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Conserved domains on  [gi|24663131|ref|NP_524033|]
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ypsilon schachtel, isoform A [Drosophila melanogaster]

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;
62-131 2.05e-28

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 105.02  E-value: 2.05e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24663131    62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANVTGP 131
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
62-131 2.05e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 105.02  E-value: 2.05e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24663131    62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANVTGP 131
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 ...
 62-130 1.91e-22

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: 89.17  E-value: 1.91e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24663131  62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANVTG 130
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
62-129 2.23e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 81.01  E-value: 2.23e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24663131  62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRS----GFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 63-131 9.38e-15

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: 68.01  E-value: 9.38e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24663131     63 TGTVKWFNvkSGYGFINRNDTREDVFVHQSAIarnnpKKAVRSVGDGEVVEFDVVI--GEKGNEAANVTGP 131
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSpeGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
60-129 1.26e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.14  E-value: 1.26e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24663131   60 TKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVI 67
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
62-131 2.05e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 105.02  E-value: 2.05e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24663131    62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANVTGP 131
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 ...
 62-130 1.91e-22

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: 89.17  E-value: 1.91e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24663131  62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANVTG 130
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
62-129 2.23e-19

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 81.01  E-value: 2.23e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24663131  62 VTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRS----GFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 63-131 9.38e-15

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: 68.01  E-value: 9.38e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24663131     63 TGTVKWFNvkSGYGFINRNDTREDVFVHQSAIarnnpKKAVRSVGDGEVVEFDVVI--GEKGNEAANVTGP 131
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI-----QGGLKSLREGDEVEFKVVSpeGGEKPEAENVVKL 64
cspE PRK09507
cold shock-like protein CspE;
60-129 1.26e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 68.14  E-value: 1.26e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24663131   60 TKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN----GFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
58-129 1.92e-14

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 67.31  E-value: 1.92e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24663131   58 IATKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNPKkavrSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYK----SLDEGQKVSFTIESGAKGPAAGNVT 68
PRK09890 PRK09890
cold shock protein CspG; Provisional
 58-128 1.56e-13

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 64.79  E-value: 1.56e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24663131   58 IATKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNpkkaVRSVGDGEVVEFDVVIGEKGNEAANV 128
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 61-129 7.39e-11

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 57.39  E-value: 7.39e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24663131   61 KVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVT 129
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN----GFKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 63-136 2.63e-09

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 53.13  E-value: 2.63e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24663131   63 TGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAANVTGPSGEPV 136
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAEAV 72
PRK09937 PRK09937
cold shock-like protein CspD;
64-126 3.35e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 52.81  E-value: 3.35e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24663131   64 GTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNnpkkAVRSVGDGEVVEFDVVIGEKGNEAA 126
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD----GYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 58-128 1.45e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 47.97  E-value: 1.45e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24663131   58 IATKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIArnnpKKAVRSVGDGEVVEFDVVIGEKGNEAANV 128
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALN----LRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 58-128 4.63e-05

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 41.24  E-value: 4.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24663131   58 IATKVTGTVKWFNVKSGYGFINRNDTREDVFVHQSAIARNNPKKAVRSVGdgevVEFDVVIGEKGNEAANV 128
Cdd:PRK15464   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLR----VEFCRVNGLRGPTAANV 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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