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Conserved domains on  [gi|1958747461|ref|XP_038953975|]
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ATP-dependent RNA helicase DDX39A isoform X1 [Rattus norvegicus]

Protein Classification

DEAD/DEAH box helicase domain-containing protein( domain architecture ID 1000559)

DEAD/DEAH box helicase domain-containing protein may function as an RNA helicase

CATH:  3.40.50.300|1.20.1320.20
EC:  3.6.4.-
Gene Ontology:  GO:0005524|GO:0004386|GO:0003676
PubMed:  20206133

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SrmB super family cl33924
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
27-247 7.78e-62

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


The actual alignment was detected with superfamily member COG0513:

Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 199.60  E-value: 7.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLaaNM--RRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYYVKLKDSEKNRKLF 104
Cdd:COG0513   157 ML--DMgfIEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENA-TAETIEQRYYLVDKRDKLELLR 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 105 DLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIV 184
Cdd:COG0513   234 RLLRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV 313

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958747461 185 FNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKILNDVQD--RFEVNVAELPEEIDIST 247
Cdd:COG0513   314 INYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPD-ERRLLRAIEKliGQKIEEEELPGFEPVEE 377
 
Name Accession Description Interval E-value
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
27-247 7.78e-62

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 199.60  E-value: 7.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLaaNM--RRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYYVKLKDSEKNRKLF 104
Cdd:COG0513   157 ML--DMgfIEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENA-TAETIEQRYYLVDKRDKLELLR 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 105 DLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIV 184
Cdd:COG0513   234 RLLRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV 313

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958747461 185 FNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKILNDVQD--RFEVNVAELPEEIDIST 247
Cdd:COG0513   314 INYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPD-ERRLLRAIEKliGQKIEEEELPGFEPVEE 377
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 87-216 4.86e-53

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 168.07  E-value: 4.86e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  87 LQQYYVKLKDSEKNRKLF-DLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRI 165
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLlLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958747461 166 LVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFV 216
Cdd:cd18787    81 LVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
PTZ00424 PTZ00424
helicase 45; Provisional
 27-243 3.69e-46

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 158.45  E-value: 3.69e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDEtKLTLHGLQQYYVKL-KDSEKNRKLFD 105
Cdd:PTZ00424  182 MLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD-ELTLEGIRQFYVAVeKEEWKFDTLCD 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 106 LLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVF 185
Cdd:PTZ00424  261 LYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747461 186 NYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKILNDVQDRFEVNVAELPEEI 243
Cdd:PTZ00424  341 NYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD-DIEQLKEIERHYNTQIEEMPMEV 397
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 98-207 7.17e-30

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: 107.68  E-value: 7.17e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  98 EKNRKLFDLLDVLEFNQVVIFVKSVQRCMAlAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMD 177
Cdd:pfam00271   1 EKLEALLELLKKERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958747461 178 IERVNIVFNYDMPEDSDTYLHRVARAGRFG 207
Cdd:pfam00271  80 LPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
128-207 1.25e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 90.73  E-value: 1.25e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  128 LAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 207
Cdd:smart00490   3 LAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
 
Name Accession Description Interval E-value
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
27-247 7.78e-62

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 199.60  E-value: 7.78e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLaaNM--RRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYYVKLKDSEKNRKLF 104
Cdd:COG0513   157 ML--DMgfIEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENA-TAETIEQRYYLVDKRDKLELLR 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 105 DLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIV 184
Cdd:COG0513   234 RLLRDEDPERAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHV 313

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958747461 185 FNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKILNDVQD--RFEVNVAELPEEIDIST 247
Cdd:COG0513   314 INYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTPD-ERRLLRAIEKliGQKIEEEELPGFEPVEE 377
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 87-216 4.86e-53

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 168.07  E-value: 4.86e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  87 LQQYYVKLKDSEKNRKLF-DLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRI 165
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLlLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958747461 166 LVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFV 216
Cdd:cd18787    81 LVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
PTZ00424 PTZ00424
helicase 45; Provisional
 27-243 3.69e-46

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 158.45  E-value: 3.69e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDEtKLTLHGLQQYYVKL-KDSEKNRKLFD 105
Cdd:PTZ00424  182 MLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD-ELTLEGIRQFYVAVeKEEWKFDTLCD 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 106 LLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVF 185
Cdd:PTZ00424  261 LYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI 340

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958747461 186 NYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKILNDVQDRFEVNVAELPEEI 243
Cdd:PTZ00424  341 NYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD-DIEQLKEIERHYNTQIEEMPMEV 397
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 27-241 4.77e-37

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 135.31  E-value: 4.77e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTlhGLQQYYVKLKDSEKNRKLFDL 106
Cdd:PRK11776  159 MLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLP--AIEQRFYEVSPDERLPALQRL 236

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 107 LDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFN 186
Cdd:PRK11776  237 LLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVIN 316

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958747461 187 YDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDENDAKI--LNDVQDRfEVNVAELPE 241
Cdd:PRK11776  317 YELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRAnaIEDYLGR-KLNWEPLPS 372
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 27-240 3.96e-34

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 129.20  E-value: 3.96e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYYVKLKDSEKNRKLFDL 106
Cdd:PRK11634  161 MLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVT-TRPDISQSYWTVWGMRKNEALVRF 239

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 107 LDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFN 186
Cdd:PRK11634  240 LEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVN 319

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958747461 187 YDMPEDSDTYLHRVARAGRFGTKGLAVTFVsDENDAKILNDVQDRFEVNV--AELP 240
Cdd:PRK11634  320 YDIPMDSESYVHRIGRTGRAGRAGRALLFV-ENRERRLLRNIERTMKLTIpeVELP 374
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 27-225 5.67e-30

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 115.81  E-value: 5.67e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATL-SKEIRPVCRKFMQDPMEVFVD---DETKltlhGLQQYYVKLKDSEKNRK 102
Cdd:PRK11192  159 MLDMGFAQDIETIAAETRWRKQTLLFSATLeGDAVQDFAERLLNDPVEVEAEpsrRERK----KIHQWYYRADDLEHKTA 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 103 LfdLLDVLEFNQV---VIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIE 179
Cdd:PRK11192  235 L--LCHLLKQPEVtrsIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDID 312

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1958747461 180 RVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVsDENDAKIL 225
Cdd:PRK11192  313 DVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV-EAHDHLLL 357
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 98-207 7.17e-30

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: 107.68  E-value: 7.17e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  98 EKNRKLFDLLDVLEFNQVVIFVKSVQRCMAlAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMD 177
Cdd:pfam00271   1 EKLEALLELLKKERGGKVLIFSQTKKTLEA-ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1958747461 178 IERVNIVFNYDMPEDSDTYLHRVARAGRFG 207
Cdd:pfam00271  80 LPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 36-222 1.13e-29

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 115.78  E-value: 1.13e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  36 VQEIFRLTPH--EKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYYVKLKDSEKNRKLFDLLDVLEFN 113
Cdd:PRK01297  258 VRQIIRQTPRkeERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV-ASDTVEQHVYAVAGSDKYKLLYNLVTQNPWE 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 114 QVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDS 193
Cdd:PRK01297  337 RVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDP 416

                         170       180
                  ....*....|....*....|....*....
gi 1958747461 194 DTYLHRVARAGRFGTKGLAVTFVSdENDA 222
Cdd:PRK01297  417 DDYVHRIGRTGRAGASGVSISFAG-EDDA 444
DEADc_DDX39 cd17950
DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ...
 29-76 1.27e-29

DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and is required for the export of mRNA out of the nucleus. DDX39B is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. Diseases associated with DDX39A (also called UAP56-Related Helicase, 49 kDa) include gastrointestinal stromal tumor and inflammatory bowel disease 6, while diseases associated with DDX39B (also called 56 kDa U2AF65-Associated Protein) include Plasmodium vivax malaria. DDX39 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: 350708 [Multi-domain]  Cd Length: 208  Bit Score: 110.13  E-value: 1.27e-29
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  29 AANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFV 76
Cdd:cd17950   161 QLDMRRDVQEIFRATPHDKQVMMFSATLSKEIRPVCKKFMQDPLEIFV 208
PTZ00110 PTZ00110
helicase; Provisional
 46-217 8.37e-26

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 105.24  E-value: 8.37e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  46 EKQCMMFSATLSKEI----RPVCRkfmQDPMEVFVDDETKLTLHGLQQYYVKLKDSEKNRKLFDLLDVL--EFNQVVIFV 119
Cdd:PTZ00110  308 DRQTLMWSATWPKEVqslaRDLCK---EEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRImrDGDKILIFV 384

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 120 KSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHR 199
Cdd:PTZ00110  385 ETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHR 464

                         170
                  ....*....|....*...
gi 1958747461 200 VARAGRFGTKGLAVTFVS 217
Cdd:PTZ00110  465 IGRTGRAGAKGASYTFLT 482
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 34-251 8.61e-26

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 105.42  E-value: 8.61e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  34 RDVQEIFRLTPHE--KQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLHGLQQYYVKlKDSEKNRKLFDLLDVLE 111
Cdd:PRK04537  178 KDIRFLLRRMPERgtRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFP-ADEEKQTLLLGLLSRSE 256

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 112 FNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPE 191
Cdd:PRK04537  257 GARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPF 336

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 192 DSDTYLHRVARAGRFGTKGLAVTFVSdendakilndvqDRFEVNvaeLPeeiDISTYIEQ 251
Cdd:PRK04537  337 DAEDYVHRIGRTARLGEEGDAISFAC------------ERYAMS---LP---DIEAYIEQ 378
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 27-229 1.92e-24

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 101.04  E-value: 1.92e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLHGLQqyYVKLKDSEKNRKLF-D 105
Cdd:PRK10590  161 MLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQ--HVHFVDKKRKRELLsQ 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 106 LLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVF 185
Cdd:PRK10590  239 MIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVV 318

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1958747461 186 NYDMPEDSDTYLHRVARAGRFGTKGLAVTFVS-DENdaKILNDVQ 229
Cdd:PRK10590  319 NYELPNVPEDYVHRIGRTGRAAATGEALSLVCvDEH--KLLRDIE 361
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 34-252 5.89e-24

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 99.28  E-value: 5.89e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  34 RDVQEIFRLTPHEKQ--CMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKlTLHGLQQYyvklkdseknrklfdlldvle 111
Cdd:PRK04837  176 KDIRWLFRRMPPANQrlNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQK-TGHRIKEE--------------------- 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 112 fnqvvIFVKSVQRCMALAQLLVEQNFPAIAI--------------------HR-GM-----AQEERLSRYQQFKDFQRRI 165
Cdd:PRK04837  234 -----LFYPSNEEKMRLLQTLIEEEWPDRAIifantkhrceeiwghlaadgHRvGLltgdvAQKKRLRILEEFTRGDLDI 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 166 LVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEndaKILNdvqdrfevnvaeLPEeidI 245
Cdd:PRK04837  309 LVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACEE---YALN------------LPA---I 370


                  ....*..
gi 1958747461 246 STYIEQS 252
Cdd:PRK04837  371 ETYIGHS 377
HELICc smart00490
helicase superfamily c-terminal domain;
128-207 1.25e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 90.73  E-value: 1.25e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  128 LAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 207
Cdd:smart00490   3 LAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 27-253 3.02e-23

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 97.94  E-value: 3.02e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  27 MLAANMRRDVQEIFRLTPhEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTlHGLQQYYVKLKDSEKNRKLFDL 106
Cdd:PLN00206  282 MLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPN-KAVKQLAIWVETKQKKQKLFDI 359

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 107 LDVLEFNQ--VVIFVKSVQRCMALAQLL-VEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNI 183
Cdd:PLN00206  360 LKSKQHFKppAVVFVSSRLGADLLANAItVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQ 439

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 184 VFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDENDAkILNDVQDRFEVNVAELPEEIDISTYIEQSR 253
Cdd:PLN00206  440 VIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRN-LFPELVALLKSSGAAIPRELANSRYLGSGR 508
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
92-225 1.57e-12

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 66.70  E-value: 1.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  92 VKLKDSEKNRKLFDLLDVLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNL 171
Cdd:COG0514   210 VPKPPDDKLAQLLDFLKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIA 289

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1958747461 172 FGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAVTFVSDEnDAKIL 225
Cdd:COG0514   290 FGMGIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPE-DVAIQ 342
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 27-74 1.79e-11

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: 61.30  E-value: 1.79e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd00268   148 MLDMGFEEDVEKILSALPKDRQTLLFSATLPEEVKELAKKFLKNPVRI 195
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 90-207 1.41e-10

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: 57.60  E-value: 1.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  90 YYVKLKDSEKNRKLFDLLDVLEFNQ--VVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILV 167
Cdd:cd18794     6 YSVRPKDKKDEKLDLLKRIKVEHLGgsGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1958747461 168 ATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 207
Cdd:cd18794    86 ATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDG 125
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
96-253 7.47e-09

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 55.80  E-value: 7.47e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  96 DSEKNRKLFDLLD-VLEFNQVVIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGR 174
Cdd:COG1061   288 AERKDKILRELLReHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNE 367

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 175 GMDIERVNIVFnYDMPEDSDTYLH----RVARAGRFGTKGLAVTFVSdeNDAKILNDVQDRFEVNVAELPEEIDISTYIE 250
Cdd:COG1061   368 GVDVPRLDVAI-LLRPTGSPREFIqrlgRGLRPAPGKEDALVYDFVG--NDVPVLEELAKDLRDLAGYRVEFLDEEESEE 444


                  ...
gi 1958747461 251 QSR 253
Cdd:COG1061   445 LAL 447
DEADc_EIF4A cd17939
DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ...
 27-75 9.53e-08

DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350697 [Multi-domain]  Cd Length: 199  Bit Score: 50.79  E-value: 9.53e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVF 75
Cdd:cd17939   151 MLSRGFKDQIYDIFQFLPPETQVVLFSATMPHEVLEVTKKFMRDPVRIL 199
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 165-216 1.57e-07

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 47.70  E-value: 1.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958747461 165 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK-GLAVTFV 216
Cdd:cd18785    25 ILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDeGEVILFV 77
DEXDc smart00487
DEAD-like helicases superfamily;
27-90 3.23e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 46.33  E-value: 3.23e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958747461   27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVfvdDETKLTLHGLQQY 90
Cdd:smart00487 141 LLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFI---DVGFTPLEPIEQF 201
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 116-215 3.46e-06

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 47.79  E-value: 3.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 116 VIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERlSRYQQfkDFQR---RILVATNLFGRGMDIERVNIVFNYDMPED 192
Cdd:PRK11057  240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVR-ADVQE--AFQRddlQIVVATVAFGMGINKPNVRFVVHFDIPRN 316

                          90       100
                  ....*....|....*....|...
gi 1958747461 193 SDTYLHRVARAGRFGTKGLAVTF 215
Cdd:PRK11057  317 IESYYQETGRAGRDGLPAEAMLF 339
DEADc_EIF4AII_EIF4AI_DDX2 cd18046
DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ...
 27-74 1.47e-05

DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation factor 4A-I (DDX2A) and eukaryotic initiation factor 4A-II (DDX2B) are involved in cap recognition and are required for mRNA binding to ribosome. They are 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: 350804 [Multi-domain]  Cd Length: 201  Bit Score: 44.74  E-value: 1.47e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd18046   153 MLSRGFKDQIYDIFQKLPPDTQVVLLSATMPNDVLEVTTKFMRDPIRI 200
DEADc_DDX49 cd17955
DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the ...
 27-73 5.70e-05

DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) 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: 350713 [Multi-domain]  Cd Length: 204  Bit Score: 42.98  E-value: 5.70e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPME 73
Cdd:cd17955   156 LLTGSFEDDLATILSALPPKRQTLLFSATLTDALKALKELFGNKPFF 202
DEADc_DDX27 cd17947
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...
 27-75 1.10e-04

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 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: 350705 [Multi-domain]  Cd Length: 196  Bit Score: 41.86  E-value: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVF 75
Cdd:cd17947   148 MLEEGFADELKEILRLCPRTRQTMLFSATMTDEVKDLAKLSLNKPVRVF 196
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 61-216 1.13e-04

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: 41.38  E-value: 1.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  61 RPVcrkfmqdPMEVFVDDETKLTLHGLQQyyVKLKDSEKNRKLFDLLDVLEFNQVVIFVKSVQRCMALAQLLVeqnfpAI 140
Cdd:cd18795     1 RPV-------PLEEYVLGFNGLGIKLRVD--VMNKFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA-----GI 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 141 AIHR-GMAQEERLSRYQQFKDFQRRILVAT-------NLFGRGMDIERVNIVFNYDMPE-DSDTYLHRVARAGR--FGTK 209
Cdd:cd18795    67 AFHHaGLTREDRELVEELFREGLIKVLVATstlaagvNLPARTVIIKGTQRYDGKGYRElSPLEYLQMIGRAGRpgFDTR 146


                  ....*..
gi 1958747461 210 GLAVTFV 216
Cdd:cd18795   147 GEAIIMT 153
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 50-209 6.69e-04

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 40.49  E-value: 6.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  50 MMFSATLSKEIRpvcrKFMQDpMEVFVDDETkLTLHGLQQYYVKLKDSEKNRKLFDLLDVLEF----NQVVIFVKSVQRC 125
Cdd:cd09639   158 LLMSATLPKFLK----EYAEK-IGYVEENEP-LDLKPNERAPFIKIESDKVGEISSLERLLEFikkgGSVAIIVNTVDRA 231

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461 126 MALAQLLVEQN--FPAIAIHRGMAQEERLSRYQQ----FKDFQRRILVATNLFGRGMDIErVNIVFNYDMPEDSdtYLHR 199
Cdd:cd09639   232 QEFYQQLKEKGpeEEIMLIHSRFTEKDRAKKEAEllleFKKSEKFVIVATQVIEASLDIS-VDVMITELAPIDS--LIQR 308

                         170
                  ....*....|
gi 1958747461 200 VARAGRFGTK 209
Cdd:cd09639   309 LGRLHRYGEK 318
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 144-205 7.19e-04

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350188 [Multi-domain]  Cd Length: 143  Bit Score: 38.88  E-value: 7.19e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958747461 144 RGMAQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 205
Cdd:cd18801    72 KGMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR 133
DEADc_DDX59 cd17962
DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ...
 26-74 1.32e-03

DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 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: 350720 [Multi-domain]  Cd Length: 193  Bit Score: 38.68  E-value: 1.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958747461  26 SMLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd17962   144 TMLKMGFQQQVLDILENISHDHQTILVSATIPRGIEQLAGQLLQNPVRI 192
DEADc_DDX6 cd17940
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ...
 27-74 1.53e-03

DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350698 [Multi-domain]  Cd Length: 201  Bit Score: 38.43  E-value: 1.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd17940   153 LLSQDFQPIIEKILNFLPKERQILLFSATFPLTVKNFMDRHMHNPYEI 200
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 117-185 2.29e-03

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain]  Cd Length: 116  Bit Score: 36.77  E-value: 2.29e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958747461 117 IFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQEERLSRYQQ---FKDFQRRILVATNLFGRGMDI-ERVNIVF 185
Cdd:cd18799    11 IFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERGDEALIllfFGELKPPILVTVDLLTTGVDIpEVDNVVF 83
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 27-61 2.39e-03

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: 37.61  E-value: 2.39e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIR 61
Cdd:pfam00270 129 LLDMGFGPDLEEILRRLPKKRQILLLSATLPRNLE 163
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 33-76 4.13e-03

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain]  Cd Length: 198  Bit Score: 37.18  E-value: 4.13e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958747461  33 RRDVQEIFR-LTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFV 76
Cdd:cd17957   153 REQTDEILAaCTNPNLQRSLFSATIPSEVEELARSVMKDPIRIIV 197
DEADc_DDX10 cd17941
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ...
 44-76 5.18e-03

DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 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: 350699 [Multi-domain]  Cd Length: 198  Bit Score: 36.88  E-value: 5.18e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958747461  44 PHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFV 76
Cdd:cd17941   165 PKSRQTLLFSATQTKSVKDLARLSLKNPEYISV 197
DEADc_EIF4AIII_DDX48 cd18045
DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ...
 27-74 5.73e-03

DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor 4A-III (EIF4AIII, also known as DDX48) is part of the exon junction complex (EJC) that plays a major role in posttranscriptional regulation of mRNA. EJC consists of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. DDX48 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: 350803 [Multi-domain]  Cd Length: 201  Bit Score: 37.06  E-value: 5.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd18045   153 MLNKGFKEQIYDVYRYLPPATQVVLVSATLPQDILEMTNKFMTDPIRI 200
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 27-74 6.74e-03

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 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: 350712 [Multi-domain]  Cd Length: 203  Bit Score: 36.53  E-value: 6.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958747461  27 MLAANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd17954   155 LLNMDFEPEIDKILKVIPRERTTYLFSATMTTKVAKLQRASLKNPVKI 202
DEADc_DDX19_DDX25 cd17963
DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ...
 27-74 8.02e-03

DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called DEAD box RNA helicase DEAD5) and DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH)) are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.


Pssm-ID: 350721 [Multi-domain]  Cd Length: 196  Bit Score: 36.40  E-value: 8.02e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958747461  27 MLA-ANMRRDVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEV 74
Cdd:cd17963   147 MLDtQGHGDQSIRIKRMLPRNCQILLFSATFPDSVRKFAEKIAPNANTI 195
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 99-203 9.27e-03

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350189 [Multi-domain]  Cd Length: 142  Bit Score: 35.64  E-value: 9.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  99 KNRKLFDLLDVL--EFNQV-----VIFVKSVQRCMALAQLLVE--QNFPAIAIH-------RGMAQEERLSRYQQ---FK 159
Cdd:cd18802     5 VIPKLQKLIEILreYFPKTpdfrgIIFVERRATAVVLSRLLKEhpSTLAFIRCGfligrgnSSQRKRSLMTQRKQketLD 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1958747461 160 DFQR---RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARA 203
Cdd:cd18802    85 KFRDgelNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGRA 131
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 99-209 9.45e-03

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. 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: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 35.53  E-value: 9.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  99 KNRKLFDLLDVLEFNQ--VVIFVKSVQrcMA--LAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQ--RRILVATNLF 172
Cdd:cd18793    12 KLEALLELLEELREPGekVLIFSQFTD--TLdiLEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPdiRVFLLSTKAG 89

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1958747461 173 GRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 209
Cdd:cd18793    90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQK 126
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
99-188 9.60e-03

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 37.02  E-value: 9.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958747461  99 KNRKLFDLLD-VLEFN---QVVIFVKSVQRCMALAQLLVEQNFPAIAI--------HRGMAQEERLSRYQQFKDFQRRIL 166
Cdd:COG1111   336 KLSKLREILKeQLGTNpdsRIIVFTQYRDTAEMIVEFLSEPGIKAGRFvgqaskegDKGLTQKEQIEILERFRAGEFNVL 415

                          90       100
                  ....*....|....*....|..
gi 1958747461 167 VATNLFGRGMDIERVNIVFNYD 188
Cdd:COG1111   416 VATSVAEEGLDIPEVDLVIFYE 437
 
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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