 EKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQ 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 486 GRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLTLLF 565
Cdd:COG0187 436 GRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFY 515
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 566 RYMRPLIELGHVFIAMPPLYRLKWTNaPHEYVFSDAERDRKLEEGRAAGKripkdNGIQRYKGLGEMDWRELQTTTMDRD 645
Cdd:COG0187 516 RYMRPLIEAGHVYIAQPPLYRIKKGK-KTYYAYSDAELDELLKELKGKKK-----VEIQRYKGLGEMNPEQLWETTMDPE 589
|
650 660 670 680
....*....|....*....|....*....|....*....|....*.
gi 514222659 646 LRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAKDVRFLDI 691
Cdd:COG0187 590 TRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
11-691 |
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: 925.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 11 YDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHPT 90
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 91 EKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEETTETGT 170
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 171 SVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRpvedpvdddlpdldnldqdvdendgindaarpteaga 250
Cdd:TIGR01059 161 TVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER------------------------------------- 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 251 dtaeKPKTKSVTFLYEQGLEDFVKYINKQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTINTHEGG 330
Cdd:TIGR01059 204 ----DGKGKKVTFHYEGGIKSFVKYLNRNK--EPLHEEIIYIKGEKEG--IEVEVALQWNDGYSENILSFVNNINTREGG 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 331 THEEGFRSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLAD 410
Cdd:TIGR01059 276 THLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTE 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 411 WASAHPNEMKTIVTKAQSAAAAREAARKARDATRRKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAVSGRDPK 490
Cdd:TIGR01059 356 FFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRR 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 491 TQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLTLLFRYMRP 570
Cdd:TIGR01059 436 FQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRP 515
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 571 LIELGHVFIAMPPLYRLKWTNAP--------------------HEYVFSDAERDRKLEEGRAAGKRipKDNGIQRYKGLG 630
Cdd:TIGR01059 516 LIENGYVYIAQPPLYKVKKGKKEryikddkekdlvgealedlkALYIYSDKEKEEAKTQIPVHLGR--KGIEIQRYKGLG 593
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 514222659 631 EMDWRELQTTTMDRDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAKDVRFLDI 691
Cdd:TIGR01059 594 EMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLDV 654
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
11-691 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 878.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 11 YDASDITVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHP 89
Cdd:PRK14939 7 YGASSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIPTDIHP 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 90 TEKKPAVELVLTVLHAggkfggggyavsggLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEETTETG 169
Cdd:PRK14939 87 EEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTG 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 170 TSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRPVedpvdddlpdldnldqdvdendgindaarpteag 249
Cdd:PRK14939 167 TEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG---------------------------------- 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 250 adtaekpktKSVTFLYEQGLEDFVKYINKQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTINTHEG 329
Cdd:PRK14939 213 ---------KEEEFHYEGGIKAFVEYLNRNK--TPLHPNIFYFSGEKDG--IGVEVALQWNDSYQENVLCFTNNIPQRDG 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 330 GTHEEGFRSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLA 409
Cdd:PRK14939 280 GTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLS 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 410 DWASAHPNEMKTIVTKAQSAAAAREAARKARDATRRKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAVSGRDP 489
Cdd:PRK14939 360 EFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDR 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 490 KTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIG-EDFDPTKLRYHKIILMADADVDGQHICTLLLTLLFRYM 568
Cdd:PRK14939 440 KFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQM 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 569 RPLIELGHVFIAMPPLYR---------LKWTNAPHEYVFSDAERDRKLEEGRAAG------------------------K 615
Cdd:PRK14939 520 PELIERGHLYIAQPPLYKvkkgkqeqyLKDDEALDDYLIELALEGATLHLADGPAisgealeklvkeyravrkiidrleR 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 616 RIP----------------------------------------------------------------------------- 618
Cdd:PRK14939 600 RYPravlealiyapaldlddladeaavaaldadfltsaeyrrlvelaeklrglieegaylergerkqpvssfeealdwll 679
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 514222659 619 ----KDNGIQRYKGLGEMDWRELQTTTMDRDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAKDVRFLDI 691
Cdd:PRK14939 680 aearKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
7-686 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 813.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 7 NAPHYDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVA 86
Cdd:PRK05559 4 MTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 87 MHPTEKKPAVELVLTVLHAggkfggggyavsggLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEETT 166
Cdd:PRK05559 84 IHPEEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 167 E--TGTSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRPVEdpvdddlpdldnldqdvdendgindaar 244
Cdd:PRK05559 164 KrkTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ---------------------------- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 245 pteagadtaekpktksvTFLYEQGLEDFVKYINKQKraEVIHPE-IISFESEDTDhmISVEIAMQWTSAYSESVHTYANT 323
Cdd:PRK05559 216 -----------------TFHYENGLKDYLAELNEGK--ETLPEEfVGSFEGEAEG--EAVEWALQWTDEGGENIESYVNL 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 324 INTHEGGTHEEGFRSALTGVINRYARANNLMKeKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKV 403
Cdd:PRK05559 275 IPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGV 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 404 MTDKLADWASAHPNEMKTIVTKAQSAAAAREAARKARdaTRRKSPLETGgMPGKLRDCSSRNPAISEIFIVEGDSAGGSA 483
Cdd:PRK05559 354 VKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKKKTSGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSA 430
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 484 VSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLTL 563
Cdd:PRK05559 431 KQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTF 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 564 LFRYMRPLIELGHVFIAMPPLYRLKwTNAPHEYVFSDAERDRKLEEGRAAGKRIPkdngIQRYKGLGEMDWRELQTTTMD 643
Cdd:PRK05559 511 FYRHFPPLVEAGHVYIALPPLYRVD-KGKKKIYALDEEEKEELLKKLGKKGGKPE----IQRFKGLGEMNPDQLWETTMD 585
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 514222659 644 RDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAKDV 686
Cdd:PRK05559 586 PETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
40-684 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 772.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 40 GLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGG 119
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 120 LHGVGSSVVNALSKRLEVEIKRDGYVWRQQYT-HGVPNAPLEKGEETTETGTSVTFWADGDIFE-TTEYEFETLRKRFQQ 197
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 198 MAFLNKGLKITLTDhrpvedpvdddlpdldnldqdvdendgindaarpteagadtaeKPKTKSVTFLYEQGLEDFVKYIN 277
Cdd:smart00433 161 LAFLNKGVKITLND-------------------------------------------ERSDEEKTFLFEGGIKDYVELLN 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 278 KQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTINTHEGGTHEEGFRSALTGVINRYARANNLMKEK 357
Cdd:smart00433 198 KNK--ELLSPEPTYIEGEKDN--IRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEK 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 358 daNLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLADWASAHPNEMKTIVTKAQSAAAAREAAR 437
Cdd:smart00433 274 --NIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAK 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 438 KARDATRRKSpLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLDRALDNAE 517
Cdd:smart00433 352 KARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEE 430
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 518 VRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLTLLFRYMRPLIELGHVFIAMPPLYRLKWTNAphEYV 597
Cdd:smart00433 431 IQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKK--KYV 508
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 598 FSDAERDRKLEEGRAAGKRIPKDNgIQRYKGLGEMDWRELQTTTMDRDLRTLKQVTMDEAADADAVFSVLMGDDVDARRR 677
Cdd:smart00433 509 YSFYSLDEYEKWLEKTEGNKSKYE-IQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKE 587
|
....*..
gi 514222659 678 FIQENAK 684
Cdd:smart00433 588 WIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
8-684 |
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: 642.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 8 APHYDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAM 87
Cdd:TIGR01058 2 ASKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 88 HPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTH-GVPNAPLEKGEETT 166
Cdd:TIGR01058 82 HQDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 167 ETGTSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDHRpvedpvdddlpdldnldqdvdendgindaarpt 246
Cdd:TIGR01058 162 KTGTLVHFHPDPTIFKTTQFNSNIIKERLKESAFLLKKLKLTFTDKR--------------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 247 eagadtaekpKTKSVTFLYEQGLEDFVKYINKQKRaevIHPEIISFESEdtDHMISVEIAMQWTSAYSESVHTYANTINT 326
Cdd:TIGR01058 209 ----------TNKTTVFFYENGLVDFVDYINETKE---TLSQVTYFEGE--KNGIEVEVAFQFNDGDSENILSFANSVKT 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 327 HEGGTHEEGFRSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGEP--QFEGQTKTKLGNTIARTFVSKVM 404
Cdd:TIGR01058 274 KEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLSAIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIV 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 405 TDKLADWASAHPNEMKTIVTKAQSAAAAREAARKARDATR--RKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGS 482
Cdd:TIGR01058 354 QDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKPKKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGS 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 483 AVSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMADADVDGQHICTLLLT 562
Cdd:TIGR01058 434 AKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGTGIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLT 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 563 LLFRYMRPLIELGHVFIAMPPLYRL-KWTNAPHEYVFSDAERDRKLEEgraagkriPKDNGIQRYKGLGEMDWRELQTTT 641
Cdd:TIGR01058 514 FFYRYMRPLIELGHVYIALPPLYKLsKKDGKKVKYAWSDLELESVKKK--------LKNYTLQRYKGLGEMNADQLWETT 585
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 514222659 642 MDRDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENAK 684
Cdd:TIGR01058 586 MNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANIN 628
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
11-683 |
2.51e-151 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 461.66 E-value: 2.51e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 11 YDASDITVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHPT 90
Cdd:PTZ00109 100 YDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVSEK 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 91 EKKPAVELVLTVLH----------------------------------------AGGKFGGGGYAVSGGLHGVGSSVVNA 130
Cdd:PTZ00109 180 TGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSVVNA 259
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 131 LSKRLEVEIKRDGYVWRQQYTHGVPNAPL-EKGEETTETGTSVTFWADGD-IFETT--------------EYEFETLRKR 194
Cdd:PTZ00109 260 LSSFLKVDVFKGGKIYSIELSKGKVTKPLsVFSCPLKKRGTTIHFLPDYKhIFKTHhqhteteeeegcknGFNLDLIKNR 339
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 195 FQQMAFLNKGLKITLTDHRpvedpvdddlpdldnldqDVDENdgindAARPTEagadtaekpktksvTFLYEQGLEDFVK 274
Cdd:PTZ00109 340 IHELSYLNPGLTFYLVDER------------------IANEN-----NFYPYE--------------TIKHEGGTREFLE 382
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 275 YINKQKRAEVIHPEIISFESEDTDhmISVEIAMQWTS-AYSESVHTYANTINThEGGTHEEGFRSALTGVINRYARANNL 353
Cdd:PTZ00109 383 ELIKDKTPLYKDINIISIRGVIKN--VNVEVSLSWSLeSYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGY 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 354 MKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLADWASAHPNEMKTIVTKAQSAAAAR 433
Cdd:PTZ00109 460 FKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAF 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 434 EAARKARDATRRK-SPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLD-R 511
Cdd:PTZ00109 540 EEAKAAKDLIRQKnNQYYSTILPGKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkK 619
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 512 ALDNAEVRSLITAFGTGIGED--------------------------------FDPTKLRYHKIILMADADVDGQHICTL 559
Cdd:PTZ00109 620 VFENSEIKLLITSIGLSVNPVtwrqydlshgtkaskdesvqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRIL 699
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 560 LLTLLFRYMRPLIELGHVFIAMPPLYRL--------------------KWTN--------------APHEYVFSDAERDR 605
Cdd:PTZ00109 700 LLTLLYRFCPSLYEHGRVYVACPPLYRItnnrmkqfnvstknskkyiyTWSDeelnvlikllnkdySSKETTRSVEEKGN 779
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 606 KLEEGR---------------------------------------AAGKRIPKDNG---IQRYKGLGEMDWRELQTTTMD 643
Cdd:PTZ00109 780 APDLDNeyedekldnknmrennvdevelktelgtnvadteqtdelDINKAFFKFSKhyeIQRFKGLGEMMADQLWETTMD 859
|
810 820 830 840
....*....|....*....|....*....|....*....|
gi 514222659 644 RDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQENA 683
Cdd:PTZ00109 860 PKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
11-681 |
1.41e-148 |
|
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: 445.90 E-value: 1.41e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 11 YDASDITVLEGLEAVRKRPGMYIGSTGergLHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHPT 90
Cdd:TIGR01055 4 YSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 91 EKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEETTE--T 168
Cdd:TIGR01055 81 EGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 169 GTSVTFWADGDIFETTEYEFETLRKRFQQMAFLNKGLKITLTDhrpvedpvdddlpdldnldqdvdendgindaarptea 248
Cdd:TIGR01055 161 GTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFED------------------------------------- 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 249 gadtaeKPKTKSVTFLYEQGLEDFVkyINKQKRAEVIHPEIIS--FESEDtdhmISVEIAMQW----TSAYSESvhtYAN 322
Cdd:TIGR01055 204 ------EVNNTKALWNYPDGLKDYL--SEAVNGDNTLPPKPFSgnFEGDD----EAVEWALLWlpegGELFMES---YVN 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 323 TINTHEGGTHEEGFRSALTGVINRYARANNLmKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSK 402
Cdd:TIGR01055 269 LIPTPQGGTHVNGLRQGLLDALREFCEMRNN-LPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSG 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 403 VMTDKLADWAsahpNEMKTIVTKAQSAA-AAREAARKARDATRRKSPLETGGMPGKLRDCSSRNPAISEIFIVEGDSAGG 481
Cdd:TIGR01055 348 VIKDAFDLWL----NQNVQLAEHLAEHAiSSAQRRKRAAKKVVRKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGG 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 482 SAVSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDfDPTKLRYHKIILMADADVDGQHICTLLL 561
Cdd:TIGR01055 424 SAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGIDPDSN-DLSQLRYGKICILADADSDGLHIATLLC 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 562 TLLFRYMRPLIELGHVFIAMPPLYRLKWTNAPHeYVFSDAERDRKLEEGRAAGKRIpkdnGIQRYKGLGEMDWRELQTTT 641
Cdd:TIGR01055 503 ALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVY-YALDEEEKEKLLYKLKKKKGKP----NVQRFKGLGEMNPAQLRETT 577
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 514222659 642 MDRDLRTLKQVTMDEAAD--ADAVFSVLMGDDV-DARRRFIQE 681
Cdd:TIGR01055 578 MDPNTRRLVQLTLDDVQDqrVDKIMDMLLAKKRsEDRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
41-213 |
6.20e-88 |
|
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: 272.87 E-value: 6.20e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 41 LHHLVYEIVDNSVDEALAGYASEITVDVLEDGGVRVIDDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGL 120
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 121 HGVGSSVVNALSKRLEVEIKRDGYVWRQQYTHGVPNAPLEKGEETTETGTSVTFWADGDIFETTEYEFETLRKRFQQMAF 200
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160
|
170
....*....|...
gi 514222659 201 LNKGLKITLTDHR 213
Cdd:cd16928 161 LNKGLKIVLEDER 173
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
469-582 |
3.18e-72 |
|
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: 229.08 E-value: 3.18e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 469 SEIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDFDPTKLRYHKIILMAD 548
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 514222659 549 ADVDGQHICTLLLTLLFRYMRPLIELGHVFIAMP 582
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
268-425 |
3.19e-71 |
|
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: 228.60 E-value: 3.19e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 268 GLEDFVKYINKQKraEVIHPEIISFESEDTDhmISVEIAMQWTSAYSESVHTYANTINTHEGGTHEEGFRSALTGVINRY 347
Cdd:cd00822 2 GLKDFVEELNKDK--EPLHEEPIYIEGEKDG--VEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDY 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514222659 348 ARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLADWASAHPNEMKTIVTK 425
Cdd:cd00822 78 AKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
268-425 |
1.31e-65 |
|
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: 214.02 E-value: 1.31e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 268 GLEDFVKYINKQKraEVIHPEIISFESEDTDHMISVEIAMQWTSAYSESVHTYANTINTHEGGTHEEGFRSALTGVINRY 347
Cdd:pfam00204 1 GLKDFVEELNKDK--KPLHKEIIYFEGESPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEY 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514222659 348 ARANNLMKEKDANLTGEDIREGLTAVVSVKLGEPQFEGQTKTKLGNTIARTFVSKVMTDKLADWASAHPNEMKTIVTK 425
Cdd:pfam00204 79 AKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
469-582 |
2.60e-61 |
|
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: 200.42 E-value: 2.60e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 469 SEIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIG-EDFDPTKLRYHKIILMA 547
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 514222659 548 DADVDGQHICTLLLTLLFRYMRPLIELGHVFIAMP 582
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
14-680 |
8.09e-32 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 131.03 E-value: 8.09e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 14 SDITVLEGLEAVRKRPGMYIGSTG----ER-------------GLHHLVYEIVDNSVDEALAG---YASEITVDVlEDGG 73
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 74 VRVIDDGRGIPVAMHPT---EKKPAVELVLTVLHAGGKFGGGGYAVSGgLHGVGSSVVNALSKRLeVEIKRDGyvwRQQY 150
Cdd:PHA02569 81 VTVSDNGRGIPQAMVTTpegEEIPGPVAAWTRTKAGSNFDDTNRVTGG-MNGVGSSLTNFFSVLF-IGETCDG---KNEV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 151 THGVPNAPLEKGEETT---ETGTSVTFWADGDIFETTEYEFETL---RKRFQQMAflnkglkitltdhrpvedpvdddlp 224
Cdd:PHA02569 156 TVNCSNGAENISWSTKpgkGKGTSVTFIPDFSHFEVNGLDQQYLdiiLDRLQTLA------------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 225 dldnldqdvdendgindAARPteagadtaekpktkSVTFLY--EQGLEDFVKYinkqkrAEVIHPEIISFESEDtdhmIS 302
Cdd:PHA02569 211 -----------------VVFP--------------DIKFTFngKKVSGKFKKY------AKQFGDDTIVQENDN----VS 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 303 VEIAmqwTSAYSESVHTYANTINTHEGGTHEEGFRSALtgvinryarANNLM----KEKDANLTGEDIREGLTAVVSVK- 377
Cdd:PHA02569 250 IALA---PSPDGFRQLSFVNGLHTKNGGHHVDCVMDDI---------CEELIpmikKKHKIEVTKARVKECLTIVLFVRn 317
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 378 LGEPQFEGQTKTKLGNTIARtFVSKVMTD--KLADWASAHPNemktIVTKAQSAAAAREAARKARDATR-RKSPLET--- 451
Cdd:PHA02569 318 MSNPRFDSQTKERLTSPFGE-IRNHIDLDykKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKaAKKAKKAkva 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 452 ----GGMPGKLRDcssrnpaiSEIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGT 527
Cdd:PHA02569 393 khikANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGL 464
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 528 GIGEDFDPTKlrYHKIILMADADVDGQ-HICTLLLTLLFRYMRpLIELGHVFIAMPPLYRLkwTNAPHEYVFSDaerdrk 606
Cdd:PHA02569 465 VLGEKAENMN--YKNIAIMTDADVDGKgSIYPLLLAFFSRWPE-LFEQGRIRFVKTPVIIA--QVGKETKWFYS------ 533
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514222659 607 LEEGRAAGKRIPKDNgIQRYKGLGEMdwRELQTTTMDRDLrTLKQVTMDEaaDADAVFSVLMGDDVDARRRFIQ 680
Cdd:PHA02569 534 LDEFEKAKDSLKKWS-IRYIKGLGSL--RKSEYRRVINNP-VYDVVVLPD--DWKELFEMLFGDDADLRKDWMS 601
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
19-681 |
7.09e-27 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 117.45 E-value: 7.09e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 19 LEGLEAVRKRPGMYIGSTgER------------------------GLHHLVYEI----VDNSVDEALAGYASEITVDVLE 70
Cdd:PTZ00108 13 KTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKVTIDE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 71 DGG-VRVIDDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEI--KRDGYVWR 147
Cdd:PTZ00108 92 ENGeISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSKSGKKFK 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 148 QQYTHGVPN--APLEKGEETTETGTSVTFWADGDIFETTEYEFET---LRKRFQQMAFLNKGLKITLTDHRPvedpvddd 222
Cdd:PTZ00108 172 MTWTDNMSKksEPRITSYDGKKDYTKVTFYPDYAKFGMTEFDDDMlrlLKKRVYDLAGCFGKLKVYLNGERI-------- 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 223 lpdldnldqdvdendGINDaarpTEAGADTAEKPKTKSVTFLYEQgledfvKYINKQKRAEVIhpeiISFeSEDTDHMIS 302
Cdd:PTZ00108 244 ---------------AIKS----FKDYVDLYLPDGEEGKKPPYPF------VYTSVNGRWEVV----VSL-SDGQFQQVS 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 303 VeiamqwtsaysesvhtyANTINTHEGGTHEEGFRSALTGVINRYARAnnlMKEKDANLTGEDIREGLTAVVSVKLGEPQ 382
Cdd:PTZ00108 294 F-----------------VNSICTTKGGTHVNYILDQLISKLQEKAKK---KKKKGKEIKPNQIKNHLWVFVNCLIVNPS 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 383 FEGQTKTKLGNTIARtFVSK-VMTDKLAD-------------WASAHPN-----EMKTivtkaqsaaaareaarkardaT 443
Cdd:PTZ00108 354 FDSQTKETLTTKPSK-FGSTcELSEKLIKyvlkspileniveWAQAKLAaelnkKMKA---------------------G 411
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 444 RRKSPLetgGMPgKLRDCSSRNPAISEI---FIVEGDSA-----GGSAVSGRDpkTQAILPIRGKILNVEKARLDRALDN 515
Cdd:PTZ00108 412 KKSRIL---GIP-KLDDANDAGGKNSEEctlILTEGDSAkalalAGLSVVGRD--YYGVFPLRGKLLNVRDASLKQLMNN 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 516 AEVRSLITAFGTGIGEDFDPTK-LRYHKIILMADADVDGQHICTLLLTL-------LFRY-------MRPLIEL------ 574
Cdd:PTZ00108 486 KEIQNLFKILGLDIGKKYEDPKgLRYGSLMIMTDQDHDGSHIKGLLINMihhfwpsLLKNpgflkefITPIVKAtkkgnq 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 575 GHVFIAMPPLYRLKWTNAPHEYvfsdaerdrkleegraagkripkdnGIQRYKGLGEMDWRELQTTTMDRDLRTLKQVTM 654
Cdd:PTZ00108 566 VISFFTIPDFEKWKQTVGLKGW-------------------------KIKYYKGLGTSTDKEGKEYFSNIDKHRIRFVYV 620
|
730 740
....*....|....*....|....*....
gi 514222659 655 DEAADA--DAVFSvlmGDDVDARRRFIQE 681
Cdd:PTZ00108 621 DDSDDDsiDLAFS---KKRVEDRKEWITN 646
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
623-680 |
1.46e-26 |
|
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: 102.84 E-value: 1.46e-26
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 514222659 623 IQRYKGLGEMDWRELQTTTMDRDLRTLKQVTMDEAADADAVFSVLMGDDVDARRRFIQ 680
Cdd:pfam00986 6 IQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
22-690 |
9.10e-26 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 113.65 E-value: 9.10e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 22 LEAVRKRPGMYIGSTGERGLHHLVYE---IVDNSV----------DEALAGYAS-----------EITVDVlEDGGVRVI 77
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHTQTLWVYEggeMVNREVtyvpglykifDEILVNAADnkqrdpsmdslKVDIDV-EQNTISVY 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 78 DDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEI------KRDGYVWRQQYT 151
Cdd:PLN03128 92 NNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETadgnrgKKYKQVFTNNMS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 152 hgVPNAPLEKGEETTETGTSVTFWADGDIFETTEYEFET---LRKRFQQMA-FLNKGLKITLTDHR-PVedpvdddlpdl 226
Cdd:PLN03128 172 --VKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKKlPV----------- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 227 dnldqdvdendgindaarpteagadtaekpktksvtflyeQGLEDFVKYINKQKRAEVIHPeiisfesedtdhMISVEIA 306
Cdd:PLN03128 239 ----------------------------------------KSFQDYVGLYLGPNSREDPLP------------RIYEKVN 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 307 MQWTSAYS------ESVhTYANTINTHEGGTHEEgfrSALTGVINRYARANNLMKEKDANLTGEDIREGLTAVVSVKLGE 380
Cdd:PLN03128 267 DRWEVCVSlsdgsfQQV-SFVNSIATIKGGTHVD---YVADQIVKHIQEKVKKKNKNATHVKPFQIKNHLWVFVNCLIEN 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 381 PQFEGQTKTKLgNTIARTFVSKV--------------MTDKLADWA-SAHPNEMKtivtkaqsaaaareaarkARDATRR 445
Cdd:PLN03128 343 PTFDSQTKETL-TTRPSSFGSKCelseeflkkvekcgVVENILSWAqFKQQKELK------------------KKDGAKR 403
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 446 KSPLetgGMPgKLRDCSSRNPAISE---IFIVEGDSAGGSAVSG-----RDpkTQAILPIRGKILNVEKARLDRALDNAE 517
Cdd:PLN03128 404 QRLT---GIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGlsvvgRD--HYGVFPLRGKLLNVREASHKQIMKNAE 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 518 VRSLITAFGTGIGEDFDPT---KLRYHKIILMADADVDGQHICTLLLTlLFRYMRP--------LIElghvFIAmpPLyr 586
Cdd:PLN03128 478 ITNIKQILGLQFGKTYDEEntkSLRYGHLMIMTDQDHDGSHIKGLIIN-FFHSFWPsllkipgfLVE----FIT--PI-- 548
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 587 LKWTNAPHEYVF-SDAERDRKLEEGRAAGKRIPkdngIQRYKGLGEMDWRELQTTTMDRDLRTlKQVTMDEAADADAVFS 665
Cdd:PLN03128 549 VKATKGGKSLSFyTMPEYEAWKESLEGETKGWT----IKYYKGLGTSTSEEAKEYFSNLDIHK-KEFLWQSDEDGDLIDM 623
|
730 740
....*....|....*....|....*
gi 514222659 666 VLMGDDVDARRRFIQENAKDVrFLD 690
Cdd:PLN03128 624 AFSKKRVEDRKIWLNNYEPGT-FLD 647
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
269-392 |
5.20e-20 |
|
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: 85.39 E-value: 5.20e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 269 LEDFVKYINKQKraevIHPEIISFESEDTDhmISVEIAMQWTS---AYSESVHTYANTINTHEGGTHEEGFRSALTGVIN 345
Cdd:cd00329 1 LKDRLAEILGDK----VADKLIYVEGESDG--FRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 514222659 346 ryarannlmkekdanltGEDIREGLTAVVSVKL--GEPQFE-GQTKTKLG 392
Cdd:cd00329 75 -----------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
22-690 |
1.72e-19 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 93.77 E-value: 1.72e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 22 LEAVRKRPGMYIGSTGERGLHHLVYE---IVDNSV----------DEALAGYAS-----------EITVDVlEDGGVRVI 77
Cdd:PLN03237 38 LEHILLRPDTYIGSIEKHTQTLWVYEtdkMVQRSVtyvpglykifDEILVNAADnkqrdpkmdslRVVIDV-EQNLISVY 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 78 DDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYAVSGGLHGVGSSVVNALSKRLEVEIKrDGYvwRQQ-YTHGVPN 156
Cdd:PLN03237 117 NNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEFVIETA-DGK--RQKkYKQVFSN 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 157 APLEKGE------ETTETGTSVTFWADGDIFETTEYEFET---LRKRFQQMA-FLNKGLKITLTDHR-PVEdpvdddlpd 225
Cdd:PLN03237 194 NMGKKSEpvitkcKKSENWTKVTFKPDLAKFNMTHLEDDVvalMKKRVVDIAgCLGKTVKVELNGKRiPVK--------- 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 226 ldnldqdvdendGINDAarpTEAGADTAEKPKTKSVTFLYEqgledfvkyiNKQKRAEVIhpeiISFeSEDTDHMISvei 305
Cdd:PLN03237 265 ------------SFSDY---VDLYLESANKSRPENLPRIYE----------KVNDRWEVC----VSL-SEGQFQQVS--- 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 306 amqwtsaysesvhtYANTINTHEGGTHEEGFRSALTG----VINRyarannlmKEKDANLTGEDIREGLTAVVSVKLGEP 381
Cdd:PLN03237 312 --------------FVNSIATIKGGTHVDYVTNQIANhvmeAVNK--------KNKNANIKAHNVKNHLWVFVNALIDNP 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 382 QFEGQTKTKLgNTIARTFVSKV--------------MTDKLADWASAHPN-EMKtivtkaqsaaaareaarkaRDATRRK 446
Cdd:PLN03237 370 AFDSQTKETL-TLRQSSFGSKCelsedflkkvmksgIVENLLSWADFKQSkELK-------------------KTDGAKT 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 447 SPLEtgGMPgKLRDCSS---RNPAISEIFIVEGDSAGGSAVSGRDPKTQ---AILPIRGKILNVEKARLDRALDNAEVRS 520
Cdd:PLN03237 430 TRVT--GIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSVVGRnyyGVFPLRGKLLNVREASHKQIMNNAEIEN 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 521 LITAFGTGIGEDFDPTK-LRYHKIILMADADVDGQHICTLLLTLLFRYMRPLIELGHVFIA-MPPLYRLKWTNAPHEYVF 598
Cdd:PLN03237 507 IKQILGLQHGKQYESVKsLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVPSFLVEfITPIVKATRRGKKVLSFY 586
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 599 SDAERDRKLE--EGRAAGKripkdnGIQRYKGLGEMDWRELQTTTMDRDLRTLKQVTMDEaADADAVFSVLMGDDVDARR 676
Cdd:PLN03237 587 SMPEYEEWKEslGGNATGW------SIKYYKGLGTSTAKEGKEYFKNLGKHKKDFVWEDE-QDGDAIELAFSKKKIEARK 659
|
730 740
....*....|....*....|...
gi 514222659 677 R---------FIQENAKDVRFLD 690
Cdd:PLN03237 660 NwlrqyepgtHLDQTQKDVKYSD 682
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
475-564 |
1.44e-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: 81.96 E-value: 1.44e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 475 EGDSAGGSAVSGR---DPKTQAILPIRGKILNVEKARLDRALDNAEVRSLITAFGTGIGEDF--DPTKLRYHKIILMADA 549
Cdd:cd03365 7 EGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMIMTDQ 86
|
90
....*....|....*
gi 514222659 550 DVDGQHICTLLLTLL 564
Cdd:cd03365 87 DHDGSHIKGLLINFI 101
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
470-582 |
1.37e-14 |
|
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: 69.69 E-value: 1.37e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 470 EIFIVEGDSAGGSAVSGRDPKTQAILPIRGKILNVEKARLDRALDNaevrslitafgtgigedFDPTKLRYHKIILMADA 549
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|...
gi 514222659 550 DVDGQHICTLLLTlLFRYMRPLIelGHVFIAMP 582
Cdd:pfam01751 64 DREGEAIALKLLE-LKELLENAG--GRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
38-175 |
2.94e-11 |
|
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: 60.84 E-value: 2.94e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 38 ERGLHHLVYEIVDNSVDEAlaGYASEITVDVLEDGG--VRVIDDGRGIPVAMHPTEKKPAVElvltvlhaggkfgggGYA 115
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLPRIFEPFST---------------ADK 65
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 116 VSGGLHGVGSSVVNALSKRLeveikrDGYVWRqqythgvpnaplekgEETTETGTSVTFW 175
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELL------GGTITV---------------ESEPGGGTTVTLT 104
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
38-143 |
1.65e-10 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 58.43 E-value: 1.65e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 38 ERGLHHLVYEIVDNSVDEALAGyaSEITVDVLEDGG---VRVIDDGRGIPvamhptekkpaVELVLTVLHAGGKFGGGGY 114
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGDhveITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRSR 69
|
90 100
....*....|....*....|....*....
gi 514222659 115 AVSGglHGVGSSVVNALSKRLEVEIKRDG 143
Cdd:smart00387 70 KIGG--TGLGLSIVKKLVELHGGEISVES 96
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
469-575 |
2.06e-05 |
|
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: 43.18 E-value: 2.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 469 SEIFIVEGDSAGGSAVSGRDpKTQAILPIRGKILNVEKARLDRALDnaevrslitafgtgigedfdptklRYHKIILMAD 548
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90 100
....*....|....*....|....*..
gi 514222659 549 ADVDGQHICTLLLTLLFRYMRPLIELG 575
Cdd:cd00188 56 ADREGEAIALRLLELLKSLGKKVRRLL 82
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
47-84 |
2.55e-05 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 47.35 E-value: 2.55e-05
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 514222659 47 EIVDNSVDealAGyASEITVDVlEDGGV---RVIDDGRGIP 84
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEI-EEGGKsliRVTDNGCGMS 65
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
45-84 |
7.79e-05 |
|
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: 43.96 E-value: 7.79e-05
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 514222659 45 VYEIVDNSVDealAGyASEITVDVlEDGG---VRVIDDGRGIP 84
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEI-EEGGlklIRVTDNGSGIS 55
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
45-84 |
1.84e-04 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 44.82 E-value: 1.84e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 514222659 45 VYEIVDNSVDealAGyASEITVDvLEDGGV---RVIDDGRGIP 84
Cdd:PRK00095 27 VKELVENALD---AG-ATRIDIE-IEEGGLkliRVRDNGCGIS 64
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
41-89 |
7.01e-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: 39.51 E-value: 7.01e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 514222659 41 LHHLVYEIVDNSVDEALAGyaSEITVDVLEDGG---VRVIDDGRGIPVAMHP 89
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLE 50
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
40-177 |
1.74e-03 |
|
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: 39.24 E-value: 1.74e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514222659 40 GLHHLVYEIV----DNSVDEALAGYAsEITVDVlEDGGVRVIDDGRGIPVAMHPTEKKPAVELVLTVLHAGGKFGGGGYA 115
Cdd:cd16930 4 GLYKIFDEILvnaaDNKQRDKSMTCI-KVTIDP-ENNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKK 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 514222659 116 VSGGLHGVGSSVVNALSKRLEVEI--KRDGYVWRQQYTH--GVPNAPLEKGEETTETGTSVTFWAD 177
Cdd:cd16930 82 VTGGRNGYGAKLCNIFSTEFTVETadSESKKKFKQTWTNnmGKASEPKITPYEKGKDYTKVTFKPD 147
|
|
| |
