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Conserved domains on  [gi|1267754425|ref|WP_098502255|]
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cold-shock protein [Priestia megaterium]

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];
7-75 3.40e-26

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 90.64  E-value: 3.40e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENG-PDLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSG------FRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-75 3.40e-26

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 90.64  E-value: 3.40e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENG-PDLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSG------FRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
7-75 8.73e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 84.60  E-value: 8.73e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENG-PDLFVHFTAIERTkgtegvIIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGD------GFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-74 5.80e-23

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: 82.63  E-value: 5.80e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1267754425  7 GTVKWFNHEKGFGFITPEN-GPDLFVHFTAIertkgtEGVIIKSLKEGQKVTFVVVNGQRGMQAEMVRV 74
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDgGEDVFVHISAL------EGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-75 3.65e-20

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 75.78  E-value: 3.65e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1267754425  1 MAERQVGTVKWFNHEKGFGFITPENGP-DLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDG------YKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-75 1.70e-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: 58.76  E-value: 1.70e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1267754425   7 GTVKWFNheKGFGFITPENG-PDLFVHFTAIERTKgtegviiKSLKEGQKVTFVVV--NGQRGMQAEMVRVL 75
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQGGL-------KSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
7-75 3.40e-26

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 90.64  E-value: 3.40e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENG-PDLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSG------FRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
7-75 8.73e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 84.60  E-value: 8.73e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENG-PDLFVHFTAIERTkgtegvIIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGD------GFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 7-74 5.80e-23

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: 82.63  E-value: 5.80e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1267754425  7 GTVKWFNHEKGFGFITPEN-GPDLFVHFTAIertkgtEGVIIKSLKEGQKVTFVVVNGQRGMQAEMVRV 74
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDgGEDVFVHISAL------EGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-75 3.65e-20

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 75.78  E-value: 3.65e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1267754425  1 MAERQVGTVKWFNHEKGFGFITPENGP-DLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDG------YKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-75 4.58e-19

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 72.88  E-value: 4.58e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1267754425  1 MAERQVGTVKWFNHEKGFGFITPENGP-DLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNE------FRTLNENQKVEFSIEQGQRGPAAANVVTL 70
cspE PRK09507
cold shock-like protein CspE;
7-75 1.17e-17

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 69.30  E-value: 1.17e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1267754425  7 GTVKWFNHEKGFGFITPENGP-DLFVHFTAIErtkgTEGviIKSLKEGQKVTFVVVNGQRGMQAEMVRVL 75
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSkDVFVHFSAIQ----TNG--FKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 7-75 1.70e-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: 58.76  E-value: 1.70e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1267754425   7 GTVKWFNheKGFGFITPENG-PDLFVHFTAIERTKgtegviiKSLKEGQKVTFVVV--NGQRGMQAEMVRVL 75
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQGGL-------KSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK09937 PRK09937
cold shock-like protein CspD;
7-72 2.53e-13

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 58.59  E-value: 2.53e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1267754425  7 GTVKWFNHEKGFGFITPE-NGPDLFVHFTAIErtkgTEGViiKSLKEGQKVTFVVVNGQRGMQAEMV 72
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQ----MDGY--RTLKAGQSVQFDVHQGPKGNHASVI 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 7-69 2.73e-13

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 58.54  E-value: 2.73e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1267754425  7 GTVKWFNHEKGFGFITPENGP-DLFVHFTAIertkgtEGVIIKSLKEGQKVTFVVVNGQRGMQA 69
Cdd:PRK10943   6 GQVKWFNESKGFGFITPADGSkDVFVHFSAI------QGNGFKTLAEGQNVEFEIQDGQKGPAA 63
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 5-72 2.13e-12

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 56.21  E-value: 2.13e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1267754425  5 QVGTVKWFNHEKGFGFITPE-NGPDLFVHFTAIERTKgtegviIKSLKEGQKVTFVVVNGQRGMQAEMV 72
Cdd:PRK14998   2 ETGTVKWFNNAKGFGFICPEgGGEDIFAHYSTIQMDG------YRTLKAGQSVRFDVHQGPKGNHASVI 64
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-72 6.74e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.20  E-value: 6.74e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1267754425  1 MAERQVGTVKWFNHEKGFGFITPENG-PDLFVHFTAIeRTKGTEgviikSLKEGQKVTFVVVNGQRGMQAEMV 72
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGrKDVQVHISAL-NLRDAE-----ELTTGLRVEFCRINGLRGPTAANV 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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