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Conserved domains on  [gi|489712355|ref|WP_003616492|]
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MULTISPECIES: cold-shock protein [Lactobacillus]

Protein Classification

cold-shock protein( domain architecture ID 10003418)

cold-shock protein (Csp) such as bacterial CspA and CspB involved in cold stress response; it is up-regulated by an abrupt drop in growth temperature, and preferentially binds poly-pyrimidine region of single-stranded RNA and DNA

Gene Ontology:  GO:0005829|GO:0003676|GO:0003723|GO:0001072
PubMed:  12530521|10322168|17437059

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-64 2.42e-33

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.36  E-value: 2.42e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489712355  1 MQNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRV 66
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-64 2.42e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.36  E-value: 2.42e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489712355  1 MQNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-64 2.66e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.78  E-value: 2.66e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489712355   2 QNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 2-64 4.86e-29

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: 97.26  E-value: 4.86e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489712355  2 QNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGgeDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-64 1.83e-25

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 88.49  E-value: 1.83e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGskDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-63 3.89e-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: 67.24  E-value: 3.89e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489712355    4 GTVKWFNadKGFGFITGSDG--DVFVHFSSIKTnGFKSLEEGQKVSYDVE--QGNRGPQATNVV 63
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgkDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-64 2.42e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.36  E-value: 2.42e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489712355  1 MQNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRV 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-64 2.66e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.78  E-value: 2.66e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489712355   2 QNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 2-64 4.86e-29

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: 97.26  E-value: 4.86e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489712355  2 QNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDGgeDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-64 1.83e-25

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 88.49  E-value: 1.83e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGskDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-63 1.70e-24

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 86.36  E-value: 1.70e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVV 63
Cdd:PRK09890  7 GLVKWFNADKGFGFITPDDGskDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVV 68
cspE PRK09507
cold shock-like protein CspE;
4-63 1.59e-23

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 83.93  E-value: 1.59e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVV 63
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGskDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK09937 PRK09937
cold shock-like protein CspD;
1-64 1.46e-19

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 74.00  E-value: 1.46e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489712355  1 MQNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGgeDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVP 66
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-62 2.37e-19

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 73.18  E-value: 2.37e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNV 62
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGskDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNV 66
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-64 2.09e-18

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 70.85  E-value: 2.09e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489712355  1 MQNGTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNVVP 64
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGgeDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-63 3.89e-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: 67.24  E-value: 3.89e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489712355    4 GTVKWFNadKGFGFITGSDG--DVFVHFSSIKTnGFKSLEEGQKVSYDVE--QGNRGPQATNVV 63
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgkDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 4-62 1.15e-08

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 46.05  E-value: 1.15e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNV 62
Cdd:PRK15463  7 GIVKTFDGKSGKGLITPSDGrkDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 4-62 1.24e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 35.84  E-value: 1.24e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489712355  4 GTVKWFNADKGFGFITGSDG--DVFVHFSSIKTNGFKSLEEGQKVSYDVEQGNRGPQATNV 62
Cdd:PRK15464  7 GIVKTFDRKSGKGFIIPSDGrkEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 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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