|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
32-739 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 985.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 32 GAYSYAVPEGVHVEPGSVVQVPVGPRQLIGVVWDGDNDDRLDPKKLRPITLVFDC-PPLSKEMRDFVDWVASYTLSPPGL 110
Cdd:PRK05580 15 RPFDYLIPEGLEVQPGDRVRVPFGNRKLIGVVVGVEEGSEVPADKLKPILEVLDLePLLPPELLRLLDWAADYYLSPLGE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 111 VARMAVRAPaaldpepmveglrylggqperltpararvldlageeeipwtrsgLAHAAgvSMSVVDGLTAQGIFETVFLP 190
Cdd:PRK05580 95 VLRLALLAE--------------------------------------------LALAA--SSAVLKGLVKKGLIELEEVE 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 191 PPPVVALPDPDYITPRIEGPQKQAsvdiLDSIRAG-GFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTS 269
Cdd:PRK05580 129 VLRLRPPPDPAFEPPTLNPEQAAA----VEAIRAAaGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTP 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 270 SFLERFQERFGAKPGEWHSDLAPRMREKVWRGVVTGEVKVVAGARSALFLPFEDLGLIIVDEEHDPAYKQEDRVFYNARD 349
Cdd:PRK05580 205 QMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHDSSYKQQEGPRYHARD 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 350 MAVVRARIGDFPIVLVSATPSVESQVNGLAGRYNTVHLPTRFGDAAMPDLHLIDMRRHPP-ERGGFLSPVLLRAMKKTLE 428
Cdd:PRK05580 285 LAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAGGARLPEVEIIDMRELLRgENGSFLSPPLLEAIKQRLE 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 429 RNEQSLLFLNRRGYAPLTLCRVCGHRFQCPQCSSWLVEHRFKRQIQCHQCGYSERTPEACPECGTfDHLVACGPGVERIA 508
Cdd:PRK05580 365 RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGS-TDLVPVGPGTERLE 443
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 509 EEVEKHFPEARTIVMSSDLLGGVKRMRLELEAIAKGEADIVIGTQLVAKGHNFPLMTLVGIVDSDLGLSNGDPRAAERTF 588
Cdd:PRK05580 444 EELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTF 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 589 QLLSQVTGRAGRTGLKSHGLLQTFQPQHPVMQAIVSGDAGAFYEREIAEREKAILPPFGRLASLIVSADTRADAEAHARG 668
Cdd:PRK05580 524 QLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFGRLALLRASAKDEEKAEKFAQQ 603
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004165 669 LRAAAPKV---TGISVLGPAEAPLALVRGRHRFRLLVHGRRNSDMQAFLRAMLENGPK--QRGSVQIQLDIDPQSF 739
Cdd:PRK05580 604 LAALLPNLlplLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKlpQARKVRWSIDVDPQSF 679
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
32-738 |
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: 970.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 32 GAYSYAVPEGV-HVEPGSVVQVPVGPRQLIGVVWDGDNDDRLDPKKLRPITLVFD-CPPLSKEMRDFVDWVASYTLSPPG 109
Cdd:COG1198 14 RPFDYLVPEGLeLVQPGSRVLVPFGRRQVVGIVVGLKEESDVDPAKLKPILAVLDdEPLLPEELLELLRWVADYYLCPLG 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 110 LVARMAVRAPAALDPEPMVEGLRY----LGGQPERLTPARARVLDLAGEEEIPWTRSGLAHAAGVSMSVVDGLTAQGIFE 185
Cdd:COG1198 94 EVLRLALPAGLRQGYPARIKTERYvrltLGEELPKRAPKQRRVLEALREHGGPLTLSELAKEAGVSRSVLKALVKKGLLE 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 186 TVF-LPPPPVVALPDPDYITPRIEGPQKQAsvdiLDSIRA--GGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILL 262
Cdd:COG1198 174 IEErEVDRDPFAPDVPAEPPPTLNEEQQAA----VEAIRAaaGGFSVFLLHGVTGSGKTEVYLQAIAEVLAQGKQALVLV 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 263 PEIALTSSFLERFQERFGAKPGEWHSDLAPRMREKVWRGVVTGEVKVVAGARSALFLPFEDLGLIIVDEEHDPAYKQEDR 342
Cdd:COG1198 250 PEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGLIIVDEEHDSSYKQEDG 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 343 VFYNARDMAVVRARIGDFPIVLVSATPSVESQVNGLAGRYNTVHLPTRFGDAAMPDLHLIDMRRHPPERGGFLSPVLLRA 422
Cdd:COG1198 330 PRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDMREEPLEGGRILSPPLLEA 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 423 MKKTLERNEQSLLFLNRRGYAPLTLCRVCGHRFQCPQCSSWLVEHRFKRQIQCHQCGYSERTPEACPECGTfDHLVACGP 502
Cdd:COG1198 410 IEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCPECGS-DSLRPFGP 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 503 GVERIAEEVEKHFPEARTIVMSSDLLGGVKRMRLELEAIAKGEADIVIGTQLVAKGHNFPLMTLVGIVDSDLGLSNGDPR 582
Cdd:COG1198 489 GTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLGLNSPDFR 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 583 AAERTFQLLSQVTGRAGRTGLKSHGLLQTFQPQHPVMQAIVSGDAGAFYEREIAEREKAILPPFGRLASLIVSADTRADA 662
Cdd:COG1198 569 AAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFGRLALLRASGKDEEAA 648
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 663 EAHARGLRAAAPKV---TGISVLGPAEAPLALVRGRHRFRLLVHGRRNSDMQAFLRAMLENGPK-QRGSVQIQLDIDPQS 738
Cdd:COG1198 649 EEFAQALARALRALlsaDGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLEKpLPRKVRWSIDVDPQS 728
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
231-736 |
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: 606.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 231 LIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPGEWHSDLAPRMREKVWRGVVTGEVKVV 310
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 311 AGARSALFLPFEDLGLIIVDEEHDPAYKQEDRVFYNARDMAVVRARIGDFPIVLVSATPSVESQVNGLAGRYNTVHLPTR 390
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 391 FGDAAMPDLHLIDMRRHPPErgGFLSPVLLRAMKKTLERNEQSLLFLNRRGYAPLTLCRVCGHRFQCPQCSSWLVEHRFK 470
Cdd:TIGR00595 161 VSGRKPPEVKLIDMRKEPRQ--SFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 471 RQIQCHQCGYSERTPEACPECGTFdHLVACGPGVERIAEEVEKHFPEARTIVMSSDLLGGVKRMRLELEAIAKGEADIVI 550
Cdd:TIGR00595 239 GKLRCHYCGYQEPIPKTCPQCGSE-DLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 551 GTQLVAKGHNFPLMTLVGIVDSDLGLSNGDPRAAERTFQLLSQVTGRAGRTGLKSHGLLQTFQPQHPVMQAIVSGDAGAF 630
Cdd:TIGR00595 318 GTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAF 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 631 YEREIAEREKAILPPFGRLASLIVSADTRADAEAHARGLRAAAPKV--TGISVLGPAEAPLALVRGRHRFRLLVHGRRNS 708
Cdd:TIGR00595 398 YEQELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNldEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFL 477
|
490 500
....*....|....*....|....*...
gi 2229004165 709 DMQAFLRAMLENGPKQRGsVQIQLDIDP 736
Cdd:TIGR00595 478 VLQKLVNKTLLKEIPSSS-VYCEVDVDP 504
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
399-639 |
4.70e-103 |
|
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: 315.72 E-value: 4.70e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 399 LHLIDMRRHppERGGFLSPVLLRAMKKTLERNEQSLLFLNRRGYAPLTLCRVCGHRFQCPQCSSWLVEHRFKRQIQCHQC 478
Cdd:cd18804 1 IEIVDMKEE--ELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYC 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 479 GYSERTPEACPECGTFDhLVACGPGVERIAEEVEKHFPEARTIVMSSDLLGGVKRMRLELEAIAKGEADIVIGTQLVAKG 558
Cdd:cd18804 79 GYQEPIPKQCPECGSED-LVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKG 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 559 HNFPLMTLVGIVDSDLGLSNGDPRAAERTFQLLSQVTGRAGRTGLKSHGLLQTFQPQHPVMQAIVSGDAGAFYEREIAER 638
Cdd:cd18804 158 LDFPNVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAER 237
|
.
gi 2229004165 639 E 639
Cdd:cd18804 238 K 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
211-390 |
5.22e-82 |
|
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: 258.29 E-value: 5.22e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSirAGGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPGEWHSDL 290
Cdd:cd17929 1 QRKAYEAIVSS--LGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 291 APRMREKVWRGVVTGEVKVVAGARSALFLPFEDLGLIIVDEEHDPAYKQEDRVFYNARDMAVVRARIGDFPIVLVSATPS 370
Cdd:cd17929 79 SDKERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPS 158
|
170 180
....*....|....*....|
gi 2229004165 371 VESQVNGLAGRYNTVHLPTR 390
Cdd:cd17929 159 LESYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
36-733 |
2.54e-32 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 133.52 E-value: 2.54e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 36 YAVPEGV--HVEPGSVVQVPVGPRQLIGVVWDgdNDDRLDPK-KLRPITLVF-DCPPLSKEMRDFVDWVASYTLSPPGLV 111
Cdd:PRK14873 31 YLVPEELsdDAQPGVRVRVRFGGRLVDGFVLE--RRSDSDHEgKLRWLERVVsPEPVLTPEIRRLARAVADRYAGTRADV 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 112 ARMAVrapaaldpepmveglrylggqperltPAR-ARVldlagEEEIPWTRSGLAHAAGVSMSVVDGLTAQGIFetvflp 190
Cdd:PRK14873 109 LRLAV--------------------------PPRhARV-----EKEPVATPPPPLTAPPPDPSGWAAYGRGPRF------ 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 191 pppvvalpdpdyitpriegpqkqasvdiLDSIRAGGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSS 270
Cdd:PRK14873 152 ----------------------------LAALAAGRAARAVWQALPGEDWARRLAAAAAATLRAGRGALVVVPDQRDVDR 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 271 FLERFQERFGAKP-GEWHSDLAPRMREKVWRGVVTGEVKVVAGARSALFLPFEDLGLIIVDEEHDPAYkQEDRVFY-NAR 348
Cdd:PRK14873 204 LEAALRALLGAGDvAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLL-AEPRAPYpHAR 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 349 DMAVVRARIGDFPIVLVSATPSVESQVNGLAGRYNTVHLPTRFGDAAMPDLHL-----IDMRRHPPERGGFLSPVLLRAM 423
Cdd:PRK14873 283 EVALLRAHQHGCALLIGGHARTAEAQALVESGWAHDLVAPRPVVRARAPRVRAlgdsgLALERDPAARAARLPSLAFRAA 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 424 KKTLERNEqSLLFLNRRGYAPLTLCRVCGHRFQCPQCSSWLVEHRFKRQIQCHQCGYSErTPEACPECGTfDHLVACGPG 503
Cdd:PRK14873 363 RDALEHGP-VLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA-PDWRCPRCGS-DRLRAVVVG 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 504 VERIAEEVEKHFPEARTIVMSSDLLggvkrmrleLEAIAKGEAdIVIGTQ----LVAKGHNFPLmtlvgIVDSDLGLSNG 579
Cdd:PRK14873 440 ARRTAEELGRAFPGVPVVTSGGDQV---------VDTVDAGPA-LVVATPgaepRVEGGYGAAL-----LLDAWALLGRQ 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 580 DPRAAERTfqlLSQVTGRAGRTGLKSHGLLQTF--QPQHPVMQAIVSGDAGAFYEREIAEREKAILPPFGRLASLIVSAD 657
Cdd:PRK14873 505 DLRAAEDT---LRRWMAAAALVRPRADGGQVVVvaESSLPTVQALIRWDPVGHAERELAERAEVGFPPAVRMAAVDGRPA 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 658 TRADAEAHARGLRAAapkvtgiSVLGPAEAPLALVR------GRHRFRLLV---HGRRNSDMQAFLRAMLENGPKQR-GS 727
Cdd:PRK14873 582 AVAALLEAAGLPDGA-------EVLGPVPLPPGVRRpagidaREDRVRALVrvpRARGAELAAALRRAVAVRSARREpGP 654
|
....*.
gi 2229004165 728 VQIQLD 733
Cdd:PRK14873 655 LRVQID 660
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
32-116 |
5.97e-23 |
|
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: 93.68 E-value: 5.97e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 32 GAYSYAVPEGVHVEPGSVVQVPVGPRQLIGVVWDGDNDDRLDPKKLRPITLVFD-CPPLSKEMRDFVDWVASYTLSPPGL 110
Cdd:pfam17764 10 RPFDYRVPEELAVKIGMRVLVPFGKRKVTGIVVGLSEESEVDPEKLKPILEVLDeEPLLTPELLELARWMAEYYLCPLGE 89
|
....*.
gi 2229004165 111 VARMAV 116
Cdd:pfam17764 90 VLRAAL 95
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
645-736 |
1.81e-20 |
|
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: 86.51 E-value: 1.81e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 645 PFGRLASLIVSADTRADAEAHARGLRA---AAPKVTGISVLGPAEAPLALVRGRHRFRLLVHGRRNSDMQAFLRAMLEN- 720
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAEllkELLKLQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEEl 80
|
90
....*....|....*.
gi 2229004165 721 GPKQRGSVQIQLDIDP 736
Cdd:pfam18074 81 QKLPKRKVRISIDVDP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
231-368 |
3.05e-16 |
|
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: 76.29 E-value: 3.05e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 231 LIDGVTGSGKTEVYFEAIA-ETLRRGKQVLILLPEIALTSSFLERFQERF--GAKPGEWHSDLAPRMREKVWRG---VVT 304
Cdd:cd00046 5 LITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEEREKNKLGdadIII 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2229004165 305 GEVKVVAGARSALFLPFE-DLGLIIVDEEHdpAYKQEDRVFYNArDMAVVRARIGDFPIVLVSAT 368
Cdd:cd00046 85 ATPDMLLNLLLREDRLFLkDLKLIIVDEAH--ALLIDSRGALIL-DLAVRKAGLKNAQVILLSAT 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
211-374 |
1.37e-15 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 75.99 E-value: 1.37e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSIRAGgfsasLIDGVTGSGKTEVYFEAIAETLRRG--KQVLILLPEIALTSSFLERFQERFGAKPGEWHS 288
Cdd:smart00487 13 QKEAIEALLSGLRDV-----ILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 289 DLAPRMREKVWRGVVTGEVKVVAGARSALF-------LPFEDLGLIIVDEEHD-PAYKQEDRVfynardMAVVRARIGDF 360
Cdd:smart00487 88 LYGGDSKREQLRKLESGKTDILVTTPGRLLdllendkLSLSNVDLVILDEAHRlLDGGFGDQL------EKLLKLLPKNV 161
|
170
....*....|....
gi 2229004165 361 PIVLVSATPSVESQ 374
Cdd:smart00487 162 QLLLLSATPPEEIE 175
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
210-437 |
1.06e-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: 77.22 E-value: 1.06e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 210 PQKQASVDILDSIRAGgfSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFgakpgewhsd 289
Cdd:COG4098 114 AQQKASDELLEAIKKK--EEHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAF---------- 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 290 laPRMREKVWRGVVTGEVK----VVAGARSAL-----FlpfeDlgLIIVDE------EHDPAYKQedrvfynardmAVVR 354
Cdd:COG4098 182 --PGVDIAALYGGSEEKYRyaqlVIATTHQLLrfyqaF----D--LLIIDEvdafpySGDPMLQY-----------AVKR 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 355 ARIGDFPIVLVSATPSVE--SQVNGlaGRYNTVHLPTRFgdaampdlHlidmrRHP-PE-------------RGGFLSPV 418
Cdd:COG4098 243 ARKPDGKLIYLTATPSKAlqRQVKR--GKLKVVKLPARY--------H-----GHPlPVpkfkwlgnwkkrlRRGKLPRK 307
|
250
....*....|....*....
gi 2229004165 419 LLRAMKKTLERNEQSLLFL 437
Cdd:COG4098 308 LLKWLKKRLKEGRQLLIFV 326
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
231-370 |
1.22e-13 |
|
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: 69.19 E-value: 1.22e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 231 LIDGVTGSGKTEVYFEAIAETLRR---GKQVLILLPEIALTSSFLERFQERFGAKPGEWHSDLAPRMREKVWRGVvtGEV 307
Cdd:pfam00270 18 LVQAPTGSGKTLAFLLPALEALDKldnGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGDSRKEQLEKL--KGP 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2229004165 308 KVVAGARSALFL------PFEDLGLIIVDEEHdpaykqedRVFYNAR--DMAVVRARI-GDFPIVLVSATPS 370
Cdd:pfam00270 96 DILVGTPGRLLDllqerkLLKNLKLLVLDEAH--------RLLDMGFgpDLEEILRRLpKKRQILLLSATLP 159
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
211-369 |
2.18e-12 |
|
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: 66.44 E-value: 2.18e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSIRAGGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPGEwhSDL 290
Cdd:cd17991 20 QLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFANFPVN--VEL 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 291 APRMR-----EKVWRGVVTGEVKVVAGARSALF--LPFEDLGLIIVDEEHDPAYKQEDRvfynardmavVRARIGDFPIV 363
Cdd:cd17991 98 LSRFTtaaeqREILEGLKEGKVDIVIGTHRLLSkdVEFKNLGLLIIDEEQRFGVKQKEK----------LKELRPNVDVL 167
|
....*.
gi 2229004165 364 LVSATP 369
Cdd:cd17991 168 TLSATP 173
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
210-339 |
1.85e-10 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 59.99 E-value: 1.85e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 210 PQKQASVDILDSIRAGGFSAsLIDGVTGSGKTEVYFEAIAETLRRG--KQVLILLPEIALTSSFLERFQERFGAK---PG 284
Cdd:pfam04851 7 YQIEAIENLLESIKNGQKRG-LIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPNYveiGE 85
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2229004165 285 EWHSDLAPRMRekvwrgvvtGEVKVVAGARSALFLPFEDL---------GLIIVDEEH---DPAYKQ 339
Cdd:pfam04851 86 IISGDKKDESV---------DDNKIVVTTIQSLYKALELAslellpdffDVIIIDEAHrsgASSYRN 143
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
211-369 |
2.41e-10 |
|
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: 60.12 E-value: 2.41e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSIRAGGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFgakpgewhsdl 290
Cdd:cd17918 20 QAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFL----------- 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 291 aPRMR-EKVWRGV---VTGEVKVVAGARSALFL--PFEDLGLIIVDEEHDPAYKQEDRVfYNARDMAvvrarigdfpIVL 364
Cdd:cd17918 89 -PFINvELVTGGTkaqILSGISLLVGTHALLHLdvKFKNLDLVIVDEQHRFGVAQREAL-YNLGATH----------FLE 156
|
....*
gi 2229004165 365 VSATP 369
Cdd:cd17918 157 ATATP 161
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
231-343 |
3.16e-08 |
|
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: 57.37 E-value: 3.16e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 231 LIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPG--EWHSDLAPRMREK-VWRGVVTGEV 307
Cdd:TIGR00580 476 LVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVtiELLSRFRSAKEQNeILKELASGKI 555
|
90 100 110
....*....|....*....|....*....|....*...
gi 2229004165 308 KVVAGARSAL--FLPFEDLGLIIVDEEHDPAYKQEDRV 343
Cdd:TIGR00580 556 DILIGTHKLLqkDVKFKDLGLLIIDEEQRFGVKQKEKL 593
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
457-483 |
6.33e-08 |
|
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: 48.68 E-value: 6.33e-08
10 20
....*....|....*....|....*..
gi 2229004165 457 CPQCSSWLVEHRFKRQIQCHQCGYSER 483
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
231-369 |
4.38e-07 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 53.60 E-value: 4.38e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 231 LIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPgeWHSDLAPRMR-----EKVWRGVVTG 305
Cdd:PRK10689 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWP--VRIEMLSRFRsakeqTQILAEAAEG 702
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004165 306 EVKVVAGARSALF--LPFEDLGLIIVDEEHDPAYKQEDRvfynardmavVRARIGDFPIVLVSATP 369
Cdd:PRK10689 703 KIDILIGTHKLLQsdVKWKDLGLLIVDEEHRFGVRHKER----------IKAMRADVDILTLTATP 758
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
211-279 |
6.95e-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: 49.22 E-value: 6.95e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2229004165 211 QKQASVDILDSIRAGGfsASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERF 279
Cdd:cd17925 2 QQKASNALVETIDAKE--DLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAF 68
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
211-369 |
3.77e-06 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 50.41 E-value: 3.77e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSIRAGGFSAsLIDGVTGSGKTEVyFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPGewhsdl 290
Cdd:COG1061 85 QQEALEALLAALERGGGRG-LVVAPTGTGKTVL-ALALAAELLRGKRVLVLVPRRELLEQWAEELRRFLGDPLA------ 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 291 APRMREKVWRGVVTGeVKVVAgARSALFLPFEDLGLIIVDEEHD-PAykqedRVFYNARDMAVVRARIGdfpivlVSATP 369
Cdd:COG1061 157 GGGKKDSDAPITVAT-YQSLA-RRAHLDELGDRFGLVIIDEAHHaGA-----PSYRRILEAFPAAYRLG------LTATP 223
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
211-333 |
3.36e-05 |
|
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: 45.60 E-value: 3.36e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSIRAGGFSASLIDGVTGSGKTEVYFEAIAETLRRGKQVLILLP-EIaLTSSFLERFQERF---GAKPGEW 286
Cdd:cd17992 50 QKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKLLeplGIRVALL 128
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 2229004165 287 HSDLAPRMREKVWRGVVTGEVKVVAGARsALF---LPFEDLGLIIVDEEH 333
Cdd:cd17992 129 TGSTKAKEKREILEKIASGEIDIVIGTH-ALIqedVEFHNLGLVIIDEQH 177
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
210-333 |
1.29e-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: 42.68 E-value: 1.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 210 PQKQASVDILDSIRAGGfsaSLIDGVTGSGKTEVYFEAIAETLRRGkqVLILLPEIALTSSFLERFQERFGAKPgewhsd 289
Cdd:cd17926 4 YQEEALEAWLAHKNNRR---GILVLPTGSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFEDFLGDSS------ 72
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 2229004165 290 laprmrekvwRGVVTGEVKVVAGARSALF--------------LPFEDLGLIIVDEEH 333
Cdd:cd17926 73 ----------IGLIGGGKKKDFDDANVVVatyqslsnlaeeekDLFDQFGLLIVDEAH 120
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
236-375 |
1.34e-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: 43.68 E-value: 1.34e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 236 TGSGKTEVYfeaIAETLRRGKQVLILLPEIALTSSFLERFQERfGAKPGEWHSDLAPRMREKVWRGVVTGEVKVV----A 311
Cdd:cd17920 36 TGGGKSLCY---QLPALLLDGVTLVVSPLISLMQDQVDRLQQL-GIRAAALNSTLSPEEKREVLLRIKNGQYKLLyvtpE 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 312 GARSALFLPF-------EDLGLIIVDEEH-------D--PAYKQedrvfynardMAVVRARIGDFPIVLVSAT--PSVES 373
Cdd:cd17920 112 RLLSPDFLELlqrlperKRLALIVVDEAHcvsqwghDfrPDYLR----------LGRLRRALPGVPILALTATatPEVRE 181
|
..
gi 2229004165 374 QV 375
Cdd:cd17920 182 DI 183
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
509-602 |
2.12e-04 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 40.27 E-value: 2.12e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 509 EEVEKHFPEA--RTIVMSSDLLggvKRMRLE-LEAIAKGEADIVIGTQLVAKGHNFPLMTLVGIVDSDlglsngdpraae 585
Cdd:smart00490 1 EELAELLKELgiKVARLHGGLS---QEEREEiLDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP------------ 65
|
90
....*....|....*..
gi 2229004165 586 RTFQLLSQVTGRAGRTG 602
Cdd:smart00490 66 WSPASYIQRIGRAGRAG 82
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
211-421 |
2.98e-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: 42.66 E-value: 2.98e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 211 QKQASVDILDSiRAGGFsasLI-DGVtGSGKTevyFEA---IAETLRRG--KQVLILLPEiALTSSFLERFQERFGAKPG 284
Cdd:cd18011 5 QIDAVLRALRK-PPVRL---LLaDEV-GLGKT---IEAgliIKELLLRGdaKRVLILCPA-SLVEQWQDELQDKFGLPFL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 285 EWHSDLAPRMREKVWRG------VVTGEVKVVAGARSALFLPFEDLGLIIVDEEHDPAYKQEDRvfYNARdMAVVRARIG 358
Cdd:cd18011 76 ILDRETAAQLRRLIGNPfeefpiVIVSLDLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGGGK--ETKR-YKLGRLLAK 152
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2229004165 359 DFP-IVLVSATPsvesqVNG-LAGRYNTVHL--PTRFGDaampdlhLIDMRRHPPERGGfLSPVLLR 421
Cdd:cd18011 153 RARhVLLLTATP-----HNGkEEDFRALLSLldPGRFAV-------LGRFLRLDGLREV-LAKVLLR 206
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
236-368 |
8.02e-04 |
|
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: 41.09 E-value: 8.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 236 TGSGKTEVYFEAIAETLRRGKQVLI-LLPEIALTSSFLERFQERFGAKPGewhsdlaprmreKVwrGVVTGEVKV----V 310
Cdd:cd17921 26 TSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGK------------NV--GLLTGDPSVnkllL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 311 AGARSALFLP--------------FEDLGLIIVDEEHDpaYKQEDRvfynardmAVV--------RARIGDFPIVLVSAT 368
Cdd:cd17921 92 AEADILVATPekldlllrnggerlIQDVRLVVVDEAHL--IGDGER--------GVVlelllsrlLRINKNARFVGLSAT 161
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
236-349 |
1.04e-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: 41.10 E-value: 1.04e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 236 TGSGKTEV-------YFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAKPGEWHSDlaprMREKVWRGVVTGEVK 308
Cdd:cd18034 25 TGSGKTLIavmlikeMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGE----MGVDKWTKERWKEEL 100
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90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 2229004165 309 -----VVAGARSAL------FLPFEDLGLIIVDEEH----DPAYKQEDRVFYNARD 349
Cdd:cd18034 101 ekydvLVMTAQILLdalrhgFLSLSDINLLIFDECHhatgDHPYARIMKEFYHLEG 156
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|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
236-314 |
1.04e-03 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 42.62 E-value: 1.04e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2229004165 236 TGSGKTEVYFEAIAETLRRGKQVLILLPEIALTSSFLERFQERFGAkpgewhsdlaprmrEKVwrGVVTGEVKVVAGAR 314
Cdd:COG4581 49 TGSGKTLVAEFAIFLALARGRRSFYTAPIKALSNQKFFDLVERFGA--------------ENV--GLLTGDASVNPDAP 111
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| SF2_C_UvrB |
cd18790 |
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
506-600 |
3.33e-03 |
|
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: 39.15 E-value: 3.33e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2229004165 506 RIAEEVEKHFPEA--RTIVMSSDLlGGVKRMRLeLEAIAKGEADIVIGTQLVAKGHNFPLMTLVGIVDSDlglSNGDPRa 583
Cdd:cd18790 38 RMAEDLTEYLQELgvKVRYLHSEI-DTLERVEI-IRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDAD---KEGFLR- 111
|
90
....*....|....*..
gi 2229004165 584 AERTfqlLSQVTGRAGR 600
Cdd:cd18790 112 SETS---LIQTIGRAAR 125
|
|
| COG2888 |
COG2888 |
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ... |
448-493 |
7.16e-03 |
|
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];
Pssm-ID: 442134 [Multi-domain] Cd Length: 52 Bit Score: 35.09 E-value: 7.16e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 2229004165 448 CRVCG--------HRFQCPQCSswlvEHRFKRqiqCHQCGYSERTPEACPECGT 493
Cdd:COG2888 3 CPSCGreiapeggVAFYCPNCG----EALIIR---CPKCRKQSNALYFCPKCGF 49
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