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Conserved domains on  [gi|1779108733|ref|WP_155162062|]
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cold-shock protein [Sansalvadorimonas verongulae]

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];
7-70 1.85e-31

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.85e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-70 1.85e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.85e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-69 1.20e-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: 94.18  E-value: 1.20e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1779108733  7 TGTVKWFNESKGYGFIEQDN-GPDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEV 69
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
7-70 4.90e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 92.69  E-value: 4.90e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
4-70 9.24e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 84.70  E-value: 9.24e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1779108733  4 SETTGTVKWFNESKGYGFIEQDNGP-DVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-70 2.57e-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: 65.70  E-value: 2.57e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1779108733   7 TGTVKWFNesKGYGFIEQDNG-PDVFAHFRAIVGsGFRTLVEGQRVKFNVT--QGQKGPQAENIEVI 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 8-70 3.24e-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: 52.57  E-value: 3.24e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1779108733  8 GTVKWFNESKGYGFIEQDNGPDVFAHFRAIVGSGfRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-70 1.85e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.85e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-69 1.20e-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: 94.18  E-value: 1.20e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1779108733  7 TGTVKWFNESKGYGFIEQDN-GPDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEV 69
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
7-70 4.90e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 92.69  E-value: 4.90e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
4-70 9.24e-24

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 84.70  E-value: 9.24e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1779108733  4 SETTGTVKWFNESKGYGFIEQDNGP-DVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-67 8.24e-21

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 77.11  E-value: 8.24e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  4 SETTGTVKWFNESKGYGFIEQDNGP-DVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENI 67
Cdd:PRK09890   3 NKMTGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
7-70 9.60e-21

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 76.94  E-value: 9.60e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNGP-DVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-70 8.04e-19

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 72.02  E-value: 8.04e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1779108733  4 SETTGTVKWFNESKGYGFIEQDNGP-DVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:PRK10943   2 AKIKGQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
8-67 8.61e-17

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 67.06  E-value: 8.61e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1779108733  8 GTVKWFNESKGYGFI-EQDNGPDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENI 67
Cdd:PRK09937   4 GTVKWFNNAKGFGFIcPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVI 64
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 7-67 2.00e-16

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 66.23  E-value: 2.00e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1779108733  7 TGTVKWFNESKGYGFI-EQDNGPDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENI 67
Cdd:PRK14998   3 TGTVKWFNNAKGFGFIcPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVI 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-70 2.57e-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: 65.70  E-value: 2.57e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1779108733   7 TGTVKWFNesKGYGFIEQDNG-PDVFAHFRAIVGsGFRTLVEGQRVKFNVT--QGQKGPQAENIEVI 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 8-70 3.24e-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: 52.57  E-value: 3.24e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1779108733  8 GTVKWFNESKGYGFIEQDNGPDVFAHFRAIVGSGfRTLVEGQRVKFNVTQGQKGPQAENIEVI 70
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 7-67 4.04e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 39.88  E-value: 4.04e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1779108733  7 TGTVKWFNESKGYGFIEQDNG-PDVFAHFRAIVGSGFRTLVEGQRVKFNVTQGQKGPQAENI 67
Cdd:PRK15463   6 TGIVKTFDGKSGKGLITPSDGrKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 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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