|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
1-691 |
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 489287962 1 MTELSQvSVTALKGVGEAMAEKLAKVGLENLQDVLFHLPLRYQDRTRVVPIGHLRPGQDAVIEGTVSGADVVM--GKRRS 78
Cdd:COG1200 1 MAPLDT-PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 79 LVVRLQDGTGGLSLRFYHFsNAQKEGLKRGTRVRCYGEARPGASGLEIYHPEYRAItGDEPPPVDTTLTPIYPLTEGLTQ 158
Cdd:COG1200 80 LEVTLSDGTGSLTLVFFNQ-PYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELL-DEEEAELAGRLTPVYPLTEGLSQ 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 159 QRLRQLCMQTLTMLGPQsLPDWLPLELARDYQLAPLADAIRYLHHPPADADVdelalghHWAQHRLAFEELLTHQLSQQR 238
Cdd:COG1200 158 KTLRKLIRQALDLLAPD-LPEPLPEELRARYGLPSLAEALRNIHFPPSDEDL-------HPARRRLAFEELLALQLALLL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 239 LRESMRSLRAPAMPKATRLPAQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGY 318
Cdd:COG1200 230 RRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGY 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 319 QVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVAALEQIAAG-APMVVGTHALFQDEVQFKNLALVIIDE 397
Cdd:COG1200 310 QAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGeADIVVGTHALIQDDVEFKNLGLVVIDE 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 398 QHRFGVQQRLALRQKGVggrmNPHQLIMTATPIPRTLAMSAYADLDTSILDELPPGRTPVNTVLVTDTRRVEVIERVRGA 477
Cdd:COG1200 390 QHRFGVEQRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREE 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 478 CAEGRQAYWVCTLIEESEELTCQAAETTYEDLTSALGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDV 557
Cdd:COG1200 466 IAKGRQAYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 558 PNASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLYHPPLSQIGRQRLGIMRETNDGFVIAEKDLELRGPGEMLGTR 637
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTR 625
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 489287962 638 QTGLLQFKVADLMRDADLLPAVRDAAQALLERWPDHVS-PLLNRWLR---HGQQYGQV 691
Cdd:COG1200 626 QSGLPDLRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGlrfRDEDYLEV 683
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
1-691 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 1068.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 1 MTELSQVSVTALKGVGEAMAEKLAKVGLENLQDVLFHLPLRYQDRTRVVPIGHLRPGQDAVIEGTVSGADVVMGKRRSLV 80
Cdd:PRK10917 3 LLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRRLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 81 VRLQDGTGGLSLRFYHFSNAQ-KEGLKRGTRVRCYGEARPGASGLEIYHPEYRAITGDEPPPVDTtLTPIYPLTEGLTQQ 159
Cdd:PRK10917 83 VTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGR-LTPVYPLTEGLKQK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 160 RLRQLCMQTLTMLGPqsLPDWLPLELARDYQLAPLADAIRYLHHPPADADVdelalghHWAQHRLAFEELLTHQLSQQRL 239
Cdd:PRK10917 162 TLRKLIKQALELLDA--LPELLPEELLEKYGLLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLLLL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 240 RESMRSLRAPAMPKATRLPAQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGYQ 319
Cdd:PRK10917 233 RAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQ 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 320 VALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVAALEQIAAG-APMVVGTHALFQDEVQFKNLALVIIDEQ 398
Cdd:PRK10917 313 AALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGeADIVIGTHALIQDDVEFHNLGLVIIDEQ 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 399 HRFGVQQRLALRQKGVggrmNPHQLIMTATPIPRTLAMSAYADLDTSILDELPPGRTPVNTVLVTDTRRVEVIERVRGAC 478
Cdd:PRK10917 393 HRFGVEQRLALREKGE----NPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEI 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 479 AEGRQAYWVCTLIEESEELTCQAAETTYEDLTSALGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVP 558
Cdd:PRK10917 469 AKGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 559 NASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLYHPPLSQIGRQRLGIMRETNDGFVIAEKDLELRGPGEMLGTRQ 638
Cdd:PRK10917 549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQ 628
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|...
gi 489287962 639 TGLLQFKVADLMRDADLLPAVRDAAQALLERWPDHVSPLLNRWLRHGQQYGQV 691
Cdd:PRK10917 629 SGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
27-663 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 782.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 27 GLENLQDVLFHLPLRYQDRTRVVPIGHLRPGQDAVIEGTVSGADVVM-GKRRSLVVRLQD-GTGGLSLRFYHfSNAQKEG 104
Cdd:TIGR00643 2 GIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGfKRRKVLKLRLKDgGYKKLELRFFN-RAFLKKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 105 LKRGTRVRCYGEARPGASGLEIYHPEYraITGDEPPPVDTTLTPIYPLTEGLTQQRLRQLCMQTLTMLgPQSLPDWLPLE 184
Cdd:TIGR00643 81 FKVGSKVVVYGKVKSSKFKAYLIHPEF--ISEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDQL-DKSLEDPLPEE 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 185 LARDYQLAPLADAIRYLHHPPadaDVDELALghhwAQHRLAFEELLTHQLS--QQRLRESMRSLRAPAMPKATRLpAQYL 262
Cdd:TIGR00643 158 LREKYGLLSLEDALRAIHFPK---TLSLLEL----ARRRLIFDEFFYLQLAmlARRLGEKQQFSAPPANPSEELL-TKFL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 263 ANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGYQVALMAPTEILAEQHFITFKRWLE 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 343 PLGLEVAWLAGKLKGKNRVAALEQIAAGA-PMVVGTHALFQDEVQFKNLALVIIDEQHRFGVQQRLALRQKGVGGrMNPH 421
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQiHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGG-FTPH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 422 QLIMTATPIPRTLAMSAYADLDTSILDELPPGRTPVNTVLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELTCQA 501
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKA 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 502 AETTYEDLTSALGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRG 581
Cdd:TIGR00643 469 AEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRG 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 582 RVGRGSAASHCVLLYHPPLSQIGRQRLGIMRETNDGFVIAEKDLELRGPGEMLGTRQTGLLQFKVADLMRDADLLPAVRD 661
Cdd:TIGR00643 549 RVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEARE 628
|
..
gi 489287962 662 AA 663
Cdd:TIGR00643 629 DA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
224-451 |
1.99e-110 |
|
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: 332.58 E-value: 1.99e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 224 LAFEELLTHQLSQQRLRESMRSLRAPAMPKATRLPAQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKT 303
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 304 VVAALAALQALEAGYQVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVAALEQIAAG-APMVVGTHALFQ 382
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGeIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489287962 383 DEVQFKNLALVIIDEQHRFGVQQRLALRQKGVggrmNPHQLIMTATPIPRTLAMSAYADLDTSILDELP 451
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE----TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
166-640 |
1.87e-97 |
|
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: 320.84 E-value: 1.87e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 166 MQTLTMLGpqSLPDWLPLELA-RDYQLAPL--ADAI-RYLHHPPADADVDELAlGHHW----AQHRLAFEELLTHQLSQQ 237
Cdd:TIGR00580 347 LETLEVGG--IERDYLVLEYAgEDKLYVPVeqLHLIsRYVGGSGKNPALDKLG-GKSWektkAKVKKSVREIAAKLIELY 423
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 238 RLRESMRSLrapAMPKATRLPAQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAG 317
Cdd:TIGR00580 424 AKRKAIKGH---AFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG 500
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 318 YQVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVAALEQIAAGA-PMVVGTHALFQDEVQFKNLALVIID 396
Cdd:TIGR00580 501 KQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKiDILIGTHKLLQKDVKFKDLGLLIID 580
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 397 EQHRFGVQQRLALRQKgvggRMNPHQLIMTATPIPRTLAMSAYADLDTSILDELPPGRTPVNTVLV--TDTRRVEVIERv 474
Cdd:TIGR00580 581 EEQRFGVKQKEKLKEL----RTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMeyDPELVREAIRR- 655
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 475 rgACAEGRQAYWVCTLIEESEELtcqaaETTYEDLTSalgELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVG 554
Cdd:TIGR00580 656 --ELLRGGQVFYVHNRIESIEKL-----ATQLRELVP---EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETG 725
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 555 VDVPNASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLYHP--PLSQIGRQRLGIMRETND---GFVIAEKDLELRG 629
Cdd:TIGR00580 726 IDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHqkALTEDAQKRLEAIQEFSElgaGFKIALHDLEIRG 805
|
490
....*....|.
gi 489287962 630 PGEMLGTRQTG 640
Cdd:TIGR00580 806 AGNLLGEEQSG 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
266-640 |
5.87e-82 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 281.57 E-value: 5.87e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 266 GFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKT---------VVAAlaalqaleaGYQVALMAPTEILAEQHFIT 336
Cdd:COG1197 584 PYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafkAVMD---------GKQVAVLVPTTLLAQQHYET 654
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 337 FKRWLEPLGLEVAWL-----AGKLKgknrvAALEQIAAG-APMVVGTHALFQDEVQFKNLALVIIDEQHRFGVQQRLALR 410
Cdd:COG1197 655 FKERFAGFPVRVEVLsrfrtAKEQK-----ETLEGLADGkVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHKEKLK 729
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 411 QKgvggRMNPHQLIMTATPIPRTLAMSayadL----DTSILDELPPGRTPVNT-VLVTDTRRV-EVIER--VRGacaeGr 482
Cdd:COG1197 730 AL----RANVDVLTLTATPIPRTLQMS----LsgirDLSIIATPPEDRLPVKTfVGEYDDALIrEAILRelLRG----G- 796
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 483 QAYWVCTLIEESEEltcqaaetTYEDLTSALGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASL 562
Cdd:COG1197 797 QVFYVHNRVEDIEK--------VAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANT 868
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 563 MIIENPERLGLAQLHQLRGRVGRGSAASHCVLLYHP--PLSQIGRQRLGIMRETND---GFVIAEKDLELRGPGEMLGTR 637
Cdd:COG1197 869 IIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPdkVLTEDAEKRLEAIQEFTElgaGFKLAMHDLEIRGAGNLLGEE 948
|
...
gi 489287962 638 QTG 640
Cdd:COG1197 949 QSG 951
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
456-613 |
2.92e-75 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350198 [Multi-domain] Cd Length: 159 Bit Score: 238.78 E-value: 2.92e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 456 PVNTVLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELTCQAAETTYEDLTSAL-GELKVGLIHGRMKPAEKAAVM 534
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489287962 535 AEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLYHPPLSQIGRQRLGIMRE 613
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
456-613 |
2.74e-65 |
|
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: 212.51 E-value: 2.74e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 456 PVNTVLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELTCQAAETTYEDLTSALGELKVGLIHGRMKPAEKAAVMA 535
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 536 EFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLY--HPPLSQIGRQRLGIMRE 613
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYpdPKKLTETAKKRLRAIAE 160
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
267-640 |
2.33e-57 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 210.76 E-value: 2.33e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 267 FAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGYQVALMAPTEILAEQHFITFK----RWle 342
Cdd:PRK10689 599 FETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRdrfaNW-- 676
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 343 PLGLEVawLAGKLKGKNRVAALEQIAAG-APMVVGTHALFQDEVQFKNLALVIIDEQHRFGVQQRLalRQKGVggRMNPH 421
Cdd:PRK10689 677 PVRIEM--LSRFRSAKEQTQILAEAAEGkIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKE--RIKAM--RADVD 750
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 422 QLIMTATPIPRTLAMSAYADLDTSILDELPPGRTPVNTvLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELTCQA 501
Cdd:PRK10689 751 ILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKT-FVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERL 829
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 502 AETtyedltsaLGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERLGLAQLHQLRG 581
Cdd:PRK10689 830 AEL--------VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRG 901
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489287962 582 RVGRGSAASHCVLLYHPP--LSQIGRQRLGIMRETND---GFVIAEKDLELRGPGEMLGTRQTG 640
Cdd:PRK10689 902 RVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSG 965
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
259-437 |
5.87e-54 |
|
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: 183.54 E-value: 5.87e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 259 AQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGYQVALMAPTEILAEQHFITFK 338
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 339 RWLEPLGLEVAWLAGKLKGKNRVAALEQIAAG-APMVVGTHALFQDEVQFKNLALVIIDEQHRFGVQQRLALRQKgvggR 417
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGkVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL----R 161
|
170 180
....*....|....*....|
gi 489287962 418 MNPHQLIMTATPIPRTLAMS 437
Cdd:cd17991 162 PNVDVLTLSATPIPRTLHMA 181
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
259-448 |
6.54e-54 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 183.00 E-value: 6.54e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 259 AQYLANLGFAPTGAQQRVGNEIAYDLSQQEPMLRLIQGDVGAGKTVVAALAALQALEAGYQVALMAPTEILAEQHFITFK 338
Cdd:cd17918 6 QELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEAR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 339 RWLEPLGLEVawlagkLKGKNRvaalEQIAAGAPMVVGTHALFQDEVQFKNLALVIIDEQHRFGVQQRLALRQKGvggrm 418
Cdd:cd17918 86 KFLPFINVEL------VTGGTK----AQILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLG----- 150
|
170 180 190
....*....|....*....|....*....|
gi 489287962 419 NPHQLIMTATPIPRTLAMSAYADLDTSILD 448
Cdd:cd17918 151 ATHFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
469-613 |
2.37e-30 |
|
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: 116.67 E-value: 2.37e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 469 EVIERvrgACAEGRQAYWVCTLIEESEELtcqaaETTYEDLTSalgELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVAT 548
Cdd:cd18810 16 EAIER---ELLRGGQVFYVHNRIESIEKL-----ATQLRQLVP---EARIAIAHGQMTENELEEVMLEFAKGEYDILVCT 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489287962 549 TVIEVGVDVPNASLMIIENPERLGLAQLHQLRGRVGRGSAASHCVLLY--HPPLSQIGRQRLGIMRE 613
Cdd:cd18810 85 TIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYpdQKKLTEDALKRLEAIQE 151
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
13-170 |
7.54e-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: 89.80 E-value: 7.54e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 13 KGVGEAMAEKLAKVGLENLQDVLFHLPLRYQDRTRVVPIGHLRPGQDAVIEGTVSGADVV-MGKRRSLVVRLQDGTGGLS 91
Cdd:pfam17191 6 KGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETKkIGSLVIISAVLSDGIGQVL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 92 LRFYHFSNAQKEgLKRGTRVRCYGEARPGASG-LEIYHPEYRAITGDEPppvdTTLTPIYPLTEGLTQQRLRQLCMQTLT 170
Cdd:pfam17191 86 LKWFNQEYIKKF-LQKGKEVYITGTVKEGPFGpIEMNNPEIEEITGEQE----REILPVYPLTEGISQKNMRKIVKENIS 160
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
61-134 |
1.49e-20 |
|
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.
Pssm-ID: 239934 [Multi-domain] Cd Length: 75 Bit Score: 86.09 E-value: 1.49e-20
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489287962 61 VIEGTVSGADVV-MGKRRSLVVRLQDGTGGLSLRFYHFSNAQKEGLKRGTRVRCYGEARPGASGLEIYHPEYRAI 134
Cdd:cd04488 1 TVEGTVVSVEVVpRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYELL 75
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
293-436 |
3.21e-20 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 88.07 E-value: 3.21e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 293 LIQGDVGAGKTVVAAL---AALQALEAGYQVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGklkGKNRVAALEQIaA 369
Cdd:pfam00270 18 LVQAPTGSGKTLAFLLpalEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG---GDSRKEQLEKL-K 93
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489287962 370 GAPMVVGTH----ALFQDEVQFKNLALVIIDEQHRFGVQQRLALrQKGVGGRMNPHQ--LIMTATPiPRTLAM 436
Cdd:pfam00270 94 GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPD-LEEILRRLPKKRqiLLLSATL-PRNLED 164
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
499-585 |
1.37e-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: 1.37e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 499 CQAAETTYEDLTSALGELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQ 578
Cdd:pfam00271 22 SQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQ 100
|
....*..
gi 489287962 579 LRGRVGR 585
Cdd:pfam00271 101 RIGRAGR 107
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
263-455 |
1.58e-18 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 84.47 E-value: 1.58e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 263 ANLGFAPTGAQQRVGNEIAydlsqQEPMLRLIQGDVGAGKTVVAAL--AALQALEAGYQVALMAPTEILAEQHFITFKRW 340
Cdd:smart00487 3 KFGFEPLRPYQKEAIEALL-----SGLRDVILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 341 LEPLGLEVawlAGKLKGKNRVAALEQIAAG-APMVVGT-----HALFQDEVQFKNLALVIIDEQHRFGVQ-QRLALRQKG 413
Cdd:smart00487 78 GPSLGLKV---VGLYGGDSKREQLRKLESGkTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLEKLL 154
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 489287962 414 VGGRMNPHQLIMTATP---IPRTLAMSAYADLDTSILDELPPGRT 455
Cdd:smart00487 155 KLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
507-585 |
7.88e-18 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 78.41 E-value: 7.88e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 507 EDLTSALGEL--KVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPeRLGLAQLHQLRGRVG 584
Cdd:smart00490 1 EELAELLKELgiKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAG 79
|
.
gi 489287962 585 R 585
Cdd:smart00490 80 R 80
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
614-683 |
1.42e-16 |
|
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: 75.20 E-value: 1.42e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489287962 614 TNDGFVIAEKDLELRGPGEMLGTRQTGL-LQFKVADLMRDADLLPAVRDAAQALLERWPDHVSP---LLNRWLR 683
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIaFDLKIADIARDGQLLQLARTEAEEIIDNDPECSLPenaVLWRQLK 74
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
299-673 |
8.73e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 80.84 E-value: 8.73e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 299 GAGKTVVAALAALQALEAGyQVALMAPTEILAEQHFITFKRWLeplglevawlagklkgKNRVAALEQIAAGAPMVVGTH 378
Cdd:COG1061 110 GTGKTVLALALAAELLRGK-RVLVLVPRRELLEQWAEELRRFL----------------GDPLAGGGKKDSDAPITVATY 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 379 ALFQDEVQFKNLA----LVIIDEQHRFGVQQRLALRQkgvggRMNPHQLI-MTATPI---PRTLAMSAYA------DLDT 444
Cdd:COG1061 173 QSLARRAHLDELGdrfgLVIIDEAHHAGAPSYRRILE-----AFPAAYRLgLTATPFrsdGREILLFLFDgivyeySLKE 247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 445 -------------SILDELPPGR-------TPVNTVLVTDTRRV-EVIERVRGACAEGRQAYWVCTLIEESEELtcqaae 503
Cdd:COG1061 248 aiedgylappeyyGIRVDLTDERaeydalsERLREALAADAERKdKILRELLREHPDDRKTLVFCSSVDHAEAL------ 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 504 ttYEDLTSAlgELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMII----ENPerlglAQLHQL 579
Cdd:COG1061 322 --AELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILlrptGSP-----REFIQR 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 580 RGRVGRGSAASHCVLLYH------PPLSQI-GRQRLGIMRETNDGFVIAEKDLELRGPGEMLGTRQTGLLQFKVADLMRD 652
Cdd:COG1061 393 LGRGLRPAPGKEDALVYDfvgndvPVLEELaKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELL 472
|
410 420
....*....|....*....|.
gi 489287962 653 ADLLPAVRDAAQALLERWPDH 673
Cdd:COG1061 473 EDALLLVLAELLLLELLALAL 493
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
371-557 |
9.46e-10 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 61.64 E-value: 9.46e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 371 APMVVGT-----HALF----QDEVQFKNLA--LVIIDEqhrfgVQ----QRLAL------RQKGVGGRMnphqLIMTAT- 428
Cdd:COG1203 239 APVVVTTidqlfESLFsnrkGQERRLHNLAnsVIILDE-----VQayppYMLALllrlleWLKNLGGSV----ILMTATl 309
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 429 -PIPRTLAMSAYAdldtsILDELPPGRTPVNTVLVTdtRRVEV----------IERVRGACAEGRQAYWVCTLIEESEEL 497
Cdd:COG1203 310 pPLLREELLEAYE-----LIPDEPEELPEYFRAFVR--KRVELkegplsdeelAELILEALHKGKSVLVIVNTVKDAQEL 382
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489287962 498 tcqaaettYEDLTSALGELKVGLIHGRMKPAEK----AAVMAEFKAGNLQLLVATTVIEVGVDV 557
Cdd:COG1203 383 --------YEALKEKLPDEEVYLLHSRFCPADRseieKEIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
390-585 |
8.52e-09 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 57.82 E-value: 8.52e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 390 LALVIIDEQHRFGVQQRL-------ALRQKGVggrmnPHqLIMTATpIP---RTLAMSAYADLDTSILDELPPGRTPVNT 459
Cdd:cd09639 124 NSLLIFDEVHFYDEYTLAlilavleVLKDNDV-----PI-LLMSAT-LPkflKEYAEKIGYVEENEPLDLKPNERAPFIK 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 460 VLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELtcqaaettYEDLTSALGELKVGLIHGRMKP---AEKAA-VMA 535
Cdd:cd09639 197 IESDKVGEISSLERLLEFIKKGGSVAIIVNTVDRAQEF--------YQQLKEKGPEEEIMLIHSRFTEkdrAKKEAeLLL 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 489287962 536 EFKAGNLQLLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 585
Cdd:cd09639 269 EFKKSEKFVIVATQVIEASLDI-SVDVMITE------LAPIDSLIQRLGR 311
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
542-586 |
1.08e-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: 52.32 E-value: 1.08e-08
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 489287962 542 LQLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVGRG 586
Cdd:cd18785 23 LEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRG 66
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
273-399 |
1.67e-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: 54.52 E-value: 1.67e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 273 QQRVGNEIAYDLSQQEPMLrlIQGDVGAGKTVVAALAALQALEAGYQVALMAPtEI-LAEQhfiTFKRWLEPLGLEVAWL 351
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFL--LHGVTGSGKTEVYIELIEKVLAKGKQVLVLVP-EIsLTPQ---LIKRFKKRFGDKVAVL 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 489287962 352 AGKLKGKNRVAALEQIAAG-APMVVGTH-ALFqdeVQFKNLALVIIDEQH 399
Cdd:cd17929 75 HSKLSDKERADEWRKIKRGeAKVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
498-564 |
5.04e-08 |
|
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: 52.12 E-value: 5.04e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489287962 498 TCQAAETTYEDLTSAlgELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMI 564
Cdd:cd18787 36 TKKRVDRLAELLEEL--GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
390-585 |
5.35e-08 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 55.54 E-value: 5.35e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 390 LALVIIDEQHRFGVQQRL-------ALRQKGVggrmnPHqLIMTATpIPRTLaMSAYADLDTSILDELPP-------GRT 455
Cdd:TIGR01587 125 NSLLIFDEVHFYDEYTLAlilavleVLKDNDV-----PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDlkeerrfENH 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 456 PVNTVLVTDTRRVEVIERVRGACAEGRQAYWVCTLIEESEELtcqaaettYEDLTSALGELKVGLIHGRMKP---AEKAA 532
Cdd:TIGR01587 197 RFILIESDKVGEISSLERLLEFIKKGGSIAIIVNTVDRAQEF--------YQQLKEKAPEEEIILYHSRFTEkdrAKKEA 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 489287962 533 -VMAEFKAGNLQ-LLVATTVIEVGVDVpNASLMIIEnperlgLAQLHQLRGRVGR 585
Cdd:TIGR01587 269 eLLREMKKSNEKfVIVATQVIEASLDI-SADVMITE------LAPIDSLIQRLGR 316
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
299-429 |
8.96e-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: 52.82 E-value: 8.96e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 299 GAGKT---VVAALAALQALEAGYQ--VALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVaalEQIAAGAPM 373
Cdd:cd17927 27 GSGKTfvaVLICEHHLKKFPAGRKgkVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV---EQIVESSDV 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489287962 374 VVGTHALFQD------EVQFKNLALVIIDEQHR------FGVQQRLALRQKGVGGRMNPHQLIMTATP 429
Cdd:cd17927 104 IIVTPQILVNdlksgtIVSLSDFSLLVFDECHNttknhpYNEIMFRYLDQKLGSSGPLPQILGLTASP 171
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
290-428 |
1.22e-07 |
|
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: 51.25 E-value: 1.22e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 290 MLRLIQGDVGAGKT-VVAALAALQALEAGYQVALMAPTEILAEQHFITFKRWLEPlGLEVAWLAGklkgknRVAALEQIA 368
Cdd:cd00046 2 ENVLITAPTGSGKTlAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVG------GSSAEEREK 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489287962 369 AG---APMVVGTHALFQDEVQ------FKNLALVIIDEQHRFGVQQRLALRQKGVGGRMNPH--QLI-MTAT 428
Cdd:cd00046 75 NKlgdADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALILDLAVRKAGLKnaQVIlLSAT 146
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
299-585 |
1.61e-06 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 51.05 E-value: 1.61e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 299 GAGKTVVAALAALQALEAGYQVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAG------KLKGKNRVaaleqiaagap 372
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGdydsddEWLGRYDI----------- 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 373 mVVGT----HALFQDEVQF-KNLALVIIDEQHRFGVQQR-------LA-LRQKGVGGRM--------NPHQL--IMTATP 429
Cdd:COG1204 117 -LVATpeklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevlLArLRRLNPEAQIvalsatigNAEEIaeWLDAEL 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 430 I---------------PRTLAM------SAYADLDTsILDELPPGRTpvNTVLVTDTRRVEVI-ERVRGACAEGRQAYWV 487
Cdd:COG1204 196 VksdwrpvplnegvlyDGVLRFddgsrrSKDPTLAL-ALDLLEEGGQ--VLVFVSSRRDAESLaKKLADELKRRLTPEER 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 488 CTLIEESEEL-TCQAAETTYEDLTSALgELKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPnASLMIIE 566
Cdd:COG1204 273 EELEELAEELlEVSEETHTNEKLADCL-EKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIIR 350
|
330 340
....*....|....*....|....
gi 489287962 567 NPERLGLAQL-----HQLRGRVGR 585
Cdd:COG1204 351 DTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
518-585 |
6.16e-06 |
|
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: 46.78 E-value: 6.16e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489287962 518 VGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPnASLMIIENPER--------LGLAQLHQLRGRVGR 585
Cdd:cd18795 66 IAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVIIKGTQRydgkgyreLSPLEYLQMIGRAGR 140
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
293-429 |
8.58e-06 |
|
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: 46.74 E-value: 8.58e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 293 LIQGDVGAGKTVVAAL-AALQALEAGYQVALMAPTEILAEQHFITFKRWLEpLGLEVAWLAGKLKGKNRVAALE--QIAA 369
Cdd:cd18035 20 LIVLPTGLGKTIIAILvAADRLTKKGGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEERAERWDasKIIV 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489287962 370 GAPMVVgTHALFQDEVQFKNLALVIIDEQHR-FGVQQRLALRQKGVGGRMNPHQLIMTATP 429
Cdd:cd18035 99 ATPQVI-ENDLLAGRITLDDVSLLIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
299-429 |
4.85e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 46.65 E-value: 4.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 299 GAGKTVVAALAALQA-LEAGYQVALMAPTEILAEQHFITFKRWLEPLGLEVAWLAGKLKGKNRVAALEQiaagAPMVVGT 377
Cdd:COG1111 27 GLGKTAVALLVIAERlHKKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWEK----ARIIVAT 102
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 489287962 378 -HALFQD----EVQFKNLALVIIDEQHR-FGVQQRLALRQKGVGGRMNPHQLIMTATP 429
Cdd:COG1111 103 pQVIENDliagRIDLDDVSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
65-132 |
5.55e-05 |
|
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: 41.84 E-value: 5.55e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489287962 65 TVSGadVVMGKRRS----LVVRLQDGTGGLSLRFYH-FSNAQKEGLKRGTRVRCYGEARP-GASGLEIYHPEYR 132
Cdd:pfam01336 2 TVAG--RVTSIRRSggklLFLTLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKrKGGELELVVEEIE 73
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
537-595 |
1.03e-04 |
|
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: 42.96 E-value: 1.03e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 489287962 537 FKAGNLQLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRvGRgSAASHCVLL 595
Cdd:cd18802 86 FRDGELNLLIATSVLEEGIDVPACNLVIRFDLPK-TLRSYIQSRGR-AR-APNSKYILM 141
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
507-598 |
2.10e-04 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 44.37 E-value: 2.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 507 EDLTSALGE--LKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLmII-----ENPErlglAQLHql 579
Cdd:COG0513 255 DRLAEKLQKrgISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSH-VInydlpEDPE----DYVH-- 327
|
90 100
....*....|....*....|
gi 489287962 580 R-GRVGRGSAASHCVLLYHP 598
Cdd:COG0513 328 RiGRTGRAGAEGTAISLVTP 347
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
293-430 |
2.70e-04 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 41.89 E-value: 2.70e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 293 LIQGDVGAGKTVVAALAALQALEAGYQ--VALMAPTEILAEQHFITFKRWLEplglEVAWLAGKLKGKNRVAALEQIaag 370
Cdd:pfam04851 27 LIVMATGSGKTLTAAKLIARLFKKGPIkkVLFLVPRKDLLEQALEEFKKFLP----NYVEIGEIISGDKKDESVDDN--- 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489287962 371 aPMVVGT-HALFQDEVQFKNLA------LVIIDEQHRFG--VQQRLALRQKgvggrmNPHQLIMTATPI 430
Cdd:pfam04851 100 -KIVVTTiQSLYKALELASLELlpdffdVIIIDEAHRSGasSYRNILEYFK------PAFLLGLTATPE 161
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
317-585 |
3.11e-04 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 44.04 E-value: 3.11e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 317 GYQVALMAPTEILAEQHFITFKRWlEPLGLEVAWLAGKLKGKnrvaalEQIAAGAPMVVGTHALFQDEVQ-----FKNLA 391
Cdd:PRK00254 68 GGKAVYLVPLKALAEEKYREFKDW-EKLGLRVAMTTGDYDST------DEWLGKYDIIIATAEKFDSLLRhgsswIKDVK 140
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 392 LVIIDEQHRFGVQQRLALRQKGVGGRMNPHQLIMTATPI--PRTLAMSAYADL--------------------------- 442
Cdd:PRK00254 141 LVVADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVgnAEELAEWLNAELvvsdwrpvklrkgvfyqgflfwedgki 220
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 443 -------DTSILDELPPGRtpvNTVLVTDTRRVEviERVRGACAEGRQAYWVCTLIEESEELTCQAAET-TYEDLTSALG 514
Cdd:PRK00254 221 erfpnswESLVYDAVKKGK---GALVFVNTRRSA--EKEALELAKKIKRFLTKPELRALKELADSLEENpTNEKLKKALR 295
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489287962 515 ElKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPnASLMIIENP--------ERLGLAQLHQLRGRVGR 585
Cdd:PRK00254 296 G-GVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLP-AFRVIIRDTkrysnfgwEDIPVLEIQQMMGRAGR 372
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
525-595 |
5.39e-04 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 40.80 E-value: 5.39e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489287962 525 MKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERLGLAQLhQLRGRVGRGSAASHCVLL 595
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRKRQGRVVVLL 143
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
507-596 |
5.92e-04 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 43.35 E-value: 5.92e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 507 EDLTSALGEL--KVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVG 584
Cdd:PLN03137 694 EKVAERLQEFghKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPK-SIEGYHQECGRAG 772
|
90
....*....|..
gi 489287962 585 RGSAASHCVLLY 596
Cdd:PLN03137 773 RDGQRSSCVLYY 784
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
299-438 |
6.50e-04 |
|
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: 41.09 E-value: 6.50e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 299 GAGKTVVAALAALQALEAGYQVAL-MAPTEILAEQHFITFKRWLEPLGLEVAWLAGklkgkNRVAALEQIaAGAPMVVGT 377
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTG-----DPSVNKLLL-AEADILVAT 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489287962 378 HALFQ------DEVQFKNLALVIIDEQHRFGVQQRLALRQKGVggrmnphQLIMTATPIPRTLAMSA 438
Cdd:cd17921 101 PEKLDlllrngGERLIQDVRLVVVDEAHLIGDGERGVVLELLL-------SRLLRINKNARFVGLSA 160
|
|
| PTZ00110 |
PTZ00110 |
helicase; Provisional |
521-615 |
7.28e-04 |
|
helicase; Provisional
Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 42.84 E-value: 7.28e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 521 IHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMI-------IENperlglaQLHQLrGRVGRGSAASHCV 593
Cdd:PTZ00110 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVInfdfpnqIED-------YVHRI-GRTGRAGAKGASY 478
|
90 100
....*....|....*....|..
gi 489287962 594 LLYHPPLSQIGRQRLGIMRETN 615
Cdd:PTZ00110 479 TFLTPDKYRLARDLVKVLREAK 500
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
293-399 |
1.00e-03 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 42.45 E-value: 1.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 293 LIQGDVGAGKTVVAALAALQALEAGYQVALMAPtEI-LAEQhfiTFKRWLEPLGLEVAWLAGKLKGKNRVAALEQIAAG- 370
Cdd:PRK05580 166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQ---MLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGe 241
|
90 100 110
....*....|....*....|....*....|
gi 489287962 371 APMVVGTH-ALFqdeVQFKNLALVIIDEQH 399
Cdd:PRK05580 242 AKVVIGARsALF---LPFKNLGLIIVDEEH 268
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
507-611 |
1.91e-03 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 41.24 E-value: 1.91e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 507 EDLTSALGE--LKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMIIENPERlGLAQLHQLRGRVG 584
Cdd:PRK11057 250 EDTAARLQSrgISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR-NIESYYQETGRAG 328
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 489287962 585 RGSAASHCVLLYHP----------------PLSQIGRQRLGIM 611
Cdd:PRK11057 329 RDGLPAEAMLFYDPadmawlrrcleekpagQQQDIERHKLNAM 371
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
295-564 |
2.60e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 40.58 E-value: 2.60e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 295 QGDVGAGKT---VVAALAALQALEAGYQVALMAPTEILAEQhfitFKRWLEPLG--LEVAWLAGkLKGKNRVAALEQIAA 369
Cdd:PTZ00424 71 QAQSGTGKTatfVIAALQLIDYDLNACQALILAPTRELAQQ----IQKVVLALGdyLKVRCHAC-VGGTVVRDDINKLKA 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 370 GAPMVVGTHALFQDEVQFK-----NLALVIIDEQHRFgVQQRLALRQKGVGGRMNPH-QLIMTATPIPRTLAmsayaDLD 443
Cdd:PTZ00424 146 GVHMVVGTPGRVYDMIDKRhlrvdDLKLFILDEADEM-LSRGFKGQIYDVFKKLPPDvQVALFSATMPNEIL-----ELT 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 444 TSILdelppgRTPVNTVLVTDTRRVEVIERVRgaCAEGRQAYWVCTLIEESEELTCQAA------ETTYEDLTSALGE-- 515
Cdd:PTZ00424 220 TKFM------RDPKRILVKKDELTLEGIRQFY--VAVEKEEWKFDTLCDLYETLTITQAiiycntRRKVDYLTKKMHErd 291
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 489287962 516 LKVGLIHGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMI 564
Cdd:PTZ00424 292 FTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
527-595 |
5.93e-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: 37.62 E-value: 5.93e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489287962 527 PAEKAAVMAEFKAGNLQLLVATTVIEVGVDVpnASL---MIIENPErlGLAQLHQLRGRVGRGSAASHCVLL 595
Cdd:cd18797 78 AEDRREIEAELFNGELLGVVATNALELGIDI--GGLdavVLAGYPG--SLASLWQQAGRAGRRGKDSLVILV 145
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
500-595 |
6.68e-03 |
|
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: 37.63 E-value: 6.68e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489287962 500 QAAETTYEDLTSALGELKVGLI----HGRMKPAEKAAVMAEFKAGNLQLLVATTVIEVGVDVPNASLMI-IENPerLGLA 574
Cdd:cd18796 49 SQAERLAQRLRELCPDRVPPDFialhHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVA 126
|
90 100
....*....|....*....|..
gi 489287962 575 QLHQLRGRVG-RGSAASHCVLL 595
Cdd:cd18796 127 RLLQRLGRSGhRPGAASKGRLV 148
|
|
| |
