|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
1-693 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 1065.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 1 MSQQLLDGVPLTALSGVGAAISEKLSRIGINNVQDLLFHLPMRYEDRTRITPIADVRPESFATVEGFVQLTEVQFGRRPI 80
Cdd:PRK10917 1 PSLLLLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 81 LSTTISDGTSKITLKFFNFNAGM-KNSLATGVRVKAFGEIKRGRFMAEIHHPEYQIIRGNQPlELAETLTPIYPTTEGLK 159
Cdd:PRK10917 81 LTVTVSDGTGNLTLRFFNFNQPYlKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEESP-ELEGRLTPVYPLTEGLK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 160 QASLRKLTDQALALLErvQVAELLPDEFNPHK--YSLKEALQLLHRPPPSVSSelldkgeHPAQKRLIFEELLAHNLAMQ 237
Cdd:PRK10917 160 QKTLRKLIKQALELLD--ALPELLPEELLEKYglLSLAEALRAIHFPPSDEDL-------HPARRRLKFEELFALQLSLL 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 238 QVRMGVQQHFAEPLCYQTDLKQRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNG 317
Cdd:PRK10917 231 LLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAG 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 318 KQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIID 397
Cdd:PRK10917 311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIID 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 398 EQHRFGVHQRLTLREKGAKgdvyPHQLIMTATPIPRTLAMTVYADLDTSIIDELPPGRTPITTVAISEDRRDEVVRRVYQ 477
Cdd:PRK10917 391 EQHRFGVEQRLALREKGEN----PHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIRE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 478 ACKnEKRQAYWVCTLIDESEVLEAQAAAAIAEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGV 557
Cdd:PRK10917 467 EIA-KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 558 DVPNASLMIIENSERLGLAQLHQLRGRVGRGATASHCVLMYKAPLGKISSKRLQVLRDSQDGFVIAEKDLEIRGPGEVLG 637
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLG 625
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*.
gi 737522233 638 TKQTGMAEFKIANLMRDRKMIPLVQNYAKQLTLKYPDTAKQLIRRWLDEKTVYSNA 693
Cdd:PRK10917 626 TRQSGLPEFKVADLVRDEELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
10-687 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 1040.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 10 PLTALSGVGAAISEKLSRIGINNVQDLLFHLPMRYEDRTRITPIADVRPESFATVEGFVQLTEVQF--GRRPILSTTISD 87
Cdd:COG1200 7 PLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRrrRRRRILEVTLSD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 88 GTSKITLKFFNFNAgMKNSLATGVRVKAFGEIKRGRFMAEIHHPEYQIIrGNQPLELAETLTPIYPTTEGLKQASLRKLT 167
Cdd:COG1200 87 GTGSLTLVFFNQPY-LKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELL-DEEEAELAGRLTPVYPLTEGLSQKTLRKLI 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 168 DQALALLERvQVAELLPDEFNpHKY---SLKEALQLLHRPPPSVSselldkgEHPAQKRLIFEELLAHNLAMQQVRMGVQ 244
Cdd:COG1200 165 RQALDLLAP-DLPEPLPEELR-ARYglpSLAEALRNIHFPPSDED-------LHPARRRLAFEELLALQLALLLRRARRR 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 245 QHFAEPLCYQTDLKQRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMA 324
Cdd:COG1200 236 KRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMA 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 325 PTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGV 404
Cdd:COG1200 316 PTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGV 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 405 HQRLTLREKGAkgdvYPHQLIMTATPIPRTLAMTVYADLDTSIIDELPPGRTPITTVAISEDRRDEVVRRVYQACKnEKR 484
Cdd:COG1200 396 EQRLALREKGE----APHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIA-KGR 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 485 QAYWVCTLIDESEVLEAQAAAAIAEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASL 564
Cdd:COG1200 471 QAYVVCPLIEESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATV 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 565 MIIENSERLGLAQLHQLRGRVGRGATASHCVLMYKAPLGKISSKRLQVLRDSQDGFVIAEKDLEIRGPGEVLGTKQTGMA 644
Cdd:COG1200 551 MVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLP 630
|
650 660 670 680
....*....|....*....|....*....|....*....|....
gi 737522233 645 EFKIANLMRDRKMIPLVQNYAKQLTLKYPDTAK-QLIRRWLDEK 687
Cdd:COG1200 631 DLRIADLVRDADLLEAAREDAEELLEEDPELAShPALRRWLGLR 674
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
28-665 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 872.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 28 IGINNVQDLLFHLPMRYEDRTRITPIADVRPESFATVEGFVQ-LTEVQFGRRPILSTTISD-GTSKITLKFFNfNAGMKN 105
Cdd:TIGR00643 1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLsHCIFGFKRRKVLKLRLKDgGYKKLELRFFN-RAFLKK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 106 SLATGVRVKAFGEIKRGRFMAEIHHPEYQIIRGNQPLELaeTLTPIYPTTEGLKQASLRKLTDQALALLERVqVAELLPD 185
Cdd:TIGR00643 80 KFKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFEL--KILPVYPLTEGLTQKKLRKLIQQALDQLDKS-LEDPLPE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 186 EFNP--HKYSLKEALQLLHRPPpsvSSELLdkgeHPAQKRLIFEELLAHNLAMQQVRMGVQQHF-AEPLCYQTDLKQRFL 262
Cdd:TIGR00643 157 ELREkyGLLSLEDALRAIHFPK---TLSLL----ELARRRLIFDEFFYLQLAMLARRLGEKQQFsAPPANPSEELLTKFL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 263 ATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLR 342
Cdd:TIGR00643 230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLA 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 343 PFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQRLTLREKGAKGdVYPH 422
Cdd:TIGR00643 310 PLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGG-FTPH 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 423 QLIMTATPIPRTLAMTVYADLDTSIIDELPPGRTPITTVAISEDRRDEVVRRVyQACKNEKRQAYWVCTLIDESEVLEAQ 502
Cdd:TIGR00643 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFI-EEEIAKGRQAYVVYPLIEESEKLDLK 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 503 AAAAIAEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGLAQLHQLR 582
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 583 GRVGRGATASHCVLMYKAPLGKISSKRLQVLRDSQDGFVIAEKDLEIRGPGEVLGTKQTGMAEFKIANLMRDRKMIPLVQ 662
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAR 627
|
...
gi 737522233 663 NYA 665
Cdd:TIGR00643 628 EDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
224-452 |
5.45e-118 |
|
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: 352.22 E-value: 5.45e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 224 LIFEELLAHNLAMQQVRMGVQQHFAEPLCYQTDLKQRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKT 303
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 304 LVAALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQ 383
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 737522233 384 DQVEFHHLALVIIDEQHRFGVHQRLTLREKGAkgdvYPHQLIMTATPIPRTLAMTVYADLDTSIIDELP 452
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGE----TPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
259-642 |
8.16e-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: 337.79 E-value: 8.16e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 259 QRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNFA 338
Cdd:TIGR00580 442 QEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFK 521
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 339 NWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQRLTLREKGAKGD 418
Cdd:TIGR00580 522 ERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVD 601
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 419 VyphqLIMTATPIPRTLAMTVYADLDTSIIDELPPGRTPITTVAISEDrrDEVVRrvyQACKNEKR---QAYWVCTLIDE 495
Cdd:TIGR00580 602 V----LTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYD--PELVR---EAIRRELLrggQVFYVHNRIES 672
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 496 SEVLEaqaaaaiaEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGL 575
Cdd:TIGR00580 673 IEKLA--------TQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGL 744
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 737522233 576 AQLHQLRGRVGRGATASHCVLMY--KAPLGKISSKRLQVLRDSQD---GFVIAEKDLEIRGPGEVLGTKQTG 642
Cdd:TIGR00580 745 AQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEAIQEFSElgaGFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
255-645 |
4.25e-98 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 326.25 E-value: 4.25e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 255 TDLKQRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKT--------LVaalaallaIDNGKQVALMAPT 326
Cdd:COG1197 573 TPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTevalraafKA--------VMDGKQVAVLVPT 644
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 327 EILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQ 406
Cdd:COG1197 645 TLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRH 724
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 407 --RL-TLREkgakgDVypHQLIMTATPIPRTLAMTVyADL-DTSIIDELPPGRTPITTVAISEDrrDEVVRrvyQACKNE 482
Cdd:COG1197 725 keKLkALRA-----NV--DVLTLTATPIPRTLQMSL-SGIrDLSIIATPPEDRLPVKTFVGEYD--DALIR---EAILRE 791
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 483 -KR--QAYWVC----TlIDEsevleaqaaaaIAEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEV 555
Cdd:COG1197 792 lLRggQVFYVHnrveD-IEK-----------VAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIET 859
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 556 GVDVPNASLMIIENSERLGLAQLHQLRGRVGRGATASHCVLMYKA--PLGKISSKRLQVLRDSQD---GFVIAEKDLEIR 630
Cdd:COG1197 860 GIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPdkVLTEDAEKRLEAIQEFTElgaGFKLAMHDLEIR 939
|
410
....*....|....*.
gi 737522233 631 GPGEVLGTKQTG-MAE 645
Cdd:COG1197 940 GAGNLLGEEQSGhIAE 955
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
259-645 |
3.85e-70 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 248.51 E-value: 3.85e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 259 QRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNF- 337
Cdd:PRK10689 591 QLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFr 670
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 338 ---ANWlrPFGIEVgwLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQRLTLREKG 414
Cdd:PRK10689 671 drfANW--PVRIEM--LSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMR 746
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 415 AKGDVyphqLIMTATPIPRTLAMTVYADLDTSIIDELPPGRTPITTVAISEDrrDEVVRrvyQACKNEKRQAYWVCTLID 494
Cdd:PRK10689 747 ADVDI----LTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYD--SLVVR---EAILREILRGGQVYYLYN 817
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 495 ESEVLEAQAaaaiaEDLQCALPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLG 574
Cdd:PRK10689 818 DVENIQKAA-----ERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG 892
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 737522233 575 LAQLHQLRGRVGRGATASHCVLMYKAP--LGKISSKRLQVLRDSQD---GFVIAEKDLEIRGPGEVLGTKQTGMAE 645
Cdd:PRK10689 893 LAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSGQME 968
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
457-615 |
1.33e-65 |
|
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: 213.36 E-value: 1.33e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 457 PITTVAISEDRRDEVVRRVyQACKNEKRQAYWVCTLIDESEVLEAQAAAAIAEDLQCAL-PDLRIGLVHGRMKPQEKQAI 535
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFV-REEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 536 MAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGLAQLHQLRGRVGRGATASHCVLMYKAPLGKISSKRLQVLRD 615
Cdd:cd18811 80 MAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
259-449 |
1.32e-61 |
|
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: 203.96 E-value: 1.32e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 259 QRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNFA 338
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 339 NWLRPFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQRLTLREKgaKGD 418
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL--RPN 163
|
170 180 190
....*....|....*....|....*....|.
gi 737522233 419 VypHQLIMTATPIPRTLAMTVYADLDTSIID 449
Cdd:cd17991 164 V--DVLTLSATPIPRTLHMALSGIRDLSVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
256-449 |
5.03e-57 |
|
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: 191.48 E-value: 5.03e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 256 DLKQRFLATLPFQPTNAQSRVTAEIEQDLAKPFPMMRLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAH 335
Cdd:cd17918 3 ALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 336 NFANWLRPFGIEVgwlagkVKGkARTAQLEAIKNgdvqMIIGTHALFQDQVEFHHLALVIIDEQHRFGVHQRLTLREKGA 415
Cdd:cd17918 83 EARKFLPFINVEL------VTG-GTKAQILSGIS----LLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA 151
|
170 180 190
....*....|....*....|....*....|....
gi 737522233 416 kgdvyPHQLIMTATPIPRTLAMTVYADLDTSIID 449
Cdd:cd17918 152 -----THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
457-615 |
1.11e-56 |
|
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: 189.79 E-value: 1.11e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 457 PITTVAISEDRRDEVVRRVYQaCKNEKRQAYWVCTLIDESEVLEAQAAAAIAEDLQCALPDLRIGLVHGRMKPQEKQAIM 536
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIER-ELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 537 AEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGLAQLHQLRGRVGRGATASHCVLMYKAP--LGKISSKRLQVLR 614
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPkkLTETAKKRLRAIA 159
|
.
gi 737522233 615 D 615
Cdd:cd18792 160 E 160
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
516-613 |
7.62e-29 |
|
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: 112.44 E-value: 7.62e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 516 PDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGLAQLHQLRGRVGRGATASHCV 595
Cdd:cd18810 50 PEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAY 129
|
90 100
....*....|....*....|
gi 737522233 596 LMY--KAPLGKISSKRLQVL 613
Cdd:cd18810 130 FLYpdQKKLTEDALKRLEAI 149
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
16-166 |
1.61e-27 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 109.06 E-value: 1.61e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 16 GVGAAISEKLSRIGINNVQDLLFHLPMRYEDRTRITPIADVRPESFATVEGFVQLTEV-QFGRRPILSTTISDGTSKITL 94
Cdd:pfam17191 7 GVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETkKIGSLVIISAVLSDGIGQVLL 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 737522233 95 KFFNfNAGMKNSLATGVRVKAFGEIKRGRFMA-EIHHPEYQIIRGNQPLElaetLTPIYPTTEGLKQASLRKL 166
Cdd:pfam17191 87 KWFN-QEYIKKFLQKGKEVYITGTVKEGPFGPiEMNNPEIEEITGEQERE----ILPVYPLTEGISQKNMRKI 154
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
261-456 |
3.94e-21 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 91.78 E-value: 3.94e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 261 FLATLPFQPTNAQSRVTAEIEQDLakpfpMMRLVQGDVGSGKTLVAALAALLAIDNG--KQVALMAPTEILAEQHAHNFA 338
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 339 NWLRPFGIEVgwlAGKVKGKARTAQLEAIKNGDVQMIIGT-----HALFQDQVEFHHLALVIIDEQHRFGVH-QRLTLRE 412
Cdd:smart00487 76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 737522233 413 KGAKGDVYPHQLIMTATP---IPRTLAMTVYADLDTSIIDELPPGRT 456
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
293-438 |
4.08e-21 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 90.76 E-value: 4.08e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 293 LVQGDVGSGKTLVAAL---AALLAIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGkvkGKARTAQLEAIKN 369
Cdd:pfam00270 18 LVQAPTGSGKTLAFLLpalEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG---GDSRKEQLEKLKG 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 737522233 370 GDVqmIIGTH----ALFQDQVEFHHLALVIIDEQHRFGVH-QRLTLREKGAKGDVYPHQLIMTATPiPRTLAMT 438
Cdd:pfam00270 95 PDI--LVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRLPKKRQILLLSATL-PRNLEDL 165
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
63-136 |
4.06e-19 |
|
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: 81.86 E-value: 4.06e-19
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 737522233 63 TVEGFVQLTEVQFGR-RPILSTTISDGTSKITLKFFNFNAGMKNSLATGVRVKAFGEIKRGRFMAEIHHPEYQII 136
Cdd:cd04488 1 TVEGTVVSVEVVPRRgRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYELL 75
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
517-587 |
6.82e-18 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 79.56 E-value: 6.82e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 737522233 517 DLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERlGLAQLHQLRGRVGR 587
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
517-587 |
6.48e-17 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 75.71 E-value: 6.48e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 737522233 517 DLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSeRLGLAQLHQLRGRVGR 587
Cdd:smart00490 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
293-598 |
4.73e-12 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 68.90 E-value: 4.73e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 293 LVQGDVGSGKTLVAALAALLaIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGwlagkvkgkartaqleaIKNGDV 372
Cdd:COG1061 104 LVVAPTGTGKTVLALALAAE-LLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAGGG-----------------KKDSDA 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 373 QMIIGTHALFQDQVEFHHLA----LVIIDEQHRFGVHQ-RLTLREKGAKgdvypHQLIMTATPIpRTLAMTVYADLDTSI 447
Cdd:COG1061 166 PITVATYQSLARRAHLDELGdrfgLVIIDEAHHAGAPSyRRILEAFPAA-----YRLGLTATPF-RSDGREILLFLFDGI 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 448 IDELPPGR-------TPITTVAISED------------------------RRDEVVRRVYQACKNEKRqAYWVCTLIDES 496
Cdd:COG1061 240 VYEYSLKEaiedgylAPPEYYGIRVDltderaeydalserlrealaadaeRKDKILRELLREHPDDRK-TLVFCSSVDHA 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 497 EVLeaqaaaaiAEDLQcaLPDLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIeNSERLGLA 576
Cdd:COG1061 319 EAL--------AELLN--EAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL-LRPTGSPR 387
|
330 340
....*....|....*....|..
gi 737522233 577 QLHQLRGRVGRGATASHCVLMY 598
Cdd:COG1061 388 EFIQRLGRGLRPAPGKEDALVY 409
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
293-429 |
5.91e-12 |
|
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: 63.96 E-value: 5.91e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 293 LVQGDVGSGKTLVAALAALLAID-NGKQVALMAPTEILAEQHAHNFANWLRPfGIEVGWLAGKVKGKARtaqlEAIKNGD 371
Cdd:cd00046 5 LITAPTGSGKTLAALLAALLLLLkKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEER----EKNKLGD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 372 VQMIIGTHA------LFQDQVEFHHLALVIIDEQHRFGVHQR------LTLREKGAKgdvYPHQLIMTAT 429
Cdd:cd00046 80 ADIIIATPDmllnllLREDRLFLKDLKLIIVDEAHALLIDSRgalildLAVRKAGLK---NAQVILLSAT 146
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
616-673 |
1.24e-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: 1.24e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 737522233 616 SQDGFVIAEKDLEIRGPGEVLGTKQTGMA-EFKIANLMRDRKMIPLVQNYAKQLTLKYP 673
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEEIIDNDP 59
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
273-400 |
5.48e-11 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 61.84 E-value: 5.48e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 273 QSRVTAEIEQDLA--KPFpmmrLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPtEI-LAEQHAHNFANwlrPFGIEVG 349
Cdd:cd17929 1 QRKAYEAIVSSLGgfKTF----LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVP-EIsLTPQLIKRFKK---RFGDKVA 72
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 737522233 350 WLAGKVKGKARTAQLEAIKNGDVQMIIGTH-ALFqdqVEFHHLALVIIDEQH 400
Cdd:cd17929 73 VLHSKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
293-400 |
5.75e-07 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 52.85 E-value: 5.75e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 293 LVQGDVGSGKTLVAALAALLAIDNGKQVALMAPtEI-LAEQHAHNFANwlRpFGIEVGWLAGKVKGKARTAQLEAIKNGD 371
Cdd:PRK05580 166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaLTPQMLARFRA--R-FGAPVAVLHSGLSDGERLDEWRKAKRGE 241
|
90 100 110
....*....|....*....|....*....|
gi 737522233 372 VQMIIGTH-ALFqdqVEFHHLALVIIDEQH 400
Cdd:PRK05580 242 AKVVIGARsALF---LPFKNLGLIIVDEEH 268
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
63-136 |
8.31e-07 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 46.84 E-value: 8.31e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 737522233 63 TVEGFVqlTEVQFGRRPILSTTISDGTSKITLKFFNFNAG-MKNSLATGVRVKAFGEIKRGRFMA-EIHHPEYQII 136
Cdd:pfam01336 2 TVAGRV--TSIRRSGGKLLFLTLRDGTGSIQVVVFKEEAEkLAKKLKEGDVVRVTGKVKKRKGGElELVVEEIELL 75
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
253-400 |
1.16e-06 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 52.04 E-value: 1.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 253 YQTDLKQRFLATLPFQPTNAQSRVTAEIEQDLA--KPFpmmrLVQGDVGSGKTLVAALAALLAIDNGKQVALMAPtEI-L 329
Cdd:COG1198 180 DRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGgfSVF----LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVP-EIaL 254
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 737522233 330 AEQHAHNFANWlrpFGIEVGWLAGKVKGKARTAQLEAIKNGDVQMIIGTH-ALFqdqVEFHHLALVIIDEQH 400
Cdd:COG1198 255 TPQTVERFRAR---FGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
546-590 |
1.54e-06 |
|
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: 46.16 E-value: 1.54e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 737522233 546 LLVATTVIEVGVDVPNASLMIIENSERlGLAQLHQLRGRVGRGAT 590
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGK 68
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
391-587 |
5.25e-06 |
|
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: 48.97 E-value: 5.25e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 391 LALVIIDEQHRFGVHQR---LTLREKGAKGDVyPHqLIMTATpIPRTLaMTVYADLDTSIIDELPP------GRTPITTV 461
Cdd:cd09639 124 NSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEENEPLDlkpnerAPFIKIES 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 462 AISEDRRdeVVRRVYQACKNEKRQAYwVCTLIDESEVLEAQaaaaiaedLQCALPDLRIGLVHGRMKP---QEKQA-IMA 537
Cdd:cd09639 200 DKVGEIS--SLERLLEFIKKGGSVAI-IVNTVDRAQEFYQQ--------LKEKGPEEEIMLIHSRFTEkdrAKKEAeLLL 268
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 737522233 538 EFKAANIDLLVATTVIEVGVDVpNASLMIIENSErlgLAQLHQLRGRVGR 587
Cdd:cd09639 269 EFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHR 314
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
515-597 |
6.82e-06 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 46.43 E-value: 6.82e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 515 LPDLRIGLVHGR----------MKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIienseRLGLA----QLHQ 580
Cdd:cd18802 52 LAFIRCGFLIGRgnssqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPktlrSYIQ 126
|
90
....*....|....*..
gi 737522233 581 LRGRvGRgATASHCVLM 597
Cdd:cd18802 127 SRGR-AR-APNSKYILM 141
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
299-430 |
1.23e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 46.66 E-value: 1.23e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAID-----NGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQleAIKNGDVq 373
Cdd:cd17927 27 GSGKTFVAVLICEHHLKkfpagRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQ--IVESSDV- 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 737522233 374 mIIGTHALFQD------QVEFHHLALVIIDEQHR------FGVHQRLTLREKGAKGDVYPHQLIMTATP 430
Cdd:cd17927 104 -IIVTPQILVNdlksgtIVSLSDFSLLVFDECHNttknhpYNEIMFRYLDQKLGSSGPLPQILGLTASP 171
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
391-587 |
1.51e-05 |
|
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: 47.83 E-value: 1.51e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 391 LALVIIDEQHRFGVHQR---LTLREKGAKGDVyPHqLIMTATpIPRTLaMTVYADLDTSIIDELPP----GRTPITTVAI 463
Cdd:TIGR01587 125 NSLLIFDEVHFYDEYTLaliLAVLEVLKDNDV-PI-LLMSAT-LPKFL-KEYAEKIGYVEFNEPLDlkeeRRFENHRFIL 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 464 SEDRRDEVVR---RVYQACKNEKRQAYwVCTLIDESEVLEAQaaaaiaedLQCALPDLRIGLVHGRMKP---QEKQA-IM 536
Cdd:TIGR01587 201 IESDKVGEISsleRLLEFIKKGGSIAI-IVNTVDRAQEFYQQ--------LKEKAPEEEIILYHSRFTEkdrAKKEAeLL 271
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 737522233 537 AEFKAANID-LLVATTVIEVGVDVpNASLMIIENSErlgLAQLHQLRGRVGR 587
Cdd:TIGR01587 272 REMKKSNEKfVIVATQVIEASLDI-SADVMITELAP---IDSLIQRLGRLHR 319
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
517-566 |
4.15e-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: 43.65 E-value: 4.15e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 737522233 517 DLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMI 566
Cdd:cd18787 51 GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI 100
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
299-430 |
6.91e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 46.26 E-value: 6.91e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDN-GKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKARTAQLEaikngDVQMIIG 377
Cdd:COG1111 27 GLGKTAVALLVIAERLHKkGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWE-----KARIIVA 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 737522233 378 ThalfqDQVEFHHL----------ALVIIDEQHR-FGVHQRLTLREKGAKGDVYPHQLIMTATP 430
Cdd:COG1111 102 T-----PQVIENDLiagridlddvSLLIFDEAHRaVGNYAYVYIAERYHEDAKDPLILGMTASP 160
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
299-431 |
1.31e-04 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 43.04 E-value: 1.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDNG--KQVALMAPTEILAEQHAHNFanwlRPFGIEVGWLAGKVKGKARTaqleaIKNGDVQMII 376
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEF----KKFLPNYVEIGEIISGDKKD-----ESVDDNKIVV 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 737522233 377 GT-HALFQDQVEFHHLA------LVIIDEQHRFG--VHQRLTLREKgakgdvYPHQLIMTATPI 431
Cdd:pfam04851 104 TTiQSLYKALELASLELlpdffdVIIIDEAHRSGasSYRNILEYFK------PAFLLGLTATPE 161
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
388-587 |
1.47e-04 |
|
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: 45.07 E-value: 1.47e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 388 FHHLA--LVIIDEQHRFGVHQ----RLTLRE-KGAKGDVyphqLIMTAT-PIPRTLAMTVYADLDTSIIDELPPGRTPIT 459
Cdd:COG1203 264 LHNLAnsVIILDEVQAYPPYMlallLRLLEWlKNLGGSV----ILMTATlPPLLREELLEAYELIPDEPEELPEYFRAFV 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 460 --TVAISEDR--RDEVVRRVYQACKNEKRQAyWVCTLIDES-EVLEAqaaaaiaedLQCALPDLRIGLVHGRMKPQEKQA 534
Cdd:COG1203 340 rkRVELKEGPlsDEELAELILEALHKGKSVL-VIVNTVKDAqELYEA---------LKEKLPDEEVYLLHSRFCPADRSE 409
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 737522233 535 IMAE----FKAANIDLLVATTVIEVGVDVpNASLMIIENSerlGLAQLHQLRGRVGR 587
Cdd:COG1203 410 IEKEikerLERGKPCILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQRAGRCNR 462
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
299-587 |
1.92e-04 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 44.50 E-value: 1.92e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGkvkgkARTAQLEAIKNGDVqmIIGT 378
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTG-----DYDSDDEWLGRYDI--LVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 379 ----HALFQDQVEF-HHLALVIIDEQHRFGVHQR-------LT-LREKGAKGdvyphQLI-MTAT--------------- 429
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevlLArLRRLNPEA-----QIVaLSATignaeeiaewldael 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 430 ------PIPRTLAmtVYADLDTSIIDELPPGRTPITTVA---ISED--------RRDEVV---RRVYQACKNEKRQAYWV 489
Cdd:COG1204 196 vksdwrPVPLNEG--VLYDGVLRFDDGSRRSKDPTLALAldlLEEGgqvlvfvsSRRDAEslaKKLADELKRRLTPEERE 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 490 CTLIDESEVLEAQAAAAIAEDL-QCALpdLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPnASLMIIE 568
Cdd:COG1204 274 ELEELAEELLEVSEETHTNEKLaDCLE--KGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIIR 350
|
330 340
....*....|....*....|....
gi 737522233 569 NSERLGLAQL-----HQLRGRVGR 587
Cdd:COG1204 351 DTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| polC |
PRK00448 |
DNA polymerase III PolC; Validated |
50-132 |
4.27e-04 |
|
DNA polymerase III PolC; Validated
Pssm-ID: 234767 [Multi-domain] Cd Length: 1437 Bit Score: 43.67 E-value: 4.27e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 50 ITPIADVRPESF-ATVEGFVQLTEVQFGR--RPILSTTISDGTSKITLKFFNFNAG---MKNSLATGVRVKAFGEIKRGR 123
Cdd:PRK00448 226 ITPMKEINEEERrVVVEGYVFKVEIKELKsgRHILTFKITDYTSSIIVKKFSRDKEdlkKFDEIKKGDWVKVRGSVQNDT 305
|
90
....*....|....*....
gi 737522233 124 FM----------AEIHHPE 132
Cdd:PRK00448 306 FTrdlvmnaqdiNEIKHPE 324
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
299-398 |
4.43e-04 |
|
DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 42.04 E-value: 4.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTL-------VAALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLAGKVKGKartAQLEAIKNGd 371
Cdd:cd00268 37 GSGKTLafllpilEKLLPEPKKKGRGPQALVLAPTRELAMQIAEVARKLGKGTGLKVAAIYGGAPIK---KQIEALKKG- 112
|
90 100 110
....*....|....*....|....*....|..
gi 737522233 372 VQMIIGT-----HALFQDQVEFHHLALVIIDE 398
Cdd:cd00268 113 PDIVVGTpgrllDLIERGKLDLSNVKYLVLDE 144
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
295-566 |
4.67e-04 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 43.28 E-value: 4.67e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 295 QGDVGSGKTLVAALAALLAID---NGKQVALMAPTEILAEQhAHNFANWLRPFgIEVGWLAGkVKGKARTAQLEAIKNGd 371
Cdd:PTZ00424 71 QAQSGTGKTATFVIAALQLIDydlNACQALILAPTRELAQQ-IQKVVLALGDY-LKVRCHAC-VGGTVVRDDINKLKAG- 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 372 VQMIIGTHALFQDQVEFHHL-----ALVIIDEQHRfgvhqrltLREKGAKGDVYPhqlimTATPIPRTLAMTVYADLDTS 446
Cdd:PTZ00424 147 VHMVVGTPGRVYDMIDKRHLrvddlKLFILDEADE--------MLSRGFKGQIYD-----VFKKLPPDVQVALFSATMPN 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 447 IIDELPPG--RTPITTVAISEDRRDEVVRRVYQACKNEKrqaYWVCTLIDESEVLEAQAAAAIAED--------LQCALP 516
Cdd:PTZ00424 214 EILELTTKfmRDPKRILVKKDELTLEGIRQFYVAVEKEE---WKFDTLCDLYETLTITQAIIYCNTrrkvdyltKKMHER 290
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 737522233 517 DLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMI 566
Cdd:PTZ00424 291 DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
299-430 |
1.08e-03 |
|
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: 40.58 E-value: 1.08e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDN-GKQVALMAPTEILAEQHAHNFANWLRpFGIEVGWLAGKVKGKARTAQLEAIKngdvqMIIG 377
Cdd:cd18035 26 GLGKTIIAILVAADRLTKkGGKVLILAPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEERAERWDASK-----IIVA 99
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 737522233 378 T-----HALFQDQVEFHHLALVIIDEQHR-FGVHQRLTLREKGAKGDVYPHQLIMTATP 430
Cdd:cd18035 100 TpqvieNDLLAGRITLDDVSLLIFDEAHHaVGNYAYVYIAHRYKREANNPLILGLTASP 158
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
292-397 |
1.83e-03 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase 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: 350682 [Multi-domain] Cd Length: 189 Bit Score: 40.00 E-value: 1.83e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 292 RLVQGD-------VGSGKTLVAALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLRPFGIEVGWLA--GKVKGKARTA 362
Cdd:cd17924 28 RLLRGKsfaiiapTGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILVyhSRLKKKEKEE 107
|
90 100 110
....*....|....*....|....*....|....*...
gi 737522233 363 QLEAIKNGDVQMIIGTHALFQDQVEF---HHLALVIID 397
Cdd:cd17924 108 LLEKIEKGDFDILVTTNQFLSKNFDLlsnKKFDFVFVD 145
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
299-407 |
2.00e-03 |
|
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: 39.94 E-value: 2.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDNGKQVAL-MAPTEILAEQHAHNFANWLRPFGIEVGWLAGkvkgkARTAQLEAIKNGDV----- 372
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTG-----DPSVNKLLLAEADIlvatp 101
|
90 100 110
....*....|....*....|....*....|....*....
gi 737522233 373 ----QMIIGTHALFQDQVEfhhlaLVIIDEQHRFGVHQR 407
Cdd:cd17921 102 ekldLLLRNGGERLIQDVR-----LVVVDEAHLIGDGER 135
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
509-588 |
2.11e-03 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 40.31 E-value: 2.11e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 509 EDLQCALPDLRIGlvhgRM------KPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIEN------------S 570
Cdd:cd18804 108 EELKTLFPEARIA----RIdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNadsglnspdfraS 183
|
90
....*....|....*....
gi 737522233 571 ERLglAQL-HQLRGRVGRG 588
Cdd:cd18804 184 ERA--FQLlTQVSGRAGRG 200
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
527-599 |
2.58e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 41.01 E-value: 2.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 527 MKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMI-----------IenserlglaqlhQLRGRVGRGATASHCV 595
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIfyepvpseirsI------------QRKGRTGRQEEGRVVV 474
|
....
gi 737522233 596 LMYK 599
Cdd:PRK13766 475 LIAK 478
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
527-599 |
2.60e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 41.25 E-value: 2.60e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 737522233 527 MKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMII-EN--SE-RlglaqLHQLRGRVGRGATASHCVLMYK 599
Cdd:COG1111 395 LTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFyEPvpSEiR-----SIQRKGRTGRKREGRVVVLIAK 466
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
524-598 |
2.87e-03 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 41.03 E-value: 2.87e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 737522233 524 HGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLmIIENSERLGLAQLHQLRGRVGRGATASHCVLMY 598
Cdd:PLN03137 711 HGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRF-VIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYY 784
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
299-430 |
3.96e-03 |
|
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: 39.38 E-value: 3.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 299 GSGKTLVAALAALLAIDNGKQ------VALMAPTEILAEQHAHNFANWLRPfGIEVGWLAGKVKGKARTAQLeaIKNGDV 372
Cdd:cd18036 27 GSGKTRVAVYICRHHLEKRRSagekgrVVVLVNKVPLVEQQLEKFFKYFRK-GYKVTGLSGDSSHKVSFGQI--VKASDV 103
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 737522233 373 qmIIGTHALFQ---------DQVEFHHLALVIIDE------QHRFGVHQRLTLREKGAKGDVYPHQLIMTATP 430
Cdd:cd18036 104 --IICTPQILInnllsgreeERVYLSDFSLLIFDEchhtqkEHPYNKIMRMYLDKKLSSQGPLPQILGLTASP 174
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
527-588 |
5.21e-03 |
|
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: 38.11 E-value: 5.21e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 737522233 527 MKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMIIENSERLGLAQLhQLRGRVGRG 588
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRK 134
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
517-574 |
5.22e-03 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 38.00 E-value: 5.22e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 737522233 517 DLRIGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPNASLMII---------ENSERLG 574
Cdd:cd18789 68 RLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQisghggsrrQEAQRLG 134
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
297-438 |
5.51e-03 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 38.79 E-value: 5.51e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 297 DVGSGKTLV-------AALAALLAIDNGKQVALMAPTEILAEQHAHNFANWLrpfGIEVGWLAGK--VKGKARTAQLEAI 367
Cdd:cd18034 24 PTGSGKTLIavmlikeMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHT---DLKVGEYSGEmgVDKWTKERWKEEL 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 737522233 368 KNGDVqmIIGTHALFQD-----QVEFHHLALVIIDEQHRfgvhqrltlrekgAKGDvYPHQLIM-------TATPIPRTL 435
Cdd:cd18034 101 EKYDV--LVMTAQILLDalrhgFLSLSDINLLIFDECHH-------------ATGD-HPYARIMkefyhleGRTSRPRIL 164
|
...
gi 737522233 436 AMT 438
Cdd:cd18034 165 GLT 167
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
520-587 |
8.33e-03 |
|
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: 37.53 E-value: 8.33e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 737522233 520 IGLVHGRMKPQEKQAIMAEFKAANIDLLVATTVIEVGVDVPnASLMII--------ENSERLGLAQLHQLRGRVGR 587
Cdd:cd18795 66 IAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLP-ARTVIIkgtqrydgKGYRELSPLEYLQMIGRAGR 140
|
|
| |
