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Conserved domains on  [gi|2536469840|ref|WP_293208411|]
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cold-shock protein [Parvibaculum sp.]

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];
1-58 8.49e-30

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2536469840  1 MASGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKG 58
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-58 8.49e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2536469840  1 MASGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKG 58
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-59 1.92e-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: 91.10  E-value: 1.92e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGR 59
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGP 58
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 4.03e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 85.37  E-value: 4.03e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRfSAEELVL 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGP-QAANVTK 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-58 1.58e-20

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 76.17  E-value: 1.58e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2536469840  3 SGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 3.68e-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: 67.62  E-value: 3.68e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2536469840   4 GVVKWFNatKGYGFIAPADGGKDVFVHISAVErAGQKSLQEGQQIQYELV-EGRNGRFSAEELVL 67
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVsPEGGEKPEAENVVK 63
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-58 8.49e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 8.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 2536469840  1 MASGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKG 58
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-59 1.92e-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: 91.10  E-value: 1.92e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGR 59
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGP 58
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 4.03e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 85.37  E-value: 4.03e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRfSAEELVL 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGP-QAANVTK 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-58 1.58e-20

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 76.17  E-value: 1.58e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2536469840  3 SGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG 61
cspE PRK09507
cold shock-like protein CspE;
4-58 1.65e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 76.23  E-value: 1.65e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG 60
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-67 1.08e-18

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 71.72  E-value: 1.08e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2536469840  3 SGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRFSAEELVL 67
Cdd:PRK09890   6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-58 1.88e-17

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 68.56  E-value: 1.88e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2536469840  4 GVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNG 58
Cdd:PRK10943   6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG 60
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 3.68e-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: 67.62  E-value: 3.68e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2536469840   4 GVVKWFNatKGYGFIAPADGGKDVFVHISAVErAGQKSLQEGQQIQYELV-EGRNGRFSAEELVL 67
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVsPEGGEKPEAENVVK 63
PRK09937 PRK09937
cold shock-like protein CspD;
1-62 2.30e-16

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 65.91  E-value: 2.30e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2536469840  1 MASGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRFSA 62
Cdd:PRK09937   1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-62 4.28e-15

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 62.76  E-value: 4.28e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2536469840  1 MASGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRFSA 62
Cdd:PRK14998   1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-62 1.71e-10

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 51.06  E-value: 1.71e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2536469840  3 SGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRFSA 62
Cdd:PRK15463   6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAA 65
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-62 6.56e-07

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 42.01  E-value: 6.56e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2536469840  3 SGVVKWFNATKGYGFIAPADGGKDVFVHISAVERAGQKSLQEGQQIQYELVEGRNGRFSA 62
Cdd:PRK15464   6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAA 65
 
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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