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Conserved domains on  [gi|40068489|ref|NP_690019|]
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probable ATP-dependent RNA helicase DDX17 isoform 3 [Mus musculus]

Protein Classification

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 ...
 22-120 4.66e-28

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: 112.17  E-value: 4.66e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRggggGGG 101
Cdd:PTZ00110 442 DVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNER----SNG 517

                         90
                 ....*....|....*....
gi 40068489  102 KGGRSRYRTTSSANNPNLM 120
Cdd:PTZ00110 518 TERRRWGGYGRFSNNVNNI 536
 
Name Accession Description Interval E-value
PTZ00110 PTZ00110
helicase; Provisional
 22-120 4.66e-28

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 112.17  E-value: 4.66e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRggggGGG 101
Cdd:PTZ00110 442 DVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNER----SNG 517

                         90
                 ....*....|....*....
gi 40068489  102 KGGRSRYRTTSSANNPNLM 120
Cdd:PTZ00110 518 TERRRWGGYGRFSNNVNNI 536
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 22-61 3.82e-19

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: 81.01  E-value: 3.82e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 40068489  22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFF 61
Cdd:cd18787  92 DIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
22-86 2.43e-18

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 83.66  E-value: 2.43e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 40068489  22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPgnlKQARELIKVLEEANQAINPK 86
Cdd:COG0513 306 DIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTP---DERRLLRAIEKLIGQKIEEE 367
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 22-50 1.41e-08

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: 51.44  E-value: 1.41e-08
                          10        20
                  ....*....|....*....|....*....
gi 40068489    22 DVEDVKFVINYDYPNSSEDYVHRIGRTAR 50
Cdd:pfam00271  79 DLPDVDLVINYDLPWNPASYIQRIGRAGR 107
HELICc smart00490
helicase superfamily c-terminal domain;
22-50 1.32e-07

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 47.98  E-value: 1.32e-07
                           10        20
                   ....*....|....*....|....*....
gi 40068489     22 DVEDVKFVINYDYPNSSEDYVHRIGRTAR 50
Cdd:smart00490  52 DLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
 
Name Accession Description Interval E-value
PTZ00110 PTZ00110
helicase; Provisional
 22-120 4.66e-28

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 112.17  E-value: 4.66e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEEANQAINPKLMQLVDHRggggGGG 101
Cdd:PTZ00110 442 DVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELEKLSNER----SNG 517

                         90
                 ....*....|....*....
gi 40068489  102 KGGRSRYRTTSSANNPNLM 120
Cdd:PTZ00110 518 TERRRWGGYGRFSNNVNNI 536
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 22-61 3.82e-19

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: 81.01  E-value: 3.82e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 40068489  22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFF 61
Cdd:cd18787  92 DIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
22-86 2.43e-18

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 83.66  E-value: 2.43e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 40068489  22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPgnlKQARELIKVLEEANQAINPK 86
Cdd:COG0513 306 DIDDVSHVINYDLPEDPEDYVHRIGRTGRAGAEGTAISLVTP---DERRLLRAIEKLIGQKIEEE 367
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 22-57 8.45e-12

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 64.58  E-value: 8.45e-12
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTA 57
Cdd:PRK11192 310 DIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTA 345
PTZ00424 PTZ00424
helicase 45; Provisional
 22-72 1.64e-10

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 60.61  E-value: 1.64e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQAREL 72
Cdd:PTZ00424 332 DVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEI 382
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 22-63 7.05e-10

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 59.04  E-value: 7.05e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTP 63
Cdd:PRK11776 307 DIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAP 348
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 25-60 4.11e-09

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 56.52  E-value: 4.11e-09
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 40068489   25 DVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTF 60
Cdd:PRK04837 323 AVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 22-109 9.77e-09

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 55.56  E-value: 9.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEEANQAInPKlmQLVDHRGGGGGGG 101
Cdd:PLN00206 433 DLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPELVALLKSSGAAI-PR--ELANSRYLGSGRK 509


                 ....*...
gi 40068489  102 KGGRSRYR 109
Cdd:PLN00206 510 RKKKRRYG 517
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 22-50 1.41e-08

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: 51.44  E-value: 1.41e-08
                          10        20
                  ....*....|....*....|....*....
gi 40068489    22 DVEDVKFVINYDYPNSSEDYVHRIGRTAR 50
Cdd:pfam00271  79 DLPDVDLVINYDLPWNPASYIQRIGRAGR 107
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 23-60 3.95e-08

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 53.80  E-value: 3.95e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 40068489   23 VEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTF 60
Cdd:PRK04537 323 IDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 22-77 5.68e-08

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 53.27  E-value: 5.68e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLE 77
Cdd:PRK10590 310 DIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLK 365
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 22-60 9.52e-08

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 52.54  E-value: 9.52e-08
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 40068489   22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTF 60
Cdd:PRK11634 310 DVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLF 348
HELICc smart00490
helicase superfamily c-terminal domain;
22-50 1.32e-07

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 47.98  E-value: 1.32e-07
                           10        20
                   ....*....|....*....|....*....
gi 40068489     22 DVEDVKFVINYDYPNSSEDYVHRIGRTAR 50
Cdd:smart00490  52 DLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 23-60 1.44e-06

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 48.76  E-value: 1.44e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 40068489   23 VEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTF 60
Cdd:PRK01297 401 IDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISF 438
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 22-62 5.49e-04

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


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 37.68  E-value: 5.49e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 40068489  22 DVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFT 62
Cdd:cd18785  37 DVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGEVILFV 77
SF2_C_RecQ cd18794
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...
 25-50 6.47e-03

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: 36.03  E-value: 6.47e-03
                        10        20
                ....*....|....*....|....*.
gi 40068489  25 DVKFVINYDYPNSSEDYVHRIGRTAR 50
Cdd:cd18794  98 DVRFVIHYSLPKSMESYYQESGRAGR 123
 
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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