|
Name |
Accession |
Description |
Interval |
E-value |
| gyrB |
PRK05644 |
DNA gyrase subunit B; Validated |
7-644 |
0e+00 |
|
DNA gyrase subunit B; Validated
Pssm-ID: 235542 [Multi-domain] Cd Length: 638 Bit Score: 1226.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 7 DVNNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGI 86
Cdd:PRK05644 1 KEEKAQEYDASQIQVLEGLEAVRKRPGMYIGSTGERGLHHLVYEIVDNSIDEALAGYCDHIEVTINEDGSITVTDNGRGI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 87 PVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVG 166
Cdd:PRK05644 81 PVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 167 TTDKTGTVIRFKADGEIFtETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENvREDSYHYEGGIKSYVELLNENKEP 246
Cdd:PRK05644 161 ETDETGTTVTFKPDPEIF-ETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEE-KEETFHYEGGIKEYVEYLNRNKEP 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 247 IHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDT 326
Cdd:PRK05644 239 LHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 327 REGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRK 406
Cdd:PRK05644 319 REGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRK 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 407 SALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFG 486
Cdd:PRK05644 399 SALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 487 TGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKyYVYNDRELDKLK 566
Cdd:PRK05644 479 TGIGDDFDISKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEIL 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 567 SEL--NPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVY-ANLD 643
Cdd:PRK05644 558 AELklKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSILMGDDVEPRREFIEENAKYvRNLD 637
|
.
gi 996919738 644 F 644
Cdd:PRK05644 638 I 638
|
|
| GyrB |
COG0187 |
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]; |
9-643 |
0e+00 |
|
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
Pssm-ID: 439957 [Multi-domain] Cd Length: 635 Bit Score: 1169.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 9 NNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPV 88
Cdd:COG0187 1 AKKSNYDASSIQVLEGLEAVRKRPGMYIGSTDERGLHHLVWEIVDNSIDEALAGYCDRIEVTLHADGSVTVEDNGRGIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 89 DIQEKMGRPAVEVILTVLHAggkfggggykvsggLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTT 168
Cdd:COG0187 81 DIHPKEGKSALEVVLTVLHAggkfdggsykvsggLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 169 DKTGTVIRFKADGEIFtETTVYNYETLQQRIRELAFLNKGIQITLRDERDEEnVREDSYHYEGGIKSYVELLNENKEPIH 248
Cdd:COG0187 161 DRTGTTVRFKPDPEIF-ETTEFDYETLAERLRELAFLNKGLTITLTDEREEE-PKEETFHYEGGIKDFVEYLNEDKEPLH 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 249 DEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTRE 328
Cdd:COG0187 239 PEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVRE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 329 GMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSA 408
Cdd:COG0187 319 GLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSA 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 409 LDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTG 488
Cdd:COG0187 399 LESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 489 IGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSE 568
Cdd:COG0187 479 IGDDFDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLKE 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 996919738 569 LNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA-NLD 643
Cdd:COG0187 559 LKGKKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIFSLLMGDKVEPRREFIEENAKFVrNLD 634
|
|
| gyrB |
PRK14939 |
DNA gyrase subunit B; Provisional |
9-644 |
0e+00 |
|
DNA gyrase subunit B; Provisional
Pssm-ID: 237860 [Multi-domain] Cd Length: 756 Bit Score: 1009.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 9 NNTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSE-RGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIP 87
Cdd:PRK14939 2 MMSNSYGASSIKVLKGLDAVRKRPGMYIGDTDDgTGLHHMVYEVVDNAIDEALAGHCDDITVTIHADGSVSVSDNGRGIP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 88 VDIQEKMGRPAVEVILTVLHAggkfggggykvsggLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGT 167
Cdd:PRK14939 82 TDIHPEEGVSAAEVIMTVLHAggkfdqnsykvsggLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 168 TDKTGTVIRFKADGEIFTeTTVYNYETLQQRIRELAFLNKGIQITLRDERDEenvREDSYHYEGGIKSYVELLNENKEPI 247
Cdd:PRK14939 162 TDKTGTEVRFWPSPEIFE-NTEFDYDILAKRLRELAFLNSGVRIRLKDERDG---KEEEFHYEGGIKAFVEYLNRNKTPL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 248 HDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTR 327
Cdd:PRK14939 238 HPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAR 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 328 EGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKS 407
Cdd:PRK14939 318 EGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKG 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 408 ALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGT 487
Cdd:PRK14939 398 ALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGC 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 488 GIG-GDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDK-- 564
Cdd:PRK14939 478 GIGrDEFNPDKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDyl 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 565 ----------------------LKSELN---------------------------------------------------- 570
Cdd:PRK14939 558 ielalegatlhladgpaisgeaLEKLVKeyravrkiidrlerrypravlealiyapaldlddladeaavaaldadfltsa 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 571 -------------------------------PTPK-------------WSIARYKGLGEMNADQLWETTMNPEHRALLQV 606
Cdd:PRK14939 638 eyrrlvelaeklrglieegaylergerkqpvSSFEealdwllaearkgLSIQRYKGLGEMNPEQLWETTMDPENRRLLQV 717
|
730 740 750
....*....|....*....|....*....|....*....
gi 996919738 607 KLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYA-NLDF 644
Cdd:PRK14939 718 TIEDAIAADEIFTTLMGDEVEPRREFIEENALNVaNLDV 756
|
|
| gyrB |
TIGR01059 |
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ... |
14-643 |
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: 994.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 14 YGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEK 93
Cdd:TIGR01059 1 YDASSIKVLEGLEAVRKRPGMYIGSTGETGLHHLVYEVVDNSIDEAMAGYCDTISVTINDDGSVTVEDNGRGIPVDIHPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 94 MGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGT 173
Cdd:TIGR01059 81 EGISAVEVVLTVLHAGGKFDKDSYKVSGGLHGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 174 VIRFKADGEIFtETTVYNYETLQQRIRELAFLNKGIQITLRDERDEeNVREDSYHYEGGIKSYVELLNENKEPIHDEPIY 253
Cdd:TIGR01059 161 TVRFWPDPEIF-ETTEFDFDILAKRLRELAFLNSGVKISLEDERDG-KGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 254 IHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTREGMTAI 333
Cdd:TIGR01059 239 IKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAV 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 334 ISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVAS 413
Cdd:TIGR01059 319 ISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGG 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 414 LPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDF 493
Cdd:TIGR01059 399 LPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKDF 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 494 DLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQ--------------------- 552
Cdd:TIGR01059 479 DLEKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKeryikddkekdlvgealedlk 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 553 KYYVYNDRELDKLKSELNPTP---KWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENR 629
Cdd:TIGR01059 559 ALYIYSDKEKEEAKTQIPVHLgrkGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIFSTLMGDEVEPR 638
|
650
....*....|....*
gi 996919738 630 RQFIEDNAVYA-NLD 643
Cdd:TIGR01059 639 REFIEANALDVkNLD 653
|
|
| TOP2c |
smart00433 |
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE |
43-638 |
0e+00 |
|
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
Pssm-ID: 214659 [Multi-domain] Cd Length: 594 Bit Score: 886.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 43 GLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGG 122
Cdd:smart00433 1 GLHHLVDEIVDNAADEALAGYMDTIKVTIDKDNSISVEDNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 123 LHGVGSSVVNALSQDLEVYVHRNETIYHQAYKK-GVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRE 201
Cdd:smart00433 81 LHGVGASVVNALSTEFEVEVARDGKEYKQSFSNnGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGMTTDDDFELLKRRLRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 202 LAFLNKGIQITLRDERDEEnvrEDSYHYEGGIKSYVELLNENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYA 281
Cdd:smart00433 161 LAFLNKGVKITLNDERSDE---EKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFV 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 282 NNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKdrLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVD 361
Cdd:smart00433 238 NNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVE 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 362 KLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKsALDVASLPGKLADCSSKSPEECEIFLVEGDSAGG 441
Cdd:smart00433 316 KIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGG 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 442 STKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLL 521
Cdd:smart00433 395 SAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIGKDFDIEKLRYGKIIIMTDADVDGSHIKGLLL 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 522 TFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYV--YNDRE-LDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNP 598
Cdd:smart00433 475 TFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYVYsfYSLDEyEKWLEKTEGNKSKYEIQRYKGLGEMNADQLWETTMDP 554
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 996919738 599 EHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAV 638
Cdd:smart00433 555 ERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENAP 594
|
|
| PRK05559 |
PRK05559 |
DNA topoisomerase IV subunit B; Reviewed |
10-643 |
0e+00 |
|
DNA topoisomerase IV subunit B; Reviewed
Pssm-ID: 235501 [Multi-domain] Cd Length: 631 Bit Score: 886.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 10 NTDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVD 89
Cdd:PRK05559 4 MTNNYNADSIEVLEGLEPVRKRPGMYIGSTDTRGLHHLVQEVIDNSVDEALAGHGKRIEVTLHADGSVSVRDNGRGIPVG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 90 IQEKMGRPAVEVILTVLHAggkfggggykvsggLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTT- 168
Cdd:PRK05559 84 IHPEEGKSGVEVILTKLHAggkfsnkaykfsggLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAg 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 169 -DKTGTVIRFKADGEIFtETTVYNYETLQQRIRELAFLNKGIQITLRDERDEEnvredSYHYEGGIKSYVELLNENKEPI 247
Cdd:PRK05559 164 kRKTGTRVRFWPDPKIF-DSPKFSPERLKERLRSKAFLLPGLTITLNDERERQ-----TFHYENGLKDYLAELNEGKETL 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 248 HDEPI-YIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDrLSGEDT 326
Cdd:PRK05559 238 PEEFVgSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKK-LEGEDV 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 327 REGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGImaARARVAAKKAREVTRRK 406
Cdd:PRK05559 317 REGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAI--KAAQARLRAAKKVKRKK 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 407 SALdVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFG 486
Cdd:PRK05559 395 KTS-GPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIG 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 487 TGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLK 566
Cdd:PRK05559 474 IGPGDSFDLEDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELL 553
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 996919738 567 SEL-NPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLD 643
Cdd:PRK05559 554 KKLgKKGGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLVDMLMGKKAEPRREWIEENGDFAEEE 631
|
|
| parE_Gpos |
TIGR01058 |
DNA topoisomerase IV, B subunit, Gram-positive; Operationally, topoisomerase IV is a type II ... |
13-636 |
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: 706.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 13 NYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQE 92
Cdd:TIGR01058 4 KYNADAIKILEGLDAVRKRPGMYIGSTDSKGLHHLVWEIVDNSVDEVLAGYADNITVTLHKDNSITVQDDGRGIPTGIHQ 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 93 KMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKK-GVPQFDLKEVGTTDKT 171
Cdd:TIGR01058 84 DGNISTVETVFTVLHAGGKFDQGGYKTAGGLHGVGASVVNALSSWLEVTVKRDGQIYQQRFENgGKIVQSLKKIGTTKKT 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 172 GTVIRFKADGEIFTeTTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVredSYHYEGGIKSYVELLNENKEpIHDEP 251
Cdd:TIGR01058 164 GTLVHFHPDPTIFK-TTQFNSNIIKERLKESAFLLKKLKLTFTDKRTNKTT---VFFYENGLVDFVDYINETKE-TLSQV 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 252 IYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTREGMT 331
Cdd:TIGR01058 239 TYFEGEKNGIEVEVAFQFNDGDSENILSFANSVKTKEGGTHENGFKLAITDVINSYARKYNLLKEKDKNLEGSDIREGLS 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 332 AIISIKHGDP--QFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTR--RKS 407
Cdd:TIGR01058 319 AIISVRIPEEliQFEGQTKSKLFSPEARNVVDEIVQDHLFFFLEENNNDAKLLIDKAIKARDAKEAAKKAREEKKsgKKP 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 408 ALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGT 487
Cdd:TIGR01058 399 KKEKGILSGKLTPAQSKNPAKNELFLVEGDSAGGSAKQGRDRKFQAILPLRGKVLNVEKAKLADILKNEEINTIIFCIGT 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 488 GIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQK--YYVYNDRELDKL 565
Cdd:TIGR01058 479 GIGADFSIKDLKYDKIIIMTDADTDGAHIQVLLLTFFYRYMRPLIELGHVYIALPPLYKLSKKDGKkvKYAWSDLELESV 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 996919738 566 KSELNptpKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDN 636
Cdd:TIGR01058 559 KKKLK---NYTLQRYKGLGEMNADQLWETTMNPETRTLVRVKIDDLARAERQINTLMGDKVEPRKKWIEAN 626
|
|
| parE_Gneg |
TIGR01055 |
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ... |
11-635 |
8.84e-171 |
|
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: 500.99 E-value: 8.84e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 11 TDNYGAGQIQVLEGLEAVRKRPGMYIGSTSergLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDI 90
Cdd:TIGR01055 1 TTNYSAKDIEVLDGLEPVRKRPGMYTDTTR---PNHLVQEVIDNSVDEALAGFASIIMVILHQDQSIEVFDNGRGMPVDI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 91 QEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDK 170
Cdd:TIGR01055 78 HPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 171 --TGTVIRFKADGEIFTETTvYNYETLQQRIRELAFLNKGIQITLrdeRDEENVREDSYHYEGGIKSYVELLNENKEPIH 248
Cdd:TIGR01055 158 rlTGTSVHFTPDPEIFDSLH-FSVSRLYHILRAKAVLCRGVEIEF---EDEVNNTKALWNYPDGLKDYLSEAVNGDNTLP 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 249 DEPIYIHQSKDDIEVEIAIQY-NSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGlSSKIMKEEKDRLSGEDTR 327
Cdd:TIGR01055 234 PKPFSGNFEGDDEAVEWALLWlPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFC-EMRNNLPRGVKLTAEDIW 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 328 EGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKArevTRRKS 407
Cdd:TIGR01055 313 DRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKK---VVRKK 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 408 ALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGT 487
Cdd:TIGR01055 390 LTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGI 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 488 GIGGDfDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKS 567
Cdd:TIGR01055 470 DPDSN-DLSQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYYALDEEEKEKLLY 548
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 996919738 568 EL-NPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDA--IEADQTFEMLMG-DVVENRRQFIED 635
Cdd:TIGR01055 549 KLkKKKGKPNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDDVqdQRVDKIMDMLLAkKRSEDRFNWLQE 620
|
|
| PTZ00109 |
PTZ00109 |
DNA gyrase subunit b; Provisional |
11-637 |
1.62e-166 |
|
DNA gyrase subunit b; Provisional
Pssm-ID: 240272 [Multi-domain] Cd Length: 903 Bit Score: 499.41 E-value: 1.62e-166
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 11 TDNYGAGQIQVLEGLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDI 90
Cdd:PTZ00109 97 CSEYDADDIVVLEGLEAVRKRPGMYIGNTDEKGLHQLLFEILDNSVDEYLAGECNKITVVLHKDGSVEISDNGRGIPCDV 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 91 QEKMGRPAVEVILTVLH----------------------------------------AGGKFGGGGYKVSGGLHGVGSSV 130
Cdd:PTZ00109 177 SEKTGKSGLETVLTVLHsggkfqdtfpknsrsdksedkndtksskkgksshvkgpkeAKEKESSQMYEYSSGLHGVGLSV 256
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 131 VNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVG-TTDKTGTVIRFKADGE-IFTETT-------------VYNYETL 195
Cdd:PTZ00109 257 VNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFScPLKKRGTTIHFLPDYKhIFKTHHqhteteeeegcknGFNLDLI 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 196 QQRIRELAFLNKGIQITLRDERDEENV---REDSYHYEGGIKSYVELLNENKEPIHDEPIYIHQS--KDDIEVEIAIQYN 270
Cdd:PTZ00109 337 KNRIHELSYLNPGLTFYLVDERIANENnfyPYETIKHEGGTREFLEELIKDKTPLYKDINIISIRgvIKNVNVEVSLSWS 416
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 271 SG-YATNLLTYANNIHTyEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTREGMTAIISIKHGDPQFEGQTKT 349
Cdd:PTZ00109 417 LEsYTALIKSFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKT 495
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 350 KLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVAS-LPGKLADCSSKSPEE 428
Cdd:PTZ00109 496 KLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDDIER 575
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 429 CEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLD-RILNNNEIRQMITAFGTGIGGD--------------- 492
Cdd:PTZ00109 576 NELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVtwrqydlshgtkask 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 493 -----------------FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKY- 554
Cdd:PTZ00109 656 desvqnnnstltkkknsLFDTPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQf 735
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 555 -----------YVYNDRELDKLKSELNP---------------------------------------------------- 571
Cdd:PTZ00109 736 nvstknskkyiYTWSDEELNVLIKLLNKdysskettrsveekgnapdldneyedekldnknmrennvdevelktelgtnv 815
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 572 ------------------TPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFI 633
Cdd:PTZ00109 816 adteqtdeldinkaffkfSKHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASELIFLLMGEDVQSRKQFI 895
|
....
gi 996919738 634 EDNA 637
Cdd:PTZ00109 896 FENS 899
|
|
| HATPase_GyrB-like |
cd16928 |
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ... |
44-222 |
6.62e-88 |
|
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.
Pssm-ID: 340405 [Multi-domain] Cd Length: 180 Bit Score: 271.33 E-value: 6.62e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 44 LHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGL 123
Cdd:cd16928 1 LHHLVWEIVDNSIDEALAGYATEIEVTLHEDNSITVEDNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 124 HGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFtETTVYNYETLQQRIRELA 203
Cdd:cd16928 81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIF-EKTEFDFDTLKRRLRELA 159
|
170
....*....|....*....
gi 996919738 204 FLNKGIQITLRDERDEENV 222
Cdd:cd16928 160 FLNKGLKIVLEDERTGKEE 178
|
|
| TOPRIM_TopoIIA_GyrB |
cd03366 |
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
429-542 |
1.29e-79 |
|
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: 247.57 E-value: 1.29e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 429 CEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTD 508
Cdd:cd03366 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIGEDFDLEKLRYHKIIIMTD 80
|
90 100 110
....*....|....*....|....*....|....
gi 996919738 509 ADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQP 542
Cdd:cd03366 81 ADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
|
|
| TopoII_Trans_DNA_gyrase |
cd00822 |
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ... |
231-387 |
1.44e-75 |
|
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: 239.00 E-value: 1.44e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 231 GGIKSYVELLNENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLS 310
Cdd:cd00822 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 996919738 311 SKIMKEEKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGI 387
Cdd:cd00822 81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAI 157
|
|
| DNA_gyraseB |
pfam00204 |
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ... |
232-387 |
3.00e-69 |
|
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: 222.49 E-value: 3.00e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 232 GIKSYVELLNENKEPIHDEPIYI--HQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGL 309
Cdd:pfam00204 1 GLKDFVEELNKDKKPLHKEIIYFegESPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 996919738 310 SSKIMKEEKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGI 387
Cdd:pfam00204 81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKAL 158
|
|
| TOPRIM_TopoIIA_like |
cd01030 |
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ... |
429-542 |
3.11e-67 |
|
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: 215.06 E-value: 3.11e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 429 CEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGG-DFDLAKARYHKIVIMT 507
Cdd:cd01030 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKdDFDLDKLRYGKIIIMT 80
|
90 100 110
....*....|....*....|....*....|....*
gi 996919738 508 DADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQP 542
Cdd:cd01030 81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
|
|
| 39 |
PHA02569 |
DNA topoisomerase II large subunit; Provisional |
18-633 |
7.12e-55 |
|
DNA topoisomerase II large subunit; Provisional
Pssm-ID: 177398 [Multi-domain] Cd Length: 602 Bit Score: 197.28 E-value: 7.12e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 18 QIQVLEGLEAVRKRPGMYIGSTS----ER-------------GLHHLVWEIVDNSIDEALAG---YANQIEVVIeKDNWI 77
Cdd:PHA02569 3 EFKVLSDREHILKRPGMYIGSVAyeahERflfgkftqveyvpGLVKIIDEIIDNSVDEAIRTnfkFANKIDVTI-KNNQV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 78 KVTDNGRGIPvdiQEKMGRPAVEVILTVLHAGGKFG-----GGGYKVSGGLHGVGSSVVNALSQ-------DLEVYVHRN 145
Cdd:PHA02569 82 TVSDNGRGIP---QAMVTTPEGEEIPGPVAAWTRTKagsnfDDTNRVTGGMNGVGSSLTNFFSVlfigetcDGKNEVTVN 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 146 ETiyhqaykKGVPQFDLKEVGTTDKtGTVIRFKADGEIFTETTVYN--YETLQQRIRELAFLNKGIQITLRDERdeenvr 223
Cdd:PHA02569 159 CS-------NGAENISWSTKPGKGK-GTSVTFIPDFSHFEVNGLDQqyLDIILDRLQTLAVVFPDIKFTFNGKK------ 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 224 edsyhYEGGIKSYVELLNENKepihdepiyIHQSKDDIEVEIAiqyNSGYATNLLTYANNIHTYEGGTHEDGFKRALtrv 303
Cdd:PHA02569 225 -----VSGKFKKYAKQFGDDT---------IVQENDNVSIALA---PSPDGFRQLSFVNGLHTKNGGHHVDCVMDDI--- 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 304 lnSYGLSSKIMKEEKDRLSGEDTREGMTAIISIKH-GDPQFEGQTKTKLGNS--EVRQVVDkLFSEHFERFLYENPQVAR 380
Cdd:PHA02569 285 --CEELIPMIKKKHKIEVTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgEIRNHID-LDYKKIAKQILKTEAIIM 361
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 381 TVVEKGI---MAARARVAAKKAREVTRRKSALDV-ASLPGKLADCSskspeeceIFLVEGDSAGGSTKSGRDSRTQAILP 456
Cdd:PHA02569 362 PIIEAALarkLAAEKAAETKAAKKAKKAKVAKHIkANLIGKDAETT--------LFLTEGDSAIGYLIEVRDEELHGGYP 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 457 LRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKarYHKIVIMTDADVDG-AHIRTLLLTFFYRFMRpLIEAG 535
Cdd:PHA02569 434 LRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENMN--YKNIAIMTDADVDGkGSIYPLLLAFFSRWPE-LFEQG 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 536 YVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELnptPKWSIARYKGLGEMNADQLWETTMNPEHRallQVKLEDaiEAD 615
Cdd:PHA02569 511 RIRFVKTPVIIAQVGKETKWFYSLDEFEKAKDSL---KKWSIRYIKGLGSLRKSEYRRVINNPVYD---VVVLPD--DWK 582
|
650
....*....|....*...
gi 996919738 616 QTFEMLMGDVVENRRQFI 633
Cdd:PHA02569 583 ELFEMLFGDDADLRKDWM 600
|
|
| DNA_gyraseB_C |
pfam00986 |
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ... |
574-634 |
1.00e-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: 134.04 E-value: 1.00e-37
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 996919738 574 KWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIE 634
Cdd:pfam00986 3 KVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIFSTLMGDKVEPRREFIE 63
|
|
| PLN03128 |
PLN03128 |
DNA topoisomerase 2; Provisional |
25-584 |
1.27e-37 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215593 [Multi-domain] Cd Length: 1135 Bit Score: 150.24 E-value: 1.27e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 25 LEAVRKRPGMYIGSTSERGLHHLVWE---IVDNSI----------DEALAGYA---------NQIEVVIEKD-NWIKVTD 81
Cdd:PLN03128 13 LEHILLRPDTYIGSTEKHTQTLWVYEggeMVNREVtyvpglykifDEILVNAAdnkqrdpsmDSLKVDIDVEqNTISVYN 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 82 NGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYV---HRNETiYHQAYKKGVP 158
Cdd:PLN03128 93 NGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETadgNRGKK-YKQVFTNNMS 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 159 QFDLKEVGTTDK--TGTVIRFKADGEIFTETTVYN--YETLQQRIRELA-FLNKGIQITLRDERDEENvredsyhyegGI 233
Cdd:PLN03128 172 VKSEPKITSCKAseNWTKITFKPDLAKFNMTRLDEdvVALMSKRVYDIAgCLGKKLKVELNGKKLPVK----------SF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 234 KSYVEL-LNENKEPiHDEPIYIHQSKDDIEVEIAIqynSGYATNLLTYANNIHTYEGGTHEDgfkrALTRVLNSYgLSSK 312
Cdd:PLN03128 242 QDYVGLyLGPNSRE-DPLPRIYEKVNDRWEVCVSL---SDGSFQQVSFVNSIATIKGGTHVD----YVADQIVKH-IQEK 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 313 IMKEEKD--RLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEvrqvvdKLFSEHFE---RFLyenpqvaRTVVEKGI 387
Cdd:PLN03128 313 VKKKNKNatHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRP------SSFGSKCElseEFL-------KKVEKCGV 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 388 MAARARVAAKKAREVTRRKSALDVASLPG--KLADCS---SKSPEECEIFLVEGDSA-----GGSTKSGRDSrtQAILPL 457
Cdd:PLN03128 380 VENILSWAQFKQQKELKKKDGAKRQRLTGipKLDDANdagGKKSKDCTLILTEGDSAkalamSGLSVVGRDH--YGVFPL 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 458 RGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKA---RYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIE- 533
Cdd:PLN03128 458 RGKLLNVREASHKQIMKNAEITNIKQILGLQFGKTYDEENTkslRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKi 537
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 996919738 534 AGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNP-TPKWSIARYKGLG 584
Cdd:PLN03128 538 PGFLVEFITPIVKATKGGKSLSFYTMPEYEAWKESLEGeTKGWTIKYYKGLG 589
|
|
| PTZ00108 |
PTZ00108 |
DNA topoisomerase 2-like protein; Provisional |
18-584 |
1.21e-33 |
|
DNA topoisomerase 2-like protein; Provisional
Pssm-ID: 240271 [Multi-domain] Cd Length: 1388 Bit Score: 138.26 E-value: 1.21e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 18 QIQVLEGLEAVRKRPGMYIGSTsER------------------------GLHHLVWEI----VDNSIDEALAGYANQIEV 69
Cdd:PTZ00108 9 RYQKKTQIEHILLRPDTYIGSI-ETqtedmwvydeeknrmvyktityvpGLYKIFDEIlvnaADNKARDKGGHRMTYIKV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 70 VI-EKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYV--HRNE 146
Cdd:PTZ00108 88 TIdEENGEISVYNDGEGIPVQIHKEHKIYVPEMIFGHLLTSSNYDDTEKRVTGGRNGFGAKLTNIFSTKFTVECvdSKSG 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 147 TIYHQAYKKGVPQFDLKEVGTTDKTG--TVIRFKADGEIF--TETTVYNYETLQQRIRELAFLNKGIQITLRDERdeenV 222
Cdd:PTZ00108 168 KKFKMTWTDNMSKKSEPRITSYDGKKdyTKVTFYPDYAKFgmTEFDDDMLRLLKKRVYDLAGCFGKLKVYLNGER----I 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 223 REDSYhyeggiKSYVEL-LNENKEPIHDEPIYIHQSKDDiEVEIAIQY-NSGYatNLLTYANNIHTYEGGTHedgfkraL 300
Cdd:PTZ00108 244 AIKSF------KDYVDLyLPDGEEGKKPPYPFVYTSVNG-RWEVVVSLsDGQF--QQVSFVNSICTTKGGTH-------V 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 301 TRVLNSygLSSKIMKEEK-DRLSGEDTREGMtaiisIKHG----------DPQFEGQTKTKLGNSEVRQVVDKLFSEHFE 369
Cdd:PTZ00108 308 NYILDQ--LISKLQEKAKkKKKKGKEIKPNQ-----IKNHlwvfvnclivNPSFDSQTKETLTTKPSKFGSTCELSEKLI 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 370 RFLYENPQVARTVvekGIMAARARVAAKKAREVTRRKSALdvaSLPgKLADCSS---KSPEECEIFLVEGDSA-----GG 441
Cdd:PTZ00108 381 KYVLKSPILENIV---EWAQAKLAAELNKKMKAGKKSRIL---GIP-KLDDANDaggKNSEECTLILTEGDSAkalalAG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 442 STKSGRDSrtQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKA-RYHKIVIMTDADVDGAHIRTLL 520
Cdd:PTZ00108 454 LSVVGRDY--YGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGlRYGSLMIMTDQDHDGSHIKGLL 531
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 996919738 521 LTFFYRFMRPLIEA-GYVYIAQPPLYKLTQ-GKQKYYVYNDRELDKLKSElNPTPKWSIARYKGLG 584
Cdd:PTZ00108 532 INMIHHFWPSLLKNpGFLKEFITPIVKATKkGNQVISFFTIPDFEKWKQT-VGLKGWKIKYYKGLG 596
|
|
| PLN03237 |
PLN03237 |
DNA topoisomerase 2; Provisional |
25-584 |
5.40e-25 |
|
DNA topoisomerase 2; Provisional
Pssm-ID: 215641 [Multi-domain] Cd Length: 1465 Bit Score: 111.11 E-value: 5.40e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 25 LEAVRKRPGMYIGSTSERGLHHLVWE---IVDNSI----------DEALAGYANQ---------IEVVIEKD-NWIKVTD 81
Cdd:PLN03237 38 LEHILLRPDTYIGSIEKHTQTLWVYEtdkMVQRSVtyvpglykifDEILVNAADNkqrdpkmdsLRVVIDVEqNLISVYN 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 82 NGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQD--LEVYVHRNETIYHQAY-----K 154
Cdd:PLN03237 118 NGDGVPVEIHQEEGVYVPEMIFGHLLTSSNYDDNEKKTTGGRNGYGAKLTNIFSTEfvIETADGKRQKKYKQVFsnnmgK 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 155 KGVPQFdlkevgTTDKTG---TVIRFKADGEIFTETTVYN--YETLQQRIRELA-FLNKGIQITLRDERdeenVREDSYh 228
Cdd:PLN03237 198 KSEPVI------TKCKKSenwTKVTFKPDLAKFNMTHLEDdvVALMKKRVVDIAgCLGKTVKVELNGKR----IPVKSF- 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 229 yeggiKSYVEL-LNENKEPIHDEPIYIHQSKDDiEVEIAIQYNSGYATNLlTYANNIHTYEGGTHEDgfkrALTRVLNSY 307
Cdd:PLN03237 267 -----SDYVDLyLESANKSRPENLPRIYEKVND-RWEVCVSLSEGQFQQV-SFVNSIATIKGGTHVD----YVTNQIANH 335
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 308 gLSSKIMKEEKD-RLSGEDTREGMTAIISIKHGDPQFEGQTKTKLgnsEVRQvvdKLFSEHFErfLYENpqVARTVVEKG 386
Cdd:PLN03237 336 -VMEAVNKKNKNaNIKAHNVKNHLWVFVNALIDNPAFDSQTKETL---TLRQ---SSFGSKCE--LSED--FLKKVMKSG 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 387 IMAARARVAAKKAREVTRRKSALDVASLPG--KL---ADCSSKSPEECEIFLVEGDSA-----GGSTKSGRDSrtQAILP 456
Cdd:PLN03237 405 IVENLLSWADFKQSKELKKTDGAKTTRVTGipKLedaNEAGGKNSEKCTLILTEGDSAkalavAGLSVVGRNY--YGVFP 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 457 LRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKA-RYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEA- 534
Cdd:PLN03237 483 LRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSlRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKVp 562
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 996919738 535 GYVYIAQPPLYKLT-QGKQKYYVYNDRELDKLKSELNPTPK-WSIARYKGLG 584
Cdd:PLN03237 563 SFLVEFITPIVKATrRGKKVLSFYSMPEYEEWKESLGGNATgWSIKYYKGLG 614
|
|
| TopoII_MutL_Trans |
cd00329 |
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ... |
233-352 |
2.07e-20 |
|
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.
Pssm-ID: 238202 [Multi-domain] Cd Length: 107 Bit Score: 86.55 E-value: 2.07e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 233 IKSYVELLNENKepIHDEPIYIHQSKDDIEVEIAIQYNS---GYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNsygl 309
Cdd:cd00329 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 996919738 310 sskimkeekdrlsGEDTREGMTAIISIKH--GDPQFE-GQTKTKLG 352
Cdd:cd00329 75 -------------GDDVRRYPVAVLSLKIppSLVDVNvHPTKEEVR 107
|
|
| TOPRIM_TopoIIA |
cd03365 |
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
429-527 |
2.93e-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: 86.59 E-value: 2.93e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 429 CEIFLVEGDSAGGSTKSGR---DSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDF--DLAKARYHKI 503
Cdd:cd03365 1 CTLILTEGDSAKALAVAGLsvvGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDyeSTKSLRYGRL 80
|
90 100
....*....|....*....|....
gi 996919738 504 VIMTDADVDGAHIRTLLLTFFYRF 527
Cdd:cd03365 81 MIMTDQDHDGSHIKGLLINFIHSF 104
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
430-542 |
5.72e-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: 70.46 E-value: 5.72e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 430 EIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNneirqmitafgtgiggdFDLAKARYHKIVIMTDA 509
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKA-----------------LKELALKAKEVILATDP 63
|
90 100 110
....*....|....*....|....*....|....*
gi 996919738 510 DVDGAHIRTLLLTFfyrfmRPLIEA--GYVYIAQP 542
Cdd:pfam01751 64 DREGEAIALKLLEL-----KELLENagGRVEFSEL 93
|
|
| HATPase_c |
pfam02518 |
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ... |
41-147 |
1.26e-13 |
|
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.
Pssm-ID: 460579 [Multi-domain] Cd Length: 109 Bit Score: 67.39 E-value: 1.26e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 41 ERGLHHLVWEIVDNSIDEAlaGYANQIEVVIEKDNW--IKVTDNGRGIPVDIQEKMGRPAVEViltvlhaggkfggggYK 118
Cdd:pfam02518 3 ELRLRQVLSNLLDNALKHA--AKAGEITVTLSEGGEltLTVEDNGIGIPPEDLPRIFEPFSTA---------------DK 65
|
90 100
....*....|....*....|....*....
gi 996919738 119 VSGGLHGVGSSVVNALSQDLEVYVHRNET 147
Cdd:pfam02518 66 RGGGGTGLGLSIVRKLVELLGGTITVESE 94
|
|
| HATPase_c |
smart00387 |
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. |
41-145 |
2.76e-12 |
|
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
Pssm-ID: 214643 [Multi-domain] Cd Length: 111 Bit Score: 63.44 E-value: 2.76e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 41 ERGLHHLVWEIVDNSIDEALAGyaNQIEVVIEKDN---WIKVTDNGRGIPVDIQEKMGRPAVEViltvlhaggkfggGGY 117
Cdd:smart00387 3 PDRLRQVLSNLLDNAIKYTPEG--GRITVTLERDGdhvEITVEDNGPGIPPEDLEKIFEPFFRT-------------DKR 67
|
90 100
....*....|....*....|....*...
gi 996919738 118 KVSGGLHGVGSSVVNALSQDLEVYVHRN 145
Cdd:smart00387 68 SRKIGGTGLGLSIVKKLVELHGGEISVE 95
|
|
| mutL |
PRK00095 |
DNA mismatch repair endonuclease MutL; |
50-89 |
1.17e-05 |
|
DNA mismatch repair endonuclease MutL;
Pssm-ID: 234630 [Multi-domain] Cd Length: 617 Bit Score: 48.29 E-value: 1.17e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 996919738 50 EIVDNSIDealAGyANQIEVVIEKD--NWIKVTDNGRGIPVD 89
Cdd:PRK00095 29 ELVENALD---AG-ATRIDIEIEEGglKLIRVRDNGCGISKE 66
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| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
429-535 |
1.77e-05 |
|
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 43.57 E-value: 1.77e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 996919738 429 CEIFLVEGDSAGGSTKSGRdSRTQAILPLRGKILNVEKARLDRILNnneirqmitafgtgiggdfdlakaRYHKIVIMTD 508
Cdd:cd00188 1 KKLIIVEGPSDALALAQAG-GYGGAVVALGGHALNKTRELLKRLLG------------------------EAKEVIIATD 55
|
90 100
....*....|....*....|....*..
gi 996919738 509 ADVDGAHIRTLLLTFFYRFMRPLIEAG 535
Cdd:cd00188 56 ADREGEAIALRLLELLKSLGKKVRRLL 82
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| MutL |
COG0323 |
DNA mismatch repair ATPase MutL [Replication, recombination and repair]; |
50-89 |
4.40e-05 |
|
DNA mismatch repair ATPase MutL [Replication, recombination and repair];
Pssm-ID: 440092 [Multi-domain] Cd Length: 515 Bit Score: 46.58 E-value: 4.40e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 996919738 50 EIVDNSIDealAGyANQIEVVIEKD--NWIKVTDNGRGIPVD 89
Cdd:COG0323 30 ELVENAID---AG-ATRIEVEIEEGgkSLIRVTDNGCGMSPE 67
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| HATPase_LytS-like |
cd16957 |
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to ... |
51-100 |
4.67e-05 |
|
Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis LytS and Staphylococcus aureus LytS; This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis LytS, a HK of the two-component system (TCS) LytS-LytR needed for growth on pyruvate, and Staphylococcus aureus LytS-LytR TCS involved in the adaptation of S. aureus to cationic antimicrobial peptides. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and a GAF sensor domain; most contain a DUF3816 domain.
Pssm-ID: 340433 [Multi-domain] Cd Length: 106 Bit Score: 42.80 E-value: 4.67e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 996919738 51 IVDNSIDEALAG--YANQIEVVIEKDN---WIKVTDNGRGIPVDIQEKMGRPAVE 100
Cdd:cd16957 9 LVENAIRHAFPKrkENNEVRVVVKKDQhkvHVSVSDNGQGIPEERLDLLGKTTVT 63
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|
| HATPase |
cd00075 |
Histidine kinase-like ATPase domain; This superfamily includes the histidine kinase-like ... |
44-97 |
5.48e-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: 42.59 E-value: 5.48e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 996919738 44 LHHLVWEIVDNSIDEALAGyaNQIEVVIEKDN---WIKVTDNGRGIPVDIQEKMGRP 97
Cdd:cd00075 1 LEQVLSNLLDNALKYSPPG--GTIEISLRQEGdgvVLEVEDNGPGIPEEDLERIFER 55
|
|
| HATPase_MutL-MLH-PMS-like |
cd16926 |
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, ... |
50-89 |
8.63e-05 |
|
Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains; This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease.
Pssm-ID: 340403 [Multi-domain] Cd Length: 188 Bit Score: 43.96 E-value: 8.63e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 996919738 50 EIVDNSIDealAGyANQIEVVIEKD--NWIKVTDNGRGIPVD 89
Cdd:cd16926 20 ELVENSID---AG-ATRIDVEIEEGglKLIRVTDNGSGISRE 57
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