NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1907188396|ref|XP_036009806|]
View 

probable ATP-dependent RNA helicase DDX60 isoform X2 [Mus musculus]

Protein Classification

DEXHc_DDX60 and SF2_C_Ski2 domain-containing protein( domain architecture ID 13408691)

DEXHc_DDX60 and SF2_C_Ski2 domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 357-534 6.07e-116

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 359.76  E-value: 6.07e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  357 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 435
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  436 LCGVFTRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSAT 514
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|
gi 1907188396  515 ISNPQHLTEWLQSVKRYWKQ 534
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKA 180
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
362-1036 1.18e-39

Replicative superfamily II helicase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1204:

Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 155.44  E-value: 1.18e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESLcGVF 440
Cdd:COG1204     27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIKV-GVS 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  441 TRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP---FLAL 511
Cdd:COG1204    101 TGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPeaqIVAL 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  512 SATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCSVRQGd 591
Cdd:COG1204    178 SATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRSKDPT- 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  592 vcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKYEESLK 671
Cdd:COG1204    229 ---------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRDAESLA 256

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  672 EEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEKKQEek 751
Cdd:COG1204    257 KKLADELKRRLTPEER----------------------------------------------EELEELAEELLEVSEE-- 288

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  752 rppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkaiddqll 831
Cdd:COG1204    289 --------------------------------------------THT--------------------------------- 291

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  832 qrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA----QNSVY 907
Cdd:COG1204    292 ------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVP 359

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  908 LDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KADDLEDg 979
Cdd:COG1204    360 IPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFANSREE- 436

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  980 kakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1036
Cdd:COG1204    437 ---LLDFLENTFYAYQYDK--GDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 357-534 6.07e-116

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 359.76  E-value: 6.07e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  357 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 435
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  436 LCGVFTRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSAT 514
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|
gi 1907188396  515 ISNPQHLTEWLQSVKRYWKQ 534
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKA 180
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
362-1036 1.18e-39

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 155.44  E-value: 1.18e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESLcGVF 440
Cdd:COG1204     27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIKV-GVS 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  441 TRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP---FLAL 511
Cdd:COG1204    101 TGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPeaqIVAL 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  512 SATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCSVRQGd 591
Cdd:COG1204    178 SATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRSKDPT- 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  592 vcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKYEESLK 671
Cdd:COG1204    229 ---------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRDAESLA 256

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  672 EEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEKKQEek 751
Cdd:COG1204    257 KKLADELKRRLTPEER----------------------------------------------EELEELAEELLEVSEE-- 288

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  752 rppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkaiddqll 831
Cdd:COG1204    289 --------------------------------------------THT--------------------------------- 291

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  832 qrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA----QNSVY 907
Cdd:COG1204    292 ------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVP 359

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  908 LDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KADDLEDg 979
Cdd:COG1204    360 IPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFANSREE- 436

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  980 kakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1036
Cdd:COG1204    437 ---LLDFLENTFYAYQYDK--GDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 791-934 9.50e-35

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: 130.37  E-value: 9.50e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  791 LDESVMHETEHNYLLQTLEKNLEIPKDCTYANQKAIDD--QLLqrVFhrvRFERKG--ETLKRLAerGIGYHHSSMSAKE 866
Cdd:cd18795      5 LEEYVLGFNGLGIKLRVDVMNKFDSDIIVLLKIETVSEgkPVL--VF---CSSRKEceKTAKDLA--GIAFHHAGLTRED 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907188396  867 KQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVY-------LDALNYRQMSGRAGRRGQDLLGDVYFF 934
Cdd:cd18795     78 RELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLEYLQMIGRAGRPGFDTRGEAIIM 152
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 362-516 5.37e-22

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: 94.23  E-value: 5.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLCGVF 440
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907188396  441 TRDYRHDAL-NCQVLITVPacfEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPFLALSATIS 516
Cdd:pfam00270   84 SRKEQLEKLkGPDILVGTP---GRLLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSATLP 159
DEXDc smart00487
DEAD-like helicases superfamily;
356-547 3.30e-18

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 84.47  E-value: 3.30e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396   356 FIPDTWQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNmpaGE 434
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL---GL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396   435 SLCGVFTRDYRHDAL------NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--C 506
Cdd:smart00487   84 KVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPknV 161

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|.
gi 1907188396   507 PFLALSATISNPQHLTEWLqsvkrYWKQVDSTMEERTVSKR 547
Cdd:smart00487  162 QLLLLSATPPEEIENLLEL-----FLNDPVFIDVGFTPLEP 197
PRK02362 PRK02362
ATP-dependent DNA helicase;
738-1041 2.35e-17

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 87.71  E-value: 2.35e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  738 ENAFEFLEKKQEEKRPPKADkeartTANKLRKvkkslekqkTVDEKGQ----KSSRRLDESvmhetehnyllqtleknle 813
Cdd:PRK02362   212 GGAIHFDDSQREVEVPSKDD-----TLNLVLD---------TLEEGGQclvfVSSRRNAEG------------------- 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  814 IPKDCTYANQKAIDDQL---LQRVFHRVRFERKGETLKRLA---ERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGT 887
Cdd:PRK02362   259 FAKRAASALKKTLTAAEraeLAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPT 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  888 LALGINMPCKSVV------FAQNS--VYLDALNYRQMSGRAGRRGQDLLG----------------DVYFFDIPLPkigk 943
Cdd:PRK02362   339 LAAGLNLPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLDPYGeavllaksydeldelfERYIWADPED---- 414

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  944 lIKSKvpelrgqfpLSISLILRLMLLASKADDLEDGKAKALSVLKHSLLSFKQP------RAIDMlklyflySLQFLVKE 1017
Cdd:PRK02362   415 -VRSK---------LATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDdtgrleRVVDD-------VLDFLERN 477

                          330       340
                   ....*....|....*....|....*..
gi 1907188396 1018 GHIDQEGN---PTGFAGLVSHLhYHEP 1041
Cdd:PRK02362   478 GMIEEDGEtleATELGHLVSRL-YIDP 503
HELICc smart00490
helicase superfamily c-terminal domain;
848-924 8.65e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 8.65e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907188396   848 KRLAERGIGY--HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 924
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 362-523 2.20e-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: 78.34  E-value: 2.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLDVVDNYESAVIVAPTSSGKTYAsyYC---MEKVLKESDeGVVVYVAPTKALVN-QVAATVEyrYAKNMPAGESlC 437
Cdd:COG1205     61 QAEAIEAARAGKNVVIATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALARdQLRRLRE--LAEALGLGVR-V 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 GVFT----RDYRHDAL-NCQVLITVPacfEIL---LLaPHRQNWV---KRIRYVIFDEVHCLGGEIGAeiweHLLVMIR- 505
Cdd:COG1205    135 ATYDgdtpPEERRWIReHPDIVLTNP---DMLhygLL-PHHTRWArffRNLRYVVIDEAHTYRGVFGS----HVANVLRr 206

                          170       180
                   ....*....|....*....|....*....
gi 1907188396  506 ----CP-------FLALSATISNPQHLTE 523
Cdd:COG1205    207 lrriCRhygsdpqFILASATIGNPAEHAE 235
PRK00254 PRK00254
ski2-like helicase; Provisional
 373-535 3.11e-12

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 71.00  E-value: 3.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCM-EKVLKESdeGVVVYVAPTKALvnqvaATVEYRYAKNMPAGESLCGVFTRDY------- 444
Cdd:PRK00254    40 KNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL-----AEEKYREFKDWEKLGLRVAMTTGDYdstdewl 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  445 -RHDalncqVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGG-EIGAE---IWEHLLVmiRCPFLALSATISNPQ 519
Cdd:PRK00254   113 gKYD-----IIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGSyDRGATlemILTHMLG--RAQILGLSATVGNAE 183

                          170
                   ....*....|....*...
gi 1907188396  520 HLTEWLQS--VKRYWKQV 535
Cdd:PRK00254   184 ELAEWLNAelVVSDWRPV 201
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 845-924 2.59e-09

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: 56.06  E-value: 2.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  845 ETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 924
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI-NYDLPWNPASYIQRIGRAGRAG 109
 
Name Accession Description Interval E-value
DEXHc_DDX60 cd18025
DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an ...
 357-534 6.07e-116

DEXH-box helicase domain of DEAD box protein 60; DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 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: 350783 [Multi-domain]  Cd Length: 192  Bit Score: 359.76  E-value: 6.07e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  357 IPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGES 435
Cdd:cd18025      1 NPDAWQRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  436 LCGVFTRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSAT 514
Cdd:cd18025     81 LWGVFTRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSAT 160

                          170       180
                   ....*....|....*....|
gi 1907188396  515 ISNPQHLTEWLQSVKRYWKQ 534
Cdd:cd18025    161 IGNPQKFHEWLQSVQRARKA 180
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 359-528 3.65e-47

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: 167.05  E-value: 3.65e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  359 DTWQRELLDVVDNY-ESAVIVAPTSSGKTYASYYCMEKVLKESdEGVVVYVAPTKALVNQVAATVEYRYAKNMpageSLC 437
Cdd:cd17921      3 NPIQREALRALYLSgDSVLVSAPTSSGKTLIAELAILRALATS-GGKAVYIAPTRALVNQKEADLRERFGPLG----KNV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 GVFTRDYRHDAL---NCQVLITVPACFEILLLAPHrQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR-----CPFL 509
Cdd:cd17921     78 GLLTGDPSVNKLllaEADILVATPEKLDLLLRNGG-ERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLrinknARFV 156

                          170
                   ....*....|....*....
gi 1907188396  510 ALSATISNPQHLTEWLQSV 528
Cdd:cd17921    157 GLSATLPNAEDLAEWLGVE 175
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
362-1036 1.18e-39

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 155.44  E-value: 1.18e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESLcGVF 440
Cdd:COG1204     27 QAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIKV-GVS 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  441 TRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP---FLAL 511
Cdd:COG1204    101 TGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPeaqIVAL 177

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  512 SATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCSVRQGd 591
Cdd:COG1204    178 SATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRSKDPT- 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  592 vcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKYEESLK 671
Cdd:COG1204    229 ---------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRDAESLA 256

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  672 EEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEKKQEek 751
Cdd:COG1204    257 KKLADELKRRLTPEER----------------------------------------------EELEELAEELLEVSEE-- 288

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  752 rppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkaiddqll 831
Cdd:COG1204    289 --------------------------------------------THT--------------------------------- 291

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  832 qrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA----QNSVY 907
Cdd:COG1204    292 ------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkrGGMVP 359

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  908 LDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KADDLEDg 979
Cdd:COG1204    360 IPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFANSREE- 436

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  980 kakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1036
Cdd:COG1204    437 ---LLDFLENTFYAYQYDK--GDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 791-934 9.50e-35

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: 130.37  E-value: 9.50e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  791 LDESVMHETEHNYLLQTLEKNLEIPKDCTYANQKAIDD--QLLqrVFhrvRFERKG--ETLKRLAerGIGYHHSSMSAKE 866
Cdd:cd18795      5 LEEYVLGFNGLGIKLRVDVMNKFDSDIIVLLKIETVSEgkPVL--VF---CSSRKEceKTAKDLA--GIAFHHAGLTRED 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907188396  867 KQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVY-------LDALNYRQMSGRAGRRGQDLLGDVYFF 934
Cdd:cd18795     78 RELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLEYLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
354-999 5.64e-32

Superfamily II RNA helicase [Replication, recombination and repair];


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 134.68  E-value: 5.64e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  354 QDFIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQ-VAATVEyRYaknmpa 432
Cdd:COG4581     22 RGFELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQkFFDLVE-RF------ 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  433 GESLCGVFTRDYR--HDAlncQVLI-TVpacfEILL-LAPHRQNWVKRIRYVIFDEVHCLG-GEIGAeIWEhlLVMIRCP 507
Cdd:COG4581     93 GAENVGLLTGDASvnPDA---PIVVmTT----EILRnMLYREGADLEDVGVVVMDEFHYLAdPDRGW-VWE--EPIIHLP 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  508 ----FLALSATISNPQHLTEWLQSVkrywkqvdstmeertvskrtgtsRGSyykdqaqarqsykVRLVLYGERyndleky 583
Cdd:COG4581    163 arvqLVLLSATVGNAEEFAEWLTRV-----------------------RGE-------------TAVVVSEER------- 199

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  584 lcsvrqgdvcfdhfhpcaaltidhiekygfPSDLalspresIQLYdtmcqvwkswpqaqSLCPENFTQFKnkiVIKKLda 663
Cdd:COG4581    200 ------------------------------PVPL-------EFHY--------------LVTPRLFPLFR---VNPEL-- 223

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  664 rkyeeslkeeftnwvkngneeearmvlkKLSPDYHEhsgrmldffpcLVEKLRKMEKLPALFFLFklniveecaenafef 743
Cdd:COG4581    224 ----------------------------LRPPSRHE-----------VIEELDRGGLLPAIVFIF--------------- 249

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  744 lekkqeekrppkadkearttanklrkvkkslekqktvdekgqksSRR-LDESVMhetehnyllQTLEKNLeipkdCTYAN 822
Cdd:COG4581    250 --------------------------------------------SRRgCDEAAQ---------QLLSARL-----TTKEE 271

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  823 QKAIDDQLLQRvfhRVRFE-RKGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVF 901
Cdd:COG4581    272 RAEIREAIDEF---AEDFSvLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVF 348

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  902 AQNS-------VYLDALNYRQMSGRAGRRGQDLLGDVY----FFDIPlPKIGKLIKSKVPELRGQFPLSISLILRlmLLA 970
Cdd:COG4581    349 TKLSkfdgerhRPLTAREFHQIAGRAGRRGIDTEGHVVvlapEHDDP-KKFARLASARPEPLRSSFRPSYNMVLN--LLA 425

                          650       660
                   ....*....|....*....|....*....
gi 1907188396  971 SkaddleDGKAKALSVLKHSLLSFKQPRA 999
Cdd:COG4581    426 R------PGLERARELLEDSFAQFQADRS 448
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 362-516 5.37e-22

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: 94.23  E-value: 5.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLCGVF 440
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGD 83

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907188396  441 TRDYRHDAL-NCQVLITVPacfEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPFLALSATIS 516
Cdd:pfam00270   84 SRKEQLEKLkGPDILVGTP---GRLLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSATLP 159
DEXDc smart00487
DEAD-like helicases superfamily;
356-547 3.30e-18

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 84.47  E-value: 3.30e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396   356 FIPDTWQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNmpaGE 434
Cdd:smart00487    7 EPLRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL---GL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396   435 SLCGVFTRDYRHDAL------NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--C 506
Cdd:smart00487   84 KVVGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPknV 161

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|.
gi 1907188396   507 PFLALSATISNPQHLTEWLqsvkrYWKQVDSTMEERTVSKR 547
Cdd:smart00487  162 QLLLLSATPPEEIENLLEL-----FLNDPVFIDVGFTPLEP 197
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 373-525 2.26e-17

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: 80.71  E-value: 2.26e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYC-MEKVLKESDEGV-VVYVAPTKALVNQVAATVEyRYAKNMPAGESLcGVFTRDY----RH 446
Cdd:cd17922      2 RNVLIAAPTGSGKTEAAFLPaLSSLADEPEKGVqVLYISPLKALINDQERRLE-EPLDEIDLEIPV-AVRHGDTsqseKA 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  447 DALNC--QVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCL-GGEIGAEI---WEHLLVMIRCPF--LALSATISNP 518
Cdd:cd17922     80 KQLKNppGILITTPESLELLLVNKKLRELFAGLRYVVVDEIHALlGSKRGVQLellLERLRKLTGRPLrrIGLSATLGNL 159


                   ....*..
gi 1907188396  519 QHLTEWL 525
Cdd:cd17922    160 EEAAAFL 166
PRK02362 PRK02362
ATP-dependent DNA helicase;
738-1041 2.35e-17

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 87.71  E-value: 2.35e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  738 ENAFEFLEKKQEEKRPPKADkeartTANKLRKvkkslekqkTVDEKGQ----KSSRRLDESvmhetehnyllqtleknle 813
Cdd:PRK02362   212 GGAIHFDDSQREVEVPSKDD-----TLNLVLD---------TLEEGGQclvfVSSRRNAEG------------------- 258

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  814 IPKDCTYANQKAIDDQL---LQRVFHRVRFERKGETLKRLA---ERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGT 887
Cdd:PRK02362   259 FAKRAASALKKTLTAAEraeLAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPT 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  888 LALGINMPCKSVV------FAQNS--VYLDALNYRQMSGRAGRRGQDLLG----------------DVYFFDIPLPkigk 943
Cdd:PRK02362   339 LAAGLNLPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLDPYGeavllaksydeldelfERYIWADPED---- 414

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  944 lIKSKvpelrgqfpLSISLILRLMLLASKADDLEDGKAKALSVLKHSLLSFKQP------RAIDMlklyflySLQFLVKE 1017
Cdd:PRK02362   415 -VRSK---------LATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDdtgrleRVVDD-------VLDFLERN 477

                          330       340
                   ....*....|....*....|....*..
gi 1907188396 1018 GHIDQEGN---PTGFAGLVSHLhYHEP 1041
Cdd:PRK02362   478 GMIEEDGEtleATELGHLVSRL-YIDP 503
DEXHc_Mtr4-like cd18024
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ...
 340-530 4.33e-17

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: 81.34  E-value: 4.33e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  340 YLIREERKDPDPRVQDFIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQva 419
Cdd:cd18024     15 PISAHKPPGNPARTYPFTLDPFQKTAIACIERNESVLVSAHTSAGKTVVAEYAIAQSLRDKQR--VIYTSPIKALSNQ-- 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  420 atvEYRyakNMPAGESLCGVFTRDYR-HDALNCQVLITvpacfEILLLAPHRQNWVKR-IRYVIFDEVHCLGGEIGAEIW 497
Cdd:cd18024     91 ---KYR---ELQEEFGDVGLMTGDVTiNPNASCLVMTT-----EILRSMLYRGSEIMReVAWVIFDEIHYMRDKERGVVW 159

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1907188396  498 EHLLV----MIRcpFLALSATISNPQHLTEWLQSVKR 530
Cdd:cd18024    160 EETIIllpdKVR--YVFLSATIPNARQFAEWICKIHK 194
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 362-525 3.06e-16

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: 78.14  E-value: 3.06e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLkeSDEGVVVYVAPTKALVNQvaatvEYRYAKNMPAGESLCGVF 440
Cdd:cd18028      6 QAEAVRaGLLKGENLLISIPTASGKTLIAEMAMVNTL--LEGGKALYLVPLRALASE-----KYEEFKKLEEIGLKVGIS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  441 TRDYRHDAL---NCQVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR-----CPFLALS 512
Cdd:cd18028     79 TGDYDEDDEwlgDYDIIVATYEKFDSLL--RHSPSWLRDVGVVVVDEIHLISDEERGPTLESIVARLRrlnpnTQIIGLS 156

                          170
                   ....*....|...
gi 1907188396  513 ATISNPQHLTEWL 525
Cdd:cd18028    157 ATIGNPDELAEWL 169
PRK01172 PRK01172
ATP-dependent DNA helicase;
845-1050 8.90e-16

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 82.62  E-value: 8.90e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  845 ETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQ-------NSVYLDALNYRQMS 917
Cdd:PRK01172   278 DSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDitrygngGIRYLSNMEIKQMI 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  918 GRAGRRGQDLLGDVYFF---------------DIPLPKIGKLIKSKvpELRGQFPLSISlilrlMLLASKADDLEDgkak 982
Cdd:PRK01172   358 GRAGRPGYDQYGIGYIYaaspasydaakkylsGEPEPVISYMGSQR--KVRFNTLAAIS-----MGLASSMEDLIL---- 426

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  983 alsvLKHSLLSFKQpRAIDMLKLYFLYSLQFLVKEGHIDQEG--NPTGFAGLVSHLHYHEPSNLVFVSFL 1050
Cdd:PRK01172   427 ----FYNETLMAIQ-NGVDEIDYYIESSLKFLKENGFIKGDVtlRATRLGKLTSDLYIDPESALILKSAF 491
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 362-526 1.24e-15

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: 77.01  E-value: 1.24e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELL-DVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEG-----VVVYVAPTKALVNQVAAtvEYRyAKNMPAGES 435
Cdd:cd18023      6 QSEVFpDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYD--DWK-EKFGPLGLS 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  436 lCGVFTRDYRHDAL----NCQVLITVPACFE-ILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIwE---------HLL 501
Cdd:cd18023     83 -CAELTGDTEMDDTfeiqDADIILTTPEKWDsMTRRWRDNGNLVQLVALVLIDEVHIIKENRGATL-EvvvsrmktlSSS 160

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1907188396  502 VMIRCP------FLALSATISNPQHLTEWLQ 526
Cdd:cd18023    161 SELRGStvrpmrFVAVSATIPNIEDLAEWLG 191
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 373-525 3.18e-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: 75.49  E-value: 3.18e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNMpaGES---LCGVFTRDYRhDAL 449
Cdd:cd18022     18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKRFEEKL--GKKvveLTGDVTPDMK-ALA 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  450 NCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGA----------EIWEHLLVMIRcpFLALSATISNPQ 519
Cdd:cd18022     95 DADIIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLGSDRGPvlevivsrmnYISSQTEKPVR--LVGLSTALANAG 172


                   ....*.
gi 1907188396  520 HLTEWL 525
Cdd:cd18022    173 DLANWL 178
DEXHc_SKIV2L cd18027
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ...
 356-538 3.31e-15

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: 74.99  E-value: 3.31e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  356 FIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQvaatvEYRYAKNMPAGes 435
Cdd:cd18027      7 FELDVFQKQAILHLEAGDSVFVAAHTSAGKTVVAEYAIALAQKHMTR--TIYTSPIKALSNQ-----KFRDFKNTFGD-- 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  436 lCGVFTRDYR-HDALNCQVLITvpacfEILLLAPHRQNWVKR-IRYVIFDEVHCLGGEIGAEIWEHLLVMI--RCPFLAL 511
Cdd:cd18027     78 -VGLITGDVQlNPEASCLIMTT-----EILRSMLYNGSDVIRdLEWVIFDEVHYINDAERGVVWEEVLIMLpdHVSIILL 151

                          170       180
                   ....*....|....*....|....*..
gi 1907188396  512 SATISNPQHLTEWLQSVKRYWKQVDST 538
Cdd:cd18027    152 SATVPNTVEFADWIGRIKKKNIYVIST 178
HELICc smart00490
helicase superfamily c-terminal domain;
848-924 8.65e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 8.65e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907188396   848 KRLAERGIGY--HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 924
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 362-523 2.20e-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: 78.34  E-value: 2.20e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLDVVDNYESAVIVAPTSSGKTYAsyYC---MEKVLKESDeGVVVYVAPTKALVN-QVAATVEyrYAKNMPAGESlC 437
Cdd:COG1205     61 QAEAIEAARAGKNVVIATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALARdQLRRLRE--LAEALGLGVR-V 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 GVFT----RDYRHDAL-NCQVLITVPacfEIL---LLaPHRQNWV---KRIRYVIFDEVHCLGGEIGAeiweHLLVMIR- 505
Cdd:COG1205    135 ATYDgdtpPEERRWIReHPDIVLTNP---DMLhygLL-PHHTRWArffRNLRYVVIDEAHTYRGVFGS----HVANVLRr 206

                          170       180
                   ....*....|....*....|....*....
gi 1907188396  506 ----CP-------FLALSATISNPQHLTE 523
Cdd:COG1205    207 lrriCRhygsdpqFILASATIGNPAEHAE 235
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 361-514 1.16e-13

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: 69.64  E-value: 1.16e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  361 WQRELLDVVDNYES---AVIVAPTSSGKTYASYYCMEKVLKESdegvVVYVAPTKALVNQVAAtveyRYAKnmPAGESLC 437
Cdd:cd17926      4 YQEEALEAWLAHKNnrrGILVLPTGSGKTLTALALIAYLKELR----TLIVVPTDALLDQWKE----RFED--FLGDSSI 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 GVFTRDYRHDALNCQVLITVP----ACFEILLLAPHRQNwvkrirYVIFDEVHclggEIGAEIWEHLLVMIRCPF-LALS 512
Cdd:cd17926     74 GLIGGGKKKDFDDANVVVATYqslsNLAEEEKDLFDQFG------LLIVDEAH----HLPAKTFSEILKELNAKYrLGLT 143


                   ..
gi 1907188396  513 AT 514
Cdd:cd17926    144 AT 145
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 373-525 2.61e-13

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: 69.98  E-value: 2.61e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNMPAG-ESLCGVFTRDYRHDALNc 451
Cdd:cd18021     20 DNVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGPLLGKKvVKLTGETSTDLKLLAKS- 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  452 QVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAeIWEHLLVMIR---------CPFLALSATISNPQHLT 522
Cdd:cd18021     99 DVILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGENGP-VYEVVVSRMRyissqlekpIRIVGLSSSLANARDVG 177


                   ...
gi 1907188396  523 EWL 525
Cdd:cd18021    178 EWL 180
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
339-514 4.61e-13

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 73.52  E-value: 4.61e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  339 HYLIREERKDPDPRVQ-DFIPDTWQRELLD-----VVDNYESAVIVAPTSSGKTYASYYCMEKVLKesdEGVVVYVAPTK 412
Cdd:COG1061     61 ELAEAEALEAGDEASGtSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRR 137

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  413 ALVNQVAATveyrYAKNMPAGESLCGVFTRDYRHdalncqVLITVpacfEILLLAPHRQNWVKRIRYVIFDEVHclggEI 492
Cdd:COG1061    138 ELLEQWAEE----LRRFLGDPLAGGGKKDSDAPI------TVATY----QSLARRAHLDELGDRFGLVIIDEAH----HA 199

                          170       180
                   ....*....|....*....|...
gi 1907188396  493 GAEIWEHLLVMIRCPF-LALSAT 514
Cdd:COG1061    200 GAPSYRRILEAFPAAYrLGLTAT 222
PRK00254 PRK00254
ski2-like helicase; Provisional
 845-970 5.40e-13

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 73.70  E-value: 5.40e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  845 ETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVYLD-------ALNYRQMS 917
Cdd:PRK00254   288 EKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNfgwedipVLEIQQMM 367

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907188396  918 GRAGRRGQDLLGD---VYFFDIPLPKIGKLIKSKVPELRGQfpLSISLILRLMLLA 970
Cdd:PRK00254   368 GRAGRPKYDEVGEaiiVATTEEPSKLMERYIFGKPEKLFSM--LSNESAFRSQVLA 421
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 373-514 8.44e-13

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: 67.04  E-value: 8.44e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCMEKVLkESDEGVVVYVAPTKALVNQVAATVEYRYAKNMPageslCGVFTRD------YRH 446
Cdd:cd00046      2 ENVLITAPTGSGKTLAALLAALLLL-LKKGKKVLVLVPTKALALQTAERLRELFGPGIR-----VAVLVGGssaeerEKN 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907188396  447 DALNCQVLITVPACFEILLLAPHRQnWVKRIRYVIFDEVHCLGGeIGAEIWEHLLVMIR-----CPFLALSAT 514
Cdd:cd00046     76 KLGDADIIIATPDMLLNLLLREDRL-FLKDLKLIIVDEAHALLI-DSRGALILDLAVRKaglknAQVILLSAT 146
PRK00254 PRK00254
ski2-like helicase; Provisional
 373-535 3.11e-12

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 71.00  E-value: 3.11e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCM-EKVLKESdeGVVVYVAPTKALvnqvaATVEYRYAKNMPAGESLCGVFTRDY------- 444
Cdd:PRK00254    40 KNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL-----AEEKYREFKDWEKLGLRVAMTTGDYdstdewl 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  445 -RHDalncqVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGG-EIGAE---IWEHLLVmiRCPFLALSATISNPQ 519
Cdd:PRK00254   113 gKYD-----IIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGSyDRGATlemILTHMLG--RAQILGLSATVGNAE 183

                          170
                   ....*....|....*...
gi 1907188396  520 HLTEWLQS--VKRYWKQV 535
Cdd:PRK00254   184 ELAEWLNAelVVSDWRPV 201
ResIII pfam04851
Type III restriction enzyme, res subunit;
375-514 2.11e-11

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 63.46  E-value: 2.11e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  375 AVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQvaaTVEyRYAKNMPAGESLCGVFT-RDYRHDALNCQV 453
Cdd:pfam04851   26 GLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQ---ALE-EFKKFLPNYVEIGEIISgDKKDESVDDNKI 101

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907188396  454 LI-TVPACFEILLLAPHrQNWVKRIRYVIFDEVHclggEIGAEIWEHLLVMIRCPF-LALSAT 514
Cdd:pfam04851  102 VVtTIQSLYKALELASL-ELLPDFFDVIIIDEAH----RSGASSYRNILEYFKPAFlLGLTAT 159
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 362-520 3.25e-11

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: 63.37  E-value: 3.25e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  362 QRELLDVVDNYESAVIVAPTSSGKTYAsyY---CMEKVLKESdEGVVVYVAPTKALVN-QVAATVEyrYAKNMPAGESlC 437
Cdd:cd17923      5 QAEAIEAARAGRSVVVTTGTASGKSLC--YqlpILEALLRDP-GSRALYLYPTKALAQdQLRSLRE--LLEQLGLGIR-V 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 GVFTRDYRHDA------LNCQVLITVPACFEILLLAPHRQ--NWVKRIRYVIFDEVHCLGGEIGAeiweHLLVMIR---- 505
Cdd:cd17923     79 ATYDGDTPREErraiirNPPRILLTNPDMLHYALLPHHDRwaRFLRNLRYVVLDEAHTYRGVFGS----HVALLLRrlrr 154

                          170       180
                   ....*....|....*....|....
gi 1907188396  506 -CP-------FLALSATISNP-QH 520
Cdd:cd17923    155 lCRrygadpqFILTSATIGNPaEH 178
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 845-924 2.59e-09

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: 56.06  E-value: 2.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  845 ETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 924
Cdd:pfam00271   31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI-NYDLPWNPASYIQRIGRAGRAG 109
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 834-925 6.36e-09

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: 56.12  E-value: 6.36e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  834 VFH--RVRFERKGETLKRLAERG-----IGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINM-PCKSVVfaQNS 905
Cdd:cd18796     43 VFTntRSQAERLAQRLRELCPDRvppdfIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIgDVDLVI--QIG 120

                           90       100
                   ....*....|....*....|
gi 1907188396  906 VYLDALNYRQMSGRAGRRGQ 925
Cdd:cd18796    121 SPKSVARLLQRLGRSGHRPG 140
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
350-525 7.60e-08

Lhr-like helicase [Replication, recombination and repair];


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 57.03  E-value: 7.60e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  350 DPRVQDFIPDTW------QRELLDVVDNYESAVIVAPTSSGKTYASY------YCMEKVLKESDEGV-VVYVAPTKALVN 416
Cdd:COG1201     11 HPAVRAWFAARFgaptppQREAWPAIAAGESTLLIAPTGSGKTLAAFlpaldeLARRPRPGELPDGLrVLYISPLKALAN 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  417 QVaatveyryAKNM---------PAGESLCGV----------------FTRDYRHdalncqVLITVPACFEILLLAPHRQ 471
Cdd:COG1201     91 DI--------ERNLrapleeigeAAGLPLPEIrvgvrtgdtpaserqrQRRRPPH------ILITTPESLALLLTSPDAR 156

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907188396  472 NWVKRIRYVIFDEVHCLGG-------EIGAEIWEHL----LVMIrcpflALSATISNPQHLTEWL 525
Cdd:COG1201    157 ELLRGVRTVIVDEIHALAGskrgvhlALSLERLRALaprpLQRI-----GLSATVGPLEEVARFL 216
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 356-486 2.08e-07

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: 52.86  E-value: 2.08e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  356 FIPDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKE----SDEGVVVYVAPTKALVNQvAATVEYRYAKNMP 431
Cdd:cd18036      1 LELRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKrrsaGEKGRVVVLVNKVPLVEQ-QLEKFFKYFRKGY 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907188396  432 AGESLCGVFTRD--YRHDALNCQVLITVPACFEILLLAPhRQNwvKRIRY-----VIFDEVH 486
Cdd:cd18036     80 KVTGLSGDSSHKvsFGQIVKASDVIICTPQILINNLLSG-REE--ERVYLsdfslLIFDECH 138
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 376-514 3.17e-07

DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain]  Cd Length: 186  Bit Score: 51.91  E-value: 3.17e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  376 VIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVA----------------------ATVEYRYAKNMPAG 433
Cdd:cd17930      5 ILEAPTGSGKTEAALLWALKLAARGGKRRIIYALPTRATINQMYerireilgrlddedkvlllhskAALELLESDEEPDD 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  434 ESLCGVFTRDYRHDALNCQVLITVPacFEILL-LAPHRQNWVK--RI--RYVIFDEVHCLGGEIGAEIWEHLLVMIR--- 505
Cdd:cd17930     85 DPVEAVDWALLLKRSWLAPIVVTTI--DQLLEsLLKYKHFERRlhGLanSVVVLDEVQAYDPEYMALLLKALLELLGelg 162


                   ....*....
gi 1907188396  506 CPFLALSAT 514
Cdd:cd17930    163 GPVVLMTAT 171
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 231-514 4.46e-06

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: 50.85  E-value: 4.46e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  231 KAQVERVGLQACLKAWKEHCQAEGETTKDLSIAVNMMKRIHSLLDKHSELLQEADQKLIARCLKYLGFCELAVSLYPTQD 310
Cdd:COG1203     11 GALALAALLLLLLALLLAALLLLLLAALLLALLLALLLLAALELALLLLLLLLLLLLLLLLLLDLLLDDLAFLFLLLLID 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  311 A----SDGIKMKKKNKysvgigpARFQLQYMGHYLirEERKDPDPRVqdfipDTWQRELLDVVDNYESA-----VIVAPT 381
Cdd:COG1203     91 AdwldSANFDMARQAL-------DHLLAERLERLL--PKKSKPRTPI-----NPLQNEALELALEAAEEepglfILTAPT 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  382 SSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVA-----------------ATVEYRYAKNMPAGESlcgvftRDY 444
Cdd:COG1203    157 GGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYdrlrdlfgedvllhhslADLDLLEEEEEYESEA------RWL 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  445 RH--DALNCQVLITVPACFEILLLAPHRQNWVKRIRY----VIFDEVHClggeIGAEIWEHLLVMIR------CPFLALS 512
Cdd:COG1203    231 KLlkELWDAPVVVTTIDQLFESLFSNRKGQERRLHNLansvIILDEVQA----YPPYMLALLLRLLEwlknlgGSVILMT 306


                   ..
gi 1907188396  513 AT 514
Cdd:COG1203    307 AT 308
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 358-521 1.58e-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: 47.43  E-value: 1.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  358 PDTWQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLK---ESDEGVVVYVAPTKALVNQvAATVEYRYAKNMP--- 431
Cdd:cd17927      3 PRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKkfpAGRKGKVVFLANKVPLVEQ-QKEVFRKHFERPGykv 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  432 ---AGESLCGVFTRDYrhdALNCQVLITVPACFEILLLApHRQNWVKRIRYVIFDEVHCLGGEigaeiWEHLLVMIRCPF 508
Cdd:cd17927     82 tglSGDTSENVSVEQI---VESSDVIIVTPQILVNDLKS-GTIVSLSDFSLLVFDECHNTTKN-----HPYNEIMFRYLD 152

                          170
                   ....*....|...
gi 1907188396  509 LALSATISNPQHL 521
Cdd:cd17927    153 QKLGSSGPLPQIL 165
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 821-925 1.70e-05

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: 45.66  E-value: 1.70e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  821 ANQKAIDDQLLQRVFHR-------VRFERKGETL-KRLAERGI--GYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLAL 890
Cdd:cd18794     13 KKDEKLDLLKRIKVEHLggsgiiyCLSRKECEQVaARLQSKGIsaAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGM 92

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1907188396  891 GINMPckSVVF-AQNSVYLDALNYRQMSGRAGRRGQ 925
Cdd:cd18794     93 GIDKP--DVRFvIHYSLPKSMESYYQESGRAGRDGL 126
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
857-943 2.14e-05

Superfamily II helicase, archaea-specific [Replication, recombination and repair];


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 49.12  E-value: 2.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  857 YHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVYLDALN---YRQMSGRAGRRGQDLLGDVYF 933
Cdd:COG1202    453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSvqeFHQMLGRAGRPDYHDRGKVYL 532

                           90
                   ....*....|
gi 1907188396  934 fdipLPKIGK 943
Cdd:COG1202    533 ----LVEPGK 538
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 848-928 2.36e-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: 48.68  E-value: 2.36e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  848 KRLAERGIGY----HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCksvvfaqnsvyLDA----------LNY 913
Cdd:COG1205    310 RALREPDLADrvaaYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGG-----------LDAvvlagypgtrASF 378

                           90
                   ....*....|....*
gi 1907188396  914 RQMSGRAGRRGQDLL 928
Cdd:COG1205    379 WQQAGRAGRRGQDSL 393
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 373-517 6.81e-05

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: 45.44  E-value: 6.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCM----EKVLKES-----DEGVVVYVAPTKALVNQVAATVEYRYAK-NMPAGE-----SLC 437
Cdd:cd18019     34 ENLLLCAPTGAGKTNVALLTIlreiGKHRNPDgtinlDAFKIVYIAPMKALVQEMVGNFSKRLAPyGITVAEltgdqQLT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  438 gvftrdyRHDALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGA--------EIW--EHLLVMIRcp 507
Cdd:cd18019    114 -------KEQISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDDRGPvlesivarTIRqiEQTQEYVR-- 184

                          170
                   ....*....|
gi 1907188396  508 FLALSATISN 517
Cdd:cd18019    185 LVGLSATLPN 194
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 373-517 1.18e-04

N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350778 [Multi-domain]  Cd Length: 199  Bit Score: 44.73  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  373 ESAVIVAPTSSGKTYASYYCMEKVLKES---------DEGVVVYVAPTKALVNQVAATVEYRYAK-NMPAGEslcgvFTR 442
Cdd:cd18020     18 ENMLICAPTGAGKTNIAMLTILHEIRQHvnqggvikkDDFKIVYIAPMKALAAEMVEKFSKRLAPlGIKVKE-----LTG 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  443 DY---RHDALNCQVLITVPACFEILLLAPHRQN-WVKRIRYVIFDEVHCLGGEIGAEIwEHLLV-----------MIRcp 507
Cdd:cd18020     93 DMqltKKEIAETQIIVTTPEKWDVVTRKSSGDVaLSQLVRLLIIDEVHLLHDDRGPVI-ESLVArtlrqvestqsMIR-- 169

                          170
                   ....*....|
gi 1907188396  508 FLALSATISN 517
Cdd:cd18020    170 IVGLSATLPN 179
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 356-517 1.76e-04

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: 44.18  E-value: 1.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  356 FIPDTWQRELLDVVDNyESAVIVAPTSSGKTYASyyCM------EKVLKESDEG-VVVYVAPTKALVNQVAATVE-YRYA 427
Cdd:cd18034      1 FTPRSYQLELFEAALK-RNTIVVLPTGSGKTLIA--VMlikemgELNRKEKNPKkRAVFLVPTVPLVAQQAEAIRsHTDL 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  428 KNMP-AGESLCGVFTRDYRHDAL-NCQVLITVPACFEILLlaphRQNWVK--RIRYVIFDEVH-CLGGEIGAEI---WEH 499
Cdd:cd18034     78 KVGEySGEMGVDKWTKERWKEELeKYDVLVMTAQILLDAL----RHGFLSlsDINLLIFDECHhATGDHPYARImkeFYH 153

                          170
                   ....*....|....*....
gi 1907188396  500 LLVMIRCP-FLALSATISN 517
Cdd:cd18034    154 LEGRTSRPrILGLTASPVN 172
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
377-486 2.09e-04

ERCC4-related helicase [Replication, recombination and repair];


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 45.88  E-value: 2.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  377 IVAPTSSGKTYASYYCMEKVLKESDeGVVVYVAPTKALVNQVAATveyrYAKNMPAGESLCGVFTRDYRHD---AL--NC 451
Cdd:COG1111     22 VVLPTGLGKTAVALLVIAERLHKKG-GKVLFLAPTKPLVEQHAEF----FKEALNIPEDEIVVFTGEVSPEkrkELweKA 96

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1907188396  452 QVLITVPACFEILLLAphrqnwvKRIR-----YVIFDEVH 486
Cdd:COG1111     97 RIIVATPQVIENDLIA-------GRIDlddvsLLIFDEAH 129
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 837-928 2.99e-04

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: 42.63  E-value: 2.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  837 RVRFERKGETLKRLAE-RGiGYhhssmSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCksvvfaqnsvyLDAL---- 911
Cdd:cd18797     56 KARLVEEGPLASKVASyRA-GY-----LAEDRREIEAELFNGELLGVVATNALELGIDIGG-----------LDAVvlag 118

                           90       100
                   ....*....|....*....|...
gi 1907188396  912 ------NYRQMSGRAGRRGQDLL 928
Cdd:cd18797    119 ypgslaSLWQQAGRAGRRGKDSL 141
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
833-895 5.74e-04

Lhr-like helicase [Replication, recombination and repair];


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 44.32  E-value: 5.74e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907188396  833 RVFHRvrferkgetLKRLAERG---IGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMP 895
Cdd:COG1201    287 RLFQR---------LNELNPEDalpIAAHHGSLSREQRLEVEEALKAGELRAVVATSSLELGIDIG 343
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 374-486 1.60e-03

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350793 [Multi-domain]  Cd Length: 181  Bit Score: 40.96  E-value: 1.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  374 SAVIVAPTSSGKTYASYYCMEKVLKESDeGVVVYVAPTKALVNQVAATveYRYAKNMPAG-ESLCGVFTRDYRHDALN-C 451
Cdd:cd18035     18 NTLIVLPTGLGKTIIAILVAADRLTKKG-GKVLILAPSRPLVEQHAEN--LKRVLNIPDKiTSLTGEVKPEERAERWDaS 94

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1907188396  452 QVLITVPACFEILLLApHRQNwVKRIRYVIFDEVH 486
Cdd:cd18035     95 KIIVATPQVIENDLLA-GRIT-LDDVSLLIFDEAH 127
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 845-924 1.90e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.39  E-value: 1.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  845 ETLKRLAERGI--GYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPckSVVFAqnsVYLD----ALNYRQMSG 918
Cdd:PRK11057   251 DTAARLQSRGIsaAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKP--NVRFV---VHFDiprnIESYYQETG 325


                   ....*.
gi 1907188396  919 RAGRRG 924
Cdd:PRK11057   326 RAGRDG 331
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 837-895 2.25e-03

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 42.57  E-value: 2.25e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  837 RVRFERKGETLKRLAERGIGYHHSSMSaKEKQL-VEILFRKGFIRVVTATGTLALGINMP 895
Cdd:PRK13767   299 RVLYNLRKRFPEEYDEDNIGAHHSSLS-REVRLeVEEKLKRGELKVVVSSTSLELGIDIG 357
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 848-934 4.75e-03

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: 41.01  E-value: 4.75e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  848 KRLAERGIGYHHSSMSA-KEKqlVEIlFRKGFIRVVTATGTLALGINMPCKSV--VFAQNSVY-LDALnyRQMSGRAGRR 923
Cdd:COG4098    341 KLFPEERIAGVHAEDPErKEK--VQA-FRDGEIPILVTTTILERGVTFPNVDVavLGADHPVFtEAAL--VQIAGRVGRS 415

                           90
                   ....*....|.
gi 1907188396  924 GQDLLGDVYFF 934
Cdd:COG4098    416 ADYPTGEVIFF 426
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 376-485 5.28e-03

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: 39.73  E-value: 5.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  376 VIVAPTSSGKTYAsyYCM---EKVLKESDEG-----VVVyVAPTKALVNQVAATVEyRYAKNMPAgESLC---GVftrDY 444
Cdd:cd00268     31 IGQAQTGSGKTLA--FLLpilEKLLPEPKKKgrgpqALV-LAPTRELAMQIAEVAR-KLGKGTGL-KVAAiygGA---PI 102

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1907188396  445 RHDAL----NCQVLITVPACFeILLLAPHRQNwVKRIRYVIFDEV 485
Cdd:cd00268    103 KKQIEalkkGPDIVVGTPGRL-LDLIERGKLD-LSNVKYLVLDEA 145
DEADc_MRH4 cd17965
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ...
 367-484 7.42e-03

DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 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: 350723 [Multi-domain]  Cd Length: 251  Bit Score: 39.67  E-value: 7.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  367 DVVDNYESAVIVAPTSSGKTYAsyYCMEKV--LKESDEGV------------------VVYVAPTKALVNQVAATVEyry 426
Cdd:cd17965     56 NEEPKLEVFLLAAETGSGKTLA--YLAPLLdyLKRQEQEPfeeaeeeyesakdtgrprSVILVPTHELVEQVYSVLK--- 130

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907188396  427 AKNMPAGESLCGV---FTRDYRHDALN----CQVLITVPacFEILLLAPHRQNWVKRIRYVIFDE 484
Cdd:cd17965    131 KLSHTVKLGIKTFssgFGPSYQRLQLAfkgrIDILVTTP--GKLASLAKSRPKILSRVTHLVVDE 193
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
842-925 8.60e-03

Superfamily II DNA helicase RecQ [Replication, recombination and repair];


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 40.12  E-value: 8.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  842 RKG--ETLKRLAERGI--GYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGIN-----------MPcKSVVfaqnsv 906
Cdd:COG0514    240 RKKveELAEWLREAGIraAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDkpdvrfvihydLP-KSIE------ 312

                           90
                   ....*....|....*....
gi 1907188396  907 yldalNYRQMSGRAGRRGQ 925
Cdd:COG0514    313 -----AYYQEIGRAGRDGL 326
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 851-922 8.72e-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: 38.48  E-value: 8.72e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907188396  851 AERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVYLDALNYRQMSGRAGR 922
Cdd:cd18811     60 PELNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGR 131
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 837-925 9.42e-03

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 40.65  E-value: 9.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907188396  837 RVRFERKGETLKRLAERGiGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPckSVVFA-QNSVYLDALNYRQ 915
Cdd:PLN03137   690 RMDCEKVAERLQEFGHKA-AFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKP--DVRFViHHSLPKSIEGYHQ 766

                           90
                   ....*....|
gi 1907188396  916 MSGRAGRRGQ 925
Cdd:PLN03137   767 ECGRAGRDGQ 776
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH