|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
1-638 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1363.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 1 MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGI 80
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 81 PVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIG 160
Cdd:PRK05644 81 PVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 161 ETDHTGTTTHFVPDPEIFsETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVV 240
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKEYVEYLNRNKEPL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 241 HEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVR 320
Cdd:PRK05644 240 HEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 321 EGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKS 400
Cdd:PRK05644 320 EGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 401 ALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGT 480
Cdd:PRK05644 400 ALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGT 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 481 GIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRvEYAYNDKELEELLK 560
Cdd:PRK05644 480 GIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGK-EYAYSDEELDEILA 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 561 TLPQ--TPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI 638
Cdd:PRK05644 559 ELKLkgNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYVRNLDI 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
3-638 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1307.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 3 QQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPV 82
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 83 GIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGET 162
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 163 DHTGTTTHFVPDPEIFsETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHE 242
Cdd:COG0187 161 DRTGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKDFVEYLNEDKEPLHP 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 243 EPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREG 322
Cdd:COG0187 240 EVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 323 LTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSAL 402
Cdd:COG0187 320 LTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSAL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 403 EISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGI 482
Cdd:COG0187 400 ESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 483 GEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTL 562
Cdd:COG0187 480 GDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKEL 559
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16077074 563 PQTPKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI 638
Cdd:COG0187 560 KGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVRNLDI 635
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
8-638 |
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: 1173.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 8 YDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEK 87
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 88 MGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGT 167
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 168 TTHFVPDPEIFsETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKNEYHYEGGIKSYVEYLNRSKEVVHEEPIYI 247
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDGKGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 248 EGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAII 327
Cdd:TIGR01059 240 KGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVI 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 328 SIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISNL 407
Cdd:TIGR01059 320 SVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 408 PGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFN 487
Cdd:TIGR01059 400 PGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDFD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 488 LEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGK---------------------RV 546
Cdd:TIGR01059 480 LEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKkeryikddkekdlvgealedlKA 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 547 EYAYNDKELEELLKTLPQTP---KPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRR 623
Cdd:TIGR01059 560 LYIYSDKEKEEAKTQIPVHLgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPRR 639
|
650
....*....|....*
gi 16077074 624 NFIEANARYVKNLDI 638
Cdd:TIGR01059 640 EFIEANALDVKNLDV 654
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
2-638 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1152.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 2 EQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTN-SKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGI 80
Cdd:PRK14939 1 SMMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDdGTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 81 PVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIG 160
Cdd:PRK14939 81 PTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 161 ETDHTGTTTHFVPDPEIFsETTEYDYDLLANRVRELAFLTKGVNITIEDKREGqeRKNEYHYEGGIKSYVEYLNRSKEVV 240
Cdd:PRK14939 161 ETDKTGTEVRFWPSPEIF-ENTEFDYDILAKRLRELAFLNSGVRIRLKDERDG--KEEEFHYEGGIKAFVEYLNRNKTPL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 241 HEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVR 320
Cdd:PRK14939 238 HPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 321 EGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKS 400
Cdd:PRK14939 318 EGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKG 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 401 ALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGT 480
Cdd:PRK14939 398 ALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGC 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 481 GIG-EDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELE--- 556
Cdd:PRK14939 478 GIGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDdyl 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 --------------------------------------------------------------------------------
Cdd:PRK14939 558 ielalegatlhladgpaisgealeklvkeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsa 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 557 -----------------------------------ELLKTLPQTPKPGL--QRYKGLGEMNATQLWETTMDPSSRTLLQV 599
Cdd:PRK14939 638 eyrrlvelaeklrglieegaylergerkqpvssfeEALDWLLAEARKGLsiQRYKGLGEMNPEQLWETTMDPENRRLLQV 717
|
730 740 750
....*....|....*....|....*....|....*....
gi 16077074 600 TLEDAMDADETFEMLMGDKVEPRRNFIEANARYVKNLDI 638
Cdd:PRK14939 718 TIEDAIAADEIFTTLMGDEVEPRREFIEENALNVANLDV 756
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
1-633 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 990.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 1 MEQQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGI 80
Cdd:PRK05559 1 AAMMTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 81 PVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIG 160
Cdd:PRK05559 81 PVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 161 ET--DHTGTTTHFVPDPEIFsETTEYDYDLLANRVRELAFLTKGVNITIEDKREGQErkneYHYEGGIKSYVEYLNRSKE 238
Cdd:PRK05559 161 TAgkRKTGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERERQT----FHYENGLKDYLAELNEGKE 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 239 VVHEEPI-YIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKeNDPNLSGD 317
Cdd:PRK05559 236 TLPEEFVgSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLP-KGKKLEGE 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 318 DVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKarELTR 397
Cdd:PRK05559 315 DVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAK--KVKR 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 398 RKSALEiSNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITA 477
Cdd:PRK05559 393 KKKTSG-PALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVA 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 478 LGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEE 557
Cdd:PRK05559 472 IGIGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEE 551
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16077074 558 LLKTLPQT-PKPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARYV 633
Cdd:PRK05559 552 LLKKLGKKgGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFA 628
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
37-631 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 966.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 37 GLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGG 116
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 117 LHGVGASVVNALSTELDVTVHRDGKIHRQTYKR-GVPVTDLEIIGETDHTGTTTHFVPDPEIFSETTEYDYDLLANRVRE 195
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 196 LAFLTKGVNITIEDKREGQERknEYHYEGGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTN 275
Cdd:smart00433 161 LAFLNKGVKITLNDERSDEEK--TFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVN 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 276 NINTYEGGTHEAGFKTGLTRVINDYARKKGLIKEndPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDT 355
Cdd:smart00433 239 NIATTEGGTHENGFKDALTRVINEYAKKKKKLKE--KNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEK 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 356 LFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKsALEISNLPGKLADCSSKDPSISELYIVEGDSAGGS 435
Cdd:smart00433 317 IVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGS 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 436 AKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLT 515
Cdd:smart00433 396 AKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLLT 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 516 FFYRYMRQIIENGYVYIAQPPLYKVQQGKRvEYAYNDKELEELLKTLPQTP----KPGLQRYKGLGEMNATQLWETTMDP 591
Cdd:smart00433 476 FFYRYMPPLIEAGFVYIAIPPLYKVTKGKK-KYVYSFYSLDEYEKWLEKTEgnksKYEIQRYKGLGEMNADQLWETTMDP 554
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 16077074 592 SSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANAR 631
Cdd:smart00433 555 ERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
6-632 |
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: 805.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 6 NSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIH 85
Cdd:TIGR01058 3 SKYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIH 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 86 EKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKR-GVPVTDLEIIGETDH 164
Cdd:TIGR01058 83 QDGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKK 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 165 TGTTTHFVPDPEIFSeTTEYDYDLLANRVRELAFLTKGVNITIEDKREGQerKNEYHYEGGIKSYVEYLNRSKEVVHEEp 244
Cdd:TIGR01058 163 TGTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNK--TTVFFYENGLVDFVDYINETKETLSQV- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 245 IYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLT 324
Cdd:TIGR01058 239 TYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLS 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 325 AIISIKHPDP--QFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTR--RKS 400
Cdd:TIGR01058 319 AIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKP 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 401 ALEISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGT 480
Cdd:TIGR01058 399 KKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGT 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 481 GIGEDFNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQ--GKRVEYAYNDKELEEL 558
Cdd:TIGR01058 479 GIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKkdGKKVKYAWSDLELESV 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16077074 559 LKTLPQTPkpgLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIEANARY 632
Cdd:TIGR01058 559 KKKLKNYT---LQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEANINF 629
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
3-630 |
0e+00 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 552.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 3 QQQNSYDENQIQVLEGLEAVRKRPGMYIGSTNSKGLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPV 82
Cdd:PTZ00109 95 QRCSEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPC 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 83 GIHEKMGRPAVEVIMTVLHAGGKF-DGSG---------------------------------------YKVSGGLHGVGA 122
Cdd:PTZ00109 175 DVSEKTGKSGLETVLTVLHSGGKFqDTFPknsrsdksedkndtksskkgksshvkgpkeakekessqmYEYSSGLHGVGL 254
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 123 SVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGE-TDHTGTTTHFVPD-PEIFSETTE-------------YDYD 187
Cdd:PTZ00109 255 SVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCpLKKRGTTIHFLPDyKHIFKTHHQhteteeeegckngFNLD 334
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 188 LLANRVRELAFLTKGVNITIEDKREGQErKNEYHYE-----GGIKSYVEYLNRSKEVVHEEP--IYIEGEKDGITVEVAL 260
Cdd:PTZ00109 335 LIKNRIHELSYLNPGLTFYLVDERIANE-NNFYPYEtikheGGTREFLEELIKDKTPLYKDIniISIRGVIKNVNVEVSL 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 261 QYN-DSYTSNIYSFTNNINTyEGGTHEAGFKTGLTRVINDYARKKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQ 339
Cdd:PTZ00109 414 SWSlESYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQ 492
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 340 TKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKARELTRRKSALEISN-LPGKLADCSSKD 418
Cdd:PTZ00109 493 TKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDD 572
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 419 PSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLD-KILSNNEVRSMITALGTGIGED------------ 485
Cdd:PTZ00109 573 IERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtk 652
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 486 --------------------FNLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKV----- 540
Cdd:PTZ00109 653 askdesvqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRItnnrm 732
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 541 -------QQGKRVEYAYNDKELEELLKTL-----------------------------------------PQTPKPG--- 569
Cdd:PTZ00109 733 kqfnvstKNSKKYIYTWSDEELNVLIKLLnkdysskettrsveekgnapdldneyedekldnknmrennvDEVELKTelg 812
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 570 --------------------------LQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRR 623
Cdd:PTZ00109 813 tnvadteqtdeldinkaffkfskhyeIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRK 892
|
....*..
gi 16077074 624 NFIEANA 630
Cdd:PTZ00109 893 QFIFENS 899
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
7-628 |
0e+00 |
|
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 130127 [Multi-domain] Cd Length: 625 Bit Score: 547.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 7 SYDENQIQVLEGLEAVRKRPGMYIGSTNskgLHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHE 86
Cdd:TIGR01055 3 NYSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDIHP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 87 KMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDH-- 164
Cdd:TIGR01055 80 KEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrl 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 165 TGTTTHFVPDPEIFSEtTEYDYDLLANRVRELAFLTKGVNITIEDKREGQERKneYHYEGGIKSYVEYLNRSKEVVHEEP 244
Cdd:TIGR01055 160 TGTSVHFTPDPEIFDS-LHFSVSRLYHILRAKAVLCRGVEIEFEDEVNNTKAL--WNYPDGLKDYLSEAVNGDNTLPPKP 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 245 IYIEGEKDGITVEVALQYNDSYTSNIY-SFTNNINTYEGGTHEAGFKTGLTRVINDYARKKGlIKENDPNLSGDDVREGL 323
Cdd:TIGR01055 237 FSGNFEGDDEAVEWALLWLPEGGELFMeSYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRN-NLPRGVKLTAEDIWDRC 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 324 TAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDKGLMAARARMAAKKArelTRRKSALE 403
Cdd:TIGR01055 316 SYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKK---VVRKKLTS 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 404 ISNLPGKLADCSSKDPSISELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALgtGIG 483
Cdd:TIGR01055 393 GPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVAL--GID 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 484 EDFN-LEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTL 562
Cdd:TIGR01055 471 PDSNdLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLYKL 550
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 563 PQTP-KPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMD--ADETFEMLMGDKV-EPRRNFIEA 628
Cdd:TIGR01055 551 KKKKgKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVQDqrVDKIMDMLLAKKRsEDRFNWLQE 620
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
38-216 |
7.34e-116 |
|
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: 343.36 E-value: 7.34e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 38 LHHLVWEIVDNSIDEALAGYCTDINIQIEKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGL 117
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 118 HGVGASVVNALSTELDVTVHRDGKIHRQTYKRGVPVTDLEIIGETDHTGTTTHFVPDPEIFsETTEYDYDLLANRVRELA 197
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170
....*....|....*....
gi 16077074 198 FLTKGVNITIEDKREGQER 216
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEE 178
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
224-378 |
2.36e-89 |
|
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: 274.82 E-value: 2.36e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 224 GGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYARK 303
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16077074 304 KGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDK 378
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEK 155
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
422-535 |
7.73e-86 |
|
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: 263.36 E-value: 7.73e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 422 SELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKARYHKVVIMTD 501
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 16077074 502 ADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQP 535
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
225-378 |
3.53e-76 |
|
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: 240.60 E-value: 3.53e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 225 GIKSYVEYLNRSKEVVHEEPIYIEGE--KDGITVEVALQYNDSYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINDYAR 302
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16077074 303 KKGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLGNSEARTITDTLFSTAMETFMLENPDAAKKIVDK 378
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEK 156
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
422-535 |
8.84e-71 |
|
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: 224.31 E-value: 8.84e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 422 SELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIG-EDFNLEKARYHKVVIMT 500
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGkDDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 16077074 501 DADVDGAHIRTLLLTFFYRYMRQIIENGYVYIAQP 535
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
11-626 |
7.37e-60 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 210.77 E-value: 7.37e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 11 NQIQVLEGLEAVRKRPGMYIGSTNSK-----------------GLHHLVWEIVDNSIDEALAG---YCTDINIQIeKDNS 70
Cdd:PHA02569 2 DEFKVLSDREHILKRPGMYIGSVAYEaherflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 71 ITVVDNGRGIPVGI-----HEKMGRPavEVIMTVLHAGGKFDGSGyKVSGGLHGVGASVVNALSTELdVTVHRDGkihrq 145
Cdd:PHA02569 81 VTVSDNGRGIPQAMvttpeGEEIPGP--VAAWTRTKAGSNFDDTN-RVTGGMNGVGSSLTNFFSVLF-IGETCDG----- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 146 tyKRGVPVT---DLEIIGETDH----TGTTTHFVPDPEIFSETT--EYDYDLLANRVRELAFLTKGVNITIEDKRegqer 216
Cdd:PHA02569 152 --KNEVTVNcsnGAENISWSTKpgkgKGTSVTFIPDFSHFEVNGldQQYLDIILDRLQTLAVVFPDIKFTFNGKK----- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 217 kneyhYEGGIKSYVEYLNrskevvhEEPIYIEGEKDGITVEVAlqyNDSYTSNiySFTNNINTYEGGTHEAGFKTGLTRV 296
Cdd:PHA02569 225 -----VSGKFKKYAKQFG-------DDTIVQENDNVSIALAPS---PDGFRQL--SFVNGLHTKNGGHHVDCVMDDICEE 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 297 INDYARKKGLIKENDPNlsgddVREGLTAIISIKH-PDPQFEGQTKTKLGNS--EARTITDtLFSTAMETFMLENPDAAK 373
Cdd:PHA02569 288 LIPMIKKKHKIEVTKAR-----VKECLTIVLFVRNmSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEAIIM 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 374 KIVDKGLMAAR---ARMAAKKARELTRRKSALEI-SNLPGKLADcsskdpsiSELYIVEGDSAGGSAKQGRDRHFQAILP 449
Cdd:PHA02569 362 PIIEAALARKLaaeKAAETKAAKKAKKAKVAKHIkANLIGKDAE--------TTLFLTEGDSAIGYLIEVRDEELHGGYP 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 450 LRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDfnLEKARYHKVVIMTDADVDG-AHIRTLLLTFFYRYmRQIIENG 528
Cdd:PHA02569 434 LRGKVLNTWGMSYADILKNKELFDICAITGLVLGEK--AENMNYKNIAIMTDADVDGkGSIYPLLLAFFSRW-PELFEQG 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 529 YVYIAQPPLYKVQQGKRVEYAYNDKELEELLKTLpqtPKPGLQRYKGLGEMNATQLWETTMDPssrTLLQVTLEDamDAD 608
Cdd:PHA02569 511 RIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSL---KKWSIRYIKGLGSLRKSEYRRVINNP---VYDVVVLPD--DWK 582
|
650
....*....|....*...
gi 16077074 609 ETFEMLMGDKVEPRRNFI 626
Cdd:PHA02569 583 ELFEMLFGDDADLRKDWM 600
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
9-577 |
8.05e-47 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 178.32 E-value: 8.05e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 9 DENQIQVLEGLEAVRKRPGMYIGSTNSK-----------------------GLHHLVWEI----VDNSIDEALAGYCTDI 61
Cdd:PTZ00108 6 VEERYQKKTQIEHILLRPDTYIGSIETQtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 62 NIQI-EKDNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDVTV--HR 138
Cdd:PTZ00108 86 KVTIdEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 139 DGKIHRQTYKRGVPVTDLEII----GETDHTGTTthFVPDPEIF--SETTEYDYDLLANRVRELAFLTKGVNITIEDKRE 212
Cdd:PTZ00108 166 SGKKFKMTWTDNMSKKSEPRItsydGKKDYTKVT--FYPDYAKFgmTEFDDDMLRLLKKRVYDLAGCFGKLKVYLNGERI 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 213 gqerkneyhyegGIKSYVEY-----LNRSKEVVHEEPIYIEGEKDGitVEVALQYNDSyTSNIYSFTNNINTYEGGTHEA 287
Cdd:PTZ00108 244 ------------AIKSFKDYvdlylPDGEEGKKPPYPFVYTSVNGR--WEVVVSLSDG-QFQQVSFVNSICTTKGGTHVN 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 288 GFKTGLTRVINDYARKKgliKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTK-------TKLGNSeaRTITDTLFSTA 360
Cdd:PTZ00108 309 YILDQLISKLQEKAKKK---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKetlttkpSKFGST--CELSEKLIKYV 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 361 METFMLEN----------PDAAKKIvdKGlmaararmaakkarelTRRKSALEISnlpgKLADCSSKDPSISE---LYIV 427
Cdd:PTZ00108 384 LKSPILENivewaqaklaAELNKKM--KA----------------GKKSRILGIP----KLDDANDAGGKNSEectLILT 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 428 EGDSA-----GGSAKQGRDRHfqAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDF-NLEKARYHKVVIMTD 501
Cdd:PTZ00108 442 EGDSAkalalAGLSVVGRDYY--GVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYeDPKGLRYGSLMIMTD 519
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16077074 502 ADVDGAHIRTLLLTFFYRYMRQIIE-NGYVYIAQPPLYKVQQ-GKRVEYAYNDKELEELLKTLPqTPKPGLQRYKGLG 577
Cdd:PTZ00108 520 QDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQTVG-LKGWKIKYYKGLG 596
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
19-577 |
1.14e-46 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 177.59 E-value: 1.14e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 19 LEAVRKRPGMYIGST-----------NSK----------GLHHLVWEIVDNSIDEALAGYCTD---INIQIEKdNSITVV 74
Cdd:PLN03128 13 LEHILLRPDTYIGSTekhtqtlwvyeGGEmvnrevtyvpGLYKIFDEILVNAADNKQRDPSMDslkVDIDVEQ-NTISVY 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 75 DNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDV-TVH-RDGKIHRQTYKRGVP 152
Cdd:PLN03128 92 NNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVeTADgNRGKKYKQVFTNNMS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 153 VTDLEIIG--ETDHTGTTTHFVPDPEIFSETT--EYDYDLLANRVRELA-FLTKGVNITIEDKREgqerkneyhyegGIK 227
Cdd:PLN03128 172 VKSEPKITscKASENWTKITFKPDLAKFNMTRldEDVVALMSKRVYDIAgCLGKKLKVELNGKKL------------PVK 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 228 SYVEYLN---RSKEVVHEEPIYIEGEKDGITVEVALQyNDSYTSniYSFTNNINTYEGGTHEAGFKTGLTRVINDYARKK 304
Cdd:PLN03128 240 SFQDYVGlylGPNSREDPLPRIYEKVNDRWEVCVSLS-DGSFQQ--VSFVNSIATIKGGTHVDYVADQIVKHIQEKVKKK 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 305 gliKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKLgnsearTITDTLFSTAMETfmleNPDAAKKIVDKGLMAAR 384
Cdd:PLN03128 317 ---NKNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETL------TTRPSSFGSKCEL----SEEFLKKVEKCGVVENI 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 385 ARMAAKKARELTRRKSALEISNLPG--KLADCS---SKDPSISELYIVEGDSA-----GGSAKQGRDRHfqAILPLRGKI 454
Cdd:PLN03128 384 LSWAQFKQQKELKKKDGAKRQRLTGipKLDDANdagGKKSKDCTLILTEGDSAkalamSGLSVVGRDHY--GVFPLRGKL 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 455 LNVEKARLDKILSNNEVRSMITALGTGIGEDFNLEKA---RYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQIIE-NGYV 530
Cdd:PLN03128 462 LNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENTkslRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKiPGFL 541
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 16077074 531 YIAQPPLYKVQQGKRVEYAYNDKELEELLKTL-PQTPKPGLQRYKGLG 577
Cdd:PLN03128 542 VEFITPIVKATKGGKSLSFYTMPEYEAWKESLeGETKGWTIKYYKGLG 589
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
567-627 |
3.12e-39 |
|
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: 137.89 E-value: 3.12e-39
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16077074 567 KPGLQRYKGLGEMNATQLWETTMDPSSRTLLQVTLEDAMDADETFEMLMGDKVEPRRNFIE 627
Cdd:pfam00986 3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
19-577 |
1.16e-30 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 128.83 E-value: 1.16e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 19 LEAVRKRPGMYIGS---------------------TNSKGLHHLVWEIVDNSIDEALAGYCTD-INIQIEKD-NSITVVD 75
Cdd:PLN03237 38 LEHILLRPDTYIGSiekhtqtlwvyetdkmvqrsvTYVPGLYKIFDEILVNAADNKQRDPKMDsLRVVIDVEqNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 76 NGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELdVTVHRDG---KIHRQTYKRGVP 152
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEF-VIETADGkrqKKYKQVFSNNMG 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 153 VTDLEIIGETDHTG--TTTHFVPDPEIFSeTTEYDYD---LLANRVRELA-FLTKGVNITIEDKREgqerkneyhyegGI 226
Cdd:PLN03237 197 KKSEPVITKCKKSEnwTKVTFKPDLAKFN-MTHLEDDvvaLMKKRVVDIAgCLGKTVKVELNGKRI------------PV 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 227 KSYVEYLN---RSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIySFTNNINTYEGGTHeagfKTGLTRVINDYARK 303
Cdd:PLN03237 264 KSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTH----VDYVTNQIANHVME 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 304 KGLIKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKtklgnsEARTITDTLFSTAMETfmleNPDAAKKIVDKGLMAA 383
Cdd:PLN03237 339 AVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTK------ETLTLRQSSFGSKCEL----SEDFLKKVMKSGIVEN 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 384 RARMAAKKARELTRRKSALEISNLPG--KLADCSSKDPSISE---LYIVEGDSAGGSAKQGR---DRHFQAILPLRGKIL 455
Cdd:PLN03237 409 LLSWADFKQSKELKKTDGAKTTRVTGipKLEDANEAGGKNSEkctLILTEGDSAKALAVAGLsvvGRNYYGVFPLRGKLL 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 456 NVEKARLDKILSNNEVRSMITALGTGIGEDF-NLEKARYHKVVIMTDADVDGAHIRTLLLTFFYRYMRQI--IENGYVYI 532
Cdd:PLN03237 489 NVREASHKQIMNNAEIENIKQILGLQHGKQYeSVKSLRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLlkVPSFLVEF 568
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 16077074 533 AQPPLYKVQQGKRVEYAYNDKELEELLKTLPQTPKP-GLQRYKGLG 577
Cdd:PLN03237 569 ITPIVKATRRGKKVLSFYSMPEYEEWKESLGGNATGwSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
226-345 |
4.06e-25 |
|
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: 100.03 E-value: 4.06e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 226 IKSYVEYLNRSKevVHEEPIYIEGEKDGITVEVALQYND---SYTSNIYSFTNNINTYEGGTHEAGFKTGLTRVINdyar 302
Cdd:cd00329 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 16077074 303 kkglikendpnlsGDDVREGLTAIISIKHPD--PQFE-GQTKTKLG 345
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
424-520 |
1.57e-20 |
|
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173785 [Multi-domain] Cd Length: 120 Bit Score: 87.36 E-value: 1.57e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 424 LYIVEGDSAGGSAKQGR---DRHFQAILPLRGKILNVEKARLDKILSNNEVRSMITALGTGIGEDF--NLEKARYHKVVI 498
Cdd:cd03365 3 LILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRLMI 82
|
90 100
....*....|....*....|..
gi 16077074 499 MTDADVDGAHIRTLLLTFFYRY 520
Cdd:cd03365 83 MTDQDHDGSHIKGLLINFIHSF 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
423-535 |
4.97e-18 |
|
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: 79.32 E-value: 4.97e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 423 ELYIVEGDSAGGSAKQGRDRHFQAILPLRGKILNVEKARLDKILSNnevrsmitalgtgigedFNLEKARYHKVVIMTDA 502
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 16077074 503 DVDGAHIRTLLLTFfyrymRQIIEN--GYVYIAQP 535
Cdd:pfam01751 64 DREGEAIALKLLEL-----KELLENagGRVEFSEL 93
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
33-146 |
1.12e-16 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 76.15 E-value: 1.12e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 33 TNSKGLHHLVWEIVDNSIDEALAGycTDINIQIEKDN---SITVVDNGRGIPvgihekmgrpaVEVIMTVLHAGGKFDGS 109
Cdd:smart00387 1 GDPDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIP-----------PEDLEKIFEPFFRTDKR 67
|
90 100 110
....*....|....*....|....*....|....*..
gi 16077074 110 GYKVSGglHGVGASVVNALSTELDVTVHRDGKIHRQT 146
Cdd:smart00387 68 SRKIGG--TGLGLSIVKKLVELHGGEISVESEPGGGT 102
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
33-146 |
2.25e-15 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 72.40 E-value: 2.25e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 33 TNSKGLHHLVWEIVDNSIDEAlaGYCTDINIQIEKDN--SITVVDNGRGIPVGIHEKMgrpavevimtvlhaGGKFDgSG 110
Cdd:pfam02518 1 GDELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGelTLTVEDNGIGIPPEDLPRI--------------FEPFS-TA 63
|
90 100 110
....*....|....*....|....*....|....*.
gi 16077074 111 YKVSGGLHGVGASVVNALSTELDVTVHRDGKIHRQT 146
Cdd:pfam02518 64 DKRGGGGTGLGLSIVRKLVELLGGTITVESEPGGGT 99
|
|
| HATPase_TopII-like |
cd16930 |
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ... |
58-174 |
1.48e-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: 65.44 E-value: 1.48e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 58 CTDINIQIEKdNSITVVDNGRGIPVGIHEKMGRPAVEVIMTVLHAGGKFDGSGYKVSGGLHGVGASVVNALSTELDV-TV 136
Cdd:cd16930 28 CIKVTIDPEN-NEISVWNNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFTVeTA 106
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 16077074 137 HRD-GKIHRQTY-----KRGVPVTdLEIIGETDHTGTTthFVPD 174
Cdd:cd16930 107 DSEsKKKFKQTWtnnmgKASEPKI-TPYEKGKDYTKVT--FKPD 147
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
422-525 |
2.56e-07 |
|
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: 48.58 E-value: 2.56e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 422 SELYIVEGDSAGGSAKQGRDrHFQAILPLRGKILNVEKARLDKILSnnevrsmitalgtgigedfnlekaRYHKVVIMTD 501
Cdd:cd00188 1 KKLIIVEGPSDALALAQAGG-YGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90 100
....*....|....*....|....
gi 16077074 502 ADVDGAHIRTLLLTFFYRYMRQII 525
Cdd:cd00188 56 ADREGEAIALRLLELLKSLGKKVR 79
|
|
| TopoIIA_Trans_ScTopoIIA |
cd03481 |
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
224-344 |
1.69e-05 |
|
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.
Pssm-ID: 239563 [Multi-domain] Cd Length: 153 Bit Score: 45.36 E-value: 1.69e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 224 GGIKSYVEYLNRSKEVVHEEPIYIEGEKDGITVEVALQYNDSYTSNIySFTNNINTYEGGTHEAGFKTGLTRVINDYARK 303
Cdd:cd03481 1 KSFKDYVKLYLKDANKEDGPPPPVVYEPVNDRWEVAVALSDGQFQQV-SFVNSIATTKGGTHVDYVADQIVKKLDEVVKK 79
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 16077074 304 KgliKENDPNLSGDDVREGLTAIISIKHPDPQFEGQTKTKL 344
Cdd:cd03481 80 K---NKGGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL 117
|
|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
38-137 |
1.01e-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: 41.82 E-value: 1.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 38 LHHLVWEIVDNSIDEALAGycTDINIQIEKDNS---ITVVDNGRGIPVGIHEKMGRPavevimtvlhaggkFDGSGYKVS 114
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGDgvvLEVEDNGPGIPEEDLERIFER--------------FYRGDKSRE 64
|
90 100
....*....|....*....|...
gi 16077074 115 GGLHGVGASVVNALSTELDVTVH 137
Cdd:cd00075 65 GGGTGLGLAIVRRIVEAHGGRIT 87
|
|
| COG1389 |
COG1389 |
DNA topoisomerase VI, subunit B [Replication, recombination and repair]; |
35-123 |
1.29e-03 |
|
DNA topoisomerase VI, subunit B [Replication, recombination and repair];
Pssm-ID: 440999 [Multi-domain] Cd Length: 530 Bit Score: 41.74 E-value: 1.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 35 SKGLHHLVWEIVDNSIDEA-LAGYCTDINIQIEKDNS-----ITVVDNGRGIPvgiHEKMGRpaveVIMTVLhAGGKFdg 108
Cdd:COG1389 33 ARALYTTVKEAVDNSLDACeEAGILPDIKVSIERVDGkdiyrVTVEDNGPGIP---PEQIPK----VFGKLL-YGSKF-- 102
|
90
....*....|....*
gi 16077074 109 SGYKVSGGLHGVGAS 123
Cdd:COG1389 103 HVLRQSRGQQGIGIS 117
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
44-81 |
1.61e-03 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 41.36 E-value: 1.61e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 16077074 44 EIVDNSIDealAGyCTDINIQIEKD--NSITVVDNGRGIP 81
Cdd:PRK00095 29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGIS 64
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
44-81 |
1.68e-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: 40.11 E-value: 1.68e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 16077074 44 EIVDNSIDealAGyCTDINIQIEKD--NSITVVDNGRGIP 81
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGIS 55
|
|
| HATPase_TopVIB-like |
cd16933 |
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family ... |
20-125 |
1.92e-03 |
|
Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B; This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends.
Pssm-ID: 340410 [Multi-domain] Cd Length: 203 Bit Score: 40.02 E-value: 1.92e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 20 EAVRKRPGMyIGSTN-SKGLHHLVWEIVDNSIDEA-LAGYCTDINIQIEKDN----SITVVDNGRGIPvgiHEKMGRpav 93
Cdd:cd16933 2 EFFRKNKEM-LGFDNpIRSLYTTVRELVENSLDATeEAGILPDIKVEIEEIGkdhyKVIVEDNGPGIP---EEQIPK--- 74
|
90 100 110
....*....|....*....|....*....|..
gi 16077074 94 eVIMTVLhAGGKFdgsGYKVSGGLHGVGASVV 125
Cdd:cd16933 75 -VFGKVL-YGSKY---HNKQSRGQQGLGISAA 101
|
|
| PRK04184 |
PRK04184 |
DNA topoisomerase VI subunit B; Validated |
36-125 |
2.73e-03 |
|
DNA topoisomerase VI subunit B; Validated
Pssm-ID: 235246 [Multi-domain] Cd Length: 535 Bit Score: 40.65 E-value: 2.73e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16077074 36 KGLHHLVWEIVDNSIDEA-LAGYCTDINIQIEKDN------SITVVDNGRGIPvgihekmgrpaVEVIMTVLhagGK-FD 107
Cdd:PRK04184 35 RALYTTVKELVDNSLDACeEAGILPDIKIEIKRVDegkdhyRVTVEDNGPGIP-----------PEEIPKVF---GKlLY 100
|
90 100
....*....|....*....|.
gi 16077074 108 GSGYKV---SGGLHGVGASVV 125
Cdd:PRK04184 101 GSKFHNlrqSRGQQGIGISAA 121
|
|
| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
44-81 |
3.30e-03 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 40.41 E-value: 3.30e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 16077074 44 EIVDNSIDealAGyCTDINIQIEKD--NSITVVDNGRGIP 81
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGgkSLIRVTDNGCGMS 65
|
|
| |
