|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
1-692 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 1072.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 1 MSQLLSAIPLNSLSGVGAKVAEKLEKVGLNNVQDLLFHLPLRYEDRTRIYPIVKLHAGLWAAVQGKVMHVDTIFGKRKML 80
Cdd:PRK10917 2 SLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRRL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 81 AVKISDGNGTITLRFFNFTAGM-KNNFAEGKQVHAYGEIKRGNMGLEIVHPDYKFFAPRQQPDVEAnLTPVYPTTEGLRQ 159
Cdd:PRK10917 82 TVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGR-LTPVYPLTEGLKQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 160 VTLRNLTDQALELIDkaAVNELLPSGLYDHQ--ITLAQALHTIHRPPPGIDLelfdegkHPAQLRLIMEELLAQNLSMLS 237
Cdd:PRK10917 161 KTLRKLIKQALELLD--ALPELLPEELLEKYglLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLLL 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 238 VRSKGQQDKAMPFPPVNTLKDKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHGQ 317
Cdd:PRK10917 232 LRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGY 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 318 QVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQEHVEFKNLGLVIIDE 397
Cdd:PRK10917 312 QAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDE 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 398 QHRFGVHQRLELREKGAKqgyyPHQLVMTATPIPRTLAMTAYADLETSIIDELPPGRAPIQTVAIPDTKRDDIVERVKNA 477
Cdd:PRK10917 392 QHRFGVEQRLALREKGEN----PHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREE 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 478 ClNEGKQAYWVCTLIDESEVLEAQAAADTAEELQRKLPDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVD 557
Cdd:PRK10917 468 I-AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVD 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 558 VPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLYHSPLSKTAQKRLGVLRESNDGFVIAQRDLEIRGPGELLGT 637
Cdd:PRK10917 547 VPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGT 626
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 1140790570 638 KQTGLADFKIADLVRDQRLIPEVQRIARHIHDSYPDNAKAIINRWLGERDVYSKA 692
Cdd:PRK10917 627 RQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
1-686 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 1051.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 1 MSQLlsAIPLNSLSGVGAKVAEKLEKVGLNNVQDLLFHLPLRYEDRTRIYPIVKLHAGLWAAVQGKVMHVDTIF--GKRK 78
Cdd:COG1200 1 MAPL--DTPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRR 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 79 MLAVKISDGNGTITLRFFNFtAGMKNNFAEGKQVHAYGEIKRGNMGLEIVHPDYKFFAPRQQPDVEAnLTPVYPTTEGLR 158
Cdd:COG1200 79 ILEVTLSDGTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDEEEAELAGR-LTPVYPLTEGLS 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 159 QVTLRNLTDQALELIDKAaVNELLPSGLYDHQ--ITLAQALHTIHRPPPGIDLelfdegkHPAQLRLIMEELLAQNLSML 236
Cdd:COG1200 157 QKTLRKLIRQALDLLAPD-LPEPLPEELRARYglPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALL 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 237 SVRSKGQQDKAMPFPPVNTLKDKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHG 316
Cdd:COG1200 229 LRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAG 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 317 QQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQEHVEFKNLGLVIID 396
Cdd:COG1200 309 YQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVID 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 397 EQHRFGVHQRLELREKGAkqgyYPHQLVMTATPIPRTLAMTAYADLETSIIDELPPGRAPIQTVAIPDTKRDDIVERVKN 476
Cdd:COG1200 389 EQHRFGVEQRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIRE 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 477 AClNEGKQAYWVCTLIDESEVLEAQAAADTAEELQRKLPDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGV 556
Cdd:COG1200 465 EI-AKGRQAYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGV 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 557 DVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLYHSPLSKTAQKRLGVLRESNDGFVIAQRDLEIRGPGELLG 636
Cdd:COG1200 544 DVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLG 623
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|.
gi 1140790570 637 TKQTGLADFKIADLVRDQRLIPEVQRIARHIHDSYPDNAK-AIINRWLGER 686
Cdd:COG1200 624 TRQSGLPDLRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLR 674
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
28-664 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 817.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 28 GLNNVQDLLFHLPLRYEDRTRIYPIVKLHAGLWAAVQGKVMHVDTI-FGKRKMLAVKISDGNG-TITLRFFNfTAGMKNN 105
Cdd:TIGR00643 2 GIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFgFKRRKVLKLRLKDGGYkKLELRFFN-RAFLKKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 106 FAEGKQVHAYGEIKRGNMGLEIVHPDYKffAPRQQPDVEANLTPVYPTTEGLRQVTLRNLTDQALELIDKAaVNELLPSG 185
Cdd:TIGR00643 81 FKVGSKVVVYGKVKSSKFKAYLIHPEFI--SEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPEE 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 186 LYD--HQITLAQALHTIHRPPpgiDLELfdegKHPAQLRLIMEELLAQNLSMLSVRSKG-QQDKAMPFPPVNTLKDKLLA 262
Cdd:TIGR00643 158 LREkyGLLSLEDALRAIHFPK---TLSL----LELARRRLIFDEFFYLQLAMLARRLGEkQQFSAPPANPSEELLTKFLA 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 263 QLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEA 342
Cdd:TIGR00643 231 SLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAP 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 343 MGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKGaKQGYYPHQ 422
Cdd:TIGR00643 311 LGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKG-QGGFTPHV 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 423 LVMTATPIPRTLAMTAYADLETSIIDELPPGRAPIQTVAIPDTKRDdIVERVKNACLNEGKQAYWVCTLIDESEVLEAQA 502
Cdd:TIGR00643 390 LVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKD-IVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKA 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 503 AADTAEELQRKLPDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRG 582
Cdd:TIGR00643 469 AEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRG 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 583 RVGRGSVASHCVLLYHSPLSKTAQKRLGVLRESNDGFVIAQRDLEIRGPGELLGTKQTGLADFKIADLVRDQRLIPEVQR 662
Cdd:TIGR00643 549 RVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEARE 628
|
..
gi 1140790570 663 IA 664
Cdd:TIGR00643 629 DA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
223-451 |
1.21e-112 |
|
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: 338.35 E-value: 1.21e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 223 LIMEELLAQNLSMLSVRSKGQQDKAMPFPPVNTLKDKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKT 302
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 303 LVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQ 382
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1140790570 383 EHVEFKNLGLVIIDEQHRFGVHQRLELREKgakqGYYPHQLVMTATPIPRTLAMTAYADLETSIIDELP 451
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREK----GETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
220-641 |
9.73e-106 |
|
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: 342.80 E-value: 9.73e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 220 QLRLIMEELLaqnlsmlSVRSKGQQDKAMPFPPVNTLKDKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGS 299
Cdd:TIGR00580 411 SVREIAAKLI-------ELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGF 483
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 300 GKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHA 379
Cdd:TIGR00580 484 GKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK 563
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 380 LFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKGAKQgyypHQLVMTATPIPRTLAMTAYADLETSIIDELPPGRAPIQT 459
Cdd:TIGR00580 564 LLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSV----DVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRT 639
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 460 VAIPdtkRDDIVerVKNACLNE---GKQAYWVCTLIDESEVLEAQaaadtaeeLQRKLPDVKIGLVHGRMKPAEKQAVMQ 536
Cdd:TIGR00580 640 FVME---YDPEL--VREAIRREllrGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVML 706
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 537 EFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLYHS--PLSKTAQKRLGVLRE 614
Cdd:TIGR00580 707 EFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHqkALTEDAQKRLEAIQE 786
|
410 420 430
....*....|....*....|....*....|
gi 1140790570 615 SND---GFVIAQRDLEIRGPGELLGTKQTG 641
Cdd:TIGR00580 787 FSElgaGFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
246-641 |
1.71e-102 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 338.19 E-value: 1.71e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 246 KAMPFPPVNTLKDKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTlvaalaavralE----------- 314
Cdd:COG1197 565 KGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKT-----------Evalraafkavm 633
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 315 HGQQVALMAPTELLAEQHAINFANWFEAMGIQVGWL-----AGKLKgktrETeLARIASGEAQMVVGTHALFQEHVEFKN 389
Cdd:COG1197 634 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLsrfrtAKEQK----ET-LEGLADGKVDIVIGTHRLLSKDVKFKD 708
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 390 LGLVIIDEQHRFGVHQ--RL-ELREKgakqgyyPHQLVMTATPIPRTL--AMTAYADLetSIIDELPPGRAPIQTVAIPd 464
Cdd:COG1197 709 LGLLIIDEEQRFGVRHkeKLkALRAN-------VDVLTLTATPIPRTLqmSLSGIRDL--SIIATPPEDRLPVKTFVGE- 778
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 465 tkRDDIVerVKNACLNE---GKQAYWVC----TlIDEsevleaqaaadTAEELQRKLPDVKIGLVHGRMKPAEKQAVMQE 537
Cdd:COG1197 779 --YDDAL--IREAILREllrGGQVFYVHnrveD-IEK-----------VAARLQELVPEARIAVAHGQMSERELERVMLD 842
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 538 FKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLY--HSPLSKTAQKRLGVLRES 615
Cdd:COG1197 843 FYEGEFDVLVCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYppDKVLTEDAEKRLEAIQEF 922
|
410 420
....*....|....*....|....*....
gi 1140790570 616 ND---GFVIAQRDLEIRGPGELLGTKQTG 641
Cdd:COG1197 923 TElgaGFKLAMHDLEIRGAGNLLGEEQSG 951
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
456-614 |
1.79e-75 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 239.55 E-value: 1.79e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 456 PIQTVAIPDTKRDDIVERVKNaCLNEGKQAYWVCTLIDESEVLEAQAAADTAEELQRKL-PDVKIGLVHGRMKPAEKQAV 534
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVRE-EIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 535 MQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLYHSPLSKTAQKRLGVLRE 614
Cdd:cd18811 80 MAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
265-641 |
6.29e-69 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 244.65 E-value: 6.29e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 265 PFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMG 344
Cdd:PRK10689 598 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWP 677
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 345 IQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKGAKQGYyphqLV 424
Cdd:PRK10689 678 VRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDI----LT 753
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 425 MTATPIPRTL--AMTAYADLetSIIDELPPGRAPIQTVAipdTKRDDIVerVKNACLNE---GKQAYWVctlidESEVLE 499
Cdd:PRK10689 754 LTATPIPRTLnmAMSGMRDL--SIIATPPARRLAVKTFV---REYDSLV--VREAILREilrGGQVYYL-----YNDVEN 821
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 500 AQAAADTAEELqrkLPDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQ 579
Cdd:PRK10689 822 IQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQ 898
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1140790570 580 LRGRVGRGSVASHCVLLYHSP--LSKTAQKRLGVLRESND---GFVIAQRDLEIRGPGELLGTKQTG 641
Cdd:PRK10689 899 LRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSG 965
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
456-614 |
8.82e-67 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases 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: 350179 [Multi-domain] Cd Length: 160 Bit Score: 216.75 E-value: 8.82e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 456 PIQTVAIPDTKRDDIVERVKNaCLNEGKQAYWVCTLIDESEVLEAQAAADTAEELQRKLPDVKIGLVHGRMKPAEKQAVM 535
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIER-ELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 536 QEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLY--HSPLSKTAQKRLGVLR 613
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYpdPKKLTETAKKRLRAIA 159
|
.
gi 1140790570 614 E 614
Cdd:cd18792 160 E 160
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
258-448 |
4.07e-55 |
|
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: 186.62 E-value: 4.07e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 258 DKLLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFA 337
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 338 NWFEAMGIQVGWLAGKLKGKTRETELARIASGEAQMVVGTHALFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKgakqg 417
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL----- 160
|
170 180 190
....*....|....*....|....*....|....*
gi 1140790570 418 yYP--HQLVMTATPIPRTL--AMTAYADLetSIID 448
Cdd:cd17991 161 -RPnvDVLTLSATPIPRTLhmALSGIRDL--SVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
260-448 |
2.77e-54 |
|
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: 184.16 E-value: 2.77e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 260 LLAQLPFSPTNAQARVTQEIEADLEKPHPMMRLVQGDVGSGKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFANW 339
Cdd:cd17918 8 LCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 340 FEAMGIQVgwlagkLKGKTRETELAriasgEAQMVVGTHALFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKGAkqgyy 419
Cdd:cd17918 88 LPFINVEL------VTGGTKAQILS-----GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA----- 151
|
170 180
....*....|....*....|....*....
gi 1140790570 420 PHQLVMTATPIPRTLAMTAYADLETSIID 448
Cdd:cd17918 152 THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
456-614 |
1.01e-33 |
|
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: 126.30 E-value: 1.01e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 456 PIQTVAIPdtkRDDIVerVKNACLNE---GKQAYWVCTLIDESEVLEAQaaadtaeeLQRKLPDVKIGLVHGRMKPAEKQ 532
Cdd:cd18810 1 PVRTYVMP---YDDEL--IREAIEREllrGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 533 AVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERLGLAQLHQLRGRVGRGSVASHCVLLY--HSPLSKTAQKRLG 610
Cdd:cd18810 68 EVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYpdQKKLTEDALKRLE 147
|
....
gi 1140790570 611 VLRE 614
Cdd:cd18810 148 AIQE 151
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
9-165 |
1.45e-21 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 92.12 E-value: 1.45e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 9 PLNSLSGVGAKVAEKLEKVGLNNVQDLLFHLPLRYEDRTRIYPIVKLHAGLWAAVQGKVMHVDTI-FGKRKMLAVKISDG 87
Cdd:pfam17191 1 PIKYAKGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETKkIGSLVIISAVLSDG 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1140790570 88 NGTITLRFFNfTAGMKNNFAEGKQVHAYGEIKRGNMG-LEIVHPDYKFFAPRQqpdvEANLTPVYPTTEGLRQVTLRNL 165
Cdd:pfam17191 81 IGQVLLKWFN-QEYIKKFLQKGKEVYITGTVKEGPFGpIEMNNPEIEEITGEQ----EREILPVYPLTEGISQKNMRKI 154
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
292-437 |
5.29e-21 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 90.38 E-value: 5.29e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 292 LVQGDVGSGKT---LVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGklkGKTRETELARIAs 368
Cdd:pfam00270 18 LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG---GDSRKEQLEKLK- 93
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1140790570 369 gEAQMVVGTH----ALFQEHVEFKNLGLVIIDEQHRFGVHQRLELREKGAKQGYYPHQ-LVMTATPiPRTLAMT 437
Cdd:pfam00270 94 -GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKRQiLLLSATL-PRNLEDL 165
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
63-135 |
6.47e-21 |
|
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.
Pssm-ID: 239934 [Multi-domain] Cd Length: 75 Bit Score: 86.86 E-value: 6.47e-21
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1140790570 63 VQGKVMHVDTI-FGKRKMLAVKISDGNGTITLRFFNFTAGMKNNFAEGKQVHAYGEIKRGNMGLEIVHPDYKFF 135
Cdd:cd04488 2 VEGTVVSVEVVpRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYELL 75
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
264-454 |
5.24e-20 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 88.70 E-value: 5.24e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 264 LPFSPTNAQARVTQEIEADLekphpMMRLVQGDVGSGKTLVAAL--AAVRALEHGQQVALMAPTELLAEQHAINFANWFE 341
Cdd:smart00487 5 GFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLGP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 342 AMGIQVgwlAGKLKGKTRETELARIASGEAQMVVGT-----HALFQEHVEFKNLGLVIIDEQHRFGVHQRLE-LREKGAK 415
Cdd:smart00487 80 SLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDqLEKLLKL 156
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1140790570 416 QGYYPHQLVMTATP---IPRTLAMTAYADLETSIIDELPPGR 454
Cdd:smart00487 157 LPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
466-586 |
2.90e-18 |
|
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: 80.72 E-value: 2.90e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 466 KRDDIVERVKnacLNEGKQAYWVCTLIDESEvleaqaaadtAEELQRKLpDVKIGLVHGRMKPAEKQAVMQEFKENKLHL 545
Cdd:pfam00271 2 KLEALLELLK---KERGGKVLIFSQTKKTLE----------AELLLEKE-GIKVARLHGDLSQEEREEILEDFRKGKIDV 67
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1140790570 546 LVATTVIEVGVDVPNSSLMIIENPERlGLAQLHQLRGRVGR 586
Cdd:pfam00271 68 LVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
507-586 |
1.77e-17 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 77.64 E-value: 1.77e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 507 AEELQRKlpDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPeRLGLAQLHQLRGRVGR 586
Cdd:smart00490 4 AELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGR 80
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
615-685 |
2.32e-14 |
|
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 68.65 E-value: 2.32e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1140790570 615 SNDGFVIAQRDLEIRGPGELLGTKQTGLA-DFKIADLVRDQRLIPEVQRIARHIHDSYPDNAK---AIINRWLGE 685
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEEIIDNDPECSLpenAVLWRQLKE 75
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
262-597 |
1.14e-12 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 71.21 E-value: 1.14e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 262 AQLPFSPTNAQARVTQEIEADLEKPHPMMrLVQGDVGSGKTLVAALAAVRALEhGQQVALMAPTELLAEQhainfanWFE 341
Cdd:COG1061 75 SGTSFELRPYQQEALEALLAALERGGGRG-LVVAPTGTGKTVLALALAAELLR-GKRVLVLVPRRELLEQ-------WAE 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 342 AMgiqVGWLAGKLKGKTRETELARIasgeaqmVVGTHALFQEHVEFKNL----GLVIIDEQHRFGVHQRLELREKGAKqg 417
Cdd:COG1061 146 EL---RRFLGDPLAGGGKKDSDAPI-------TVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPA-- 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 418 yyPHQLVMTATPIpRTLAMTAYADLETSIIDELPPGRA-------PIQTVAIPD------TKRDDIVERVKNACLNEGKQ 484
Cdd:COG1061 214 --AYRLGLTATPF-RSDGREILLFLFDGIVYEYSLKEAiedgylaPPEYYGIRVdltderAEYDALSERLREALAADAER 290
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 485 AYWVCTLIDESEVLEAQA---AA--DTAEELQRKL--PDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVD 557
Cdd:COG1061 291 KDKILRELLREHPDDRKTlvfCSsvDHAEALAELLneAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVD 370
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 1140790570 558 VPNSSLMII----ENPerlglAQLHQLRGRVGRGSVASHCVLLY 597
Cdd:COG1061 371 VPRLDVAILlrptGSP-----REFIQRLGRGLRPAPGKEDALVY 409
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
272-399 |
1.58e-11 |
|
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: 63.38 E-value: 1.58e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 272 QARVTQEIEADLE--KPHpmmrLVQGDVGSGKTLVAALAAVRALEHGQQVALMAPTELLAEQhainFANWFEA-MGIQVG 348
Cdd:cd17929 1 QRKAYEAIVSSLGgfKTF----LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQ----LIKRFKKrFGDKVA 72
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 1140790570 349 WLAGKLKGKTRETELARIASGEAQMVVGTH-ALFqehVEFKNLGLVIIDEQH 399
Cdd:cd17929 73 VLHSKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
423-558 |
9.24e-10 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 61.64 E-value: 9.24e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 423 LVMTAT-PIPRTLAMTAYADLETSIIDELPPGRAPIQ----TVAIPDTKRDDIVERVKNAcLNEGKQAYWVCTLIDEsev 497
Cdd:COG1203 303 ILMTATlPPLLREELLEAYELIPDEPEELPEYFRAFVrkrvELKEGPLSDEELAELILEA-LHKGKSVLVIVNTVKD--- 378
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1140790570 498 leaqaAADTAEELQRKLPDVKIGLVHGRMKPAEKQAVMQE----FKENKLHLLVATTVIEVGVDV 558
Cdd:COG1203 379 -----AQELYEALKEKLPDEEVYLLHSRFCPADRSEIEKEikerLERGKPCILVSTQVVEAGVDI 438
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
292-428 |
1.17e-09 |
|
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: 57.41 E-value: 1.17e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 292 LVQGDVGSGKTLVAALA-AVRALEHGQQVALMAPTELLAEQHAINFANWFeAMGIQVGWLAGklkGKTREtELARIASGE 370
Cdd:cd00046 5 LITAPTGSGKTLAALLAaLLLLLKKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVG---GSSAE-EREKNKLGD 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1140790570 371 AQMVVGTHA------LFQEHVEFKNLGLVIIDEQHRFG----VHQRLELREKGAKQGYYPhQLVMTAT 428
Cdd:cd00046 80 ADIIIATPDmllnllLREDRLFLKDLKLIIVDEAHALLidsrGALILDLAVRKAGLKNAQ-VILLSAT 146
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
392-586 |
8.03e-09 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 57.82 E-value: 8.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 392 LVIIDEQHRFGVHQR------LE-LREKGAKQgyyphqLVMTATpIPRTLaMTAYADLETSIIDELPPgRAPIQTVAIPd 464
Cdd:cd09639 126 LLIFDEVHFYDEYTLalilavLEvLKDNDVPI------LLMSAT-LPKFL-KEYAEKIGYVEENEPLD-LKPNERAPFI- 195
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 465 tKRDD-------IVERVKNACLNEGKQAYwVCTLIDEsevleAQAAADTAEElqrKLPDVKIGLVHGRMKP---AEKQA- 533
Cdd:cd09639 196 -KIESdkvgeisSLERLLEFIKKGGSVAI-IVNTVDR-----AQEFYQQLKE---KGPEEEIMLIHSRFTEkdrAKKEAe 265
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1140790570 534 VMQEFKENKLHLLVATTVIEVGVDVpNSSLMIIEnperlgLAQLHQLRGRVGR 586
Cdd:cd09639 266 LLLEFKKSEKFVIVATQVIEASLDI-SVDVMITE------LAPIDSLIQRLGR 311
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
392-586 |
1.90e-08 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 56.69 E-value: 1.90e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 392 LVIIDEQHRFGVHQR------LE-LREKGAKQgyyphqLVMTATpIPRTLaMTAYADLETSIIDELPPGRAPIQTVAIPD 464
Cdd:TIGR01587 127 LLIFDEVHFYDEYTLalilavLEvLKDNDVPI------LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDLKEERRFENHRF 198
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 465 TKRDD-------IVERVKNACLNEGKQAYwVCTLIDESEVLEAQaaadtaeeLQRKLPDVKIGLVHGRMKP---AEKQA- 533
Cdd:TIGR01587 199 ILIESdkvgeisSLERLLEFIKKGGSIAI-IVNTVDRAQEFYQQ--------LKEKAPEEEIILYHSRFTEkdrAKKEAe 269
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1140790570 534 VMQEF-KENKLHLLVATTVIEVGVDVpNSSLMIIEnperlgLAQLHQLRGRVGR 586
Cdd:TIGR01587 270 LLREMkKSNEKFVIVATQVIEASLDI-SADVMITE------LAPIDSLIQRLGR 316
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
218-399 |
7.87e-08 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 55.51 E-value: 7.87e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 218 PAQLRLImeELLAQNLSMLSVRskgQQDKAMPF--PPVNTLKDK------------------LLAQLPFSPTNAQARVTQ 277
Cdd:COG1198 131 PKQRRVL--EALREHGGPLTLS---ELAKEAGVsrSVLKALVKKglleieerevdrdpfapdVPAEPPPTLNEEQQAAVE 205
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 278 EIEADLEKPHPMmrLVQGDVGSGKTlvaalaavralE-----------HGQQVALMAPtEL-LAEQHAINFANWFeamGI 345
Cdd:COG1198 206 AIRAAAGGFSVF--LLHGVTGSGKT-----------EvylqaiaevlaQGKQALVLVP-EIaLTPQTVERFRARF---GA 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1140790570 346 QVGWLAGKLKGKTRETELARIASGEAQMVVGTH-ALFqehVEFKNLGLVIIDEQH 399
Cdd:COG1198 269 RVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
221-399 |
8.31e-08 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 55.55 E-value: 8.31e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 221 LRLIMEELLAQNLSMLSVRS---KGQ-QDKAMPFPPVNTLKDKLLAQLPFSPTNAQArVTQEIEADLEKPHpmmrLVQGD 296
Cdd:PRK05580 96 LRLALLAELALAASSAVLKGlvkKGLiELEEVEVLRLRPPPDPAFEPPTLNPEQAAA-VEAIRAAAGFSPF----LLDGV 170
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 297 VGSGKTLVAALAAVRALEHGQQVALMAPtEL-LAEQhainFANWFEA-MGIQVGWLAGKLKGKTRETELARIASGEAQMV 374
Cdd:PRK05580 171 TGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQ----MLARFRArFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVV 245
|
170 180
....*....|....*....|....*.
gi 1140790570 375 VGTH-ALFqehVEFKNLGLVIIDEQH 399
Cdd:PRK05580 246 IGARsALF---LPFKNLGLIIVDEEH 268
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
63-133 |
1.89e-07 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 48.77 E-value: 1.89e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1140790570 63 VQGKVMHVDTifGKRKMLAVKISDGNGTITLRFFNFTAG-MKNNFAEGKQVHAYGEIKRGNMG-LEIVHPDYK 133
Cdd:pfam01336 3 VAGRVTSIRR--SGGKLLFLTLRDGTGSIQVVVFKEEAEkLAKKLKEGDVVRVTGKVKKRKGGeLELVVEEIE 73
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
541-587 |
2.09e-07 |
|
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: 48.85 E-value: 2.09e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 1140790570 541 NKLHLLVATTVIEVGVDVPNSSLMIIENPERlGLAQLHQLRGRVGRG 587
Cdd:cd18785 21 SSLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRG 66
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
505-565 |
6.39e-07 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 49.04 E-value: 6.39e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1140790570 505 DTAEELQRKLP--DVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMI 565
Cdd:cd18787 38 KRVDRLAELLEelGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
508-596 |
4.47e-06 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 46.82 E-value: 4.47e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 508 EELQRKLPDVKIGLVHGR----------MKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERlGLAQL 577
Cdd:cd18802 46 KEHPSTLAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSY 124
|
90
....*....|....*....
gi 1140790570 578 HQLRGRvGRgSVASHCVLL 596
Cdd:cd18802 125 IQSRGR-AR-APNSKYILM 141
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
298-586 |
1.56e-05 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 47.97 E-value: 1.56e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 298 GSGKTLVAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGwlagklkGKTRETELARIASGEAQMVVGT 377
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVG-------VSTGDYDSDDEWLGRYDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 378 ----HALFQEHVEF-KNLGLVIIDEQHRFGVHQR---LE-----LREKGAKQgyyphQLV-MTAT--------------- 428
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptLEvllarLRRLNPEA-----QIVaLSATignaeeiaewldael 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 429 ------PIPRTLAMtaYADLETSIIDELPPGRAPIQTVAIpDTKRDD----IVERVKNACLNEGKQAYWVCTLIDES--- 495
Cdd:COG1204 196 vksdwrPVPLNEGV--LYDGVLRFDDGSRRSKDPTLALAL-DLLEEGgqvlVFVSSRRDAESLAKKLADELKRRLTPeer 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 496 --------EVLEAQAAADTAEELQRKLPDvKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPnSSLMIIE 567
Cdd:COG1204 273 eeleelaeELLEVSEETHTNEKLADCLEK-GVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIIR 350
|
330 340
....*....|....*....|....
gi 1140790570 568 NPERLGLAQL-----HQLRGRVGR 586
Cdd:COG1204 351 DTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
298-406 |
4.44e-05 |
|
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: 44.56 E-value: 4.44e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 298 GSGKTL-VAALAAVRALEHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGwlagklkGKTRETELARIASGEAQMVVG 376
Cdd:cd17921 27 SSGKTLiAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVG-------LLTGDPSVNKLLLAEADILVA 99
|
90 100 110
....*....|....*....|....*....|....*.
gi 1140790570 377 THALFQ------EHVEFKNLGLVIIDEQHRFGVHQR 406
Cdd:cd17921 100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGER 135
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
316-438 |
4.68e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family 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: 350685 [Multi-domain] Cd Length: 201 Bit Score: 45.12 E-value: 4.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 316 GQQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELARiasgEAQMVVGTHALFQ------EHVEFKN 389
Cdd:cd17927 50 KGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQIVE----SSDVIIVTPQILVndlksgTIVSLSD 125
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1140790570 390 LGLVIIDEQHRfgvhqrlelrekgaKQGYYPHQLVMT---------ATPIPRTLAMTA 438
Cdd:cd17927 126 FSLLVFDECHN--------------TTKNHPYNEIMFryldqklgsSGPLPQILGLTA 169
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
316-429 |
1.06e-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: 43.66 E-value: 1.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 316 GQQVALMAPTELLAEQHAINFANWFEaMGIQVGWLAGKLKGKTRET--ELARIASGEAQMVvgTHALFQEHVEFKNLGLV 393
Cdd:cd18035 45 GGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEERAErwDASKIIVATPQVI--ENDLLAGRITLDDVSLL 121
|
90 100 110
....*....|....*....|....*....|....*..
gi 1140790570 394 IIDEQHR-FGVHQRLELREKGAKQGYYPHQLVMTATP 429
Cdd:cd18035 122 IFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
519-586 |
1.42e-04 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 42.54 E-value: 1.42e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1140790570 519 IGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPnSSLMIIENPER--------LGLAQLHQLRGRVGR 586
Cdd:cd18795 66 IAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVIIKGTQRydgkgyreLSPLEYLQMIGRAGR 140
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
505-587 |
5.82e-04 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases 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: 350188 [Multi-domain] Cd Length: 143 Bit Score: 40.80 E-value: 5.82e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 505 DTAEELQRKL----PDVK----IGLVHGR----MKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERL 572
Cdd:cd18801 41 DSAEEIVNFLskirPGIRatrfIGQASGKsskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPS 120
|
90
....*....|....*
gi 1140790570 573 GLAQLhQLRGRVGRG 587
Cdd:cd18801 121 PIRMI-QRMGRTGRK 134
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
314-429 |
7.58e-04 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 42.79 E-value: 7.58e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 314 EHGQQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKGKTRETELAriasgEAQMVVGT-----HALFQEHVEFK 388
Cdd:COG1111 44 KKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWE-----KARIIVATpqvieNDLIAGRIDLD 118
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 1140790570 389 NLGLVIIDEQHR-FGVHQRLELREKGAKQGYYPHQLVMTATP 429
Cdd:COG1111 119 DVSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
|
|
| RPA2_OBF_family |
cd03524 |
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ... |
63-128 |
1.37e-03 |
|
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).
Pssm-ID: 239601 [Multi-domain] Cd Length: 75 Bit Score: 37.73 E-value: 1.37e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1140790570 63 VQGKVMHVDTIFGKRKMLAVKISDG-NGTITLRFF-NFTAGMKNNFAEGKQVHAYGEIKRGNMGLEIV 128
Cdd:cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGtGGTIRVTLFgELAEELENLLKEGQVVYIKGKVKKFRGRLQLI 69
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
518-597 |
1.62e-03 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 41.81 E-value: 1.62e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 518 KIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERlGLAQLHQLRGRVGRGSVASHCVLLY 597
Cdd:PLN03137 706 KAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAGRDGQRSSCVLYY 784
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
298-430 |
2.57e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 39.19 E-value: 2.57e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 298 GSGKTLVAALAAVRALEHG--QQVALMAPTELLAEQHAINFANWFEAMGIQVGWLAGKLKgktretelaRIASGEAQMVV 375
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPNYVEIGEIISGDKK---------DESVDDNKIVV 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1140790570 376 GT-HALF------QEHVEFKNLGLVIIDEQHRFG--VHQRLELREKgakqgyYPHQLVMTATPI 430
Cdd:pfam04851 104 TTiQSLYkalelaSLELLPDFFDVIIIDEAHRSGasSYRNILEYFK------PAFLLGLTATPE 161
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
505-560 |
2.94e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 40.52 E-value: 2.94e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1140790570 505 DTAEELQRKLPD--VKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPN 560
Cdd:COG0513 252 RGADRLAEKLQKrgISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDD 309
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
507-629 |
3.61e-03 |
|
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: 39.54 E-value: 3.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 507 AEELQRKLPDVKIGlvhgRM------KPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIEN------------ 568
Cdd:cd18804 107 EEELKTLFPEARIA----RIdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNadsglnspdfra 182
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1140790570 569 PERLglAQL-HQLRGRVGRGSVASHCVLLYHSPLSKTAQKrlgVLRESNDGFviAQRDLEIR 629
Cdd:cd18804 183 SERA--FQLlTQVSGRAGRGDKPGKVIIQTYNPEHPLIQA---AKEEDYEAF--YEEELAER 237
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
505-597 |
4.76e-03 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 37.96 E-value: 4.76e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 505 DTAEELQRKLpdVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMI-------IENperlglaqL 577
Cdd:cd18794 45 QVAARLQSKG--ISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIhyslpksMES--------Y 114
|
90 100
....*....|....*....|
gi 1140790570 578 HQLRGRVGRGSVASHCVLLY 597
Cdd:cd18794 115 YQESGRAGRDGLPSECILFY 134
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
382-430 |
5.34e-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: 38.81 E-value: 5.34e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1140790570 382 QEHVEFKNLGLVIIDEQHRFGV------HQRLELREKGAKQGyyPHQLVMTATPI 430
Cdd:cd18011 113 RGLLLSEEWDLVVVDEAHKLRNsgggkeTKRYKLGRLLAKRA--RHVLLLTATPH 165
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
358-627 |
8.53e-03 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 39.31 E-value: 8.53e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 358 TRETEL---ARIASGEAQMV-VGTHAL----FQEHVEFKNLGLVIIDEQH---RFGVHQRLELREKGAKQGYYPHQLVMt 426
Cdd:PRK11057 100 TREQQLevmAGCRTGQIKLLyIAPERLmmdnFLEHLAHWNPALLAVDEAHcisQWGHDFRPEYAALGQLRQRFPTLPFM- 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 427 atpiprtlAMTAYADLETSI-IDELPPGRAPIQTVAIPDTK--RDDIVERVKNacLNE---------GKQAYWVCTLIDE 494
Cdd:PRK11057 179 --------ALTATADDTTRQdIVRLLGLNDPLIQISSFDRPniRYTLVEKFKP--LDQlmryvqeqrGKSGIIYCNSRAK 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1140790570 495 SEvleaqaaaDTAEELQRKlpDVKIGLVHGRMKPAEKQAVMQEFKENKLHLLVATTVIEVGVDVPNSSLMIIENPERlGL 574
Cdd:PRK11057 249 VE--------DTAARLQSR--GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR-NI 317
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|...
gi 1140790570 575 AQLHQLRGRVGRGSVASHCVLLYhSPLSKTAQKRLgvLRESNDGfviAQRDLE 627
Cdd:PRK11057 318 ESYYQETGRAGRDGLPAEAMLFY-DPADMAWLRRC--LEEKPAG---QQQDIE 364
|
|
| |
