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Conserved domains on  [gi|738135872|ref|WP_036093504|]
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MULTISPECIES: cold-shock protein [Listeria]

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 8.03e-31

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.19  E-value: 8.03e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 738135872  1 MQNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 8.03e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.19  E-value: 8.03e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 738135872  1 MQNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-66 1.16e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.23  E-value: 1.16e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738135872   2 QNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 2-65 9.51e-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: 91.87  E-value: 9.51e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 738135872  2 QNGKVKWFSNEKGYGFLEIEN-GEDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKK 65
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-66 1.85e-21

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 78.48  E-value: 1.85e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 738135872  4 GKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGsKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-66 3.82e-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: 64.93  E-value: 3.82e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738135872    4 GKVKWFSneKGYGFLEIENG-EDIFIHFTAIQGdGYKTLDEGQSVTFEVV--EGNRGPQATNVKKL 66
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 8.03e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 102.19  E-value: 8.03e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 738135872  1 MQNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-66 1.16e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.23  E-value: 1.16e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738135872   2 QNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 2-65 9.51e-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: 91.87  E-value: 9.51e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 738135872  2 QNGKVKWFSNEKGYGFLEIEN-GEDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKK 65
Cdd:cd04458   1 VTGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-66 1.85e-21

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 78.48  E-value: 1.85e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 738135872  4 GKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGsKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
cspE PRK09507
cold shock-like protein CspE;
4-66 2.23e-21

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 78.54  E-value: 2.23e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 738135872  4 GKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGsKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09937 PRK09937
cold shock-like protein CspD;
1-61 7.02e-19

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 72.46  E-value: 7.02e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 738135872  1 MQNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQAT 61
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-66 7.30e-19

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 72.10  E-value: 7.30e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 738135872  4 GKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:PRK09890  7 GLVKWFNADKGFGFITPDDGsKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-66 4.49e-18

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 70.10  E-value: 4.49e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 738135872  4 GKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQATNVKKL 66
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGsKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-61 2.70e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 68.15  E-value: 2.70e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 738135872  1 MQNGKVKWFSNEKGYGFLEIENG-EDIFIHFTAIQGDGYKTLDEGQSVTFEVVEGNRGPQAT 61
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-66 3.82e-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: 64.93  E-value: 3.82e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738135872    4 GKVKWFSneKGYGFLEIENG-EDIFIHFTAIQGdGYKTLDEGQSVTFEVV--EGNRGPQATNVKKL 66
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK05054 PRK05054
exoribonuclease II; Provisional
 4-28 2.12e-03

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 34.08  E-value: 2.12e-03
                         10        20
                 ....*....|....*....|....*
gi 738135872   4 GKVKwfSNEKGYGFLEIENGEDIFI 28
Cdd:PRK05054  24 GVVK--ATEKGFGFLEVDAQKSYFI 46
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 4-36 5.09e-03

Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.


Pssm-ID: 429863 [Multi-domain]  Cd Length: 58  Bit Score: 31.35  E-value: 5.09e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 738135872   4 GKVKwfSNEKGYGFLEIE-NGEDIFIHF----TAIQGD 36
Cdd:pfam08206  1 GTVR--GHKKGFGFLIPDdEEDDIFIPPnqmkKAMHGD 36
 
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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