|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
1-693 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 1094.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 1 MTGRLLDAVPLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISFGGRRM 80
Cdd:PRK10917 1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 81 MTCQISDGSGILTMRFFNFSAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLStPELQETLTPVYPTTEGVK 159
Cdd:PRK10917 81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEES-PELEGRLTPVYPLTEGLK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 160 QATLRKLTDQALDLLDtcAIEELLPPELSQ--GMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 238 ALRAGAQRFHAQPLSANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 318 KQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRH 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 478 AcITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGV 557
Cdd:PRK10917 467 E-IAKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*.
gi 15833781 638 TRQTGNAEFKVADLLRDQAMIPEVQRLARHIHERYPQQAKALIERWMPETERYSNA 693
Cdd:PRK10917 626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
10-689 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 1063.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 10 PLSSLTGVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCNISF--GGRRMMTCQISD 87
Cdd:COG1200 7 PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLSD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 88 GSGILTMRFFNFsAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDlSTPELQETLTPVYPTTEGVKQATLRKLT 167
Cdd:COG1200 87 GTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDE-EEAELAGRLTPVYPLTEGLSQKTLRKLI 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 168 DQALDLLDTcAIEELLPPEL--SQGMMTLPEALRTLHRPPPTLQLsdletgqHPAQRRLILEELLAHNLSMLALRAGAQR 245
Cdd:COG1200 165 RQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLLRRARRRK 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 246 FHAQPLSANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAP 325
Cdd:COG1200 237 RKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAP 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 326 TELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVH 405
Cdd:COG1200 317 TEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVE 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 406 QRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRTDIIDRVRHACiTEGRQ 485
Cdd:COG1200 397 QRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI-AKGRQ 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 486 AYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLM 565
Cdd:COG1200 472 AYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVM 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 566 IIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:COG1200 552 VIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPD 631
|
650 660 670 680
....*....|....*....|....*....|....*....|....*
gi 15833781 646 FKVADLLRDQAMIPEVQRLARHIHERYPQQAK-ALIERWMPETER 689
Cdd:COG1200 632 LRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLRFR 676
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
28-665 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 949.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 28 INLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLN-CNISFGGRRMMTCQISD-GSGILTMRFFNfSAAMKN 105
Cdd:TIGR00643 1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRVQGDLSTPELqeTLTPVYPTTEGVKQATLRKLTDQALDLLDTCaIEELLPP 185
Cdd:TIGR00643 80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 186 ELSQ--GMMTLPEALRTLHrPPPTLQLsdletgQHPAQRRLILEELLAHNLSMLALRAG-AQRFHAQPLSANDALKNKLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKTLSL------LELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 263 AALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFE 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 343 PLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRtDIIDRVRHACITEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 503 AAEATWEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 583 GRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAMIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627
|
...
gi 15833781 663 RLA 665
Cdd:TIGR00643 628 EDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
224-452 |
7.57e-117 |
|
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: 349.52 E-value: 7.57e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 224 LILEELLAHNLSMLALRAGAQRFHAQPLSANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKT 303
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 304 LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQ 383
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15833781 384 EQVQFNGLALVIIDEQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELP 452
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE----TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
226-642 |
6.39e-103 |
|
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: 335.48 E-value: 6.39e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 226 LEELLAHNLSMLALRAgAQRFHAQPlsANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLV 305
Cdd:TIGR00580 412 VREIAAKLIELYAKRK-AIKGHAFP--PDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV 488
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 306 AALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQ 385
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKD 568
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 386 VQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPD 465
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQK----EKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEY 644
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 466 TRRTdiidrVRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQG 542
Cdd:TIGR00580 645 DPEL-----VREAIRREllrGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVMLEFYKG 711
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 543 ELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLY--KTPLSKTAQIRLQVLRDSND-- 618
Cdd:TIGR00580 712 EFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEAIQEFSElg 791
|
410 420
....*....|....*....|....*
gi 15833781 619 -GFVIAQKDLEIRGPGELLGTRQTG 642
Cdd:TIGR00580 792 aGFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
238-643 |
2.59e-93 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 313.16 E-value: 2.59e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 238 ALRAGAQRFhaqPLSANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTlvaalaalraiahG 317
Cdd:COG1197 559 AERAARKGF---AFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafkavmdG 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 318 KQVALMAPTELLAEQHANNFRNWFEPLGIEVGWL-----AGKQKgKARlsqqEAIASGQVQMIVGTHAIFQEQVQFNGLA 392
Cdd:COG1197 636 KQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLsrfrtAKEQK-ETL----EGLADGKVDIVIGTHRLLSKDVKFKDLG 710
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 393 LVIIDEQHRFGVHQ--RL-ALWEkgqqqgfHPHQLIMTATPIPRTLAMtAYADL-DTSVIDELPPGRTPVTTVAIPdtrR 468
Cdd:COG1197 711 LLIIDEEQRFGVRHkeKLkALRA-------NVDVLTLTATPIPRTLQM-SLSGIrDLSIIATPPEDRLPVKTFVGE---Y 779
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 469 TDIIdrVRHACITE---GRQAYWVCTLIEEselLEAQAaeatwEELKLALPELNVGLVHGRMKPAEKQAVMASFKQGELH 545
Cdd:COG1197 780 DDAL--IREAILREllrGGQVFYVHNRVED---IEKVA-----ARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFD 849
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 546 LLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYK--TPLSKTAQIRLQVLRDSND---GF 620
Cdd:COG1197 850 VLVCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPpdKVLTEDAEKRLEAIQEFTElgaGF 929
|
410 420
....*....|....*....|...
gi 15833781 621 VIAQKDLEIRGPGELLGTRQTGN 643
Cdd:COG1197 930 KLAMHDLEIRGAGNLLGEEQSGH 952
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
457-615 |
2.21e-84 |
|
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: 262.67 E-value: 2.21e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 457 PVTTVAIPDTRRtDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLAL-PELNVGLVHGRMKPAEKQAV 535
Cdd:cd18811 1 PITTYLIFHTRL-DKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 536 MASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTPLSKTAQIRLQVLRD 615
Cdd:cd18811 80 MAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
457-615 |
1.76e-72 |
|
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: 231.77 E-value: 1.76e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 457 PVTTVAIPDTRrTDIIDRVRHACITEGRQAYWVCTLIEESELLEAQAAEATWEELKLALPELNVGLVHGRMKPAEKQAVM 536
Cdd:cd18792 1 PIRTYVIPHDD-LDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 537 ASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKTP--LSKTAQIRLQVLR 614
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPkkLTETAKKRLRAIA 159
|
.
gi 15833781 615 D 615
Cdd:cd18792 160 E 160
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
264-645 |
3.97e-66 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 236.56 E-value: 3.97e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 264 ALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFR----N 339
Cdd:PRK10689 596 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRdrfaN 675
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 340 WfePLGIEVgwLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGF 419
Cdd:PRK10689 676 W--PVRIEM--LSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK----ERIKAMRA 747
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 420 HPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVaipdTRRTDIIdRVRHACITE---GRQAYWVCTLIEES 496
Cdd:PRK10689 748 DVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTF----VREYDSL-VVREAILREilrGGQVYYLYNDVENI 822
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 497 ElleaqAAEATWEELklaLPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLA 576
Cdd:PRK10689 823 Q-----KAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLA 894
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15833781 577 QLHQLRGRVGRGAVASHCVLLYKTP--LSKTAQIRLQV---LRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:PRK10689 895 QLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAiasLEDLGAGFALATHDLEIRGAGELLGEEQSGQME 968
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
263-449 |
1.15e-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: 188.16 E-value: 1.15e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 263 AALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFE 342
Cdd:cd17991 10 ASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFA 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 343 PLGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPH 422
Cdd:cd17991 90 NFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQK----EKLKELRPNVD 165
|
170 180
....*....|....*....|....*....
gi 15833781 423 QLIMTATPIPRTL--AMTAYADLdtSVID 449
Cdd:cd17991 166 VLTLSATPIPRTLhmALSGIRDL--SVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
254-449 |
1.08e-52 |
|
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: 179.92 E-value: 1.08e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 254 NDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMMRLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQH 333
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 334 ANNFRNWFEPLGIEVGWLAGKQKgkarlsqqeaiASGQVQMIVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:cd17918 81 YEEARKFLPFINVELVTGGTKAQ-----------ILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|....*.
gi 15833781 414 GQqqgfhPHQLIMTATPIPRTLAMTAYADLDTSVID 449
Cdd:cd17918 150 GA-----THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
475-613 |
6.91e-32 |
|
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: 120.91 E-value: 6.91e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 475 VRHACITE---GRQAYWVCTLIEESELLEAQaaeatweeLKLALPELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATT 551
Cdd:cd18810 14 IREAIEREllrGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTT 85
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15833781 552 VIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKT--PLSKTAQIRLQVL 613
Cdd:cd18810 86 IIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDqkKLTEDALKRLEAI 149
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
63-135 |
8.77e-23 |
|
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: 92.26 E-value: 8.77e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15833781 63 TVEGEVLNCNI-SFGGRRMMTCQISDGSGILTMRFFNFSAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRV 135
Cdd:cd04488 1 TVEGTVVSVEVvPRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYEL 74
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
270-438 |
2.39e-22 |
|
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: 94.23 E-value: 2.39e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 270 TGAQARVVAEI--ERDMaldvpmmrLVQGDVGSGKT---LVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPL 344
Cdd:pfam00270 1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 345 GIEVGWLAGkqkGKARLSQQEAIASgqVQMIVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFH 420
Cdd:pfam00270 73 GLKVASLLG---GDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK 147
|
170
....*....|....*....
gi 15833781 421 PHQLI-MTATPiPRTLAMT 438
Cdd:pfam00270 148 KRQILlLSATL-PRNLEDL 165
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
261-456 |
7.20e-22 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 94.10 E-value: 7.20e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 261 LLAALPFKPTGAQARVVAEIERDMaldvpMMRLVQGDVGSGKTLVAAL--AALRAIAHGKQVALMAPTELLAEQHANNFR 338
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 339 NWFEPLGIEVgwlAGKQKGKARLSQQEAIASGQVQMIVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:smart00487 76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 15833781 414 -GQQQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 153 lLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
16-166 |
3.46e-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: 90.96 E-value: 3.46e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 16 GVGAALSNKLAKINLHTVQDLLLHLPLRYEDRTHLYPIGELLPGVYATVEGEVLNCN-ISFGGRRMMTCQISDGSGILTM 94
Cdd:pfam17191 7 GVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFEtKKIGSLVIISAVLSDGIGQVLL 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15833781 95 RFFNfSAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRVQGDlsTPELQetLTPVYPTTEGVKQATLRKL 166
Cdd:pfam17191 87 KWFN-QEYIKKFLQKGKEVYITGTVKEGPFGPiEMNNPEIEEITG--EQERE--ILPVYPLTEGISQKNMRKI 154
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
517-587 |
3.49e-19 |
|
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: 83.41 E-value: 3.49e-19
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833781 517 ELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGR 587
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
509-587 |
7.03e-18 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 78.79 E-value: 7.03e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPeRLGLAQLHQLRGRVG 586
Cdd:smart00490 1 EELAELLKELGikVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAG 79
|
.
gi 15833781 587 R 587
Cdd:smart00490 80 R 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
263-598 |
4.98e-12 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 68.90 E-value: 4.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 263 AALPFKPTGAQARVVAEIERDMALDVPMMrLVQGDVGSGKTLVAALAALRAIaHGKQVALMAPTELLAEQHANNFRNWFe 342
Cdd:COG1061 75 SGTSFELRPYQQEALEALLAALERGGGRG-LVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFL- 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 343 plgievgwlagkqkGKARLSQQEAIASGQVqmIVGTHAIFQEQVQFNGLA----LVIIDEQHRFG--VHQRLAlwekgqq 416
Cdd:COG1061 152 --------------GDPLAGGGKKDSDAPI--TVATYQSLARRAHLDELGdrfgLVIIDEAHHAGapSYRRIL------- 208
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 417 QGFHPHQLI-MTATPIpRTLAMTAYADLDTSVIDELPPGR-------TPVTTVAIPD----------------------- 465
Cdd:COG1061 209 EAFPAAYRLgLTATPF-RSDGREILLFLFDGIVYEYSLKEaiedgylAPPEYYGIRVdltderaeydalserlrealaad 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 466 -TRRTDIIDRVRHACiTEGRQAYWVCTLIEEselleaqaAEATWEELKLAlpELNVGLVHGRMKPAEKQAVMASFKQGEL 544
Cdd:COG1061 288 aERKDKILRELLREH-PDDRKTLVFCSSVDH--------AEALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGEL 356
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 15833781 545 HLLVATTVIEVGVDVPNASLMII----ENPerlglAQLHQLRGRVGRGAVASHCVLLY 598
Cdd:COG1061 357 RILVTVDVLNEGVDVPRLDVAILlrptGSP-----REFIQRLGRGLRPAPGKEDALVY 409
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
616-674 |
2.60e-10 |
|
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: 57.48 E-value: 2.60e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 616 SNDGFVIAQKDLEIRGPGELLGTRQTGNA-EFKVADLLRDQAMIPEVQRLARHIHERYPQ 674
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEEIIDNDPE 60
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
293-429 |
5.69e-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: 55.10 E-value: 5.69e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 293 LVQGDVGSGKTLVAALA-ALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPlGIEVGWLAgkqkGKARLSQQEAIASGQ 371
Cdd:cd00046 5 LITAPTGSGKTLAALLAaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLV----GGSSAEEREKNKLGD 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15833781 372 VQMIVGTHAIFQEQVQFNGLA------LVIIDEQHRFGV--HQRLALWEKGQQQGFHPHQLI-MTAT 429
Cdd:cd00046 80 ADIIIATPDMLLNLLLREDRLflkdlkLIIVDEAHALLIdsRGALILDLAVRKAGLKNAQVIlLSAT 146
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
317-439 |
1.79e-08 |
|
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: 55.13 E-value: 1.79e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 317 GKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARLsqQEAIASGQVqmIVGTHAIFQ------EQVQFNG 390
Cdd:cd17927 50 KGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV--EQIVESSDV--IIVTPQILVndlksgTIVSLSD 125
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 15833781 391 LALVIIDEQHRfgvhqrlalwekgqQQGFHPHQLIMT---------ATPIPRTLAMTA 439
Cdd:cd17927 126 FSLLVFDECHN--------------TTKNHPYNEIMFryldqklgsSGPLPQILGLTA 169
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
63-135 |
1.90e-08 |
|
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: 51.47 E-value: 1.90e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15833781 63 TVEGEVLNcnISFGGRRMMTCQISDGSGILTMRFFN-FSAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRV 135
Cdd:pfam01336 2 TVAGRVTS--IRRSGGKLLFLTLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKRKGGElELVVEEIEL 74
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
543-589 |
2.30e-08 |
|
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: 51.55 E-value: 2.30e-08
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 15833781 543 ELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGA 589
Cdd:cd18785 22 SLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGG 67
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
390-587 |
6.36e-08 |
|
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: 55.13 E-value: 6.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTsVIDELPPGRTPVTTVAIP-- 464
Cdd:cd09639 123 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGY-VEENEPLDLKPNERAPFIki 197
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 465 ---DTRRTDIIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-VMA 537
Cdd:cd09639 198 esdKVGEISSLERLLEFIKKGGSVAI-IVNTVDR--------AQEFYQQLKEKGPEEEIMLIHSRFTEkdrAKKEAeLLL 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 15833781 538 SFKQGELHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 587
Cdd:cd09639 269 EFKKSEKFVIVATQVIEASLDI-SVDVMITE------LAPIDSLIQRLGR 311
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
293-400 |
1.38e-07 |
|
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: 51.83 E-value: 1.38e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 293 LVQGDVGSGKTLVAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFeplGIEVGWLAGKQKGKARLSQQEAIASGQV 372
Cdd:cd17929 19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF---GDKVAVLHSKLSDKERADEWRKIKRGEA 95
|
90 100
....*....|....*....|....*....
gi 15833781 373 QMIVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:cd17929 96 KVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
424-559 |
4.70e-07 |
|
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: 53.16 E-value: 4.70e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 424 LIMTAT-PIPRTLAMTAYADL-------DTSVIDELPPGRTPVTTVAIPDTrrtDIIDRVRhACITEGRQAYWVCTLIee 495
Cdd:COG1203 303 ILMTATlPPLLREELLEAYELipdepeeLPEYFRAFVRKRVELKEGPLSDE---ELAELIL-EALHKGKSVLVIVNTV-- 376
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15833781 496 selleaQAAEATWEELKLALPELNVGLVHGRMKPAEKQA----VMASFKQGELHLLVATTVIEVGVDV 559
Cdd:COG1203 377 ------KDAQELYEALKEKLPDEEVYLLHSRFCPADRSEiekeIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
509-597 |
1.20e-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: 48.36 E-value: 1.20e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 509 EELKLALPELNVGLVHGR----------MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQL 578
Cdd:cd18802 46 KEHPSTLAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSY 124
|
90
....*....|....*....
gi 15833781 579 HQLRGRvGRgAVASHCVLL 597
Cdd:cd18802 125 IQSRGR-AR-APNSKYILM 141
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
390-587 |
1.30e-06 |
|
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: 50.92 E-value: 1.30e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTSVIDELPPGRTPVTTVAIPDT 466
Cdd:TIGR01587 124 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDLKEERRFENHRFI 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 467 RRTD-------IIDRVRHACITEGRQAYwVCTLIEEselleaqaAEATWEELKLALPELNVGLVHGRMKP---AEKQA-V 535
Cdd:TIGR01587 200 LIESdkvgeisSLERLLEFIKKGGSIAI-IVNTVDR--------AQEFYQQLKEKAPEEEIILYHSRFTEkdrAKKEAeL 270
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 15833781 536 MASF-KQGELHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 587
Cdd:TIGR01587 271 LREMkKSNEKFVIVATQVIEASLDI-SADVMITE------LAPIDSLIQRLGR 316
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
509-566 |
4.24e-06 |
|
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: 46.73 E-value: 4.24e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 509 EELKLALPELN--VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:cd18787 41 DRLAELLEELGikVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
316-430 |
4.65e-06 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 50.11 E-value: 4.65e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 316 HGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:COG1111 45 KGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKR---KELWEKARI--IVAT-----PQVIENDLiagr 114
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 15833781 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:COG1111 115 idlddvSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
317-430 |
1.31e-05 |
|
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: 46.35 E-value: 1.31e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 317 GKQVALMAPTELLAEQHANNFRNWFEpLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGT-----HAIFQEQVQFNGL 391
Cdd:cd18035 45 GGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEER---AERWDASKI--IVATpqvieNDLLAGRITLDDV 118
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 15833781 392 ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:cd18035 119 SLLIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
299-412 |
1.57e-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: 46.10 E-value: 1.57e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 299 GSGKTLVAALAALRAIAHGKQVAL-MAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKgkarlSQQEAIASGQVqmIVG 377
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPS-----VNKLLLAEADI--LVA 99
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 15833781 378 THAIFQ------EQVQFNGLALVIIDEQHRFGVHQRLALWE 412
Cdd:cd17921 100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGERGVVLE 140
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
502-587 |
6.76e-05 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 43.41 E-value: 6.76e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 502 QAAEATWEELKLALPE----LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI-IENPerLGLA 576
Cdd:cd18796 49 SQAERLAQRLRELCPDrvppDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVA 126
|
90
....*....|.
gi 15833781 577 QLHQLRGRVGR 587
Cdd:cd18796 127 RLLQRLGRSGH 137
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
297-439 |
2.03e-04 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 43.02 E-value: 2.03e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 297 DVGSGKTL-------VAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWfepLGIEVGWLAGKQ--KGKARLSQQEAI 367
Cdd:cd18034 24 PTGSGKTLiavmlikEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSH---TDLKVGEYSGEMgvDKWTKERWKEEL 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 368 ASGQVqmIVGTHAIF-----QEQVQFNGLALVIIDEQHrfgvHQRlalwekgqqqGFHPHQLIM-------TATPIPRTL 435
Cdd:cd18034 101 EKYDV--LVMTAQILldalrHGFLSLSDINLLIFDECH----HAT----------GDHPYARIMkefyhleGRTSRPRIL 164
|
....
gi 15833781 436 AMTA 439
Cdd:cd18034 165 GLTA 168
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
520-587 |
2.13e-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: 42.15 E-value: 2.13e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15833781 520 VGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPnASLMIIENPER--------LGLAQLHQLRGRVGR 587
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 ... |
527-588 |
2.47e-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: 41.96 E-value: 2.47e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15833781 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLhQLRGRVGRG 588
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRK 134
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
223-430 |
3.67e-04 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 43.61 E-value: 3.67e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 223 RLILEELLAHNLSMLALRA----GAQRFHAQPLSANDALKNKLLAALPFkpTGAQARVVAEIERDMALDVPmmrLVQGDV 298
Cdd:PRK05580 97 RLALLAELALAASSAVLKGlvkkGLIELEEVEVLRLRPPPDPAFEPPTL--NPEQAAAVEAIRAAAGFSPF---LLDGVT 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 299 GSGKTLVAALAALRAIAHGKQVALMAPtEL-LAEQHANNFRNWFeplGIEVG-W---LAGKQKGKARLsqqeAIASGQVQ 373
Cdd:PRK05580 172 GSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQMLARFRARF---GAPVAvLhsgLSDGERLDEWR----KAKRGEAK 243
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 374 MIVGTH-AIFqeqVQFNGLALVIIDEQH----------RFgvHQR-LALWeKGQQQGFhphQLIM-TATP 430
Cdd:PRK05580 244 VVIGARsALF---LPFKNLGLIIVDEEHdssykqqegpRY--HARdLAVV-RAKLENI---PVVLgSATP 304
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
183-400 |
8.02e-04 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 42.80 E-value: 8.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 183 LPPELSQGMMTLPEALRTLhrpppTLQLSDLETGQHPAQRRLiLEELLAHN----LSMLALRAGAQRFHAQPL------- 251
Cdd:COG1198 100 LPAGLRQGYPARIKTERYV-----RLTLGEELPKRAPKQRRV-LEALREHGgpltLSELAKEAGVSRSVLKALvkkglle 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 252 -----SANDALKNKLLAALPFKPTGAQARVVAEIERDMALDVPMmrLVQGDVGSGKTLVAALAALRAIAHGKQVALMAPt 326
Cdd:COG1198 174 ieereVDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVP- 250
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15833781 327 EL-LAEQHANNFRNWFeplGIEVGWLAGKQKGKARLSQQEAIASGQVQMIVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:COG1198 251 EIaLTPQTVERFRARF---GARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
524-611 |
1.54e-03 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 41.81 E-value: 1.54e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 524 HGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGAVASHCVLLYktplS 603
Cdd:PLN03137 711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAGRDGQRSSCVLYY----S 785
|
....*...
gi 15833781 604 KTAQIRLQ 611
Cdd:PLN03137 786 YSDYIRVK 793
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
299-431 |
2.94e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 38.81 E-value: 2.94e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 299 GSGKTL--VAALAALRAIAHGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKgkarlsqqeAIASGQVQMIV 376
Cdd:pfam04851 33 GSGKTLtaAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYVEIGEIISGDKK---------DESVDDNKIVV 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15833781 377 GT-HAIF------QEQVQFNGLALVIIDEQHRFG--VHQRLALWEKgqqqgfHPHQLIMTATPI 431
Cdd:pfam04851 104 TTiQSLYkalelaSLELLPDFFDVIIIDEAHRSGasSYRNILEYFK------PAFLLGLTATPE 161
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
317-587 |
3.76e-03 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 40.57 E-value: 3.76e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 317 GKQVALMaPTELLAEQHANNFRNWfEPLGIEVGWLAGKQKgkarlSQQEAIasGQVQMIVGTHAIFQEQVQ-----FNGL 391
Cdd:PRK00254 69 GKAVYLV-PLKALAEEKYREFKDW-EKLGLRVAMTTGDYD-----STDEWL--GKYDIIIATAEKFDSLLRhgsswIKDV 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 392 ALVIIDEQHRFGVHQRLALWEKGQQQGFHPHQLIMTATPI--PRTLAMTAYADL-------------------------- 443
Cdd:PRK00254 140 KLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVgnAEELAEWLNAELvvsdwrpvklrkgvfyqgflfwedgk 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 444 --------DTSVIDELPPGRTPVTTVaipDTRRTdiidRVRHACITEGRQAYWVcTLIEESELLE-AQAAEA--TWEELK 512
Cdd:PRK00254 220 ierfpnswESLVYDAVKKGKGALVFV---NTRRS----AEKEALELAKKIKRFL-TKPELRALKElADSLEEnpTNEKLK 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 513 LALPElNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPnASLMIIENP--------ERLGLAQLHQLRGR 584
Cdd:PRK00254 292 KALRG-GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLP-AFRVIIRDTkrysnfgwEDIPVLEIQQMMGR 369
|
...
gi 15833781 585 VGR 587
Cdd:PRK00254 370 AGR 372
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
518-566 |
5.12e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 39.75 E-value: 5.12e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 15833781 518 LNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMI 566
Cdd:COG0513 266 ISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVI 314
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
527-599 |
7.06e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.86 E-value: 7.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 527 MKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMIIENP--------ERlglaqlhqlRGRVGRGAVASHCVLLY 598
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvpseirsiQR---------KGRTGRQEEGRVVVLIA 477
|
.
gi 15833781 599 K 599
Cdd:PRK13766 478 K 478
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
517-567 |
8.29e-03 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 37.61 E-value: 8.29e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 15833781 517 ELNVGLVHGRMKPAEKQAVMASFKQGELHLLVATTVIEVGVDVPNASLMII 567
Cdd:cd18789 68 RLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
529-597 |
8.78e-03 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 37.24 E-value: 8.78e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15833781 529 PAEKQAVMASFKQGELHLLVATTVIEVGVDVpnASL---MIIENPErlGLAQLHQLRGRVGRGAVASHCVLL 597
Cdd:cd18797 78 AEDRREIEAELFNGELLGVVATNALELGIDI--GGLdavVLAGYPG--SLASLWQQAGRAGRRGKDSLVILV 145
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
316-430 |
9.21e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.47 E-value: 9.21e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833781 316 HGKQVALMAPTELLAEQHANNFRNWFEPLGIEVGWLAGKQKGKARlsqQEAIASGQVqmIVGThaifqEQVQFNGL---- 391
Cdd:PRK13766 57 KGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKR---AELWEKAKV--IVAT-----PQVIENDLiagr 126
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 15833781 392 ------ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:PRK13766 127 isledvSLLIFDEAHRaVGNYAYVYIAERYHEDAKNPLVLGLTASP 172
|
|
| |
