|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
2-674 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 1039.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 2 TSVQQLQGVGAAAATLLEKLHIFSTDDLLFHLPRDYEDRSTIIPMNQLMVGRSYLLEGEVRSIDFPP--GKKKSLAALLQ 79
Cdd:COG1200 6 TPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 80 DDFGKVTLRFYHiYKGLTDRIQVGNRLRIFGEVRVGARGLELYHPEIQVILQHTPLPKTQLTAIYPSTEGLTQPKLREYV 159
Cdd:COG1200 86 DGTGSLTLVFFN-QPYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDEEEAELAGRLTPVYPLTEGLSQKTLRKLI 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 160 RQALAHHSDDLAELLPSKYSNGY---ELKQALHYIHEPPIDANmlqlnqgSHPAQQRLIFEELVAHQISLLTRRAYIRQI 236
Cdd:COG1200 165 RQALDLLAPDLPEPLPEELRARYglpSLAEALRNIHFPPSDED-------LHPARRRLAFEELLALQLALLLRRARRRKR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 237 AAPQFTSSKVLAKQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPT 316
Cdd:COG1200 238 KGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPT 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 317 EILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQ 396
Cdd:COG1200 318 EILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVEQ 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 397 RLALRNKGAdqfTPHQLVMTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTVTIPLDRREEVLQRIAQNCREGKQAYW 476
Cdd:COG1200 398 RLALREKGE---APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIAKGRQAYV 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 477 VCTLVEQSETLDAQAAEATYQEIKERFPDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIE 556
Cdd:COG1200 475 VCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 557 NAERLGLSQLHQLRGRVGRGATASFCALLYKTPLSQNGQERLSILRESNDGFVIAEKDLEIRGPGELLGTKQTGDMGFRV 636
Cdd:COG1200 555 NAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPDLRI 634
|
650 660 670
....*....|....*....|....*....|....*....
gi 491228584 637 ARLERDDHLLTQAHYVAEQILKDYPQHAEG-LLKRWLPE 674
Cdd:COG1200 635 ADLVRDADLLEAAREDAEELLEEDPELASHpALRRWLGL 673
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
2-678 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 1027.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 2 TSVQQLQGVGAAAATLLEKLHIFSTDDLLFHLPRDYEDRSTIIPMNQLMVGRSYLLEGEVRSIDFPPGKKKSLAALLQDD 81
Cdd:PRK10917 9 APLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRRLTVTVSDG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 82 FGKVTLRFYHIYKG-LTDRIQVGNRLRIFGEVRVGARGLELYHPEIQVILQHTPLPKTQLTAIYPSTEGLTQPKLREYVR 160
Cdd:PRK10917 89 TGNLTLRFFNFNQPyLKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGRLTPVYPLTEGLKQKTLRKLIK 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 161 QALAHHsDDLAELLPSKYSNGY---ELKQALHYIHEPPIDANmlqlnqgSHPAQQRLIFEELVAHQISLLTRRAYIRQIA 237
Cdd:PRK10917 169 QALELL-DALPELLPEELLEKYgllSLAEALRAIHFPPSDED-------LHPARRRLKFEELFALQLSLLLLRAGRRSKK 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 238 APQFTSSKVLAKQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPTE 317
Cdd:PRK10917 241 AGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 318 ILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQR 397
Cdd:PRK10917 321 ILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQR 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 398 LALRNKGADqftPHQLVMTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTVTIPLDRREEVLQRIAQNCREGKQAYWV 477
Cdd:PRK10917 401 LALREKGEN---PHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVV 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 478 CTLVEQSETLDAQAAEATYQEIKERFPDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIEN 557
Cdd:PRK10917 478 CPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIEN 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 558 AERLGLSQLHQLRGRVGRGATASFCALLYKTPLSQNGQERLSILRESNDGFVIAEKDLEIRGPGELLGTKQTGDMGFRVA 637
Cdd:PRK10917 558 AERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVA 637
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 491228584 638 RLERDDHLLTQAHYVAEQILKDYPQHAEGLLKRWLPEAPRY 678
Cdd:PRK10917 638 DLVRDEELLEEARKDARELLERDPELAEALLERWLGERERY 678
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
21-653 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 770.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 21 LHIFSTDDLLFHLPRDYEDRSTIIPMNQLMVGRSYLLEGEVRSIDFPP-GKKKSLAALLQDDFGKV-TLRFYHiYKGLTD 98
Cdd:TIGR00643 1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGfKRRKVLKLRLKDGGYKKlELRFFN-RAFLKK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 99 RIQVGNRLRIFGEVRVGARGLELYHPEIQvILQHTPLPKTQLTAIYPSTEGLTQPKLREYVRQALAHHSDDLAELLPSKY 178
Cdd:TIGR00643 80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFI-SEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDQLDKSLEDPLPEEL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 179 SNGYEL---KQALHYIHEPPIDANMlqlnqgsHPAQQRLIFEELVAHQISLLTRRAYIR-QIAAPQFTSSKVLAKQLLES 254
Cdd:TIGR00643 159 REKYGLlslEDALRAIHFPKTLSLL-------ELARRRLIFDEFFYLQLAMLARRLGEKqQFSAPPANPSEELLTKFLAS 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 255 LPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWFEPL 334
Cdd:TIGR00643 232 LPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPL 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 335 GIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQRLALRNKGADQFTPHQLV 414
Cdd:TIGR00643 312 GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGFTPHVLV 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 415 MTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTVTIPLDRREEVLQRIAQNCREGKQAYWVCTLVEQSETLDAQAAEA 494
Cdd:TIGR00643 392 MSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEA 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 495 TYQEIKERFPDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVG 574
Cdd:TIGR00643 472 LYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVG 551
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491228584 575 RGATASFCALLYKTPLSQNGQERLSILRESNDGFVIAEKDLEIRGPGELLGTKQTGDMGFRVARLERDDHLLTQAHYVA 653
Cdd:TIGR00643 552 RGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAREDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
214-441 |
4.99e-123 |
|
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: 364.93 E-value: 4.99e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 214 LIFEELVAHQISLLTRRAYIRQIAAPQFTSSKVLAKQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKT 293
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 294 LVAAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQ 373
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491228584 374 DNVAFSKLGLVIIDEQHRFGVDQRLALRNKGAdqfTPHQLVMTATPIPRTLAMSAYGDLDTSVIDELP 441
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE---TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
217-632 |
1.14e-104 |
|
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: 339.72 E-value: 1.14e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 217 EELVAHQISLLTRRAYIRQIAAPQFTSskvlAKQLLES-LPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLV 295
Cdd:TIGR00580 413 REIAAKLIELYAKRKAIKGHAFPPDLE----WQQEFEDsFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEV 488
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 296 AAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDN 375
Cdd:TIGR00580 489 AMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKD 568
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 376 VAFSKLGLVIIDEQHRFGVDQRLALRNKGAdqfTPHQLVMTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTVTIPLD 455
Cdd:TIGR00580 569 VKFKDLGLLIIDEEQRFGVKQKEKLKELRT---SVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYD 645
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 456 rrEEVLQR-IAQNCREGKQAYWVCTLVEQSETLDAQaaeatyqeIKERFPDLNVGLVHGKMKADEKQAVMQAFKDNQSQL 534
Cdd:TIGR00580 646 --PELVREaIRRELLRGGQVFYVHNRIESIEKLATQ--------LRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQV 715
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 535 LIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVGRGATASFCALLY--KTPLSQNGQERLSILRESND---GFV 609
Cdd:TIGR00580 716 LVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEAIQEFSElgaGFK 795
|
410 420
....*....|....*....|...
gi 491228584 610 IAEKDLEIRGPGELLGTKQTGDM 632
Cdd:TIGR00580 796 IALHDLEIRGAGNLLGEEQSGHI 818
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
233-634 |
1.19e-98 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 327.41 E-value: 1.19e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 233 IRQIAA--------------PQFTSSKVLAKQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAI 298
Cdd:COG1197 547 VRDIAAellklyaeraarkgFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALR 626
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 299 AACHALEAEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSgkqkgKARTQAEQH-----IREGHSQLIVGTHALFQ 373
Cdd:COG1197 627 AAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLS-----RFRTAKEQKetlegLADGKVDIVIGTHRLLS 701
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 374 DNVAFSKLGLVIIDEQHRFGVDQ--RL-ALRNkgadqfTPHQLVMTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTV 450
Cdd:COG1197 702 KDVKFKDLGLLIIDEEQRFGVRHkeKLkALRA------NVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTF 775
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 451 TIPLDR---REEVLQRIAqncREGkQAYWVCTLVEqseTLDAQAAEatyqeIKERFPDLNVGLVHGKMKADEKQAVMQAF 527
Cdd:COG1197 776 VGEYDDaliREAILRELL---RGG-QVFYVHNRVE---DIEKVAAR-----LQELVPEARIAVAHGQMSERELERVMLDF 843
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 528 KDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVGRGATASFCALLYK--TPLSQNGQERLSILRESN 605
Cdd:COG1197 844 YEGEFDVLVCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPpdKVLTEDAEKRLEAIQEFT 923
|
410 420 430
....*....|....*....|....*....|....*
gi 491228584 606 D---GFVIAEKDLEIRGPGELLGTKQTGDM---GF 634
Cdd:COG1197 924 ElgaGFKLAMHDLEIRGAGNLLGEEQSGHIaevGF 958
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
446-603 |
9.07e-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: 237.24 E-value: 9.07e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 446 PIQTVTIPLDRREEVLQRIAQNCREGKQAYWVCTLVEQSETLDAQAAEATYQEIKERF-PDLNVGLVHGKMKADEKQAVM 524
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491228584 525 QAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVGRGATASFCALLYKTPLSQNGQERLSILRE 603
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
253-632 |
2.63e-72 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 254.28 E-value: 2.63e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 253 ESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWFE 332
Cdd:PRK10689 595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA 674
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 333 PLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQRLALRNKGADQftpHQ 412
Cdd:PRK10689 675 NWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADV---DI 751
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 413 LVMTATPIPRTLAMSAYGDLDTSVIDELPPGRTPIQTVTIPLDR---REEVLQRIAQncreGKQAYWVCTLVEQSEtlda 489
Cdd:PRK10689 752 LTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSlvvREAILREILR----GGQVYYLYNDVENIQ---- 823
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 490 QAAeatyQEIKERFPDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQL 569
Cdd:PRK10689 824 KAA----ERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQL 899
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491228584 570 RGRVGRGATASFCALLYKTP--LSQNGQERLSILRESND---GFVIAEKDLEIRGPGELLGTKQTGDM 632
Cdd:PRK10689 900 RGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSGQM 967
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
446-603 |
1.14e-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: 213.28 E-value: 1.14e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 446 PIQTVTIPLDRREEVLQRIAQNCREGKQAYWVCTLVEQSETLDAQAAEATYQEIKERFPDLNVGLVHGKMKADEKQAVMQ 525
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 526 AFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVGRGATASFCALLYKTPLSQN--GQERLSILRE 603
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTetAKKRLRAIAE 160
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
249-438 |
6.92e-63 |
|
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: 207.42 E-value: 6.92e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 249 KQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLNFK 328
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 329 RWFEPLGIDVAWLSGKQKGKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQRLALRNKGADQf 408
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKELRPNV- 164
|
170 180 190
....*....|....*....|....*....|
gi 491228584 409 tpHQLVMTATPIPRTLAMSAYGDLDTSVID 438
Cdd:cd17991 165 --DVLTLSATPIPRTLHMALSGIRDLSVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
247-438 |
7.54e-62 |
|
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: 204.19 E-value: 7.54e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 247 LAKQLLESLPFQMTNAQKRVSKEILQDLKQQQPMLRLVQGDVGAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLN 326
Cdd:cd17918 4 LIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 327 FKRWFEPlgIDVAWLSGKQKGKARTQAEqhireghsqLIVGTHALFQDNVAFSKLGLVIIDEQHRFGVDQRLALRNKGAd 406
Cdd:cd17918 84 ARKFLPF--INVELVTGGTKAQILSGIS---------LLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA- 151
|
170 180 190
....*....|....*....|....*....|..
gi 491228584 407 qftPHQLVMTATPIPRTLAMSAYGDLDTSVID 438
Cdd:cd17918 152 ---THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
446-603 |
2.97e-31 |
|
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: 119.37 E-value: 2.97e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 446 PIQTVTIPLDrrEEVLQR-IAQNCREGKQAYWVCTLVEQSETLDAQaaeatyqeIKERFPDLNVGLVHGKMKADEKQAVM 524
Cdd:cd18810 1 PVRTYVMPYD--DELIREaIERELLRGGQVFYVHNRIESIEKLATQ--------LRQLVPEARIAIAHGQMTENELEEVM 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 525 QAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERLGLSQLHQLRGRVGRGATASFCALLYKT--PLSQNGQERLSILR 602
Cdd:cd18810 71 LEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDqkKLTEDALKRLEAIQ 150
|
.
gi 491228584 603 E 603
Cdd:cd18810 151 E 151
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
260-426 |
5.89e-25 |
|
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: 101.55 E-value: 5.89e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 260 TNAQKRVSKEILQ--DLkqqqpmlrLVQGDVGAGKTLVAAIAACHALEAEW---QVALMAPTEILAEQHYLNFKRWFEPL 334
Cdd:pfam00270 1 TPIQAEAIPAILEgrDV--------LVQAPTGSGKTLAFLLPALEALDKLDngpQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 335 GIDVAWLSGkqkGKARTQAEQHIRegHSQLIVGTH----ALFQDNVAFSKLGLVIIDEQHRFGVDQRLALRNKGADQFTP 410
Cdd:pfam00270 73 GLKVASLLG---GDSRKEQLEKLK--GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK 147
|
170
....*....|....*...
gi 491228584 411 HQ--LVMTATPiPRTLAM 426
Cdd:pfam00270 148 KRqiLLLSATL-PRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
251-445 |
3.38e-23 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 97.95 E-value: 3.38e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 251 LLESLPFQMTNAQKRVSKEILQDLKQqqpmlRLVQGDVGAGKTLVAAIAACHAL--EAEWQVALMAPTEILAEQHYLNFK 328
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLRD-----VILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 329 RWFEPLGIDVAwlsGKQKGKARTQAEQHIREGHSQLIVGT-----HALFQDNVAFSKLGLVIIDEQHRFGV-DQRLALRN 402
Cdd:smart00487 76 KLGPSLGLKVV---GLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDgGFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 491228584 403 KGADQFTPHQLV-MTATP---IPRTLAMSAYGDLDTSVIDELPPGRT 445
Cdd:smart00487 153 LLKLLPKNVQLLlLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
8-161 |
1.31e-21 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 92.12 E-value: 1.31e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 8 QGVGAAAATLLEKLHIFSTDDLLFHLPRDYEDRSTIIPMNQLMVGRSYLLEGEVrsIDFPPGKKKSL---AALLQDDFGK 84
Cdd:pfam17191 6 KGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKI--VNFETKKIGSLviiSAVLSDGIGQ 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491228584 85 VTLR-FYHIYkgLTDRIQVGNRLRIFGEVRVGARG-LELYHPEIQVILQHTPLpktQLTAIYPSTEGLTQPKLREYVRQ 161
Cdd:pfam17191 84 VLLKwFNQEY--IKKFLQKGKEVYITGTVKEGPFGpIEMNNPEIEEITGEQER---EILPVYPLTEGISQKNMRKIVKE 157
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
221-679 |
1.17e-19 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 93.17 E-value: 1.17e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 221 AHQISLLTRRAYIRQIAAPQFTSSKVLAKQLLE------SLPFQMTNAQKRVSKEILQDLKQQQPMLrLVQGDVGAGKTL 294
Cdd:COG1061 37 ARRLAIKEGTREDGRRLPEEDTERELAEAEALEagdeasGTSFELRPYQQEALEALLAALERGGGRG-LVVAPTGTGKTV 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 295 VAAIAACHALEAEwQVALMAPTEILAEQHYLNFKRWFeplgiDVAWLSGKQKgkartqaeqhirEGHSQLIVGTHALFQD 374
Cdd:COG1061 116 LALALAAELLRGK-RVLVLVPRRELLEQWAEELRRFL-----GDPLAGGGKK------------DSDAPITVATYQSLAR 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 375 NVAFSKL----GLVIIDEQHRFGVDQRLALRNKGADQFTphqLVMTATPIpRTLAMSAYGDLDTSVIDELPPGR------ 444
Cdd:COG1061 178 RAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYR---LGLTATPF-RSDGREILLFLFDGIVYEYSLKEaiedgy 253
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 445 -TPIQTVTIPLD------------------------RREEVLQRIAQNCREGKQAYWVCTLVEQsetldaqaAEATYQEI 499
Cdd:COG1061 254 lAPPEYYGIRVDltderaeydalserlrealaadaeRKDKILRELLREHPDDRKTLVFCSSVDH--------AEALAELL 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 500 KERfpDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIenaerLG----LSQLHQLRGRVGR 575
Cdd:COG1061 326 NEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL-----LRptgsPREFIQRLGRGLR 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 576 GATASFCALLY-----KTPLSQN--GQERLSILRESNDGFVIAEKDLEIRGPGELLGTKQTGDMGFRVARLERDDHLLTQ 648
Cdd:COG1061 399 PAPGKEDALVYdfvgnDVPVLEElaKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLL 478
|
490 500 510
....*....|....*....|....*....|.
gi 491228584 649 AHYVAEQILKDYPQHAEGLLKRWLPEAPRYA 679
Cdd:COG1061 479 VLAELLLLELLALALELLELAKAEGKAEEEE 509
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
280-418 |
1.08e-17 |
|
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: 80.14 E-value: 1.08e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 280 MLRLVQGDVGAGKTLVAAIAA-CHALEAEWQVALMAPTEILAEQHYLNFKRWFEPlGIDVAWLSGkqkgkARTQAEQH-I 357
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAAlLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVG-----GSSAEEREkN 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491228584 358 REGHSQLIVGTHALFQDNVA------FSKLGLVIIDEQHRFGVDQRLALRNKGADQF----TPHQLVMTAT 418
Cdd:cd00046 76 KLGDADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALILDLAVRKaglkNAQVILLSAT 146
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
57-129 |
3.02e-17 |
|
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: 76.46 E-value: 3.02e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491228584 57 LEGEVRSIDFPPGKKKS-LAALLQDDFGKVTLRFYHIYKGLTDRIQVGNRLRIFGEVRVGARGLELYHPEIQVI 129
Cdd:cd04488 2 VEGTVVSVEVVPRRGRRrLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYELL 75
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
505-575 |
3.17e-17 |
|
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: 77.64 E-value: 3.17e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491228584 505 DLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAERlGLSQLHQLRGRVGR 575
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
493-575 |
7.71e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 72.63 E-value: 7.71e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 493 EATYQEIKERfpDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVIENAeRLGLSQLHQLRGR 572
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGR 77
|
...
gi 491228584 573 VGR 575
Cdd:smart00490 78 AGR 80
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
283-575 |
3.80e-14 |
|
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: 74.39 E-value: 3.80e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 283 LVQGDVGAGKTLVAAIAACHALEA--EWQVALMAPTEILAEQHYLNFKRWF--EPLGIDVAWLSG-KQKGKARTQAEQHI 357
Cdd:cd09639 3 VIEAPTGYGKTEAALLWALHSLKSqkADRVIIALPTRATINAMYRRAKEAFgeTGLYHSSILSSRiKEMGDSEEFEHLFP 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 358 REGHSQLIV---------------------GTHALFQDNVAFSklgLVIIDEQHRFGVDQR---LALRNKGADQFTPHqL 413
Cdd:cd09639 83 LYIHSNDTLfldpitvctidqvlksvfgefGHYEFTLASIANS---LLIFDEVHFYDEYTLaliLAVLEVLKDNDVPI-L 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 414 VMTATpIPRTLaMSAYGDLDTsVIDELPPGRTPIQTVTIPL-----DRREEVLQRIAQNCREGKQAYWVCTLVEQsetld 488
Cdd:cd09639 159 LMSAT-LPKFL-KEYAEKIGY-VEENEPLDLKPNERAPFIKiesdkVGEISSLERLLEFIKKGGSVAIIVNTVDR----- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 489 aqaAEATYQEIKERFPDLNVGLVHGKM----KADEKQAVMQAFKDNQSQLLIATTVIEVGVDVpNASIMVIENAErlgLS 564
Cdd:cd09639 231 ---AQEFYQQLKEKGPEEEIMLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---ID 303
|
330
....*....|.
gi 491228584 565 QLHQLRGRVGR 575
Cdd:cd09639 304 SLIQRLGRLHR 314
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
263-575 |
6.85e-14 |
|
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: 74.73 E-value: 6.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 263 QKRVSKEILQDLKQQQPMLRLVqgdV--GAGKTLVAAIAAcHALEAEWQ-----VALmaPTEILAEQHYLNFKRWFEP-L 334
Cdd:COG1203 132 QNEALELALEAAEEEPGLFILT---AptGGGKTEAALLFA-LRLAAKHGgrriiYAL--PFTSIINQTYDRLRDLFGEdV 205
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 335 GI-----DVAWLSGKQKGKARTQAEQHIREG-HSQLIVGT-----HALF----QDNVAFSKLG--LVIIDEQHRFGVDQR 397
Cdd:COG1203 206 LLhhslaDLDLLEEEEEYESEARWLKLLKELwDAPVVVTTidqlfESLFsnrkGQERRLHNLAnsVIILDEVQAYPPYML 285
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 398 LALRN--KGADQFTPHQLVMTAT--PIPRTLAMSAYGDLDTSVIDEL----PPGRTPIQTVTIPLDRrEEVLQRIAQNCR 469
Cdd:COG1203 286 ALLLRllEWLKNLGGSVILMTATlpPLLREELLEAYELIPDEPEELPeyfrAFVRKRVELKEGPLSD-EELAELILEALH 364
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 470 EGKQAYWVCTLVEqsetlDAQAAeatYQEIKERFPDLNVGLVHGKMKADEKQA----VMQAFKDNQSQLLIATTVIEVGV 545
Cdd:COG1203 365 KGKSVLVIVNTVK-----DAQEL---YEALKEKLPDEEVYLLHSRFCPADRSEiekeIKERLERGKPCILVSTQVVEAGV 436
|
330 340 350
....*....|....*....|....*....|
gi 491228584 546 DVpNASIMVIENAerlGLSQLHQLRGRVGR 575
Cdd:COG1203 437 DI-DFDVVIRDLA---PLDSLIQRAGRCNR 462
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
604-662 |
1.46e-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: 60.95 E-value: 1.46e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491228584 604 SNDGFVIAEKDLEIRGPGELLGTKQTGdMGF--RVARLERDDHLLTQAHYVAEQILKDYPQ 662
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSG-IAFdlKIADIARDGQLLQLARTEAEEIIDNDPE 60
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
289-575 |
2.45e-11 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 66.46 E-value: 2.45e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGkqkgkARTQAEQHIREghSQLIVGT 368
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTG-----DYDSDDEWLGR--YDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 369 ----HALFQDNVAF-SKLGLVIIDEQHRFGVDQR----------LALRNKGAdqftphQLV-MTAT-------------- 418
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevllarLRRLNPEA------QIVaLSATignaeeiaewldae 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 419 -------PIPRTLAMSAYGDLDTSviDELPPGRTPIQTVTIPL------------DRR--EEVLQRIAQNCREGKQAywv 477
Cdd:COG1204 195 lvksdwrPVPLNEGVLYDGVLRFD--DGSRRSKDPTLALALDLleeggqvlvfvsSRRdaESLAKKLADELKRRLTP--- 269
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 478 ctlvEQSETLDAQAAEAtyQEIKERFP---DLN------VGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVP 548
Cdd:COG1204 270 ----EEREELEELAEEL--LEVSEETHtneKLAdclekgVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP 343
|
330 340 350
....*....|....*....|....*....|..
gi 491228584 549 nASIMVIENAERLGLSQL-----HQLRGRVGR 575
Cdd:COG1204 344 -ARRVIIRDTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
257-420 |
7.08e-10 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 58.07 E-value: 7.08e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 257 FQMTNAQKRVSKEILQDLKQQQPMLrLVQGDVGAGKTLVAA--IAACHALEAEWQVALMAPTEILAEQHYLNFKRWFEpl 334
Cdd:pfam04851 2 LELRPYQIEAIENLLESIKNGQKRG-LIVMATGSGKTLTAAklIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLP-- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 335 giDVAWLSGKQKGKartqaEQHIREGHSQLIVGT-HALFQDNVAFSKL------GLVIIDEQHRFGVD--QRLALRNKga 405
Cdd:pfam04851 79 --NYVEIGEIISGD-----KKDESVDDNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGASsyRNILEYFK-- 149
|
170
....*....|....*
gi 491228584 406 dqfTPHQLVMTATPI 420
Cdd:pfam04851 150 ---PAFLLGLTATPE 161
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
289-397 |
1.03e-09 |
|
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: 58.04 E-value: 1.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAEWQVAL-MAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKgkartqaEQHIREGHSQLIVG 367
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPS-------VNKLLLAEADILVA 99
|
90 100 110
....*....|....*....|....*....|....*.
gi 491228584 368 THALFQ------DNVAFSKLGLVIIDEQHRFGVDQR 397
Cdd:cd17921 100 TPEKLDlllrngGERLIQDVRLVVVDEAHLIGDGER 135
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
263-390 |
2.58e-09 |
|
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: 56.83 E-value: 2.58e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 263 QKRVSKEILQDLKQQQPMLrlVQGDVGAGKTLVAAIAACHALEAEWQVALMAPtEI-LAEQHYLNFKRWFeplGIDVAWL 341
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFL--LHGVTGSGKTEVYIELIEKVLAKGKQVLVLVP-EIsLTPQLIKRFKKRF---GDKVAVL 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 491228584 342 SGKQKGKARTQAEQHIREGHSQLIVGTH-ALFqdnVAFSKLGLVIIDEQH 390
Cdd:cd17929 75 HSKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
289-391 |
4.65e-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: 53.98 E-value: 4.65e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAEWQ-----VALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTqaeQHIREGHSQ 363
Cdd:cd17927 27 GSGKTFVAVLICEHHLKKFPAgrkgkVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV---EQIVESSDV 103
|
90 100 110
....*....|....*....|....*....|...
gi 491228584 364 LIVGTHALFQD-----NVAFSKLGLVIIDEQHR 391
Cdd:cd17927 104 IIVTPQILVNDlksgtIVSLSDFSLLVFDECHN 136
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
533-586 |
3.33e-07 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 48.08 E-value: 3.33e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 491228584 533 QLLIATTVIEVGVDVPNASIMVIENAERlGLSQLHQLRGRVGRGATASFCALLY 586
Cdd:cd18785 24 EILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGKDEGEVILF 76
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
280-425 |
3.53e-07 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 52.30 E-value: 3.53e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 280 MLRLVQG---------DVGAGKTL--VAAIAACHALEAEWQVA--LMAPTEILaEQHYLNFKRWFEPLGIDVAWLSGKQK 346
Cdd:pfam00176 9 MLSLENNlgrggiladEMGLGKTLqtISLLLYLKHVDKNWGGPtlIVVPLSLL-HNWMNEFERWVSPPALRVVVLHGNKR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 347 GKARTQAEQHIREGHSQLIVGTHALFQDNVAFSKLG--LVIIDEQHRFGVDQrlALRNKGADQF-TPHQLVMTATPIPRT 423
Cdd:pfam00176 88 PQERWKNDPNFLADFDVVITTYETLRKHKELLKKVHwhRIVLDEGHRLKNSK--SKLSKALKSLkTRNRWILTGTPLQNN 165
|
..
gi 491228584 424 LA 425
Cdd:pfam00176 166 LE 167
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
209-390 |
4.50e-07 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 53.20 E-value: 4.50e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 209 PAQQRLIfeELVAHQISLLTRRayirQIAAPQFTSSKVL----AKQLLESL-----------------PFQMTNAQKRVS 267
Cdd:COG1198 131 PKQRRVL--EALREHGGPLTLS----ELAKEAGVSRSVLkalvKKGLLEIEerevdrdpfapdvpaepPPTLNEEQQAAV 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 268 KEILQDLKQQQPMLrlVQGDVGAGKTLV--AAIAacHALEAEWQVALMAPtEI-LAEQHYLNFKRWFeplGIDVAWLSGK 344
Cdd:COG1198 205 EAIRAAAGGFSVFL--LHGVTGSGKTEVylQAIA--EVLAQGKQALVLVP-EIaLTPQTVERFRARF---GARVAVLHSG 276
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 491228584 345 QKGKARTQAEQHIREGHSQLIVGTH-ALFqdnVAFSKLGLVIIDEQH 390
Cdd:COG1198 277 LSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
256-390 |
2.00e-06 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 50.93 E-value: 2.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 256 PFQMTNAQKRVSKEILQDLKQQQPMLrlvQGDVGAGKTLV--AAIAAChaLEAEWQVALMAPtEI-LAEQHYLNFKRWFe 332
Cdd:PRK05580 142 PPTLNPEQAAAVEAIRAAAGFSPFLL---DGVTGSGKTEVylQAIAEV--LAQGKQALVLVP-EIaLTPQMLARFRARF- 214
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 333 plGIDVA-WLSGKQKGKaRTQAEQHIREGHSQLIVGTH-ALFqdnVAFSKLGLVIIDEQH 390
Cdd:PRK05580 215 --GAPVAvLHSGLSDGE-RLDEWRKAKRGEAKVVIGARsALF---LPFKNLGLIIVDEEH 268
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
55-129 |
3.72e-06 |
|
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: 44.92 E-value: 3.72e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 491228584 55 YLLEGEVRSIDFPPGKKKSLaaLLQDDFGKVTLRFYH-IYKGLTDRIQVGNRLRIFGEVRV-GARGLELYHPEIQVI 129
Cdd:pfam01336 1 VTVAGRVTSIRRSGGKLLFL--TLRDGTGSIQVVVFKeEAEKLAKKLKEGDVVRVTGKVKKrKGGELELVVEEIELL 75
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
289-397 |
5.58e-06 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type 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: 350786 [Multi-domain] Cd Length: 177 Bit Score: 47.33 E-value: 5.58e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAEWQVALMAPTEILAEQHYLNFKRWfEPLGIDVAWLSGKQKGKARTQAEQHIreghsqlIVGT 368
Cdd:cd18028 27 ASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKL-EEIGLKVGISTGDYDEDDEWLGDYDI-------IVAT 98
|
90 100 110
....*....|....*....|....*....|....
gi 491228584 369 HALFQDNVAFSK-----LGLVIIDEQHRFGVDQR 397
Cdd:cd18028 99 YEKFDSLLRHSPswlrdVGVVVVDEIHLISDEER 132
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
289-391 |
8.00e-06 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 49.34 E-value: 8.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAE-WQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKGKARTQAeqhirEGHSQLIVG 367
Cdd:COG1111 27 GLGKTAVALLVIAERLHKKgGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKEL-----WEKARIIVA 101
|
90 100
....*....|....*....|....*....
gi 491228584 368 T-HALFQDNVA----FSKLGLVIIDEQHR 391
Cdd:COG1111 102 TpQVIENDLIAgridLDDVSLLIFDEAHR 130
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
287-421 |
1.95e-05 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins 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: 350677 [Multi-domain] Cd Length: 182 Bit Score: 45.63 E-value: 1.95e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 287 DVGAGKTLVAaIAACHALEAE----WQVALMAPTEILaeQHYLN-FKRWFEPLgiDVAWLSGKQKgkARTQAEQHIREGH 361
Cdd:cd17919 27 EMGLGKTLQA-IAFLAYLLKEgkerGPVLVVCPLSVL--ENWEReFEKWTPDL--RVVVYHGSQR--ERAQIRAKEKLDK 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 362 SQLIVGTHALFQDNVAFSKL---GLVIIDEQHRfgvdqrlaLRNKGADQF-------TPHQLVMTATPIP 421
Cdd:cd17919 100 FDVVLTTYETLRRDKASLRKfrwDLVVVDEAHR--------LKNPKSQLSkalkalrAKRRLLLTGTPLQ 161
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
490-575 |
2.06e-05 |
|
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: 44.42 E-value: 2.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 490 QAAEATYQEIKERfpDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASiMVI-----ENAErlglS 564
Cdd:cd18787 38 KRVDRLAELLEEL--GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVD-HVInydlpRDAE----D 110
|
90
....*....|..
gi 491228584 565 QLHqlR-GRVGR 575
Cdd:cd18787 111 YVH--RiGRTGR 120
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
289-419 |
2.16e-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: 45.58 E-value: 2.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAE-WQVALMAPTEILAEQHYLNFKRWFEpLGIDVAWLSGKQKGKARTQAEQhiregHSQLIVG 367
Cdd:cd18035 26 GLGKTIIAILVAADRLTKKgGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEERAERWD-----ASKIIVA 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 368 T-----HALFQDNVAFSKLGLVIIDEQHRFGVDQR---LALRNKGADQfTPHQLVMTATP 419
Cdd:cd18035 100 TpqvieNDLLAGRITLDDVSLLIFDEAHHAVGNYAyvyIAHRYKREAN-NPLILGLTASP 158
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
287-420 |
5.62e-05 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 44.59 E-value: 5.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 287 DVGAGKTLVAAIAAC-HALEAEW-QVALMAPTeILAEQ--HYLNFKRWFEPLGIDvaWLSGKQKGKARTQAEQHiregHS 362
Cdd:cd18011 25 EVGLGKTIEAGLIIKeLLLRGDAkRVLILCPA-SLVEQwqDELQDKFGLPFLILD--RETAAQLRRLIGNPFEE----FP 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491228584 363 QLIVGTHALFQDN-----VAFSKLGLVIIDEQHRFGVD------QRLALRNKGADQfTPHQLVMTATPI 420
Cdd:cd18011 98 IVIVSLDLLKRSEerrglLLSEEWDLVVVDEAHKLRNSgggketKRYKLGRLLAKR-ARHVLLLTATPH 165
|
|
| DEXHc_ASCC3_1 |
cd18020 |
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
283-390 |
1.60e-04 |
|
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350778 [Multi-domain] Cd Length: 199 Bit Score: 43.19 E-value: 1.60e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 283 LVQGDVGAGKTLVAAIAACHALEA-----------EWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGK-QKGKAR 350
Cdd:cd18020 21 LICAPTGAGKTNIAMLTILHEIRQhvnqggvikkdDFKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDmQLTKKE 100
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 491228584 351 TQAEQHIREGHSQLIVGTHALFQDNVAFSKLGLVIIDEQH 390
Cdd:cd18020 101 IAETQIIVTTPEKWDVVTRKSSGDVALSQLVRLLIIDEVH 140
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
505-581 |
2.66e-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: 41.85 E-value: 2.66e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 505 DLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMVI---------ENAERLGlsqlHQLRGRVGR 575
Cdd:cd18789 68 RLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQisghggsrrQEAQRLG----RILRPKKGG 143
|
....*.
gi 491228584 576 GATASF 581
Cdd:cd18789 144 GKNAFF 149
|
|
| DEXHc_ERCC6 |
cd18000 |
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ... |
287-424 |
3.30e-04 |
|
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 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: 350758 [Multi-domain] Cd Length: 193 Bit Score: 42.31 E-value: 3.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 287 DVGAGKTL--VAAIAACHALEAEWQVALM-APTEILAeqHYLN-FKRWFEPLGIDVAWLSG-----KQKGKARTQAEQHI 357
Cdd:cd18000 27 EMGLGKTIqiIAFLAALHHSKLGLGPSLIvCPATVLK--QWVKeFHRWWPPFRVVVLHSSGsgtgsEEKLGSIERKSQLI 104
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491228584 358 RE--GHSQLIVGTHALFQDNVAF---SKLGLVIIDEQHRfgvdqrlaLRNKGAD------QF-TPHQLVMTATPIPRTL 424
Cdd:cd18000 105 RKvvGDGGILITTYEGFRKHKDLllnHNWQYVILDEGHK--------IRNPDAEitlackQLrTPHRLILSGTPIQNNL 175
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
289-390 |
7.99e-04 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 41.31 E-value: 7.99e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAEWQ------VALMAPTEILAEQHYLNFKRWFEPlGIDVAWLSGKQKGKARTqaeQHIREGhS 362
Cdd:cd18036 27 GSGKTRVAVYICRHHLEKRRSagekgrVVVLVNKVPLVEQQLEKFFKYFRK-GYKVTGLSGDSSHKVSF---GQIVKA-S 101
|
90 100 110
....*....|....*....|....*....|....*..
gi 491228584 363 QLIVGTHALFQDN---------VAFSKLGLVIIDEQH 390
Cdd:cd18036 102 DVIICTPQILINNllsgreeerVYLSDFSLLIFDECH 138
|
|
| DEXHc_RIG-I_DDX58 |
cd18073 |
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ... |
289-428 |
1.09e-03 |
|
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I 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: 350831 [Multi-domain] Cd Length: 202 Bit Score: 40.96 E-value: 1.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALE-----AEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQkgkARTQAEQHIREgHSQ 363
Cdd:cd18073 27 GCGKTFVSLLICEHHLKkfpqgQKGKVVFFATKVPVYEQQKSVFSKYFERHGYRVTGISGAT---AENVPVEQIIE-NND 102
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 491228584 364 LIVGTHALFQDNV------AFSKLGLVIIDEQHRFGVDQRLalrNKGADQFTPHQLVMTATPIPRTLAMSA 428
Cdd:cd18073 103 IIILTPQILVNNLkkgtipSLSIFTLMIFDECHNTSGNHPY---NMIMFRYLDQKLGGSSGPLPQIIGLTA 170
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
289-419 |
1.45e-03 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are 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: 350684 [Multi-domain] Cd Length: 146 Bit Score: 39.60 E-value: 1.45e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 289 GAGKTLVAAIAACHALEAewQVALMAPTEILAEQHYLNFKRWFEPlgidvawlsgKQKGKARTQAEQHIREGhsQLIVGT 368
Cdd:cd17926 28 GSGKTLTALALIAYLKEL--RTLIVVPTDALLDQWKERFEDFLGD----------SSIGLIGGGKKKDFDDA--NVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 491228584 369 -----HALFQDNVAFSKLGLVIIDEQHRFGVDQ--RLALRNKGadqftPHQLVMTATP 419
Cdd:cd17926 94 yqslsNLAEEEKDLFDQFGLLIVDEAHHLPAKTfsEILKELNA-----KYRLGLTATP 146
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
283-583 |
1.71e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 41.29 E-value: 1.71e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 283 LVQGDVGAGKTLVAAIAACHALEAEW----QVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKgkARTQAEQhIR 358
Cdd:COG0513 43 LGQAQTGTGKTAAFLLPLLQRLDPSRprapQALILAPTRELALQVAEELRKLAKYLGLRVATVYGGVS--IGRQIRA-LK 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 359 EGhSQLIVGT------HaLFQDNVAFSKLGLVIIDEqhrfgvdqrlalrnkgADqftphqlvmtatpipRTLAMSAYGDL 432
Cdd:COG0513 120 RG-VDIVVATpgrlldL-IERGALDLSGVETLVLDE----------------AD---------------RMLDMGFIEDI 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 433 DTsVIDELPPGRtpiQTV----TIP------------------LDRREEVLQRIaqncregKQAYWvctLVEQSETLDA- 489
Cdd:COG0513 167 ER-ILKLLPKER---QTLlfsaTMPpeirklakrylknpvrieVAPENATAETI-------EQRYY---LVDKRDKLELl 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 490 -------------------QAAEATYQEIKERfpDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNA 550
Cdd:COG0513 233 rrllrdedperaivfcntkRGADRLAEKLQKR--GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDV 310
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 491228584 551 SiMVI-----ENAE----RLGlsqlhqlR-GRVGRGATA-SFCA 583
Cdd:COG0513 311 S-HVInydlpEDPEdyvhRIG-------RtGRAGAEGTAiSLVT 346
|
|
| PTZ00110 |
PTZ00110 |
helicase; Provisional |
511-605 |
1.76e-03 |
|
helicase; Provisional
Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 41.30 E-value: 1.76e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 511 VHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMV-------IENaerlglsQLHQLrGRVGRgATASFCA 583
Cdd:PTZ00110 407 IHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVInfdfpnqIED-------YVHRI-GRTGR-AGAKGAS 477
|
90 100
....*....|....*....|...
gi 491228584 584 LLYKTP-LSQNGQERLSILRESN 605
Cdd:PTZ00110 478 YTFLTPdKYRLARDLVKVLREAK 500
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
497-554 |
1.87e-03 |
|
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: 39.11 E-value: 1.87e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491228584 497 QEIKERFPDLNVGLVHG----------KMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMV 554
Cdd:cd18802 46 KEHPSTLAFIRCGFLIGrgnssqrkrsLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI 113
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
262-388 |
2.28e-03 |
|
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350683 [Multi-domain] Cd Length: 143 Bit Score: 38.82 E-value: 2.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 262 AQKRVSKEILQDLKQQQPMlrLVQGDVGAGKT--LVAAIAAchALEAEWQVALMAP-TEILAEQHYlNFKRWFEPLGIDV 338
Cdd:cd17925 1 GQQKASNALVETIDAKEDL--LVWAVTGAGKTemLFPAIAQ--ALRQGGRVAIASPrIDVCLELAP-RLKAAFPGAAIVL 75
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 491228584 339 awLSGKQKGKARtqaeqhiregHSQLIVGT-HALFQDNVAFSklgLVIIDE 388
Cdd:cd17925 76 --LHGGSEDQYQ----------RSPLVIATtHQLLRFYRAFD---LLIIDE 111
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
283-390 |
3.14e-03 |
|
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350777 [Multi-domain] Cd Length: 214 Bit Score: 39.66 E-value: 3.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 283 LVQGDVGAGKTLVAAIAACHALE-----------AEWQVALMAPTEILAEQHYLNFKRWFEPLGIDVAWLSGKQKgkart 351
Cdd:cd18019 37 LLCAPTGAGKTNVALLTILREIGkhrnpdgtinlDAFKIVYIAPMKALVQEMVGNFSKRLAPYGITVAELTGDQQ----- 111
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 491228584 352 QAEQHIREghSQLIVGTHALFQ------DNVAFSKL-GLVIIDEQH 390
Cdd:cd18019 112 LTKEQISE--TQIIVTTPEKWDiitrksGDRTYTQLvRLIIIDEIH 155
|
|
| PRK09694 |
PRK09694 |
CRISPR-associated helicase/endonuclease Cas3; |
431-547 |
3.44e-03 |
|
CRISPR-associated helicase/endonuclease Cas3;
Pssm-ID: 182031 [Multi-domain] Cd Length: 878 Bit Score: 40.56 E-value: 3.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 431 DLDTSVIDELPPGRTPIQTVTIPLDR---REEVLQRIAQNCREGKQAYWVCTLVEqsetlDAQAaeaTYQEIKE-RFPDL 506
Cdd:PRK09694 517 RFDLSAHPEQLPARFTIQLEPICLADmlpDLTLLQRMIAAANAGAQVCLICNLVD-----DAQK---LYQRLKElNNTQV 588
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 491228584 507 NVGLVHGKMKADEKQA----VMQAF----KDNQSQLLIATTVIEVGVDV 547
Cdd:PRK09694 589 DIDLFHARFTLNDRREkeqrVIENFgkngKRNQGRILVATQVVEQSLDL 637
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
290-343 |
3.87e-03 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 40.57 E-value: 3.87e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 491228584 290 AGKTLVAAIAACHALEAEWQVAL-MAPTEILAEQHYLNFKRWfEPLGIDVAWLSG 343
Cdd:PRK00254 50 SGKTLVAEIVMVNKLLREGGKAVyLVPLKALAEEKYREFKDW-EKLGLRVAMTTG 103
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
490-575 |
6.39e-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: 6.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 490 QAAEATYQEIKERFPD----LNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASiMVIENAERLGLSQ 565
Cdd:cd18796 49 SQAERLAQRLRELCPDrvppDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVD-LVIQIGSPKSVAR 127
|
90
....*....|
gi 491228584 566 LHQLRGRVGR 575
Cdd:cd18796 128 LLQRLGRSGH 137
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
497-579 |
8.44e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 39.04 E-value: 8.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491228584 497 QEIKERfpDLNVGLVHGKMKADEKQAVMQAFKDNQSQLLIATTVIEVGVDVPNASIMV-------IEN-AERLGLSqlhq 568
Cdd:PTZ00424 285 KKMHER--DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVInydlpasPENyIHRIGRS---- 358
|
90
....*....|.
gi 491228584 569 lrGRVGRGATA 579
Cdd:PTZ00424 359 --GRFGRKGVA 367
|
|
| |
