NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1954872925|gb|QQM89221|]
View 

cold shock domain-containing protein (plasmid) [Klebsiella variicola]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-36 7.25e-10

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 48.27  E-value: 7.25e-10
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISAFP 36
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQ 35
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-36 7.25e-10

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 48.27  E-value: 7.25e-10
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISAFP 36
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQ 35
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-41 1.61e-09

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: 47.19  E-value: 1.61e-09
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISAFPEMVCR 41
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFR 39
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
7-34 8.61e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 38.03  E-value: 8.61e-06
                         10        20
                 ....*....|....*....|....*....
gi 1954872925  7 LVRW-NGDKGFGFVRCDMDQKEYFVHISA 34
Cdd:PRK10354   8 IVKWfNADKGFGFITPDDGSKDVFVHFSA 36
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-35 1.45e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 37.22  E-value: 1.45e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1954872925  4 KGTlVRW-NGDKGFGFVRCDMDQKEYFVHISAF 35
Cdd:pfam00313  2 TGT-VKWfNAKKGFGFITPEDGDKDVFVHFSAI 33
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-35 2.39e-05

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: 36.81  E-value: 2.39e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1954872925   4 KGTLVRWNgdKGFGFVRCDMDQKEYFVHISAF 35
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI 30
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-36 7.25e-10

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 48.27  E-value: 7.25e-10
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISAFP 36
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQ 35
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-41 1.61e-09

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: 47.19  E-value: 1.61e-09
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISAFPEMVCR 41
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFR 39
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
7-34 8.61e-06

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 38.03  E-value: 8.61e-06
                         10        20
                 ....*....|....*....|....*....
gi 1954872925  7 LVRW-NGDKGFGFVRCDMDQKEYFVHISA 34
Cdd:PRK10354   8 IVKWfNADKGFGFITPDDGSKDVFVHFSA 36
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-35 1.45e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 37.22  E-value: 1.45e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 1954872925  4 KGTlVRW-NGDKGFGFVRCDMDQKEYFVHISAF 35
Cdd:pfam00313  2 TGT-VKWfNAKKGFGFITPEDGDKDVFVHFSAI 33
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-35 2.39e-05

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: 36.81  E-value: 2.39e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1954872925   4 KGTLVRWNgdKGFGFVRCDMDQKEYFVHISAF 35
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQI 30
PRK09890 PRK09890
cold shock protein CspG; Provisional
 7-34 5.20e-05

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 36.28  E-value: 5.20e-05
                         10        20
                 ....*....|....*....|....*....
gi 1954872925  7 LVRW-NGDKGFGFVRCDMDQKEYFVHISA 34
Cdd:PRK09890   8 LVKWfNADKGFGFITPDDGSKDVFVHFTA 36
PRK05054 PRK05054
exoribonuclease II; Provisional
 4-38 9.67e-04

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 34.08  E-value: 9.67e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1954872925   4 KGTlvrwngDKGFGFVRCDmDQKEYFVhisAFPEM 38
Cdd:PRK05054   27 KAT------EKGFGFLEVD-AQKSYFI---PPPQM 51
cspE PRK09507
cold shock-like protein CspE;
4-34 1.51e-03

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 32.32  E-value: 1.51e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 1954872925  4 KGTLVRWNGDKGFGFVRCDMDQKEYFVHISA 34
Cdd:PRK09507   5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSA 35
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH