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Conserved domains on  [gi|34098946|ref|NP_004550|]
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Y-box-binding protein 1 [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
PubMed:  12530521|10322168|17437059
SCOP:  4001909

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
59-128 1.53e-25

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.53e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946    59 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 128
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
59-128 1.53e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.53e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946    59 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 128
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 ...
 61-127 1.69e-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: 91.49  E-value: 1.69e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 34098946  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 127
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
61-126 2.50e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 80.24  E-value: 2.50e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 34098946  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:COG1278   4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 61-128 3.42e-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: 71.86  E-value: 3.42e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946     61 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 128
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
57-126 3.42e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 69.30  E-value: 3.42e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946   57 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
59-128 1.53e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 96.93  E-value: 1.53e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946    59 VLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTGP 128
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 ...
 61-127 1.69e-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: 91.49  E-value: 1.69e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 34098946  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVTG 127
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
61-126 2.50e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 80.24  E-value: 2.50e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 34098946  61 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIkknnPRKYLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:COG1278   4 GTVKWFNAEKGFGFITPDDGGEDVFVHISAL----QRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 61-128 3.42e-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: 71.86  E-value: 3.42e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946     61 GTVKWFNvrNGYGFINRNDTKEDVFVHQTAIKKNnprkyLRSVGDGETVEFDVV--EGEKGAEAANVTGP 128
Cdd:smart00357   2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQGG-----LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
57-126 3.42e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 69.30  E-value: 3.42e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946   57 TKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG----FKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 55-125 1.93e-14

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 67.10  E-value: 1.93e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 34098946   55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANV 125
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
55-126 7.27e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 65.77  E-value: 7.27e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 34098946   55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 58-126 1.71e-11

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 58.93  E-value: 1.71e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 34098946   58 KVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVT 126
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
61-134 5.83e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 52.04  E-value: 5.83e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 34098946   61 GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpggVPVQ 134
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVQFDVHQGPKGNHASVI-----VPVE 68
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 60-139 8.89e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 48.89  E-value: 8.89e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 34098946   60 LGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNprkyLRSVGDGETVEFDVVEGEKGAEAANVtgpggVPVQGSKYA 139
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG----YRTLKAGQSVRFDVHQGPKGNHASVI-----VPIEAEAVA 73
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 55-125 6.49e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 43.35  E-value: 6.49e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 34098946   55 IATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRkylrSVGDGETVEFDVVEGEKGAEAANV 125
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.
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