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Conserved domains on  [gi|504005346|ref|WP_014239340|]
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MULTISPECIES: cold-shock protein [Alphaproteobacteria]

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];
1-69 1.65e-33

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 109.13  E-value: 1.65e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504005346  1 MPVGTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKrgKTSAENLKAV 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-69 1.65e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 109.13  E-value: 1.65e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504005346  1 MPVGTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKrgKTSAENLKAV 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-58 2.79e-28

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: 95.72  E-value: 2.79e-28
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKR 58
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG 57
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-69 1.27e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 86.53  E-value: 1.27e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504005346   4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKrgKTSAENLKAV 69
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK--GPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-69 1.96e-19

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: 73.40  E-value: 1.96e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504005346    4 GTVKWFNstKGYGFIQPDNGGADVFVHISAVErAGLRSLNEGQKVSYEEQRDPKRGKTSAENLKAV 69
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-50 2.79e-19

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 73.09  E-value: 2.79e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSY 50
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF 53
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-69 1.65e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 109.13  E-value: 1.65e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504005346  1 MPVGTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKrgKTSAENLKAV 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-58 2.79e-28

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: 95.72  E-value: 2.79e-28
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKR 58
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG 57
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-69 1.27e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 86.53  E-value: 1.27e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504005346   4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKrgKTSAENLKAV 69
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK--GPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-69 1.96e-19

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: 73.40  E-value: 1.96e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504005346    4 GTVKWFNstKGYGFIQPDNGGADVFVHISAVErAGLRSLNEGQKVSYEEQRDPKRGKTSAENLKAV 69
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-50 2.79e-19

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 73.09  E-value: 2.79e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSY 50
Cdd:PRK10354  7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF 53
cspE PRK09507
cold shock-like protein CspE;
4-51 2.16e-18

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 70.84  E-value: 2.16e-18
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYE 51
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFE 53
PRK09937 PRK09937
cold shock-like protein CspD;
1-62 8.57e-18

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 69.76  E-value: 8.57e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504005346  1 MPVGTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKRGKTS 62
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-56 8.62e-18

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 69.41  E-value: 8.62e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSY---EEQRDP 56
Cdd:PRK09890  7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFsieQGQRGP 62
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-62 4.88e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 67.77  E-value: 4.88e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504005346  1 MPVGTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQRDPKRGKTS 62
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-62 4.29e-15

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 62.78  E-value: 4.29e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSYEEQrDPKRGKTS 62
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQ-DGQKGPAA 63
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 4-50 1.05e-05

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 38.73  E-value: 1.05e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISAVERAGLRSLNEGQKVSY 50
Cdd:PRK15463  7 GIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF 53
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 4-33 2.61e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 32.76  E-value: 2.61e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 504005346  4 GTVKWFNSTKGYGFIQPDNGGADVFVHISA 33
Cdd:PRK15464  7 GIVKTFDRKSGKGFIIPSDGRKEVQVHISA 36
Rho_RNA_bind pfam07497
Rho termination factor, RNA-binding domain; The Rho termination factor disengages newly ...
 14-59 3.64e-03

Rho termination factor, RNA-binding domain; The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers.


Pssm-ID: 462182 [Multi-domain]  Cd Length: 72  Bit Score: 32.35  E-value: 3.64e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 504005346  14 GYGFIQPDN---GGADVFVHISAVERAGLRSlneGQKVSyEEQRDPKRG 59
Cdd:pfam07497 10 GYGFLRSSNylpGPDDIYVSPSQIRRFGLRT---GDIVE-GQVRPPKEG 54
VacB COG0557
Exoribonuclease R [Transcription];
13-30 3.99e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 33.54  E-value: 3.99e-03
                         10
                 ....*....|....*...
gi 504005346  13 KGYGFIQPDNGGADVFVH 30
Cdd:COG0557   79 DGFGFVIPDDGEEDIFIP 96
 
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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