|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
3-807 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1485.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 3 SEAPAEYGADSIRVLKGLDAVRKRPGMYIGDTDDGSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGI 82
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 83 PTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTG 162
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 163 DAgSETGTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRRHAdvKEQELHYDGGLVEFVKYIDQSKKSL 242
Cdd:PRK14939 161 ET-DKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG--KEEEFHYEGGIKAFVEYLNRNKTPL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 243 LEEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKVQLTGDDCR 322
Cdd:PRK14939 238 HPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 323 EGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDITR-KS 401
Cdd:PRK14939 318 EGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRrKG 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 402 NLSVTSLPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGT 481
Cdd:PRK14939 398 ALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGC 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 482 SIGKDEthgFNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYIKNEAAFE 561
Cdd:PRK14939 478 GIGRDE---FNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALD 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 562 DFLIETGLEETTLELVTGEMRAGPDLRSVVEDARTLRQLLHGLHTRYDRSVVEQAAIAGLLNPDASRDNAtaqhsadtva 641
Cdd:PRK14939 555 DYLIELALEGATLHLADGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEA---------- 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 642 krldmiseetergwsghvmedggyrfermvrgvkDIAILDMALLGSADARQVDRVAGRMAEIFMEPPVLRRKDKVESLSG 721
Cdd:PRK14939 625 ----------------------------------AVAALDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSS 670
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 722 PVALLDAVFATGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNALN 801
Cdd:PRK14939 671 FEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIFTTLMGDEVEPRREFIEENALN 750
|
....*.
gi 479375216 802 VANLDV 807
Cdd:PRK14939 751 VANLDV 756
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
4-807 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1037.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 4 EAPAEYGADSIRVLKGLDAVRKRPGMYIGDTDDgSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIP 83
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDE-RGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 84 TDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGD 163
Cdd:COG0187 80 VDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 164 AGsETGTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRRHADVKEQELHYDGGLVEFVKYIDQSKKSLL 243
Cdd:COG0187 160 TD-RTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKDFVEYLNEDKEPLH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 244 EEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKVQLTGDDCRE 323
Cdd:COG0187 239 PEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVRE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 324 GLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDIT-RKSN 402
Cdd:COG0187 319 GLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVrRKSA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 403 LSVTSLPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTS 482
Cdd:COG0187 399 LESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 483 IGKDethgFNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYIKNEAAfed 562
Cdd:COG0187 479 IGDD----FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAE--- 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 563 flietgLEETTLELvtgemragpdlrsvvedartlrqllhglhtrydrsvveqaaiagllnpdasrdnataqhsadtvak 642
Cdd:COG0187 552 ------LDELLKEL------------------------------------------------------------------ 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 643 rldmiseetergwsghvmedggyrfermvrgvkdiaildmallgsadarqvdrvagrmaeifmeppvlrrkdkveslsgp 722
Cdd:COG0187 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 723 valldavfaTGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNALNV 802
Cdd:COG0187 560 ---------KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFV 630
|
....*
gi 479375216 803 ANLDV 807
Cdd:COG0187 631 RNLDI 635
|
|
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
2-807 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1034.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 2 NSEAPAEYGADSIRVLKGLDAVRKRPGMYIGDTDDgSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRG 81
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGE-RGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 82 IPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVT 161
Cdd:PRK05644 80 IPVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVI 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 162 GDAgSETGTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRRHADVKEQELHYDGGLVEFVKYIDQSKKS 241
Cdd:PRK05644 160 GET-DETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNKEP 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 242 LLEEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKVQLTGDDC 321
Cdd:PRK05644 239 LHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 322 REGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDIT-RK 400
Cdd:PRK05644 319 REGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTrRK 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 401 SNLSVTSLPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALG 480
Cdd:PRK05644 399 SALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 481 TSIGKDethgFNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKsSQYIKNEAAF 560
Cdd:PRK05644 479 TGIGDD----FDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGG-KEYAYSDEEL 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 561 EDFLIETGleettlelvtgemragpdlrsvvedartlrqllhglhtrydrsvveqaaiagllnpdasrdnataqhsadtv 640
Cdd:PRK05644 554 DEILAELK------------------------------------------------------------------------ 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 641 akrldmiseetergwsghvmedggyrfermvrgvkdiaildmallgsadarqvdrvagrmaeifmeppvlrrkdkvesls 720
Cdd:PRK05644 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 721 gpvalldavfATGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNAL 800
Cdd:PRK05644 562 ----------LKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAK 631
|
....*..
gi 479375216 801 NVANLDV 807
Cdd:PRK05644 632 YVRNLDI 638
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
9-807 |
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: 1015.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 9 YGADSIRVLKGLDAVRKRPGMYIGDTDDgSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIHK 88
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGE-TGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 89 EEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGDAgSET 168
Cdd:TIGR01059 80 EEGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGET-KKT 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 169 GTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRRHADVKEQELHYDGGLVEFVKYIDQSKKSLLEEPIY 248
Cdd:TIGR01059 159 GTTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 249 IRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKVQLTGDDCREGLTAV 328
Cdd:TIGR01059 239 IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 329 LSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDITR-KSNLSVTS 407
Cdd:TIGR01059 319 ISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRrKSALDSGG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 408 LPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDe 487
Cdd:TIGR01059 399 LPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 488 thgFNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYIKNEAAFEdfLIET 567
Cdd:TIGR01059 478 ---FDLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKEKD--LVGE 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 568 GLEEttlelvtgemragpdlrsvvedartlrqllhglhtrydrsvveqaaiagllnpdasrdnataqhsadtvAKRLDMI 647
Cdd:TIGR01059 553 ALED---------------------------------------------------------------------LKALYIY 563
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 648 SEETERGWsghvmedggyrfermvrgvkdiaildmallgsadarqvdrvagrmaeifmeppvlrrKDKVESLsgpvalld 727
Cdd:TIGR01059 564 SDKEKEEA---------------------------------------------------------KTQIPVH-------- 578
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 728 avfaTGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNALNVANLDV 807
Cdd:TIGR01059 579 ----LGRKGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRREFIEANALDVKNLDV 654
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
5-799 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 813.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 5 APAEYGADSIRVLKGLDAVRKRPGMYIGDTDDgSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPT 84
Cdd:PRK05559 4 MTNNYNADSIEVLEGLEPVRKRPGMYIGSTDT-RGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 85 DIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGDA 164
Cdd:PRK05559 83 GIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTA 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 165 GSE-TGTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRRhadvKEQELHYDGGLVEFVKYIDQSKKSL- 242
Cdd:PRK05559 163 GKRkTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDER----ERQTFHYENGLKDYLAELNEGKETLp 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 243 LEEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKvQLTGDDCR 322
Cdd:PRK05559 239 EEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 323 EGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQaaAAREAARKARDITRKSN 402
Cdd:PRK05559 318 EGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIK--AAQARLRAAKKVKRKKK 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 403 LSVTSLPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTS 482
Cdd:PRK05559 396 TSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIG 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 483 IGKDethgFNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYikneaafed 562
Cdd:PRK05559 476 PGDS----FDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIY--------- 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 563 flietgleettlelvtgemragpdlrsvvedARTlrqllhglhtrydrsvveqaaiagllnpDASRDNATAQhsadtvak 642
Cdd:PRK05559 543 -------------------------------ALD----------------------------EEEKEELLKK-------- 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 643 rldmiseetergwsghvmedggyrfermvrgvkdiaildmallgsadarqvdrvagrmaeifmeppvlrrkdkveslsgp 722
Cdd:PRK05559 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 479375216 723 valldavFATGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNA 799
Cdd:PRK05559 556 -------LGKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENG 625
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
39-799 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 757.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 39 GLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGG 118
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 119 LHGVGVSVVNALSIWLKLKIRRAGKIHEMSFT-HGVADAPLVVTGDAGsETGTEVSFLPSPDTFSM-VEFDYETLERRLR 196
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTK-KDGTKVTFKPDLEIFGMtTDDDFELLKRRLR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 197 ELAFLNSGVRIKLADRRHAdvKEQELHYDGGLVEFVKYIDQSKKSLLEEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFT 276
Cdd:smart00433 160 ELAFLNKGVKITLNDERSD--EEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFV 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 277 NNIPQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKvqLTGDDCREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVE 356
Cdd:smart00433 238 NNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 357 GLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDITRKSNLSVTSLPGKLADCQERDPAKSEIFIVEGDSAGGS 436
Cdd:smart00433 316 KIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKKKLSSISLPGKLADASSAGPKKCELFLVEGDSAGGS 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 437 AKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDethgFNADKLRYHKIIIMTDADVDGAHIRT 516
Cdd:smart00433 396 AKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKD----FDIEKLRYGKIIIMTDADVDGSHIKG 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 517 LLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYIkNEAAFEDFLIETGLEEttlelvtgemragpdlrsvvedart 596
Cdd:smart00433 472 LLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVY-SFYSLDEYEKWLEKTE------------------------- 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 597 lrqllhglhtrydrsvveqaaiagllnpdasrdnataqhsadtvakrldmiseetergwsghvmedggyrfermvrgvkd 676
Cdd:smart00433 --------------------------------------------------------------------------------
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 677 iaildmallgsadarqvdrvagrmaeifmeppvlrrkdkveslsgpvalldavfaTGRKGLTLQRYKGLGEMNAEQLWET 756
Cdd:smart00433 526 -------------------------------------------------------GNKSKYEIQRYKGLGEMNADQLWET 550
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 479375216 757 TLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQDNA 799
Cdd:smart00433 551 TMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
8-799 |
0e+00 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 542.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 8 EYGADSIRVLKGLDAVRKRPGMYIGDTDDgSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIH 87
Cdd:PTZ00109 99 EYDADDIVVLEGLEAVRKRPGMYIGNTDE-KGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDVS 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 88 KEEGVSAAEVIMTQLHAGGKF--------------DQNS--------------------------YKVSGGLHGVGVSVV 127
Cdd:PTZ00109 178 EKTGKSGLETVLTVLHSGGKFqdtfpknsrsdkseDKNDtksskkgksshvkgpkeakekessqmYEYSSGLHGVGLSVV 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 128 NALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGDAGSETGTEVSFLPSPDTF---------------SMVEFDYETLE 192
Cdd:PTZ00109 258 NALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLKKRGTTIHFLPDYKHIfkthhqhteteeeegCKNGFNLDLIK 337
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 193 RRLRELAFLNSGVRIKLADRRHAD----VKEQELHYDGGLVEFVKYIDQSKKSLLEEP--IYIRSEKDGMTVEVAMWWN- 265
Cdd:PTZ00109 338 NRIHELSYLNPGLTFYLVDERIANennfYPYETIKHEGGTREFLEELIKDKTPLYKDIniISIRGVIKNVNVEVSLSWSl 417
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 266 DSYHEKVLCFTNNIpQRDGGTHLAGFRGALTRQITGYADSSGMTKKEKVQLTGDDCREGLTAVLSVKVPDPKFSSQTKDK 345
Cdd:PTZ00109 418 ESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTK 496
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 346 LVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQAAAAREAARKARDITRK--SNLSVTSLPGKLADCQERDPAKS 423
Cdd:PTZ00109 497 LGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQknNQYYSTILPGKLVDCISDDIERN 576
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 424 EIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFD-RMISSDQVGTLITALGTSIGK------DETHGFNADK- 495
Cdd:PTZ00109 577 ELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPvtwrqyDLSHGTKASKd 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 496 ---------------------LRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYI 554
Cdd:PTZ00109 657 esvqnnnstltkkknslfdtpLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQFN 736
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 555 KNEAAfEDFLIETGLEETTLELVtgemragpdlrsvvedartlrqllhglhtrydrsvveqaaiaGLLNPDASrdnatAQ 634
Cdd:PTZ00109 737 VSTKN-SKKYIYTWSDEELNVLI------------------------------------------KLLNKDYS-----SK 768
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 635 HSADTVAKRLDMISEETERGWSGHVMEDGGYrfermvRGVKDIAILDMALLGSADARQVDRVAgrmaeifmeppvlrrkd 714
Cdd:PTZ00109 769 ETTRSVEEKGNAPDLDNEYEDEKLDNKNMRE------NNVDEVELKTELGTNVADTEQTDELD----------------- 825
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 715 kveslsgpvalLDAVFATGRKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREF 794
Cdd:PTZ00109 826 -----------INKAFFKFSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQF 894
|
....*
gi 479375216 795 IQDNA 799
Cdd:PTZ00109 895 IFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
9-557 |
3.48e-158 |
|
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: 474.41 E-value: 3.48e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 9 YGADSIRVLKGLDAVRKRPGMYIgdtdDGSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIHK 88
Cdd:TIGR01055 4 YSAKDIEVLDGLEPVRKRPGMYT----DTTRPNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 89 EEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGDAGSE- 167
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKRl 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 168 TGTEVSFLPSPDTFSMVEFDYETLERRLRELAFLNSGVRIKLADRrhADVKEQELHYDGGLVEFVKYIDQSKKSLLEEPI 247
Cdd:TIGR01055 160 TGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKALWNYPDGLKDYLSEAVNGDNTLPPKPF 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 248 YIRSEKDGMTVEVAMWWNDSYHEKVL-CFTNNIPQRDGGTHLAGFRGALTRQITGYADSSGMtKKEKVQLTGDDCREGLT 326
Cdd:TIGR01055 238 SGNFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNN-LPRGVKLTAEDIWDRCS 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 327 AVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIqaAAAREAARKARDITRKSNLSVT 406
Cdd:TIGR01055 317 YVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAI--SSAQRRKRAAKKVVRKKLTSGP 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 407 SLPGKLADCQERDPAKSEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGtsIGKD 486
Cdd:TIGR01055 395 ALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALG--IDPD 472
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 479375216 487 EThgfNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQPPLYKVTRGKSSQYIKNE 557
Cdd:TIGR01055 473 SN---DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDE 540
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
40-214 |
2.00e-100 |
|
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: 308.31 E-value: 2.00e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 40 LHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGL 119
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 120 HGVGVSVVNALSIWLKLKIRRAGKIHEMSFTHGVADAPLVVTGDAgSETGTEVSFLPSPDTFSMVEFDYETLERRLRELA 199
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGET-KKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELA 159
|
170
....*....|....*
gi 479375216 200 FLNSGVRIKLADRRH 214
Cdd:cd16928 160 FLNKGLKIVLEDERT 174
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
226-383 |
4.03e-80 |
|
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: 254.79 E-value: 4.03e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 226 GGLVEFVKYIDQSKKSLLEEPIYIRSEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYADS 305
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 479375216 306 SGMTKKEKVQLTGDDCREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQ 383
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
423-540 |
1.71e-74 |
|
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173786 [Multi-domain] Cd Length: 114 Bit Score: 237.55 E-value: 1.71e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 423 SEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDethgFNADKLRYHKII 502
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGED----FDLEKLRYHKII 76
|
90 100 110
....*....|....*....|....*....|....*...
gi 479375216 503 IMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQP 540
Cdd:cd03366 77 IMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
423-540 |
1.76e-65 |
|
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: 213.52 E-value: 1.76e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 423 SEIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDEthgFNADKLRYHKII 502
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDD---FDLDKLRYGKII 77
|
90 100 110
....*....|....*....|....*....|....*...
gi 479375216 503 IMTDADVDGAHIRTLLLTFFFRQMPELIERGHIYIAQP 540
Cdd:cd01030 78 IMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
227-383 |
3.76e-62 |
|
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: 206.70 E-value: 3.76e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 227 GLVEFVKYIDQSKKSLLEEPIYIR--SEKDGMTVEVAMWWNDSYHEKVLCFTNNIPQRDGGTHLAGFRGALTRQITGYAD 304
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEgeSPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 479375216 305 SSGMTKKEKVQLTGDDCREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPAGGKIVVEKVIQ 383
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
12-563 |
3.29e-49 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 183.80 E-value: 3.29e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 12 DSIRVLKGLDAVRKRPGMYIGDTD--------DGS--------GLHHMVYEVVDNAIDEALAG---HATLVTVTLNaDGS 72
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAyeaherflFGKftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTIK-NNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 73 CTVTDNGRGIP----TDIHKEEgVSAAEVIMTQLHAGGKFDqNSYKVSGGLHGVGVSVVNALSIWL---------KLKIR 139
Cdd:PHA02569 81 VTVSDNGRGIPqamvTTPEGEE-IPGPVAAWTRTKAGSNFD-DTNRVTGGMNGVGSSLTNFFSVLFigetcdgknEVTVN 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 140 RAGKIHEMSFThgvaDAPlvvtgdaGSETGTEVSFLPSPDTFSMVEFDYETLE---RRLRELAFLNSGVRIKLADRRHad 216
Cdd:PHA02569 159 CSNGAENISWS----TKP-------GKGKGTSVTFIPDFSHFEVNGLDQQYLDiilDRLQTLAVVFPDIKFTFNGKKV-- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 217 vkeqelhyDGGLVEFVKYIDqskksllEEPIYIRSEKDGMTVEVAmwwNDSYheKVLCFTNNIPQRDGGTHLAGFRGALT 296
Cdd:PHA02569 226 --------SGKFKKYAKQFG-------DDTIVQENDNVSIALAPS---PDGF--RQLSFVNGLHTKNGGHHVDCVMDDIC 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 297 RQITgyadsSGMTKKEKVQLTGDDCREGLTAVLSVK-VPDPKFSSQTKDKLVSS--EVRPVVEgLVNEALSTWLEEHPAg 373
Cdd:PHA02569 286 EELI-----PMIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEA- 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 374 gkiVVEKVIQAAAAREAARKARDITRK----SNLSV-----TSLPGKLADcqerdpakSEIFIVEGDSAGGSAKSGRSRQ 444
Cdd:PHA02569 359 ---IIMPIIEAALARKLAAEKAAETKAakkaKKAKVakhikANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEE 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 445 NQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDethgfnADKLRYHKIIIMTDADVDG-AHIRTLLLTFFF 523
Cdd:PHA02569 428 LHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEK------AENMNYKNIAIMTDADVDGkGSIYPLLLAFFS 501
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 479375216 524 RqMPELIERGHIYIAQPPLYKVTRGKSSQYIKNEAAFEDF 563
Cdd:PHA02569 502 R-WPELFEQGRIRFVKTPVIIAQVGKETKWFYSLDEFEKA 540
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
26-554 |
4.10e-45 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 176.01 E-value: 4.10e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 26 RPGMYIGDT----------DDGSGlhHMVYEVVD--------------NAID----EALAGHATLVTVTLN-ADGSCTVT 76
Cdd:PTZ00108 22 RPDTYIGSIetqtedmwvyDEEKN--RMVYKTITyvpglykifdeilvNAADnkarDKGGHRMTYIKVTIDeENGEISVY 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 77 DNGRGIPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIR--RAGKIHEMSFTHGV- 153
Cdd:PTZ00108 100 NDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECVdsKSGKKFKMTWTDNMs 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 154 -ADAPLVVTGDaGSETGTEVSFLPSPDTFSMVEFDYET---LERRLRELAFLNSGVRIKLADRRHAdVKeqelhydgglv 229
Cdd:PTZ00108 180 kKSEPRITSYD-GKKDYTKVTFYPDYAKFGMTEFDDDMlrlLKKRVYDLAGCFGKLKVYLNGERIA-IK----------- 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 230 EFVKYIDQSKKSLLEEPIYIRSEKDGMT---VEVAMWWNDSYHEKVlCFTNNIPQRDGGTHLAGFRGALTRQITGYADSS 306
Cdd:PTZ00108 247 SFKDYVDLYLPDGEEGKKPPYPFVYTSVngrWEVVVSLSDGQFQQV-SFVNSICTTKGGTHVNYILDQLISKLQEKAKKK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 307 gmtKKEKVQLTGDDCREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEHPaggkiVVEKVIQAAA 386
Cdd:PTZ00108 326 ---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP-----ILENIVEWAQ 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 387 AREAARKARDITRKSNLSVTSLPgKLADCQERDPAKSEI---FIVEGDSAGGSAKSGRS---RQNQAILPLRGKILNVER 460
Cdd:PTZ00108 398 AKLAAELNKKMKAGKKSRILGIP-KLDDANDAGGKNSEEctlILTEGDSAKALALAGLSvvgRDYYGVFPLRGKLLNVRD 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 461 VRFDRMISSDQVGTLITALGTSIGKDEThgfNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIE-RGHIYIAQ 539
Cdd:PTZ00108 477 ASLKQLMNNKEIQNLFKILGLDIGKKYE---DPKGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFI 553
|
570
....*....|....*
gi 479375216 540 PPLYKVTRgKSSQYI 554
Cdd:PTZ00108 554 TPIVKATK-KGNQVI 567
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
26-561 |
5.93e-45 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 174.90 E-value: 5.93e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 26 RPGMYIGDT----------DDGS----------GLHHMVYEVVDNAIDEALAgHATL--VTVTLNAD-GSCTVTDNGRGI 82
Cdd:PLN03128 19 RPDTYIGSTekhtqtlwvyEGGEmvnrevtyvpGLYKIFDEILVNAADNKQR-DPSMdsLKVDIDVEqNTISVYNNGKGI 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 83 PTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVSGGLHGVGVSVVNALSIWLKLKIR--RAGKIHEMSFTHG--VADAPL 158
Cdd:PLN03128 98 PVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFTNNmsVKSEPK 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 159 VVTGDAgSETGTEVSFLPSPDTFSMVEFDYET---LERRLRELA-FLNSGVRIKLADrRHADVKeqelhydgGLVEFVKY 234
Cdd:PLN03128 178 ITSCKA-SENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNG-KKLPVK--------SFQDYVGL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 235 IDQSKKSllEEPIYIRSEKDGMTVEVAMWWNDSYHEKVlCFTNNIPQRDGGTHLAgfrgALTRQITGYADSSgMTKKEK- 313
Cdd:PLN03128 248 YLGPNSR--EDPLPRIYEKVNDRWEVCVSLSDGSFQQV-SFVNSIATIKGGTHVD----YVADQIVKHIQEK-VKKKNKn 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 314 -VQLTGDDCREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPVVEGLVNEALSTWLEEhpAGgkiVVEKVIQ-AAAAREAA 391
Cdd:PLN03128 320 aTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSEEFLKKVEK--CG---VVENILSwAQFKQQKE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 392 RKARDITRKSNLsvTSLPgKLADCQERDPAKSE---IFIVEGDSAGGSAKSGRS---RQNQAILPLRGKILNVERVRFDR 465
Cdd:PLN03128 395 LKKKDGAKRQRL--TGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLSvvgRDHYGVFPLRGKLLNVREASHKQ 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 466 MISSDQVGTLITALGTSIGKDETHGfNADKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIER-GHIYIAQPPLYK 544
Cdd:PLN03128 472 IMKNAEITNIKQILGLQFGKTYDEE-NTKSLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIpGFLVEFITPIVK 550
|
570
....*....|....*..
gi 479375216 545 VTRGKSSQYIKNEAAFE 561
Cdd:PLN03128 551 ATKGGKSLSFYTMPEYE 567
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
734-796 |
4.54e-37 |
|
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: 132.89 E-value: 4.54e-37
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 479375216 734 RKGLTLQRYKGLGEMNAEQLWETTLDPNVRSLLQVKVNDATDADSLFSRLMGDEVEPRREFIQ 796
Cdd:pfam00986 1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
39-531 |
2.47e-32 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 135.76 E-value: 2.47e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 39 GLHHMVYEVVDNAIDEALAgHATLVT--VTLNADGSC-TVTDNGRGIPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKV 115
Cdd:PLN03237 77 GLYKIFDEILVNAADNKQR-DPKMDSlrVVIDVEQNLiSVYNNGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKT 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 116 SGGLHGVGVSVVNALSIWLKLKI---RRAGKIHEM-SFTHGVADAPlVVTGDAGSETGTEVSFLPSPDTFSMVEFDYET- 190
Cdd:PLN03237 156 TGGRNGYGAKLTNIFSTEFVIETadgKRQKKYKQVfSNNMGKKSEP-VITKCKKSENWTKVTFKPDLAKFNMTHLEDDVv 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 191 --LERRLRELA-FLNSGVRIKLADRRhADVKeqelhydgglvEFVKYID---QSKKSLLEEPIYIRSEKDGMTVEVAMWW 264
Cdd:PLN03237 235 alMKKRVVDIAgCLGKTVKVELNGKR-IPVK-----------SFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSL 302
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 265 NDSYHEKVlCFTNNIPQRDGGTHLagfrGALTRQITGYAdSSGMTKKEK-VQLTGDDCREGLTAVLSVKVPDPKFSSQTK 343
Cdd:PLN03237 303 SEGQFQQV-SFVNSIATIKGGTHV----DYVTNQIANHV-MEAVNKKNKnANIKAHNVKNHLWVFVNALIDNPAFDSQTK 376
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 344 DKLVsseVRPVVEGLVNEALSTWLEEHPAGGkiVVEKVIQ-AAAAREAARKARDITRKSNlsVTSLPgKLADCQE---RD 419
Cdd:PLN03237 377 ETLT---LRQSSFGSKCELSEDFLKKVMKSG--IVENLLSwADFKQSKELKKTDGAKTTR--VTGIP-KLEDANEaggKN 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 420 PAKSEIFIVEGDSAGGSAKSGRS---RQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDEThgfNADKL 496
Cdd:PLN03237 449 SEKCTLILTEGDSAKALAVAGLSvvgRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYE---SVKSL 525
|
490 500 510
....*....|....*....|....*....|....*
gi 479375216 497 RYHKIIIMTDADVDGAHIRTLLLTFFFRQMPELIE 531
Cdd:PLN03237 526 RYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
429-532 |
1.71e-21 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 90.44 E-value: 1.71e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 429 EGDSAGGSAKSGRS---RQNQAILPLRGKILNVERVRFDRMISSDQVGTLITALGTSIGKDETHgfNADKLRYHKIIIMT 505
Cdd:cd03365 7 EGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYE--STKSLRYGRLMIMT 84
|
90 100
....*....|....*....|....*..
gi 479375216 506 DADVDGAHIRTLLLTFFFRQMPELIER 532
Cdd:cd03365 85 DQDHDGSHIKGLLINFIHSFWPSLLKI 111
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
228-346 |
6.98e-19 |
|
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: 82.69 E-value: 6.98e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 228 LVEFVKYIdqSKKSLLEEPIYIRSEKDGMTVEVAMWWND---SYHEKVLCFTNNIPQRDGGTHLAGFRGALTRqitgyad 304
Cdd:cd00329 1 LKDRLAEI--LGDKVADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTR------- 71
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 479375216 305 ssgmtkkekvQLTGDDCREGLTAVLSVKVPD--PKFS-SQTKDKL 346
Cdd:cd00329 72 ----------ALNGDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
424-540 |
3.47e-15 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 71.62 E-value: 3.47e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 424 EIFIVEGDSAGGSAKSGRSRQNQAILPLRGKILNVERvrfdrmissdqvGTLITALGTsigkdethgFNADKLRYHKIII 503
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEK------------GPKKKALKA---------LKELALKAKEVIL 59
|
90 100 110
....*....|....*....|....*....|....*....
gi 479375216 504 MTDADVDGAHIRTLLLTFFfrqmpELIER--GHIYIAQP 540
Cdd:pfam01751 60 ATDPDREGEAIALKLLELK-----ELLENagGRVEFSEL 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
36-143 |
8.36e-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: 8.36e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 36 DGSGLHHMVYEVVDNAIDEALAGhaTLVTVTLNADG---SCTVTDNGRGIPtdihkeegvsaAEVIMTQLHAGGKFDQNS 112
Cdd:smart00387 2 DPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIP-----------PEDLEKIFEPFFRTDKRS 68
|
90 100 110
....*....|....*....|....*....|.
gi 479375216 113 YKVSGglHGVGVSVVNALSIWLKLKIRRAGK 143
Cdd:smart00387 69 RKIGG--TGLGLSIVKKLVELHGGEISVESE 97
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
35-140 |
5.95e-14 |
|
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: 68.55 E-value: 5.95e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 35 DDGSGLHHMVYEVVDNAIDEALAGHATLVTVTLNADGSCTVTDNGRGIPTDIHKeegvsaaevimtqlHAGGKFDQnSYK 114
Cdd:pfam02518 1 GDELRLRQVLSNLLDNALKHAAKAGEITVTLSEGGELTLTVEDNGIGIPPEDLP--------------RIFEPFST-ADK 65
|
90 100
....*....|....*....|....*.
gi 479375216 115 VSGGLHGVGVSVVNALSIWLKLKIRR 140
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELLGGTITV 91
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
39-176 |
9.57e-12 |
|
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: 63.51 E-value: 9.57e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 39 GLHHMVYEVVDNAID-EALAGHATLVTVTLNAD-GSCTVTDNGRGIPTDIHKEEGVSAAEVIMTQLHAGGKFDQNSYKVS 116
Cdd:cd16930 4 GLYKIFDEILVNAADnKQRDKSMTCIKVTIDPEnNEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVT 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 479375216 117 GGLHGVGVSVVNALSiwLKLKI----RRAGKIHEMSFTH--GVADAPlVVTGDAGSETGTEVSFLP 176
Cdd:cd16930 84 GGRNGYGAKLCNIFS--TEFTVetadSESKKKFKQTWTNnmGKASEP-KITPYEKGKDYTKVTFKP 146
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
40-130 |
1.09e-05 |
|
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains.
Pssm-ID: 340391 [Multi-domain] Cd Length: 102 Bit Score: 44.90 E-value: 1.09e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 40 LHHMVYEVVDNAIDEALAGhaTLVTVTLNADGS---CTVTDNGRGIPTDIhkeegvsaaevimtQLHAGGKFDQNSYKVS 116
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEED--------------LERIFERFYRGDKSRE 64
|
90
....*....|....
gi 479375216 117 GGLHGVGVSVVNAL 130
Cdd:cd00075 65 GGGTGLGLAIVRRI 78
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
423-525 |
4.07e-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: 42.80 E-value: 4.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 423 SEIFIVEGDSAGGSAKSGRSRqNQAILPLRGKILNvERVRFDRMISSdqvgtlitalgtsigkdethgfnadklRYHKII 502
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGGY-GGAVVALGGHALN-KTRELLKRLLG---------------------------EAKEVI 51
|
90 100
....*....|....*....|...
gi 479375216 503 IMTDADVDGAHIRTLLLTFFFRQ 525
Cdd:cd00188 52 IATDADREGEAIALRLLELLKSL 74
|
|
| GyrB_insert |
pfam18053 |
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ... |
604-692 |
2.98e-03 |
|
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.
Pssm-ID: 465629 Cd Length: 167 Bit Score: 39.43 E-value: 2.98e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 479375216 604 LHTRYDRSVVEQAAIAGLLNPDASRDNATAQHSADTVAKRLDMISEETERgWSGHVMED---GGYRFE--RMVRGVKDIA 678
Cdd:pfam18053 34 LSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLGGPR-YRVSVEEDterGKYLLRvtRRHHGNETVY 112
|
90
....*....|....
gi 479375216 679 ILDMALLGSADARQ 692
Cdd:pfam18053 113 VLDADFFESGDYRA 126
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
44-83 |
6.17e-03 |
|
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.
Pssm-ID: 340403 [Multi-domain] Cd Length: 188 Bit Score: 38.57 E-value: 6.17e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 479375216 44 VYEVVDNAIDealAGhATLVTVTLNADGSC--TVTDNGRGIP 83
Cdd:cd16926 18 VKELVENSID---AG-ATRIDVEIEEGGLKliRVTDNGSGIS 55
|
|
| |
