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Conserved domains on  [gi|655472371|ref|WP_028855210|]
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MULTISPECIES: cold-shock protein [Psychrilyobacter]

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];
1-66 8.53e-30

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.53e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655472371  1 MLKGTVKWFNDDKGFGFISAEDG-NDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 8.53e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.53e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655472371  1 MLKGTVKWFNDDKGFGFISAEDG-NDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-63 6.15e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.62  E-value: 6.15e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 655472371   2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANV 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-63 6.58e-26

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: 6.58e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 655472371  3 KGTVKWFNDDKGFGFISAED-GNDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
cspE PRK09507
cold shock-like protein CspE;
2-66 1.28e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 86.63  E-value: 1.28e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK09507  4 IKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-63 6.42e-17

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: 66.85  E-value: 6.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 655472371    3 KGTVKWFNddKGFGFISAEDG-NDYFAHFSQINKeGFKTLKEGEEVTFEIT--EGAKGPQASNI 63
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENV 61
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 8.53e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.53e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655472371  1 MLKGTVKWFNDDKGFGFISAEDG-NDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-63 6.15e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.62  E-value: 6.15e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 655472371   2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANV 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-63 6.58e-26

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: 6.58e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 655472371  3 KGTVKWFNDDKGFGFISAED-GNDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
cspE PRK09507
cold shock-like protein CspE;
2-66 1.28e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 86.63  E-value: 1.28e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK09507  4 IKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
2-66 3.71e-21

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 77.71  E-value: 3.71e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK10354  5 MTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
PRK09937 PRK09937
cold shock-like protein CspD;
1-66 9.38e-20

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 74.38  E-value: 9.38e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 655472371  1 MLKGTVKWFNDDKGFGFISAEDG-NDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 2-66 6.86e-19

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 72.10  E-value: 6.86e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK09890  5 MTGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 2-66 2.58e-18

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 70.48  E-value: 2.58e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNIETV 66
Cdd:PRK10943  4 IKGQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-63 1.16e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 68.92  E-value: 1.16e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 655472371  1 MLKGTVKWFNDDKGFGFISAE-DGNDYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVI 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-63 6.42e-17

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: 66.85  E-value: 6.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 655472371    3 KGTVKWFNddKGFGFISAEDG-NDYFAHFSQINKeGFKTLKEGEEVTFEIT--EGAKGPQASNI 63
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENV 61
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 2-63 4.21e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 39.50  E-value: 4.21e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 655472371  2 LKGTVKWFNDDKGFGFISAEDGN-DYFAHFSQINKEGFKTLKEGEEVTFEITEGAKGPQASNI 63
Cdd:PRK15463  5 MTGIVKTFDGKSGKGLITPSDGRkDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 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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