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Conserved domains on  [gi|488409693|ref|WP_002479078|]
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MULTISPECIES: cold-shock protein [Staphylococcus]

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 1.02e-31

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 104.12  E-value: 1.02e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488409693  1 MNNGTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 1.02e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 104.12  E-value: 1.02e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488409693  1 MNNGTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-65 2.51e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.78  E-value: 2.51e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693   3 NGTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVV 65
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-65 4.83e-27

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: 92.64  E-value: 4.83e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488409693  4 GTVKWFNAEKGFGFIERED-GNDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVV 65
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
4-66 4.20e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 85.09  E-value: 4.20e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-65 1.16e-16

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: 66.08  E-value: 1.16e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488409693    4 GTVKWFNaeKGFGFIEREDG-NDVFVHFSGIAGeGYKTLEEGQKVEFDIT--EGQRGDQATNVVV 65
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVK 63
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 4-63 1.13e-11

retron Se72 family effector protein; Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance.


Pssm-ID: 439537  Cd Length: 62  Bit Score: 53.34  E-value: 1.13e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488409693  4 GTVKWFNAEKGFGFIEREDGNDVFVHFSGIAGEGYkTLEEGQKVEFDITEGQRGDQATNV 63
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEGD-DIIEGDKVSFEVRKTPKGPRAYNI 59
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 1.02e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 104.12  E-value: 1.02e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488409693  1 MNNGTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-65 2.51e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.78  E-value: 2.51e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693   3 NGTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVV 65
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-65 4.83e-27

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: 92.64  E-value: 4.83e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488409693  4 GTVKWFNAEKGFGFIERED-GNDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVV 65
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
4-66 4.20e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 85.09  E-value: 4.20e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-66 6.70e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 79.81  E-value: 6.70e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:PRK09890  7 GLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-63 7.00e-22

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 79.63  E-value: 7.00e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNV 63
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-66 3.70e-19

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 72.79  E-value: 3.70e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVVVM 66
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
1-64 5.79e-19

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 72.46  E-value: 5.79e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488409693  1 MNNGTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVV 64
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-64 1.07e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 69.31  E-value: 1.07e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488409693  1 MNNGTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNVV 64
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIV 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-65 1.16e-16

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: 66.08  E-value: 1.16e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488409693    4 GTVKWFNaeKGFGFIEREDG-NDVFVHFSGIAGeGYKTLEEGQKVEFDIT--EGQRGDQATNVVV 65
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVK 63
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 4-63 1.13e-11

retron Se72 family effector protein; Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance.


Pssm-ID: 439537  Cd Length: 62  Bit Score: 53.34  E-value: 1.13e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488409693  4 GTVKWFNAEKGFGFIEREDGNDVFVHFSGIAGEGYkTLEEGQKVEFDITEGQRGDQATNV 63
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEGD-DIIEGDKVSFEVRKTPKGPRAYNI 59
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 4-63 3.68e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.20  E-value: 3.68e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488409693  4 GTVKWFNAEKGFGFIEREDGN-DVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNV 63
Cdd:PRK15463  7 GIVKTFDGKSGKGLITPSDGRkDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 4-63 1.98e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 35.46  E-value: 1.98e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488409693  4 GTVKWFNAEKGFGFIEREDG-NDVFVHFSGIAGEGYKTLEEGQKVEFDITEGQRGDQATNV 63
Cdd:PRK15464  7 GIVKTFDRKSGKGFIIPSDGrKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
PRK09439 PRK09439
PTS system glucose-specific transporter subunit; Provisional
 3-51 1.38e-03

PTS system glucose-specific transporter subunit; Provisional


Pssm-ID: 181859 [Multi-domain]  Cd Length: 169  Bit Score: 34.57  E-value: 1.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488409693   3 NGTV-KWFNAEKGFGfIEREDGNDVFVHFsGIA-----GEGYKTL-EEGQKV-------EFDI 51
Cdd:PRK09439  65 DGTIgKIFETNHAFS-IESDSGVELFVHF-GIDtvelkGEGFKRIaEEGQRVkvgdpiiEFDL 125
 
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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