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Conserved domains on  [gi|1907113873|ref|XP_036015440|]
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probable ATP-dependent RNA helicase DDX17 isoform X2 [Mus musculus]

Protein Classification

DEAD/DEAH box helicase family protein( domain architecture ID 1000205)

DEAD/DEAH box helicase family protein such as a DEAD/DEAH box-containing ATP-dependent helicase, which catalyzes the unwinding of DNA or RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 1-226 4.96e-95

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


The actual alignment was detected with superfamily member PTZ00110:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 545  Bit Score: 293.99  E-value: 4.96e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDY-TQINVGNLELSANHNILQIVDVCMESEKDHKLIQLMEEIMAEKeNKTIIFVETKRRCD 79
Cdd:PTZ00110  313 MWSATWPKEVQSLARDLCKEEpVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDG-DKILIFVETKKGAD 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  80 DLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARS 159
Cdd:PTZ00110  392 FLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA 471

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907113873 160 TNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRGGGGGGGGRSRYRttSSANNPNLM 226
Cdd:PTZ00110  472 GAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRWGGYG--RFSNNVNNI 536
 
Name Accession Description Interval E-value
PTZ00110 PTZ00110
helicase; Provisional
 1-226 4.96e-95

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 293.99  E-value: 4.96e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDY-TQINVGNLELSANHNILQIVDVCMESEKDHKLIQLMEEIMAEKeNKTIIFVETKRRCD 79
Cdd:PTZ00110  313 MWSATWPKEVQSLARDLCKEEpVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDG-DKILIFVETKKGAD 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  80 DLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARS 159
Cdd:PTZ00110  392 FLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA 471

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907113873 160 TNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRGGGGGGGGRSRYRttSSANNPNLM 226
Cdd:PTZ00110  472 GAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRWGGYG--RFSNNVNNI 536
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
3-194 3.60e-68

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 220.79  E-value: 3.60e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   3 SATWPKEVRQLAEDFLRDYTQINVGNLELSANhNILQIVdvcMESEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLT 82
Cdd:COG0513   183 SATMPPEIRKLAKRYLKNPVRIEVAPENATAE-TIEQRY---YLVDKRDKLELLRRLLRDEDPERAIVFCNTKRGADRLA 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  83 RRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNK 162
Cdd:COG0513   259 EKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE 338

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1907113873 163 GTAYTFFTPgnlKQARELIKVLEEANQAINPK 194
Cdd:COG0513   339 GTAISLVTP---DERRLLRAIEKLIGQKIEEE 367
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 37-169 6.33e-63

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: 197.34  E-value: 6.33e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  37 ILQIVDVCMESEKDHKLIQLmeEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKA 116
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLLL--LLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907113873 117 PILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFF 169
Cdd:cd18787    79 RVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 52-158 6.39e-38

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: 131.95  E-value: 6.39e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  52 KLIQLMEEIMAEKENKTIIFVETKRRCDdLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDV 131
Cdd:pfam00271   2 KLEALLELLKKERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80

                          90       100
                  ....*....|....*....|....*..
gi 1907113873 132 EDVKFVINYDYPNSSEDYVHRIGRTAR 158
Cdd:pfam00271  81 PDVDLVINYDLPWNPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
79-158 6.10e-29

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 107.30  E-value: 6.10e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   79 DDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTAR 158
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
 
Name Accession Description Interval E-value
PTZ00110 PTZ00110
helicase; Provisional
 1-226 4.96e-95

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 293.99  E-value: 4.96e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDY-TQINVGNLELSANHNILQIVDVCMESEKDHKLIQLMEEIMAEKeNKTIIFVETKRRCD 79
Cdd:PTZ00110  313 MWSATWPKEVQSLARDLCKEEpVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDG-DKILIFVETKKGAD 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  80 DLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARS 159
Cdd:PTZ00110  392 FLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA 471

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907113873 160 TNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRGGGGGGGGRSRYRttSSANNPNLM 226
Cdd:PTZ00110  472 GAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNERSNGTERRRWGGYG--RFSNNVNNI 536
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
3-194 3.60e-68

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 220.79  E-value: 3.60e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   3 SATWPKEVRQLAEDFLRDYTQINVGNLELSANhNILQIVdvcMESEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLT 82
Cdd:COG0513   183 SATMPPEIRKLAKRYLKNPVRIEVAPENATAE-TIEQRY---YLVDKRDKLELLRRLLRDEDPERAIVFCNTKRGADRLA 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  83 RRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNK 162
Cdd:COG0513   259 EKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAE 338

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1907113873 163 GTAYTFFTPgnlKQARELIKVLEEANQAINPK 194
Cdd:COG0513   339 GTAISLVTP---DERRLLRAIEKLIGQKIEEE 367
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 37-169 6.33e-63

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: 197.34  E-value: 6.33e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  37 ILQIVDVCMESEKDHKLIQLmeEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKA 116
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLLLL--LLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907113873 117 PILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFF 169
Cdd:cd18787    79 RVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 3-171 2.20e-42

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 153.80  E-value: 2.20e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   3 SATWPKEVRQLAEDFLRDYTQInvgnlELSANHNILQIVDVCMESEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLT 82
Cdd:PRK11776  185 SATYPEGIAAISQRFQRDPVEV-----KVESTHDLPAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVA 259

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  83 RRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNK 162
Cdd:PRK11776  260 DALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSK 339


                  ....*....
gi 1907113873 163 GTAYTFFTP 171
Cdd:PRK11776  340 GLALSLVAP 348
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 52-158 6.39e-38

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: 131.95  E-value: 6.39e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  52 KLIQLMEEIMAEKENKTIIFVETKRRCDdLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDV 131
Cdd:pfam00271   2 KLEALLELLKKERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80

                          90       100
                  ....*....|....*....|....*..
gi 1907113873 132 EDVKFVINYDYPNSSEDYVHRIGRTAR 158
Cdd:pfam00271  81 PDVDLVINYDLPWNPASYIQRIGRAGR 107
PTZ00424 PTZ00424
helicase 45; Provisional
 1-180 8.01e-37

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 137.65  E-value: 8.01e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNLELSAnHNILQI-VDVCMESEKDHKLIQLMEEIMAekeNKTIIFVETKRRCD 79
Cdd:PTZ00424  206 LFSATMPNEILELTTKFMRDPKRILVKKDELTL-EGIRQFyVAVEKEEWKFDTLCDLYETLTI---TQAIIYCNTRRKVD 281

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  80 DLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARS 159
Cdd:PTZ00424  282 YLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRF 361

                         170       180
                  ....*....|....*....|.
gi 1907113873 160 TNKGTAYTFFTPGNLKQAREL 180
Cdd:PTZ00424  362 GRKGVAINFVTPDDIEQLKEI 382
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 49-165 2.00e-31

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 123.51  E-value: 2.00e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  49 KDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRG 128
Cdd:PRK11192  229 LEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARG 308

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907113873 129 LDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTA 165
Cdd:PRK11192  309 IDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTA 345
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 1-168 8.69e-30

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 118.54  E-value: 8.69e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNLELSAnHNILQIVDVCMESEKDHKLIQLMEEimaEKENKTIIFVETKRRCDD 80
Cdd:PRK04837  195 LFSATLSYRVRELAFEHMNNPEYVEVEPEQKTG-HRIKEELFYPSNEEKMRLLQTLIEE---EWPDRAIIFANTKHRCEE 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  81 LTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARST 160
Cdd:PRK04837  271 IWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAG 350


                  ....*...
gi 1907113873 161 NKGTAYTF 168
Cdd:PRK04837  351 ASGHSISL 358
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 1-185 1.23e-29

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 118.76  E-value: 1.23e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNLElSANHNILQIVDVCMESEKDHKLIQLmeeIMAEKENKTIIFVETKRRCDD 80
Cdd:PRK10590  185 LFSATFSDDIKALAEKLLHNPLEIEVARRN-TASEQVTQHVHFVDKKRKRELLSQM---IGKGNWQQVLVFTRTKHGANH 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  81 LTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARST 160
Cdd:PRK10590  261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAA 340

                         170       180
                  ....*....|....*....|....*
gi 1907113873 161 NKGTAYTFFTPGNLKQARELIKVLE 185
Cdd:PRK10590  341 ATGEALSLVCVDEHKLLRDIEKLLK 365
HELICc smart00490
helicase superfamily c-terminal domain;
79-158 6.10e-29

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 107.30  E-value: 6.10e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   79 DDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTAR 158
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 1-168 3.24e-27

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 113.02  E-value: 3.24e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNlELSANHNILQIVDVCMESEKDHKLIQLMEeimAEKENKTIIFVETKRRCDD 80
Cdd:PRK11634  185 LFSATMPEAIRRITRRFMKEPQEVRIQS-SVTTRPDISQSYWTVWGMRKNEALVRFLE---AEDFDAAIIFVRTKNATLE 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  81 LTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARST 160
Cdd:PRK11634  261 VAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340


                  ....*...
gi 1907113873 161 NKGTAYTF 168
Cdd:PRK11634  341 RAGRALLF 348
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 1-168 4.71e-26

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 109.66  E-value: 4.71e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNLELSANHnILQIVDVCMESEKdhklIQLMEEIMAEKEN-KTIIFVETKRRCD 79
Cdd:PRK04537  197 LFSATLSHRVLELAYEHMNEPEKLVVETETITAAR-VRQRIYFPADEEK----QTLLLGLLSRSEGaRTMVFVNTKAFVE 271

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  80 DLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARS 159
Cdd:PRK04537  272 RVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARL 351


                  ....*....
gi 1907113873 160 TNKGTAYTF 168
Cdd:PRK04537  352 GEEGDAISF 360
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 1-168 3.02e-25

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 106.54  E-value: 3.02e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVgNLELSANHNILQIVDVCMESEKdHKLIQLMeeIMAEKENKTIIFVETKRRCDD 80
Cdd:PRK01297  275 LFSATFTDDVMNLAKQWTTDPAIVEI-EPENVASDTVEQHVYAVAGSDK-YKLLYNL--VTQNPWERVMVFANRKDEVRR 350

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  81 LTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARST 160
Cdd:PRK01297  351 IEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430


                  ....*...
gi 1907113873 161 NKGTAYTF 168
Cdd:PRK01297  431 ASGVSISF 438
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 1-215 4.46e-25

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 106.41  E-value: 4.46e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVGNLElSANHNILQIVdVCMES-EKDHKLIqlmeEIMAEKEN---KTIIFVETKR 76
Cdd:PLN00206  305 LFSATVSPEVEKFASSLAKDIILISIGNPN-RPNKAVKQLA-IWVETkQKKQKLF----DILKSKQHfkpPAVVFVSSRL 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  77 RCDDLTRRMRR-DGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGR 155
Cdd:PLN00206  379 GADLLANAITVvTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGR 458

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907113873 156 TARSTNKGTAYTFFTPGNLKQARELIKVLEEANQAInPKlmQLVDHRG--GGGGGGGRSRYR 215
Cdd:PLN00206  459 ASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAI-PR--ELANSRYlgSGRKRKKKRRYG 517
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
30-162 2.68e-17

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 83.63  E-value: 2.68e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  30 ELSANHNILQIVDVCMESEKDH-KLIQLMEEI----MAEKENKTIIFVETKRRCDDLTRRMRRDGWPAM------CIHGD 98
Cdd:COG1111   313 RLVSDPRFRKAMRLAEEADIEHpKLSKLREILkeqlGTNPDSRIIVFTQYRDTAEMIVEFLSEPGIKAGrfvgqaSKEGD 392

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907113873  99 K--SQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDyPNSSE-DYVHRIGRTARSTNK 162
Cdd:COG1111   393 KglTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYE-PVPSEiRSIQRKGRTGRKREG 458
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
45-166 1.20e-15

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 78.14  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  45 MESEKDHKLIQLMEEIMAEKenKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDV 124
Cdd:COG1061   287 DAERKDKILRELLREHPDDR--KTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDV 364

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1907113873 125 ASRGLDVEDVKFVInYDYPNSSE-DYVHRIGRTAR-STNKGTAY 166
Cdd:COG1061   365 LNEGVDVPRLDVAI-LLRPTGSPrEFIQRLGRGLRpAPGKEDAL 407
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 46-156 2.39e-14

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 74.49  E-value: 2.39e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  46 ESEKDHKLIQLMEEIMAEKEnKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAP--ILIATD 123
Cdd:COG0553   531 RSAKLEALLELLEELLAEGE-KVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEApvFLISLK 609

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1907113873 124 VASRGLDVEDVKFVINYDYP------NSSEDYVHRIGRT 156
Cdd:COG0553   610 AGGEGLNLTAADHVIHYDLWwnpaveEQAIDRAHRIGQT 648
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 42-158 6.04e-13

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: 65.31  E-value: 6.04e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  42 DVCMESEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIA 121
Cdd:cd18794     7 SVRPKDKKDEKLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVA 86

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1907113873 122 TDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTAR 158
Cdd:cd18794    87 TVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGR 123
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
36-181 1.13e-12

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 69.01  E-value: 1.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  36 NI-LQIVDVcmesEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSG 114
Cdd:COG0514   204 NLrLEVVPK----PPDDKLAQLLDFLKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRD 279

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1907113873 115 KAPILIATdVA-SRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELI 181
Cdd:COG0514   280 EVDVIVAT-IAfGMGIDKPDVRFVIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQRFFI 346
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 47-161 1.99e-12

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: 64.15  E-value: 1.99e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  47 SEKDHKLIQ-LMEEIMAEKENKTIIFVETKR-------------------RCDDLTRRMRRDGWPAMcIHGDKSQPErdw 106
Cdd:cd18802     6 IPKLQKLIEiLREYFPKTPDFRGIIFVERRAtavvlsrllkehpstlafiRCGFLIGRGNSSQRKRS-LMTQRKQKE--- 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907113873 107 VLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRtARSTN 161
Cdd:cd18802    82 TLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-ARAPN 135
DEADc_DDX17 cd18050
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...
 1-27 2.74e-12

DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 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: 350808 [Multi-domain]  Cd Length: 271  Bit Score: 66.57  E-value: 2.74e-12
                          10        20
                  ....*....|....*....|....*..
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVG 27
Cdd:cd18050   245 MWSATWPKEVRQLAEDFLRDYVQINIG 271
DEADc_DDX5 cd18049
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...
 1-27 3.73e-12

DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 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: 350807 [Multi-domain]  Cd Length: 234  Bit Score: 65.42  E-value: 3.73e-12
                          10        20
                  ....*....|....*....|....*..
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVG 27
Cdd:cd18049   207 MWSATWPKEVRQLAEDFLKDYIHINIG 233
DEADc_DDX5_DDX17 cd17966
DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ...
 1-25 3.50e-11

DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 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: 350724 [Multi-domain]  Cd Length: 197  Bit Score: 62.00  E-value: 3.50e-11
                          10        20
                  ....*....|....*....|....*
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQIN 25
Cdd:cd17966   173 MWSATWPKEVRRLAEDFLKDYIQVN 197
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 37-154 1.03e-10

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: 59.03  E-value: 1.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  37 ILQIVDVCMEsekdhKLIQLMEEIMAEKEnKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKA 116
Cdd:cd18793     5 IEEVVSGKLE-----ALLELLEELREPGE-KVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1907113873 117 P--ILIATDVASRGLDVEDVKFVINYDYP-NSS-----EDYVHRIG 154
Cdd:cd18793    79 IrvFLLSTKAGGVGLNLTAANRVILYDPWwNPAveeqaIDRAHRIG 124
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 67-170 5.18e-10

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: 55.40  E-value: 5.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  67 KTIIFVETKRRCDDLTRRMRrdgwpamcihgdksqperdwvlnefrsgkapILIATDVASRGLDVEDVKFVINYDYPNSS 146
Cdd:cd18785     5 KIIVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPPSSA 53

                          90       100
                  ....*....|....*....|....
gi 1907113873 147 EDYVHRIGRTARSTNKGTAYTFFT 170
Cdd:cd18785    54 ASYIQRVGRAGRGGKDEGEVILFV 77
PRK13766 PRK13766
Hef nuclease; Provisional
 30-160 8.56e-10

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 60.27  E-value: 8.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  30 ELSANHNILQIVDVCMESEKDH----KLIQLMEEIMAEKEN-KTIIFVETKRRCDDLTRRMRRDGWPAM------CIHGD 98
Cdd:PRK13766  325 RLVEDPRFRKAVRKAKELDIEHpkleKLREIVKEQLGKNPDsRIIVFTQYRDTAEKIVDLLEKEGIKAVrfvgqaSKDGD 404

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907113873  99 K--SQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDyPNSSE-DYVHRIGRTARST 160
Cdd:PRK13766  405 KgmSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEiRSIQRKGRTGRQE 468
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 53-161 2.57e-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: 55.35  E-value: 2.57e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  53 LIQLMEEImaEKENKTIIFVETKRRCDDLTRRMRR----DGWP--AMCIHGDKSQPERDWVLNEFRSGKAPILIATDVAS 126
Cdd:cd18796    28 YAEVIFLL--ERHKSTLVFTNTRSQAERLAQRLRElcpdRVPPdfIALHHGSLSRELREEVEAALKRGDLKVVVATSSLE 105

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1907113873 127 RGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTN 161
Cdd:cd18796   106 LGIDIGDVDLVIQIGSPKSVARLLQRLGRSGHRPG 140
SF2_C_UvrB cd18790
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...
 56-161 2.42e-08

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350177 [Multi-domain]  Cd Length: 171  Bit Score: 53.02  E-value: 2.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  56 LMEEI--MAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVED 133
Cdd:cd18790    16 LLGEIrkRVARGERVLVTTLTKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPE 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907113873 134 VKFVINYD-----YPNSSEDYVHRIGRTARSTN 161
Cdd:cd18790    96 VSLVAILDadkegFLRSETSLIQTIGRAARNVN 128
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 48-186 2.71e-08

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 55.49  E-value: 2.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  48 EKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASR 127
Cdd:PRK11057  219 EKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGM 298

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907113873 128 GLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQAReliKVLEE 186
Cdd:PRK11057  299 GINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR---RCLEE 354
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 48-158 1.57e-07

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: 50.05  E-value: 1.57e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  48 EKDHKLIQLMEEIMAE--------KENKTIIFVETKRRCDDLTRRMRRDGW---PAMCI-HGDK------SQPERDWVLN 109
Cdd:cd18801     5 EKIHPKLEKLEEIVKEhfkkkqegSDTRVIIFSEFRDSAEEIVNFLSKIRPgirATRFIgQASGksskgmSQKEQKEVIE 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1907113873 110 EFRSGKAPILIATDVASRGLDVEDVKFVINYDyPNSSE-DYVHRIGRTAR 158
Cdd:cd18801    85 QFRKGGYNVLVATSIGEEGLDIGEVDLIICYD-ASPSPiRMIQRMGRTGR 133
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 63-169 8.31e-06

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350176 [Multi-domain]  Cd Length: 153  Bit Score: 45.32  E-value: 8.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  63 EKENKTIIFVETKrrcDDLTRRMRRDGWPAmcIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVED--VKFVINY 140
Cdd:cd18789    47 EQGDKIIVFTDNV---EALYRYAKRLLKPF--ITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEanVAIQISG 121

                          90       100
                  ....*....|....*....|....*....
gi 1907113873 141 DYpNSSEDYVHRIGRTARSTNKGTAYTFF 169
Cdd:cd18789   122 HG-GSRRQEAQRLGRILRPKKGGGKNAFF 149
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 69-181 2.92e-05

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 46.04  E-value: 2.92e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   69 IIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFVINYDYPNSSED 148
Cdd:PLN03137   684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEG 763

                           90       100       110
                   ....*....|....*....|....*....|...
gi 1907113873  149 YVHRIGRTARSTNKGTAYTFFTPGNLKQARELI 181
Cdd:PLN03137   764 YHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMI 796
DEADc_DDX3_DDX4 cd17967
DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ...
 1-27 4.41e-05

DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 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: 350725 [Multi-domain]  Cd Length: 221  Bit Score: 44.01  E-value: 4.41e-05
                          10        20
                  ....*....|....*....|....*..
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVG 27
Cdd:cd17967   192 MFSATFPREIQRLAADFLKNYIFLTVG 218
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 3-158 2.14e-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: 42.80  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   3 SATWPKEVRQLAEDFLRDytqINVGNLELSANHNILQIVdvcMESEKDHKlIQLMEEIMAE--KENKTIIFVETKRRCDD 80
Cdd:cd09639   161 SATLPKFLKEYAEKIGYV---EENEPLDLKPNERAPFIK---IESDKVGE-ISSLERLLEFikKGGSVAIIVNTVDRAQE 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  81 LTRRMRRDG--WPAMCIHG-----DKSQPERDwVLNEFRSGKAPILIATDVASRGLDVeDVKFVINYDYPNSSedYVHRI 153
Cdd:cd09639   234 FYQQLKEKGpeEEIMLIHSrftekDRAKKEAE-LLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAPIDS--LIQRL 309


                  ....*
gi 1907113873 154 GRTAR 158
Cdd:cd09639   310 GRLHR 314
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 1-24 2.93e-04

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: 41.27  E-value: 2.93e-04
                          10        20
                  ....*....|....*....|....
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQI 24
Cdd:cd00268   172 LFSATLPEEVKELAKKFLKNPVRI 195
DEADc_DDX3 cd18051
DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ...
 1-27 7.49e-04

DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD box, X isoform, or DDX14) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. Diseases associated with DDX3 include mental retardation, X-linked 102 and agenesis of the corpus callosum, with facial anomalies and robin sequence. DDX3 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: 350809 [Multi-domain]  Cd Length: 249  Bit Score: 40.79  E-value: 7.49e-04
                          10        20
                  ....*....|....*....|....*..
gi 1907113873   1 MWSATWPKEVRQLAEDFLRDYTQINVG 27
Cdd:cd18051   219 MFSATFPKEIQMLARDFLDNYIFLAVG 245
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 41-122 8.27e-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: 39.46  E-value: 8.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873  41 VDVCMESEKDHKLIQLMEEIMAEKenKTIIFVETKRRCDDLTRRMRrdgwpamCI---HGDKSQPERDWVLNEFRSGKAP 117
Cdd:cd18795    21 VDVMNKFDSDIIVLLKIETVSEGK--PVLVFCSSRKECEKTAKDLA-------GIafhHAGLTREDRELVEELFREGLIK 91


                  ....*
gi 1907113873 118 ILIAT 122
Cdd:cd18795    92 VLVAT 96
Cas3 COG1203
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...
 3-138 9.45e-04

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: 41.22  E-value: 9.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907113873   3 SATWPKEVRQLAEDFLRDYTQiNVGNLELSANHNILQIVDVCMESEKDHKLIQLMEEImAEKENKTIIFVETKRRCDDLT 82
Cdd:COG1203   306 TATLPPLLREELLEAYELIPD-EPEELPEYFRAFVRKRVELKEGPLSDEELAELILEA-LHKGKSVLVIVNTVKDAQELY 383

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907113873  83 RRMRRDGW--PAMCIHG-----DKSQPERDwVLNEFRSGKAPILIATDVASRGLDVeDVKFVI 138
Cdd:COG1203   384 EALKEKLPdeEVYLLHSrfcpaDRSEIEKE-IKERLERGKPCILVSTQVVEAGVDI-DFDVVI 444
SF2_C_EcoAI-like cd18799
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...
 67-138 1.51e-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: 37.92  E-value: 1.51e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907113873  67 KTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWV---LNEFRSGKAPILIATDVASRGLDVEDVKFVI 138
Cdd:cd18799     8 KTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERGDEaliLLFFGELKPPILVTVDLLTTGVDIPEVDNVV 82
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 95-131 4.04e-03

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350198 [Multi-domain]  Cd Length: 159  Bit Score: 37.71  E-value: 4.04e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907113873  95 IHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDV 131
Cdd:cd18811    67 LHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDV 103
DEADc_DDX4 cd18052
DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ...
 1-29 4.26e-03

DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are 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: 350810 [Multi-domain]  Cd Length: 264  Bit Score: 38.41  E-value: 4.26e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1907113873   1 MWSATWPKEVRQLAEDFLR-DYTQINVGNL 29
Cdd:cd18052   234 MFSATFPEEIQRLAAEFLKeDYLFLTVGRV 263
 
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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