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Conserved domains on  [gi|488617988|ref|WP_002554837|]
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MULTISPECIES: cold-shock protein [Gammaproteobacteria]

Protein Classification

cold-shock protein( domain architecture ID 10003418)

cold-shock protein (Csp) such as bacterial CspA and CspB involved in cold stress response

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  9371456|12530521

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-69 5.15e-31

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.58  E-value: 5.15e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988  4 RQTGTVKWFNDEKGFGFITP-QSGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPdDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-69 5.15e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.58  E-value: 5.15e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988  4 RQTGTVKWFNDEKGFGFITP-QSGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPdDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 1.49e-29

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.49e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488617988   5 QTGTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-68 5.33e-28

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: 94.95  E-value: 5.33e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488617988  5 QTGTVKWFNDEKGFGFITP-QSGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQV 68
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPdDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-69 1.06e-25

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 89.65  E-value: 1.06e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488617988  1 MSNRQTGTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:PRK10354  1 MSGKMTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-69 8.23e-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: 61.85  E-value: 8.23e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988    6 TGTVKWFNdeKGFGFITPQSGD-DLFVHFKAIQsDGFKSLKEGQQVSF--IATRGQKGMQAEEVQVI 69
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGkDVFVHPSQIQ-GGLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-69 5.15e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.58  E-value: 5.15e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988  4 RQTGTVKWFNDEKGFGFITP-QSGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPdDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 1.49e-29

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 98.85  E-value: 1.49e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488617988   5 QTGTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-68 5.33e-28

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: 94.95  E-value: 5.33e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488617988  5 QTGTVKWFNDEKGFGFITP-QSGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQV 68
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPdDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-69 1.06e-25

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 89.65  E-value: 1.06e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488617988  1 MSNRQTGTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:PRK10354  1 MSGKMTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
cspE PRK09507
cold shock-like protein CspE;
7-69 5.03e-22

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 80.08  E-value: 5.03e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488617988  7 GTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-66 8.26e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 79.81  E-value: 8.26e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988  1 MSNRQTGTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEV 66
Cdd:PRK09890  1 MSNKMTGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
PRK09937 PRK09937
cold shock-like protein CspD;
5-63 5.07e-19

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 72.84  E-value: 5.07e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488617988  5 QTGTVKWFNDEKGFGFITPQSG-DDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQA 63
Cdd:PRK09937  2 EKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHA 61
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 5-63 1.36e-18

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 71.62  E-value: 1.36e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488617988  5 QTGTVKWFNDEKGFGFITPQ-SGDDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQA 63
Cdd:PRK14998  2 ETGTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHA 61
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 7-69 1.71e-16

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 66.25  E-value: 1.71e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488617988  7 GTVKWFNDEKGFGFITPQSGD-DLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEVQVI 69
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-69 8.23e-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: 61.85  E-value: 8.23e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988    6 TGTVKWFNdeKGFGFITPQSGD-DLFVHFKAIQsDGFKSLKEGQQVSF--IATRGQKGMQAEEVQVI 69
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGkDVFVHPSQIQ-GGLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-66 2.57e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.97  E-value: 2.57e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488617988  1 MSNRQTGTVKWFNDEKGFGFITPQSG-DDLFVHFKAIQSDGFKSLKEGQQVSFIATRGQKGMQAEEV 66
Cdd:PRK15463  1 MSRKMTGIVKTFDGKSGKGLITPSDGrKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 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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