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Conserved domains on  [gi|515521900|ref|WP_016955154|]
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cold-shock protein [Catenovulum agarivorans]

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 2.42e-30

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 101.04  E-value: 2.42e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENVVPA 70
Cdd:COG1278   4 GTVKWFNAEKGFGFITPDdGGEDVFVHISALQ-RSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-70 2.42e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 101.04  E-value: 2.42e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENVVPA 70
Cdd:COG1278   4 GTVKWFNAEKGFGFITPDdGGEDVFVHISALQ-RSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 5.16e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 95.00  E-value: 5.16e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515521900   5 VIGTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEdGDKDVFVHFSAIQG-DGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-69 1.49e-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: 93.80  E-value: 1.49e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDdGGEDVFVHISALE-GDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-69 1.83e-23

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 83.87  E-value: 1.83e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515521900  1 MSNQVIGTVKWFNDEKGFGFIE-QEGGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:PRK10354  1 MSGKMTGIVKWFNADKGFGFITpDDGSKDVFVHFSAIQN-DGYKSLDEGQKVSFTIESGAKGPAAGNVTS 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-68 5.42e-18

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: 69.94  E-value: 5.42e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900    7 GTVKWFNdeKGFGFIEQE-GGKDVFVHYSAIQtaGGRRTLAEGQQVTMTVT--QGQKGPQAENVV 68
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDdGGKDVFVHPSQIQ--GGLKSLREGDEVEFKVVspEGGEKPEAENVV 62
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 7-67 3.19e-13

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: 57.58  E-value: 3.19e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515521900  7 GTVKWFNDEKGFGFIEQEGGKDVFVHYSAIqtAGGRRTLAEGQQVTMTVTQGQKGPQAENV 67
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDI--NDEGDDIIEGDKVSFEVRKTPKGPRAYNI 59
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-70 2.42e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 101.04  E-value: 2.42e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENVVPA 70
Cdd:COG1278   4 GTVKWFNAEKGFGFITPDdGGEDVFVHISALQ-RSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 5.16e-28

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 95.00  E-value: 5.16e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 515521900   5 VIGTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEdGDKDVFVHFSAIQG-DGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-69 1.49e-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: 93.80  E-value: 1.49e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDdGGEDVFVHISALE-GDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-69 1.83e-23

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 83.87  E-value: 1.83e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515521900  1 MSNQVIGTVKWFNDEKGFGFIE-QEGGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:PRK10354  1 MSGKMTGIVKWFNADKGFGFITpDDGSKDVFVHFSAIQN-DGYKSLDEGQKVSFTIESGAKGPAAGNVTS 69
cspE PRK09507
cold shock-like protein CspE;
3-68 1.75e-22

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 81.24  E-value: 1.75e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 515521900  3 NQVIGTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVV 68
Cdd:PRK09507  2 SKIKGNVKWFNESKGFGFITPEdGSKDVFVHFSAIQT-NGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-68 8.14e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 79.81  E-value: 8.14e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 515521900  1 MSNQVIGTVKWFNDEKGFGFIE-QEGGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVV 68
Cdd:PRK09890  1 MSNKMTGLVKWFNADKGFGFITpDDGSKDVFVHFTAIQS-NEFRTLNENQKVEFSIEQGQRGPAAANVV 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-68 5.42e-18

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: 69.94  E-value: 5.42e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900    7 GTVKWFNdeKGFGFIEQE-GGKDVFVHYSAIQtaGGRRTLAEGQQVTMTVT--QGQKGPQAENVV 68
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDdGGKDVFVHPSQIQ--GGLKSLREGDEVEFKVVspEGGEKPEAENVV 62
PRK09937 PRK09937
cold shock-like protein CspD;
7-69 1.51e-17

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 68.99  E-value: 1.51e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:PRK09937  4 GTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQM-DGYRTLKAGQSVQFDVHQGPKGNHASVIVP 66
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 7-69 1.38e-16

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 66.61  E-value: 1.38e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 515521900  7 GTVKWFNDEKGFGFIEQE-GGKDVFVHYSAIQTaGGRRTLAEGQQVTMTVTQGQKGPQAENVVP 69
Cdd:PRK14998  4 GTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQM-DGYRTLKAGQSVRFDVHQGPKGNHASVIVP 66
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-67 2.08e-16

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 65.86  E-value: 2.08e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 515521900  4 QVIGTVKWFNDEKGFGFIE-QEGGKDVFVHYSAIQtAGGRRTLAEGQQVTMTVTQGQKGPQAENV 67
Cdd:PRK10943  3 KIKGQVKWFNESKGFGFITpADGSKDVFVHFSAIQ-GNGFKTLAEGQNVEFEIQDGQKGPAAVNV 66
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 7-67 3.19e-13

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: 57.58  E-value: 3.19e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 515521900  7 GTVKWFNDEKGFGFIEQEGGKDVFVHYSAIqtAGGRRTLAEGQQVTMTVTQGQKGPQAENV 67
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDI--NDEGDDIIEGDKVSFEVRKTPKGPRAYNI 59
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-67 5.83e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.20  E-value: 5.83e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 515521900  1 MSNQVIGTVKWFNDEKGFGFIE-QEGGKDVFVHYSAIQTAgGRRTLAEGQQVTMTVTQGQKGPQAENV 67
Cdd:PRK15463  1 MSRKMTGIVKTFDGKSGKGLITpSDGRKDVQVHISALNLR-DAEELTTGLRVEFCRINGLRGPTAANV 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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