|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
7-660 |
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: 968.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 7 ILRVAVPSPLWQSFDYLpLNAEIQSLQPGMRLKVPFGRRETVGILLDVVTHSTLPLSKLKPIIEIIDEVALIPASLLKLY 86
Cdd:COG1198 3 IAEVALPVPLDRPFDYL-VPEGLELVQPGSRVLVPFGRRQVVGIVVGLKEESDVDPAKLKPILAVLDDEPLLPEELLELL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 87 CWASDYYHYPIGEIILGSLPRLFRQGKTIISEKI----------------------------------EELNQAAP---- 128
Cdd:COG1198 82 RWVADYYLCPLGEVLRLALPAGLRQGYPARIKTEryvrltlgeelpkrapkqrrvlealrehggpltlSELAKEAGvsrs 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 129 ------------------------------PSLELNEYQQNAVNQIMASK-GFQTFLLAGVTGSGKTEVYLRCIEKLIQQ 177
Cdd:COG1198 162 vlkalvkkglleieerevdrdpfapdvpaePPPTLNEEQQAAVEAIRAAAgGFSVFLLHGVTGSGKTEVYLQAIAEVLAQ 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 178 EKQALILVPEIGLTPQTLNRFRERFNVPTAVLHSSLTDKKRAQAWMMAKRGTAKIVIGTRSAIFTPLLNPGIIILDEEHD 257
Cdd:COG1198 242 GKQALVLVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGLIIVDEEHD 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 258 TSFKQQSGFRYSARDLAVMRGQFENIPVVLGSATPSLESLYNVERRRYQLLSLPGRAGKAKLPSLTIVDLRQKKLIAGM- 336
Cdd:COG1198 322 SSYKQEDGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVDMREEPLEGGRi 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 337 -SEDLLISIEKHIKNKGQVLLFLNRRGYAPTLLCHGCGWVMHCDRCDARLTLHYFPKRLYCHHCGAAKKIPPTCPQCHQQ 415
Cdd:COG1198 402 lSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCPECGSD 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 416 ELIDVGLGTERLEAALQQRFPNDDIVRIDRDSTRTKNSMENKLNLIHNREAPILIGTQMIAKGHHFSHLTLVAIIDADSG 495
Cdd:COG1198 482 SLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 496 LYSADFRATERMGQLLTQVAGRAGRVDRQGEVLIQTHQPNNPFLTLLLQEGYEAFAQALLKERQLVQLPPFTYLALLRTE 575
Cdd:COG1198 562 LNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFGRLALLRAS 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 576 AVKQNLPLDFLTKIKELMVNELK-EEVDLLGPVSAGMERKAGRYRYQLLFQSKHRKHLHSVLNKLISLL-ATQRTKVRWS 653
Cdd:COG1198 642 GKDEEAAEEFAQALARALRALLSaDGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLeKPLPRKVRWS 721
|
....*..
gi 499260921 654 LDIDPQE 660
Cdd:COG1198 722 IDVDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
7-660 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 934.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 7 ILRVAVPSPLWQSFDYLPlnAEIQSLQPGMRLKVPFGRRETVGILLDVVTHSTLPLSKLKPIIEIIDEVALIPASLLKLY 86
Cdd:PRK05580 4 IARVLLPVPLPRPFDYLI--PEGLEVQPGDRVRVPFGNRKLIGVVVGVEEGSEVPADKLKPILEVLDLEPLLPPELLRLL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 87 CWASDYYHYPIGEIILGSLPR-------------LFRQGKTIISEKIEELNQAAP----PSLELNEYQQNAVNQIMASKG 149
Cdd:PRK05580 82 DWAADYYLSPLGEVLRLALLAelalaassavlkgLVKKGLIELEEVEVLRLRPPPdpafEPPTLNPEQAAAVEAIRAAAG 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 150 FQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERFNVPTAVLHSSLTDKKRAQAWMMAKRGT 229
Cdd:PRK05580 162 FSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 230 AKIVIGTRSAIFTPLLNPGIIILDEEHDTSFKQQSGFRYSARDLAVMRGQFENIPVVLGSATPSLESLYNVERRRYQLLS 309
Cdd:PRK05580 242 AKVVIGARSALFLPFKNLGLIIVDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLR 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 310 LPGRAGKAKLPSLTIVDLRQ---KKLIAGMSEDLLISIEKHIKNKGQVLLFLNRRGYAPTLLCHGCGWVMHCDRCDARLT 386
Cdd:PRK05580 322 LTKRAGGARLPEVEIIDMREllrGENGSFLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLT 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 387 LHYFPKRLYCHHCGAAKKIPPTCPQCHQQELIDVGLGTERLEAALQQRFPNDDIVRIDRDSTRTKNSMENKLNLIHNREA 466
Cdd:PRK05580 402 LHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEA 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 467 PILIGTQMIAKGHHFSHLTLVAIIDADSGLYSADFRATERMGQLLTQVAGRAGRVDRQGEVLIQTHQPNNPFLTLLLQEG 546
Cdd:PRK05580 482 DILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQD 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 547 YEAFAQALLKERQLVQLPPFTYLALLRTEAVKQNLPLDFLTKIKELMVNELK-EEVDLLGPVSAGMERKAGRYRYQLLFQ 625
Cdd:PRK05580 562 YDAFAEQELEERRAAGYPPFGRLALLRASAKDEEKAEKFAQQLAALLPNLLPlLDVEVLGPAPAPIAKIAGRYRYQLLLK 641
|
650 660 670
....*....|....*....|....*....|....*..
gi 499260921 626 SKHRKHLHSVLNKLISLLAT--QRTKVRWSLDIDPQE 660
Cdd:PRK05580 642 SPSRADLQKLLRAWLALLQKlpQARKVRWSIDVDPQS 678
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
154-658 |
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: 615.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 154 LLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERFNVPTAVLHSSLTDKKRAQAWMMAKRGTAKIV 233
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 234 IGTRSAIFTPLLNPGIIILDEEHDTSFKQQSGFRYSARDLAVMRGQFENIPVVLGSATPSLESLYNVERRRYQLLSLPGR 313
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 314 AGKAKLPSLTIVDLRQKKLIAGMSEDLLISIEKHIKNKGQVLLFLNRRGYAPTLLCHGCGWVMHCDRCDARLTLHYFPKR 393
Cdd:TIGR00595 161 VSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 394 LYCHHCGAAKKIPPTCPQCHQQELIDVGLGTERLEAALQQRFPNDDIVRIDRDSTRTKNSMENKLNLIHNREAPILIGTQ 473
Cdd:TIGR00595 241 LRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 474 MIAKGHHFSHLTLVAIIDADSGLYSADFRATERMGQLLTQVAGRAGRVDRQGEVLIQTHQPNNPFLTLLLQEGYEAFAQA 553
Cdd:TIGR00595 321 MIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFYEQ 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 554 LLKERQLVQLPPFTYLALLRTEAVKQNLPLDFLTKIKELMVNELKEEVDLLGPVSAGMERKAGRYRYQLLFQSKHRKHLH 633
Cdd:TIGR00595 401 ELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLVLQ 480
|
490 500
....*....|....*....|....*.
gi 499260921 634 SVLNKliSLLATQRT-KVRWSLDIDP 658
Cdd:TIGR00595 481 KLVNK--TLLKEIPSsSVYCEVDVDP 504
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
324-559 |
2.64e-111 |
|
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: 334.60 E-value: 2.64e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 324 IVDLRQKKLIAGMSEDLLISIEKHIKNKGQVLLFLNRRGYAPTLLCHGCGWVMHCDRCDARLTLHYFPKRLYCHHCGAAK 403
Cdd:cd18804 3 IVDMKEEELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGYQE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 404 KIPPTCPQCHQQELIDVGLGTERLEAALQQRFPNDDIVRIDRDSTRTKNSMENKLNLIHNREAPILIGTQMIAKGHHFSH 483
Cdd:cd18804 83 PIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPN 162
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499260921 484 LTLVAIIDADSGLYSADFRATERMGQLLTQVAGRAGRVDRQGEVLIQTHQPNNPFLTLLLQEGYEAFAQALLKERQ 559
Cdd:cd18804 163 VTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAERK 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
137-313 |
6.11e-94 |
|
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: 287.57 E-value: 6.11e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 137 QQNAVNQIMASK-GFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERFNVPTAVLHSSLTD 215
Cdd:cd17929 1 QRKAYEAIVSSLgGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKLSD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 216 KKRAQAWMMAKRGTAKIVIGTRSAIFTPLLNPGIIILDEEHDTSFKQQSGFRYSARDLAVMRGQFENIPVVLGSATPSLE 295
Cdd:cd17929 81 KERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSLE 160
|
170
....*....|....*...
gi 499260921 296 SLYNVERRRYQLLSLPGR 313
Cdd:cd17929 161 SYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
7-608 |
4.05e-33 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 135.45 E-value: 4.05e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 7 ILRVAVPSP---LWQSFDYLPLNAEIQSLQPGMRLKVPFGRRETVGILLDVVTHSTlPLSKLKPIIEIIDEVALIPASLL 83
Cdd:PRK14873 13 VARVLPDLGlphLDRLFDYLVPEELSDDAQPGVRVRVRFGGRLVDGFVLERRSDSD-HEGKLRWLERVVSPEPVLTPEIR 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 84 KLYCWASDYYHYPIGEII-LGSLPRLFRQGKTIISEKIEELNQAAPPSLELNEYQQNavnqimaskgfQTFLLAGVTGSG 162
Cdd:PRK14873 92 RLARAVADRYAGTRADVLrLAVPPRHARVEKEPVATPPPPLTAPPPDPSGWAAYGRG-----------PRFLAALAAGRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 163 KTEVYL--------RCIEKLIQQE----KQALILVPEIGLTPQTLNRFRERFNV-PTAVLHSSLTDKKRAQAWMMAKRGT 229
Cdd:PRK14873 161 ARAVWQalpgedwaRRLAAAAAATlragRGALVVVPDQRDVDRLEAALRALLGAgDVAVLSAGLGPADRYRRWLAVLRGQ 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 230 AKIVIGTRSAIFTPLLNPG-IIILDE------EHDTSFKQqsgfrysARDLAVMRGQFENIPVVLGSATPSLESLYNVE- 301
Cdd:PRK14873 241 ARVVVGTRSAVFAPVEDLGlVAIWDDgddllaEPRAPYPH-------AREVALLRAHQHGCALLIGGHARTAEAQALVEs 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 302 -------------RRRYQLLSLPGR----------AGKAKLPSLTIVDLRqkkliagmseDLLISiekhiknkGQVLLFL 358
Cdd:PRK14873 314 gwahdlvaprpvvRARAPRVRALGDsglalerdpaARAARLPSLAFRAAR----------DALEH--------GPVLVQV 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 359 NRRGYAPTLLCHGCGWVMHCDRCDARLTLHYFPKRLYCHHCGAAkKIPPTCPQCHQQELIDVGLGTERLEAALQQRFPNd 438
Cdd:PRK14873 376 PRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRA-APDWRCPRCGSDRLRAVVVGARRTAEELGRAFPG- 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 439 diVRIdRDSTRtknsmENKLNLIhnREAPILI----GTQMIAKGHHFShltlVAIIDADSGLYSADFRATE----RMGQL 510
Cdd:PRK14873 454 --VPV-VTSGG-----DQVVDTV--DAGPALVvatpGAEPRVEGGYGA----ALLLDAWALLGRQDLRAAEdtlrRWMAA 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 511 LTQVAGRAgrvdRQGEVLIqthqpnnpfltllLQEGYEAFAQAL------------LKERQLVQLPPFTYLALL--RTEA 576
Cdd:PRK14873 520 AALVRPRA----DGGQVVV-------------VAESSLPTVQALirwdpvghaereLAERAEVGFPPAVRMAAVdgRPAA 582
|
650 660 670
....*....|....*....|....*....|..
gi 499260921 577 VKqnlplDFLTKIkelmvnELKEEVDLLGPVS 608
Cdd:PRK14873 583 VA-----ALLEAA------GLPDGAEVLGPVP 603
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
9-106 |
5.21e-33 |
|
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: 122.18 E-value: 5.21e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 9 RVAVPSPLWQSFDYLPlnAEIQSLQPGMRLKVPFGRRETVGILLDVVTHSTLPLSKLKPIIEIIDEVALIPASLLKLYCW 88
Cdd:pfam17764 1 EVAVPLPLDRPFDYRV--PEELAVKIGMRVLVPFGKRKVTGIVVGLSEESEVDPEKLKPILEVLDEEPLLTPELLELARW 78
|
90
....*....|....*...
gi 499260921 89 ASDYYHYPIGEIILGSLP 106
Cdd:pfam17764 79 MAEYYLCPLGEVLRAALP 96
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
565-658 |
1.26e-25 |
|
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: 101.14 E-value: 1.26e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 565 PFTYLALLRTEAVKQNLPLDFLTKIKELMVNELK-EEVDLLGPVSAGMERKAGRYRYQLLFQSKHRKHLHSVLNKLISLL 643
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAELLKELLKlQGVEILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEEL 80
|
90
....*....|....*.
gi 499260921 644 ATQ-RTKVRWSLDIDP 658
Cdd:pfam18074 81 QKLpKRKVRISIDVDP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
153-291 |
5.86e-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: 95.16 E-value: 5.86e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 153 FLLAGVTGSGKTEVYLRCIE-KLIQQEKQALILVPEIGLTPQTLNRFRERF--NVPTAVLHSSLTDKKRAQAWmmakRGT 229
Cdd:cd00046 4 VLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEEREKNK----LGD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 230 AKIVIGTRSAIFTPLLNPG--------IIILDEEHDTSFKQQSGFRYSARDLAVMRGqfeNIPVVLGSAT 291
Cdd:cd00046 80 ADIIIATPDMLLNLLLREDrlflkdlkLIIVDEAHALLIDSRGALILDLAVRKAGLK---NAQVILLSAT 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
131-311 |
1.81e-20 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 89.86 E-value: 1.81e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 131 LELNEYQQNAVNQIMasKGFQTFLLAGVTGSGKTEVYLRCIEKLIQQE--KQALILVPEIGLTPQTLNRFRERFNVPTAV 208
Cdd:smart00487 7 EPLRPYQKEAIEALL--SGLRDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELKKLGPSLGLK 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 209 LHSSLTDKKRAQAWMMAKRGTAKIVIGTRSAIFTPLLNP-------GIIILDEEHDTSfkqQSGFRYSARDLavMRGQFE 281
Cdd:smart00487 85 VVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDklslsnvDLVILDEAHRLL---DGGFGDQLEKL--LKLLPK 159
|
170 180 190
....*....|....*....|....*....|
gi 499260921 282 NIPVVLGSATPSleslYNVERRRYQLLSLP 311
Cdd:smart00487 160 NVQLLLLSATPP----EEIENLLELFLNDP 185
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
134-293 |
4.12e-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: 87.68 E-value: 4.12e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 134 NEYQQNAVNQIMASKGFqtfLLAGVTGSGKTEVYLRCIEKLIQQEK---QALILVPEIGLTPQTLNRFRERFNVPTAVLH 210
Cdd:pfam00270 1 TPIQAEAIPAILEGRDV---LVQAPTGSGKTLAFLLPALEALDKLDngpQALVLAPTRELAEQIYEELKKLGKGLGLKVA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 211 SSLTDKKRAQAWMMAKRgtAKIVIGTRSAIFTPLL------NPGIIILDEEHDTSfkqQSGFRysaRDLAVMRGQF-ENI 283
Cdd:pfam00270 78 SLLGGDSRKEQLEKLKG--PDILVGTPGRLLDLLQerkllkNLKLLVLDEAHRLL---DMGFG---PDLEEILRRLpKKR 149
|
170
....*....|
gi 499260921 284 PVVLGSATPS 293
Cdd:pfam00270 150 QILLLSATLP 159
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
131-292 |
2.72e-16 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 76.56 E-value: 2.72e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 131 LELNEYQQNAVNQIMAS--KGFQTFLLAGVTGSGKTEVYLRCIEKLIQQ--EKQALILVPEIGLTPQTLNRFRERFnvPT 206
Cdd:pfam04851 2 LELRPYQIEAIENLLESikNGQKRGLIVMATGSGKTLTAAKLIARLFKKgpIKKVLFLVPRKDLLEQALEEFKKFL--PN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 207 AVLHSSLTDKKRaqawMMAKRGTAKIVIGTRSAIFTPLLNP---------GIIILDEEHDTSFKqqsgfrySARDLAvmr 277
Cdd:pfam04851 80 YVEIGEIISGDK----KDESVDDNKIVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGAS-------SYRNIL--- 145
|
170
....*....|....*.
gi 499260921 278 gQFENIPVVLG-SATP 292
Cdd:pfam04851 146 -EYFKPAFLLGlTATP 160
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
154-292 |
2.49e-13 |
|
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: 69.14 E-value: 2.49e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 154 LLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERFN---VPTAVLHSSLTDKKRAQAWMMAKRGTA 230
Cdd:cd17991 40 LICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFAnfpVNVELLSRFTTAAEQREILEGLKEGKV 119
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499260921 231 KIVIGTRSaiftpLL-------NPGIIILDEEHdtsfkqqsgfRYSARDLAVMRGQFENIPVVLGSATP 292
Cdd:cd17991 120 DIVIGTHR-----LLskdvefkNLGLLIIDEEQ----------RFGVKQKEKLKELRPNVDVLTLSATP 173
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
115-292 |
1.06e-12 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 70.82 E-value: 1.06e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 115 IISEKIEELNQAAPPSLELNEYQQNAVNQIMA--SKGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKqALILVPEIGLTP 192
Cdd:COG1061 63 AEAEALEAGDEASGTSFELRPYQQEALEALLAalERGGGRGLVVAPTGTGKTVLALALAAELLRGKR-VLVLVPRRELLE 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 193 QTLNRFRERFNVPTAVLHSsltdkkraqawmmaKRGTAKIVIGT-----RSAIFTPLLN-PGIIILDEEHdtsfkqqsgf 266
Cdd:COG1061 142 QWAEELRRFLGDPLAGGGK--------------KDSDAPITVATyqslaRRAHLDELGDrFGLVIIDEAH---------- 197
|
170 180
....*....|....*....|....*..
gi 499260921 267 RYSARDLAVMRGQFeNIPVVLG-SATP 292
Cdd:COG1061 198 HAGAPSYRRILEAF-PAAYRLGlTATP 223
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
154-360 |
2.62e-10 |
|
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: 63.92 E-value: 2.62e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 154 LLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERF-NVPTAV-LHSSLTDKKRAQAWMMA-KRGTA 230
Cdd:TIGR00580 476 LVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFaNFPVTIeLLSRFRSAKEQNEILKElASGKI 555
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 231 KIVIGTRSAIFTPLL--NPGIIILDEEHdtsfkqqsgfRYSARDLAVMRGQFENIPVVLGSATPSLESLYnverrryqlL 308
Cdd:TIGR00580 556 DILIGTHKLLQKDVKfkDLGLLIIDEEQ----------RFGVKQKEKLKELRTSVDVLTLSATPIPRTLH---------M 616
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 499260921 309 SLpgrAGKAKLPSLTIVDLRQKKLIAGMSE--DLLIS--IEKHIKNKGQVLLFLNR 360
Cdd:TIGR00580 617 SM---SGIRDLSIIATPPEDRLPVRTFVMEydPELVReaIRRELLRGGQVFYVHNR 669
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
117-256 |
2.23e-09 |
|
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: 57.93 E-value: 2.23e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 117 SEKIEELNQAAPpsLELNEYQQNAVNQI---MASKGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVP-EIgLTP 192
Cdd:cd17992 32 GELLKKFLEALP--FELTGAQKRVIDEIlrdLASEKPMNRLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAE 108
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499260921 193 QTLNRFRERF---NVPTAVLHSSLTDKKRAQAWMMAKRGTAKIVIGTRSAIFTPLL--NPGIIILDEEH 256
Cdd:cd17992 109 QHYDSLKKLLeplGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEfhNLGLVIIDEQH 177
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
378-404 |
3.86e-09 |
|
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: 52.14 E-value: 3.86e-09
10 20
....*....|....*....|....*..
gi 499260921 378 CDRCDARLTLHYFPKRLYCHHCGAAKK 404
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
118-292 |
8.96e-09 |
|
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: 55.50 E-value: 8.96e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 118 EKIEELNQAAPpsLELNEYQQNAVNQI---MASKGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQT 194
Cdd:cd17918 3 ALIQELCKSLP--FSLTKDQAQAIKDIekdLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 195 LNRFRERF-NVPTAVLHSSLTDKKRAQawmmakrgtAKIVIGTRSAIF--TPLLNPGIIILDEEHDTSFKQQSgfrysar 271
Cdd:cd17918 81 YEEARKFLpFINVELVTGGTKAQILSG---------ISLLVGTHALLHldVKFKNLDLVIVDEQHRFGVAQRE------- 144
|
170 180
....*....|....*....|.
gi 499260921 272 dlAVMRGQFENIPVVlgSATP 292
Cdd:cd17918 145 --ALYNLGATHFLEA--TATP 161
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
132-528 |
1.82e-08 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 57.19 E-value: 1.82e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 132 ELNEYQQNAVNQIMAS-KGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIG----LTPqtlnRFRERF-NVP 205
Cdd:COG4098 110 TLTPAQQKASDELLEAiKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDvvleLAP----RLQQAFpGVD 185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 206 TAVLHSSLTDKKRaqawmmakrgTAKIVIGT-------RSAiFTpllnpgIIILDEEhDtsfkqqsGFRYSARDL---AV 275
Cdd:COG4098 186 IAALYGGSEEKYR----------YAQLVIATthqllrfYQA-FD------LLIIDEV-D-------AFPYSGDPMlqyAV 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 276 MRGQFENIPVVLGSATPSLESLYNVERRRYQLLSLPGRAGKAKL--PSLTIVDLRQKKLIAG-MSEDLLISIEKHIKNKG 352
Cdd:COG4098 241 KRARKPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYHGHPLpvPKFKWLGNWKKRLRRGkLPRKLLKWLKKRLKEGR 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 353 QVLLFLnrrgyaPTllchgcgwvmhcdrcdarltlhyfpkrlychhcgaakkipptcpqchqqelIDVGlgtERLEAALQ 432
Cdd:COG4098 321 QLLIFV------PT---------------------------------------------------IELL---EQLVALLQ 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 433 QRFPNddiVRID----RDSTRtknsmENKLNLIHNREAPILIGTQMIAKGHHFSHLTlVAIIDADSGLYSAdfratermg 508
Cdd:COG4098 341 KLFPE---ERIAgvhaEDPER-----KEKVQAFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPVFTE--------- 402
|
410 420
....*....|....*....|..
gi 499260921 509 QLLTQVAGRAGR-VDRQ-GEVL 528
Cdd:COG4098 403 AALVQIAGRVGRsADYPtGEVI 424
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
113-361 |
4.19e-08 |
|
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: 56.24 E-value: 4.19e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 113 KTIISEKIEE-LNQAAPPSLELNEYQQNAVNQI--MASKGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQA-LILV-PE 187
Cdd:COG1203 107 DHLLAERLERlLPKKSKPRTPINPLQNEALELAleAAEEEPGLFILTAPTGGGKTEAALLFALRLAAKHGGRrIIYAlPF 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 188 IGLTPQTLNRFRERFNVPTAVLHSSL--------TDKKRAQAWM-MAKRG-TAKIVIGTRSAIFTPLLNPG--------- 248
Cdd:COG1203 187 TSIINQTYDRLRDLFGEDVLLHHSLAdldlleeeEEYESEARWLkLLKELwDAPVVVTTIDQLFESLFSNRkgqerrlhn 266
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 249 ----IIILDEEHDtsfkqqsgfrYSARDLAVMRGQFE-----NIPVVLGSAT-PSLESLYNVErrRYQLLSLPGRAGKAK 318
Cdd:COG1203 267 lansVIILDEVQA----------YPPYMLALLLRLLEwlknlGGSVILMTATlPPLLREELLE--AYELIPDEPEELPEY 334
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 499260921 319 LPSLT--IVDLRQKKLiagMSEDLLISIEKHIKNKGQVLLFLNRR 361
Cdd:COG1203 335 FRAFVrkRVELKEGPL---SDEELAELILEALHKGKSVLVIVNTV 376
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
154-292 |
5.65e-08 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 56.29 E-value: 5.65e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 154 LLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERF-NVPT--AVLHSSLTDKKRAQAWMMAKRGTA 230
Cdd:PRK10689 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFaNWPVriEMLSRFRSAKEQTQILAEAAEGKI 704
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499260921 231 KIVIGTRSAIFTPLL--NPGIIILDEEHdtsfkqQSGFRYSARdLAVMRGqfeNIPVVLGSATP 292
Cdd:PRK10689 705 DILIGTHKLLQSDVKwkDLGLLIVDEEH------RFGVRHKER-IKAMRA---DVDILTLTATP 758
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
133-292 |
7.39e-08 |
|
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: 51.92 E-value: 7.39e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 133 LNEYQQNAVNQIMASKGFQTFLLAGVTGSGKTEVYLRCIEKLiqQEKQALILVPEIGLTPQTLNRFrERFNVPTAVLHSS 212
Cdd:cd17926 1 LRPYQEEALEAWLAHKNNRRGILVLPTGSGKTLTALALIAYL--KELRTLIVVPTDALLDQWKERF-EDFLGDSSIGLIG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 213 LTDKKraqawmmaKRGTAKIVIGTRSAIF-------TPLLNPGIIILDEEHdtsfkqqsgfRYSARDLAVMRGQFENIPV 285
Cdd:cd17926 78 GGKKK--------DFDDANVVVATYQSLSnlaeeekDLFDQFGLLIVDEAH----------HLPAKTFSEILKELNAKYR 139
|
....*..
gi 499260921 286 VLGSATP 292
Cdd:cd17926 140 LGLTATP 146
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
137-256 |
4.33e-07 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 53.23 E-value: 4.33e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 137 QQNAVNQIMA--SKGFQT-FLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVP-EIgLTPQ---TLNRFRERFNVPTAVL 209
Cdd:PRK10917 266 QKRVVAEILAdlASPKPMnRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPtEI-LAEQhyeNLKKLLEPLGIRVALL 344
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 499260921 210 HSSLTDKKRAQAWMMAKRGTAKIVIGT-----RSAIFTPLlnpGIIILDEEH 256
Cdd:PRK10917 345 TGSLKGKERREILEAIASGEADIVIGThaliqDDVEFHNL---GLVIIDEQH 393
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
137-256 |
8.77e-06 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 48.89 E-value: 8.77e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 137 QQNAVNQI---MASkGFQTF-LLAGVTGSGKTEVYLRCIEKLIQQEKQALILVP-EIgLTPQ---TLNRFRERFNVPTAV 208
Cdd:COG1200 264 QKRVIAEIaadLAS-PHPMNrLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPtEI-LAEQhyrSLSKLLEPLGIRVAL 341
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 499260921 209 LHSSLTDKKRAQAWMMAKRGTAKIVIGTRsAIFTP---LLNPGIIILDEEH 256
Cdd:COG1200 342 LTGSTKAKERREILAALASGEADIVVGTH-ALIQDdveFKNLGLVVIDEQH 391
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
425-520 |
2.18e-05 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 42.97 E-value: 2.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 425 ERLEAALQQRfpNDDIVRIDrdSTRTKNSMENKLNLIHNREAPILIGTQMIAKGHHFSHLTLVAIIDADSGLysadfrat 504
Cdd:smart00490 1 EELAELLKEL--GIKVARLH--GGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSP-------- 68
|
90
....*....|....*.
gi 499260921 505 ermgQLLTQVAGRAGR 520
Cdd:smart00490 69 ----ASYIQRIGRAGR 80
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
133-256 |
5.91e-05 |
|
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: 44.09 E-value: 5.91e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 133 LNEYQQNAVNQIMAS--KGFQTFLLAGVTGSGKTEVYLRCIEKLIQQE--KQALILVPEIGLTPQTLNRFRERFNVPTAV 208
Cdd:cd18032 1 PRYYQQEAIEALEEAreKGQRRALLVMATGTGKTYTAAFLIKRLLEANrkKRILFLAHREELLEQAERSFKEVLPDGSFG 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 499260921 209 LHSSLTDKKRAqawmmakrgtAKIVIGT----RSAIFTPLLNPG---IIILDEEH 256
Cdd:cd18032 81 NLKGGKKKPDD----------ARVVFATvqtlNKRKRLEKFPPDyfdLIIIDEAH 125
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
131-259 |
1.50e-04 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 43.23 E-value: 1.50e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 131 LELNEYQQNAVNQimASKGFQTFLLAGvTGSGKTEVYLRCIEKLIQQEKQA------LILVPEIGLTPQTLNRF----RE 200
Cdd:cd18036 1 LELRNYQLELVLP--ALRGKNTIICAP-TGSGKTRVAVYICRHHLEKRRSAgekgrvVVLVNKVPLVEQQLEKFfkyfRK 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499260921 201 RFNVptAVLHSSLTDKKraqawmmakrGTAKIVIGTRSAIFTP-----LLNPG------------IIILDEEHDTS 259
Cdd:cd18036 78 GYKV--TGLSGDSSHKV----------SFGQIVKASDVIICTPqilinNLLSGreeervylsdfsLLIFDECHHTQ 141
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
137-291 |
1.92e-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: 42.91 E-value: 1.92e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 137 QQNAVNQIMAskGFQTFLLAGvTGSGKTEVYlrciekliQ-----QEKQALILVPEIGLTPQTLNRFRERfNVPTAVLHS 211
Cdd:cd17920 17 QLEAINAVLA--GRDVLVVMP-TGGGKSLCY--------QlpallLDGVTLVVSPLISLMQDQVDRLQQL-GIRAAALNS 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 212 SLTDKKRAQAWMMAKRGTAKIVIGT----RSAIFTPLLN-------PGIIILDEEHDTSfkqQSG--FRYSARDLAVMRG 278
Cdd:cd17920 85 TLSPEEKREVLLRIKNGQYKLLYVTperlLSPDFLELLQrlperkrLALIVVDEAHCVS---QWGhdFRPDYLRLGRLRR 161
|
170
....*....|...
gi 499260921 279 QFENIPVVLGSAT 291
Cdd:cd17920 162 ALPGVPILALTAT 174
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
159-258 |
7.26e-04 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain] Cd Length: 181 Bit Score: 40.96 E-value: 7.26e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 159 TGSGKTEVYLRCIEKLIQQEK-QALILVPEIGLTPQTLNRFRERFNVPTAV--LHSSLTDKKRAQAWmmakrGTAKIVIG 235
Cdd:cd18035 25 TGLGKTIIAILVAADRLTKKGgKVLILAPSRPLVEQHAENLKRVLNIPDKItsLTGEVKPEERAERW-----DASKIIVA 99
|
90 100 110
....*....|....*....|....*....|
gi 499260921 236 TRSAIFTPLLNPGI-------IILDEEHDT 258
Cdd:cd18035 100 TPQVIENDLLAGRItlddvslLIFDEAHHA 129
|
|
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
132-195 |
3.44e-03 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 40.71 E-value: 3.44e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499260921 132 ELNEYQQNAVNQIMAskGFQT-----FLLAgvTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTL 195
Cdd:COG4889 169 TLRPHQQEAIEAVLA--GFKThdrgkLIMA--CGTGKTFTSLRIAEELAGKGGRVLFLVPSISLLSQTL 233
|
|
| DUF35_N |
pfam12172 |
Rubredoxin-like zinc ribbon domain (DUF35_N); This domain has no known function and is found ... |
374-401 |
3.80e-03 |
|
Rubredoxin-like zinc ribbon domain (DUF35_N); This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Swiss:O53566. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment.
Pssm-ID: 463482 Cd Length: 37 Bit Score: 35.38 E-value: 3.80e-03
10 20
....*....|....*....|....*...
gi 499260921 374 WVMHCDRCDArltlHYFPKRLYCHHCGA 401
Cdd:pfam12172 10 VGQRCPDCGT----VRFPPRAVCPHCGS 33
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
132-202 |
4.98e-03 |
|
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: 38.40 E-value: 4.98e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499260921 132 ELNEYQQNAVNQIMASKGfqTFLLAGVTGSGKTEVYLRCIEK-LIQQEKQALILVPEIGLTPQTLNRFRERF 202
Cdd:cd17921 1 LLNPIQREALRALYLSGD--SVLVSAPTSSGKTLIAELAILRaLATSGGKAVYIAPTRALVNQKEADLRERF 70
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
136-236 |
6.00e-03 |
|
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: 37.66 E-value: 6.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 136 YQQNAVNQIMAS-KGFQTFLLAGVTGSGKTEVYLRCIEKLIQQEKQALILVPEIGLTPQTLNRFRERF-NVPTAVLHSSL 213
Cdd:cd17925 1 GQQKASNALVETiDAKEDLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFpGAAIVLLHGGS 80
|
90 100
....*....|....*....|...
gi 499260921 214 TDKKRAqawmmakrgtAKIVIGT 236
Cdd:cd17925 81 EDQYQR----------SPLVIAT 93
|
|
| COG2888 |
COG2888 |
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ... |
369-412 |
7.72e-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: 7.72e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 499260921 369 CHGCGWVMHCDRCDARltlhYFPK-----RLYCHHCGAAKKIPPTCPQC 412
Cdd:COG2888 3 CPSCGREIAPEGGVAF----YCPNcgealIIRCPKCRKQSNALYFCPKC 47
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
136-314 |
9.96e-03 |
|
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: 38.04 E-value: 9.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 136 YQQNAVNQIMAsKGFQTFLLAGVTGSGKTevylrcIEK-LIQQE-------KQALILVPEiGLTPQTLNRFRERFNVPTA 207
Cdd:cd18011 4 HQIDAVLRALR-KPPVRLLLADEVGLGKT------IEAgLIIKElllrgdaKRVLILCPA-SLVEQWQDELQDKFGLPFL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499260921 208 VLHSSLTDKKRAQAWMMakRGTAKIVI--------GTRSAIFTPLLNPGIIILDEEHDTSFkqqSGFRYSARDLAVMRGQ 279
Cdd:cd18011 76 ILDRETAAQLRRLIGNP--FEEFPIVIvsldllkrSEERRGLLLSEEWDLVVVDEAHKLRN---SGGGKETKRYKLGRLL 150
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 499260921 280 FENIP-VVLGSATP---SLESLYNverrryqLLSL--PGRA 314
Cdd:cd18011 151 AKRARhVLLLTATPhngKEEDFRA-------LLSLldPGRF 184
|
|
| |
