|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
1-730 |
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: 1091.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 1 MPVARVALPVPLARTFDYLLPDAMT-AAAGCRVRVPFGRQQLVGVVVAVGEESDLPRSELKSVVEVLDGASLYPPTLWRM 79
Cdd:COG1198 1 MKIAEVALPVPLDRPFDYLVPEGLElVQPGSRVLVPFGRRQVVGIVVGLKEESDVDPAKLKPILAVLDDEPLLPEELLEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 80 LLWAADYYHHPLGEVLLHALPVLLRQGKPASPAPLWYWFATEEGQAvdlnsLKRSPKQQQALAALRQ--GRLWRHEVAQM 157
Cdd:COG1198 81 LRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRLTLGEEL-----PKRAPKQRRVLEALREhgGPLTLSELAKE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 158 A-FNDAALQALRTKGLCELgSELPPVADWRSQFSVAGDRLRLNTEQATAVGAIRGEADNFCAWLLAGVTGSGKTEVYLSV 236
Cdd:COG1198 156 AgVSRSVLKALVKKGLLEI-EEREVDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYLQA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 237 LENTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGEAAIVIGTRSALFTPFKNLGVI 316
Cdd:COG1198 235 IAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGLI 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 317 VIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLHNVRQRKYRVLKLTHRAGNARPAQQHVLDLKGQ 396
Cdd:COG1198 315 IVDEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDMREE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 397 ALQAG--LAPALVARMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHQLRCHHCDSQRPVPRQ 474
Cdd:COG1198 395 PLEGGriLSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQ 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 475 CPGCGSTHLVPVGLGTEQLEQSLAPLFPGVPLSRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVA 554
Cdd:COG1198 475 CPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVG 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 555 LLDVDGALFCADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLHQGYDAFADQALAERSSVWLPPYSS 634
Cdd:COG1198 555 VLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFGR 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 635 HILIRAEDHHNQDAPAFLQQLRNLLQASpLADDKLWLLGPVPALQPKRGGRYRWQLLLQHPSRLQLQRIVAGSLPLVGTl 714
Cdd:COG1198 635 LALLRASGKDEEAAEEFAQALARALRAL-LSADGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLEK- 712
|
730
....*....|....*.
gi 742406948 715 PAARKVKWTLDVDPTE 730
Cdd:COG1198 713 PLPRKVRWSIDVDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
1-730 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 1048.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 1 MPVARVALPVPLARTFDYLLPDAMTAAAGCRVRVPFGRQQLVGVVVAVGEESDLPRSELKSVVEVLDGASLYPPTLWRML 80
Cdd:PRK05580 2 MKIARVLLPVPLPRPFDYLIPEGLEVQPGDRVRVPFGNRKLIGVVVGVEEGSEVPADKLKPILEVLDLEPLLPPELLRLL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 81 LWAADYYHHPLGEVLLHALPVLLRQgkpaspaplwywfateegqavdlnslkrspkqqqalaalrqgrlwrhevaqmAFN 160
Cdd:PRK05580 82 DWAADYYLSPLGEVLRLALLAELAL----------------------------------------------------AAS 109
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 161 DAALQALRTKGLCELGSELPPVADWRSQFsvAGDRLRLNTEQATAVGAIRgEADNFCAWLLAGVTGSGKTEVYLSVLENT 240
Cdd:PRK05580 110 SAVLKGLVKKGLIELEEVEVLRLRPPPDP--AFEPPTLNPEQAAAVEAIR-AAAGFSPFLLDGVTGSGKTEVYLQAIAEV 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 241 LAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGEAAIVIGTRSALFTPFKNLGVIVIDE 320
Cdd:PRK05580 187 LAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDE 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 321 EHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLHNVRQRKYRVLKLTHRAGNARPAQQHVLDLKGQALQA 400
Cdd:PRK05580 267 EHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMRELLRGE 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 401 ---GLAPALVARMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHQLRCHHCDSQRPVPRQCPG 477
Cdd:PRK05580 347 ngsFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPE 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 478 CGSTHLVPVGLGTEQLEQSLAPLFPGVPLSRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLD 557
Cdd:PRK05580 427 CGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLD 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 558 VDGALFCADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLHQGYDAFADQALAERSSVWLPPYSSHIL 637
Cdd:PRK05580 507 ADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFGRLAL 586
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 638 IRAEDHHNQDAPAFLQQLRNLLQASPLaDDKLWLLGPVPALQPKRGGRYRWQLLLQHPSRLQLQRIVAGSLPLVGTLPAA 717
Cdd:PRK05580 587 LRASAKDEEKAEKFAQQLAALLPNLLP-LLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKLPQA 665
|
730
....*....|...
gi 742406948 718 RKVKWTLDVDPTE 730
Cdd:PRK05580 666 RKVRWSIDVDPQS 678
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
220-728 |
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: 779.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGEAAIV 299
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 300 IGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLHNVRQRKYRVLKLTHR 379
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 380 AGNARPAQQHVLDLKGQALQAGLAPALVARMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHQ 459
Cdd:TIGR00595 161 VSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 460 LRCHHCDSQRPVPRQCPGCGSTHLVPVGLGTEQLEQSLAPLFPGVPLSRIDRDTTSRKGALEQQLAEVHRGGARILIGTQ 539
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 540 MLAKGHHFPDVTLVALLDVDGALFCADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLHQGYDAFADQ 619
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 620 ALAERSSVWLPPYSSHILIRAEDHHNQDAPAFLQQLRNLLqaSPLADDKLWLLGPVPALQPKRGGRYRWQLLLQHPSRLQ 699
Cdd:TIGR00595 401 ELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELL--KQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLV 478
|
490 500
....*....|....*....|....*....
gi 742406948 700 LQRIVAGSlpLVGTLPAArKVKWTLDVDP 728
Cdd:TIGR00595 479 LQKLVNKT--LLKEIPSS-SVYCEVDVDP 504
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
389-624 |
7.61e-126 |
|
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: 374.27 E-value: 7.61e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 389 HVLDLKGQALQAGLAPALVARMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHQLRCHHCDSQ 468
Cdd:cd18804 2 EIVDMKEEELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGYQ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 469 RPVPRQCPGCGSTHLVPVGLGTEQLEQSLAPLFPGVPLSRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFP 548
Cdd:cd18804 82 EPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDFP 161
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742406948 549 DVTLVALLDVDGALFCADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLHQGYDAFADQALAER 624
Cdd:cd18804 162 NVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAER 237
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
202-379 |
9.18e-100 |
|
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: 304.52 E-value: 9.18e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 202 QATAVGAIRGEADNFCAWLLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSALND 281
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 282 SERLAAWLKAKSGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALE 361
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|....*...
gi 742406948 362 TLHNVRQRKYRVLKLTHR 379
Cdd:cd17929 161 SYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
2-676 |
1.71e-38 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 152.40 E-value: 1.71e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 2 PVARVALPVPLA---RTFDYLLPDAMTAAA--GCRVRVPFGRQQLVGVVVAVGEESDlPRSELKSVVEVLDGASLYPPTL 76
Cdd:PRK14873 12 PVARVLPDLGLPhldRLFDYLVPEELSDDAqpGVRVRVRFGGRLVDGFVLERRSDSD-HEGKLRWLERVVSPEPVLTPEI 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 77 WRMLLWAADYYHHPLGEVLLHALPVllRQGK--PASPAPLWYWFATEEgqaVDLNSLKRSPKQQQALAALRQGRLWRhev 154
Cdd:PRK14873 91 RRLARAVADRYAGTRADVLRLAVPP--RHARveKEPVATPPPPLTAPP---PDPSGWAAYGRGPRFLAALAAGRAAR--- 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 155 aqmafndAALQALrtkglcelgselpPVADWRSQFsvagdrlrlnteqATAVGAirgeadnfcawllagvtgsgktevyl 234
Cdd:PRK14873 163 -------AVWQAL-------------PGEDWARRL-------------AAAAAA-------------------------- 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 235 svlenTLAQGKQALVLVPEIGLTPQTIARFRERFNA-PVEVLHSALNDSERLAAWLKAKSGEAAIVIGTRSALFTPFKNL 313
Cdd:PRK14873 184 -----TLRAGRGALVVVPDQRDVDRLEAALRALLGAgDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDL 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 314 GVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALET-----------LHNVRQRKYRVLKLTHRAGn 382
Cdd:PRK14873 259 GLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAqalvesgwahdLVAPRPVVRARAPRVRALG- 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 383 aRPAQQHVLDLkgQALQAGLAPALVARMRQHLQADnQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHQLRC 462
Cdd:PRK14873 338 -DSGLALERDP--AARAARLPSLAFRAARDALEHG-PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRC 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 463 HHCDSQRPVPRqCPGCGSTHLVPVGLGTEQLEQSLAPLFPGVPLsridrdTTSRKgalEQQLAEVhRGGARILIGT---Q 539
Cdd:PRK14873 414 RWCGRAAPDWR-CPRCGSDRLRAVVVGARRTAEELGRAFPGVPV------VTSGG---DQVVDTV-DAGPALVVATpgaE 482
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 540 MLAKGHHfpdvTLVALLDVDGALFCADFRSAE----RFAQLYTQVAGRAgragkQGEVVLQTHHPEHPLLQTLLHQGYDA 615
Cdd:PRK14873 483 PRVEGGY----GAALLLDAWALLGRQDLRAAEdtlrRWMAAAALVRPRA-----DGGQVVVVAESSLPTVQALIRWDPVG 553
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742406948 616 FADQALAERSSVWLPPYSSHILIRAedhhnqdAPAFLQQLRNLLQASPLADdklwLLGPVP 676
Cdd:PRK14873 554 HAERELAERAEVGFPPAVRMAAVDG-------RPAAVAALLEAAGLPDGAE----VLGPVP 603
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
5-100 |
1.53e-32 |
|
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: 121.03 E-value: 1.53e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 5 RVALPVPLARTFDYLLPDAMTAAAGCRVRVPFGRQQLVGVVVAVGEESDLPRSELKSVVEVLDGASLYPPTLWRMLLWAA 84
Cdd:pfam17764 1 EVAVPLPLDRPFDYRVPEELAVKIGMRVLVPFGKRKVTGIVVGLSEESEVDPEKLKPILEVLDEEPLLTPELLELARWMA 80
|
90
....*....|....*.
gi 742406948 85 DYYHHPLGEVLLHALP 100
Cdd:pfam17764 81 EYYLCPLGEVLRAALP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
219-357 |
2.81e-28 |
|
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: 110.57 E-value: 2.81e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 219 WLLAGVTGSGKTEVYLSVLE-NTLAQGKQALVLVPEIGLTPQTIARFRERF--NAPVEVLHSALNDSERLAAWLkaksGE 295
Cdd:cd00046 4 VLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEEREKNKL----GD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 296 AAIVIGTRSALFTP--------FKNLGVIVIDEEHDSSYKQQEGWRYharDLAVYRAHSEQIPIILGSAT 357
Cdd:cd00046 80 ADIIIATPDMLLNLllredrlfLKDLKLIIVDEAHALLIDSRGALIL---DLAVRKAGLKNAQVILLSAT 146
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
631-728 |
5.28e-22 |
|
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: 91.13 E-value: 5.28e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 631 PYSSHILIRAEDHHNQDAPAFLQQLRNLLQASpLADDKLWLLGPVPALQPKRGGRYRWQLLLQHPSRLQLQRIVAGSLPL 710
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAELLKEL-LKLQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEE 79
|
90
....*....|....*...
gi 742406948 711 VGTLPaARKVKWTLDVDP 728
Cdd:pfam18074 80 LQKLP-KRKVRISIDVDP 96
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
202-359 |
3.95e-21 |
|
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: 90.76 E-value: 3.95e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 202 QATAVGAIRGEADNfcawLLAGVTGSGKTEVY-LSVLE--NTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSA 278
Cdd:pfam00270 4 QAEAIPAILEGRDV----LVQAPTGSGKTLAFlLPALEalDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 279 LNDSERLAAWLKAKsgEAAIVIGTRSALFT------PFKNLGVIVIDEEHDSSYK-QQEGWRYHARDLavyrahSEQIPI 351
Cdd:pfam00270 80 LGGDSRKEQLEKLK--GPDILVGTPGRLLDllqerkLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRL------PKKRQI 151
|
....*...
gi 742406948 352 ILGSATPA 359
Cdd:pfam00270 152 LLLSATLP 159
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
202-389 |
5.31e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 82.93 E-value: 5.31e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 202 QATAVGAIRGEADNFcawLLAGVTGSGKTEVYLSVLENTLAQG--KQALVLVPEIGLTPQTIARFRERFNAPVEVLHSAL 279
Cdd:smart00487 13 QKEAIEALLSGLRDV---ILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLY 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 280 NDSERLAAWLKAKSGEAAIVIGTRSALF-------TPFKNLGVIVIDEEHDSSYKqqeGWRYHARDLAvyRAHSEQIPII 352
Cdd:smart00487 90 GGDSKREQLRKLESGKTDILVTTPGRLLdllendkLSLSNVDLVILDEAHRLLDG---GFGDQLEKLL--KLLPKNVQLL 164
|
170 180 190
....*....|....*....|....*....|....*..
gi 742406948 353 LGSATPALETLHNVRQRKYRVLKLTHRAGNARPAQQH 389
Cdd:smart00487 165 LLSATPPEEIENLLELFLNDPVFIDVGFTPLEPIEQF 201
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
220-364 |
1.19e-17 |
|
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: 81.85 E-value: 1.19e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERF-NAPVEV--LHSALNDSERLAAWLKAKSGEA 296
Cdd:cd17991 40 LICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFaNFPVNVelLSRFTTAAEQREILEGLKEGKV 119
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 297 AIVIGTRSALF--TPFKNLGVIVIDEEHDSSYKQQEGWryhardlavyRAHSEQIPIILGSATPALETLH 364
Cdd:cd17991 120 DIVIGTHRLLSkdVEFKNLGLLIIDEEQRFGVKQKEKL----------KELRPNVDVLTLSATPIPRTLH 179
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
201-364 |
1.36e-14 |
|
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: 77.78 E-value: 1.36e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 201 EQATAVGAIRGEADNFCAW--LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERF-NAPV--EVL 275
Cdd:TIGR00580 455 DQLKAIEEIKADMESPRPMdrLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFaNFPVtiELL 534
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 276 HSALNDSERLAAWLKAKSGEAAIVIGTRSALFTP--FKNLGVIVIDEEHDSSYKQQE---GWRYHARDLAVyrahseqip 350
Cdd:TIGR00580 535 SRFRSAKEQNEILKELASGKIDILIGTHKLLQKDvkFKDLGLLIIDEEQRFGVKQKEklkELRTSVDVLTL--------- 605
|
170
....*....|....
gi 742406948 351 iilgSATPALETLH 364
Cdd:TIGR00580 606 ----SATPIPRTLH 615
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
220-358 |
1.01e-11 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 63.85 E-value: 1.01e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQG--KQALVLVPEIGLTPQTIARFRERFnaPVEVLHSALNDSERlaawLKAKSGEAA 297
Cdd:pfam04851 27 LIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFL--PNYVEIGEIISGDK----KDESVDDNK 100
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742406948 298 IVIGTRSALFTPFKNL---------GVIVIDEEHDSSYKqqeGWryhaRDLAVYRAHseqiPIILG-SATP 358
Cdd:pfam04851 101 IVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGAS---SY----RNILEYFKP----AFLLGlTATP 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
197-363 |
4.30e-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: 62.43 E-value: 4.30e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 197 RLNTEQATAVGAIRGEADNFCAW--LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERF-NAPVE 273
Cdd:cd17918 15 SLTKDQAQAIKDIEKDLHSPEPMdrLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLpFINVE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 274 VLHSALNDserlaawlKAKSGeAAIVIGTRSALF--TPFKNLGVIVIDEEHDSSYKQQEgwryhardlAVYRAhsEQIPI 351
Cdd:cd17918 95 LVTGGTKA--------QILSG-ISLLVGTHALLHldVKFKNLDLVIVDEQHRFGVAQRE---------ALYNL--GATHF 154
|
170
....*....|..
gi 742406948 352 ILGSATPALETL 363
Cdd:cd17918 155 LEATATPIPRTL 166
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
220-322 |
2.11e-10 |
|
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: 61.39 E-value: 2.11e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVP-EIgLTPQ---TIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGE 295
Cdd:cd17992 70 LLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQhydSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGE 148
|
90 100 110
....*....|....*....|....*....|
gi 742406948 296 AAIVIGTRsALFTP---FKNLGVIVIDEEH 322
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 ... |
444-470 |
2.84e-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: 55.61 E-value: 2.84e-10
10 20
....*....|....*....|....*..
gi 742406948 444 CPRCDHYYTLHQAQHQLRCHHCDSQRP 470
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
220-322 |
3.80e-10 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 63.25 E-value: 3.80e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVP-EIgLTPQ---TIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGE 295
Cdd:PRK10917 286 LLQGDVGSGKTVVAALAALAAIEAGYQAALMAPtEI-LAEQhyeNLKKLLEPLGIRVALLTGSLKGKERREILEAIASGE 364
|
90 100 110
....*....|....*....|....*....|
gi 742406948 296 AAIVIGTRsALFTP---FKNLGVIVIDEEH 322
Cdd:PRK10917 365 ADIVIGTH-ALIQDdveFHNLGLVIIDEQH 393
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
220-322 |
5.11e-10 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 62.76 E-value: 5.11e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEV----YLSVLENtlaqGKQALVLVP-EIgLTPQ---TIARFRERFNAPVEVLHSALNDSERLAAWLKA 291
Cdd:COG1200 284 LLQGDVGSGKTVVallaMLAAVEA----GYQAALMAPtEI-LAEQhyrSLSKLLEPLGIRVALLTGSTKAKERREILAAL 358
|
90 100 110
....*....|....*....|....*....|....
gi 742406948 292 KSGEAAIVIGTRsALFTP---FKNLGVIVIDEEH 322
Cdd:COG1200 359 ASGEADIVVGTH-ALIQDdveFKNLGLVVIDEQH 391
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
491-588 |
9.73e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 49.90 E-value: 9.73e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 491 EQLEQSLAPLfpGVPLSRIDRDTTSRKgaLEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALfcadfrsa 570
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEE--REEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSP-------- 68
|
90
....*....|....*...
gi 742406948 571 erfaQLYTQVAGRAGRAG 588
Cdd:smart00490 69 ----ASYIQRIGRAGRAG 82
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
197-322 |
1.09e-07 |
|
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: 52.34 E-value: 1.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 197 RLNTEQATAVGAIRGEADNFcawLLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLH 276
Cdd:cd18028 1 ELYPPQAEAVRAGLLKGENL---LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLEEIGLKVGI 77
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 742406948 277 SaLNDSERLAAWLkaksGEAAIVIGTRSAL-----FTP--FKNLGVIVIDEEH 322
Cdd:cd18028 78 S-TGDYDEDDEWL----GDYDIIVATYEKFdsllrHSPswLRDVGVVVVDEIH 125
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
220-363 |
1.31e-07 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 55.14 E-value: 1.31e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERF-NAPV--EVLHSALNDSERLAAWLKAKSGEA 296
Cdd:PRK10689 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFaNWPVriEMLSRFRSAKEQTQILAEAAEGKI 704
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742406948 297 AIVIGTRSALFTP--FKNLGVIVIDEEHdssykqqegwRYHARDLAVYRAHSEQIPIILGSATPALETL 363
Cdd:PRK10689 705 DILIGTHKLLQSDvkWKDLGLLIVDEEH----------RFGVRHKERIKAMRADVDILTLTATPIPRTL 763
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
228-322 |
6.16e-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: 6.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 228 GKTEV-----YLSVLEntlaqGKQALVLVPeiglTpqTI-AR-----FRERF-NAPV--EVLhSALNDSERLAAWLKA-K 292
Cdd:COG1197 619 GKTEValraaFKAVMD-----GKQVAVLVP----T--TLlAQqhyetFKERFaGFPVrvEVL-SRFRTAKEQKETLEGlA 686
|
90 100 110
....*....|....*....|....*....|...
gi 742406948 293 SGEAAIVIGTrSALFTP---FKNLGVIVIDEEH 322
Cdd:COG1197 687 DGKVDIVIGT-HRLLSKdvkFKDLGLLIIDEEQ 718
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
198-357 |
1.12e-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: 49.57 E-value: 1.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 198 LNTEQATAVGAIRGEADNFcawLLAGVTGSGKTEV-YLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERFnapvevLH 276
Cdd:cd17921 2 LNPIQREALRALYLSGDSV---LVSAPTSSGKTLIaELAILRALATSGGKAVYIAPTRALVNQKEADLRERF------GP 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 277 SALNDSERL--AAWLKAKSGEAAIVIGT----RSALFTP----FKNLGVIVIDEEH---DSSYkqqeGWRYHaRDLAVYR 343
Cdd:cd17921 73 LGKNVGLLTgdPSVNKLLLAEADILVATpeklDLLLRNGgerlIQDVRLVVVDEAHligDGER----GVVLE-LLLSRLL 147
|
170
....*....|....
gi 742406948 344 AHSEQIPIILGSAT 357
Cdd:cd17921 148 RINKNARFVGLSAT 161
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
219-424 |
6.12e-06 |
|
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: 49.49 E-value: 6.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 219 WLLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIG----LTPqtiaRFRERF-NAPVEVLHSalnDSERlaawlkaKS 293
Cdd:COG4098 132 HLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDvvleLAP----RLQQAFpGVDIAALYG---GSEE-------KY 197
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 294 GEAAIVIGTRSALFTPFKNLGVIVIDE------EHDSSYKQqegwryhardlAVYRAHSEQIPIILGSATPALETLHNVR 367
Cdd:COG4098 198 RYAQLVIATTHQLLRFYQAFDLLIIDEvdafpySGDPMLQY-----------AVKRARKPDGKLIYLTATPSKALQRQVK 266
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 368 QRKYRVLKLTHR-AGNARPAQQHVL--DLKGQALQAGLAPALVARMRQHLQADNQVILFL 424
Cdd:COG4098 267 RGKLKVVKLPARyHGHPLPVPKFKWlgNWKKRLRRGKLPRKLLKWLKKRLKEGRQLLIFV 326
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
534-597 |
9.42e-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: 9.42e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742406948 534 ILIGTQMLAKGHHFPDVTLVALLDVDgalfcadfrsaeRFAQLYTQVAGRAGRAGK-QGEVVLQT 597
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPP------------SSAASYIQRVGRAGRGGKdEGEVILFV 77
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
191-322 |
1.10e-05 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 48.87 E-value: 1.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 191 VAGDRLRLNTEQATAVGAIRGE-ADNFCAWLLAGVTGSGKTEVYLSVLENtLAQGKQALVLVPEIGLTPQTIARFRERFN 269
Cdd:COG1061 74 ASGTSFELRPYQQEALEALLAAlERGGGRGLVVAPTGTGKTVLALALAAE-LLRGKRVLVLVPRRELLEQWAEELRRFLG 152
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 742406948 270 APVEVLHSalndserlaawlkaKSGEAAIVIGT-----RSALFTPFKNL-GVIVIDEEH 322
Cdd:COG1061 153 DPLAGGGK--------------KDSDAPITVATyqslaRRAHLDELGDRfGLVIIDEAH 197
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
503-595 |
4.54e-05 |
|
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: 43.65 E-value: 4.54e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 503 GVPLSRI--DRDTTSRKGALEQqlaeVHRGGARILIGTQMLAKGHHFPDVTLVALLDvdgalFCADFRSaerfaqlYTQV 580
Cdd:cd18787 51 GIKVAALhgDLSQEERERALKK----FRSGKVRVLVATDVAARGLDIPGVDHVINYD-----LPRDAED-------YVHR 114
|
90
....*....|....*
gi 742406948 581 AGRAGRAGKQGEVVL 595
Cdd:cd18787 115 IGRTGRAGRKGTAIT 129
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
490-588 |
2.46e-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: 2.46e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 490 TEQLEQSLAPLFPGVPLSRIDRDTTSRKgaLEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALfcadfrs 569
Cdd:pfam00271 25 KKTLEAELLLEKEGIKVARLHGDLSQEE--REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNP------- 95
|
90
....*....|....*....
gi 742406948 570 aerfaQLYTQVAGRAGRAG 588
Cdd:pfam00271 96 -----ASYIQRIGRAGRAG 109
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
220-320 |
3.92e-04 |
|
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: 41.13 E-value: 3.92e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 220 LLAGVTGSGKTEVYLSVLENTLAQGKQALVLVPEIGLTPQTIARFRERF-NAPVEVLHSalnDSErlaawlkAKSGEAAI 298
Cdd:cd17925 20 LVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFpGAAIVLLHG---GSE-------DQYQRSPL 89
|
90 100
....*....|....*....|..
gi 742406948 299 VIGTRSALFTPFKNLGVIVIDE 320
Cdd:cd17925 90 VIATTHQLLRFYRAFDLLIIDE 111
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
76-454 |
4.15e-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: 43.53 E-value: 4.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 76 LWRMLLWAADYYHHPLGEVLLHALPVLLRQGKPASPAPLWYWFATEEGQAVDLNSLKRSPKQQQALAALRQGRLW----- 150
Cdd:COG1203 11 GALALAALLLLLLALLLAALLLLLLAALLLALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLlllid 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 151 --RHEVAQMAFNDAALQALRTKGLCELgseLPPVADWRSQFsvagDRLRlnTEQATAVGAIRGEADNFCawLLAGVTGSG 228
Cdd:COG1203 91 adWLDSANFDMARQALDHLLAERLERL---LPKKSKPRTPI----NPLQ--NEALELALEAAEEEPGLF--ILTAPTGGG 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 229 KTEVYLSV-LENTLAQGKQALVLV-PEIGLTPQTIARFRERFNAPVEVLHSAL--------NDSERLAAWLK--AKSGEA 296
Cdd:COG1203 160 KTEAALLFaLRLAAKHGGRRIIYAlPFTSIINQTYDRLRDLFGEDVLLHHSLAdldlleeeEEYESEARWLKllKELWDA 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 297 AIVIGTR----SALFTPFK-------NLG--VIVIDEEHDssykqqegwrYHARDLA-----VYRAHSEQIPIILGSAT- 357
Cdd:COG1203 240 PVVVTTIdqlfESLFSNRKgqerrlhNLAnsVIILDEVQA----------YPPYMLAlllrlLEWLKNLGGSVILMTATl 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 358 PALEtlhnvRQRKYRVLKL-----THRAGNARPAQQHVLDLKGQALQaglAPALVARMRQHLQADNQVILFLNRRgfAPA 432
Cdd:COG1203 310 PPLL-----REELLEAYELipdepEELPEYFRAFVRKRVELKEGPLS---DEELAELILEALHKGKSVLVIVNTV--KDA 379
|
410 420
....*....|....*....|..
gi 742406948 433 LLCHDcgWIAECPRCDHYYTLH 454
Cdd:COG1203 380 QELYE--ALKEKLPDEEVYLLH 399
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
225-377 |
6.32e-04 |
|
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: 41.75 E-value: 6.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 225 TGSGKTEVY-LSvlenTLAQGKQALVLVPEIGLTPQTIARFRERfNAPVEVLHSALNDSERLAAWLKAKSGEAAIVI--- 300
Cdd:cd17920 36 TGGGKSLCYqLP----ALLLDGVTLVVSPLISLMQDQVDRLQQL-GIRAAALNSTLSPEEKREVLLRIKNGQYKLLYvtp 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 301 ------GTRSALFTP--FKNLGVIVIDEEHDSSykqQEG--WRYHARDLAVYRAHSEQIPIILGSATPALETLHNVRQRk 370
Cdd:cd17920 111 erllspDFLELLQRLpeRKRLALIVVDEAHCVS---QWGhdFRPDYLRLGRLRRALPGVPILALTATATPEVREDILKR- 186
|
....*..
gi 742406948 371 yrvLKLT 377
Cdd:cd17920 187 ---LGLR 190
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
225-358 |
7.84e-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: 7.84e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 225 TGSGKTEVYLSVLENTLAQGkqALVLVPEIGLTPQTIARFrERFNAPVEVLhsaLNDSERlaawlKAKSGEAAIVIGTRS 304
Cdd:cd17926 27 TGSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERF-EDFLGDSSIG---LIGGGK-----KKDFDDANVVVATYQ 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742406948 305 ALF-------TPFKNLGVIVIDEEHDSSYKqqeGWRY-HARDLAVYRahseqipiiLG-SATP 358
Cdd:cd17926 96 SLSnlaeeekDLFDQFGLLIVDEAHHLPAK---TFSEiLKELNAKYR---------LGlTATP 146
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
225-359 |
8.90e-04 |
|
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: 41.10 E-value: 8.90e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 225 TGSGKTEVYLSVLE-------NTLAQGKQALVLVPEIGLTPQTIARFRERFNAPVEVLHSALNDSERLAAWLKAKSGEAA 297
Cdd:cd18034 25 TGSGKTLIAVMLIKemgelnrKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEMGVDKWTKERWKEELEKYD 104
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742406948 298 IVIGT----RSAL---FTPFKNLGVIVIDEEHdssykqqegwryHARDLAVYR---------AHSEQIPIILG-SATPA 359
Cdd:cd18034 105 VLVMTaqilLDALrhgFLSLSDINLLIFDECH------------HATGDHPYArimkefyhlEGRTSRPRILGlTASPV 171
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
196-325 |
2.32e-03 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members 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: 350794 [Multi-domain] Cd Length: 204 Bit Score: 40.15 E-value: 2.32e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 196 LRLNTEQATAV-GAIRGEADNFCAwllagVTGSGKTEVYLSVLENTL----AQGKQA--LVLVPEIGLTPQTIARFRERF 268
Cdd:cd18036 1 LELRNYQLELVlPALRGKNTIICA-----PTGSGKTRVAVYICRHHLekrrSAGEKGrvVVLVNKVPLVEQQLEKFFKYF 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 742406948 269 NAPVEVlhSALNDSERLaawlkaKSGEAAIVIGTRSALFTP-----------------FKNLGVIVIDEEHDSS 325
Cdd:cd18036 76 RKGYKV--TGLSGDSSH------KVSFGQIVKASDVIICTPqilinnllsgreeervyLSDFSLLIFDECHHTQ 141
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
198-322 |
3.58e-03 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 40.65 E-value: 3.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742406948 198 LNTEQATAVGAIRGEADNFcawLLAGVTGSGKTEV-YLSVLeNTLAQGKQALVLVPEIGLTPQTIARFRERF---NAPVE 273
Cdd:COG1204 23 LYPPQAEALEAGLLEGKNL---VVSAPTASGKTLIaELAIL-KALLNGGKALYIVPLRALASEKYREFKRDFeelGIKVG 98
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 742406948 274 VLHSALNDSERLAawlkaksGEAAIVIGT----RSAL---FTPFKNLGVIVIDEEH 322
Cdd:COG1204 99 VSTGDYDSDDEWL-------GRYDILVATpeklDSLLrngPSWLRDVDLVVVDEAH 147
|
|
| |
