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Conserved domains on  [gi|21356601|ref|NP_648920|]
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uncharacterized protein Dmel_CG9705, isoform A [Drosophila melanogaster]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10138668)

cold shock domain-containing protein similar to mammalian calcium-regulated heat-stable protein 1, which binds mRNA and regulates the stability of target mRNA

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  2184368|10377894|10322168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 55-120 1.22e-20

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: 79.16  E-value: 1.22e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356601  55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE--YVPMPGDEVKYRLCAIPPKYekhQAVHVQI 120
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGDKGP---QAVNVRL 65
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 55-120 1.22e-20

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: 79.16  E-value: 1.22e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356601  55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE--YVPMPGDEVKYRLCAIPPKYekhQAVHVQI 120
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGDKGP---QAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
55-120 5.52e-15

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.83  E-value: 5.52e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356601  55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYV--PMPGDEVKYRLCAIPpkyEKHQAVHVQI 120
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEFEVEQGD---KGPQAVNVRV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 56-121 8.37e-13

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: 59.15  E-value: 8.37e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21356601     56 TGMVKSFSrtKGHGFITPNAGGEDVFCHVSDIE-GEYVPMPGDEVKYRLCAiPPKYEKHQAVHVQIS 121
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
55-90 1.28e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 53.79  E-value: 1.28e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 21356601    55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE 90
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGD 36
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
55-88 3.13e-08

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 47.66  E-value: 3.13e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIE 88
Cdd:PRK10354   5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQ 38
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 55-120 1.22e-20

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: 79.16  E-value: 1.22e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356601  55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE--YVPMPGDEVKYRLCAIPPKYekhQAVHVQI 120
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDgfRSLEEGDRVEFELEEGDKGP---QAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
55-120 5.52e-15

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.83  E-value: 5.52e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21356601  55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGEYV--PMPGDEVKYRLCAIPpkyEKHQAVHVQI 120
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFrtLREGQRVEFEVEQGD---KGPQAVNVRV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 56-121 8.37e-13

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: 59.15  E-value: 8.37e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21356601     56 TGMVKSFSrtKGHGFITPNAGGEDVFCHVSDIE-GEYVPMPGDEVKYRLCAiPPKYEKHQAVHVQIS 121
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQgGLKSLREGDEVEFKVVS-PEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
55-90 1.28e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 53.79  E-value: 1.28e-10
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 21356601    55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE 90
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGD 36
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
55-88 3.13e-08

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 47.66  E-value: 3.13e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIE 88
Cdd:PRK10354   5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQ 38
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 55-89 1.95e-07

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 45.44  E-value: 1.95e-07
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEG 89
Cdd:PRK10943   4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQG 38
cspE PRK09507
cold shock-like protein CspE;
55-90 3.76e-07

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 44.64  E-value: 3.76e-07
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIEGE 90
Cdd:PRK09507   4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN 39
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 56-88 6.15e-07

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 44.27  E-value: 6.15e-07
                         10        20        30
                 ....*....|....*....|....*....|...
gi 21356601   56 TGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIE 88
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK09937 PRK09937
cold shock-like protein CspD;
57-88 1.95e-06

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 43.18  E-value: 1.95e-06
                         10        20        30
                 ....*....|....*....|....*....|..
gi 21356601   57 GMVKSFSRTKGHGFITPNAGGEDVFCHVSDIE 88
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQ 35
PRK09890 PRK09890
cold shock protein CspG; Provisional
 55-88 2.44e-06

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 42.83  E-value: 2.44e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVSDIE 88
Cdd:PRK09890   5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQ 38
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 55-85 3.92e-04

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 36.80  E-value: 3.92e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVS 85
Cdd:PRK15463   5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHIS 35
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 55-85 8.42e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 35.84  E-value: 8.42e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 21356601   55 VTGMVKSFSRTKGHGFITPNAGGEDVFCHVS 85
Cdd:PRK15464   5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHIS 35
 
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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