|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
1-731 |
0e+00 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 1116.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 1 MPVAHVALPVPLPRTFDYLLPEGMT-VKAGCRVRVPFGKQQeRIGVVVSVSDVSELPLNELKAVVEVLDVEPVFTHSVWR 79
Cdd:COG1198 1 MKIAEVALPVPLDRPFDYLVPEGLElVQPGSRVLVPFGRRQ-VVGIVVGLKEESDVDPAKLKPILAVLDDEPLLPEELLE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 80 LLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAvdlnsLKRSPKQQQALAALRQ--GKIWRDQVAE 157
Cdd:COG1198 80 LLRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRLTLGEEL-----PKRAPKQRRVLEALREhgGPLTLSELAK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 158 -LEFNDAALQALRKKGLCDLASETPEFSDWRTNyAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLS 236
Cdd:COG1198 155 eAGVSRSVLKALVKKGLLEIEEREVDRDPFAPD-VPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYLQ 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 237 VLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGV 316
Cdd:COG1198 234 AIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGL 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 317 IVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKG 396
Cdd:COG1198 314 IIVDEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDMRE 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 397 QKVQAG--LAPALITRMRQHLQANNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQQHLRCHHCDSQRPVPR 474
Cdd:COG1198 394 EPLEGGriLSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPK 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 475 QCPSCGSTHLVPVGLGTEQLEQTLAPLFPDVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLV 554
Cdd:COG1198 474 QCPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLV 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 555 ALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWT 634
Cdd:COG1198 554 GVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFG 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 635 SHVIVRAEDHNNQHAPLFLQQLRNLiLSSPLADDKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIISGTLALINT 714
Cdd:COG1198 634 RLALLRASGKDEEAAEEFAQALARA-LRALLSADGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLEK 712
|
730
....*....|....*..
gi 485691697 715 iPDSRKVKWVLDVDPIE 731
Cdd:COG1198 713 -PLPRKVRWSIDVDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
1-731 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 1072.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 1 MPVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQeRIGVVVSVSDVSELPLNELKAVVEVLDVEPVFTHSVWRL 80
Cdd:PRK05580 2 MKIARVLLPVPLPRPFDYLIPEGLEVQPGDRVRVPFGNRK-LIGVVVGVEEGSEVPADKLKPILEVLDLEPLLPPELLRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 81 LLWAADYYHHPIGDVLFHALPILLrqgrpaanapmwywfateqgqavdlnslkrspkqqqalaalrqgkiwrdqvaELEF 160
Cdd:PRK05580 81 LDWAADYYLSPLGEVLRLALLAEL----------------------------------------------------ALAA 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 161 NDAALQALRKKGLCDLASETPEFSDWRTNyaVSGERLRLNTEQATAVGAIHsAADTFSAWLLAGVTGSGKTEVYLSVLEN 240
Cdd:PRK05580 109 SSAVLKGLVKKGLIELEEVEVLRLRPPPD--PAFEPPTLNPEQAAAVEAIR-AAAGFSPFLLDGVTGSGKTEVYLQAIAE 185
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 241 VLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVID 320
Cdd:PRK05580 186 VLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVD 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 321 EEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLK---GQ 397
Cdd:PRK05580 266 EEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMRellRG 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 398 KVQAGLAPALITRMRQHLQANNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQQHLRCHHCDSQRPVPRQCP 477
Cdd:PRK05580 346 ENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACP 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 478 SCGSTHLVPVGLGTEQLEQTLAPLFPDVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALL 557
Cdd:PRK05580 426 ECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVL 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 558 DVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHV 637
Cdd:PRK05580 506 DADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFGRLA 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 638 IVRAEDHNNQHAPLFLQQLRNlILSSPLADDKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIISGTLALINTIPD 717
Cdd:PRK05580 586 LLRASAKDEEKAEKFAQQLAA-LLPNLLPLLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKLPQ 664
|
730
....*....|....
gi 485691697 718 SRKVKWVLDVDPIE 731
Cdd:PRK05580 665 ARKVRWSIDVDPQS 678
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
221-730 |
0e+00 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 833.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIV 300
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 301 IGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRR 380
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 381 AGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQANNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQQH 460
Cdd:TIGR00595 161 VSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 461 LRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPDVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQ 540
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 541 MLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQ 620
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 621 ALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLIlsSPLADDKLWVLGPVPALAPKRGGRWRWQILLQHPSRVR 700
Cdd:TIGR00595 401 ELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELL--KQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLV 478
|
490 500 510
....*....|....*....|....*....|
gi 485691697 701 LQHIISGTlaLINTIPDSrKVKWVLDVDPI 730
Cdd:TIGR00595 479 LQKLVNKT--LLKEIPSS-SVYCEVDVDPI 505
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
390-626 |
5.07e-130 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 385.06 E-value: 5.07e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 390 HVLDLKGQKVQAGLAPALITRMRQHLQANNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQQHLRCHHCDSQ 469
Cdd:cd18804 2 EIVDMKEEELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGYQ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 470 RPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPDVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFP 549
Cdd:cd18804 82 EPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDFP 161
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485691697 550 DVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERR 626
Cdd:cd18804 162 NVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAERK 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
203-380 |
1.14e-102 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 312.22 E-value: 1.14e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 203 QATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLND 282
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 283 SERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALE 362
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|....*...
gi 485691697 363 TLCNVQQKKYRLLRLTRR 380
Cdd:cd17929 161 SYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
2-632 |
6.58e-40 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 156.64 E-value: 6.58e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 2 PVAHVALPVPLP---RTFDYLLPEGMTVKA--GCRVRVPFGKQQ------ERigvvvsvsDVSELPLNELKAVVEVLDVE 70
Cdd:PRK14873 12 PVARVLPDLGLPhldRLFDYLVPEELSDDAqpGVRVRVRFGGRLvdgfvlER--------RSDSDHEGKLRWLERVVSPE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 71 PVFTHSVWRLLLWAADYYHHPIGDVLFHALPIllRQGR--PAANAPMWYWFATEqgqAVDLNSLKRSPKQQQALAALRQG 148
Cdd:PRK14873 84 PVLTPEIRRLARAVADRYAGTRADVLRLAVPP--RHARveKEPVATPPPPLTAP---PPDPSGWAAYGRGPRFLAALAAG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 149 KIWRdqvaelefndAALQALrkkglcdlasetPEfSDWRTNYAVsgerlrlnteqatAVGAihsaadtfsawllagvtgs 228
Cdd:PRK14873 159 RAAR----------AVWQAL------------PG-EDWARRLAA-------------AAAA------------------- 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 229 gktevylsvlenVLAQGKQALVMVPEIGLTPQTIARFRERFNA-PVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSAL 307
Cdd:PRK14873 184 ------------TLRAGRGALVVVPDQRDVDRLEAALRALLGAgDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAV 251
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 308 FTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALEtlcnVQQ-------KKYRLLRLTRR 380
Cdd:PRK14873 252 FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAE----AQAlvesgwaHDLVAPRPVVR 327
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 381 AgnARPAIQHVLDLKGQKVQAGLAPAL------ITRMRQHLQAnNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTL 454
Cdd:PRK14873 328 A--RAPRVRALGDSGLALERDPAARAArlpslaFRAARDALEH-GPVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGL 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 455 HQAQQHLRCHHCDSQRPVPRqCPSCGSTHLVPVGLGTEQLEQTLAPLFPDVPIsridrdTTSRKgalEQQLAEVhRGGAR 534
Cdd:PRK14873 405 PSAGGTPRCRWCGRAAPDWR-CPRCGSDRLRAVVVGARRTAEELGRAFPGVPV------VTSGG---DQVVDTV-DAGPA 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 535 ILIGT---QMLAKGHHfpdvTLVALLDVDGALFSADFRSAE----RFAQLYTQVAGRAgragkQGEVVLQTHHPEHPLLQ 607
Cdd:PRK14873 474 LVVATpgaEPRVEGGY----GAALLLDAWALLGRQDLRAAEdtlrRWMAAAALVRPRA-----DGGQVVVVAESSLPTVQ 544
|
650 660
....*....|....*....|....*
gi 485691697 608 TLLYKGYDAFAEQALAERRMMQLPP 632
Cdd:PRK14873 545 ALIRWDPVGHAERELAERAEVGFPP 569
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
6-101 |
1.10e-35 |
|
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.
Pssm-ID: 465491 [Multi-domain] Cd Length: 96 Bit Score: 129.89 E-value: 1.10e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 6 VALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQeRIGVVVSVSDVSELPLNELKAVVEVLDVEPVFTHSVWRLLLWAA 85
Cdd:pfam17764 2 VAVPLPLDRPFDYRVPEELAVKIGMRVLVPFGKRK-VTGIVVGLSEESEVDPEKLKPILEVLDEEPLLTPELLELARWMA 80
|
90
....*....|....*.
gi 485691697 86 DYYHHPIGDVLFHALP 101
Cdd:pfam17764 81 EYYLCPLGEVLRAALP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
218-358 |
8.63e-29 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 112.11 E-value: 8.63e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 218 SAWLLAGVTGSGKTEVYLSVLENVLA-QGKQALVMVPEIGLTPQTIARFRERF--NAPVEVLHSGLNDSERlsawLKAKN 294
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLkKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEER----EKNKL 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485691697 295 GEAAIVIGTRSALFTP--------FKNLGVIVIDEEHDSSYKQQEGWRYharDLAVYRAHSEQIPIILGSAT 358
Cdd:cd00046 78 GDADIIIATPDMLLNLllredrlfLKDLKLIIVDEAHALLIDSRGALIL---DLAVRKAGLKNAQVILLSAT 146
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
203-360 |
3.50e-22 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 93.85 E-value: 3.50e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 203 QATAVGAIHSAADTfsawLLAGVTGSGKTEVY-LSVLENV--LAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSG 279
Cdd:pfam00270 4 QAEAIPAILEGRDV----LVQAPTGSGKTLAFlLPALEALdkLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 280 LNDSERLSAWLKAKNgeAAIVIGTRSALFT------PFKNLGVIVIDEEHDSSYK-QQEGWRYHARDLavyrahSEQIPI 352
Cdd:pfam00270 80 LGGDSRKEQLEKLKG--PDILVGTPGRLLDllqerkLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRL------PKKRQI 151
|
....*...
gi 485691697 353 ILGSATPA 360
Cdd:pfam00270 152 LLLSATLP 159
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
632-729 |
7.71e-19 |
|
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB).
Pssm-ID: 465633 [Multi-domain] Cd Length: 96 Bit Score: 81.88 E-value: 7.71e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 632 PWTSHVIVRAEDHNNQHAPLFLQQLRNLiLSSPLADDKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIISGTLAL 711
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAEL-LKELLKLQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEE 79
|
90
....*....|....*...
gi 485691697 712 INTIPdSRKVKWVLDVDP 729
Cdd:pfam18074 80 LQKLP-KRKVRISIDVDP 96
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
221-334 |
2.10e-18 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 83.78 E-value: 2.10e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERF-NAPVEVLH-SGLNDSERLSAWLKA-KNGEA 297
Cdd:cd17991 40 LICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFaNFPVNVELlSRFTTAAEQREILEGlKEGKV 119
|
90 100 110
....*....|....*....|....*....|....*....
gi 485691697 298 AIVIGTRSALF--TPFKNLGVIVIDEEHDSSYKQQEGWR 334
Cdd:cd17991 120 DIVIGTHRLLSkdVEFKNLGLLIIDEEQRFGVKQKEKLK 158
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
221-362 |
1.57e-16 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 78.69 E-value: 1.57e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVY-LSVLENVLAQ-GKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAA 298
Cdd:smart00487 28 ILAAPTGSGKTLAAlLPALEALKRGkGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTD 107
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 485691697 299 IVIGTRSALF-------TPFKNLGVIVIDEEHDSSYKqqeGWRYHARDLAvyRAHSEQIPIILGSATPALE 362
Cdd:smart00487 108 ILVTTPGRLLdllendkLSLSNVDLVILDEAHRLLDG---GFGDQLEKLL--KLLPKNVQLLLLSATPPEE 173
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
221-364 |
6.70e-13 |
|
transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273152 [Multi-domain] Cd Length: 926 Bit Score: 72.39 E-value: 6.70e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERF-NAPV--EVLHSGLNDSERLSAWLKAKNGEA 297
Cdd:TIGR00580 476 LVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFaNFPVtiELLSRFRSAKEQNEILKELASGKI 555
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 485691697 298 AIVIGTRSALFTP--FKNLGVIVIDEEHDSSYKQQE---GWRYHARDLAVyrahseqipiilgSATPALETL 364
Cdd:TIGR00580 556 DILIGTHKLLQKDvkFKDLGLLIIDEEQRFGVKQKEklkELRTSVDVLTL-------------SATPIPRTL 614
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
221-359 |
3.18e-12 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 65.00 E-value: 3.18e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQG--KQALVMVPEIGLTPQTIARFRERFnaPVEVLHSGLNDSERLSAWLKAKNgeaa 298
Cdd:pfam04851 27 LIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFL--PNYVEIGEIISGDKKDESVDDNK---- 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 485691697 299 IVIGTRSALFTPFKNL---------GVIVIDEEHDSSYKqqeGWryhaRDLAVYRAHseqiPIILG-SATP 359
Cdd:pfam04851 101 IVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGAS---SY----RNILEYFKP----AFLLGlTATP 160
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
221-323 |
9.40e-12 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 68.25 E-value: 9.40e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVP-EIgLTPQ---TIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGE 296
Cdd:PRK10917 286 LLQGDVGSGKTVVAALAALAAIEAGYQAALMAPtEI-LAEQhyeNLKKLLEPLGIRVALLTGSLKGKERREILEAIASGE 364
|
90 100 110
....*....|....*....|....*....|
gi 485691697 297 AAIVIGTRsALFTP---FKNLGVIVIDEEH 323
Cdd:PRK10917 365 ADIVIGTH-ALIQDdveFHNLGLVIIDEQH 393
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
198-364 |
2.75e-11 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 62.82 E-value: 2.75e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 198 RLNTEQATAVGAIHS--AADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERF-NAPVE 274
Cdd:cd17918 15 SLTKDQAQAIKDIEKdlHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLpFINVE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 275 VLHSGlndserlsawLKAKNGEAA-IVIGTRSALF--TPFKNLGVIVIDEEHDSSYKQQEgwryhardlAVYRAhsEQIP 351
Cdd:cd17918 95 LVTGG----------TKAQILSGIsLLVGTHALLHldVKFKNLDLVIVDEQHRFGVAQRE---------ALYNL--GATH 153
|
170
....*....|...
gi 485691697 352 IILGSATPALETL 364
Cdd:cd17918 154 FLEATATPIPRTL 166
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
221-323 |
3.94e-11 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 66.23 E-value: 3.94e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVP-EIgLTPQ---TIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGE 296
Cdd:COG1200 284 LLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPtEI-LAEQhyrSLSKLLEPLGIRVALLTGSTKAKERREILAALASGE 362
|
90 100 110
....*....|....*....|....*....|
gi 485691697 297 AAIVIGTRsALFTP---FKNLGVIVIDEEH 323
Cdd:COG1200 363 ADIVVGTH-ALIQDdveFKNLGLVVIDEQH 391
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
221-323 |
4.67e-11 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 63.32 E-value: 4.67e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVP-EIgLTPQ---TIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGE 296
Cdd:cd17992 70 LLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQhydSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGE 148
|
90 100 110
....*....|....*....|....*....|
gi 485691697 297 AAIVIGTRsALFTP---FKNLGVIVIDEEH 323
Cdd:cd17992 149 IDIVIGTH-ALIQEdveFHNLGLVIIDEQH 177
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
445-471 |
3.32e-10 |
|
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA.
Pssm-ID: 465708 [Multi-domain] Cd Length: 27 Bit Score: 55.23 E-value: 3.32e-10
10 20
....*....|....*....|....*..
gi 485691697 445 CPRCDHYYTLHQAQQHLRCHHCDSQRP 471
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
492-589 |
4.17e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 51.06 E-value: 4.17e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 492 EQLEQTLAPLfpDVPISRIDRDTTSRKgaLEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALfsadfrsa 571
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEE--REEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSP-------- 68
|
90
....*....|....*...
gi 485691697 572 erfaQLYTQVAGRAGRAG 589
Cdd:smart00490 69 ----ASYIQRIGRAGRAG 82
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
220-425 |
6.58e-08 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 55.65 E-value: 6.58e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 220 WLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIG----LTPqtiaRFRERF-NAPVEVLHSGLNDSERLsawlkakn 294
Cdd:COG4098 132 HLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDvvleLAP----RLQQAFpGVDIAALYGGSEEKYRY-------- 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 295 geAAIVIGTRSALFTPFKNLGVIVIDE------EHDSSYKQqegwryhardlAVYRAHSEQIPIILGSATPALETLCNVQ 368
Cdd:COG4098 200 --AQLVIATTHQLLRFYQAFDLLIIDEvdafpySGDPMLQY-----------AVKRARKPDGKLIYLTATPSKALQRQVK 266
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 369 QKKYRLLRLTRR-AGNARPAIQHVLDLKGQKVQA--GLAPALITRMRQHLQANNQVILFL 425
Cdd:COG4098 267 RGKLKVVKLPARyHGHPLPVPKFKWLGNWKKRLRrgKLPRKLLKWLKKRLKEGRQLLIFV 326
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
202-364 |
3.07e-07 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 53.98 E-value: 3.07e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 202 EQATAVGAIHS------AADTfsawLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERF-NAPV- 273
Cdd:PRK10689 604 DQAQAINAVLSdmcqplAMDR----LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFaNWPVr 679
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 274 -EVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTP--FKNLGVIVIDEEHdssykqqegwRYHARDLAVYRAHSEQI 350
Cdd:PRK10689 680 iEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDvkWKDLGLLIVDEEH----------RFGVRHKERIKAMRADV 749
|
170
....*....|....
gi 485691697 351 PIILGSATPALETL 364
Cdd:PRK10689 750 DILTLTATPIPRTL 763
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
229-323 |
6.72e-07 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 53.15 E-value: 6.72e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 229 GKTEV-----YLSVLEnvlaqGKQalVMVpeigLTPQTI-AR-----FRERF-NAPVEVlhsglndsERLS--------- 287
Cdd:COG1197 619 GKTEValraaFKAVMD-----GKQ--VAV----LVPTTLlAQqhyetFKERFaGFPVRV--------EVLSrfrtakeqk 679
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 485691697 288 AWLKA-KNGEAAIVIGTrSALFTP---FKNLGVIVIDEEH 323
Cdd:COG1197 680 ETLEGlADGKVDIVIGT-HRLLSKdvkFKDLGLLIIDEEQ 718
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
199-358 |
3.04e-06 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 48.03 E-value: 3.04e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 199 LNTEQATAVGAIHSAADTFsawLLAGVTGSGKTEV-YLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFnapvevLH 277
Cdd:cd17921 2 LNPIQREALRALYLSGDSV---LVSAPTSSGKTLIaELAILRALATSGGKAVYIAPTRALVNQKEADLRERF------GP 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 278 SGLNDSERLSA--WLKAKNGEAAIVIGT----RSALFTP----FKNLGVIVIDEEH---DSSYkqqeGWRYHaRDLAVYR 344
Cdd:cd17921 73 LGKNVGLLTGDpsVNKLLLAEADILVATpeklDLLLRNGgerlIQDVRLVVVDEAHligDGER----GVVLE-LLLSRLL 147
|
170
....*....|....
gi 485691697 345 AHSEQIPIILGSAT 358
Cdd:cd17921 148 RINKNARFVGLSAT 161
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
535-598 |
9.44e-06 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 44.23 E-value: 9.44e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485691697 535 ILIGTQMLAKGHHFPDVTLVALLDVDgalfsadfrsaeRFAQLYTQVAGRAGRAGK-QGEVVLQT 598
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPP------------SSAASYIQRVGRAGRGGKdEGEVILFV 77
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
221-321 |
7.59e-05 |
|
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350683 [Multi-domain] Cd Length: 143 Bit Score: 43.44 E-value: 7.59e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERF-NAPVEVLHSGLNDserlsawlkaKNGEAAI 299
Cdd:cd17925 20 LVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFpGAAIVLLHGGSED----------QYQRSPL 89
|
90 100
....*....|....*....|..
gi 485691697 300 VIGTRSALFTPFKNLGVIVIDE 321
Cdd:cd17925 90 VIATTHQLLRFYRAFDLLIIDE 111
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
151-323 |
8.73e-05 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 45.79 E-value: 8.73e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 151 WRDQVAELEFNDAALQALRKKGLCDLASETPEFSDWRTNYAV---------SGERLRLNTEQATAVGAIHSAADT-FSAW 220
Cdd:COG1061 24 ERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAealeagdeaSGTSFELRPYQQEALEALLAALERgGGRG 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 221 LLAGVTGSGKTEVYLSVLENvLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSglndserlsawlkaKNGEAAIV 300
Cdd:COG1061 104 LVVAPTGTGKTVLALALAAE-LLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAGGGK--------------KDSDAPIT 168
|
170 180
....*....|....*....|....*....
gi 485691697 301 IGT-----RSALFTPFKNL-GVIVIDEEH 323
Cdd:COG1061 169 VATyqslaRRAHLDELGDRfGLVIIDEAH 197
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
198-323 |
9.21e-05 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 43.86 E-value: 9.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 198 RLNTEQATAVGAIHSAADTFsawLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEV-L 276
Cdd:cd18028 1 ELYPPQAEAVRAGLLKGENL---LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLEEIGLKVgI 77
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 485691697 277 HSGLNDSErlSAWLkaknGEAAIVIGTRSAL-----FTP--FKNLGVIVIDEEH 323
Cdd:cd18028 78 STGDYDED--DEWL----GDYDIIVATYEKFdsllrHSPswLRDVGVVVVDEIH 125
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
522-596 |
1.17e-04 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 42.49 E-value: 1.17e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485691697 522 EQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDvdgalFSADFRSaerfaqlYTQVAGRAGRAGKQGEVVL 596
Cdd:cd18787 67 ERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYD-----LPRDAED-------YVHRIGRTGRAGRKGTAIT 129
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
75-455 |
1.66e-04 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 45.07 E-value: 1.66e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 75 HSVWRLLLWAADYYHHPIGDVLFHALpILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRD- 153
Cdd:COG1203 15 LAALLLLLLALLLAALLLLLLAALLL-ALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLLLLIDADw 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 154 -QVAELEFNDAALQALRKKGLcdlASETPEFSDWRTnyavsgerlRLNTEQATAVGAIHSAADTFSAW-LLAGVTGSGKT 231
Cdd:COG1203 94 lDSANFDMARQALDHLLAERL---ERLLPKKSKPRT---------PINPLQNEALELALEAAEEEPGLfILTAPTGGGKT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 232 EVYLSV-LENVLAQGKQALVMV-PEIGLTPQTIARFRERFNAPVEVLHS--------GLNDSERLSAWLK--AKNGEAAI 299
Cdd:COG1203 162 EAALLFaLRLAAKHGGRRIIYAlPFTSIINQTYDRLRDLFGEDVLLHHSladldlleEEEEYESEARWLKllKELWDAPV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 300 VIGTR----SALFTPFK-------NLG--VIVIDEEHDssykqqegwrYHARDLA-----VYRAHSEQIPIILGSAT-PA 360
Cdd:COG1203 242 VVTTIdqlfESLFSNRKgqerrlhNLAnsVIILDEVQA----------YPPYMLAlllrlLEWLKNLGGSVILMTATlPP 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 361 LEtlcnvqqkKYRLLRLTRRAGNA--------RPAIQHVLDLKGQKVQaglAPALITRMRQHLQANNQVILFLNRRgfAP 432
Cdd:COG1203 312 LL--------REELLEAYELIPDEpeelpeyfRAFVRKRVELKEGPLS---DEELAELILEALHKGKSVLVIVNTV--KD 378
|
410 420
....*....|....*....|...
gi 485691697 433 ALLCHDcgWIAECPRCDHYYTLH 455
Cdd:COG1203 379 AQELYE--ALKEKLPDEEVYLLH 399
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
491-589 |
2.35e-04 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 41.04 E-value: 2.35e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 491 TEQLEQTLAPLFPDVPISRIDRDTTSRKgaLEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALfsadfrs 570
Cdd:pfam00271 25 KKTLEAELLLEKEGIKVARLHGDLSQEE--REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNP------- 95
|
90
....*....|....*....
gi 485691697 571 aerfaQLYTQVAGRAGRAG 589
Cdd:pfam00271 96 -----ASYIQRIGRAGRAG 109
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
226-359 |
7.93e-04 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 40.37 E-value: 7.93e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 226 TGSGKTEVYLSVLENvLAQGKqALVMVPEIGLTPQTIARFrERFNAPVEVlhsGLNDSERlsawlKAKNGEAAIVIGTRS 305
Cdd:cd17926 27 TGSGKTLTALALIAY-LKELR-TLIVVPTDALLDQWKERF-EDFLGDSSI---GLIGGGK-----KKDFDDANVVVATYQ 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 485691697 306 ALF-------TPFKNLGVIVIDEEHDSSYKqqeGWRY-HARDLAVYRahseqipiiLG-SATP 359
Cdd:cd17926 96 SLSnlaeeekDLFDQFGLLIVDEAHHLPAK---TFSEiLKELNAKYR---------LGlTATP 146
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
226-320 |
1.19e-03 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 40.77 E-value: 1.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 226 TGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIAR---FRERFNAPVEVL--HSGLNDSERLSAWLKAKNGEAAIV 300
Cdd:cd17924 41 TGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERlskYAEKAGVEVKILvyHSRLKKKEKEELLEKIEKGDFDIL 120
|
90 100
....*....|....*....|....*
gi 485691697 301 IGTRSALFTPFKNLG-----VIVID 320
Cdd:cd17924 121 VTTNQFLSKNFDLLSnkkfdFVFVD 145
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
226-360 |
3.09e-03 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 39.56 E-value: 3.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 226 TGSGKTEVYLSVLENVL-------AQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAA 298
Cdd:cd18034 25 TGSGKTLIAVMLIKEMGelnrkekNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEMGVDKWTKERWKEELEKYD 104
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485691697 299 IVIGT----RSAL---FTPFKNLGVIVIDEEHdssykqqegwryHARDLAVYR---------AHSEQIPIILG-SATPA 360
Cdd:cd18034 105 VLVMTaqilLDALrhgFLSLSDINLLIFDECH------------HATGDHPYArimkefyhlEGRTSRPRILGlTASPV 171
|
|
| COG2888 |
COG2888 |
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ... |
439-480 |
4.20e-03 |
|
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];
Pssm-ID: 442134 [Multi-domain] Cd Length: 52 Bit Score: 35.86 E-value: 4.20e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 485691697 439 CGW--------IAECPRCDHYytlhqaqQHLRCHHCDSQRPVPRQCPSCG 480
Cdd:COG2888 6 CGReiapeggvAFYCPNCGEA-------LIIRCPKCRKQSNALYFCPKCG 48
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
203-358 |
4.38e-03 |
|
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.
Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 39.05 E-value: 4.38e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 203 QATAVGAIHSAADTFsawLLAGvTGSGKTEVYLSVLenvLAQGKQALVMVPEIGLTPQTIARFRERfNAPVEVLHSGLND 282
Cdd:cd17920 17 QLEAINAVLAGRDVL---VVMP-TGGGKSLCYQLPA---LLLDGVTLVVSPLISLMQDQVDRLQQL-GIRAAALNSTLSP 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485691697 283 SERLSAWLKAKNGEAAIVI---------GTRSALFTP--FKNLGVIVIDEEHDSSykqQEG--WRYHARDLAVYRAHSEQ 349
Cdd:cd17920 89 EEKREVLLRIKNGQYKLLYvtperllspDFLELLQRLpeRKRLALIVVDEAHCVS---QWGhdFRPDYLRLGRLRRALPG 165
|
....*....
gi 485691697 350 IPIILGSAT 358
Cdd:cd17920 166 VPILALTAT 174
|
|
| DEXHc_UvrB |
cd17916 |
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) ... |
222-274 |
6.97e-03 |
|
DEXH-box helicase domain of excinuclease ABC subunit B; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II) and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350674 [Multi-domain] Cd Length: 299 Bit Score: 39.11 E-value: 6.97e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 485691697 222 LAGVTGSGKTevylSVLENVLAQ-GKQALVMVPEIGLTPQTIARFRERF--NApVE 274
Cdd:cd17916 33 LLGVTGSGKT----FTIANVIAQvNKPTLVIAHNKTLAAQLYSEFKEFFpeNA-VE 83
|
|
| |
