|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
5-737 |
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: 1104.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 5 ILRLALPSPLRRLFDYRAPRGIPRsaLQPGIRLLLPFGRRELVGVLIEVTDRSEVPEDKLKPALRVLDAKPPMPAHLLEL 84
Cdd:COG1198 3 IAEVALPVPLDRPFDYLVPEGLEL--VQPGSRVLVPFGRRQVVGIVVGLKEESDVDPAKLKPILAVLDDEPLLPEELLEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 85 CRWTAQYYQHSLGDTLSWALPNLLRQGEPAEARQQRFWHATAQSSLDdprlARAPRQRQALAILKQHPHGVS-HELLNQL 163
Cdd:COG1198 81 LRWVADYYLCPLGEVLRLALPAGLRQGYPARIKTERYVRLTLGEELP----KRAPKQRRVLEALREHGGPLTlSELAKEA 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 164 EINKDSLDLLKEKGLVELEVRRHSTPPREGGWLAQAELPLNPEQRAAFEAVRASHGGFHCFLLAGVTGSGKTEVYLQLIR 243
Cdd:COG1198 157 GVSRSVLKALVKKGLLEIEEREVDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYLQAIA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 244 ETLAAGRQALVLIPEINLGPQTLARFERRFNARIALLHSALTDRERLDAWLAARDGEADIVIGTRSALFTPLKRPGLIIV 323
Cdd:COG1198 237 EVLAQGKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGLIIV 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 324 DEEHDASYKQQDGLRYHARDLALVRARLENVPILLGSATPALESLHNAQAGRYGLLRLTQRAGGAHPPKFIRLDVKSMPL 403
Cdd:COG1198 317 DEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDMREEPL 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 404 DAG--LSRPLQQAIGDTLAAGQQVLVFLNRRGFAPTLLCHDCGWISQCPRCDARMTVHQGSGELRCHHCDHRQRPPMNCP 481
Cdd:COG1198 397 EGGriLSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCP 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 482 QCGKLDLRPLGAGTERAEERLRILFPNHPVLRIDRDSTSRKHAMRDLFATINSGEPCILVGTQMLAKGHHFPRVTLVAIL 561
Cdd:COG1198 477 ECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVL 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 562 DADGGLFSADFRASERMAQQIVQVAGRAGRAEEPGRVLIQTHLADHPLLVQLTEDGYFAFAEQALSERRAAGLPPFAHLA 641
Cdd:COG1198 557 DADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFGRLA 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 642 LLRAEAHKPGQAEAFLDSACSAAEQLLEQmggPEVELLGPVPAPMERRAGKHRAQLLLQCMSRAPLHRLLTPWLQSLEQl 721
Cdd:COG1198 637 LLRASGKDEEAAEEFAQALARALRALLSA---DGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLEK- 712
|
730
....*....|....*.
gi 15600243 722 PGGRQVRWSLDIDPID 737
Cdd:COG1198 713 PLPRKVRWSIDVDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
5-738 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 1023.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 5 ILRLALPSPLRRLFDYRAPRGIPrsaLQPGIRLLLPFGRRELVGVLIEVTDRSEVPEDKLKPALRVLDAKPPMPAHLLEL 84
Cdd:PRK05580 4 IARVLLPVPLPRPFDYLIPEGLE---VQPGDRVRVPFGNRKLIGVVVGVEEGSEVPADKLKPILEVLDLEPLLPPELLRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 85 CRWTAQYYQHSLGDTLSWALPNLLrqgepaearqqrfwhataqsslddprlaraprqrqalailkqhphgvshellnQLE 164
Cdd:PRK05580 81 LDWAADYYLSPLGEVLRLALLAEL-----------------------------------------------------ALA 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 165 INKDSLDLLKEKGLVELEVRRHSTPPREGgWLAQAELPLNPEQRAAFEAVRAShGGFHCFLLAGVTGSGKTEVYLQLIRE 244
Cdd:PRK05580 108 ASSAVLKGLVKKGLIELEEVEVLRLRPPP-DPAFEPPTLNPEQAAAVEAIRAA-AGFSPFLLDGVTGSGKTEVYLQAIAE 185
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 245 TLAAGRQALVLIPEINLGPQTLARFERRFNARIALLHSALTDRERLDAWLAARDGEADIVIGTRSALFTPLKRPGLIIVD 324
Cdd:PRK05580 186 VLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVD 265
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 325 EEHDASYKQQDGLRYHARDLALVRARLENVPILLGSATPALESLHNAQAGRYGLLRLTQRAGGAHPPKFIRLDVKSMPLD 404
Cdd:PRK05580 266 EEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMRELLRG 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 405 A---GLSRPLQQAIGDTLAAGQQVLVFLNRRGFAPTLLCHDCGWISQCPRCDARMTVHQGSGELRCHHCDHRQRPPMNCP 481
Cdd:PRK05580 346 EngsFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACP 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 482 QCGKLDLRPLGAGTERAEERLRILFPNHPVLRIDRDSTSRKHAMRDLFATINSGEPCILVGTQMLAKGHHFPRVTLVAIL 561
Cdd:PRK05580 426 ECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVL 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 562 DADGGLFSADFRASERMAQQIVQVAGRAGRAEEPGRVLIQTHLADHPLLVQLTEDGYFAFAEQALSERRAAGLPPFAHLA 641
Cdd:PRK05580 506 DADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFGRLA 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 642 LLRAEAHKPGQAEAFLDSACSAAEQLLeqmGGPEVELLGPVPAPMERRAGKHRAQLLLQCMSRAPLHRLLTPWLQSLEQL 721
Cdd:PRK05580 586 LLRASAKDEEKAEKFAQQLAALLPNLL---PLLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKL 662
|
730
....*....|....*..
gi 15600243 722 PGGRQVRWSLDIDPIDL 738
Cdd:PRK05580 663 PQARKVRWSIDVDPQSF 679
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
225-736 |
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: 642.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRFNARIALLHSALTDRERLDAWLAARDGEADIV 304
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 305 IGTRSALFTPLKRPGLIIVDEEHDASYKQQDGLRYHARDLALVRARLENVPILLGSATPALESLHNAQAGRYGLLRLTQR 384
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 385 AGGAHPPKFIRLDVKSMPLDAGLSRPLQQAIGDTLAAGQQVLVFLNRRGFAPTLLCHDCGWISQCPRCDARMTVHQGSGE 464
Cdd:TIGR00595 161 VSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 465 LRCHHCDHRQRPPMNCPQCGKLDLRPLGAGTERAEERLRILFPNHPVLRIDRDSTSRKHAMRDLFATINSGEPCILVGTQ 544
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 545 MLAKGHHFPRVTLVAILDADGGLFSADFRASERMAQQIVQVAGRAGRAEEPGRVLIQTHLADHPLLVQLTEDGYFAFAEQ 624
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 625 ALSERRAAGLPPFAHLALLRAEAHKPGQAEAFldsaCSAAEQLLEQMGGPEVELLGPVPAPMERRAGKHRAQLLLQCMSR 704
Cdd:TIGR00595 401 ELAQRRALNYPPFTRLIRLIFRGKNEEKAQQT----AQAAHELLKQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSF 476
|
490 500 510
....*....|....*....|....*....|..
gi 15600243 705 APLHRLLTPWLqsLEQLPgGRQVRWSLDIDPI 736
Cdd:TIGR00595 477 LVLQKLVNKTL--LKEIP-SSSVYCEVDVDPI 505
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
396-630 |
1.23e-115 |
|
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: 348.08 E-value: 1.23e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 396 LDVKSMPLDAGLSRPLQQAIGDTLAAGQQVLVFLNRRGFAPTLLCHDCGWISQCPRCDARMTVHQGSGELRCHHCDHRQR 475
Cdd:cd18804 4 VDMKEEELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGYQEP 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 476 PPMNCPQCGKLDLRPLGAGTERAEERLRILFPNHPVLRIDRDSTSRKHAMRDLFATINSGEPCILVGTQMLAKGHHFPRV 555
Cdd:cd18804 84 IPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNV 163
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600243 556 TLVAILDADGGLFSADFRASERMAQQIVQVAGRAGRAEEPGRVLIQTHLADHPLLVQLTEDGYFAFAEQALSERR 630
Cdd:cd18804 164 TLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAERK 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
207-384 |
2.12e-96 |
|
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: 296.04 E-value: 2.12e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 207 QRAAFEAVRASHGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRFNARIALLHSALTD 286
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 287 RERLDAWLAARDGEADIVIGTRSALFTPLKRPGLIIVDEEHDASYKQQDGLRYHARDLALVRARLENVPILLGSATPALE 366
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|....*...
gi 15600243 367 SLHNAQAGRYGLLRLTQR 384
Cdd:cd17929 161 SYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
14-689 |
2.64e-40 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 157.79 E-value: 2.64e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 14 LRRLFDYRAPRGIPRSAlQPGIRLLLPFGRRELVGVLIEVTDRSEvPEDKLKPALRVLDAKPPMPAHLLELCRWTAQYYQ 93
Cdd:PRK14873 25 LDRLFDYLVPEELSDDA-QPGVRVRVRFGGRLVDGFVLERRSDSD-HEGKLRWLERVVSPEPVLTPEIRRLARAVADRYA 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 94 HSLGDTLSWALPnllrqgePAEARQQRFWHATAQSSLDDPRLARAPrqrqalaiLKQHPHGVShellnqleinkdsldll 173
Cdd:PRK14873 103 GTRADVLRLAVP-------PRHARVEKEPVATPPPPLTAPPPDPSG--------WAAYGRGPR----------------- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 174 kekglvELEVRRHSTPPReGGWLAqaeLPLNPEQRAAFEAVRAshggfhcfllagvtgsgktevylqlireTLAAGRQAL 253
Cdd:PRK14873 151 ------FLAALAAGRAAR-AVWQA---LPGEDWARRLAAAAAA----------------------------TLRAGRGAL 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 254 VLIPEINLGPQTLARFERRFNA-RIALLHSALTDRERLDAWLAARDGEADIVIGTRSALFTPLKRPGLIIVDEehDASYK 332
Cdd:PRK14873 193 VVVPDQRDVDRLEAALRALLGAgDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIWD--DGDDL 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 333 QQDGLR-Y-HARDLALVRARLENVPILLGSATPALESlhnaqagrygllRLTQRAGGAHPPKFIRLDVKS-MPLDAGLSR 409
Cdd:PRK14873 271 LAEPRApYpHAREVALLRAHQHGCALLIGGHARTAEA------------QALVESGWAHDLVAPRPVVRArAPRVRALGD 338
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 410 PLQ------------------QAIGDTLAAGqQVLVFLNRRGFAPTLLCHDCGWISQCPRCDARMTVHQGSGELRCHHCD 471
Cdd:PRK14873 339 SGLalerdpaaraarlpslafRAARDALEHG-PVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCG 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 472 hRQRPPMNCPQCGKLDLRPLGAGTERAEERLRILFPNHPVLridrdsTSRKHAMRDLFAtinsGEPCILVGT---QMLAK 548
Cdd:PRK14873 418 -RAAPDWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVV------TSGGDQVVDTVD----AGPALVVATpgaEPRVE 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 549 GHHfprvTLVAILDADGGLFSADFRASE----RMAQQIVQVAGRAgraeEPGRVLIqthLAD-HPLLVQ-LTEDGYFAFA 622
Cdd:PRK14873 487 GGY----GAALLLDAWALLGRQDLRAAEdtlrRWMAAAALVRPRA----DGGQVVV---VAEsSLPTVQaLIRWDPVGHA 555
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15600243 623 EQALSERRAAGLPPFAHLALlraeahkpgqaeafLDSACSAAEQLLEQMGGPE-VELLGPVPAPMERR 689
Cdd:PRK14873 556 ERELAERAEVGFPPAVRMAA--------------VDGRPAAVAALLEAAGLPDgAEVLGPVPLPPGVR 609
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
7-105 |
1.14e-34 |
|
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: 126.80 E-value: 1.14e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 7 RLALPSPLRRLFDYRAPRGIprsALQPGIRLLLPFGRRELVGVLIEVTDRSEVPEDKLKPALRVLDAKPPMPAHLLELCR 86
Cdd:pfam17764 1 EVAVPLPLDRPFDYRVPEEL---AVKIGMRVLVPFGKRKVTGIVVGLSEESEVDPEKLKPILEVLDEEPLLTPELLELAR 77
|
90
....*....|....*....
gi 15600243 87 WTAQYYQHSLGDTLSWALP 105
Cdd:pfam17764 78 WMAEYYLCPLGEVLRAALP 96
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
636-735 |
3.12e-29 |
|
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: 111.54 E-value: 3.12e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 636 PFAHLALLRAEAHKPGQAEAFLDSAcsaAEQLLEQMGGPEVELLGPVPAPMERRAGKHRAQLLLQCMSRAPLHRLLTPWL 715
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEEL---AELLKELLKLQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELL 77
|
90 100
....*....|....*....|
gi 15600243 716 QSLEQLPgGRQVRWSLDIDP 735
Cdd:pfam18074 78 EELQKLP-KRKVRISIDVDP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
224-362 |
1.17e-23 |
|
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: 97.47 E-value: 1.17e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 224 FLLAGVTGSGKTEVY-LQLIRETLAAGRQALVLIPEINLGPQTLARFERRF--NARIALLHSALTDRERLDAWLaardGE 300
Cdd:cd00046 4 VLITAPTGSGKTLAAlLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEEREKNKL----GD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 301 ADIVIGTRSALFTPLKRPG--------LIIVDEEHDASYKQQDGLRYharDLALVRARLENVPILLGSAT 362
Cdd:cd00046 80 ADIIIATPDMLLNLLLREDrlflkdlkLIIVDEAHALLIDSRGALIL---DLAVRKAGLKNAQVILLSAT 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
201-390 |
1.48e-20 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 90.24 E-value: 1.48e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 201 LPLNPEQRAAFEAVRASHGGFhcfLLAGVTGSGKTEVYLQLIRETLAAGR--QALVLIPEINLGPQTLARFERRFNARIA 278
Cdd:smart00487 7 EPLRPYQKEAIEALLSGLRDV---ILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELKKLGPSLGL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 279 LLHSALTDRERLDAWLAARDGEADIVIGTRSALF-------TPLKRPGLIIVDEEHDASYKQqdglryHARDLA-LVRAR 350
Cdd:smart00487 84 KVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLdllendkLSLSNVDLVILDEAHRLLDGG------FGDQLEkLLKLL 157
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 15600243 351 LENVPILLGSATPALESLHNAQAGRYGLLRLTQRAGGAHP 390
Cdd:smart00487 158 PKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
204-364 |
1.62e-20 |
|
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: 89.22 E-value: 1.62e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 204 NPEQRAAFEAVrasHGGFHCFLLAgVTGSGKTEVYLQLIRETLA---AGRQALVLIPEINLGPQTLARFERRFNARIALL 280
Cdd:pfam00270 1 TPIQAEAIPAI---LEGRDVLVQA-PTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGLKV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 281 HSALTDRERLDAWLAARdgEADIVIGTRSALFT------PLKRPGLIIVDEEHDASYK-QQDGLRYHARDLalvrarLEN 353
Cdd:pfam00270 77 ASLLGGDSRKEQLEKLK--GPDILVGTPGRLLDllqerkLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRL------PKK 148
|
170
....*....|.
gi 15600243 354 VPILLGSATPA 364
Cdd:pfam00270 149 RQILLLSATLP 159
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
200-363 |
1.93e-16 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 77.33 E-value: 1.93e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 200 ELPLNPEQRAAFEAVRASHG-GFHCFLLAGVTGSGKTEVYLQLIRETLAAG--RQALVLIPEINLGPQTLARFERRFNAr 276
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKnGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPN- 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 277 iALLHSALTDRERLDAWLaardGEADIVIGTRSALFTPLKRP---------GLIIVDEEHDASYKqqdglRYhardlalv 347
Cdd:pfam04851 80 -YVEIGEIISGDKKDESV----DDNKIVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGAS-----SY-------- 141
|
170
....*....|....*....
gi 15600243 348 RARLENVP--ILLG-SATP 363
Cdd:pfam04851 142 RNILEYFKpaFLLGlTATP 160
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
225-374 |
5.35e-16 |
|
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: 76.84 E-value: 5.35e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRFNA---RIALLHSALTDRERLDAWLAARDGEA 301
Cdd:cd17991 40 LICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFANfpvNVELLSRFTTAAEQREILEGLKEGKV 119
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600243 302 DIVIGTRSALFTPL--KRPGLIIVDEEHDASYKQQDGLryhardlalvRARLENVPILLGSATPALESLHNAQAG 374
Cdd:cd17991 120 DIVIGTHRLLSKDVefKNLGLLIIDEEQRFGVKQKEKL----------KELRPNVDVLTLSATPIPRTLHMALSG 184
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
203-599 |
5.61e-14 |
|
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: 74.91 E-value: 5.61e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAFEAVRASHGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEIN----LGPqtlaRFERRF-NARI 277
Cdd:COG4098 111 LTPAQQKASDELLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDvvleLAP----RLQQAFpGVDI 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 278 ALLHSALTDRERLdawlaardgeADIVIGT-------RSAlFTplkrpgLIIVDEEhDA-SYKQQDGLRYhardlALVRA 349
Cdd:COG4098 187 AALYGGSEEKYRY----------AQLVIATthqllrfYQA-FD------LLIIDEV-DAfPYSGDPMLQY-----AVKRA 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 350 RLENVPILLGSATPALESLHNAQAGRYGLLRLTQRAGGaHP---PKFIRL-DVKSMPLDAGLSRPLQQAIGDTLAAGQQV 425
Cdd:COG4098 244 RKPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYHG-HPlpvPKFKWLgNWKKRLRRGKLPRKLLKWLKKRLKEGRQL 322
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 426 LVFLnrrgfaPTllchdcgwISQCprcdarmtvhqgsgelrchhcdhrqrppmncpqcgkldlrplgagtERAEERLRIL 505
Cdd:COG4098 323 LIFV------PT--------IELL----------------------------------------------EQLVALLQKL 342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 506 FPNHPVlridrDSTSRKH--------AMRDlfatinsGEPCILVGTQMLAKGHHFPRVTlVAILDADGGLFSAdfrASer 577
Cdd:COG4098 343 FPEERI-----AGVHAEDperkekvqAFRD-------GEIPILVTTTILERGVTFPNVD-VAVLGADHPVFTE---AA-- 404
|
410 420
....*....|....*....|....
gi 15600243 578 maqqIVQVAGRAGR-AEEP-GRVL 599
Cdd:COG4098 405 ----LVQIAGRVGRsADYPtGEVI 424
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
178-431 |
1.12e-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: 75.09 E-value: 1.12e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 178 LVELEVRRHSTP----PREGGWLAQ--AELPLN--PEQRAAFEAVRASHGGFHCF--LLAGVTGSGKTEVYLQLIRETLA 247
Cdd:TIGR00580 419 LIELYAKRKAIKghafPPDLEWQQEfeDSFPFEetPDQLKAIEEIKADMESPRPMdrLVCGDVGFGKTEVAMRAAFKAVL 498
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 248 AGRQALVLIPEINLGPQTLARFERRFN---ARIALLHSALTDRERLDAWLAARDGEADIVIGTRSALFTPL--KRPGLII 322
Cdd:TIGR00580 499 DGKQVAVLVPTTLLAQQHFETFKERFAnfpVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVkfKDLGLLI 578
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 323 VDEEHDASYKQQDGLryhardlalvRARLENVPILLGSATPALESLHNAQAGRYGLLRLTQraggahPPKFiRLDVKS-- 400
Cdd:TIGR00580 579 IDEEQRFGVKQKEKL----------KELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIAT------PPED-RLPVRTfv 641
|
250 260 270
....*....|....*....|....*....|.
gi 15600243 401 MPLDAGLsrpLQQAIGDTLAAGQQVLVFLNR 431
Cdd:TIGR00580 642 MEYDPEL---VREAIRRELLRGGQVFYVHNR 669
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
195-382 |
1.44e-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: 63.59 E-value: 1.44e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 195 WLAQAELPLNPEQRAAFEAVR-ASHGGFHC-FLLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERR 272
Cdd:cd17918 8 LCKSLPFSLTKDQAQAIKDIEkDLHSPEPMdRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 273 F-NARIALLHSALTdrerldawlaARDGE-ADIVIGTRSALF--TPLKRPGLIIVDEEHDASYKQQDGLRyhardlalvr 348
Cdd:cd17918 88 LpFINVELVTGGTK----------AQILSgISLLVGTHALLHldVKFKNLDLVIVDEQHRFGVAQREALY---------- 147
|
170 180 190
....*....|....*....|....*....|....
gi 15600243 349 aRLENVPILLGSATPALESLhnAQAGrYGLLRLT 382
Cdd:cd17918 148 -NLGATHFLEATATPIPRTL--ALAL-SGLLDLS 177
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
225-363 |
2.07e-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: 64.09 E-value: 2.07e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEVYLQLIRETLAAGRQALVLIP-EInLGPQTLARFERRF---NARIALLHSALTDRERLDAWLAARDGE 300
Cdd:cd17992 70 LLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKLLeplGIRVALLTGSTKAKEKREILEKIASGE 148
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15600243 301 ADIVIGTRsALFTP---LKRPGLIIVDEEHDASYKQQDGLryhardlalvRARLENVPILLGSATP 363
Cdd:cd17992 149 IDIVIGTH-ALIQEdveFHNLGLVIIDEQHRFGVEQRLKL----------REKGETPHVLVMTATP 203
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
449-475 |
2.38e-11 |
|
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: 58.69 E-value: 2.38e-11
10 20
....*....|....*....|....*..
gi 15600243 449 CPRCDARMTVHQGSGELRCHHCDHRQR 475
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
191-363 |
1.16e-10 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 64.66 E-value: 1.16e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 191 REGGWLAQAELPLNPEQRAAFEAVRAS-HGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRqALVLIPEINLGPQTLARF 269
Cdd:COG1061 69 EAGDEASGTSFELRPYQQEALEALLAAlERGGGRGLVVAPTGTGKTVLALALAAELLRGKR-VLVLVPRRELLEQWAEEL 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 270 ERRFNARIALLHSaltdrerldawlaaRDGEADIVIGT------RSALFTPLKRPGLIIVDEEHDASykqqdglryhARD 343
Cdd:COG1061 148 RRFLGDPLAGGGK--------------KDSDAPITVATyqslarRAHLDELGDRFGLVIIDEAHHAG----------APS 203
|
170 180
....*....|....*....|
gi 15600243 344 LALVRARLENVPILLGSATP 363
Cdd:COG1061 204 YRRILEAFPAAYRLGLTATP 223
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
120-600 |
2.36e-10 |
|
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: 63.56 E-value: 2.36e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 120 RFWHATAQSSLDDPRLARAPRQRQALAILKQHPH-GVSHELLNQLEINKDSLDLLKEKGLV--------ELEVRRHSTPP 190
Cdd:COG1203 29 ALLLLLLAALLLALLLALLLLAALELALLLLLLLlLLLLLLLLLLDLLLDDLAFLFLLLLIdadwldsaNFDMARQALDH 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 191 REGGWLA-------QAELPLNPEQRAAFEAVR-ASHGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRQA--LVLIPEIN 260
Cdd:COG1203 109 LLAERLErllpkksKPRTPINPLQNEALELALeAAEEEPGLFILTAPTGGGKTEAALLFALRLAAKHGGRriIYALPFTS 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 261 LGPQTLARFERRFNARIALLHSAL--------TDRERLDAW--LAARDGEADIVIGTR----SALFTP-----LKRPGL- 320
Cdd:COG1203 189 IINQTYDRLRDLFGEDVLLHHSLAdldlleeeEEYESEARWlkLLKELWDAPVVVTTIdqlfESLFSNrkgqeRRLHNLa 268
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 321 ---IIVDEEHDasykqqdglrYHARDLALVRARLE-----NVPILLGSAT-PALESLHNAQAgrYGLLRLTQRAGGAHPP 391
Cdd:COG1203 269 nsvIILDEVQA----------YPPYMLALLLRLLEwlknlGGSVILMTATlPPLLREELLEA--YELIPDEPEELPEYFR 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 392 KFI--RLDVKSMPLDaglSRPLQQAIGDTLAAGQQVLVFLNRRGfaptllchdcgwisqcprcDARMTVHQGSGELRCHH 469
Cdd:COG1203 337 AFVrkRVELKEGPLS---DEELAELILEALHKGKSVLVIVNTVK-------------------DAQELYEALKEKLPDEE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 470 CDH---RQRPpmncpqcgkldlrplgagteraEERLRILfpnhpvlridrdstsrkhamRDLFATINSGEPCILVGTQML 546
Cdd:COG1203 395 VYLlhsRFCP----------------------ADRSEIE--------------------KEIKERLERGKPCILVSTQVV 432
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 547 AKG--HHFPRV-TLVAILDAdgglfsadfrasermaqqIVQVAGRA---GRAEEPGRVLI 600
Cdd:COG1203 433 EAGvdIDFDVViRDLAPLDS------------------LIQRAGRCnrhGRKEEEGNVYV 474
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
225-374 |
3.09e-09 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 60.53 E-value: 3.09e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRFN---ARIALLHSALTDRERLDAWLAARDGEA 301
Cdd:PRK10689 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFAnwpVRIEMLSRFRSAKEQTQILAEAAEGKI 704
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600243 302 DIVIGTRSALFTPLKRP--GLIIVDEEHdasykqqdglRYHARDLALVRARLENVPILLGSATPALESLHNAQAG 374
Cdd:PRK10689 705 DILIGTHKLLQSDVKWKdlGLLIVDEEH----------RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSG 769
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
205-362 |
3.79e-09 |
|
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: 57.16 E-value: 3.79e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 205 PEQRAAFEAVRAshgGFHCFLLAGvTGSGKTEVYlQLirETLAAGRQALVLIPEINLGpQTLARFERRFNARIALLHSAL 284
Cdd:cd17920 15 PGQLEAINAVLA---GRDVLVVMP-TGGGKSLCY-QL--PALLLDGVTLVVSPLISLM-QDQVDRLQQLGIRAAALNSTL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 285 TDRERLDAWLAARDGEADIVIGT-----RSALFTPL------KRPGLIIVDEEHDASykqQDGL--RYHARDLALVRARL 351
Cdd:cd17920 87 SPEEKREVLLRIKNGQYKLLYVTperllSPDFLELLqrlperKRLALIVVDEAHCVS---QWGHdfRPDYLRLGRLRRAL 163
|
170
....*....|.
gi 15600243 352 ENVPILLGSAT 362
Cdd:cd17920 164 PGVPILALTAT 174
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
225-327 |
5.63e-08 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 56.31 E-value: 5.63e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEV----YLQLIretlAAGRQALVLIP-EInLGPQ---TLARFERRFNARIALLHSALTDRERLDAWLAA 296
Cdd:PRK10917 286 LLQGDVGSGKTVVaalaALAAI----EAGYQAALMAPtEI-LAEQhyeNLKKLLEPLGIRVALLTGSLKGKERREILEAI 360
|
90 100 110
....*....|....*....|....*....|....
gi 15600243 297 RDGEADIVIGTRsALFTP---LKRPGLIIVDEEH 327
Cdd:PRK10917 361 ASGEADIVIGTH-ALIQDdveFHNLGLVIIDEQH 393
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
496-592 |
7.20e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 50.29 E-value: 7.20e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 496 ERAEERLRILfpNHPVLRIDRDSTS--RKHAMRDLfatiNSGEPCILVGTQMLAKGHHFPRVTLVAILDADGGLfsadfr 573
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQeeREEILDKF----NNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSP------ 68
|
90
....*....|....*....
gi 15600243 574 asermaQQIVQVAGRAGRA 592
Cdd:smart00490 69 ------ASYIQRIGRAGRA 81
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
203-327 |
1.04e-07 |
|
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: 51.54 E-value: 1.04e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAFEAVRASHGGFH-CFLLAgvTGSGKTEVYLQLIRETLAagRQALVLIPEINLGPQTLARFERRFNARIallh 281
Cdd:cd17926 1 LRPYQEEALEAWLAHKNNRRgILVLP--TGSGKTLTALALIAYLKE--LRTLIVVPTDALLDQWKERFEDFLGDSS---- 72
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 15600243 282 saltdRERLDAWLAARDGEADIVIGTRSALF-------TPLKRPGLIIVDEEH 327
Cdd:cd17926 73 -----IGLIGGGKKKDFDDANVVVATYQSLSnlaeeekDLFDQFGLLIVDEAH 120
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
225-327 |
1.12e-07 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 55.44 E-value: 1.12e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 225 LLAGVTGSGKTEV----YLQLIretlAAGRQALVLIP-EInLGPQ---TLARFERRFNARIALLHSALTDRERLDAWLAA 296
Cdd:COG1200 284 LLQGDVGSGKTVVallaMLAAV----EAGYQAALMAPtEI-LAEQhyrSLSKLLEPLGIRVALLTGSTKAKERREILAAL 358
|
90 100 110
....*....|....*....|....*....|....
gi 15600243 297 RDGEADIVIGTRsALFTP---LKRPGLIIVDEEH 327
Cdd:COG1200 359 ASGEADIVVGTH-ALIQDdveFKNLGLVVIDEQH 391
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
206-362 |
1.28e-07 |
|
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: 51.53 E-value: 1.28e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 206 EQRAAFEAVRASHGGFHCFLLAgVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRF-NARIALLHSAL 284
Cdd:cd17925 2 QQKASNALVETIDAKEDLLVWA-VTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFpGAAIVLLHGGS 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15600243 285 TDRERldawlaardgEADIVIGTRSALFTPLKRPGLIIVDEEHDASYKQQDGLRYHARdlalvRARLENVPILLGSAT 362
Cdd:cd17925 81 EDQYQ----------RSPLVIATTHQLLRFYRAFDLLIIDEVDAFPYAGDPMLYYAVE-----KARKEEGSLIYLTAT 143
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
202-362 |
1.27e-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: 49.18 E-value: 1.27e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 202 PLNPEQRAAFEAVRASHggfHCFLLAGVTGSGKTEV-YLQLIRETLAAGRQALVLIPEINLGPQTLARFERRFnARIALL 280
Cdd:cd17921 1 LLNPIQREALRALYLSG---DSVLVSAPTSSGKTLIaELAILRALATSGGKAVYIAPTRALVNQKEADLRERF-GPLGKN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 281 HSALTDRERLDawlAARDGEADIVIGT----RSALFTP----LKRPGLIIVDEEHDASYKQQdGLRYHaRDLALVRARLE 352
Cdd:cd17921 77 VGLLTGDPSVN---KLLLAEADILVATpeklDLLLRNGgerlIQDVRLVVVDEAHLIGDGER-GVVLE-LLLSRLLRINK 151
|
170
....*....|
gi 15600243 353 NVPILLGSAT 362
Cdd:cd17921 152 NARFVGLSAT 161
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
203-435 |
5.28e-06 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 49.89 E-value: 5.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAFEAVRASHGgfhCFLLAGVTGSGKTEVyLQL-IRETLAAGRQALVLIPEINLGPQTLARFERRF---NARIA 278
Cdd:COG1204 23 LYPPQAEALEAGLLEGK---NLVVSAPTASGKTLI-AELaILKALLNGGKALYIVPLRALASEKYREFKRDFeelGIKVG 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 279 LlhsaLT-DRERLDAWLaardGEADIVIGT----RSAL---FTPLKRPGLIIVDEEH---DASykqqDGLRYharDLALV 347
Cdd:COG1204 99 V----STgDYDSDDEWL----GRYDILVATpeklDSLLrngPSWLRDVDLVVVDEAHlidDES----RGPTL---EVLLA 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 348 RARLEN--VPILLGSAT-PALESLH---NAqagryGLLRLTQRAggahppkfIRLDV-----KSMPLDAGLSRPLQQAIG 416
Cdd:COG1204 164 RLRRLNpeAQIVALSATiGNAEEIAewlDA-----ELVKSDWRP--------VPLNEgvlydGVLRFDDGSRRSKDPTLA 230
|
250 260
....*....|....*....|..
gi 15600243 417 ---DTLAAGQQVLVFLNRRGFA 435
Cdd:COG1204 231 lalDLLEEGGQVLVFVSSRRDA 252
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
203-332 |
6.08e-06 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 46.79 E-value: 6.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAFEAVRAS-HGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRQA--LVLIPEINLGPQTLARFERrfnariAL 279
Cdd:cd18032 1 PRYYQQEAIEALEEArEKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKriLFLAHREELLEQAERSFKE------VL 74
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 280 LHSALTDRERLDawlaARDGEADIVIGTRSALFTPLK-------RPGLIIVDEEHDASYK 332
Cdd:cd18032 75 PDGSFGNLKGGK----KKPDDARVVFATVQTLNKRKRlekfppdYFDLIIIDEAHHAIAS 130
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
203-327 |
8.06e-06 |
|
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: 46.94 E-value: 8.06e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAFEAVRASHGGFhcfLLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFERRfnARIALLHS 282
Cdd:cd18028 2 LYPPQAEAVRAGLLKGENL---LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKL--EEIGLKVG 76
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 15600243 283 ALT-DRERLDAWLaardGEADIVIGTRSAL-----FTP--LKRPGLIIVDEEH 327
Cdd:cd18028 77 ISTgDYDEDDEWL----GDYDIIVATYEKFdsllrHSPswLRDVGVVVVDEIH 125
|
|
| SF2_C_UvrB |
cd18790 |
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
515-600 |
1.85e-05 |
|
C-terminal helicase domain of the UvrB family helicases; 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. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB 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: 350177 [Multi-domain] Cd Length: 171 Bit Score: 45.70 E-value: 1.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 515 DRDSTSRKHAMRDLfatiNSGEPCILVGTQMLAKGHHFPRVTLVAILDADgglfSADFRASERmaqQIVQVAGRAGRAEE 594
Cdd:cd18790 60 EIDTLERVEIIRDL----RLGEFDVLVGINLLREGLDLPEVSLVAILDAD----KEGFLRSET---SLIQTIGRAARNVN 128
|
....*.
gi 15600243 595 pGRVLI 600
Cdd:cd18790 129 -GKVIL 133
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
495-592 |
2.47e-05 |
|
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: 43.74 E-value: 2.47e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 495 TERAEERLRILFPNHPVLRIDRDSTS--RKHAMRDLfatiNSGEPCILVGTQMLAKGHHFPRVTLVAILDADGGLfsadf 572
Cdd:pfam00271 25 KKTLEAELLLEKEGIKVARLHGDLSQeeREEILEDF----RKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNP----- 95
|
90 100
....*....|....*....|
gi 15600243 573 rasermaQQIVQVAGRAGRA 592
Cdd:pfam00271 96 -------ASYIQRIGRAGRA 108
|
|
| uvrb |
TIGR00631 |
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
515-600 |
9.37e-05 |
|
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain] Cd Length: 655 Bit Score: 45.75 E-value: 9.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 515 DRDSTSRKHAMRDLFAtinsGEPCILVGTQMLAKGHHFPRVTLVAILDADgglfSADFRASERmaqQIVQVAGRAGRAEE 594
Cdd:TIGR00631 475 EIDTLERVEIIRDLRL----GEFDVLVGINLLREGLDLPEVSLVAILDAD----KEGFLRSER---SLIQTIGRAARNVN 543
|
....*.
gi 15600243 595 pGRVLI 600
Cdd:TIGR00631 544 -GKVIM 548
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
539-602 |
3.58e-04 |
|
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: 39.61 E-value: 3.58e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15600243 539 ILVGTQMLAKGHHFPRVTLVAILDADgglfsadfraseRMAQQIVQVAGRAGR-AEEPGRVLIQT 602
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPP------------SSAASYIQRVGRAGRgGKDEGEVILFV 77
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
203-381 |
5.77e-04 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is 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: 350769 [Multi-domain] Cd Length: 207 Bit Score: 41.89 E-value: 5.77e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 203 LNPEQRAAF-EAVRASHGGFhcfLLAGVTGSGKT----EVYLQLIRETLAagRQALVLIPEiNLGPQTLARFERRFNARI 277
Cdd:cd18011 1 PLPHQIDAVlRALRKPPVRL---LLADEVGLGKTieagLIIKELLLRGDA--KRVLILCPA-SLVEQWQDELQDKFGLPF 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 278 ALLHSALTDRERLDAWLAarDGEADIVI---------GTRSALFTPlKRPGLIIVDEEHDASYKqqdGLRYHARDLALVR 348
Cdd:cd18011 75 LILDRETAAQLRRLIGNP--FEEFPIVIvsldllkrsEERRGLLLS-EEWDLVVVDEAHKLRNS---GGGKETKRYKLGR 148
|
170 180 190
....*....|....*....|....*....|....
gi 15600243 349 ARLENVP-ILLGSATPalesLHNAQAGRYGLLRL 381
Cdd:cd18011 149 LLAKRARhVLLLTATP----HNGKEEDFRALLSL 178
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
233-327 |
9.53e-04 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 42.75 E-value: 9.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 233 GKTEVYLqliRetlAA------GRQALVLIPeinlgpqT--LAR-----FERRFNA---RIALLhSALTDRERLDAWLAA 296
Cdd:COG1197 619 GKTEVAL---R---AAfkavmdGKQVAVLVP-------TtlLAQqhyetFKERFAGfpvRVEVL-SRFRTAKEQKETLEG 684
|
90 100 110
....*....|....*....|....*....|....*
gi 15600243 297 -RDGEADIVIGTrSALFTP---LKRPGLIIVDEEH 327
Cdd:COG1197 685 lADGKVDIVIGT-HRLLSKdvkFKDLGLLIIDEEQ 718
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
230-329 |
1.15e-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: 40.71 E-value: 1.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 230 TGSGKTEVYLQLIRE-------TLAAGRQALVLIPEINLGPQTLARFERRFNARIALLHSAL-TDRERLDAWLAARDgEA 301
Cdd:cd18034 25 TGSGKTLIAVMLIKEmgelnrkEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGEMgVDKWTKERWKEELE-KY 103
|
90 100 110
....*....|....*....|....*....|....*
gi 15600243 302 DIVIGTRSALFTPLKRP-------GLIIVDEEHDA 329
Cdd:cd18034 104 DVLVMTAQILLDALRHGflslsdiNLLIFDECHHA 138
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
197-325 |
1.20e-03 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 42.27 E-value: 1.20e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 197 AQAELPLNPEQRAAFEAVRASHGgfhCFLLAGVTGSGKT-------EVYLQLIRET-LAA--GRQALVLIPEINLGPQTL 266
Cdd:COG0507 119 PRAGITLSDEQREAVALALTTRR---VSVLTGGAGTGKTttlrallAALEALGLRVaLAAptGKAAKRLSESTGIEARTI 195
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 15600243 267 ARferrfnariallhsaltdrerldaWLAARDGEADIVIGTRSalftPLKRPGLIIVDE 325
Cdd:COG0507 196 HR------------------------LLGLRPDSGRFRHNRDN----PLTPADLLVVDE 226
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
202-279 |
2.91e-03 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 39.47 E-value: 2.91e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 202 PLNPEQRAAFEAVRASHGGFhcFLLAGVTGSGKTEVyLQLIRETLAA-----------GRQALVLIPEINLGPQTLARFE 270
Cdd:pfam13604 1 TLNAEQAAAVRALLTSGDRV--AVLVGPAGTGKTTA-LKALREAWEAagyrviglaptGRAAKVLGEELGIPADTIAKLL 77
|
....*....
gi 15600243 271 RRFNARIAL 279
Cdd:pfam13604 78 HRLGGRAGL 86
|
|
| PksD |
COG3321 |
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites ... |
199-711 |
3.01e-03 |
|
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];
Pssm-ID: 442550 [Multi-domain] Cd Length: 1386 Bit Score: 41.01 E-value: 3.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 199 AELPLNPEQR-------AAFEAVRASHGGFHCFLLAGVTGSGKTEVYLQLIRETLAAGRQALVLIPEINLGPQTLARFER 271
Cdd:COG3321 861 VPLPTYPFQRedaaaalLAAALAAALAAAAALGALLLAALAAALAAALLALAAAAAAALALAAAALAALLALVALAAAAA 940
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 272 RFNARIALLHSALTDRERLDAWLAARDGEADIVIGTRSALFTPLKRPGLIIVDEEHDASYKQQDGLRYHARDLALVRARL 351
Cdd:COG3321 941 ALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAALALLAAAALLLAAAAAAAA 1020
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 352 ENVPILLGSATPALESLHNAQAGRYGLLRLTQRAGGAHPPKFIRLDVKSMPLDAGLSRPLQQAIGDTLAAGQQVLVFLNR 431
Cdd:COG3321 1021 LLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAAAALALALAALLLLAALAELALAAAALALAAALAAAALALALA 1100
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 432 RGFAPTLLCHDCGWISQCPRCDARMTVHQGSGELRCHHCDHRQRPPMNCPQCGKLDLRPLGAGTERAEERLRILFPNHPV 511
Cdd:COG3321 1101 ALAAALLLLALLAALALAAAAAALLALAALLAAAAAAAALAAAAAAAAALALAAAAAALAAALAAALLAAAALLLALALA 1180
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 512 LRIDRDSTSRKHAMRDLFATINSGEPCILVGTQMLAKGHHFPRVTLVAILDADGGLFSADFRASERMAQQIVQVAGRAGR 591
Cdd:COG3321 1181 LAAALAAALAGLAALLLAALLAALLAALLALALAALAAAAAALLAAAAAAAALALLALAAAAAAVAALAAAAAALLAALA 1260
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 592 AEEPGRVLIQTHLADHPLLVQLTEDGYFAFAEQALSERRAAGLPPFAHLALLRAEAHKPGQAEAFLDSACSAAEQLLEQM 671
Cdd:COG3321 1261 ALALLAAAAGLAALAAAAAAAAAALALAAAAAAAAAALAALLAAAAAAAAAAAAAAAAAALAAALLAAALAALAAAVAAA 1340
|
490 500 510 520
....*....|....*....|....*....|....*....|
gi 15600243 672 GGPEVELLGPVPAPMERRAGKHRAQLLLQCMSRAPLHRLL 711
Cdd:COG3321 1341 LALAAAAAAAAAAAAAAAAAAALAAAAGAAAAAAALALAA 1380
|
|
| DEXHc_Hrq1-like |
cd17923 |
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
212-339 |
3.85e-03 |
|
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 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: 350681 [Multi-domain] Cd Length: 182 Bit Score: 39.11 E-value: 3.85e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 212 EAVRASHGGFHcFLLAGVTGSGKTEVYLQLIRETLA--AGRQALVLIPEINLGPQTLARFERR-----FNARIALLH--S 282
Cdd:cd17923 7 EAIEAARAGRS-VVVTTGTASGKSLCYQLPILEALLrdPGSRALYLYPTKALAQDQLRSLRELleqlgLGIRVATYDgdT 85
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 15600243 283 ALTDRERLdawlaaRDGEADIVIGTRSALFTPLKRPgliivdeeHDASYKQQDGLRY 339
Cdd:cd17923 86 PREERRAI------IRNPPRILLTNPDMLHYALLPH--------HDRWARFLRNLRY 128
|
|
| DEADc_DDX28 |
cd17948 |
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
218-311 |
4.20e-03 |
|
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box 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: 350706 [Multi-domain] Cd Length: 231 Bit Score: 39.66 E-value: 4.20e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15600243 218 HGGFHCfLLAGVTGSGKTEVYL-----QLIRETLAAGRQ-----ALVLIPEINLGPQtLARFERRFNARIALLHSALTDR 287
Cdd:cd17948 25 LRGRNT-LCAAETGSGKTLTYLlpiiqRLLRYKLLAEGPfnaprGLVITPSRELAEQ-IGSVAQSLTEGLGLKVKVITGG 102
|
90 100
....*....|....*....|....
gi 15600243 288 ERLDAWLAARDGEADIVIGTRSAL 311
Cdd:cd17948 103 RTKRQIRNPHFEEVDILVATPGAL 126
|
|
| RPC10 |
COG1996 |
DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; ... |
449-478 |
4.25e-03 |
|
DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]; DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 441599 Cd Length: 48 Bit Score: 35.83 E-value: 4.25e-03
10 20 30
....*....|....*....|....*....|....
gi 15600243 449 CPRCDARMTVHQGSGELRCHHCDHRQ----RPPM 478
Cdd:COG1996 8 CPRCGAEVELDEGTPAIRCPYCGSRIfikeRPPV 41
|
|
| SRPBCC_CalC_Aha1-like_6 |
cd08899 |
Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and ... |
262-301 |
9.22e-03 |
|
Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands.
Pssm-ID: 176908 [Multi-domain] Cd Length: 157 Bit Score: 37.66 E-value: 9.22e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 15600243 262 GPQTLaRFERRFNARIALLHSALTDRERLDAWLAARDGEA 301
Cdd:cd08899 9 GGATL-RFERLLPAPIEDVWAALTDPERLARWFAPGTGDL 47
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
184-252 |
9.47e-03 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 39.54 E-value: 9.47e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15600243 184 RRHSTPPREGGWLAQAELPLNPEQRAAFEAVRASHGgfhcFLLAGVTGSGKTEVYLQLIRETLAAGRQA 252
Cdd:COG4581 7 RADARLEALADFAEERGFELDPFQEEAILALEAGRS----VLVAAPTGSGKTLVAEFAIFLALARGRRS 71
|
|
| |
