NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|187607756|ref|NP_001119929|]
View 

Y-box-binding protein 1 isoform 1 [Danio rerio]

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
PubMed:  12530521|10322168|17437059
SCOP:  4001909

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
39-108 1.22e-25

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.22e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756   39 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 108
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
39-108 1.22e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.22e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756   39 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 108
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 ...
 41-107 5.96e-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: 89.56  E-value: 5.96e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 187607756  41 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 107
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
41-106 3.59e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 79.85  E-value: 3.59e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 187607756  41 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
37-106 6.15e-16

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 71.22  E-value: 6.15e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756  37 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 41-108 7.74e-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: 70.71  E-value: 7.74e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756    41 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 108
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
39-108 1.22e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.22e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756   39 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 108
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 ...
 41-107 5.96e-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: 89.56  E-value: 5.96e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 187607756  41 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 107
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
41-106 3.59e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 79.85  E-value: 3.59e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 187607756  41 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
37-106 6.15e-16

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 71.22  E-value: 6.15e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756  37 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 41-108 7.74e-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: 70.71  E-value: 7.74e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756    41 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 108
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK09890 PRK09890
cold shock protein CspG; Provisional
 35-105 1.00e-14

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 67.87  E-value: 1.00e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 187607756  35 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANV 105
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
35-106 1.25e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 67.69  E-value: 1.25e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 187607756  35 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 38-106 4.95e-12

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 60.47  E-value: 4.95e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 187607756  38 KVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 106
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
41-114 1.53e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 53.58  E-value: 1.53e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 187607756  41 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpggVPVQ 114
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGNHASVI-----VPVE 68
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 40-119 3.32e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 49.66  E-value: 3.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 187607756  40 LGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpggVPVQGSKYA 119
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGNHASVI-----VPIEAEAVA 73
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 35-105 6.16e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 43.35  E-value: 6.16e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 187607756  35 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRkylrSVGDGETVEFDVVEGEKGAEAANV 105
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE----ELTTGLRVEFCRINGLRGPTAANV 67
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH