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Conserved domains on  [gi|490367968|ref|WP_004247631|]
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MULTISPECIES: cold-shock protein [Enterobacterales]

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];
6-69 1.31e-17

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.07  E-value: 1.31e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490367968  6 RMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-69 1.31e-17

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.07  E-value: 1.31e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490367968  6 RMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 6-68 2.14e-17

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: 68.37  E-value: 2.14e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490367968  6 RMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADV 68
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
CSD pfam00313
'Cold-shock' DNA-binding domain;
8-70 7.46e-16

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 64.57  E-value: 7.46e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490367968   8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVIG 70
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
cspE PRK09507
cold shock-like protein CspE;
8-69 3.15e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 60.44  E-value: 3.15e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490367968  8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-70 2.32e-07

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: 42.97  E-value: 2.32e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490367968    7 MGRVKWFdnNKGYGLIVAKDLEQDIYVNKKAIANTKNKaLTEGQDVEFSVIKT--AAGLEAADVIG 70
Cdd:smart00357  1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQGGLKS-LREGDEVEFKVVSPegGEKPEAENVVK 63
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-69 1.31e-17

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.07  E-value: 1.31e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490367968  6 RMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:COG1278   2 ATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 6-68 2.14e-17

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: 68.37  E-value: 2.14e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490367968  6 RMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADV 68
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
CSD pfam00313
'Cold-shock' DNA-binding domain;
8-70 7.46e-16

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 64.57  E-value: 7.46e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490367968   8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVIG 70
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
cspE PRK09507
cold shock-like protein CspE;
8-69 3.15e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 60.44  E-value: 3.15e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490367968  8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
8-68 9.94e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 54.21  E-value: 9.94e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490367968  8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADV 68
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 8-68 1.23e-10

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 51.61  E-value: 1.23e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490367968  8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADV 68
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNV 66
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 5-69 7.94e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 44.27  E-value: 7.94e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490367968  5 LRMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIV 65
PRK09937 PRK09937
cold shock-like protein CspD;
5-69 1.77e-07

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 43.57  E-value: 1.77e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490367968  5 LRMGRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADVI 69
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-70 2.32e-07

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: 42.97  E-value: 2.32e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490367968    7 MGRVKWFdnNKGYGLIVAKDLEQDIYVNKKAIANTKNKaLTEGQDVEFSVIKT--AAGLEAADVIG 70
Cdd:smart00357  1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQGGLKS-LREGDEVEFKVVSPegGEKPEAENVVK 63
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 8-68 4.56e-05

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 37.19  E-value: 4.56e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490367968  8 GRVKWFDNNKGYGLIVAKDLEQDIYVNKKAIANTKNKALTEGQDVEFSVIKTAAGLEAADV 68
Cdd:PRK15463  7 GIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 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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