|
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: 1106.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 1 MRGRLLDAVPLSSLTGVGASQSAKLAKIGLHTIQDLLLHFPLRYEDRTHLYPISDLLPGVYATVEGEVLNCNITFGGRRM 80
Cdd:PRK10917 1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 81 MTCQISDGTGILTMRFFNFNAAM-KNSLATGRRVLAYGEAKRGKYGAEMIHPEYRIQGDViTPEMQETLTPVYPTTEGVR 159
Cdd:PRK10917 81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEE-SPELEGRLTPVYPLTEGLK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 160 QATLRKLTDQALELLEtcAITELLPPELSQ--GLMSLPEALRTLHRPPPDmklEDLesgqHPAQRRLILEELLAHNLSML 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEkyGLLSLAEALRAIHFPPSD---EDL----HPARRRLKFEELFALQLSLL 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 238 ALRAGAQRYHAQPLEARDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 318 KQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQVQFNGLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 398 EQHRFGVHQRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRGDIIERVRS 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 478 AClEEGRQAYWVCTLIEESELLEAQAAEATWEELKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGV 557
Cdd:PRK10917 467 EI-AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 558 DVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKSPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*.
gi 490522288 638 TRQTGNAEFKVADLLRDQAVIPEVQRIARHIHERYPEQAAALIERWMPETERYSNA 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: 1070.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 10 PLSSLTGVGASQSAKLAKIGLHTIQDLLLHFPLRYEDRTHLYPISDLLPGVYATVEGEVLNCNITF--GGRRMMTCQISD 87
Cdd:COG1200 7 PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLSD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 88 GTGILTMRFFNFnAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRIQGDViTPEMQETLTPVYPTTEGVRQATLRKLT 167
Cdd:COG1200 87 GTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDEE-EAELAGRLTPVYPLTEGLSQKTLRKLI 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 168 DQALELLETcAITELLPPEL--SQGLMSLPEALRTLHRPPPDmklEDLesgqHPAQRRLILEELLAHNLSMLALRAGAQR 245
Cdd:COG1200 165 RQALDLLAP-DLPEPLPEELraRYGLPSLAEALRNIHFPPSD---EDL----HPARRRLAFEELLALQLALLLRRARRRK 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 246 YHAQPLEARDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANGKQVALMAP 325
Cdd:COG1200 237 RKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAP 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 326 TELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVH 405
Cdd:COG1200 317 TEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVE 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 406 QRLALWEKGQqqgfHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRGDIIERVRSAClEEGRQ 485
Cdd:COG1200 397 QRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEI-AKGRQ 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 486 AYWVCTLIEESELLEAQAAEATWEELKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLM 565
Cdd:COG1200 472 AYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVM 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 566 IIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKSPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAE 645
Cdd:COG1200 552 VIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPD 631
|
650 660 670 680
....*....|....*....|....*....|....*....|....*
gi 490522288 646 FKVADLLRDQAVIPEVQRIARHIHERYPEQAA-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: 923.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 28 IGLHTIQDLLLHFPLRYEDRTHLYPISDLLPGVYATVEGEVLN-CNITFGGRRMMTCQISD-GTGILTMRFFNfNAAMKN 105
Cdd:TIGR00643 1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLShCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 106 SLATGRRVLAYGEAKRGKYGAEMIHPEYRIQGDVITPEMqeTLTPVYPTTEGVRQATLRKLTDQALELLETCaITELLPP 185
Cdd:TIGR00643 80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 186 ELSQ--GLMSLPEALRTLHrPPPDmkledlESGQHPAQRRLILEELLAHNLSMLALRAG-AQRYHAQPLEARDALKHQLL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIH-FPKT------LSLLELARRRLIFDEFFYLQLAMLARRLGeKQQFSAPPANPSEELLTKFL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 263 ASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANGKQVALMAPTELLAEQHANNFRNWFA 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 343 PLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQqGFHPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQG-GFTPH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 423 QLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIPDTRRgDIIERVRSACLEEGRQAYWVCTLIEESELLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLK 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 503 AAEATWEELKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 583 GRVGRGAVASHCVLLYKSPLSKTAQIRLQVLRDSNDGFVIAQKDLEIRGPGELLGTRQTGNAEFKVADLLRDQAVIPEVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627
|
...
gi 490522288 663 RIA 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 |
1.51e-115 |
|
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: 346.06 E-value: 1.51e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 224 LILEELLAHNLSMLALRAGAQRYHAQPLEARDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKT 303
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 304 LVAALAALRAIANGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQ 383
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490522288 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 |
3.53e-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: 343.96 E-value: 3.53e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 226 LEELLAHNLSMLALRAgAQRYHAQPLEarDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLV 305
Cdd:TIGR00580 412 VREIAAKLIELYAKRK-AIKGHAFPPD--LEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV 488
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 306 AALAALRAIANGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQ 385
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKD 568
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 386 VQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVAIP- 464
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQK----EKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEy 644
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 465 -DTRRGDIIERVrsacLEEGRQAYWVCTLIEESELLEAQaaeatweeLKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGE 543
Cdd:TIGR00580 645 dPELVREAIRRE----LLRGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVMLEFYKGE 712
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 544 MHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKS--PLSKTAQIRLQVLRDSND--- 618
Cdd:TIGR00580 713 FQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHqkALTEDAQKRLEAIQEFSElga 792
|
410 420
....*....|....*....|....
gi 490522288 619 GFVIAQKDLEIRGPGELLGTRQTG 642
Cdd:TIGR00580 793 GFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
263-643 |
1.99e-93 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 313.54 E-value: 1.99e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 263 ASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKT-----------LvaalaalraiaNGKQVALMAPTELLAE 331
Cdd:COG1197 581 AAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafkavM-----------DGKQVAVLVPTTLLAQ 649
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 332 QHANNFRNWFAPLGIEVGWL-----AGKQKgKARqaqqEAIASGQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQ 406
Cdd:COG1197 650 QHYETFKERFAGFPVRVEVLsrfrtAKEQK-ETL----EGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRH 724
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 407 --RL-ALWEkgqqqgfHPHQLIMTATPIPRTLAMtAYADL-DTSVIDELPPGRTPVTTVAIP-DTrrgdiiERVRSACLE 481
Cdd:COG1197 725 keKLkALRA-------NVDVLTLTATPIPRTLQM-SLSGIrDLSIIATPPEDRLPVKTFVGEyDD------ALIREAILR 790
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 482 E---GRQAYWVCTLIEEselLEAQAaeatwEELKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVD 558
Cdd:COG1197 791 EllrGGQVFYVHNRVED---IEKVA-----ARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGID 862
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 559 VPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKS--PLSKTAQIRLQVLRDSND---GFVIAQKDLEIRGPG 633
Cdd:COG1197 863 IPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPdkVLTEDAEKRLEAIQEFTElgaGFKLAMHDLEIRGAG 942
|
410
....*....|
gi 490522288 634 ELLGTRQTGN 643
Cdd:COG1197 943 NLLGEEQSGH 952
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
457-615 |
1.08e-80 |
|
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: 253.04 E-value: 1.08e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 457 PVTTVAIPDTRRGDIIERVRsACLEEGRQAYWVCTLIEESELLEAQAAEATWEELKTTL-PGLNVGLVHGRMKPAEKQAV 535
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVR-EEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 536 MQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKSPLSKTAQIRLQVLRD 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 |
1.42e-69 |
|
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: 224.07 E-value: 1.42e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 457 PVTTVAIPDTRRgDIIERVRSACLEEGRQAYWVCTLIEESELLEAQAAEATWEELKTTLPGLNVGLVHGRMKPAEKQAVM 536
Cdd:cd18792 1 PIRTYVIPHDDL-DLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 537 QAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKSP--LSKTAQIRLQVLR 614
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPkkLTETAKKRLRAIA 159
|
.
gi 490522288 615 D 615
Cdd:cd18792 160 E 160
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
255-645 |
1.55e-68 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 243.88 E-value: 1.55e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 255 DALKHQLLA-SLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANGKQVALMAPTELLAEQH 333
Cdd:PRK10689 586 DREQYQLFCdSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQH 665
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 334 ANNFRNWFA--PLGIEVgwLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalw 411
Cdd:PRK10689 666 YDNFRDRFAnwPVRIEM--LSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHK---- 739
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 412 EKGQQQGFHPHQLIMTATPIPRTLAMTAYADLDTSVIDELPPGRTPVTTVaipdTRRGDIIErVRSACLEE---GRQAYW 488
Cdd:PRK10689 740 ERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTF----VREYDSLV-VREAILREilrGGQVYY 814
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 489 VCTLIEESElleaQAAeatwEELKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIE 568
Cdd:PRK10689 815 LYNDVENIQ----KAA----ERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE 886
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 569 NPERLGLAQLHQLRGRVGRGAVASHCVLLYKSP--LSKTAQIRLQV---LRDSNDGFVIAQKDLEIRGPGELLGTRQTGN 643
Cdd:PRK10689 887 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAiasLEDLGAGFALATHDLEIRGAGELLGEEQSGQ 966
|
..
gi 490522288 644 AE 645
Cdd:PRK10689 967 ME 968
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
260-449 |
7.89e-57 |
|
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: 191.25 E-value: 7.89e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 260 QLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANGKQVALMAPTELLAEQHANNFRN 339
Cdd:cd17991 7 EFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 340 WFAPLGIEVGWLAGKQKGKARQAQQEAIASGQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRlalwEKGQQQGF 419
Cdd:cd17991 87 RFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQK----EKLKELRP 162
|
170 180 190
....*....|....*....|....*....|..
gi 490522288 420 HPHQLIMTATPIPRTL--AMTAYADLdtSVID 449
Cdd:cd17991 163 NVDVLTLSATPIPRTLhmALSGIRDL--SVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
254-449 |
1.01e-55 |
|
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: 188.01 E-value: 1.01e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 254 RDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMRLVQGDVGSGKTLVAALAALRAIANGKQVALMAPTELLAEQH 333
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 334 ANNFRNWFAPLGIEVgwLAGKQKGKARQaqqeaiasgQVSMVVGTHAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:cd17918 81 YEEARKFLPFINVEL--VTGGTKAQILS---------GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|....*.
gi 490522288 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 |
6.64e-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: 6.64e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 475 VRSACLEE---GRQAYWVCTLIEESELLEAQaaeatweeLKTTLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATT 551
Cdd:cd18810 14 IREAIEREllrGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTT 85
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490522288 552 VIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGAVASHCVLLYKS--PLSKTAQIRLQVL 613
Cdd:cd18810 86 IIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDqkKLTEDALKRLEAI 149
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
16-166 |
3.88e-25 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 102.13 E-value: 3.88e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 16 GVGASQSAKLAKIGLHTIQDLLLHFPLRYEDRTHLYPISDLLPGVYATVEGEVLNCN-ITFGGRRMMTCQISDGTGILTM 94
Cdd:pfam17191 7 GVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFEtKKIGSLVIISAVLSDGIGQVLL 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490522288 95 RFFNfNAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRIQGDviTPEMQetLTPVYPTTEGVRQATLRKL 166
Cdd:pfam17191 87 KWFN-QEYIKKFLQKGKEVYITGTVKEGPFGPiEMNNPEIEEITG--EQERE--ILPVYPLTEGISQKNMRKI 154
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
63-135 |
6.30e-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: 92.64 E-value: 6.30e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490522288 63 TVEGEVLNCNI-TFGGRRMMTCQISDGTGILTMRFFNFNAAMKNSLATGRRVLAYGEAKRGKYGAEMIHPEYRI 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 |
9.82e-23 |
|
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: 95.39 E-value: 9.82e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 270 TGAQARVVAEI--ERDMaldipmmrLVQGDVGSGKT---LVAALAALRAIANGKQVALMAPTELLAEQHANNFRNWFAPL 344
Cdd:pfam00270 1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTlafLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 345 GIEVGWLAGkqkGKARQAQQEAIASGQVsmVVGTH----AIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEKGQQQGFH 420
Cdd:pfam00270 73 GLKVASLLG---GDSRKEQLEKLKGPDI--LVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK 147
|
170
....*....|....*....
gi 490522288 421 PHQLI-MTATPiPRTLAMT 438
Cdd:pfam00270 148 KRQILlLSATL-PRNLEDL 165
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
261-456 |
8.23e-22 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 93.71 E-value: 8.23e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 261 LLASLPFKPTGAQARVVAEIERDMaldipMMRLVQGDVGSGKTLVAAL--AALRAIANGKQVALMAPTELLAEQHANNFR 338
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 339 NWFAPLGIEVgwlAGKQKGKARQAQQEAIASGQVSMVVGT-----HAIFQEQVQFNGLALVIIDEQHRFGVHQRLALWEK 413
Cdd:smart00487 76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 490522288 414 -GQQQGFHPHQLIMTATP---IPRTLAMTAYADLDTSVIDELPPGRT 456
Cdd:smart00487 153 lLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
517-587 |
1.35e-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: 84.57 E-value: 1.35e-19
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490522288 517 GLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGR 587
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
517-587 |
1.85e-17 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 77.25 E-value: 1.85e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490522288 517 GLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPeRLGLAQLHQLRGRVGR 587
Cdd:smart00490 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
222-598 |
1.02e-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: 1.02e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 222 RRLILEELLAHNLSMLALRAGAQRYHAQPLEARDALKHQLLASLPFKPTGAQARVVAEIERDMALDIPMMrLVQGDVGSG 301
Cdd:COG1061 34 LVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLAALERGGGRG-LVVAPTGTG 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 302 KTLVAALAALRAIaNGKQVALMAPTELLAEQHANNFRNWFaplgievgwlaGKQKGKARQAQQEAIasgqvsMVVGTHAI 381
Cdd:COG1061 113 KTVLALALAAELL-RGKRVLVLVPRRELLEQWAEELRRFL-----------GDPLAGGGKKDSDAP------ITVATYQS 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 382 FQEQVQFNGLA----LVIIDEQHRFG--VHQRLAlwekgqqQGFHPHQLI-MTATPIpRTLAMTAYADLDTSVIDELPPG 454
Cdd:COG1061 175 LARRAHLDELGdrfgLVIIDEAHHAGapSYRRIL-------EAFPAAYRLgLTATPF-RSDGREILLFLFDGIVYEYSLK 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 455 R-------TPVTTVAIPD------------------------TRRGDIIERVRSACLeEGRQAYWVCTLIEEselleaqa 503
Cdd:COG1061 247 EaiedgylAPPEYYGIRVdltderaeydalserlrealaadaERKDKILRELLREHP-DDRKTLVFCSSVDH-------- 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 504 AEATWEELKTtlPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMII----ENPerlglAQLH 579
Cdd:COG1061 318 AEALAELLNE--AGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILlrptGSP-----REFI 390
|
410
....*....|....*....
gi 490522288 580 QLRGRVGRGAVASHCVLLY 598
Cdd:COG1061 391 QRLGRGLRPAPGKEDALVY 409
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
616-674 |
6.89e-11 |
|
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: 59.02 E-value: 6.89e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 616 SNDGFVIAQKDLEIRGPGELLGTRQTGNA-EFKVADLLRDQAVIPEVQRIARHIHERYPE 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 |
6.64e-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: 6.64e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 293 LVQGDVGSGKTLVAALA-ALRAIANGKQVALMAPTELLAEQHANNFRNWFAPlGIEVGWLAGkqkgkARQA-QQEAIASG 370
Cdd:cd00046 5 LITAPTGSGKTLAALLAaLLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVG-----GSSAeEREKNKLG 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490522288 371 QVSMVVGTHAIFQEQVQFNGLA------LVIIDEQHRFGV--HQRLALWEKGQQQGFHPHQLI-MTAT 429
Cdd:cd00046 79 DADIIIATPDMLLNLLLREDRLflkdlkLIIVDEAHALLIdsRGALILDLAVRKAGLKNAQVIlLSAT 146
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
63-135 |
8.45e-09 |
|
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: 52.62 E-value: 8.45e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490522288 63 TVEGEVLNcnITFGGRRMMTCQISDGTGILTMRFFN-FNAAMKNSLATGRRVLAYGEAKRGKYGA-EMIHPEYRI 135
Cdd:pfam01336 2 TVAGRVTS--IRRSGGKLLFLTLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKRKGGElELVVEEIEL 74
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
390-587 |
2.31e-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: 56.67 E-value: 2.31e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTsVIDELPPGRTPVTTVAIP-- 464
Cdd:cd09639 123 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGY-VEENEPLDLKPNERAPFIki 197
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 465 -DTRRGDI--IERVRSACLEEGRQAYwVCTLIEEselleaqaAEATWEELKTTLPGLNVGLVHGRMKP---AEKQA-VMQ 537
Cdd:cd09639 198 eSDKVGEIssLERLLEFIKKGGSVAI-IVNTVDR--------AQEFYQQLKEKGPEEEIMLIHSRFTEkdrAKKEAeLLL 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 490522288 538 AFKQGEMHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 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 |
3.15e-08 |
|
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: 53.75 E-value: 3.15e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 293 LVQGDVGSGKTLVAALAALRAIANGKQVALMAPTELLAEQHANNFRNWFaplGIEVGWLAGKQKGKARQAQQEAIASGQV 372
Cdd:cd17929 19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF---GDKVAVLHSKLSDKERADEWRKIKRGEA 95
|
90 100
....*....|....*....|....*....
gi 490522288 373 SMVVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:cd17929 96 KVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
424-559 |
4.14e-08 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 56.24 E-value: 4.14e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 424 LIMTAT-PIPRTLAMTAYADL-------DTSVIDELPPGRTPVTTVAIPDTrrgDIIERVRSAcLEEGRQAYWVCTLIee 495
Cdd:COG1203 303 ILMTATlPPLLREELLEAYELipdepeeLPEYFRAFVRKRVELKEGPLSDE---ELAELILEA-LHKGKSVLVIVNTV-- 376
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490522288 496 selleaQAAEATWEELKTTLPGLNVGLVHGRMKPAEK----QAVMQAFKQGEMHLLVATTVIEVGVDV 559
Cdd:COG1203 377 ------KDAQELYEALKEKLPDEEVYLLHSRFCPADRseieKEIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
543-589 |
4.65e-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: 50.40 E-value: 4.65e-08
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 490522288 543 EMHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGA 589
Cdd:cd18785 22 SLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGG 67
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
299-439 |
1.15e-07 |
|
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: 52.82 E-value: 1.15e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 299 GSGKTLVAAL-----AALRAIANGKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARqaQQEAIASGQVs 373
Cdd:cd17927 27 GSGKTFVAVLicehhLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVS--VEQIVESSDV- 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 374 mVVGTHAIFQ------EQVQFNGLALVIIDEQHRfgvhqrlalwekgqQQGFHPHQLIMT---------ATPIPRTLAMT 438
Cdd:cd17927 104 -IIVTPQILVndlksgTIVSLSDFSLLVFDECHN--------------TTKNHPYNEIMFryldqklgsSGPLPQILGLT 168
|
.
gi 490522288 439 A 439
Cdd:cd17927 169 A 169
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
509-597 |
1.25e-07 |
|
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: 51.44 E-value: 1.25e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 509 EELKTTLPGLNVGLVHGR----------MKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERlGLAQL 578
Cdd:cd18802 46 KEHPSTLAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSY 124
|
90
....*....|....*....
gi 490522288 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 |
1.13e-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: 51.30 E-value: 1.13e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 390 GLALVIIDEQHRFGVHQR---LALWEKGQQQGFhPHqLIMTATpIPRTLaMTAYADLDTSVIDELPPGRTPVTTVAIPDT 466
Cdd:TIGR01587 124 ANSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDLKEERRFENHRFI 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 467 RR-----GDI--IERVRSACLEEGRQAYwVCTLIEEselleaqaAEATWEELKTTLPGLNVGLVHGRMKPA-----EKQA 534
Cdd:TIGR01587 200 LIesdkvGEIssLERLLEFIKKGGSIAI-IVNTVDR--------AQEFYQQLKEKAPEEEIILYHSRFTEKdrakkEAEL 270
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 490522288 535 VMQAFKQGEMHLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 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 ... |
517-566 |
2.24e-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: 47.50 E-value: 2.24e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 490522288 517 GLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMI 566
Cdd:cd18787 51 GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
317-430 |
1.06e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 48.96 E-value: 1.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 317 GKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEaiasgQVSMVVGThaifqEQVQFNGL----- 391
Cdd:COG1111 46 GGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWE-----KARIIVAT-----PQVIENDLiagri 115
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 490522288 392 -----ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:COG1111 116 dlddvSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
299-412 |
1.75e-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: 45.72 E-value: 1.75e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 299 GSGKTLVAALAALRAIANGKQVAL-MAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEAIasgqvsmVVG 377
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLLAEADI-------LVA 99
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 490522288 378 THAIFQ------EQVQFNGLALVIIDEQHRFGVHQRLALWE 412
Cdd:cd17921 100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGERGVVLE 140
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
297-439 |
3.49e-05 |
|
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: 45.34 E-value: 3.49e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 297 DVGSGKTL-------VAALAALRAIANGKQVALMAPTELLAEQHANNFRNWfapLGIEVGWLAGKQ--KGKARQAQQEAI 367
Cdd:cd18034 24 PTGSGKTLiavmlikEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSH---TDLKVGEYSGEMgvDKWTKERWKEEL 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 368 ASGQVsmVVGTHAIF-----QEQVQFNGLALVIIDEQHrfgvHQRlalwekgqqqGFHPHQLIM-------TATPIPRTL 435
Cdd:cd18034 101 EKYDV--LVMTAQILldalrHGFLSLSDINLLIFDECH----HAT----------GDHPYARIMkefyhleGRTSRPRIL 164
|
....
gi 490522288 436 AMTA 439
Cdd:cd18034 165 GLTA 168
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
317-430 |
3.63e-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: 44.81 E-value: 3.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 317 GKQVALMAPTELLAEQHANNFRNWF-APLGIE--VGWLAGKQKGKARQAQQEAIASGQVSmvvgTHAIFQEQVQFNGLAL 393
Cdd:cd18035 45 GGKVLILAPSRPLVEQHAENLKRVLnIPDKITslTGEVKPEERAERWDASKIIVATPQVI----ENDLLAGRITLDDVSL 120
|
90 100 110
....*....|....*....|....*....|....*...
gi 490522288 394 VIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:cd18035 121 LIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
219-400 |
4.05e-05 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 47.04 E-value: 4.05e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 219 PAQRRLiLEELLAHN----LSMLALRAGAQRYHAQPLEA------------RDALKHQLLASLPFKPTGAQARVVAEIER 282
Cdd:COG1198 131 PKQRRV-LEALREHGgpltLSELAKEAGVSRSVLKALVKkglleieerevdRDPFAPDVPAEPPPTLNEEQQAAVEAIRA 209
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 283 DMALDIPMmrLVQGDVGSGKTLVAALAALRAIANGKQVALMAPtEL-LAEQHANNFRNWFaplGIEVGWLAGKQKGKARQ 361
Cdd:COG1198 210 AAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQTVERFRARF---GARVAVLHSGLSDGERL 283
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 490522288 362 AQQEAIASGQVSMVVGTH-AIFqeqVQFNGLALVIIDEQH 400
Cdd:COG1198 284 DEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
524-587 |
1.02e-04 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 45.27 E-value: 1.02e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490522288 524 HGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPnASLMIIENPERLGLAQL-----HQLRGRVGR 587
Cdd:COG1204 307 HAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
520-587 |
1.37e-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: 1.37e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490522288 520 VGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPnASLMIIENPER--------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 |
1.89e-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: 1.89e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490522288 527 MKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERLGLAQLhQLRGRVGRG 588
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRK 134
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
502-587 |
6.76e-04 |
|
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: 40.71 E-value: 6.76e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 502 QAAEATWEELKT----TLPGLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMI-IENPerLGLA 576
Cdd:cd18796 49 SQAERLAQRLRElcpdRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVA 126
|
90
....*....|.
gi 490522288 577 QLHQLRGRVGR 587
Cdd:cd18796 127 RLLQRLGRSGH 137
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
518-567 |
7.79e-04 |
|
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: 40.70 E-value: 7.79e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 490522288 518 LNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMII 567
Cdd:cd18789 69 LLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
524-611 |
1.32e-03 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 42.19 E-value: 1.32e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 524 HGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRGAVASHCVLLYksplS 603
Cdd:PLN03137 711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAGRDGQRSSCVLYY----S 785
|
....*...
gi 490522288 604 KTAQIRLQ 611
Cdd:PLN03137 786 YSDYIRVK 793
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
517-566 |
1.51e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 41.67 E-value: 1.51e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 490522288 517 GLNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMI 566
Cdd:COG0513 265 GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVI 314
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
317-587 |
2.10e-03 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 41.34 E-value: 2.10e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 317 GKQVALMaPTELLAEQHANNFRNWfAPLGIEVGWLAGKQKGKarqaqQEAIasGQVSMVVGTHAIFQEQVQ-----FNGL 391
Cdd:PRK00254 69 GKAVYLV-PLKALAEEKYREFKDW-EKLGLRVAMTTGDYDST-----DEWL--GKYDIIIATAEKFDSLLRhgsswIKDV 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 392 ALVIIDEQHRFGVHQRLALWEKGQQQGFHPHQLIMTATPI--PRTLAMTAYADL-------------------------- 443
Cdd:PRK00254 140 KLVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVgnAEELAEWLNAELvvsdwrpvklrkgvfyqgflfwedgk 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 444 --------DTSVIDELPPGRTPVTTVaipDTRRgdiieRVRSACLEEGRQAYWVCTLIEESELLE-AQAAEA--TWEELK 512
Cdd:PRK00254 220 ierfpnswESLVYDAVKKGKGALVFV---NTRR-----SAEKEALELAKKIKRFLTKPELRALKElADSLEEnpTNEKLK 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 513 TTLPGlNVGLVHGRMKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPnASLMIIENP--------ERLGLAQLHQLRGR 584
Cdd:PRK00254 292 KALRG-GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLP-AFRVIIRDTkrysnfgwEDIPVLEIQQMMGR 369
|
...
gi 490522288 585 VGR 587
Cdd:PRK00254 370 AGR 372
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
527-599 |
5.34e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 40.10 E-value: 5.34e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 527 MKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMI-----------IenperlglaqlhQLRGRVGRGAVASHCV 595
Cdd:COG1111 395 LTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIfyepvpseirsI------------QRKGRTGRKREGRVVV 462
|
....
gi 490522288 596 LLYK 599
Cdd:COG1111 463 LIAK 466
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
317-430 |
7.89e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.47 E-value: 7.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 317 GKQVALMAPTELLAEQHANNFRNWFAPLGIEVGWLAGKQKGKARQAQQEaiaSGQVsmVVGThaifqEQVQFNGL----- 391
Cdd:PRK13766 58 GGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE---KAKV--IVAT-----PQVIENDLiagri 127
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 490522288 392 -----ALVIIDEQHR-FGVHQRLALWEKGQQQGFHPHQLIMTATP 430
Cdd:PRK13766 128 sledvSLLIFDEAHRaVGNYAYVYIAERYHEDAKNPLVLGLTASP 172
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
293-430 |
8.13e-03 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 39.37 E-value: 8.13e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 293 LVQGDVGSGKTLVAALAALRAIANGKQVALMAPtEL-LAEQHANNFRNWFaplGIEVG-W---LAGKQKGKARqaqqEAI 367
Cdd:PRK05580 166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQMLARFRARF---GAPVAvLhsgLSDGERLDEW----RKA 237
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490522288 368 ASGQVSMVVGTH-AIFqeqVQFNGLALVIIDEQH----------RFgvHQR-LALWeKGQQQGFhphQLIM-TATP 430
Cdd:PRK05580 238 KRGEAKVVIGARsALF---LPFKNLGLIIVDEEHdssykqqegpRY--HARdLAVV-RAKLENI---PVVLgSATP 304
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
527-599 |
9.53e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 39.09 E-value: 9.53e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490522288 527 MKPAEKQAVMQAFKQGEMHLLVATTVIEVGVDVPNASLMIIENP--------ERlglaqlhqlRGRVGRGAVASHCVLLY 598
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvpseirsiQR---------KGRTGRQEEGRVVVLIA 477
|
.
gi 490522288 599 K 599
Cdd:PRK13766 478 K 478
|
|
| |
