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Conserved domains on  [gi|1729311312|gb|TXY60472|]
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cold-shock protein [Vibrio cholerae]

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];
6-70 1.82e-33

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.82e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729311312  6 TGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-70 1.82e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.82e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729311312  6 TGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-70 2.38e-30

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 101.21  E-value: 2.38e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729311312  1 MSQKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-68 2.77e-30

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: 100.73  E-value: 2.77e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729311312  5 MTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVT 68
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVR 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 7.88e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 99.62  E-value: 7.88e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1729311312  5 MTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 2.72e-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: 70.32  E-value: 2.72e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312   6 TGSVKWFNetKGFGFISQDNGGQDVFVHFKSIVSeGFKTLAEGQRVSFTVE--QGKKGPQAAQVTAL 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-70 1.82e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.82e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729311312  6 TGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-70 2.38e-30

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 101.21  E-value: 2.38e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729311312  1 MSQKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-68 2.77e-30

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: 100.73  E-value: 2.77e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1729311312  5 MTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVT 68
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVR 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 7.88e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 99.62  E-value: 7.88e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1729311312  5 MTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
4-70 4.60e-28

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 95.49  E-value: 4.60e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312  4 KMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK09507   3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-70 5.89e-27

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 92.91  E-value: 5.89e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1729311312  1 MSQKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-70 2.16e-21

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 78.57  E-value: 2.16e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312  4 KMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
7-67 5.34e-19

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 72.84  E-value: 5.34e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1729311312  7 GSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQV 67
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVI 64
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 6-70 7.91e-19

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 72.39  E-value: 7.91e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1729311312  6 TGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQVTAL 70
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 2.72e-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: 70.32  E-value: 2.72e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312   6 TGSVKWFNetKGFGFISQDNGGQDVFVHFKSIVSeGFKTLAEGQRVSFTVE--QGKKGPQAAQVTAL 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-67 9.09e-13

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 56.83  E-value: 9.09e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312  1 MSQKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQV 67
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 1-67 1.24e-09

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 48.94  E-value: 1.24e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1729311312  1 MSQKMTGSVKWFNETKGFGFISQDNGGQDVFVHFKSIVSEGFKTLAEGQRVSFTVEQGKKGPQAAQV 67
Cdd:PRK15464   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
16-61 2.34e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 34.31  E-value: 2.34e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1729311312  16 KGFGFISQDNGGQDVFVHfksivSEGFKTLAEGQRVSFTVEQGKKG 61
Cdd:COG0557    79 DGFGFVIPDDGEEDIFIP-----PRELNGALHGDRVLVRVTKEDRR 119
 
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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