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Conserved domains on  [gi|1221045215|gb|OXR32846|]
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cold-shock protein [Pseudomonas umsongensis]

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];
4-67 9.40e-28

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 94.49  E-value: 9.40e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1221045215  4 RETGNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVV 67
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-67 9.40e-28

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 94.49  E-value: 9.40e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1221045215  4 RETGNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVV 67
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 4.86e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 92.69  E-value: 4.86e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221045215  5 ETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 6-68 2.00e-25

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: 88.40  E-value: 2.00e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  6 TGNVKWFNDAKGYGFIQRED-GVDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVG 68
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
7-69 8.24e-22

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 79.70  E-value: 8.24e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  7 GNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-69 3.89e-13

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: 57.61  E-value: 3.89e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221045215   6 TGNVKWFNdaKGYGFIQREDGV-DVFVHYRAIRGeGHRSLTEGQQVEYGVV--TGEKGLQAEDVVGL 69
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 ...
 7-66 6.37e-12

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: 54.11  E-value: 6.37e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221045215  7 GNVKWFNDAKGYGFIQREDGVDVFVHYRAIRGEgHRSLTEGQQVEYGVVTGEKGLQAEDV 66
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDE-GDDIIEGDKVSFEVRKTPKGPRAYNI 59
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-67 9.40e-28

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 94.49  E-value: 9.40e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1221045215  4 RETGNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVV 67
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGeDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 4.86e-27

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 92.69  E-value: 4.86e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221045215  5 ETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 6-68 2.00e-25

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: 88.40  E-value: 2.00e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  6 TGNVKWFNDAKGYGFIQRED-GVDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVG 68
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
7-69 8.24e-22

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 79.70  E-value: 8.24e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  7 GNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-69 1.99e-19

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 73.47  E-value: 1.99e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221045215  1 MATRETGNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-69 2.82e-18

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 70.56  E-value: 2.82e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221045215  1 MATRETGNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 7-69 4.45e-17

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 67.79  E-value: 4.45e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  7 GNVKWFNDAKGYGFIQREDGV-DVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK10943   6 GQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
5-67 8.07e-16

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 64.75  E-value: 8.07e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1221045215  5 ETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVV 67
Cdd:PRK09937   2 EKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 5-69 2.69e-15

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 63.15  E-value: 2.69e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1221045215  5 ETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDVVGL 69
Cdd:PRK14998   2 ETGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-69 3.89e-13

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: 57.61  E-value: 3.89e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221045215   6 TGNVKWFNdaKGYGFIQREDGV-DVFVHYRAIRGeGHRSLTEGQQVEYGVV--TGEKGLQAEDVVGL 69
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 ...
 7-66 6.37e-12

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: 54.11  E-value: 6.37e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1221045215  7 GNVKWFNDAKGYGFIQREDGVDVFVHYRAIRGEgHRSLTEGQQVEYGVVTGEKGLQAEDV 66
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDE-GDDIIEGDKVSFEVRKTPKGPRAYNI 59
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-66 1.42e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 41.04  E-value: 1.42e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221045215  1 MATRETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDV 66
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGrKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 1-66 3.38e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 32.38  E-value: 3.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1221045215  1 MATRETGNVKWFNDAKGYGFIQREDG-VDVFVHYRAIRGEGHRSLTEGQQVEYGVVTGEKGLQAEDV 66
Cdd:PRK15464   1 MSRKMTGIVKTFDRKSGKGFIIPSDGrKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 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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