|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
1-728 |
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: 963.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 1 MIYHRIAVNVPLsDGLLTYSHSEPLPQ---GVRVLVPFRNKTVVGIVWETDITPDMDTARILSVQTAFSDEPPLPESWRD 77
Cdd:COG1198 1 MKIAEVALPVPL-DRPFDYLVPEGLELvqpGSRVLVPFGRRQVVGIVVGLKEESDVDPAKLKPILAVLDDEPLLPEELLE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 78 LLSFTSRYYHYPTGQAVFAALPQGLKETRAVEmPQPPLFYALNEAGraqtPPPARFNKKAALWDALLS--GGMTMAALKQ 155
Cdd:COG1198 80 LLRWVADYYLCPLGEVLRLALPAGLRQGYPAR-IKTERYVRLTLGE----ELPKRAPKQRRVLEALREhgGPLTLSELAK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 156 VNAQAAKLIENWAEQSWIETTEAAKPVLRSYHGQASYSEFVLNADQRQASDAIQTALGRFQPFLLYGITGSGKTEVYFDA 235
Cdd:COG1198 155 EAGVSRSVLKALVKKGLLEIEEREVDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVFLLHGVTGSGKTEVYLQA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 236 MAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFaDVPTAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRLAVFTPLPDVGL 315
Cdd:COG1198 235 IAEVLAQGKQALVLVPEIALTPQTVERFRARF-GARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGL 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 316 IVVDEEHDGSFKQDNELRYHARDLAVWRAKQGGCPIILGSATPSLESWHKAQSGAYRLLQLTERAHtAAQLPQVDILNVG 395
Cdd:COG1198 314 IIVDEEHDSSYKQEDGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAG-GAPLPEVELVDMR 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 396 RLKLDNG--FSPQALQLLKQNFEAGGMSLVYLNRRGFAPALFCGDCGHTFGCPNCSAKMVLHQRARQLRCHHCDHREPIP 473
Cdd:COG1198 393 EEPLEGGriLSPPLLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVP 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 474 FKCPDCGNQDLTAVGHGTQRVEETLRALLPKATVVRVDRDSTAHKNDWADLYRRIADNEIDILVGTQMLAKGHDFARLNL 553
Cdd:COG1198 473 KQCPECGSDSLRPFGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTL 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 554 VIVLNADGSLYSADFRAPERLFAELMQVSGRAGRADKTGKVLIQTQLPEHPVFAAVKAQDYAVFAENELNERQMFAMPPF 633
Cdd:COG1198 553 VGVLDADLGLNSPDFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPF 632
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 634 GFQTAVRADAPRVADAMEFLNAAKETLAPLL-PESVSQFGAAPMLMVRLAERERAQIFLESASRQDLHRAVSLWVQVLQQ 712
Cdd:COG1198 633 GRLALLRASGKDEEAAEEFAQALARALRALLsADGVEVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRALLALLEK 712
|
730
....*....|....*.
gi 2559311666 713 NRDGKIRWSVDVDPQE 728
Cdd:COG1198 713 PLPRKVRWSIDVDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
1-728 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 897.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 1 MIYHRIAVNVPLsDGLLTYSHSEPLPQ--GVRVLVPFRNKTVVGIVWETDITPDMDTARILSVQTAFSDEPPLPESWRDL 78
Cdd:PRK05580 2 MKIARVLLPVPL-PRPFDYLIPEGLEVqpGDRVRVPFGNRKLIGVVVGVEEGSEVPADKLKPILEVLDLEPLLPPELLRL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 79 LSFTSRYYHYPTGQAVFAALPQGLKEtravempqpplfyalnEAGRAQtppparfnkkaalwdallsggmtmaalkqvna 158
Cdd:PRK05580 81 LDWAADYYLSPLGEVLRLALLAELAL----------------AASSAV-------------------------------- 112
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 159 qaaklIENWAEQSWIETTEaaKPVLRS-YHGQASYSEFVLNADQRQASDAIQTALGrFQPFLLYGITGSGKTEVYFDAMA 237
Cdd:PRK05580 113 -----LKGLVKKGLIELEE--VEVLRLrPPPDPAFEPPTLNPEQAAAVEAIRAAAG-FSPFLLDGVTGSGKTEVYLQAIA 184
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 238 KVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPtAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRLAVFTPLPDVGLIV 317
Cdd:PRK05580 185 EVLAQGKQALVLVPEIALTPQMLARFRARFGAPV-AVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLII 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 318 VDEEHDGSFKQDNELRYHARDLAVWRAKQGGCPIILGSATPSLESWHKAQSGAYRLLQLTERAHtAAQLPQVDILNVG-R 396
Cdd:PRK05580 264 VDEEHDSSYKQQEGPRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAG-GARLPEVEIIDMReL 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 397 LKLDNG--FSPQALQLLKQNFEAGGMSLVYLNRRGFAPALFCGDCGHTFGCPNCSAKMVLHQRARQLRCHHCDHREPIPF 474
Cdd:PRK05580 343 LRGENGsfLSPPLLEAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPK 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 475 KCPDCGNQDLTAVGHGTQRVEETLRALLPKATVVRVDRDSTAHKNDWADLYRRIADNEIDILVGTQMLAKGHDFARLNLV 554
Cdd:PRK05580 423 ACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLV 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 555 IVLNADGSLYSADFRAPERLFAELMQVSGRAGRADKTGKVLIQTQLPEHPVFAAVKAQDYAVFAENELNERQMFAMPPFG 634
Cdd:PRK05580 503 GVLDADLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFG 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 635 FQTAVRADAPRVADAMEFLNAAKETLAPLLP-ESVSQFGAAPMLMVRLAERERAQIFLESASRQDLHRAVSLWVQVLQQ- 712
Cdd:PRK05580 583 RLALLRASAKDEEKAEKFAQQLAALLPNLLPlLDVEVLGPAPAPIAKIAGRYRYQLLLKSPSRADLQKLLRAWLALLQKl 662
|
730
....*....|....*.
gi 2559311666 713 NRDGKIRWSVDVDPQE 728
Cdd:PRK05580 663 PQARKVRWSIDVDPQS 678
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
219-726 |
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: 587.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 219 LLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADvPTAVLHSQMAAGRRTQDYLRAMLGQAKL 298
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS-QVAVLHSGLSDSEKLQAWRKVKNGEILV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 299 VIGTRLAVFTPLPDVGLIVVDEEHDGSFKQDNELRYHARDLAVWRAKQGGCPIILGSATPSLESWHKAQSGAYRLLQLTE 378
Cdd:TIGR00595 80 VIGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 379 RAHTAAqLPQVDILNVGRLKLDNGFSPQALQLLKQNFEAGGMSLVYLNRRGFAPALFCGDCGHTFGCPNCSAKMVLHQRA 458
Cdd:TIGR00595 160 RVSGRK-PPEVKLIDMRKEPRQSFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKE 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 459 RQLRCHHCDHREPIPFKCPDCGNQDLTAVGHGTQRVEETLRALLPKATVVRVDRDSTAHKNDWADLYRRIADNEIDILVG 538
Cdd:TIGR00595 239 GKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIG 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 539 TQMLAKGHDFARLNLVIVLNADGSLYSADFRAPERLFAELMQVSGRAGRADKTGKVLIQTQLPEHPVFAAVKAQDYAVFA 618
Cdd:TIGR00595 319 TQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEAFY 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 619 ENELNERQMFAMPPFGFQTAVRADAPRVADAMEFLNAAKETLAPLLPESVSQFGAAPMLMVRLAERERAQIFLESASRQD 698
Cdd:TIGR00595 399 EQELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLEVLGPSPAPIAKIAGRYRYQILLKSKSFLV 478
|
490 500
....*....|....*....|....*...
gi 2559311666 699 LHRAVSLWvqVLQQNRDGKIRWSVDVDP 726
Cdd:TIGR00595 479 LQKLVNKT--LLKEIPSSSVYCEVDVDP 504
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
389-626 |
1.53e-129 |
|
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: 383.52 E-value: 1.53e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 389 VDILNVGRLKLDNGFSPQALQLLKQNFEAGGMSLVYLNRRGFAPALFCGDCGHTFGCPNCSAKMVLHQRARQLRCHHCDH 468
Cdd:cd18804 1 IEIVDMKEEELKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHYCGY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 469 REPIPFKCPDCGNQDLTAVGHGTQRVEETLRALLPKATVVRVDRDSTAHKNDWADLYRRIADNEIDILVGTQMLAKGHDF 548
Cdd:cd18804 81 QEPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKGLDF 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2559311666 549 ARLNLVIVLNADGSLYSADFRAPERLFAELMQVSGRAGRADKTGKVLIQTQLPEHPVFAAVKAQDYAVFAENELNERQ 626
Cdd:cd18804 161 PNVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAERK 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
201-379 |
2.71e-101 |
|
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: 308.37 E-value: 2.71e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 201 QRQASDAIQTALGRFQPFLLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADvPTAVLHSQMA 280
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD-KVAVLHSKLS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 281 AGRRTQDYLRAMLGQAKLVIGTRLAVFTPLPDVGLIVVDEEHDGSFKQDNELRYHARDLAVWRAKQGGCPIILGSATPSL 360
Cdd:cd17929 80 DKERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPSL 159
|
170
....*....|....*....
gi 2559311666 361 ESWHKAQSGAYRLLQLTER 379
Cdd:cd17929 160 ESYYNAQQGKYRLLQLTER 178
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
235-726 |
2.26e-36 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 145.85 E-value: 2.26e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 235 AMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPTAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRLAVFTPLPDVG 314
Cdd:PRK14873 180 AAAATLRAGRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLG 259
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 315 LIVVDEEHDGSFKQDNELRYHARDLAVWRAKQGGCPIILGSATPSLESWHKAQSG-AYRLlqLTERAHTAAQLPQVDILN 393
Cdd:PRK14873 260 LVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTAEAQALVESGwAHDL--VAPRPVVRARAPRVRALG 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 394 VGRLKLDNGFSPQ-------ALQLLKQNFEAGGMsLVYLNRRGFAPALFCGDCGHTFGCPNCSAKMVLHQRARQLRCHHC 466
Cdd:PRK14873 338 DSGLALERDPAARaarlpslAFRAARDALEHGPV-LVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWC 416
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 467 DHREPiPFKCPDCGNQDLTAVGHGTQRVEETLRALLPKATVVRVDRDstahkndwadlyrRIADnEID---ILV----GT 539
Cdd:PRK14873 417 GRAAP-DWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVVTSGGD-------------QVVD-TVDagpALVvatpGA 481
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 540 QMLAKGHDFArlnlVIVLNADGSLYSADFRAPERLFAELMQVSGRAGRADKTGKVLIqtqLPEhPVFAAVKA---QDYAV 616
Cdd:PRK14873 482 EPRVEGGYGA----ALLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVV---VAE-SSLPTVQAlirWDPVG 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 617 FAENELNERQMFAMPPfgfqtAVRA---DAPRVAdAMEFLNAAKetlaplLPESVSQFGAAPM-LMVRL-------AERE 685
Cdd:PRK14873 554 HAERELAERAEVGFPP-----AVRMaavDGRPAA-VAALLEAAG------LPDGAEVLGPVPLpPGVRRpagidarEDRV 621
|
490 500 510 520
....*....|....*....|....*....|....*....|....*
gi 2559311666 686 RAQIFLESASRQD----LHRAVSlwVQVLQQnRDGKIRwsVDVDP 726
Cdd:PRK14873 622 RALVRVPRARGAElaaaLRRAVA--VRSARR-EPGPLR--VQIDP 661
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
5-99 |
3.17e-26 |
|
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: 102.92 E-value: 3.17e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 5 RIAVNVPLsDGLLTYSHSEPLPQ--GVRVLVPFRNKTVVGIVWETDITPDMDTARILSVQTAFSDEPPLPESWRDLLSFT 82
Cdd:pfam17764 1 EVAVPLPL-DRPFDYRVPEELAVkiGMRVLVPFGKRKVTGIVVGLSEESEVDPEKLKPILEVLDEEPLLTPELLELARWM 79
|
90
....*....|....*..
gi 2559311666 83 SRYYHYPTGQAVFAALP 99
Cdd:pfam17764 80 AEYYLCPLGEVLRAALP 96
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
632-726 |
6.77e-23 |
|
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: 93.44 E-value: 6.77e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 632 PFGFQTAVRADAPRVADAMEFLNAAKETLAPLLPESVSQ-FGAAPMLMVRLAERERAQIFLESASRQDLHRAVSLWVQVL 710
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAELLKELLKLQGVEiLGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRELLEEL 80
|
90
....*....|....*.
gi 2559311666 711 QQNRDGKIRWSVDVDP 726
Cdd:pfam18074 81 QKLPKRKVRISIDVDP 96
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
218-357 |
4.69e-20 |
|
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: 87.07 E-value: 4.69e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 218 FLLYGITGSGKTEVYFDAMAKVLA-QGRQVLFLLPEINLTPQLLKRVEDRFA-DVPTAVLHSQMAAGRRTqdylRAMLGQ 295
Cdd:cd00046 4 VLITAPTGSGKTLAALLAALLLLLkKGKKVLVLVPTKALALQTAERLRELFGpGIRVAVLVGGSSAEERE----KNKLGD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 296 AKLVIGTRLAVFTPL--------PDVGLIVVDEEHDGSFKQDNELRYharDLAVWRAKQGGCPIILGSAT 357
Cdd:cd00046 80 ADIIIATPDMLLNLLlredrlflKDLKLIIVDEAHALLIDSRGALIL---DLAVRKAGLKNAQVILLSAT 146
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
194-595 |
1.56e-19 |
|
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: 92.24 E-value: 1.56e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 194 EFVLNADQRQASDAIQTALGRFQPFLLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPTA 273
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKKKEEHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFPGVDIA 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 274 VLHsqmaaGRRTQDYlramlGQAKLVIGT-----RLA-VFtplpDvgLIVVDEEHDGSFKQDNELRYhardlAVWRAKQG 347
Cdd:COG4098 188 ALY-----GGSEEKY-----RYAQLVIATthqllRFYqAF----D--LLIIDEVDAFPYSGDPMLQY-----AVKRARKP 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 348 GCPIILGSATPSlESWHK-AQSGAYRLLQLTERAHTAAqLPqvdilnVGRLKLDNGfspqalqlLKQNfeaggmslvyLN 426
Cdd:COG4098 247 DGKLIYLTATPS-KALQRqVKRGKLKVVKLPARYHGHP-LP------VPKFKWLGN--------WKKR----------LR 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 427 RRGFAPALfcgdcghtfgcpncsAKMVLHQRARQLRChhcdhrepIPFkCPDcgnqdltaVGHGtQRVEETLRALLPKAT 506
Cdd:COG4098 301 RGKLPRKL---------------LKWLKKRLKEGRQL--------LIF-VPT--------IELL-EQLVALLQKLFPEER 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 507 VVRV---DRDSTAHKNDWadlyRriaDNEIDILVGTQMLAKGHDFARLNlVIVLNADGSLYSAdfraperlfAELMQVSG 583
Cdd:COG4098 348 IAGVhaeDPERKEKVQAF----R---DGEIPILVTTTILERGVTFPNVD-VAVLGADHPVFTE---------AALVQIAG 410
|
410
....*....|....
gi 2559311666 584 RAGRADK--TGKVL 595
Cdd:COG4098 411 RVGRSADypTGEVI 424
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
195-369 |
3.84e-15 |
|
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: 73.99 E-value: 3.84e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 195 FVLNADQRQASDAIQTALGRFQPF--LLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPT 272
Cdd:cd17918 14 FSLTKDQAQAIKDIEKDLHSPEPMdrLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLPFINV 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 273 AVLhsqmAAGRRTQDylramLGQAKLVIGTR--LAVFTPLPDVGLIVVDEEHDGSFKQDNELRyhardlavwraKQGGCP 350
Cdd:cd17918 94 ELV----TGGTKAQI-----LSGISLLVGTHalLHLDVKFKNLDLVIVDEQHRFGVAQREALY-----------NLGATH 153
|
170
....*....|....*....
gi 2559311666 351 IILGSATPSLESWHKAQSG 369
Cdd:cd17918 154 FLEATATPIPRTLALALSG 172
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
198-359 |
5.44e-14 |
|
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: 70.35 E-value: 5.44e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 198 NADQRQASDAIQTalGRfqPFLLYGITGSGKTEVYFDAMAKVLAQ---GRQVLFLLPEINLTPQLLKRVEDRFADVPTAV 274
Cdd:pfam00270 1 TPIQAEAIPAILE--GR--DVLVQAPTGSGKTLAFLLPALEALDKldnGPQALVLAPTRELAEQIYEELKKLGKGLGLKV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 275 LHSQmaaGRRTQDYLRAMLGQAKLVIGT--RLAVFT----PLPDVGLIVVDEEH---DGSFKQDneLRYHARDLavwrak 345
Cdd:pfam00270 77 ASLL---GGDSRKEQLEKLKGPDILVGTpgRLLDLLqerkLLKNLKLLVLDEAHrllDMGFGPD--LEEILRRL------ 145
|
170
....*....|....
gi 2559311666 346 QGGCPIILGSATPS 359
Cdd:pfam00270 146 PKKRQILLLSATLP 159
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
194-322 |
4.48e-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: 68.37 E-value: 4.48e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 194 EFVLNADQRQASDAIQTALGRFQPF--LLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVP 271
Cdd:cd17991 13 PYEETPDQLKAIEEILKDMESGKPMdrLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFANFP 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 272 TAVLH----SQMAAGRRTQDYLRAmlGQAKLVIGT-RLA----VFtplPDVGLIVVDEEH 322
Cdd:cd17991 93 VNVELlsrfTTAAEQREILEGLKE--GKVDIVIGThRLLskdvEF---KNLGLLIIDEEQ 147
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
195-361 |
1.11e-12 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 67.52 E-value: 1.11e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 195 FVLNADQRQAsdaIQTALGRFQPFLLYGITGSGKTEVYFDAMAKVLAQGR--QVLFLLPEINLTPQLLKRVEDRFAD--- 269
Cdd:smart00487 7 EPLRPYQKEA---IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELKKLGPSlgl 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 270 VPTAVLHSQmaagRRTQDYLRAMLGQAKLVIGT--RL-----AVFTPLPDVGLIVVDEEH---DGSFKQD-NELRYHARD 338
Cdd:smart00487 84 KVVGLYGGD----SKREQLRKLESGKTDILVTTpgRLldlleNDKLSLSNVDLVILDEAHrllDGGFGDQlEKLLKLLPK 159
|
170 180
....*....|....*....|...
gi 2559311666 339 lavwrakqgGCPIILGSATPSLE 361
Cdd:smart00487 160 ---------NVQLLLLSATPPEE 173
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
445-471 |
3.71e-12 |
|
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: 61.00 E-value: 3.71e-12
10 20
....*....|....*....|....*..
gi 2559311666 445 CPNCSAKMVLHQRARQLRCHHCDHREP 471
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
200-357 |
4.35e-12 |
|
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: 64.24 E-value: 4.35e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 200 DQRQASDAIQTALGRFQPFLLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPTAVLHSqm 279
Cdd:cd17925 1 GQQKASNALVETIDAKEDLLVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFPGAAIVLLHG-- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 280 aagrRTQDYLRAmlgqAKLVIGT--RLAVFTPLPDvgLIVVDEEHDGSFKQDNELRYhardlAVWRAKQGGCPIILGSAT 357
Cdd:cd17925 79 ----GSEDQYQR----SPLVIATthQLLRFYRAFD--LLIIDEVDAFPYAGDPMLYY-----AVEKARKEEGSLIYLTAT 143
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
154-592 |
8.05e-12 |
|
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: 68.92 E-value: 8.05e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 154 KQVNAQAAKLIENWAEQSWIETTeAAKPVLRSYHGQASYSEFVLNADQRQASDAIQTALGRFQPF--LLYGITGSGKTEV 231
Cdd:TIGR00580 410 KSVREIAAKLIELYAKRKAIKGH-AFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMdrLVCGDVGFGKTEV 488
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 232 YFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPT--AVLHSQMAAGRRTQDYLRAMLGQAKLVIGTR--LAVF 307
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVtiELLSRFRSAKEQNEILKELASGKIDILIGTHklLQKD 568
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 308 TPLPDVGLIVVDEEHDGSFKQDN---ELRYHARDLAVwrakqggcpiilgSATPSLESWHKAQSGAYRLLQLTERahtaa 384
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQKEklkELRTSVDVLTL-------------SATPIPRTLHMSMSGIRDLSIIATP----- 630
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 385 qlPQvdilnvGRLKLDNGFSPQALQLLKqnfEAGGMSLvylnRRGfapalfcgdcGHTFgcpncsakmVLHQRARQLrch 464
Cdd:TIGR00580 631 --PE------DRLPVRTFVMEYDPELVR---EAIRREL----LRG----------GQVF---------YVHNRIESI--- 673
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 465 hcdhrepipfkcpdcgnqdltavghgtQRVEETLRALLPKATVVrvdrdsTAH----KNDWADLYRRIADNEIDILVGTQ 540
Cdd:TIGR00580 674 ---------------------------EKLATQLRELVPEARIA------IAHgqmtENELEEVMLEFYKGEFQVLVCTT 720
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 2559311666 541 MLAKGHDFARLNLVIVLNAD--GslysadfraperlFAELMQVSGRAGRADKTG 592
Cdd:TIGR00580 721 IIETGIDIPNANTIIIERADkfG-------------LAQLYQLRGRVGRSKKKA 761
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
194-358 |
1.82e-11 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 63.07 E-value: 1.82e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 194 EFVLNADQRQASDAIQTALG-RFQPFLLYGITGSGKTEVYFDAMAKVLAQG--RQVLFLLPEINLTPQLLKRVEDRFadv 270
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKnGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFL--- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 271 PTAVLHSQMAAGRRtqdyLRAMLGQAKLVIGTRLAVFTPLPDV---------GLIVVDEEHDGSFKQdnelryhardlav 341
Cdd:pfam04851 78 PNYVEIGEIISGDK----KDESVDDNKIVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGASS------------- 140
|
170 180
....*....|....*....|
gi 2559311666 342 WR--AKQGGCPIILG-SATP 358
Cdd:pfam04851 141 YRniLEYFKPAFLLGlTATP 160
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
132-358 |
1.32e-08 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 58.11 E-value: 1.32e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 132 RFNKKAALWDALLSGGMTMAALKQVNAQAAKLIENWAEQSWIETTEAAKPVLRSY---HGQASYSEFVLNADQRQASDAI 208
Cdd:COG1061 13 KLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEAleaGDEASGTSFELRPYQQEALEAL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 209 QTALGR-FQPFLLYGITGSGKTEVYFDAMAKVLAQGRqVLFLLPEINLTPQLLKRVEDRFADVPtavlhsqmAAGRRTQD 287
Cdd:COG1061 93 LAALERgGGRGLVVAPTGTGKTVLALALAAELLRGKR-VLVLVPRRELLEQWAEELRRFLGDPL--------AGGGKKDS 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 288 ylramlgQAKLVIGT-----RLAVFTPLPD-VGLIVVDEEHdgsfkqdnelryHARDlAVWR--AKQGGCPIILG-SATP 358
Cdd:COG1061 164 -------DAPITVATyqslaRRAHLDELGDrFGLVIIDEAH------------HAGA-PSYRriLEAFPAAYRLGlTATP 223
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
195-358 |
3.12e-08 |
|
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: 54.85 E-value: 3.12e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 195 FVLNADQRQASDAIQTALGRFQPF--LLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLP-EInLTPQLLKRVEDRFA--D 269
Cdd:cd17992 44 FELTGAQKRVIDEILRDLASEKPMnrLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKLLEplG 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 270 VPTAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRlAVFTP---LPDVGLIVVDEEHDGSFKQDNELRyhardlavwraKQ 346
Cdd:cd17992 123 IRVALLTGSTKAKEKREILEKIASGEIDIVIGTH-ALIQEdveFHNLGLVIIDEQHRFGVEQRLKLR-----------EK 190
|
170
....*....|...
gi 2559311666 347 GGCP-IILGSATP 358
Cdd:cd17992 191 GETPhVLVMTATP 203
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
492-588 |
8.98e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 49.90 E-value: 8.98e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 492 QRVEETLRALlpKATVVRVDRDSTAHKNDwaDLYRRIADNEIDILVGTQMLAKGHDFARLNLVIVLNADGSlysadfrap 571
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEERE--EILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWS--------- 67
|
90
....*....|....*..
gi 2559311666 572 erlFAELMQVSGRAGRA 588
Cdd:smart00490 68 ---PASYIQRIGRAGRA 81
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
152-369 |
2.64e-07 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 54.37 E-value: 2.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 152 ALKQVNAQAAKLIENWAEQswietteAAKPVLRSYHGQASYSEFV------LNADQRQASDAIQTALgrFQPF----LLY 221
Cdd:PRK10689 557 AAEKVRDVAAELLDIYAQR-------AAKEGFAFKHDREQYQLFCdsfpfeTTPDQAQAINAVLSDM--CQPLamdrLVC 627
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 222 GITGSGKTEVYFDAMAKVLAQGRQVLFLLPEINLTPQLLKRVEDRFADVPTAV-LHSQMAAGRRTQDYL-RAMLGQAKLV 299
Cdd:PRK10689 628 GDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIeMLSRFRSAKEQTQILaEAAEGKIDIL 707
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2559311666 300 IGTR--LAVFTPLPDVGLIVVDEEHdgsfkqdnelRYHARDLAVWRAKQGGCPIILGSATPSLESWHKAQSG 369
Cdd:PRK10689 708 IGTHklLQSDVKWKDLGLLIVDEEH----------RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSG 769
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
98-322 |
6.43e-07 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 52.85 E-value: 6.43e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 98 LPQGLKEtravEMPQPPLFYALNEAGRaqtpPPARFNKKAAL----WDALLSGGMTMAALKQVNAQAAKLIenwaeqsWI 173
Cdd:PRK10917 181 LPEELLE----KYGLLSLAEALRAIHF----PPSDEDLHPARrrlkFEELFALQLSLLLLRAGRRSKKAGP-------LP 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 174 ETTEAAKPVLRSYhgqasysEFVLNADQRQASDAIQTALGRFQP--FLLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLP 251
Cdd:PRK10917 246 YDGELLKKFLASL-------PFELTGAQKRVVAEILADLASPKPmnRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAP 318
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2559311666 252 -EInLTPQLLKRVEDRFAD--VPTAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRlAVFTP---LPDVGLIVVDEEH 322
Cdd:PRK10917 319 tEI-LAEQHYENLKKLLEPlgIRVALLTGSLKGKERREILEAIASGEADIVIGTH-ALIQDdveFHNLGLVIIDEQH 393
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
195-322 |
9.73e-07 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 52.36 E-value: 9.73e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 195 FVLNADQRQASDAIQTALGRFQPF--LLYGITGSGKTEVYFDAMAKVLAQGRQVLFLLP-EI-------NLTpQLLKRve 264
Cdd:COG1200 258 FELTGAQKRVIAEIAADLASPHPMnrLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPtEIlaeqhyrSLS-KLLEP-- 334
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2559311666 265 drfADVPTAVLHSQMAAGRRTQDYLRAMLGQAKLVIGTRlAVFTPlpDV-----GLIVVDEEH 322
Cdd:COG1200 335 ---LGIRVALLTGSTKAKERREILAALASGEADIVVGTH-ALIQD--DVefknlGLVVIDEQH 391
|
|
| COG2888 |
COG2888 |
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ... |
440-482 |
1.53e-05 |
|
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: 42.80 E-value: 1.53e-05
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 2559311666 440 GHTFGCPNCSAKMVLhqrarqlRCHHCDHREPIPFKCPDCGNQ 482
Cdd:COG2888 15 GVAFYCPNCGEALII-------RCPKCRKQSNALYFCPKCGFE 50
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
491-588 |
1.86e-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: 44.12 E-value: 1.86e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 491 TQRVEETLRALLPKATVVRVDR-DSTAHKNDWADLYRRIADNEIDILVGTQMLAKGHDFARLNLVIVLNADGSLysadfr 569
Cdd:pfam00271 22 SQTKKTLEAELLLEKEGIKVARlHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNP------ 95
|
90
....*....|....*....
gi 2559311666 570 aperlfAELMQVSGRAGRA 588
Cdd:pfam00271 96 ------ASYIQRIGRAGRA 108
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
531-596 |
1.51e-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: 40.77 E-value: 1.51e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2559311666 531 NEIDILVGTQMLAKGHDFARLNLVIvlnadgslysadFRAPERLFAELMQVSGRAGRADKTGKVLI 596
Cdd:cd18785 21 SSLEILVATNVLGEGIDVPSLDTVI------------FFDPPSSAASYIQRVGRAGRGGKDEGEVI 74
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
224-322 |
2.82e-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: 39.55 E-value: 2.82e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 224 TGSGKTEVYFDAMAKVLAQGRQ-VLFLLPEINLTPQLLKRVEDRFADVPTAVlhsqmaaGRRTQDY--LRAMLGQAKLVI 300
Cdd:cd17921 26 TSSGKTLIAELAILRALATSGGkAVYIAPTRALVNQKEADLRERFGPLGKNV-------GLLTGDPsvNKLLLAEADILV 98
|
90 100 110
....*....|....*....|....*....|
gi 2559311666 301 GT--RLAVFT------PLPDVGLIVVDEEH 322
Cdd:cd17921 99 ATpeKLDLLLrnggerLIQDVRLVVVDEAH 128
|
|
| zf-NADH-PPase |
pfam09297 |
NADH pyrophosphatase zinc ribbon domain; This domain is found in between two duplicated NUDIX ... |
441-470 |
2.91e-03 |
|
NADH pyrophosphatase zinc ribbon domain; This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure.
Pssm-ID: 430510 [Multi-domain] Cd Length: 32 Bit Score: 35.65 E-value: 2.91e-03
10 20 30
....*....|....*....|....*....|
gi 2559311666 441 HTFgCPNCSAKMVLHQRARQLRCHHCDHRE 470
Cdd:pfam09297 3 HRF-CGRCGAPTVPAEGGWARVCPSCGHEH 31
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
196-252 |
4.72e-03 |
|
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain] Cd Length: 229 Bit Score: 39.14 E-value: 4.72e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 2559311666 196 VLNADQRQASDAIQTALGRFQPFLLYGITGSGKTEVYFDAMAkvlaqgrQVLFLLPE 252
Cdd:cd18038 1 ELNDEQKLAVRNIVTGTSRPPPYIIFGPPGTGKTVTLVEAIL-------QVLRQPPE 50
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
492-592 |
8.55e-03 |
|
C-terminal 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 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 37.32 E-value: 8.55e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559311666 492 QRVEETLRALLPKATVVrvdrdsTAHKNDWADLYRRI----ADNEIDILVGTQMLAKGHDFARLNLVIVLNAD--Gslys 565
Cdd:cd18810 39 EKLATQLRQLVPEARIA------IAHGQMTENELEEVmlefAKGEYDILVCTTIIESGIDIPNANTIIIERADkfG---- 108
|
90 100
....*....|....*....|....*..
gi 2559311666 566 adfraperlFAELMQVSGRAGRADKTG 592
Cdd:cd18810 109 ---------LAQLYQLRGRVGRSKERA 126
|
|
| RING-HC_TRIM13_like_C-V |
cd16581 |
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ... |
439-479 |
9.76e-03 |
|
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.
Pssm-ID: 438243 [Multi-domain] Cd Length: 50 Bit Score: 34.79 E-value: 9.76e-03
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 2559311666 439 CGHTFgCPNCSAKMvlhqrarqlrCHHCDHREPIPFKCPDC 479
Cdd:cd16581 20 CSHTF-CKNCLEKL----------LAASGYYLLASLKCPTC 49
|
|
| |
