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Conserved domains on  [gi|1101461848|gb|OIQ48263|]
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cold-shock protein [Gammaproteobacteria bacterium MedPE]

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];
5-68 2.26e-32

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 106.05  E-value: 2.26e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-68 2.26e-32

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 106.05  E-value: 2.26e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-68 4.56e-31

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 102.71  E-value: 4.56e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-67 1.02e-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: 96.88  E-value: 1.02e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1101461848  5 TGTVKWFNESKGFGFISQES-GPDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITV 67
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
1-68 8.85e-27

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 92.02  E-value: 8.85e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1101461848  1 MSTTTGTVKWFNESKGFGFISQESGP-DVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK09507   1 MSKIKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-68 4.68e-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: 72.25  E-value: 4.68e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1101461848   5 TGTVKWFNesKGFGFISQESG-PDVFAHFSAINGnGFKTLAEGQKVEFTVT--QGQKGPQAENITVV 68
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 6-68 3.45e-14

retron Se72 family effector protein; Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance.


Pssm-ID: 439537  Cd Length: 62  Bit Score: 59.89  E-value: 3.45e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1101461848  6 GTVKWFNESKGFGFISQESGPDVFAHFSAINGNGfKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-68 2.26e-32

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 106.05  E-value: 2.26e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGgEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-68 4.56e-31

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 102.71  E-value: 4.56e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGdKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-67 1.02e-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: 96.88  E-value: 1.02e-28
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1101461848  5 TGTVKWFNESKGFGFISQES-GPDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITV 67
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDDgGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
1-68 8.85e-27

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 92.02  E-value: 8.85e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1101461848  1 MSTTTGTVKWFNESKGFGFISQESGP-DVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK09507   1 MSKIKGNVKWFNESKGFGFITPEDGSkDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
5-66 2.20e-22

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 81.18  E-value: 2.20e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1101461848  5 TGTVKWFNESKGFGFISQESGP-DVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENIT 66
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 1-68 7.83e-22

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 79.73  E-value: 7.83e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1101461848  1 MSTTTGTVKWFNESKGFGFISQESGP-DVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK10943   1 MAKIKGQVKWFNESKGFGFITPADGSkDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 5-68 7.93e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 79.81  E-value: 7.93e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESGP-DVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK09890   6 TGLVKWFNADKGFGFITPDDGSkDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-68 4.68e-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: 72.25  E-value: 4.68e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1101461848   5 TGTVKWFNesKGFGFISQESG-PDVFAHFSAINGnGFKTLAEGQKVEFTVT--QGQKGPQAENITVV 68
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGgKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK09937 PRK09937
cold shock-like protein CspD;
6-68 2.85e-18

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 70.92  E-value: 2.85e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1101461848  6 GTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 5-68 1.79e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 68.54  E-value: 1.79e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 6-68 3.45e-14

retron Se72 family effector protein; Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance.


Pssm-ID: 439537  Cd Length: 62  Bit Score: 59.89  E-value: 3.45e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1101461848  6 GTVKWFNESKGFGFISQESGPDVFAHFSAINGNGfKTLAEGQKVEFTVTQGQKGPQAENITVV 68
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 5-65 6.15e-09

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 46.82  E-value: 6.15e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENI 65
Cdd:PRK15463   6 TGIVKTFDGKSGKGLITPSDGrKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 5-65 1.38e-05

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 38.54  E-value: 1.38e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1101461848  5 TGTVKWFNESKGFGFISQESG-PDVFAHFSAINGNGFKTLAEGQKVEFTVTQGQKGPQAENI 65
Cdd:PRK15464   6 TGIVKTFDRKSGKGFIIPSDGrKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
 11-50 5.15e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 31.98  E-value: 5.15e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1101461848 11 FNE--SKGFGFISQESGPDVFAHFSAINGngfkTLAEGQKVE 50
Cdd:cd12407   34 FNErgSKGFGFVTFANSADADRAREKLNG----TVVEGRKIE 71
 
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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