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Conserved domains on  [gi|552539016|ref|WP_022998017|]
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MULTISPECIES: cold-shock protein [unclassified Labrenzia]

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];
198-263 8.17e-26

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 96.80  E-value: 8.17e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQAL 263
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGD--KGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-263 8.17e-26

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 96.80  E-value: 8.17e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQAL 263
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGD--KGPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 196-261 3.03e-21

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: 84.55  E-value: 3.03e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 196 QSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQ 261
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGD--KGPQAVNVR 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
198-263 8.14e-21

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 83.45  E-value: 8.14e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016  198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEpdRRGKGPKAVNLQAL 263
Cdd:pfam00313   3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
195-263 3.33e-18

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 76.94  E-value: 3.33e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552539016 195 RQSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDrrGKGPKAVNLQAL 263
Cdd:PRK10354   4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG--AKGPAAGNVTSL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 198-263 1.33e-14

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: 66.85  E-value: 1.33e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016   198 GTVKFFknDKGFGFITPDEGDADVFVHISAVErSGFAGLDSGQRVSFETEPDRRGKGPKAVNLQAL 263
Cdd:smart00357   2 GVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-263 8.17e-26

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 96.80  E-value: 8.17e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQAL 263
Cdd:COG1278    4 GTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGD--KGPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 196-261 3.03e-21

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: 84.55  E-value: 3.03e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 196 QSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQ 261
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGD--KGPQAVNVR 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
198-263 8.14e-21

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 83.45  E-value: 8.14e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016  198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEpdRRGKGPKAVNLQAL 263
Cdd:pfam00313   3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
195-263 3.33e-18

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 76.94  E-value: 3.33e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552539016 195 RQSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDrrGKGPKAVNLQAL 263
Cdd:PRK10354   4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESG--AKGPAAGNVTSL 70
cspE PRK09507
cold shock-like protein CspE;
198-263 4.48e-17

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 73.92  E-value: 4.48e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDrrGKGPKAVNLQAL 263
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNG--AKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 195-263 6.85e-16

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 70.56  E-value: 6.85e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552539016 195 RQSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRRgkGPKAVNLQAL 263
Cdd:PRK09890   4 KMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQR--GPAAANVVTL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 198-263 1.33e-14

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: 66.85  E-value: 1.33e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016   198 GTVKFFknDKGFGFITPDEGDADVFVHISAVErSGFAGLDSGQRVSFETEPDRRGKGPKAVNLQAL 263
Cdd:smart00357   2 GVVKWF--NKGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 198-263 1.87e-13

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 63.93  E-value: 1.87e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 198 GTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRrgKGPKAVNLQAL 263
Cdd:PRK10943   6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQ--KGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
196-257 1.78e-11

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 58.59  E-value: 1.78e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 552539016 196 QSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEpdrrgKGPKA 257
Cdd:PRK09937   2 EKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVH-----QGPKG 58
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 196-257 2.82e-10

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 55.44  E-value: 2.82e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 552539016 196 QSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEpdrrgKGPKA 257
Cdd:PRK14998   2 ETGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVH-----QGPKG 58
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 195-260 6.61e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 46.05  E-value: 6.61e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 552539016 195 RQSGTVKFFKNDKGFGFITPDEGDADVFVHISAVERSGFAGLDSGQRVSFETEPDRRgkGPKAVNL 260
Cdd:PRK15463   4 KMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLR--GPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
189-257 3.88e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 38.55  E-value: 3.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552539016 189 PVERGPRQSGTVKFfkNDKGFGFITPDEGDADVFVHisaveRSGFAGLDSGQRVSFETEPDRRGKGPKA 257
Cdd:COG0557   63 LPEKLDLVEGRVRG--HRDGFGFVIPDDGEEDIFIP-----PRELNGALHGDRVLVRVTKEDRRGRPEG 124
 
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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