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Conserved domains on  [gi|568954769|ref|XP_006509456|]
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probable ATP-dependent RNA helicase DDX60 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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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 ...
 713-885 6.02e-110

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: 346.66  E-value: 6.02e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  713 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGESLCGVF 791
Cdd:cd18025     6 QRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKSLWGVF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  792 TRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSATISNPQ 870
Cdd:cd18025    86 TRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSATIGNPQ 165

                         170
                  ....*....|....*
gi 568954769  871 HLTEWLQSVKRYWKQ 885
Cdd:cd18025   166 KFHEWLQSVQRARKA 180
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
708-1387 5.48e-42

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: 163.14  E-value: 5.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGES 786
Cdd:COG1204    22 ELYPPQAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 LcGVFTRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP-- 858
Cdd:COG1204    97 V-GVSTGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPea 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  859 -FLALSATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCS 937
Cdd:COG1204   173 qIVALSATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRS 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  938 VRQGdvcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKY 1017
Cdd:COG1204   225 KDPT----------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRD 251

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1018 EESLKEEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEK 1097
Cdd:COG1204   252 AESLAKKLADELKRRLTPEER----------------------------------------------EELEELAEELLEV 285

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1098 KQEekrppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkai 1177
Cdd:COG1204   286 SEE----------------------------------------------THT---------------------------- 291

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1178 ddqllqrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA---- 1253
Cdd:COG1204   292 -----------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkr 354

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1254 QNSVYLDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KAD 1325
Cdd:COG1204   355 GGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFAN 432

                         650       660       670       680       690       700
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769 1326 DLEDgkakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1387
Cdd:COG1204   433 SREE----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 ...
 713-885 6.02e-110

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: 346.66  E-value: 6.02e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  713 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGESLCGVF 791
Cdd:cd18025     6 QRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKSLWGVF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  792 TRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSATISNPQ 870
Cdd:cd18025    86 TRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSATIGNPQ 165

                         170
                  ....*....|....*
gi 568954769  871 HLTEWLQSVKRYWKQ 885
Cdd:cd18025   166 KFHEWLQSVQRARKA 180
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
708-1387 5.48e-42

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 163.14  E-value: 5.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGES 786
Cdd:COG1204    22 ELYPPQAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 LcGVFTRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP-- 858
Cdd:COG1204    97 V-GVSTGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPea 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  859 -FLALSATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCS 937
Cdd:COG1204   173 qIVALSATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRS 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  938 VRQGdvcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKY 1017
Cdd:COG1204   225 KDPT----------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRD 251

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1018 EESLKEEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEK 1097
Cdd:COG1204   252 AESLAKKLADELKRRLTPEER----------------------------------------------EELEELAEELLEV 285

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1098 KQEekrppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkai 1177
Cdd:COG1204   286 SEE----------------------------------------------THT---------------------------- 291

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1178 ddqllqrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA---- 1253
Cdd:COG1204   292 -----------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkr 354

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1254 QNSVYLDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KAD 1325
Cdd:COG1204   355 GGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFAN 432

                         650       660       670       680       690       700
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769 1326 DLEDgkakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1387
Cdd:COG1204   433 SREE----LLDFLENTFYAYQYDK--GDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1142-1285 1.22e-34

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: 1.22e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1142 LDESVMHETEHNYLLQTLEKNLEIPKDCTYANQKAIDD--QLLqrVFhrvRFERKG--ETLKRLAerGIGYHHSSMSAKE 1217
Cdd:cd18795     5 LEEYVLGFNGLGIKLRVDVMNKFDSDIIVLLKIETVSEgkPVL--VF---CSSRKEceKTAKDLA--GIAFHHAGLTRED 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769 1218 KQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVY-------LDALNYRQMSGRAGRRGQDLLGDVYFF 1285
Cdd:cd18795    78 RELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLEYLQMIGRAGRPGFDTRGEAIIM 152
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 710-867 3.85e-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: 95.00  E-value: 3.85e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   710 YPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLC 788
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   789 GVFTRDYRHDAL-NCQVLITVPacfEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPFLALSAT 865
Cdd:pfam00270   81 GGDSRKEQLEKLkGPDILVGTP---GRLLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSAT 157


                   ..
gi 568954769   866 IS 867
Cdd:pfam00270  158 LP 159
DEXDc smart00487
DEAD-like helicases superfamily;
709-898 9.35e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 86.39  E-value: 9.35e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769    709 LYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESL 787
Cdd:smart00487    9 LRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL---GLKV 85

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769    788 CGVFTRDYRHDAL------NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPF 859
Cdd:smart00487   86 VGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPknVQL 163

                           170       180       190
                    ....*....|....*....|....*....|....*....
gi 568954769    860 LALSATISNPQHLTEWLqsvkrYWKQVDSTMEERTVSKR 898
Cdd:smart00487  164 LLLSATPPEEIENLLEL-----FLNDPVFIDVGFTPLEP 197
PRK02362 PRK02362
ATP-dependent DNA helicase;
1089-1392 3.23e-17

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 87.71  E-value: 3.23e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1089 ENAFEFLEKKQEEKRPPKADkeartTANKLRKvkkslekqkTVDEKGQ----KSSRRLDESvmhetehnyllqtleknle 1164
Cdd:PRK02362  212 GGAIHFDDSQREVEVPSKDD-----TLNLVLD---------TLEEGGQclvfVSSRRNAEG------------------- 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1165 IPKDCTYANQKAIDDQL---LQRVFHRVRFERKGETLKRLA---ERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGT 1238
Cdd:PRK02362  259 FAKRAASALKKTLTAAEraeLAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPT 338

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1239 LALGINMPCKSVV------FAQNS--VYLDALNYRQMSGRAGRRGQDLLG----------------DVYFFDIPLPkigk 1294
Cdd:PRK02362  339 LAAGLNLPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLDPYGeavllaksydeldelfERYIWADPED---- 414

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1295 lIKSKvpelrgqfpLSISLILRLMLLASKADDLEDGKAKALSVLKHSLLSFKQP------RAIDMlklyflySLQFLVKE 1368
Cdd:PRK02362  415 -VRSK---------LATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDdtgrleRVVDD-------VLDFLERN 477

                         330       340
                  ....*....|....*....|....*..
gi 568954769 1369 GHIDQEGN---PTGFAGLVSHLhYHEP 1392
Cdd:PRK02362  478 GMIEEDGEtleATELGHLVSRL-YIDP 503
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 671-874 3.09e-15

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: 81.42  E-value: 3.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  671 MKRIHSLLDKHSELLQEADQ----------------------KLIARCLKYLGFcelaVSLYPTQRELLDVVDNYESAVI 728
Cdd:COG1205     1 MARLEELLERLRASPRYGDQivhvrtiparearyapwpdwlpPELRAALKKRGI----ERLYSHQAEAIEAARAGKNVVI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  729 VAPTSSGKTYAsyYC---MEKVLKESDeGVVVYVAPTKALVN-QVAATVEyrYAKNMPAGESlCGVFT----RDYRHDAL 800
Cdd:COG1205    77 ATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALARdQLRRLRE--LAEALGLGVR-VATYDgdtpPEERRWIR 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  801 -NCQVLITVPacfEIL---LLaPHRQNWV---KRIRYVIFDEVHCLGGEIGAeiweHLLVMIR-----CP-------FLA 861
Cdd:COG1205   151 eHPDIVLTNP---DMLhygLL-PHHTRWArffRNLRYVVIDEAHTYRGVFGS----HVANVLRrlrriCRhygsdpqFIL 222

                         250
                  ....*....|...
gi 568954769  862 LSATISNPQHLTE 874
Cdd:COG1205   223 ASATIGNPAEHAE 235
HELICc smart00490
helicase superfamily c-terminal domain;
1199-1275 1.10e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 1.10e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568954769   1199 KRLAERGIGY--HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 1275
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
PRK00254 PRK00254
ski2-like helicase; Provisional
 693-886 5.73e-14

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 77.16  E-value: 5.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  693 IARCLKYLGFCELavslYPTQRELLDV-VDNYESAVIVAPTSSGKTYASYYCM-EKVLKESdeGVVVYVAPTKALvnqva 770
Cdd:PRK00254   12 IKRVLKERGIEEL----YPPQAEALKSgVLEGKNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL----- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  771 ATVEYRYAKNMPAGESLCGVFTRDY--------RHDalncqVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGG- 841
Cdd:PRK00254   81 AEEKYREFKDWEKLGLRVAMTTGDYdstdewlgKYD-----IIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGSy 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 568954769  842 EIGAE---IWEHLLVmiRCPFLALSATISNPQHLTEWLQS--VKRYWKQV 886
Cdd:PRK00254  154 DRGATlemILTHMLG--RAQILGLSATVGNAEELAEWLNAelVVSDWRPV 201
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1185-1275 3.16e-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: 3.16e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  1185 VFHRVRFERKGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNY 1264
Cdd:pfam00271   20 IFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI-NYDLPWNPASY 98

                           90
                   ....*....|.
gi 568954769  1265 RQMSGRAGRRG 1275
Cdd:pfam00271   99 IQRIGRAGRAG 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 ...
 713-885 6.02e-110

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: 346.66  E-value: 6.02e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  713 QRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNM-PAGESLCGVF 791
Cdd:cd18025     6 QRELLDIVDRRESALIVAPTSSGKTFISYYCMEKVLRESDDGVVVYVAPTKALVNQVVAEVYARFSKKYpPSGKSLWGVF 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  792 TRDYRHD-ALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIRCPFLALSATISNPQ 870
Cdd:cd18025    86 TRDYRHNnPMNCQVLITVPECLEILLLSPHNASWVPRIKYVIFDEIHSIGQSEDGAVWEQLLLLIPCPFLALSATIGNPQ 165

                         170
                  ....*....|....*
gi 568954769  871 HLTEWLQSVKRYWKQ 885
Cdd:cd18025   166 KFHEWLQSVQRARKA 180
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 708-879 6.83e-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: 166.28  E-value: 6.83e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLDVVDNY-ESAVIVAPTSSGKTYASYYCMEKVLKESdEGVVVYVAPTKALVNQVAATVEYRYAKNMpageS 786
Cdd:cd17921     1 LLNPIQREALRALYLSgDSVLVSAPTSSGKTLIAELAILRALATS-GGKAVYIAPTRALVNQKEADLRERFGPLG----K 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 LCGVFTRDYRHDAL---NCQVLITVPACFEILLLAPHrQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR-----CP 858
Cdd:cd17921    76 NVGLLTGDPSVNKLllaEADILVATPEKLDLLLRNGG-ERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLrinknAR 154

                         170       180
                  ....*....|....*....|.
gi 568954769  859 FLALSATISNPQHLTEWLQSV 879
Cdd:cd17921   155 FVGLSATLPNAEDLAEWLGVE 175
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
708-1387 5.48e-42

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 163.14  E-value: 5.48e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQVAATVEYRYAKNmpaGES 786
Cdd:COG1204    22 ELYPPQAEALEaGLLEGKNLVVSAPTASGKTLIAELAILKALLNG--GKALYIVPLRALASEKYREFKRDFEEL---GIK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 LcGVFTRDYRHDAL---NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLG-GEIGAEIwEHLLVMIR--CP-- 858
Cdd:COG1204    97 V-GVSTGDYDSDDEwlgRYDILVATPEKLDSLLR--NGPSWLRDVDLVVVDEAHLIDdESRGPTL-EVLLARLRrlNPea 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  859 -FLALSATISNPQHLTEWLQSvkrywKQVDSTmeERTVSKRTGtsrgsyykdqaqarqsykvrlVLYGERYNDLEKYLCS 937
Cdd:COG1204   173 qIVALSATIGNAEEIAEWLDA-----ELVKSD--WRPVPLNEG---------------------VLYDGVLRFDDGSRRS 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  938 VRQGdvcfdhfhpcAALTIDHIEKYGfpsdlalspresiqlydtmcqvwkswpqaQSLCpenftqFKNKivikkldaRKY 1017
Cdd:COG1204   225 KDPT----------LALALDLLEEGG-----------------------------QVLV------FVSS--------RRD 251

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1018 EESLKEEFTNWVKNGNEEEARmvlkklspdyhehsgrmldffpclveklrkmeklpalfflfklnivEECAENAFEFLEK 1097
Cdd:COG1204   252 AESLAKKLADELKRRLTPEER----------------------------------------------EELEELAEELLEV 285

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1098 KQEekrppkadkearttanklrkvkkslekqktvdekgqkssrrldesvMHEtehnyllqtleknleipkdctyanqkai 1177
Cdd:COG1204   286 SEE----------------------------------------------THT---------------------------- 291

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1178 ddqllqrvfhrvrferkGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFA---- 1253
Cdd:COG1204   292 -----------------NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRdtkr 354

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1254 QNSVYLDALNYRQMSGRAGRRGQDLLGDVYFFDIPLPKIGKL----IKSKVPELRGQfpLSISLILRLMLLAS----KAD 1325
Cdd:COG1204   355 GGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELferyILGEPEPIRSK--LANESALRTHLLALiasgFAN 432

                         650       660       670       680       690       700
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769 1326 DLEDgkakALSVLKHSLLSFKQPRaiDMLKLYFLYSLQFLVKEGHIDQEGN---PTGFAGLVSHL 1387
Cdd:COG1204   433 SREE----LLDFLENTFYAYQYDK--GDLEEVVDDALEFLLENGFIEEDGDrlrATKLGKLVSRL 491
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 1142-1285 1.22e-34

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: 1.22e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1142 LDESVMHETEHNYLLQTLEKNLEIPKDCTYANQKAIDD--QLLqrVFhrvRFERKG--ETLKRLAerGIGYHHSSMSAKE 1217
Cdd:cd18795     5 LEEYVLGFNGLGIKLRVDVMNKFDSDIIVLLKIETVSEgkPVL--VF---CSSRKEceKTAKDLA--GIAFHHAGLTRED 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769 1218 KQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVY-------LDALNYRQMSGRAGRRGQDLLGDVYFF 1285
Cdd:cd18795    78 RELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYdgkgyreLSPLEYLQMIGRAGRPGFDTRGEAIIM 152
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
704-1350 6.10e-33

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 138.15  E-value: 6.10e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  704 ELAVSLYPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESdeGVVVYVAPTKALVNQ-VAATVEyRYaknmp 782
Cdd:COG4581    21 ERGFELDPFQEEAILALEAGRSVLVAAPTGSGKTLVAEFAIFLALARG--RRSFYTAPIKALSNQkFFDLVE-RF----- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  783 aGESLCGVFTRDYR--HDAlncQVLI-TVpacfEILL-LAPHRQNWVKRIRYVIFDEVHCLG-GEIGAeIWEhlLVMIRC 857
Cdd:COG4581    93 -GAENVGLLTGDASvnPDA---PIVVmTT----EILRnMLYREGADLEDVGVVVMDEFHYLAdPDRGW-VWE--EPIIHL 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  858 P----FLALSATISNPQHLTEWLQSVkrywkqvdstmeertvskrtgtsRGSyykdqaqarqsykVRLVLYGERyndlek 933
Cdd:COG4581   162 ParvqLVLLSATVGNAEEFAEWLTRV-----------------------RGE-------------TAVVVSEER------ 199

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  934 ylcsvrqgdvcfdhfhpcaaltidhiekygfPSDLalspresIQLYdtmcqvwkswpqaqSLCPENFTQFKnkiVIKKLd 1013
Cdd:COG4581   200 -------------------------------PVPL-------EFHY--------------LVTPRLFPLFR---VNPEL- 223

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1014 arkyeeslkeeftnwvkngneeearmvlkKLSPDYHEhsgrmldffpcLVEKLRKMEKLPALFFLFklniveecaenafe 1093
Cdd:COG4581   224 -----------------------------LRPPSRHE-----------VIEELDRGGLLPAIVFIF-------------- 249

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1094 flekkqeekrppkadkearttanklrkvkkslekqktvdekgqksSRR-LDESVMhetehnyllQTLEKNLeipkdCTYA 1172
Cdd:COG4581   250 ---------------------------------------------SRRgCDEAAQ---------QLLSARL-----TTKE 270

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1173 NQKAIDDQLLQRvfhRVRFE-RKGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVV 1251
Cdd:COG4581   271 ERAEIREAIDEF---AEDFSvLFGKTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVV 347

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1252 FAQNS-------VYLDALNYRQMSGRAGRRGQDLLGDVY----FFDIPlPKIGKLIKSKVPELRGQFPLSISLILRlmLL 1320
Cdd:COG4581   348 FTKLSkfdgerhRPLTAREFHQIAGRAGRRGIDTEGHVVvlapEHDDP-KKFARLASARPEPLRSSFRPSYNMVLN--LL 424

                         650       660       670
                  ....*....|....*....|....*....|
gi 568954769 1321 ASkaddleDGKAKALSVLKHSLLSFKQPRA 1350
Cdd:COG4581   425 AR------PGLERARELLEDSFAQFQADRS 448
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 710-867 3.85e-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: 95.00  E-value: 3.85e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   710 YPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGV-VVYVAPTKALVNQVAATVEYRYAKNMPAGESLC 788
Cdd:pfam00270    1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPqALVLAPTRELAEQIYEELKKLGKGLGLKVASLL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   789 GVFTRDYRHDAL-NCQVLITVPacfEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPFLALSAT 865
Cdd:pfam00270   81 GGDSRKEQLEKLkGPDILVGTP---GRLLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPkkRQILLLSAT 157


                   ..
gi 568954769   866 IS 867
Cdd:pfam00270  158 LP 159
DEXDc smart00487
DEAD-like helicases superfamily;
709-898 9.35e-19

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 86.39  E-value: 9.35e-19
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769    709 LYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNmpaGESL 787
Cdd:smart00487    9 LRPYQKEAIEaLLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSL---GLKV 85

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769    788 CGVFTRDYRHDAL------NCQVLITVPACFEILLLapHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR--CPF 859
Cdd:smart00487   86 VGLYGGDSKREQLrklesgKTDILVTTPGRLLDLLE--NDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPknVQL 163

                           170       180       190
                    ....*....|....*....|....*....|....*....
gi 568954769    860 LALSATISNPQHLTEWLqsvkrYWKQVDSTMEERTVSKR 898
Cdd:smart00487  164 LLLSATPPEEIENLLEL-----FLNDPVFIDVGFTPLEP 197
DEXHc_archSki2 cd18028
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...
 708-876 1.68e-18

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: 84.69  E-value: 1.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLD-VVDNYESAVIVAPTSSGKTYASYYCMEKVLkeSDEGVVVYVAPTKALVNQvaatvEYRYAKNMPAGES 786
Cdd:cd18028     1 ELYPPQAEAVRaGLLKGENLLISIPTASGKTLIAEMAMVNTL--LEGGKALYLVPLRALASE-----KYEEFKKLEEIGL 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 LCGVFTRDYRHDAL---NCQVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGGEIGAEIWEHLLVMIR-----CP 858
Cdd:cd18028    74 KVGISTGDYDEDDEwlgDYDIIVATYEKFDSLL--RHSPSWLRDVGVVVVDEIHLISDEERGPTLESIVARLRrlnpnTQ 151

                         170
                  ....*....|....*...
gi 568954769  859 FLALSATISNPQHLTEWL 876
Cdd:cd18028   152 IIGLSATIGNPDELAEWL 169
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 724-876 2.93e-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: 2.93e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  724 ESAVIVAPTSSGKTYASYYC-MEKVLKESDEGV-VVYVAPTKALVNQVAATVEyRYAKNMPAGESLcGVFTRDY----RH 797
Cdd:cd17922     2 RNVLIAAPTGSGKTEAAFLPaLSSLADEPEKGVqVLYISPLKALINDQERRLE-EPLDEIDLEIPV-AVRHGDTsqseKA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  798 DALNC--QVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCL-GGEIGAEI---WEHLLVMIRCPF--LALSATISNP 869
Cdd:cd17922    80 KQLKNppGILITTPESLELLLVNKKLRELFAGLRYVVVDEIHALlGSKRGVQLellLERLRKLTGRPLrrIGLSATLGNL 159


                  ....*..
gi 568954769  870 QHLTEWL 876
Cdd:cd17922   160 EEAAAFL 166
PRK02362 PRK02362
ATP-dependent DNA helicase;
1089-1392 3.23e-17

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 87.71  E-value: 3.23e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1089 ENAFEFLEKKQEEKRPPKADkeartTANKLRKvkkslekqkTVDEKGQ----KSSRRLDESvmhetehnyllqtleknle 1164
Cdd:PRK02362  212 GGAIHFDDSQREVEVPSKDD-----TLNLVLD---------TLEEGGQclvfVSSRRNAEG------------------- 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1165 IPKDCTYANQKAIDDQL---LQRVFHRVRFERKGETLKRLA---ERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGT 1238
Cdd:PRK02362  259 FAKRAASALKKTLTAAEraeLAELAEEIREVSDTETSKDLAdcvAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPT 338

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1239 LALGINMPCKSVV------FAQNS--VYLDALNYRQMSGRAGRRGQDLLG----------------DVYFFDIPLPkigk 1294
Cdd:PRK02362  339 LAAGLNLPARRVIirdyrrYDGGAgmQPIPVLEYHQMAGRAGRPGLDPYGeavllaksydeldelfERYIWADPED---- 414

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1295 lIKSKvpelrgqfpLSISLILRLMLLASKADDLEDGKAKALSVLKHSLLSFKQP------RAIDMlklyflySLQFLVKE 1368
Cdd:PRK02362  415 -VRSK---------LATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQTDdtgrleRVVDD-------VLDFLERN 477

                         330       340
                  ....*....|....*....|....*..
gi 568954769 1369 GHIDQEGN---PTGFAGLVSHLhYHEP 1392
Cdd:PRK02362  478 GMIEEDGEtleATELGHLVSRL-YIDP 503
PRK01172 PRK01172
ATP-dependent DNA helicase;
1196-1401 8.83e-16

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 83.01  E-value: 8.83e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1196 ETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQ-------NSVYLDALNYRQMS 1268
Cdd:PRK01172  278 DSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDitrygngGIRYLSNMEIKQMI 357

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1269 GRAGRRGQDLLGDVYFF---------------DIPLPKIGKLIKSKvpELRGQFPLSISlilrlMLLASKADDLEDgkak 1333
Cdd:PRK01172  358 GRAGRPGYDQYGIGYIYaaspasydaakkylsGEPEPVISYMGSQR--KVRFNTLAAIS-----MGLASSMEDLIL---- 426

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1334 alsvLKHSLLSFKQpRAIDMLKLYFLYSLQFLVKEGHIDQEG--NPTGFAGLVSHLHYHEPSNLVFVSFL 1401
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 ...
 713-877 1.61e-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: 1.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  713 QRELL-DVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEG-----VVVYVAPTKALVNQVAAtvEYRyAKNMPAGES 786
Cdd:cd18023     6 QSEVFpDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNPLpwgnrKVVYIAPIKALCSEKYD--DWK-EKFGPLGLS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  787 lCGVFTRDYRHDAL----NCQVLITVPACFE-ILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAEIwE---------HLL 852
Cdd:cd18023    83 -CAELTGDTEMDDTfeiqDADIILTTPEKWDsMTRRWRDNGNLVQLVALVLIDEVHIIKENRGATL-EvvvsrmktlSSS 160

                         170       180       190
                  ....*....|....*....|....*....|.
gi 568954769  853 VMIRCP------FLALSATISNPQHLTEWLQ 877
Cdd:cd18023   161 SELRGStvrpmrFVAVSATIPNIEDLAEWLG 191
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 671-874 3.09e-15

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: 81.42  E-value: 3.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  671 MKRIHSLLDKHSELLQEADQ----------------------KLIARCLKYLGFcelaVSLYPTQRELLDVVDNYESAVI 728
Cdd:COG1205     1 MARLEELLERLRASPRYGDQivhvrtiparearyapwpdwlpPELRAALKKRGI----ERLYSHQAEAIEAARAGKNVVI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  729 VAPTSSGKTYAsyYC---MEKVLKESDeGVVVYVAPTKALVN-QVAATVEyrYAKNMPAGESlCGVFT----RDYRHDAL 800
Cdd:COG1205    77 ATPTASGKSLA--YLlpvLEALLEDPG-ATALYLYPTKALARdQLRRLRE--LAEALGLGVR-VATYDgdtpPEERRWIR 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  801 -NCQVLITVPacfEIL---LLaPHRQNWV---KRIRYVIFDEVHCLGGEIGAeiweHLLVMIR-----CP-------FLA 861
Cdd:COG1205   151 eHPDIVLTNP---DMLhygLL-PHHTRWArffRNLRYVVIDEAHTYRGVFGS----HVANVLRrlrriCRhygsdpqFIL 222

                         250
                  ....*....|...
gi 568954769  862 LSATISNPQHLTE 874
Cdd:COG1205   223 ASATIGNPAEHAE 235
DEXHc_Mtr4-like cd18024
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ...
 709-881 3.25e-15

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: 76.33  E-value: 3.25e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQvaatvEYRyakNMPAGESLC 788
Cdd:cd18024    33 LDPFQKTAIACIERNESVLVSAHTSAGKTVVAEYAIAQSLRDKQR--VIYTSPIKALSNQ-----KYR---ELQEEFGDV 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  789 GVFTRDYR-HDALNCQVLITvpacfEILLLAPHRQNWVKR-IRYVIFDEVHCLGGEIGAEIWEHLLV----MIRcpFLAL 862
Cdd:cd18024   103 GLMTGDVTiNPNASCLVMTT-----EILRSMLYRGSEIMReVAWVIFDEIHYMRDKERGVVWEETIIllpdKVR--YVFL 175

                         170
                  ....*....|....*....
gi 568954769  863 SATISNPQHLTEWLQSVKR 881
Cdd:cd18024   176 SATIPNARQFAEWICKIHK 194
DEXHc_ASCC3_2 cd18022
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 724-876 4.13e-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: 4.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  724 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNMpaGES---LCGVFTRDYRhDAL 800
Cdd:cd18022    18 NNVLLGAPTGSGKTIAAELAMFRAFNKYPGSKVVYIAPLKALVRERVDDWKKRFEEKL--GKKvveLTGDVTPDMK-ALA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  801 NCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGA----------EIWEHLLVMIRcpFLALSATISNPQ 870
Cdd:cd18022    95 DADIIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLGSDRGPvlevivsrmnYISSQTEKPVR--LVGLSTALANAG 172


                  ....*.
gi 568954769  871 HLTEWL 876
Cdd:cd18022   173 DLANWL 178
HELICc smart00490
helicase superfamily c-terminal domain;
1199-1275 1.10e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 1.10e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568954769   1199 KRLAERGIGY--HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNYRQMSGRAGRRG 1275
Cdd:smart00490    5 ELLKELGIKVarLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI-IYDLPWSPASYIQRIGRAGRAG 82
PRK00254 PRK00254
ski2-like helicase; Provisional
 693-886 5.73e-14

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 77.16  E-value: 5.73e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  693 IARCLKYLGFCELavslYPTQRELLDV-VDNYESAVIVAPTSSGKTYASYYCM-EKVLKESdeGVVVYVAPTKALvnqva 770
Cdd:PRK00254   12 IKRVLKERGIEEL----YPPQAEALKSgVLEGKNLVLAIPTASGKTLVAEIVMvNKLLREG--GKAVYLVPLKAL----- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  771 ATVEYRYAKNMPAGESLCGVFTRDY--------RHDalncqVLITVPACFEILLlaPHRQNWVKRIRYVIFDEVHCLGG- 841
Cdd:PRK00254   81 AEEKYREFKDWEKLGLRVAMTTGDYdstdewlgKYD-----IIIATAEKFDSLL--RHGSSWIKDVKLVVADEIHLIGSy 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 568954769  842 EIGAE---IWEHLLVmiRCPFLALSATISNPQHLTEWLQS--VKRYWKQV 886
Cdd:PRK00254  154 DRGATlemILTHMLG--RAQILGLSATVGNAEELAEWLNAelVVSDWRPV 201
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 709-865 7.86e-14

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: 70.41  E-value: 7.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYES---AVIVAPTSSGKTYASYYCMEKVLKESdegvVVYVAPTKALVNQVAAtveyRYAKnmPAGE 785
Cdd:cd17926     1 LRPYQEEALEAWLAHKNnrrGILVLPTGSGKTLTALALIAYLKELR----TLIVVPTDALLDQWKE----RFED--FLGD 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  786 SLCGVFTRDYRHDALNCQVLITVP----ACFEILLLAPHRQNwvkrirYVIFDEVHclggEIGAEIWEHLLVMIRCPF-L 860
Cdd:cd17926    71 SSIGLIGGGKKKDFDDANVVVATYqslsNLAEEEKDLFDQFG------LLIVDEAH----HLPAKTFSEILKELNAKYrL 140


                  ....*
gi 568954769  861 ALSAT 865
Cdd:cd17926   141 GLTAT 145
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
704-865 2.69e-13

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 74.68  E-value: 2.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  704 ELAVSLYPTQRELLD-----VVDNYESAVIVAPTSSGKTYASYYCMEKVLKesdEGVVVYVAPTKALVNQVAATveyrYA 778
Cdd:COG1061    76 GTSFELRPYQQEALEallaaLERGGGRGLVVAPTGTGKTVLALALAAELLR---GKRVLVLVPRRELLEQWAEE----LR 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  779 KNMPAGESLCGVFTRDYRHdalncqVLITVpacfEILLLAPHRQNWVKRIRYVIFDEVHclggEIGAEIWEHLLVMIRCP 858
Cdd:COG1061   149 RFLGDPLAGGGKKDSDAPI------TVATY----QSLARRAHLDELGDRFGLVIIDEAH----HAGAPSYRRILEAFPAA 214


                  ....*...
gi 568954769  859 F-LALSAT 865
Cdd:COG1061   215 YrLGLTAT 222
DEXHc_Brr2_2 cd18021
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ...
 724-876 3.39e-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: 3.39e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  724 ESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATVEYRYAKNMPAG-ESLCGVFTRDYRHDALNc 802
Cdd:cd18021    20 DNVFVGAPTGSGKTVCAELALLRHWRQNPKGRAVYIAPMQELVDARYKDWRAKFGPLLGKKvVKLTGETSTDLKLLAKS- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  803 QVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGAeIWEHLLVMIR---------CPFLALSATISNPQHLT 873
Cdd:cd18021    99 DVILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGENGP-VYEVVVSRMRyissqlekpIRIVGLSSSLANARDVG 177


                  ...
gi 568954769  874 EWL 876
Cdd:cd18021   178 EWL 180
DEXHc_SKIV2L cd18027
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ...
 709-889 5.37e-13

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: 68.83  E-value: 5.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEgvVVYVAPTKALVNQvaatvEYRYAKNMPAGeslC 788
Cdd:cd18027     9 LDVFQKQAILHLEAGDSVFVAAHTSAGKTVVAEYAIALAQKHMTR--TIYTSPIKALSNQ-----KFRDFKNTFGD---V 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  789 GVFTRDYR-HDALNCQVLITvpacfEILLLAPHRQNWVKR-IRYVIFDEVHCLGGEIGAEIWEHLLVMI--RCPFLALSA 864
Cdd:cd18027    79 GLITGDVQlNPEASCLIMTT-----EILRSMLYNGSDVIRdLEWVIFDEVHYINDAERGVVWEEVLIMLpdHVSIILLSA 153

                         170       180
                  ....*....|....*....|....*
gi 568954769  865 TISNPQHLTEWLQSVKRYWKQVDST 889
Cdd:cd18027   154 TVPNTVEFADWIGRIKKKNIYVIST 178
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 724-865 1.09e-12

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 67.04  E-value: 1.09e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  724 ESAVIVAPTSSGKTYASYYCMEKVLkESDEGVVVYVAPTKALVNQVAATVEYRYAKNMPageslCGVFTRD------YRH 797
Cdd:cd00046     2 ENVLITAPTGSGKTLAALLAALLLL-LKKGKKVLVLVPTKALALQTAERLRELFGPGIR-----VAVLVGGssaeerEKN 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568954769  798 DALNCQVLITVPACFEILLLAPHRQnWVKRIRYVIFDEVHCLGGeIGAEIWEHLLVMIR-----CPFLALSAT 865
Cdd:cd00046    76 KLGDADIIIATPDMLLNLLLREDRL-FLKDLKLIIVDEAHALLI-DSRGALILDLAVRKaglknAQVILLSAT 146
ResIII pfam04851
Type III restriction enzyme, res subunit;
708-865 8.37e-12

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 65.00  E-value: 8.37e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   708 SLYPTQRELLD-----VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQvaaTVEyRYAKNMP 782
Cdd:pfam04851    3 ELRPYQIEAIEnllesIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQ---ALE-EFKKFLP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769   783 AGESLCGVFT-RDYRHDALNCQVLI-TVPACFEILLLAPHrQNWVKRIRYVIFDEVHclggEIGAEIWEHLLVMIRCPF- 859
Cdd:pfam04851   79 NYVEIGEIISgDKKDESVDDNKIVVtTIQSLYKALELASL-ELLPDFFDVIIIDEAH----RSGASSYRNILEYFKPAFl 153


                   ....*.
gi 568954769   860 LALSAT 865
Cdd:pfam04851  154 LGLTAT 159
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 709-871 9.14e-12

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: 65.30  E-value: 9.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYESAVIVAPTSSGKTYAsyY---CMEKVLKESdEGVVVYVAPTKALVN-QVAATVEyrYAKNMPAG 784
Cdd:cd17923     1 LYSHQAEAIEAARAGRSVVVTTGTASGKSLC--YqlpILEALLRDP-GSRALYLYPTKALAQdQLRSLRE--LLEQLGLG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  785 ESlCGVFTRDYRHDA------LNCQVLITVPACFEILLLAPHRQ--NWVKRIRYVIFDEVHCLGGEIGAeiweHLLVMIR 856
Cdd:cd17923    76 IR-VATYDGDTPREErraiirNPPRILLTNPDMLHYALLPHHDRwaRFLRNLRYVVLDEAHTYRGVFGS----HVALLLR 150

                         170       180
                  ....*....|....*....|....*...
gi 568954769  857 -----CP-------FLALSATISNP-QH 871
Cdd:cd17923   151 rlrrlCRrygadpqFILTSATIGNPaEH 178
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 1185-1275 3.16e-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: 3.16e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  1185 VFHRVRFERKGETLKRLAERGIGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFaQNSVYLDALNY 1264
Cdd:pfam00271   20 IFSQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI-NYDLPWNPASY 98

                           90
                   ....*....|.
gi 568954769  1265 RQMSGRAGRRG 1275
Cdd:pfam00271   99 IQRIGRAGRAG 109
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 1185-1276 7.16e-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: 7.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1185 VFH--RVRFERKGETLKRLAERG-----IGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINM-PCKSVVfaQNS 1256
Cdd:cd18796    43 VFTntRSQAERLAQRLRELCPDRvppdfIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIgDVDLVI--QIG 120

                          90       100
                  ....*....|....*....|
gi 568954769 1257 VYLDALNYRQMSGRAGRRGQ 1276
Cdd:cd18796   121 SPKSVARLLQRLGRSGHRPG 140
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
711-876 1.07e-07

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 57.03  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  711 PT--QRELLDVVDNYESAVIVAPTSSGKTYASY------YCMEKVLKESDEGV-VVYVAPTKALVNQVaatveyryAKNM 781
Cdd:COG1201    25 PTppQREAWPAIAAGESTLLIAPTGSGKTLAAFlpaldeLARRPRPGELPDGLrVLYISPLKALANDI--------ERNL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  782 ---------PAGESLCGV----------------FTRDYRHdalncqVLITVPACFEILLLAPHRQNWVKRIRYVIFDEV 836
Cdd:COG1201    97 rapleeigeAAGLPLPEIrvgvrtgdtpaserqrQRRRPPH------ILITTPESLALLLTSPDARELLRGVRTVIVDEI 170

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 568954769  837 HCLGG-------EIGAEIWEHL----LVMIrcpflALSATISNPQHLTEWL 876
Cdd:COG1201   171 HALAGskrgvhlALSLERLRALaprpLQRI-----GLSATVGPLEEVARFL 216
DEXHc_cas3 cd17930
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ...
 727-865 7.21e-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: 51.14  E-value: 7.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  727 VIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVA----------------------ATVEYRYAKNMPAG 784
Cdd:cd17930     5 ILEAPTGSGKTEAALLWALKLAARGGKRRIIYALPTRATINQMYerireilgrlddedkvlllhskAALELLESDEEPDD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  785 ESLCGVFTRDYRHDALNCQVLITVPacFEILL-LAPHRQNWVK--RI--RYVIFDEVHCLGGEIGAEIWEHLLVMIR--- 856
Cdd:cd17930    85 DPVEAVDWALLLKRSWLAPIVVTTI--DQLLEsLLKYKHFERRlhGLanSVVVLDEVQAYDPEYMALLLKALLELLGelg 162


                  ....*....
gi 568954769  857 CPFLALSAT 865
Cdd:cd17930   163 GPVVLMTAT 171
DEXHc_RLR cd18036
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ...
 709-837 7.25e-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: 51.71  E-value: 7.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLKE----SDEGVVVYVAPTKALVNQvAATVEYRYAKNMPAG 784
Cdd:cd18036     3 LRNYQLELVLPALRGKNTIICAPTGSGKTRVAVYICRHHLEKrrsaGEKGRVVVLVNKVPLVEQ-QLEKFFKYFRKGYKV 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  785 ESLCGVFTRD--YRHDALNCQVLITVPACFEILLLAPhRQNwvKRIRY-----VIFDEVH 837
Cdd:cd18036    82 TGLSGDSSHKvsFGQIVKASDVIICTPQILINNLLSG-REE--ERVYLsdfslLIFDECH 138
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 1172-1276 1.84e-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: 46.05  E-value: 1.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1172 ANQKAIDDQLLQRVFHR-------VRFERKGETL-KRLAERGI--GYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLAL 1241
Cdd:cd18794    13 KKDEKLDLLKRIKVEHLggsgiiyCLSRKECEQVaARLQSKGIsaAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGM 92

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 568954769 1242 GINMPckSVVF-AQNSVYLDALNYRQMSGRAGRRGQ 1276
Cdd:cd18794    93 GIDKP--DVRFvIHYSLPKSMESYYQESGRAGRDGL 126
DEXHc_RIG-I cd17927
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ...
 707-872 2.41e-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: 47.04  E-value: 2.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  707 VSLYPTQRELLDVVDNYESAVIVAPTSSGKTYASYYCMEKVLK---ESDEGVVVYVAPTKALVNQvAATVEYRYAKNMP- 782
Cdd:cd17927     1 FKPRNYQLELAQPALKGKNTIICLPTGSGKTFVAVLICEHHLKkfpAGRKGKVVFLANKVPLVEQ-QKEVFRKHFERPGy 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  783 -----AGESLCGVFTRDYrhdALNCQVLITVPACFEILLLApHRQNWVKRIRYVIFDEVHCLGGEigaeiWEHLLVMIRC 857
Cdd:cd17927    80 kvtglSGDTSENVSVEQI---VESSDVIIVTPQILVNDLKS-GTIVSLSDFSLLVFDECHNTTKN-----HPYNEIMFRY 150

                         170
                  ....*....|....*
gi 568954769  858 PFLALSATISNPQHL 872
Cdd:cd17927   151 LDQKLGSSGPLPQIL 165
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
1208-1294 2.60e-05

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 49.12  E-value: 2.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1208 YHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCKSVVFAQNSVYLDALN---YRQMSGRAGRRGQDLLGDVYF 1284
Cdd:COG1202   453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSvqeFHQMLGRAGRPDYHDRGKVYL 532

                          90
                  ....*....|
gi 568954769 1285 fdipLPKIGK 1294
Cdd:COG1202   533 ----LVEPGK 538
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 1199-1279 3.11e-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: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1199 KRLAERGIGY----HHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCksvvfaqnsvyLDA----------LNY 1264
Cdd:COG1205   310 RALREPDLADrvaaYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGG-----------LDAvvlagypgtrASF 378

                          90
                  ....*....|....*
gi 568954769 1265 RQMSGRAGRRGQDLL 1279
Cdd:COG1205   379 WQQAGRAGRRGQDSL 393
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 709-865 5.19e-05

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: 47.77  E-value: 5.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLDVVDNYESA-----VIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVA------------- 770
Cdd:COG1203   128 INPLQNEALELALEAAEEepglfILTAPTGGGKTEAALLFALRLAAKHGGRRIIYALPFTSIINQTYdrlrdlfgedvll 207

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  771 ----ATVEYRYAKNMPAGESlcgvftRDYRH--DALNCQVLITVPACFEILLLAPHRQNWVKRIRY----VIFDEVHClg 840
Cdd:COG1203   208 hhslADLDLLEEEEEYESEA------RWLKLlkELWDAPVVVTTIDQLFESLFSNRKGQERRLHNLansvIILDEVQA-- 279

                         170       180       190
                  ....*....|....*....|....*....|.
gi 568954769  841 geIGAEIWEHLLVMIR------CPFLALSAT 865
Cdd:COG1203   280 --YPPYMLALLLRLLEwlknlgGSVILMTAT 308
DEXHc_Brr2_1 cd18019
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ...
 708-868 6.39e-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: 45.82  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  708 SLYPTQRELLDV-VDNYESAVIVAPTSSGKTYASYYCM----EKVLKES-----DEGVVVYVAPTKALVNQVAATVEYRY 777
Cdd:cd18019    17 SLNRIQSKLFPAaFETDENLLLCAPTGAGKTNVALLTIlreiGKHRNPDgtinlDAFKIVYIAPMKALVQEMVGNFSKRL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  778 AK-NMPAGE-----SLCgvftrdyRHDALNCQVLITVPACFEILLLAPHRQNWVKRIRYVIFDEVHCLGGEIGA------ 845
Cdd:cd18019    97 APyGITVAEltgdqQLT-------KEQISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDDRGPvlesiv 169

                         170       180
                  ....*....|....*....|....*..
gi 568954769  846 --EIW--EHLLVMIRcpFLALSATISN 868
Cdd:cd18019   170 arTIRqiEQTQEYVR--LVGLSATLPN 194
DEXHc_ASCC3_1 cd18020
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ...
 724-868 1.51e-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: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  724 ESAVIVAPTSSGKTYASYYCMEKVLKES---------DEGVVVYVAPTKALVNQVAATVEYRYAK-NMPAGEslcgvFTR 793
Cdd:cd18020    18 ENMLICAPTGAGKTNIAMLTILHEIRQHvnqggvikkDDFKIVYIAPMKALAAEMVEKFSKRLAPlGIKVKE-----LTG 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  794 DY---RHDALNCQVLITVPACFEILLLAPHRQN-WVKRIRYVIFDEVHCLGGEIGAEIwEHLLV-----------MIRcp 858
Cdd:cd18020    93 DMqltKKEIAETQIIVTTPEKWDVVTRKSSGDVaLSQLVRLLIIDEVHLLHDDRGPVI-ESLVArtlrqvestqsMIR-- 169

                         170
                  ....*....|
gi 568954769  859 FLALSATISN 868
Cdd:cd18020   170 IVGLSATLPN 179
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
728-837 1.64e-04

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 46.26  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  728 IVAPTSSGKTYASYYCMEKVLKESDeGVVVYVAPTKALVNQVAATveyrYAKNMPAGESLCGVFTRDYRHD---AL--NC 802
Cdd:COG1111    22 VVLPTGLGKTAVALLVIAERLHKKG-GKVLFLAPTKPLVEQHAEF----FKEALNIPEDEIVVFTGEVSPEkrkELweKA 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 568954769  803 QVLITVPACFEILLLAphrqnwvKRIR-----YVIFDEVH 837
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 ...
 1188-1279 3.85e-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: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1188 RVRFERKGETLKRLAE-RGiGYhhssmSAKEKQLVEILFRKGFIRVVTATGTLALGINMPCksvvfaqnsvyLDAL---- 1262
Cdd:cd18797    56 KARLVEEGPLASKVASyRA-GY-----LAEDRREIEAELFNGELLGVVATNALELGIDIGG-----------LDAVvlag 118

                          90       100
                  ....*....|....*....|...
gi 568954769 1263 ------NYRQMSGRAGRRGQDLL 1279
Cdd:cd18797   119 ypgslaSLWQQAGRAGRRGKDSL 141
Lhr COG1201
Lhr-like helicase [Replication, recombination and repair];
1184-1246 7.51e-04

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


Pssm-ID: 440814 [Multi-domain]  Cd Length: 850  Bit Score: 44.32  E-value: 7.51e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568954769 1184 RVFHRvrferkgetLKRLAERG---IGYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMP 1246
Cdd:COG1201   287 RLFQR---------LNELNPEDalpIAAHHGSLSREQRLEVEEALKAGELRAVVATSSLELGIDIG 343
DEXHc_dicer cd18034
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...
 707-868 1.53e-03

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350792 [Multi-domain]  Cd Length: 200  Bit Score: 41.48  E-value: 1.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  707 VSLYPTQRELLDVVDNyESAVIVAPTSSGKTYASyyCM------EKVLKESDEG-VVVYVAPTKALVNQVAATVE-YRYA 778
Cdd:cd18034     1 FTPRSYQLELFEAALK-RNTIVVLPTGSGKTLIA--VMlikemgELNRKEKNPKkRAVFLVPTVPLVAQQAEAIRsHTDL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  779 KNMP-AGESLCGVFTRDYRHDAL-NCQVLITVPACFEILLlaphRQNWVK--RIRYVIFDEVH-CLGGEIGAEI---WEH 850
Cdd:cd18034    78 KVGEySGEMGVDKWTKERWKEELeKYDVLVMTAQILLDAL----RHGFLSlsDINLLIFDECHhATGDHPYARImkeFYH 153

                         170
                  ....*....|....*....
gi 568954769  851 LLVMIRCP-FLALSATISN 868
Cdd:cd18034   154 LEGRTSRPrILGLTASPVN 172
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 725-837 1.56e-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: 41.35  E-value: 1.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  725 SAVIVAPTSSGKTYASYYCMEKVLKESDeGVVVYVAPTKALVNQVAATveYRYAKNMPAG-ESLCGVFTRDYRHDALN-C 802
Cdd:cd18035    18 NTLIVLPTGLGKTIIAILVAADRLTKKG-GKVLILAPSRPLVEQHAEN--LKRVLNIPDKiTSLTGEVKPEERAERWDaS 94

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 568954769  803 QVLITVPACFEILLLApHRQNwVKRIRYVIFDEVH 837
Cdd:cd18035    95 KIIVATPQVIENDLLA-GRIT-LDDVSLLIFDEAH 127
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 1196-1275 2.24e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 42.78  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1196 ETLKRLAERGI--GYHHSSMSAKEKQLVEILFRKGFIRVVTATGTLALGINMPckSVVFAqnsVYLD----ALNYRQMSG 1269
Cdd:PRK11057  251 DTAARLQSRGIsaAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKP--NVRFV---VHFDiprnIESYYQETG 325


                  ....*.
gi 568954769 1270 RAGRRG 1275
Cdd:PRK11057  326 RAGRDG 331
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 693-836 2.47e-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: 40.89  E-value: 2.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  693 IARCLKYLGFcelaVSLYPTQRELLDVVDNYESAVIVAPTSSGKTYAsyYCM---EKVLKESDEG-----VVVyVAPTKA 764
Cdd:cd00268     1 LLKALKKLGF----EKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLA--FLLpilEKLLPEPKKKgrgpqALV-LAPTRE 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568954769  765 LVNQVAATVEyRYAKNMPAgESLC---GVftrDYRHDAL----NCQVLITVPACFeILLLAPHRQNwVKRIRYVIFDEV 836
Cdd:cd00268    74 LAMQIAEVAR-KLGKGTGL-KVAAiygGA---PIKKQIEalkkGPDIVVGTPGRL-LDLIERGKLD-LSNVKYLVLDEA 145
PRK13767 PRK13767
ATP-dependent helicase; Provisional
 1188-1246 2.54e-03

ATP-dependent helicase; Provisional


Pssm-ID: 237497 [Multi-domain]  Cd Length: 876  Bit Score: 42.57  E-value: 2.54e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1188 RVRFERKGETLKRLAERGIGYHHSSMSaKEKQL-VEILFRKGFIRVVTATGTLALGINMP 1246
Cdd:PRK13767  299 RVLYNLRKRFPEEYDEDNIGAHHSSLS-REVRLeVEEKLKRGELKVVVSSTSLELGIDIG 357
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 1199-1285 5.35e-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: 41.40  E-value: 5.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769 1199 KRLAERGIGYHHSSMSA-KEKqlVEIlFRKGFIRVVTATGTLALGINMPCKSV--VFAQNSVY-LDALnyRQMSGRAGRR 1274
Cdd:COG4098   341 KLFPEERIAGVHAEDPErKEK--VQA-FRDGEIPILVTTTILERGVTFPNVDVavLGADHPVFtEAAL--VQIAGRVGRS 415

                          90
                  ....*....|.
gi 568954769 1275 GQDLLGDVYFF 1285
Cdd:COG4098   416 ADYPTGEVIFF 426
DEADc_MRH4 cd17965
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ...
 718-835 6.21e-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: 40.44  E-value: 6.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  718 DVVDNYESAVIVAPTSSGKTYAsyYCMEKV--LKESDEGV------------------VVYVAPTKALVNQVAATVEyry 777
Cdd:cd17965    56 NEEPKLEVFLLAAETGSGKTLA--YLAPLLdyLKRQEQEPfeeaeeeyesakdtgrprSVILVPTHELVEQVYSVLK--- 130

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769  778 AKNMPAGESLCGV---FTRDYRHDALN----CQVLITVPacFEILLLAPHRQNWVKRIRYVIFDE 835
Cdd:cd17965   131 KLSHTVKLGIKTFssgFGPSYQRLQLAfkgrIDILVTTP--GKLASLAKSRPKILSRVTHLVVDE 193
DEXHc_RE_I_III_res cd18032
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ...
 709-837 8.02e-03

DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain]  Cd Length: 163  Bit Score: 39.08  E-value: 8.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568954769  709 LYPTQRELLD-----VVDNYESAVIVAPTSSGKTYASYYCMEKVLKESDEGVVVYVAPTKALVNQVAATveyrYAKNMPA 783
Cdd:cd18032     1 PRYYQQEAIEaleeaREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERS----FKEVLPD 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568954769  784 GESlcGVFTRDyRHDALNCQVLI-TVpacfeilllaphrQNWVKRIR----------YVIFDEVH 837
Cdd:cd18032    77 GSF--GNLKGG-KKKPDDARVVFaTV-------------QTLNKRKRlekfppdyfdLIIIDEAH 125
 
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.
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