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Conserved domains on  [gi|156415990|ref|NP_057066|]
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Y-box-binding protein 2 [Homo sapiens]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10448154)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation

CATH:  2.40.50.140
Gene Ontology:  GO:0003676

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
94-163 6.73e-27

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 6.73e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156415990   94 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVTGP 163
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
PRK12323 super family cl46901
DNA polymerase III subunit gamma/tau;
304-352 8.75e-04

DNA polymerase III subunit gamma/tau;


The actual alignment was detected with superfamily member PRK14965:

Pssm-ID: 481241 [Multi-domain]  Cd Length: 576  Bit Score: 41.27  E-value: 8.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 156415990 304 PSQGPADGSRPEPQRPRNRPYFQRRRQQAPGPQQAPGPRQPAAPETSAP 352
Cdd:PRK14965 396 APAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSADPAAAA 444
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
94-163 6.73e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 6.73e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156415990   94 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVTGP 163
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 96-162 1.12e-23

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 92.64  E-value: 1.12e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 156415990  96 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVTG 162
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
96-161 6.90e-20

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 82.55  E-value: 6.90e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 156415990  96 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 96-163 5.93e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 71.48  E-value: 5.93e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156415990    96 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKRNnprkfLRSVGDGETVEFDVV--EGEKGAEATNVTGP 163
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
93-161 5.17e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 69.30  E-value: 5.17e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 156415990  93 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:PRK09507   3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 304-352 8.75e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 41.27  E-value: 8.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 156415990 304 PSQGPADGSRPEPQRPRNRPYFQRRRQQAPGPQQAPGPRQPAAPETSAP 352
Cdd:PRK14965 396 APAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSADPAAAA 444
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
94-163 6.73e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.16  E-value: 6.73e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156415990   94 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVTGP 163
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 96-162 1.12e-23

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 92.64  E-value: 1.12e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 156415990  96 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVTG 162
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
96-161 6.90e-20

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 82.55  E-value: 6.90e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 156415990  96 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 96-163 5.93e-16

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 71.48  E-value: 5.93e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 156415990    96 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKRNnprkfLRSVGDGETVEFDVV--EGEKGAEATNVTGP 163
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
93-161 5.17e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 69.30  E-value: 5.17e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 156415990  93 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:PRK09507   3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
93-161 6.06e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 66.15  E-value: 6.06e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 156415990  93 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:PRK10354   4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK09890 PRK09890
cold shock protein CspG; Provisional
 93-160 2.54e-13

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 64.40  E-value: 2.54e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 156415990  93 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNV 160
Cdd:PRK09890   4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 93-161 1.91e-12

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 62.01  E-value: 1.91e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 156415990  93 QVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVT 161
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
96-169 1.18e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 54.35  E-value: 1.18e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 156415990  96 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEATNVtgpggVPVK 169
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGNHASVI-----VPVE 68
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 95-158 2.38e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 50.43  E-value: 2.38e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 156415990  95 LGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNprkfLRSVGDGETVEFDVVEGEKGAEAT 158
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGNHAS 62
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 304-352 8.75e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 41.27  E-value: 8.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 156415990 304 PSQGPADGSRPEPQRPRNRPYFQRRRQQAPGPQQAPGPRQPAAPETSAP 352
Cdd:PRK14965 396 APAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPPARSADPAAAA 444
 
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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