|
Name |
Accession |
Description |
Interval |
E-value |
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
75-660 |
1.93e-119 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 389.25 E-value: 1.93e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 75 LPKAVLEKYHSFGVRKMFEWQAECLLLGhVLEGKNLVYSAPTSAGKTLVAELLILKRVLEtRKKALFILPFVSVAKEKKC 154
Cdd:COG1204 7 PLEKVIEFLKERGIEELYPPQAEALEAG-LLEGKNLVVSAPTASGKTLIAELAILKALLN-GGKALYIVPLRALASEKYR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 155 YLQSLFQEVGLKVDGYMGS-TSPTGQFSSLDIAVCTIERANGLVNRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLL 233
Cdd:COG1204 85 EFKRDFEELGIKVGVSTGDyDSDDEWLGRYDILVATPEKLDSLLRN--GPSWLRDVDLVVVDEAHLIDDESRGPTLEVLL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 234 TKIcyvtrksashqaesaSTLSNAVQIVGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKIGNSIYdssmklvreFQ 313
Cdd:COG1204 163 ARL---------------RRLNPEAQIVALSATIGNAEEIAEWLDAELVKSDWRPVPLNEGVLYDGVLR---------FD 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 314 PLLQVKGDEdhIVSLCYETIQDNHSVLIFCPSKKWCEKVADIIAREFYNLHHQPEglvkssefppvildQKSLLEVMDQL 393
Cdd:COG1204 219 DGSRRSKDP--TLALALDLLEEGGQVLVFVSSRRDAESLAKKLADELKRRLTPEE--------------REELEELAEEL 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 394 KR--SPSGLDSVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTP-IFSGQPLDI 470
Cdd:COG1204 283 LEvsEETHTNEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTkRGGMVPIPV 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 471 LTYKQMVGRAGRKGVDTMGESILVCKNSEKSKGIA--LLQGSLEPVHSCLqrqgEVTASMIRAILEIIVGGVASTSQDMQ 548
Cdd:COG1204 363 LEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELFerYILGEPEPIRSKL----ANESALRTHLLALIASGFANSREELL 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 549 TYAACTFLaaAIQEGKQGMQRnqddaqlgAIDACVTWLLENEFIQvaepgdgTGGKVYHPTHLGSATLSSSLSPtDTLDI 628
Cdd:COG1204 439 DFLENTFY--AYQYDKGDLEE--------VVDDALEFLLENGFIE-------EDGDRLRATKLGKLVSRLYIDP-LTAAE 500
|
570 580 590
....*....|....*....|....*....|..
gi 568996594 629 FADLQRAMKGFVleNDLHIVYLVTpVFEDWIS 660
Cdd:COG1204 501 LVDGLRKADEEF--TDLGLLHLIL-ILRDWIN 529
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
75-288 |
1.60e-108 |
|
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: 344.20 E-value: 1.60e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 75 LPKAVLEKYHSFGVRKMFEWQAECLLLGHVLEGKNLVYSAPTSAGKTLVAELLILKRVLETRKKALFILPFVSVAKEKKC 154
Cdd:cd18026 1 LPDAVREAYAKKGIKKLYDWQKECLSLPGLLEGRNLVYSLPTSGGKTLVAEILMLKRLLERRKKALFVLPYVSIVQEKVD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 155 YLQSLFQEVGLKVDGYMGS--TSPTGQFSSLDIAVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELL 232
Cdd:cd18026 81 ALSPLFEELGFRVEGYAGNkgRSPPKRRKSLSVAVCTIEKANSLVNSLIEEGRLDELGLVVVDELHMLGDGHRGALLELL 160
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 568996594 233 LTKICYVTRKSashqaesastlsnaVQIVGMSATLPNLQLVASWLNAELYHTDFRP 288
Cdd:cd18026 161 LTKLLYAAQKN--------------IQIVGMSATLPNLEELASWLRAELYTTNFRP 202
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
75-830 |
1.41e-96 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 330.38 E-value: 1.41e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 75 LPKAVLEKYHSFGVRKMFEWQAECLLLGhVLEGKNLVYSAPTSAGKTLVAELLILKRVLETrKKALFILPFVSVAKEKKC 154
Cdd:PRK02362 8 LPEGVIEFYEAEGIEELYPPQAEAVEAG-LLDGKNLLAAIPTASGKTLIAELAMLKAIARG-GKALYIVPLRALASEKFE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 155 YLQSlFQEVGLKV----------DGYMGSTsptgqfsslDIAVCTIERANGLVnrlieENK---MDLLGMVVVDELHMLG 221
Cdd:PRK02362 86 EFER-FEELGVRVgistgdydsrDEWLGDN---------DIIVATSEKVDSLL-----RNGapwLDDITCVVVDEVHLID 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 222 DSHRGYLLELLLTKIcyvtRKsashqaesastLSNAVQIVGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKIGNSI 301
Cdd:PRK02362 151 SANRGPTLEVTLAKL----RR-----------LNPDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAI 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 302 -YDSSMKLVRefqpllQVKGDEDhiVSLCYETIQDNHSVLIFCPSKKWCE----KVADIIAREFYNLhhqpeglvkssef 376
Cdd:PRK02362 216 hFDDSQREVE------VPSKDDT--LNLVLDTLEEGGQCLVFVSSRRNAEgfakRAASALKKTLTAA------------- 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 377 ppvilDQKSLLEVMDQLKR-SPSGLDSVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARR 455
Cdd:PRK02362 275 -----ERAELAELAEEIREvSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARR 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 456 VIIR-----TPIFSGQPLDILTYKQMVGRAGRKGVDTMGESILVCKNSEKSKgiALLQ----GSLEPVHSCLQRQGEvta 526
Cdd:PRK02362 350 VIIRdyrryDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYDELD--ELFEryiwADPEDVRSKLATEPA--- 424
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 527 smIRA-ILEIIVGGVASTSQDMQTYAACTFLAAaiqegkqgmQRNQDDAQLGAIDACVTWLLENEFIQvaEPGDgtggkV 605
Cdd:PRK02362 425 --LRThVLSTIASGFARTRDGLLEFLEATFYAT---------QTDDTGRLERVVDDVLDFLERNGMIE--EDGE-----T 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 606 YHPTHLGSATLSSSLSPTDTLDIfADLQRAMKGFVLENDLHIVyLVTP-VFEDWI-SID--WYRFFC------LWEKLPT 675
Cdd:PRK02362 487 LEATELGHLVSRLYIDPLSAAEI-IDGLEAAKKPTDLGLLHLV-CSTPdMYELYLrSGDyeWLNEYLyehedeLLGDVPS 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 676 SMKRVAelvgvEEGFLaRCVKgkvvarterqhrqmaihkrffTSLVLLDLISEIPLKDINQKYGCNRGQIQSLQQSAAVY 755
Cdd:PRK02362 565 EFEDDE-----FEDFL-SAVK---------------------TALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWL 617
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568996594 756 AGMITVFSNRLGWHnMELLLSQFQKRLTFGIQRELCDLIRVSLLNAQRARFLYASGFLTVADLARADSAEVEVAL 830
Cdd:PRK02362 618 LHAAERLASELDLD-LARAARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAIL 691
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
77-826 |
2.75e-76 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 270.15 E-value: 2.75e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 77 KAVLEKYhsfGVRKMFEWQAECLLLGhVLEGKNLVYSAPTSAGKTLVAELLILKRVLETRKKALFILPFVSVAKEKKCYL 156
Cdd:PRK00254 13 KRVLKER---GIEELYPPQAEALKSG-VLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREF 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 157 QSlFQEVGLKVDGYMGSTSPTGQF-SSLDIAVCTIERANGLV---NRLIEENKMdllgmVVVDELHMLGDSHRGYLLELL 232
Cdd:PRK00254 89 KD-WEKLGLRVAMTTGDYDSTDEWlGKYDIIIATAEKFDSLLrhgSSWIKDVKL-----VVADEIHLIGSYDRGATLEMI 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 233 LTKicyvtrksashqaesastLSNAVQIVGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKIGNSIYDSSMKLVREf 312
Cdd:PRK00254 163 LTH------------------MLGRAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERF- 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 313 qpllqvkgdEDHIVSLCYETIQDNHSVLIFCPSKKWCEKVADIIAREFYNLHHQPEglvkssefppvildQKSLLEVMDQ 392
Cdd:PRK00254 224 ---------PNSWESLVYDAVKKGKGALVFVNTRRSAEKEALELAKKIKRFLTKPE--------------LRALKELADS 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 393 LKRSPSglDSVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIR-TPIFSG---QPL 468
Cdd:PRK00254 281 LEENPT--NEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRdTKRYSNfgwEDI 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 469 DILTYKQMVGRAGRKGVDTMGESILVCKNSEKSKGIA-LLQGSLEPVHSCLQRQgevtaSMIRA-ILEIIVGGVASTSQD 546
Cdd:PRK00254 359 PVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMErYIFGKPEKLFSMLSNE-----SAFRSqVLALITNFGVSNFKE 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 547 MQTYAACTFLAaaiqegkqgMQRNQDDAQLGAIDACVTWLLENEFIQVaepgdgTGGKVYHPTHLGSATLSSSLSPTdTL 626
Cdd:PRK00254 434 LVNFLERTFYA---------HQRKDLYSLEEKAKEIVYFLLENEFIDI------DLEDRFIPLPLGIRTSQLYIDPL-TA 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 627 DIFAD-LQRAMKGfvlENDLHIVYLV--TPvfeDWISidwyrffclwekLPTSMKRVAELVGveegfLARCVKGKVVART 703
Cdd:PRK00254 498 KKFKDaFPKIEKN---PNPLGIFQLIasTP---DMTP------------LNYSRKEMEDLLD-----EAYEMEDRLYFNI 554
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 704 --ERQHRQMAIHKRFFTSLVLLDLISEIPLKDINQKYGCNRGQIQSLQQSAA--VYAgMITVFsnRLGWHNMELL--LSQ 777
Cdd:PRK00254 555 pyWEDYKFQKFLRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADwlMYS-LIELY--KLFEPKQEVLdyLET 631
|
730 740 750 760
....*....|....*....|....*....|....*....|....*....
gi 568996594 778 FQKRLTFGIQRELCDLIRVSLLNAQRARFLYASGFLTVADLARADSAEV 826
Cdd:PRK00254 632 LHLRVKHGVREELLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSEL 680
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
106-827 |
2.99e-75 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 265.59 E-value: 2.99e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 106 EGKNLVYSAPTSAGKTLVAELLILKRVLEtRKKALFILPFVSVAKEKKCYLQSLfQEVGLKVDGYMGSTSPTGQF-SSLD 184
Cdd:PRK01172 36 KGENVIVSVPTAAGKTLIAYSAIYETFLA-GLKSIYIVPLRSLAMEKYEELSRL-RSLGMRVKISIGDYDDPPDFiKRYD 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 185 IAVCTIERANGLVNRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYVTRKsashqaesastlsnaVQIVGMS 264
Cdd:PRK01172 114 VVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPD---------------ARILALS 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 265 ATLPNLQLVASWLNAELYHTDFRPVPLLESIKIGNSIYDSSMKlvrefqpllqvKGDEDhIVSLCYETIQDNHSVLIFCP 344
Cdd:PRK01172 177 ATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYE-----------RSQVD-INSLIKETVNDGGQVLVFVS 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 345 SKKWCEKVADIIAREFynlhhqpeglvkssefpPVILDQKSLLEVMDqlkrspsGLDSVLKNTVPWGVAFHHAGLTFEER 424
Cdd:PRK01172 245 SRKNAEDYAEMLIQHF-----------------PEFNDFKVSSENNN-------VYDDSLNEMLPHGVAFHHAGLSNEQR 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 425 DIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTPIFSG----QPLDILTYKQMVGRAGRKGVDTMGESILVCKnSEK 500
Cdd:PRK01172 301 RFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGnggiRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAA-SPA 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 501 SKGIA--LLQGSLEPVHSCLQRQGEVTASmiraILEIIVGGVASTSQDMQTYAACTFLaaAIQEGKqgmqrnqdDAQLGA 578
Cdd:PRK01172 380 SYDAAkkYLSGEPEPVISYMGSQRKVRFN----TLAAISMGLASSMEDLILFYNETLM--AIQNGV--------DEIDYY 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 579 IDACVTWLLENEFIQvaepgdgtGGKVYHPTHLGSAtlssslsptdTLDIFADLQRAMkgfvlendlhivyLVTPVFEDW 658
Cdd:PRK01172 446 IESSLKFLKENGFIK--------GDVTLRATRLGKL----------TSDLYIDPESAL-------------ILKSAFDHD 494
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 659 ISIDWYRFF-CLW-EKLPTSMKrvaELVGVEEgFLARC--VKGKVVARTerqhrqmaihkrffTSLVLLDLISEIPLKDI 734
Cdd:PRK01172 495 YDEDLALYYiSLCrEIIPANTR---DDYYAME-FLEDIgvIDGDISAAK--------------TAMVLRGWISEASMQKI 556
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 735 NQKYGCNRGQIQSLQQSA----AVYAGMITVFSNRlgwhnMELLLSQFQKRLTFGIQRELCDLIRVSLLNAQRARFLYAS 810
Cdd:PRK01172 557 TDTYGIAPGDVQARASSAdwisYSLARLSSIYKPE-----MRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDA 631
|
730
....*....|....*..
gi 568996594 811 GFLTVADLARADSAEVE 827
Cdd:PRK01172 632 GFKTVDDIARSSPERIK 648
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
287-496 |
2.89e-56 |
|
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: 192.38 E-value: 2.89e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 287 RPVPLLESIKIGNSIYDSSMKLVREfqpllqvKGDEDHIVSLCYETIQDNHSVLIFCPSKKWCEKVADIIArefynlhhq 366
Cdd:cd18795 1 RPVPLEEYVLGFNGLGIKLRVDVMN-------KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA--------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 367 peglvkssefppvildqksllevmdqlkrspsgldsvlkntvpwGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLS 446
Cdd:cd18795 65 --------------------------------------------GIAFHHAGLTREDRELVEELFREGLIKVLVATSTLA 100
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 568996594 447 SGVNLPARRVIIR-TPIFSG---QPLDILTYKQMVGRAGRKGVDTMGESILVCK 496
Cdd:cd18795 101 AGVNLPARTVIIKgTQRYDGkgyRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
91-285 |
2.73e-48 |
|
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: 170.91 E-value: 2.73e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 91 MFEWQAECLLLGHvLEGKNLVYSAPTSAGKTLVAELLILKRVLETRKKALFILPFVSVAKEKKCYLQSLFQEVGLKVDGY 170
Cdd:cd17921 2 LNPIQREALRALY-LSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 171 MGSTSPTG-QFSSLDIAVCTIERANGLVNRLiEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYVTRKsashqae 249
Cdd:cd17921 81 TGDPSVNKlLLAEADILVATPEKLDLLLRNG-GERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLRINKN------- 152
|
170 180 190
....*....|....*....|....*....|....*..
gi 568996594 250 sastlsnaVQIVGMSATLPNLQLVASWLNAE-LYHTD 285
Cdd:cd17921 153 --------ARFVGLSATLPNAEDLAEWLGVEdLIRFD 181
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
95-534 |
6.98e-38 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 154.33 E-value: 6.98e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 95 QAECLLlgHVLEGKNLVYSAPTSAGKTLVAELLILKRVLETRK-------KALfilpfvsvAKEKkcY--LQSLF--QEV 163
Cdd:COG4581 30 QEEAIL--ALEAGRSVLVAAPTGSGKTLVAEFAIFLALARGRRsfytapiKAL--------SNQK--FfdLVERFgaENV 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 164 GLkvdgyMgstspTGQfSSL----DIAVCTIERangLVNRLIEE-NKMDLLGMVVVDELHMLGDSHRGYLLEllltkicy 238
Cdd:COG4581 98 GL-----L-----TGD-ASVnpdaPIVVMTTEI---LRNMLYREgADLEDVGVVVMDEFHYLADPDRGWVWE-------- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 239 vtrksashqaESASTLSNAVQIVGMSATLPNLQLVASWLNA-----ELYHTDFRPVPLlesikignsiyDSSMKLVREFQ 313
Cdd:COG4581 156 ----------EPIIHLPARVQLVLLSATVGNAEEFAEWLTRvrgetAVVVSEERPVPL-----------EFHYLVTPRLF 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 314 PLLQVKGDEDHIVSLcYETIQ-----DNHSVLIFCPSKKWCEKVADIIAREfynlhhqpeGLVKSSEfppvildQKSLLE 388
Cdd:COG4581 215 PLFRVNPELLRPPSR-HEVIEeldrgGLLPAIVFIFSRRGCDEAAQQLLSA---------RLTTKEE-------RAEIRE 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 389 VMDQLKRSPSGLD-SVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTPI-FSGQ 466
Cdd:COG4581 278 AIDEFAEDFSVLFgKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkFDGE 357
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568996594 467 PLDILT---YKQMVGRAGRKGVDTMGESILVCKNSEKSKGIA-LLQGSLEPVHSclqrQGEVTASMIRAILE 534
Cdd:COG4581 358 RHRPLTareFHQIAGRAGRRGIDTEGHVVVLAPEHDDPKKFArLASARPEPLRS----SFRPSYNMVLNLLA 425
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
90-285 |
7.21e-35 |
|
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: 132.07 E-value: 7.21e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 90 KMFEWQAECLLLGhVLEGKNLVYSAPTSAGKTLVAELLILKRVLETrKKALFILPFVSVAKEKkcYLQ-SLFQEVGLKVD 168
Cdd:cd18028 1 ELYPPQAEAVRAG-LLKGENLLISIPTASGKTLIAEMAMVNTLLEG-GKALYLVPLRALASEK--YEEfKKLEEIGLKVG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 169 GYMGS-TSPTGQFSSLDIAVCTIERANGLVNRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKIcyvtrksashq 247
Cdd:cd18028 77 ISTGDyDEDDEWLGDYDIIVATYEKFDSLLRH--SPSWLRDVGVVVVDEIHLISDEERGPTLESIVARL----------- 143
|
170 180 190
....*....|....*....|....*....|....*...
gi 568996594 248 aesaSTLSNAVQIVGMSATLPNLQLVASWLNAELYHTD 285
Cdd:cd18028 144 ----RRLNPNTQIIGLSATIGNPDELAEWLNAELVESD 177
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
105-514 |
1.51e-31 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 134.63 E-value: 1.51e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 105 LEGKN-LVYSApTSAGKTLVAELLILKRVLETRKKALFILPFVSVAKEKkcYLQslFQEV---GLKVDGYMGS----TSP 176
Cdd:COG1202 223 LEGKDqLVVSA-TATGKTLIGELAGIKNALEGKGKMLFLVPLVALANQK--YED--FKDRygdGLDVSIRVGAsrirDDG 297
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 177 TGQFSSLDIAVCTIEranGLVNRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYVTRKSashqaesastlsn 256
Cdd:COG1202 298 TRFDPNADIIVGTYE---GIDHALRTGRDLGDIGTVVIDEVHMLEDPERGHRLDGLIARLKYYCPGA------------- 361
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 257 avQIVGMSATLPNLQLVASWLNAELYHTDFRPVPL---------LESIKIGNsiydssmKLV-REFqpllqvkgdeDHIV 326
Cdd:COG1202 362 --QWIYLSATVGNPEELAKKLGAKLVEYEERPVPLerhltfadgREKIRIIN-------KLVkREF----------DTKS 422
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 327 SLCY--ETIqdnhsvlIFCPSKKWCEKVADIIarefynlhhqpeglvkssefppvildqksllevmdqlkrspsGLDSvl 404
Cdd:COG1202 423 SKGYrgQTI-------IFTNSRRRCHEIARAL------------------------------------------GYKA-- 451
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 405 kntvpwgvAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTPIFSGQPLDILTYKQMVGRAGRKG 484
Cdd:COG1202 452 --------APYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRAGRPD 523
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 568996594 485 VDTMGES-ILV---------CKNSEKSKGIALLQGSLEPV 514
Cdd:COG1202 524 YHDRGKVyLLVepgksyhrsMEMTEDEVAFKLLKGEMEDV 563
|
|
| HTH_61 |
pfam20470 |
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ... |
489-593 |
2.06e-31 |
|
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.
Pssm-ID: 466619 [Multi-domain] Cd Length: 92 Bit Score: 118.80 E-value: 2.06e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 489 GESILVCKNSEKSKGIALLQGSLEPVHSCLQRQgevTASMIRAILEIIVGGVASTSQDMQTYAACTFLAAAIQEGKQGMQ 568
Cdd:pfam20470 1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE---KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS 77
|
90 100
....*....|....*....|....*
gi 568996594 569 rnqddaqlgaIDACVTWLLENEFIQ 593
Cdd:pfam20470 78 ----------IESSLEELVENGLIT 92
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
95-268 |
2.19e-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: 93.08 E-value: 2.19e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 95 QAECLLlgHVLEGKNLVYSAPTSAGKTLVAELLILKRVLETR--KKALFILPFVSVAKEKKCYLQSLFQEVGLKVDGYMG 172
Cdd:pfam00270 4 QAEAIP--AILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDngPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 173 STSPTGQFSSL---DIAVCTIERangLVNRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELLLtkicyvtrksashqae 249
Cdd:pfam00270 82 GDSRKEQLEKLkgpDILVGTPGR---LLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEIL---------------- 142
|
170
....*....|....*....
gi 568996594 250 saSTLSNAVQIVGMSATLP 268
Cdd:pfam00270 143 --RRLPKKRQILLLSATLP 159
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
84-297 |
7.14e-20 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 89.86 E-value: 7.14e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 84 HSFGVRKMFEWQAECLLlgHVLEG-KNLVYSAPTSAGKTLVAELLILKRVLET-RKKALFILPFVSVAKEKKCYLQSLFQ 161
Cdd:smart00487 2 EKFGFEPLRPYQKEAIE--ALLSGlRDVILAAPTGSGKTLAALLPALEALKRGkGGRVLVLVPTRELAEQWAEELKKLGP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 162 EVGLKVDGYMGSTSPTGQFSSL-----DIAVCTIERanglVNRLIEENKMDL--LGMVVVDELHMLGDSHRGYLLELLLT 234
Cdd:smart00487 80 SLGLKVVGLYGGDSKREQLRKLesgktDILVTTPGR----LLDLLENDKLSLsnVDLVILDEAHRLLDGGFGDQLEKLLK 155
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568996594 235 KicyvtrksashqaesastLSNAVQIVGMSATLP-NLQLVASWLNAELYHTDFRPVPlLESIKI 297
Cdd:smart00487 156 L------------------LPKNVQLLLLSATPPeEIENLLELFLNDPVFIDVGFTP-LEPIEQ 200
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
1853-2107 |
6.81e-19 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 93.19 E-value: 6.81e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1853 AVVVGLAVCWGAKDAYYLSLQKEqkqseispslAPPPLDATLTVKErmecLQSCLQkksDRERSVVTYDFIQTYKVLLlS 1932
Cdd:COG0749 18 AELVGISFAVEPGEAAYIPLAHG----------APEQLDLDEVLAA----LKPLLE---DPAIPKIGQNLKYDLHVLA-R 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1933 CGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHELALLEGMeTGPGIQSLGLN-VNTEHSGRYrASVESVLIFNS 2011
Cdd:COG0749 80 YGIELAGVAFDTMLASYLLNPGRRRHGLDDLAERYLGHETISYEEL-AGKGKKQLTFDqVPLEEAAEY-AAEDADITLRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 2012 MNQLNSLLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECESQKHVMQAKLDAIETQAYQLAGHSFSFTSADDIAQV 2091
Cdd:COG0749 158 HEVLKPELEEEGLLKLYEEIELPLVPVLARMERNGILVDRELLAELSAELAKRLAELEQEIYELAGEEFNLNSPKQLGEI 237
|
250
....*....|....*.
gi 568996594 2092 LFLELKLPPNGEMKTQ 2107
Cdd:COG0749 238 LFEKLGLPVGKKTKTG 253
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
95-288 |
8.09e-19 |
|
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: 87.03 E-value: 8.09e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 95 QAECLllGHVLEG-KNLVYSAPTSAGKTLVAELLILkRVL-------ETRKKALFILPFVSVAKEKKCYLQSLFQEVGLK 166
Cdd:cd18023 6 QSEVF--PDLLYSdKNFVVSAPTGSGKTVLFELAIL-RLLkernplpWGNRKVVYIAPIKALCSEKYDDWKEKFGPLGLS 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 167 VDGYMGSTS--PTGQFSSLDIAVCTIERANGLVNRLIEENKM-DLLGMVVVDELHMLGDShRGYLLELLLTKICYVTRKS 243
Cdd:cd18023 83 CAELTGDTEmdDTFEIQDADIILTTPEKWDSMTRRWRDNGNLvQLVALVLIDEVHIIKEN-RGATLEVVVSRMKTLSSSS 161
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 568996594 244 ASHQAESAStlsnaVQIVGMSATLPNLQLVASWLNAE-----LYHTDFRP 288
Cdd:cd18023 162 ELRGSTVRP-----MRFVAVSATIPNIEDLAEWLGDNpagcfSFGESFRP 206
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
107-266 |
7.45e-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: 82.45 E-value: 7.45e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 107 GKNLVYSAPTSAGKTLVAELLILKRVLETRKKALFILPFVSVAKEKKCYLQSLFQEvGLKVDGYMGSTSPTGQFS----S 182
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEEREKnklgD 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 183 LDIAVCTIERANGLVNRLIEENKMDlLGMVVVDELHMLGDSHRGYLLellltkICYVTRKSASHQaesastlsnaVQIVG 262
Cdd:cd00046 80 ADIIIATPDMLLNLLLREDRLFLKD-LKLIIVDEAHALLIDSRGALI------LDLAVRKAGLKN----------AQVIL 142
|
....
gi 568996594 263 MSAT 266
Cdd:cd00046 143 LSAT 146
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
411-484 |
1.63e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.10 E-value: 1.63e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568996594 411 GVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLP-ARRVIIrtpifSGQPLDILTYKQMVGRAGRKG 484
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVII-----YDLPWSPASYIQRIGRAGRAG 82
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
109-277 |
2.88e-15 |
|
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350777 [Multi-domain] Cd Length: 214 Bit Score: 77.03 E-value: 2.88e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 109 NLVYSAPTSAGKTLVAELLILKRVLETRK----------KALFILPFVSVAKEKKCYLQSLFQEVGLKVDGYMGSTSPTG 178
Cdd:cd18019 35 NLLLCAPTGAGKTNVALLTILREIGKHRNpdgtinldafKIVYIAPMKALVQEMVGNFSKRLAPYGITVAELTGDQQLTK 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 179 -QFSSLDIAVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGDShRGYLLELLLTKIcyvTRKSASHQAEsastlsna 257
Cdd:cd18019 115 eQISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDD-RGPVLESIVART---IRQIEQTQEY-------- 182
|
170 180
....*....|....*....|
gi 568996594 258 VQIVGMSATLPNLQLVASWL 277
Cdd:cd18019 183 VRLVGLSATLPNYEDVATFL 202
|
|
| DEXHc_ASCC3_2 |
cd18022 |
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
108-278 |
3.39e-15 |
|
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350780 [Multi-domain] Cd Length: 189 Bit Score: 75.87 E-value: 3.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 108 KNLVYSAPTSAGKTLVAELLILkRVLETR--KKALFILPFVSVAKEK-KCYLQSLFQEVGLKVDGYMGSTSPTGQ-FSSL 183
Cdd:cd18022 18 NNVLLGAPTGSGKTIAAELAMF-RAFNKYpgSKVVYIAPLKALVRERvDDWKKRFEEKLGKKVVELTGDVTPDMKaLADA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 184 DIAVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGdSHRGYLLELLLTKICYVtrksASHQAESastlsnaVQIVGM 263
Cdd:cd18022 97 DIIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLG-SDRGPVLEVIVSRMNYI----SSQTEKP-------VRLVGL 164
|
170
....*....|....*
gi 568996594 264 SATLPNLQLVASWLN 278
Cdd:cd18022 165 STALANAGDLANWLG 179
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
1828-2112 |
7.26e-15 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 80.91 E-value: 7.26e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1828 KLKQVSLPQEATVEDAGFPVRgcdgAVVVGLAVCWGAKDAYYLSLqkEQKQSEISPSLAPppldaTLtvkermeclqscl 1907
Cdd:PRK05755 311 KLKAAGLFAFDTETTSLDPMQ----AELVGLSFAVEPGEAAYIPL--DQLDREVLAALKP-----LL------------- 366
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1908 qkkSDRERSVVTYDFIQTYKVLLlSCGISLEPSYEDPKVACWLLDPDSKEpTLHSIVTSFLPHELALLEGME-TGPGIQS 1986
Cdd:PRK05755 367 ---EDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLASYLLDPGRRH-GLDSLAERYLGHKTISFEEVAgKQLTFAQ 441
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1987 LGLNVNTEHSGRyRASVesvlIFNSMNQLNS-LLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECESQKHVMQAKL 2065
Cdd:PRK05755 442 VDLEEAAEYAAE-DADV----TLRLHEVLKPkLLEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRL 516
|
250 260 270 280
....*....|....*....|....*....|....*....|....*..
gi 568996594 2066 DAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPngemktqgSKKT 2112
Cdd:PRK05755 517 AELEQEIYELAGEEFNINSPKQLGEILFEKLGLPV--------GKKT 555
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
74-484 |
4.58e-14 |
|
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: 77.95 E-value: 4.58e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 74 GLPKAVLEKYHSFGVRKMFEWQAECLllGHVLEGKNLVYSAPTSAGKTLVAELLILKRVLETRK-KALFILPFVSVAKEK 152
Cdd:COG1205 40 WLPPELRAALKKRGIERLYSHQAEAI--EAARAGKNVVIATPTASGKSLAYLLPVLEALLEDPGaTALYLYPTKALARDQ 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 153 KCYLQSLFQEVGL--KVDGYMGSTSPTGQ---FSSLDIAVCT-------IERANGLVNRLIEEnkmdlLGMVVVDELHM- 219
Cdd:COG1205 118 LRRLRELAEALGLgvRVATYDGDTPPEERrwiREHPDIVLTNpdmlhygLLPHHTRWARFFRN-----LRYVVIDEAHTy 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 220 ---LGdSHRGYLLELLLtKICyvtRKSASHqaesastlsnaVQIVGMSATLPNlqlvASWLNAELYHTDFRPV------- 289
Cdd:COG1205 193 rgvFG-SHVANVLRRLR-RIC---RHYGSD-----------PQFILASATIGN----PAEHAERLTGRPVTVVdedgspr 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 290 ---------PLLESIKIGNSIYDSSMKLVREFqpllqvkgdedhivslcyetIQDNHSVLIFCPSKKWCEKVADIIAREF 360
Cdd:COG1205 253 gertfvlwnPPLVDDGIRRSALAEAARLLADL--------------------VREGLRTLVFTRSRRGAELLARYARRAL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 361 ynlhhqPEGLVKSSefppvildqksllevmdqlkrspsgldsvlkntvpwgVAFHHAGLTFEERDIIEGAFRQGFIRVLA 440
Cdd:COG1205 313 ------REPDLADR-------------------------------------VAAYRAGYLPEERREIERGLRSGELLGVV 349
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 568996594 441 ATSTLSSGVNLP---ArrVIIrtpifSGQPLDILTYKQMVGRAGRKG 484
Cdd:COG1205 350 STNALELGIDIGgldA--VVL-----AGYPGTRASFWQQAGRAGRRG 389
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
402-484 |
5.57e-13 |
|
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: 67.24 E-value: 5.57e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 402 SVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIirtpIFSGQPLDILTYKQMVGRAG 481
Cdd:pfam00271 31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLV----INYDLPWNPASYIQRIGRAG 106
|
...
gi 568996594 482 RKG 484
Cdd:pfam00271 107 RAG 109
|
|
| DEXHc_LHR-like |
cd17922 |
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
107-277 |
1.39e-12 |
|
DEXH-box helicase domain of LHR; 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 from 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: 350680 [Multi-domain] Cd Length: 166 Bit Score: 67.61 E-value: 1.39e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 107 GKNLVYSAPTSAGKTLVAELLILKRVLETRKK---ALFILPFVSVAKEKKCYLQSLFQE--VGLKVDGYMGSTSPTGQFS 181
Cdd:cd17922 1 GRNVLIAAPTGSGKTEAAFLPALSSLADEPEKgvqVLYISPLKALINDQERRLEEPLDEidLEIPVAVRHGDTSQSEKAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 182 SL----DIAVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYVTRKSAshqaesastlsna 257
Cdd:cd17922 81 QLknppGILITTPESLELLLVNKKLRELFAGLRYVVVDEIHALLGSKRGVQLELLLERLRKLTGRPL------------- 147
|
170 180
....*....|....*....|
gi 568996594 258 vQIVGMSATLPNLQLVASWL 277
Cdd:cd17922 148 -RRIGLSATLGNLEEAAAFL 166
|
|
| DEXHc_Brr2_2 |
cd18021 |
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
109-284 |
1.84e-12 |
|
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350779 [Multi-domain] Cd Length: 191 Bit Score: 68.05 E-value: 1.84e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 109 NLVYSAPTSAGKTLVAELLILKRVLETRK-KALFILPFVSVAKEKKCYLQSLFQEV-GLKVDGYMGSTSP-TGQFSSLDI 185
Cdd:cd18021 21 NVFVGAPTGSGKTVCAELALLRHWRQNPKgRAVYIAPMQELVDARYKDWRAKFGPLlGKKVVKLTGETSTdLKLLAKSDV 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 186 AVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGDSHrGYLLELLLTKICYVtrksashqaesASTLSNAVQIVGMSA 265
Cdd:cd18021 101 ILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGEN-GPVYEVVVSRMRYI-----------SSQLEKPIRIVGLSS 168
|
170
....*....|....*....
gi 568996594 266 TLPNLQLVASWLNAELYHT 284
Cdd:cd18021 169 SLANARDVGEWLGASKSTI 187
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
90-483 |
2.42e-11 |
|
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: 2.42e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 90 KMFEWQAECL--LLGHVLEG-KNLVYSAPTSAGKTLVAeLLILKRVLeTRKKALFILPFVSVAKekkcylQSL--FQEVG 164
Cdd:COG1061 80 ELRPYQQEALeaLLAALERGgGRGLVVAPTGTGKTVLA-LALAAELL-RGKRVLVLVPRRELLE------QWAeeLRRFL 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 165 LKVDGYMGSTSPTGqfsslDIAVCTIeraNGLVNRLIEENKMDLLGMVVVDELHMLG-DSHRGyLLELLltkicyvtrks 243
Cdd:COG1061 152 GDPLAGGGKKDSDA-----PITVATY---QSLARRAHLDELGDRFGLVIIDEAHHAGaPSYRR-ILEAF----------- 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 244 ashqaesastlsNAVQIVGMSAT---LPNLQLVASWLNAELYHTD---------FRPV---PLLESIKIGNSIYDSSMKL 308
Cdd:COG1061 212 ------------PAAYRLGLTATpfrSDGREILLFLFDGIVYEYSlkeaiedgyLAPPeyyGIRVDLTDERAEYDALSER 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 309 VREFqpLLQVKGDEDHIVSLCYETIQDNHSVLIFCPSKKWCEKVADIIAREFYNlhhqpeglvkssefppvildqkslle 388
Cdd:COG1061 280 LREA--LAADAERKDKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIR-------------------------- 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 389 vmdqlkrspsgldsvlkntvpwgVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLP-ARRVIIRTPIFSGQp 467
Cdd:COG1061 332 -----------------------AAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPrLDVAILLRPTGSPR- 387
|
410
....*....|....*.
gi 568996594 468 ldilTYKQMVGRAGRK 483
Cdd:COG1061 388 ----EFIQRLGRGLRP 399
|
|
| DEXHc_ASCC3_1 |
cd18020 |
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
108-282 |
6.60e-11 |
|
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350778 [Multi-domain] Cd Length: 199 Bit Score: 63.60 E-value: 6.60e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 108 KNLVYSAPTSAGKTLVAELLILK----------RVLETRKKALFILPFVSVAKEKKCYLQSLFQEVGLKVDGYMGSTSPT 177
Cdd:cd18020 18 ENMLICAPTGAGKTNIAMLTILHeirqhvnqggVIKKDDFKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDMQLT 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 178 -GQFSSLDIAVCTIERANGLVNRLIEENKM-DLLGMVVVDELHMLGDShRGYLLEllltkiCYVTRksASHQAESASTLs 255
Cdd:cd18020 98 kKEIAETQIIVTTPEKWDVVTRKSSGDVALsQLVRLLIIDEVHLLHDD-RGPVIE------SLVAR--TLRQVESTQSM- 167
|
170 180
....*....|....*....|....*..
gi 568996594 256 naVQIVGMSATLPNLQLVASWLNAELY 282
Cdd:cd18020 168 --IRIVGLSATLPNYLDVADFLRVNPY 192
|
|
| DEXHc_Mtr4-like |
cd18024 |
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ... |
113-287 |
2.39e-09 |
|
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 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: 350782 [Multi-domain] Cd Length: 205 Bit Score: 59.38 E-value: 2.39e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 113 SAPTSAGKTLVAELLILKrVLETRKKALFILPFVSVAKEKKCYLQSLFQEVGLkvdgyMgstspTGQFSSLDIAVCTIER 192
Cdd:cd18024 53 SAHTSAGKTVVAEYAIAQ-SLRDKQRVIYTSPIKALSNQKYRELQEEFGDVGL-----M-----TGDVTINPNASCLVMT 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 193 ANGLVNRLIEENK-MDLLGMVVVDELHMLGDSHRGYLLEllltkicyvtrksashqaESASTLSNAVQIVGMSATLPNLQ 271
Cdd:cd18024 122 TEILRSMLYRGSEiMREVAWVIFDEIHYMRDKERGVVWE------------------ETIILLPDKVRYVFLSATIPNAR 183
|
170 180
....*....|....*....|...
gi 568996594 272 LVASWLnAELYH-------TDFR 287
Cdd:cd18024 184 QFAEWI-CKIHKqpchvvyTDYR 205
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
114-483 |
5.65e-09 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 61.86 E-value: 5.65e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 114 APTSAGKTLVAELLILKRVL--------ETRKKA----LFILPF----VSVAKEKKCYLQSLFQE--------VGLKVDG 169
Cdd:PRK09751 3 APTGSGKTLAAFLYALDRLFreggedtrEAHKRKtsriLYISPIkalgTDVQRNLQIPLKGIADErrrrgeteVNLRVGI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 170 YMGSTsPTGQFSSL-----DIAVCTIEranGLVNRLIEENKMDLLGM--VVVDELHMLGDSHRGYLLELLLTKIcyvtrk 242
Cdd:PRK09751 83 RTGDT-PAQERSKLtrnppDILITTPE---SLYLMLTSRARETLRGVetVIIDEVHAVAGSKRGAHLALSLERL------ 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 243 sashqaesASTLSNAVQIVGMSATLPNLQLVASWLNAElyhtdfRPVPLLE-------SIKIGNSIYDssMKLVREFQPl 315
Cdd:PRK09751 153 --------DALLHTSAQRIGLSATVRSASDVAAFLGGD------RPVTVVNppamrhpQIRIVVPVAN--MDDVSSVAS- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 316 lqVKGDED----------HIVSLCYETIQDNHSVLIFCPSKKWCEKvadIIAR--EFYnlhhqPEGLVKSsefPPVILDQ 383
Cdd:PRK09751 216 --GTGEDShagregsiwpYIETGILDEVLRHRSTIVFTNSRGLAEK---LTARlnELY-----AARLQRS---PSIAVDA 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 384 KSLLEVMDQLKRSPSGLDSVLKNTvpwgvafHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTpif 463
Cdd:PRK09751 283 AHFESTSGATSNRVQSSDVFIARS-------HHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQV--- 352
|
410 420
....*....|....*....|
gi 568996594 464 sGQPLDILTYKQMVGRAGRK 483
Cdd:PRK09751 353 -ATPLSVASGLQRIGRAGHQ 371
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
87-278 |
1.28e-07 |
|
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: 53.98 E-value: 1.28e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 87 GVRKMFEWQAECLLLghVLEGKNLVYSAPTSAGKTLvAELL-ILKRVLETRKK------ALFILP----FVSVAKEkkcy 155
Cdd:cd00268 9 GFEKPTPIQAQAIPL--ILSGRDVIGQAQTGSGKTL-AFLLpILEKLLPEPKKkgrgpqALVLAPtrelAMQIAEV---- 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 156 LQSLFQEVGLKVDGYMGSTSPTGQFSSL----DIAVCTIERanglVNRLIEENKMDL--LGMVVVDEL-HMLGDSHRGYL 228
Cdd:cd00268 82 ARKLGKGTGLKVAAIYGGAPIKKQIEALkkgpDIVVGTPGR----LLDLIERGKLDLsnVKYLVLDEAdRMLDMGFEEDV 157
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 568996594 229 LELLltkicyvtrksashqaesaSTLSNAVQIVGMSATLPN--LQLVASWLN 278
Cdd:cd00268 158 EKIL-------------------SALPKDRQTLLFSATLPEevKELAKKFLK 190
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
328-484 |
3.81e-07 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 51.06 E-value: 3.81e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 328 LCYETIQDNH---SVLIFCPSKKWCEKVADiiarefynlhhqpeglvkssefppvildqksllevmdQLKRSpsGLDSvl 404
Cdd:cd18794 19 DLLKRIKVEHlggSGIIYCLSRKECEQVAA-------------------------------------RLQSK--GISA-- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 405 kntvpwgvAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPArrviIRTPIFSGQPLDILTYKQMVGRAGRKG 484
Cdd:cd18794 58 --------AAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPD----VRFVIHYSLPKSMESYYQESGRAGRDG 125
|
|
| DNA_pol_A |
pfam00476 |
DNA polymerase family A; |
2063-2109 |
9.58e-07 |
|
DNA polymerase family A;
Pssm-ID: 459825 Cd Length: 368 Bit Score: 53.21 E-value: 9.58e-07
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 568996594 2063 AKLDAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPNGEMKTQGS 2109
Cdd:pfam00476 1 ERLKELEQEIYELAGEEFNINSPKQLGEILFEKLGLPPGKKTKTGYS 47
|
|
| DEADc_DDX28 |
cd17948 |
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
104-268 |
1.21e-06 |
|
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 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: 350706 [Multi-domain] Cd Length: 231 Bit Score: 51.60 E-value: 1.21e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 104 VLEGKNLVYSAPTSAGKTLVAELLILKRVLETRKK---------ALFILPFVSVAKEKKCYLQSLFQEVGLKVDGYMGS- 173
Cdd:cd17948 24 ILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLLaegpfnaprGLVITPSRELAEQIGSVAQSLTEGLGLKVKVITGGr 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 174 ---TSPTGQFSSLDIAVCTIERANGLVNRLIEenKMDLLGMVVVDELH-MLGDSHRGYLLELLltkicyvtRKS--ASHQ 247
Cdd:cd17948 104 tkrQIRNPHFEEVDILVATPGALSKLLTSRIY--SLEQLRHLVLDEADtLLDDSFNEKLSHFL--------RRFplASRR 173
|
170 180
....*....|....*....|.
gi 568996594 248 AESASTLSNAVQIVGMSATLP 268
Cdd:cd17948 174 SENTDGLDPGTQLVLVSATMP 194
|
|
| DEXHc_Hrq1-like |
cd17923 |
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
95-275 |
1.51e-06 |
|
DEAH-box helicase domain of Hrq1 and similar proteins; 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. Hrq1 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: 350681 [Multi-domain] Cd Length: 182 Bit Score: 50.66 E-value: 1.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 95 QAECLLlgHVLEGKNLVYSAPTSAGKTLVAELLILKRVL-ETRKKALFILPFVSVAKEKKCYLQSLFQEVGLK--VDGYM 171
Cdd:cd17923 5 QAEAIE--AARAGRSVVVTTGTASGKSLCYQLPILEALLrDPGSRALYLYPTKALAQDQLRSLRELLEQLGLGirVATYD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 172 GSTSPTgqfsslDIAVCTIERANGLV------NRLI---EENKMDLLGM---VVVDELHM----LGdSHRGYLLELLLtK 235
Cdd:cd17923 83 GDTPRE------ERRAIIRNPPRILLtnpdmlHYALlphHDRWARFLRNlryVVLDEAHTyrgvFG-SHVALLLRRLR-R 154
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 568996594 236 ICYVTRksashqaesastlsNAVQIVGMSATLPNLQLVAS 275
Cdd:cd17923 155 LCRRYG--------------ADPQFILTSATIGNPAEHAR 180
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
412-484 |
2.33e-06 |
|
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: 49.18 E-value: 2.33e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568996594 412 VAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVN---LPArrVIIrtpifSGQPLDILTYKQMVGRAGRKG 484
Cdd:cd18797 69 VASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDiggLDA--VVL-----AGYPGSLASLWQQAGRAGRRG 137
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
105-268 |
2.66e-06 |
|
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: 50.17 E-value: 2.66e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 105 LEGKNLVYSAPTSAGKTLVAeLLILKRVLETRKKA------LFILPFVSVAKEKKCYLQSLFqEVGLKVDGYMGSTS--- 175
Cdd:cd18036 15 LRGKNTIICAPTGSGKTRVA-VYICRHHLEKRRSAgekgrvVVLVNKVPLVEQQLEKFFKYF-RKGYKVTGLSGDSShkv 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 176 PTGQF-SSLDIAVCTierANGLVNRLIEENKMDLL-----GMVVVDELHMLGDSHRGYLLELlltkicyvtrksaSHQAE 249
Cdd:cd18036 93 SFGQIvKASDVIICT---PQILINNLLSGREEERVylsdfSLLIFDECHHTQKEHPYNKIMR-------------MYLDK 156
|
170
....*....|....*....
gi 568996594 250 SASTLSNAVQIVGMSATLP 268
Cdd:cd18036 157 KLSSQGPLPQILGLTASPG 175
|
|
| Lhr |
COG1201 |
Lhr-like helicase [Replication, recombination and repair]; |
212-445 |
8.84e-06 |
|
Lhr-like helicase [Replication, recombination and repair];
Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 50.87 E-value: 8.84e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 212 VVVDELHMLGDSHRGYLLELLLTKIcyvtrksashqaesASTLSNAVQIVGMSATLPNLQLVASWL-------NAELYHT 284
Cdd:COG1201 165 VIVDEIHALAGSKRGVHLALSLERL--------------RALAPRPLQRIGLSATVGPLEEVARFLvgyedprPVTIVDA 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 285 DFRPVPLLESIkignsIYDSSMKLVREFQPLLQvkgdeDHIVSLCYETIQDNHSVLIFCPSKKWCEKVadiiareFYNLh 364
Cdd:COG1201 231 GAGKKPDLEVL-----VPVEDLIERFPWAGHLW-----PHLYPRVLDLIEAHRTTLVFTNTRSQAERL-------FQRL- 292
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 365 hqpeglvkssefppvildqksllevmdqLKRSPSGLDSvlkntvpwgVAFHHAGLTFEERDIIEGAFRQGFIRVLAATST 444
Cdd:COG1201 293 ----------------------------NELNPEDALP---------IAAHHGSLSREQRLEVEEALKAGELRAVVATSS 335
|
.
gi 568996594 445 L 445
Cdd:COG1201 336 L 336
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
93-218 |
1.62e-05 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 48.03 E-value: 1.62e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 93 EWQAEclLLGHVLEgKNLVYSAPTSAGKTLVAELLIlKRVLE-------TRKKALFILPFVSVAKEKKCYLQslfQEVGL 165
Cdd:cd18034 5 SYQLE--LFEAALK-RNTIVVLPTGSGKTLIAVMLI-KEMGElnrkeknPKKRAVFLVPTVPLVAQQAEAIR---SHTDL 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568996594 166 KVDGYMGSTSPTGQ--------FSSLDIAVCTierANGLVNRLIEEN-KMDLLGMVVVDELH 218
Cdd:cd18034 78 KVGEYSGEMGVDKWtkerwkeeLEKYDVLVMT---AQILLDALRHGFlSLSDINLLIFDECH 136
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
105-218 |
1.68e-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: 47.81 E-value: 1.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 105 LEGKNLVYSAPTSAGKTLVAeLLILKRVLE-----TRKKALFILPFVSVAKEKKCYLQSLFQEVGLKVDGYMGSTSPTGQ 179
Cdd:cd17927 15 LKGKNTIICLPTGSGKTFVA-VLICEHHLKkfpagRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVS 93
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 568996594 180 FSSL----DIAVCTierANGLVNRLIEENKMDL--LGMVVVDELH 218
Cdd:cd17927 94 VEQIvessDVIIVT---PQILVNDLKSGTIVSLsdFSLLVFDECH 135
|
|
| DNA_polA_I_Bacillus_like_exo |
cd06140 |
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ... |
1853-2040 |
1.87e-05 |
|
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Pssm-ID: 176652 [Multi-domain] Cd Length: 178 Bit Score: 47.26 E-value: 1.87e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1853 AVVVGLAVcWGAKDAYYLSLQKEQKQSEispslappPLDATLtvkermeclqsclqkkSDRERSVVTYDFIQTYkVLLLS 1932
Cdd:cd06140 20 ADIIGLAL-ANGGGAYYIPLELALLDLA--------ALKEWL----------------EDEKIPKVGHDAKRAY-VALKR 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 1933 CGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHEL-ALLEGMETGPGIQSLGLNVNTEHSGRyRASVesvlIFNS 2011
Cdd:cd06140 74 HGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELpSDEEVYGKGAKFAVPDEEVLAEHLAR-KAAA----IARL 148
|
170 180
....*....|....*....|....*....
gi 568996594 2012 MNQLNSLLQKENLHDIFCKVEMPSQYCLA 2040
Cdd:cd06140 149 APKLEEELEENEQLELYYEVELPLAEVLA 177
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
90-224 |
2.74e-05 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 46.51 E-value: 2.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 90 KMFEWQAECL--LLGHVLEG-KNLVYSAPTSAGKTLVAeLLILKRVLE--TRKKALFILPFVSVAKekkcylQSL--FQE 162
Cdd:pfam04851 3 ELRPYQIEAIenLLESIKNGqKRGLIVMATGSGKTLTA-AKLIARLFKkgPIKKVLFLVPRKDLLE------QALeeFKK 75
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568996594 163 VGLKVDGYMGSTSPTGQFSSLD---IAVCTIERANGLVNRLIEENKMDLLGMVVVDELHMLGDSH 224
Cdd:pfam04851 76 FLPNYVEIGEIISGDKKDESVDdnkIVVTTIQSLYKALELASLELLPDFFDVIIIDEAHRSGASS 140
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
412-484 |
4.46e-05 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 48.56 E-value: 4.46e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568996594 412 VAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTPIfsgqPLDILTYKQMVGRAGRKG 484
Cdd:PRK11057 263 AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI----PRNIESYYQETGRAGRDG 331
|
|
| SF2_C_suv3 |
cd18805 |
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ... |
438-484 |
5.01e-05 |
|
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 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: 350192 [Multi-domain] Cd Length: 135 Bit Score: 45.24 E-value: 5.01e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 568996594 438 VLAATSTLSSGVNLPARRVIIRTPI-FSGQPLDILT---YKQMVGRAGRKG 484
Cdd:cd18805 73 VLVASDAIGMGLNLNIRRVIFSSLSkFDGNEMRPLSpseVKQIAGRAGRFG 123
|
|
| DEXHc_SKIV2L |
cd18027 |
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ... |
103-277 |
6.11e-05 |
|
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L 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: 350785 [Multi-domain] Cd Length: 179 Bit Score: 45.72 E-value: 6.11e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 103 HVLEGKNLVYSAPTSAGKTLVAELLIlKRVLETRKKALFILPFVSVAKEKKCYLQSLFQEVGLKvdgymgstspTGQFSS 182
Cdd:cd18027 19 HLEAGDSVFVAAHTSAGKTVVAEYAI-ALAQKHMTRTIYTSPIKALSNQKFRDFKNTFGDVGLI----------TGDVQL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 183 LDIAVCTIERANGLvnRLIEENKMDL---LGMVVVDELHMLGDSHRGYLLELLLTkicyvtrksashqaesasTLSNAVQ 259
Cdd:cd18027 88 NPEASCLIMTTEIL--RSMLYNGSDVirdLEWVIFDEVHYINDAERGVVWEEVLI------------------MLPDHVS 147
|
170
....*....|....*...
gi 568996594 260 IVGMSATLPNLQLVASWL 277
Cdd:cd18027 148 IILLSATVPNTVEFADWI 165
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
438-495 |
1.08e-04 |
|
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: 42.31 E-value: 1.08e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 568996594 438 VLAATSTLSSGVNLP-ARRVIIRTPIFSgqpldILTYKQMVGRAGRKGvDTMGESILVC 495
Cdd:cd18785 25 ILVATNVLGEGIDVPsLDTVIFFDPPSS-----AASYIQRVGRAGRGG-KDEGEVILFV 77
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
412-484 |
1.16e-04 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350183 [Multi-domain] Cd Length: 150 Bit Score: 44.56 E-value: 1.16e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568996594 412 VAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPA-RRVI-IrtpifsGQPLDILTYKQMVGRAGRKG 484
Cdd:cd18796 71 IALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDvDLVIqI------GSPKSVARLLQRLGRSGHRP 139
|
|
| DEXHc_RIG-I_DDX58 |
cd18073 |
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ... |
89-267 |
1.43e-04 |
|
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350831 [Multi-domain] Cd Length: 202 Bit Score: 45.20 E-value: 1.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 89 RKMFEWQAEclLLGHVLEGKNLVYSAPTSAGKTLVAeLLI----LKRVLETRK-KALFILPFVSVAKEKKCYLQSLFQEV 163
Cdd:cd18073 1 FKPRNYQLE--LALPAMKGKNTIICAPTGCGKTFVS-LLIcehhLKKFPQGQKgKVVFFATKVPVYEQQKSVFSKYFERH 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 164 GLKVDGYMGSTS---PTGQ-FSSLDIAVCTierANGLVNRLI--EENKMDLLGMVVVDELHMLGDSHRgylLELLLTKic 237
Cdd:cd18073 78 GYRVTGISGATAenvPVEQiIENNDIIILT---PQILVNNLKkgTIPSLSIFTLMIFDECHNTSGNHP---YNMIMFR-- 149
|
170 180 190
....*....|....*....|....*....|
gi 568996594 238 YVTRKSAShqaeSASTLSnavQIVGMSATL 267
Cdd:cd18073 150 YLDQKLGG----SSGPLP---QIIGLTASV 172
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
110-270 |
2.16e-04 |
|
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: 45.91 E-value: 2.16e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 110 LVYSAPTSAGKTLVAeLLILKRVLETRK--KALFILPFVSVAKEKKCYLQSLFqevGLKVDGYMGSTSPTGQFSSLD--- 184
Cdd:TIGR01587 2 LVIEAPTGYGKTEAA-LLWALHSIKSQKadRVIIALPTRATINAMYRRAKELF---GSELVGLHHSSSFSRIKEMGDsee 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 185 -------------------IAVCTIERANGLVNRLIEENKMDLLGM----VVVDELHMLGDSHRGYLLELLltkicyvtr 241
Cdd:TIGR01587 78 fehlfplyihsndklfldpITVCTIDQVLKSVFGEFGHYEFTLASIanslLIFDEVHFYDEYTLALILAVL--------- 148
|
170 180
....*....|....*....|....*....
gi 568996594 242 ksaSHQAEsastlsNAVQIVGMSATLPNL 270
Cdd:TIGR01587 149 ---EVLKD------NDVPILLMSATLPKF 168
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
74-354 |
4.62e-04 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 45.14 E-value: 4.62e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 74 GLPKAVLEKYHSFGVRKMFEWQAECLLlgHVLEGKNLVYSAPTSAGKTLvAELL-ILKRVLETRKK---ALFILP----F 145
Cdd:COG0513 8 GLSPPLLKALAELGYTTPTPIQAQAIP--LILAGRDVLGQAQTGTGKTA-AFLLpLLQRLDPSRPRapqALILAPtrelA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 146 VSVAKEkkcyLQSLFQEVGLKVDGYMGSTSPTGQFSSL----DIAVCT----IEranglvnrLIEENKMDL--LGMVVVD 215
Cdd:COG0513 85 LQVAEE----LRKLAKYLGLRVATVYGGVSIGRQIRALkrgvDIVVATpgrlLD--------LIERGALDLsgVETLVLD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 216 E----LHMlgdshrGYLLEllLTKIcyvtrksashqaesASTLSNAVQIVGMSATLPN--LQLVASWLNaelyhtdfRPV 289
Cdd:COG0513 153 EadrmLDM------GFIED--IERI--------------LKLLPKERQTLLFSATMPPeiRKLAKRYLK--------NPV 202
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568996594 290 plleSIKIGNSiyDSSMKLVREFqpLLQVkgDEDHIVSLCYETIQDNH--SVLIFCPSKKWCEKVAD 354
Cdd:COG0513 203 ----RIEVAPE--NATAETIEQR--YYLV--DKRDKLELLRRLLRDEDpeRAIVFCNTKRGADRLAE 259
|
|
| DEADc_DDX21_DDX50 |
cd17944 |
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ... |
87-222 |
8.88e-04 |
|
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members 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. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
Pssm-ID: 350702 [Multi-domain] Cd Length: 202 Bit Score: 42.91 E-value: 8.88e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 87 GVRKMFEWQAECLllGHVLEGKNLVYSAPTSAGKTL-VAELLI--LKRVLETRK-----KALFILPFVSVAKEKKCYLQS 158
Cdd:cd17944 9 GVTYLFPIQVKTF--HPVYSGKDLIAQARTGTGKTFsFAIPLIekLQEDQQPRKrgrapKVLVLAPTRELANQVTKDFKD 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 159 LFQEvgLKVDGYMGSTSPTGQF----SSLDIAVCTieraNGLVNRLIEENKMDL--LGMVVVDELHMLGD 222
Cdd:cd17944 87 ITRK--LSVACFYGGTPYQQQIfairNGIDILVGT----PGRIKDHLQNGRLDLtkLKHVVLDEVDQMLD 150
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
412-484 |
1.70e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 43.21 E-value: 1.70e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568996594 412 VAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLP-ARRVI---IrtpifsgqPLDILTYKQMVGRAGRKG 484
Cdd:COG0514 257 AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPdVRFVIhydL--------PKSIEAYYQEIGRAGRDG 325
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| DNA_pol_A_pol_I_C |
cd08637 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2055-2116 |
1.93e-03 |
|
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176474 Cd Length: 377 Bit Score: 42.79 E-value: 1.93e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568996594 2055 ESQKHVMQAKLDAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPNgeMKTqgskKTLGST 2116
Cdd:cd08637 6 EELSEELEKELAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVG--KKT----KTGYST 61
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|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
416-485 |
2.11e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 42.89 E-value: 2.11e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568996594 416 HAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIRTPIfsgqPLDILTYKQMVGRAGR---KGV 485
Cdd:PTZ00424 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDL----PASPENYIHRIGRSGRfgrKGV 366
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| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
105-218 |
3.38e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain] Cd Length: 200 Bit Score: 41.00 E-value: 3.38e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 105 LEGKNLVYSAPTSAGKTLVAeLLILKRVLETRK--KALFILPFVSVAKekkcylQSLFQEVGLKVDGYM-----GSTSPT 177
Cdd:cd18075 15 LRGKNSIIWLPTGAGKTRAA-VYVARRHLETKRgaKVAVLVNKVHLVD------QHLEKEFHVLLDKYTvtaisGDSSHK 87
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 568996594 178 GQFSSL----DIAVCTIERANGLVNRLIEENKMDL--LGMVVVDELH 218
Cdd:cd18075 88 CFFGQLargsDVVICTAQILQNALLSGEEEAHVELtdFSLLVIDECH 134
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|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
103-220 |
7.59e-03 |
|
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.
Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 39.83 E-value: 7.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568996594 103 HVLEGKNLVYSAPTSAGKTLVAEL--LILKRVletrkkALFILPFVSVAKEKKCYLQSLfqevGLKVDgYMGSTSPTGQF 180
Cdd:cd17920 23 AVLAGRDVLVVMPTGGGKSLCYQLpaLLLDGV------TLVVSPLISLMQDQVDRLQQL----GIRAA-ALNSTLSPEEK 91
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 568996594 181 SSLDIAV---------CTIERA--NGLVNRLIEENKMDLLGMVVVDELHML 220
Cdd:cd17920 92 REVLLRIkngqykllyVTPERLlsPDFLELLQRLPERKRLALIVVDEAHCV 142
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|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
410-485 |
9.60e-03 |
|
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: 38.86 E-value: 9.60e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568996594 410 WGVAFHHAGLTFEERDIIEGAFRQGFIRVLAATSTLSSGVNLPARRVIIrtpIFSGQPLDILTYKQMVGRAGRKGV 485
Cdd:cd18811 62 LNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMV---IEDAERFGLSQLHQLRGRVGRGDH 134
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