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Conserved domains on  [gi|1720424193|ref|XP_030098852|]
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probable ATP-dependent RNA helicase DHX34 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 226-337 2.19e-08

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


:

Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 51.48  E-value: 2.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424193 226 LKLVLGRGLYPQLAVPDAfnsgrkDSDQIFHTQAKQGTVLHPTCVFANSPEvlhtqgqeasgqegsqdgrdqMSCKhqLL 305
Cdd:pfam07717   1 LRAALAAGLYPNVARRDP------KGKGYTTLSDNQRVFIHPSSVLFNEKT---------------------FPPE--WV 51

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720424193 306 AFVSLLETNKPYLVNCVRIPALQsLLLFSRSI 337
Cdd:pfam07717  52 VYQELVETTKVYIRTVTAISPEW-LLLFAPHI 82
HA2 super family cl47887
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 27-73 9.19e-03

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


The actual alignment was detected with superfamily member pfam04408:

Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 36.06  E-value: 9.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720424193  27 FSLAEPVLTIAAALSVQSPFTRSAQSNLDC---------------ATARRPLESDQGDPFTL 73
Cdd:pfam04408  43 LGCLDEVLTIVAALSVRDPFVQPNFLDPRSaakaarrrrraadekARAKFARLDLEGDHLTL 104
 
Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 226-337 2.19e-08

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 51.48  E-value: 2.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424193 226 LKLVLGRGLYPQLAVPDAfnsgrkDSDQIFHTQAKQGTVLHPTCVFANSPEvlhtqgqeasgqegsqdgrdqMSCKhqLL 305
Cdd:pfam07717   1 LRAALAAGLYPNVARRDP------KGKGYTTLSDNQRVFIHPSSVLFNEKT---------------------FPPE--WV 51

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720424193 306 AFVSLLETNKPYLVNCVRIPALQsLLLFSRSI 337
Cdd:pfam07717  52 VYQELVETTKVYIRTVTAISPEW-LLLFAPHI 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 27-73 9.19e-03

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 36.06  E-value: 9.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720424193  27 FSLAEPVLTIAAALSVQSPFTRSAQSNLDC---------------ATARRPLESDQGDPFTL 73
Cdd:pfam04408  43 LGCLDEVLTIVAALSVRDPFVQPNFLDPRSaakaarrrrraadekARAKFARLDLEGDHLTL 104
 
Name Accession Description Interval E-value
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 226-337 2.19e-08

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 51.48  E-value: 2.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720424193 226 LKLVLGRGLYPQLAVPDAfnsgrkDSDQIFHTQAKQGTVLHPTCVFANSPEvlhtqgqeasgqegsqdgrdqMSCKhqLL 305
Cdd:pfam07717   1 LRAALAAGLYPNVARRDP------KGKGYTTLSDNQRVFIHPSSVLFNEKT---------------------FPPE--WV 51

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1720424193 306 AFVSLLETNKPYLVNCVRIPALQsLLLFSRSI 337
Cdd:pfam07717  52 VYQELVETTKVYIRTVTAISPEW-LLLFAPHI 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 27-73 9.19e-03

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 36.06  E-value: 9.19e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720424193  27 FSLAEPVLTIAAALSVQSPFTRSAQSNLDC---------------ATARRPLESDQGDPFTL 73
Cdd:pfam04408  43 LGCLDEVLTIVAALSVRDPFVQPNFLDPRSaakaarrrrraadekARAKFARLDLEGDHLTL 104
 
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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