|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
107-785 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 920.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 107 STPIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGY-TIISAVV 185
Cdd:COG1200 5 DTPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRRRRRrRILEVTL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 186 SDGFGQLLLKWFNQDYILQKLRRDREYLIHGLAKGTpFGPMEMNSPEIEEIQGEVP---REILPVYSLTSGISMKMMRKI 262
Cdd:COG1200 85 SDGTGSLTLVFFNQPYLKKQLKPGTRVLVSGKVERF-RGGLQMVHPEYELLDEEEAelaGRLTPVYPLTEGLSQKTLRKL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 263 VKRNLGLVRS-LDDLVPSSITTERGLLPRKHAFTAIHFPKSLYEIRKARESLAYEEFFLFETTILFRKRQIRKEyQGLQK 341
Cdd:COG1200 164 IRQALDLLAPdLPEPLPEELRARYGLPSLAEALRNIHFPPSDEDLHPARRRLAFEELLALQLALLLRRARRRKR-KGPAL 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 342 EISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAM 421
Cdd:COG1200 243 PGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPTEILAE 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 422 QHYEKIKRELSPIGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLT 501
Cdd:COG1200 323 QHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVEQRLALR 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 502 TKGRLLDSLVMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILARKRLKDLYSYISDELKMGHQAFFIYPLIEES 581
Cdd:COG1200 403 EKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIAKGRQAYVVCPLIEES 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 582 EQIDLKNATDEATKLReEVFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGM 661
Cdd:COG1200 483 EKLDLQAAEETYEELR-EAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIENAERFGL 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 662 AQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDR 741
Cdd:COG1200 562 SQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPDLRIADLVRDA 641
|
650 660 670 680
....*....|....*....|....*....|....*....|....
gi 1491784557 742 DLLFKAREDAKQLMEEDPELLEHGALRIEMERVYsERARLIEVG 785
Cdd:COG1200 642 DLLEAAREDAEELLEEDPELASHPALRRWLGLRF-RDEDYLEVG 684
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
107-779 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 876.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 107 STPIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGyTIISAVVS 186
Cdd:PRK10917 8 DAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKR-RRLTVTVS 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 187 DGFGQLLLKWF--NQDYILQKLRRDREYLIHGLAKGTPFGpMEMNSPEIEEIQGE---VPREILPVYSLTSGISMKMMRK 261
Cdd:PRK10917 87 DGTGNLTLRFFnfNQPYLKKQLKVGKRVAVYGKVKRGKYG-LEMVHPEYEVLEEEspeLEGRLTPVYPLTEGLKQKTLRK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 262 IVKRNLGLVRSLDDLVPSSITTERGLLPRKHAFTAIHFPKSLYEIRKARESLAYEEFFLFETTILfRKRQIRKEYQGLQK 341
Cdd:PRK10917 166 LIKQALELLDALPELLPEELLEKYGLLSLAEALRAIHFPPSDEDLHPARRRLKFEELFALQLSLL-LLRAGRRSKKAGPL 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 342 EISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAM 421
Cdd:PRK10917 245 PYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAE 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 422 QHYEKIKRELSPIGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLT 501
Cdd:PRK10917 325 QHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 502 TKGRLLDSLVMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILARKRLKDLYSYISDELKMGHQAFFIYPLIEES 581
Cdd:PRK10917 405 EKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEES 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 582 EQIDLKNATDEATKLREEvFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGM 661
Cdd:PRK10917 485 EKLDLQSAEETYEELQEA-FPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 662 AQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDR 741
Cdd:PRK10917 564 AQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRDE 643
|
650 660 670
....*....|....*....|....*....|....*...
gi 1491784557 742 DLLFKAREDAKQLMEEDPELLEHGALRIEMERVYSERA 779
Cdd:PRK10917 644 ELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
129-751 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 710.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 129 IETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGYTIISAVVSDGFGQLL-LKWFNQDYILQKLR 207
Cdd:TIGR00643 3 IHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLeLRFFNRAFLKKKFK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 208 RDREYLIHGLAKGTPFGPMEMNSP-EIEEIQGEVPREILPVYSLTSGISMKMMRKIVKRNLG-LVRSLDDLVPSSITTER 285
Cdd:TIGR00643 83 VGSKVVVYGKVKSSKFKAYLIHPEfISEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDqLDKSLEDPLPEELREKY 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 286 GLLPRKHAFTAIHFPKSLYEIRKARESLAYEEFFLFETTILFRKRQIRKEYQGLQKEISGVLSKRLIESLPFELTKDQVT 365
Cdd:TIGR00643 163 GLLSLEDALRAIHFPKTLSLLELARRRLIFDEFFYLQLAMLARRLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKR 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 366 AFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSL 445
Cdd:TIGR00643 243 VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 446 KKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLL---DSLVMTATPIPRTLA 522
Cdd:TIGR00643 323 KGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGftpHVLVMSATPIPRTLA 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 523 LTVYGDLDISTILTLPKGRSPVRTIILARKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATKLReEVFP 602
Cdd:TIGR00643 403 LTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLK-KAFP 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVM 682
Cdd:TIGR00643 482 KYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLL 561
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1491784557 683 VMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDRDLLFKAREDA 751
Cdd:TIGR00643 562 VYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAREDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
313-538 |
5.32e-115 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 347.21 E-value: 5.32e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 313 LAYEEFFLFETTILFRKRQIRKEyQGLQKEISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGK 392
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEEL-KGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 393 TLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALI 472
Cdd:cd17992 80 TVVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALI 159
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1491784557 473 QDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLLDSLVMTATPIPRTLALTVYGDLDISTILTLP 538
Cdd:cd17992 160 QEDVEFHNLGLVIIDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
353-728 |
2.10e-107 |
|
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: 350.12 E-value: 2.10e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELS 432
Cdd:TIGR00580 446 DSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFA 525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 433 PIGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLLDSLVM 512
Cdd:TIGR00580 526 NFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTL 605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 513 TATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILAR--KRLKDLysyISDELKMGHQAFFIYPLIEESEQIdlknat 590
Cdd:TIGR00580 606 SATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYdpELVREA---IRRELLRGGQVFYVHNRIESIEKL------ 676
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 591 deATKLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGR 670
Cdd:TIGR00580 677 --ATQLRELV-PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGR 753
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1491784557 671 VGRSNLKSICVMVM--NKAISDDALSRLR---EFASTSSGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:TIGR00580 754 VGRSKKKAYAYLLYphQKALTEDAQKRLEaiqEFSELGAGFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
109-270 |
2.89e-92 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 285.87 E-value: 2.89e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 109 PIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGYTIISAVVSDG 188
Cdd:pfam17191 1 PIKYAKGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETKKIGSLVIISAVLSDG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 189 FGQLLLKWFNQDYILQKLRRDREYLIHGLAKGTPFGPMEMNSPEIEEIQGEVPREILPVYSLTSGISMKMMRKIVKRNLG 268
Cdd:pfam17191 81 IGQVLLKWFNQEYIKKFLQKGKEVYITGTVKEGPFGPIEMNNPEIEEITGEQEREILPVYPLTEGISQKNMRKIVKENIS 160
|
..
gi 1491784557 269 LV 270
Cdd:pfam17191 161 YV 162
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
353-728 |
3.45e-92 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 312.77 E-value: 3.45e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTlvaELAM------VDNyeaGYQSALMVPTSVLAMQHYEK 426
Cdd:COG1197 581 AAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKT---EVALraafkaVMD---GKQVAVLVPTTLLAQQHYET 654
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 427 IKRELSPIGIETGLL----TgslkKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTT 502
Cdd:COG1197 655 FKERFAGFPVRVEVLsrfrT----AKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHKEKLKA 730
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 503 KGRLLDSLVMTATPIPRTL--ALTvyGDLDISTILTLPKGRSPVRTIILAR--KRLKDLysyISDELKMGHQAFFIYPLI 578
Cdd:COG1197 731 LRANVDVLTLTATPIPRTLqmSLS--GIRDLSIIATPPEDRLPVKTFVGEYddALIREA---ILRELLRGGQVFYVHNRV 805
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 579 EESEQIdlknatdeATKLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPER 658
Cdd:COG1197 806 EDIEKV--------AARLQELV-PEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERADR 876
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1491784557 659 FGMAQLHQLRGRVGRSNLKSICVMVM--NKAISDDALSRL---REFASTSSGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:COG1197 877 FGLAQLYQLRGRVGRSHRRAYAYLLYppDKVLTEDAEKRLeaiQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSG 951
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
353-728 |
1.98e-70 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 251.20 E-value: 1.98e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELS 432
Cdd:PRK10689 595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA 674
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 433 --PIGIEtgLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLLDSL 510
Cdd:PRK10689 675 nwPVRIE--MLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDIL 752
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 511 VMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILARKRLKdLYSYISDELKMGHQAFFIYPlieeseqiDLKNAT 590
Cdd:PRK10689 753 TLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLV-VREAILREILRGGQVYYLYN--------DVENIQ 823
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 591 DEATKLrEEVFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGR 670
Cdd:PRK10689 824 KAAERL-AELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGR 902
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1491784557 671 VGRSNLKSICVMVM--NKAISDDALSRLREFASTS---SGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:PRK10689 903 VGRSHHQAYAWLLTphPKAMTTDAQKRLEAIASLEdlgAGFALATHDLEIRGAGELLGEEQSG 965
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
349-536 |
9.77e-68 |
|
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: 222.06 E-value: 9.77e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 349 KRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 429 RELSPIGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLLD 508
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKELRPNVD 165
|
170 180
....*....|....*....|....*...
gi 1491784557 509 SLVMTATPIPRTLALTVYGDLDISTILT 536
Cdd:cd17991 166 VLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
351-534 |
3.19e-66 |
|
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: 217.67 E-value: 3.19e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 351 LIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRE 430
Cdd:cd17918 8 LCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 431 LSPIGIEtgLLTGSLKknEQDfvrmrlkKGEIDVVVGTHALIQDGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRlLDSL 510
Cdd:cd17918 88 LPFINVE--LVTGGTK--AQI-------LSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA-THFL 155
|
170 180
....*....|....*....|....
gi 1491784557 511 VMTATPIPRTLALTVYGDLDISTI 534
Cdd:cd17918 156 EATATPIPRTLALALSGLLDLSVI 179
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
543-701 |
8.42e-63 |
|
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: 207.58 E-value: 8.42e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 543 PVRTIILARKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATKLREEVFPGVGVELLHGRLNDNEKQEIM 622
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1491784557 623 QRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFAS 701
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
543-701 |
3.64e-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: 189.40 E-value: 3.64e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 543 PVRTIILARKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATKLREeVFPGVGVELLHGRLNDNEKQEIM 622
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKE-LVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 623 QRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVMN--KAISDDALSRLREFA 700
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPdpKKLTETAKKRLRAIA 159
|
.
gi 1491784557 701 S 701
Cdd:cd18792 160 E 160
|
|
| RecG_N |
pfam17190 |
RecG N-terminal helical domain; This four helical bundle domain is found at the N-terminus of ... |
2-89 |
8.27e-31 |
|
RecG N-terminal helical domain; This four helical bundle domain is found at the N-terminus of bacterial RecG proteins.
Pssm-ID: 407315 Cd Length: 89 Bit Score: 115.97 E-value: 8.27e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 2 LLEQFLEECERLLEAHLSGKREDNVL-PELKRFLSLLDRSELSYFSSLGEYLSKFISYLSRIDEFPHDRKVKRLKNGLEM 80
Cdd:pfam17190 1 LLEEFLDECEQLLKKVLNGKLKTNELiEEIKDNLSLLDDPLLENEEGLKEKLGQFLEYYKPIANLPPERAIKRLKNGLEM 80
|
....*....
gi 1491784557 81 IAKLRNFFL 89
Cdd:pfam17190 81 IEKLRYWFL 89
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
561-697 |
8.83e-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: 118.21 E-value: 8.83e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 561 ISDELKMGHQAFFIYPLIEESEQIdlknatdeATKLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVE 640
Cdd:cd18810 18 IERELLRGGQVFYVHNRIESIEKL--------ATQLRQLV-PEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIE 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1491784557 641 VGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVM--NKAISDDALSRLR 697
Cdd:cd18810 89 SGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYpdQKKLTEDALKRLE 147
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
351-541 |
2.55e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 107.19 E-value: 2.55e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 351 LIESLPFELTKDQVTAFEEIRDDMRaaspmNRLLQGDVGSGKTLVAELAMVDNY--EAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 429 RELSPIGIETGLLTGSLKKNEQdfvRMRLKKGEIDVVVGT-----HALIQDGVEFKNLGLVVVDEQHRFGVK-QRETLTT 502
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1491784557 503 KGRLLDS----LVMTATP---IPRTLALTVYGDLDISTILTLPKGR 541
Cdd:smart00487 153 LLKLLPKnvqlLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
360-522 |
2.35e-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: 103.09 E-value: 2.35e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 360 TKDQVTAFEEIRddmraaSPMNRLLQGDVGSGKTLVAELAM---VDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGI 436
Cdd:pfam00270 1 TPIQAEAIPAIL------EGRDVLVQAPTGSGKTLAFLLPAleaLDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 437 ETGLLTGSLKKNEQdfvRMRLKKgeIDVVVGTH----ALIQDGVEFKNLGLVVVDEQHRFGVK-QRETLTTKGRLLDS-- 509
Cdd:pfam00270 75 KVASLLGGDSRKEQ---LEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRLPKkr 149
|
170
....*....|....*
gi 1491784557 510 --LVMTATPiPRTLA 522
Cdd:pfam00270 150 qiLLLSATL-PRNLE 163
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
380-515 |
1.17e-18 |
|
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: 83.22 E-value: 1.17e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 380 MNRLLQGDVGSGKTLVAELAMVDNY-EAGYQSALMVPTSVLAMQHYEKIKRELSPiGIETGLLTGSLKKNEqdfvRMRLK 458
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLlKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEE----REKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 459 KGEIDVVVGTHALIQ------DGVEFKNLGLVVVDEQHRFGVKQRETLTTKGRLL-------DSLVMTAT 515
Cdd:cd00046 77 LGDADIIIATPDMLLnlllreDRLFLKDLKLIIVDEAHALLIDSRGALILDLAVRkaglknaQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
603-675 |
9.03e-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: 76.48 E-value: 9.03e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1491784557 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPErFGMAQLHQLRGRVGRSN 675
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
389-673 |
1.39e-16 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 83.41 E-value: 1.39e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGslkkneqDFVRMRLKKGEIDVVVGT 468
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTG-------DYDSDDEWLGRYDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 469 ----HALIQDGVEF-KNLGLVVVDEQHRFGVKQR----ETLTTK-----------------------GRLLDSLVMTAT- 515
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlEVLLARlrrlnpeaqivalsatignaeeiAEWLDAELVKSDw 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 516 -PIPRTLAL------------TVYGDLDISTIL-TLPKGRSpvrTIILA--RKRLKDLYSYISDELKMGHQAFFIYPLIE 579
Cdd:COG1204 201 rPVPLNEGVlydgvlrfddgsRRSKDPTLALALdLLEEGGQ---VLVFVssRRDAESLAKKLADELKRRLTPEEREELEE 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 580 ESEQI-DLKNATDEATKLREEVFPGVGVEllHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVIEHPER 658
Cdd:COG1204 278 LAEELlEVSEETHTNEKLADCLEKGVAFH--HAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRV-IIRDTKR 354
|
330 340
....*....|....*....|
gi 1491784557 659 FGMAQL-----HQLRGRVGR 673
Cdd:COG1204 355 GGMVPIpvlefKQMAGRAGR 374
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
603-673 |
2.03e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 2.03e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1491784557 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPeRFGMAQLHQLRGRVGR 673
Cdd:smart00490 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
279-653 |
1.50e-13 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 74.29 E-value: 1.50e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 279 SSITTERGLLPRKHAFTAIHFPKSLYEIRKARESLAYEEFFLFETTILFRKRQIRKEYQGLQKEISGVLSKRLIESLPFE 358
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 359 LTKDQVTAFEEIRDDMRAASPMNrLLQGDVGSGKTLVAELAMVDNYEAgyQSAL-MVPTSVLAMQHYEKIKRELSPIgie 437
Cdd:COG1061 81 LRPYQQEALEALLAALERGGGRG-LVVAPTGTGKTVLALALAAELLRG--KRVLvLVPRRELLEQWAEELRRFLGDP--- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 438 tglLTGSLKKNEQDfvrmrlkkgeiDVVVGTHALIQDGVEFKNL----GLVVVDEQHRFGVKQ----RETLTTKGRLLds 509
Cdd:COG1061 155 ---LAGGGKKDSDA-----------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSyrriLEAFPAAYRLG-- 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 510 lvMTATPIpRTLALTVYGDLDISTILTLPKGRspvrtiILARKRLKDLYSY-ISDELKMGHQAFFIYPLIEESEQIDLKN 588
Cdd:COG1061 219 --LTATPF-RSDGREILLFLFDGIVYEYSLKE------AIEDGYLAPPEYYgIRVDLTDERAEYDALSERLREALAADAE 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 589 ATDEA-TKLREE--------VF----------------PGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGI 643
Cdd:COG1061 290 RKDKIlRELLREhpddrktlVFcssvdhaealaellneAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGV 369
|
410
....*....|
gi 1491784557 644 DIPTATVMVI 653
Cdd:COG1061 370 DVPRLDVAIL 379
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
351-673 |
9.47e-13 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 71.84 E-value: 9.47e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 351 LIESLPFELTKDQVTAFEEIRDDMraaspmNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRe 430
Cdd:PRK01172 15 LFTGNDFELYDHQRMAIEQLRKGE------NVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELSR- 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 431 LSPIGIETGLLTGSLkKNEQDFVRmrlkkgEIDVVVGTHA-----LIQDGVEFKNLGLVVVDEQHRFGVKQR----ETLT 501
Cdd:PRK01172 88 LRSLGMRVKISIGDY-DDPPDFIK------RYDVVILTSEkadslIHHDPYIINDVGLIVADEIHIIGDEDRgptlETVL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 502 TKGRLLDslvmtatPIPRTLAL--TVYGDLDISTILTLPKGRS-----PVRTIILARKRL---------KDLYSYISDEL 565
Cdd:PRK01172 161 SSARYVN-------PDARILALsaTVSNANELAQWLNASLIKSnfrpvPLKLGILYRKRLildgyersqVDINSLIKETV 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 566 KMGHQAFFIYPLIEESEQI------------DLKNATDEATKLRE---EVFPGvGVELLHGRLNDNEKQEIMQRFRSRQS 630
Cdd:PRK01172 234 NDGGQVLVFVSSRKNAEDYaemliqhfpefnDFKVSSENNNVYDDslnEMLPH-GVAFHHAGLSNEQRRFIEEMFRNRYI 312
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 1491784557 631 MILVSTTVVEVGIDIPtATVMVIEHPERFGMA--------QLHQLRGRVGR 673
Cdd:PRK01172 313 KVIVATPTLAAGVNLP-ARLVIVRDITRYGNGgirylsnmEIKQMIGRAGR 362
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
483-674 |
5.04e-12 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 68.75 E-value: 5.04e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 483 LVVVDE----------QHRFGVKQreTLTTKGRLLdslVMTATPiPRTL-ALTVYGDLDISTILTLPKGRS-PV-RTII- 548
Cdd:COG4098 219 LLIIDEvdafpysgdpMLQYAVKR--ARKPDGKLI---YLTATP-SKALqRQVKRGKLKVVKLPARYHGHPlPVpKFKWl 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 549 ------LARKRLKD-LYSYISDELKMGHQAFFIYPLIEESEQidlknatdeATKLREEVFPGVGVELLHGRlnDNEKQEI 621
Cdd:COG4098 293 gnwkkrLRRGKLPRkLLKWLKKRLKEGRQLLIFVPTIELLEQ---------LVALLQKLFPEERIAGVHAE--DPERKEK 361
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1491784557 622 MQRFRSRQSMILVSTTVVEVGIDIPTATVMVI--EHPeRFGMAQLHQLRGRVGRS 674
Cdd:COG4098 362 VQAFRDGEIPILVTTTILERGVTFPNVDVAVLgaDHP-VFTEAALVQIAGRVGRS 415
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
389-497 |
3.59e-11 |
|
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: 62.66 E-value: 3.59e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNeqdfvrmRLKKGEIDVVVG 467
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVN-------KLLLAEADILVA 99
|
90 100 110
....*....|....*....|....*....|....*.
gi 1491784557 468 T----HALIQDGVE--FKNLGLVVVDEQHRFGVKQR 497
Cdd:cd17921 100 TpeklDLLLRNGGErlIQDVRLVVVDEAHLIGDGER 135
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
702-761 |
4.73e-11 |
|
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 59.41 E-value: 4.73e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1491784557 702 TSSGFDVAELDLRLRGPGEFLGLRQHGMPQFL-IGDIVNDRDLLFKAREDAKQLMEEDPEL 761
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAFDLkIADIARDGQLLQLARTEAEEIIDNDPEC 61
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
381-507 |
5.03e-11 |
|
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: 62.35 E-value: 5.03e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 381 NRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKReLSPIGIETGLLTGslkkneqDFVRMRLKKG 460
Cdd:cd18028 19 NLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-LEEIGLKVGISTG-------DYDEDDEWLG 90
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1491784557 461 EIDVVVGTH----ALIQDGVEF-KNLGLVVVDEQHRFGVKQR----ETLTTKGRLL 507
Cdd:cd18028 91 DYDIIVATYekfdSLLRHSPSWlRDVGVVVVDEIHLISDEERgptlESIVARLRRL 146
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
363-498 |
1.26e-10 |
|
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: 61.07 E-value: 1.26e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 363 QVTAFEEIRDDMRAASPMnrLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRElspIGIETGLLT 442
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKR---FGDKVAVLH 75
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 1491784557 443 GSLKKNEQDFVRMRLKKGEIDVVVGTH-ALIqdgVEFKNLGLVVVDEQHRFGVKQRE 498
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEHDSSYKQDS 129
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
383-673 |
1.54e-08 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 57.46 E-value: 1.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 383 LLQG-DV------GSGKT---LVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNEQd 451
Cdd:COG0513 36 ILAGrDVlgqaqtGTGKTaafLLPLLQRLDPSRPRAPQALiLAPTRELALQVAEELRKLAKYLGLRVATVYGGVSIGRQ- 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 452 fvRMRLKKGeIDVVVGT----HALIQDG-VEFKNLGLVVVDEQHRfgvkqretlttkgrLLD-------SLVMTATPIPR 519
Cdd:COG0513 115 --IRALKRG-VDIVVATpgrlLDLIERGaLDLSGVETLVLDEADR--------------MLDmgfiediERILKLLPKER 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 520 tlaltvygdldiSTIL---TLPKgrsPVRTiiLARKRLKD--LYSYISDEL---KMGHQAFFIYP---------LIEEsE 582
Cdd:COG0513 178 ------------QTLLfsaTMPP---EIRK--LAKRYLKNpvRIEVAPENAtaeTIEQRYYLVDKrdklellrrLLRD-E 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 583 QIDL-------KNATDE-ATKLREEvfpGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATvMVI- 653
Cdd:COG0513 240 DPERaivfcntKRGADRlAEKLQKR---GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVS-HVIn 315
|
330 340
....*....|....*....|....*
gi 1491784557 654 ----EHPERFgmaqLHqlR-GRVGR 673
Cdd:COG0513 316 ydlpEDPEDY----VH--RiGRTGR 334
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
363-490 |
3.67e-08 |
|
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: 54.19 E-value: 3.67e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 363 QVTAFEEIRDDmraaspmNRLLQGDVGSGKTLVAELAM----VDNYEAGY---QSALMVPTSVLAMQHYEKIKRELspiG 435
Cdd:cd18034 7 QLELFEAALKR-------NTIVVLPTGSGKTLIAVMLIkemgELNRKEKNpkkRAVFLVPTVPLVAQQAEAIRSHT---D 76
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 436 IETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGT-----HALIQDGVEFKNLGLVVVDEQH 490
Cdd:cd18034 77 LKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTaqillDALRHGFLSLSDINLLIFDECH 136
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
390-490 |
1.72e-07 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 54.90 E-value: 1.72e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 390 SGKTLVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPiGIETGLLTGS--LKKNEQDFVRmrlkkgEIDVVV 466
Cdd:COG1202 236 TGKTLIGELAGIKNALEGKGKMLfLVPLVALANQKYEDFKDRYGD-GLDVSIRVGAsrIRDDGTRFDP------NADIIV 308
|
90 100
....*....|....*....|....*...
gi 1491784557 467 GTHA----LIQDGVEFKNLGLVVVDEQH 490
Cdd:COG1202 309 GTYEgidhALRTGRDLGDIGTVVIDEVH 336
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
356-498 |
2.38e-07 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 54.39 E-value: 2.38e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 356 PFELTKDQVTAFEEIRDDMR-AASpmnrLLQGDVGSGKT-----LVAE-LAmvdnyeAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:PRK05580 142 PPTLNPEQAAAVEAIRAAAGfSPF----LLDGVTGSGKTevylqAIAEvLA------QGKQALVLVPEIALTPQMLARFR 211
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1491784557 429 RELspiGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTH-ALIqdgVEFKNLGLVVVDEQHRFGVKQRE 498
Cdd:PRK05580 212 ARF---GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARsALF---LPFKNLGLIIVDEEHDSSYKQQE 276
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
356-490 |
3.02e-07 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 53.97 E-value: 3.02e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 356 PFELTKDQVTAFEEIRDDMRAASPMnrLLQGDVGSGKT-----LVAE-LAmvdnyeAGYQSALMVPTSVLAMQHYEKIKR 429
Cdd:COG1198 193 PPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTevylqAIAEvLA------QGKQALVLVPEIALTPQTVERFRA 264
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1491784557 430 ELspiGIETGLLTGSLKKNEQDFVRMRLKKGEIDVVVGTH-ALIqdgVEFKNLGLVVVDEQH 490
Cdd:COG1198 265 RF---GARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
390-490 |
4.73e-07 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 53.42 E-value: 4.73e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 390 SGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKReLSPIGIETGLLTGSLKKNEQdfvrmRLkkGEIDVVVGTH 469
Cdd:PRK02362 50 SGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFER-FEELGVRVGISTGDYDSRDE-----WL--GDNDIIVATS 121
|
90 100
....*....|....*....|....*.
gi 1491784557 470 ----ALIQDGVEF-KNLGLVVVDEQH 490
Cdd:PRK02362 122 ekvdSLLRNGAPWlDDITCVVVDEVH 147
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
389-645 |
5.77e-07 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 52.78 E-value: 5.77e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGYQS----ALmvPTSVLAMQHYEKIKRELSP-IGIETGLLTGSLKKNEQDF------VRMRL 457
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGRriiyAL--PFTSIINQTYDRLRDLFGEdVLLHHSLADLDLLEEEEEYesearwLKLLK 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 458 KKGEIDVVVGT-----HALI--QDGVEFKNLGL----VVVDEQHRFGVKQRETLTtkgRLLDSL--------VMTATpIP 518
Cdd:COG1203 235 ELWDAPVVVTTidqlfESLFsnRKGQERRLHNLansvIILDEVQAYPPYMLALLL---RLLEWLknlggsviLMTAT-LP 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 519 rtlALTVYGDLDISTILTLPKGRSPVRTIILARKRLK---------DLYSYISDELKMGHQAFFIYPLIEESEQIdlkna 589
Cdd:COG1203 311 ---PLLREELLEAYELIPDEPEELPEYFRAFVRKRVElkegplsdeELAELILEALHKGKSVLVIVNTVKDAQEL----- 382
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 590 tdeATKLREEvFPGVGVELLHGRLNDNEK----QEIMQRFRSRQSMILVSTTVVEVGIDI 645
Cdd:COG1203 383 ---YEALKEK-LPDEEVYLLHSRFCPADRseieKEIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
163-234 |
1.95e-06 |
|
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: 46.03 E-value: 1.95e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1491784557 163 VKGRLLNFSAKKASGYTIISAVVSDGFGQLLLKWFN-QDYILQKLRRDREYLIHGLAKGTPFGPmEMNSPEIE 234
Cdd:cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNfQPYLKKQLPPGTRVRVSGKVKRFRGGL-QIVHPEYE 73
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
389-516 |
2.08e-06 |
|
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: 48.07 E-value: 2.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGyqSALMVPTSVLAMQHYEKIKRELSPIGIetGLLTGSLKKneqdfvrmrlKKGEIDVVVGT 468
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFEDFLGDSSI--GLIGGGKKK----------DFDDANVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1491784557 469 -HALIQDGVE----FKNLGLVVVDEQHRFGVKQ-RETLTtkgRLLDSLVM--TATP 516
Cdd:cd17926 94 yQSLSNLAEEekdlFDQFGLLIVDEAHHLPAKTfSEILK---ELNAKYRLglTATP 146
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
381-673 |
2.10e-06 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 51.36 E-value: 2.10e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 381 NRLLQGDVGSGKTLVAELAMVDN-YEAGYQSALMVPTSVLAMQHYEKIKrELSPIGIETGLLTGSLKKNEQDFvrmrlkk 459
Cdd:PRK00254 41 NLVLAIPTASGKTLVAEIVMVNKlLREGGKAVYLVPLKALAEEKYREFK-DWEKLGLRVAMTTGDYDSTDEWL------- 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 460 GEIDVVVGT----HALIQDGVEF-KNLGLVVVDEQHRFGVKQREtlTTKGRLLDSLVMTATPIprTLALTVYGDLDISTI 534
Cdd:PRK00254 113 GKYDIIIATaekfDSLLRHGSSWiKDVKLVVADEIHLIGSYDRG--ATLEMILTHMLGRAQIL--GLSATVGNAEELAEW 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 535 LTLPKGRSPVRTIILAR----------------KRLKDLYSYISDELKMGHQAFF------------------IYPLIEE 580
Cdd:PRK00254 189 LNAELVVSDWRPVKLRKgvfyqgflfwedgkieRFPNSWESLVYDAVKKGKGALVfvntrrsaekealelakkIKRFLTK 268
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 581 SEQIDLK--------NATDEatKLREEVFPGVGVEllHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMV 652
Cdd:PRK00254 269 PELRALKeladsleeNPTNE--KLKKALRGGVAFH--HAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVII 344
|
330 340
....*....|....*....|....*...
gi 1491784557 653 --IEHPERFGMA-----QLHQLRGRVGR 673
Cdd:PRK00254 345 rdTKRYSNFGWEdipvlEIQQMMGRAGR 372
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
382-540 |
2.17e-06 |
|
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: 48.86 E-value: 2.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 382 RLLQGD-------VGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLT--GSLKKNEQDF 452
Cdd:cd17924 28 RLLRGKsfaiiapTGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILVyhSRLKKKEKEE 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 453 VRMRLKKGEIDVVVGTHALIQDGVEF---KNLGLVVVDEqhrfgvkqretlttkgrlLDSLVMTATPIPRTLALTVYGDL 529
Cdd:cd17924 108 LLEKIEKGDFDILVTTNQFLSKNFDLlsnKKFDFVFVDD------------------VDAVLKSSKNIDRLLKLLGFGQL 169
|
170
....*....|.
gi 1491784557 530 DISTILTLPKG 540
Cdd:cd17924 170 VVSSATGRPRG 180
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
632-673 |
3.01e-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: 45.77 E-value: 3.01e-06
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1491784557 632 ILVSTTVVEVGIDIPTATVMVIEHPERFgMAQLHQLRGRVGR 673
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGR 65
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
587-673 |
3.79e-06 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 46.73 E-value: 3.79e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 587 KNATDE-ATKLREEvfpGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVI-----EHPERFg 660
Cdd:cd18787 37 KKRVDRlAELLEEL---GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDH-VInydlpRDAEDY- 111
|
90
....*....|....
gi 1491784557 661 maqLHqlR-GRVGR 673
Cdd:cd18787 112 ---VH--RiGRTGR 120
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
383-488 |
5.11e-06 |
|
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: 47.82 E-value: 5.11e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 383 LLQG-DV------GSGKTL------VAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKN 448
Cdd:cd00268 24 ILSGrDVigqaqtGSGKTLafllpiLEKLLPEPKKKGRGPQALvLAPTRELAMQIAEVARKLGKGTGLKVAAIYGGAPIK 103
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1491784557 449 EQdfvRMRLKKGeIDVVVGT----HALIQDG-VEFKNLGLVVVDE 488
Cdd:cd00268 104 KQ---IEALKKG-PDIVVGTpgrlLDLIERGkLDLSNVKYLVLDE 144
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
389-515 |
1.29e-05 |
|
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region.
Pssm-ID: 350784 [Multi-domain] Cd Length: 202 Bit Score: 46.83 E-value: 1.29e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQhyEKIkRELSPIGIETGLL----TGSLKKneqdfvRMRLKKGEIDV 464
Cdd:cd18026 43 SGGKTLVAEILMLKRLLERRKKALFVLPYVSIVQ--EKV-DALSPLFEELGFRvegyAGNKGR------SPPKRRKSLSV 113
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491784557 465 VVGT----HALIQDGVEFK---NLGLVVVDEQHRFGVKQR----ETLTTKGRLLDS----LV-MTAT 515
Cdd:cd18026 114 AVCTiekaNSLVNSLIEEGrldELGLVVVDELHMLGDGHRgallELLLTKLLYAAQkniqIVgMSAT 180
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
610-693 |
2.07e-05 |
|
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];
Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 48.29 E-value: 2.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 610 HGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPT--ATVMViehperfG----MAQLHQLRGRVGRSNLKSICVMV 683
Cdd:COG1205 325 RAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGldAVVLA-------GypgtRASFWQQAGRAGRRGQDSLVVLV 397
|
90
....*....|
gi 1491784557 684 MnkaiSDDAL 693
Cdd:COG1205 398 A----GDDPL 403
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
611-683 |
2.10e-05 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350184 [Multi-domain] Cd Length: 146 Bit Score: 44.94 E-value: 2.10e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1491784557 611 GRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPT--ATVMViEHPerFGMAQLHQLRGRVGRSNLKSICVMV 683
Cdd:cd18797 74 AGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGldAVVLA-GYP--GSLASLWQQAGRAGRRGKDSLVILV 145
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
161-236 |
1.06e-04 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 41.07 E-value: 1.06e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491784557 161 VSVKGRLLNfsaKKASGYTIISAVVSDGFGQLLLKWFNQDY--ILQKLRRDREYLIHGLAKGTPFGPMEMNSPEIEEI 236
Cdd:pfam01336 1 VTVAGRVTS---IRRSGGKLLFLTLRDGTGSIQVVVFKEEAekLAKKLKEGDVVRVTGKVKKRKGGELELVVEEIELL 75
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
389-524 |
1.83e-04 |
|
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: 43.19 E-value: 1.83e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAM---VDNYEAGYQS--ALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGslkkNEQDFVRMRLKKGEID 463
Cdd:cd17927 27 GSGKTFVAVLICehhLKKFPAGRKGkvVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSG----DTSENVSVEQIVESSD 102
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491784557 464 VVVGTHALIQD------GVEFKNLGLVVVDEQHRfGVKQRETLTTKGRLLDSLVMTATPIPRTLALT 524
Cdd:cd17927 103 VIIVTPQILVNdlksgtIVSLSDFSLLVFDECHN-TTKNHPYNEIMFRYLDQKLGSSGPLPQILGLT 168
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
389-491 |
2.63e-04 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 44.34 E-value: 2.63e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMVDNYEAGYQSALMV-PTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNEqdfvRMRLKKgEIDVVVG 467
Cdd:COG1111 27 GLGKTAVALLVIAERLHKKGGKVLFLaPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEK----RKELWE-KARIIVA 101
|
90 100
....*....|....*....|....*....
gi 1491784557 468 T-----HALIQDGVEFKNLGLVVVDEQHR 491
Cdd:COG1111 102 TpqvieNDLIAGRIDLDDVSLLIFDEAHR 130
|
|
| DEADc_DDX23 |
cd17945 |
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ... |
389-491 |
4.43e-04 |
|
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, 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: 350703 [Multi-domain] Cd Length: 220 Bit Score: 42.31 E-value: 4.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTL---------VAELAMVDNY--EAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNEQDFvrmRL 457
Cdd:cd17945 37 GSGKTAaflipllvyISRLPPLDEEtkDDGPYALILAPTRELAQQIEEETQKFAKPLGIRVVSIVGGHSIEEQAF---SL 113
|
90 100 110
....*....|....*....|....*....|....*....
gi 1491784557 458 KKGeIDVVVGTHALIQDGVEFKNLGL-----VVVDEQHR 491
Cdd:cd17945 114 RNG-CEILIATPGRLLDCLERRLLVLnqctyVVLDEADR 151
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
389-443 |
1.04e-03 |
|
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 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: 350781 [Multi-domain] Cd Length: 206 Bit Score: 41.19 E-value: 1.04e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1491784557 389 GSGKTLVAELAMV-------DNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTG 443
Cdd:cd18023 27 GSGKTVLFELAILrllkernPLPWGNRKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTG 88
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
613-684 |
1.12e-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: 39.88 E-value: 1.12e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1491784557 613 LNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMViehpeRFG----MAQLHQLRGRVGRSNlkSICVMVM 684
Cdd:cd18802 74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDlpktLRSYIQSRGRARAPN--SKYILMV 142
|
|
| DEADc_DDX1 |
cd17938 |
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
386-492 |
1.17e-03 |
|
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, 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: 350696 [Multi-domain] Cd Length: 204 Bit Score: 41.15 E-value: 1.17e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 386 GDV------GSGKTLVAELAMVDNYeagyQSALMVPTSVLAMQHYEKI---KRELSPIGIETGLLTGSLKKNEQdfvrMR 456
Cdd:cd17938 37 GDVlmaaetGSGKTGAFCLPVLQIV----VALILEPSRELAEQTYNCIenfKKYLDNPKLRVALLIGGVKAREQ----LK 108
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1491784557 457 LKKGEIDVVVGT----HALIQDG-VEFKNLGLVVVDEQHRF 492
Cdd:cd17938 109 RLESGVDIVVGTpgrlEDLIKTGkLDLSSVRFFVLDEADRL 149
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
357-517 |
1.70e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 39.96 E-value: 1.70e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 357 FELTKDQVTAFEEIRDdMRAASPMNRLLQGDVGSGKTLVAeLAMVDNY--EAGYQSALM-VPTSVLAMQHYEKIKRELSP 433
Cdd:pfam04851 2 LELRPYQIEAIENLLE-SIKNGQKRGLIVMATGSGKTLTA-AKLIARLfkKGPIKKVLFlVPRKDLLEQALEEFKKFLPN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 434 IGIETGLLTGSLKKNEQDfvrmrlkkgEIDVVVGT-HALIQDGVEFKNL------GLVVVDEQHRFGVKQREtlttkgRL 506
Cdd:pfam04851 80 YVEIGEIISGDKKDESVD---------DNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGASSYR------NI 144
|
170
....*....|....*..
gi 1491784557 507 LDS------LVMTATPI 517
Cdd:pfam04851 145 LEYfkpaflLGLTATPE 161
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
483-679 |
1.75e-03 |
|
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: 41.26 E-value: 1.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 483 LVVVDEQHRFGVKQRETLTTKGRLLDS-----LVMTATpIP---RTLALTVygDLDISTILTLPKGRSPVRTIILARKRL 554
Cdd:cd09639 126 LLIFDEVHFYDEYTLALILAVLEVLKDndvpiLLMSAT-LPkflKEYAEKI--GYVEENEPLDLKPNERAPFIKIESDKV 202
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 555 KDLYSY--ISDELKMGHQAFFIYPLIEESEQIDLKnatdeatkLREEVfPGVGVELLHGR--LNDNEKQE--IMQRFRSR 628
Cdd:cd09639 203 GEISSLerLLEFIKKGGSVAIIVNTVDRAQEFYQQ--------LKEKG-PEEEIMLIHSRftEKDRAKKEaeLLLEFKKS 273
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1491784557 629 QSMILVSTTVVEVGIDIpTATVMVIEHperfgmAQLHQLRGRVGRSNLKSI 679
Cdd:cd09639 274 EKFVIVATQVIEASLDI-SVDVMITEL------APIDSLIQRLGRLHRYGE 317
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
605-653 |
2.45e-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: 39.15 E-value: 2.45e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1491784557 605 GVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVI 653
Cdd:cd18789 70 LKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| DEADc_DDX24 |
cd17946 |
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ... |
389-491 |
5.14e-03 |
|
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 is a member of the DEAD-box helicases, 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: 350704 [Multi-domain] Cd Length: 235 Bit Score: 39.14 E-value: 5.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKTLVAELAMV-----------DNYEAGYQSALMV-PTSVLAMQHYEKIKRELSPIGIETGLLTGSLKKNEQDfvRMR 456
Cdd:cd17946 38 GSGKTLAFGIPILerllsqkssngVGGKQKPLRALILtPTRELAVQVKDHLKAIAKYTNIKIASIVGGLAVQKQE--RLL 115
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1491784557 457 LKKGEIdvVVGTH----ALIQDG----VEFKNLGLVVVDEQHR 491
Cdd:cd17946 116 KKRPEI--VVATPgrlwELIQEGnehlANLKSLRFLVLDEADR 156
|
|
| DEADc_DDX6 |
cd17940 |
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ... |
389-488 |
5.64e-03 |
|
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, 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: 350698 [Multi-domain] Cd Length: 201 Bit Score: 38.82 E-value: 5.64e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 389 GSGKT---LVAELAMVDNYEAGYQSALMVPTSVLAMQhYEKIKRELSP-IGIETGLLTG--SLKKNeqdfvRMRLKKGeI 462
Cdd:cd17940 46 GTGKTgayLIPILEKIDPKKDVIQALILVPTRELALQ-TSQVCKELGKhMGVKVMVTTGgtSLRDD-----IMRLYQT-V 118
|
90 100 110
....*....|....*....|....*....|.
gi 1491784557 463 DVVVGTHALIQDGVE-----FKNLGLVVVDE 488
Cdd:cd17940 119 HVLVGTPGRILDLAKkgvadLSHCKTLVLDE 149
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
604-673 |
7.15e-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: 37.92 E-value: 7.15e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491784557 604 VGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVIEHPERFG--------MAQLHQLRGRVGR 673
Cdd:cd18795 64 AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTV-IIKGTQRYDgkgyrelsPLEYLQMIGRAGR 140
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
305-518 |
8.10e-03 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 39.82 E-value: 8.10e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 305 EIRKARESLAYEEFFLFETTILFRKRQIRKEYQGLQKEISGVLskrliesLPFeltkdQVTAFEEIRDDMRAAspMNRLL 384
Cdd:COG0553 200 ELLLLLELLLELELLAEAAVDAFRLRRLREALESLPAGLKATL-------RPY-----QLEGAAWLLFLRRLG--LGGLL 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 385 QGDVGSGKTLVAELAMVDNYEAGYQS-ALMV-PTSVLamqhyEKIKRELS---PiGIETGLLTGSLKkneqdfvRMRLKK 459
Cdd:COG0553 266 ADDMGLGKTIQALALLLELKERGLARpVLIVaPTSLV-----GNWQRELAkfaP-GLRVLVLDGTRE-------RAKGAN 332
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491784557 460 --GEIDVVVGTHALI-QDGVEFKNL--GLVVVDEQHRfgVKQRETLTTK-GRLLDS---LVMTATPIP 518
Cdd:COG0553 333 pfEDADLVITSYGLLrRDIELLAAVdwDLVILDEAQH--IKNPATKRAKaVRALKArhrLALTGTPVE 398
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
593-698 |
8.17e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 39.42 E-value: 8.17e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 593 ATKLREEVFPgvgVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATvMVIEH-----PERFgmaqLHQL 667
Cdd:PTZ00424 284 TKKMHERDFT---VSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVS-LVINYdlpasPENY----IHRI 355
|
90 100 110
....*....|....*....|....*....|.
gi 1491784557 668 rGRVGRSNLKSICVmvmnKAISDDALSRLRE 698
Cdd:PTZ00424 356 -GRSGRFGRKGVAI----NFVTPDDIEQLKE 381
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
595-674 |
8.72e-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: 8.72e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491784557 595 KLREEVFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDI-PTATVMVIEHPerFGMAQLHQlrgRVGR 673
Cdd:cd18796 60 ELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIgDVDLVIQIGSP--KSVARLLQ---RLGR 134
|
.
gi 1491784557 674 S 674
Cdd:cd18796 135 S 135
|
|
| |
