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Conserved domains on  [gi|1261024139|gb|PFF41382|]
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cold-shock protein [Bacillus cereus]

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];
1-66 1.94e-33

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1261024139  1 MEKGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRKA 66
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 1.94e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1261024139  1 MEKGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRKA 66
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-65 1.33e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.55  E-value: 1.33e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1261024139  2 EKGNVKWFNGEKGFGFIEREGGD-DVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-65 4.68e-29

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: 97.65  E-value: 4.68e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1261024139  3 KGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDdGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
3-63 1.58e-23

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 83.93  E-value: 1.58e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  3 KGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK09507   5 KGNVKWFNESKGFGFITPEdGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-66 1.08e-16

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: 66.47  E-value: 1.08e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1261024139   3 KGNVKWFNgeKGFGFIEREGGD-DVFVHFSAIQGeGYKTLEEGQAVTFDLE--QGQRGPQASNVRKA 66
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 ...
 4-65 4.14e-11

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: 52.19  E-value: 4.14e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  4 GNVKWFNGEKGFGFIEREGGDDVFVHFSAIQGEGYkTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEGD-DIIEGDKVSFEVRKTPKGPRAYNIKK 61
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-66 1.94e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 108.74  E-value: 1.94e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1261024139  1 MEKGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRKA 66
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-65 1.33e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 101.55  E-value: 1.33e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1261024139  2 EKGNVKWFNGEKGFGFIEREGGD-DVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTK 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-65 4.68e-29

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: 97.65  E-value: 4.68e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1261024139  3 KGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:cd04458    2 TGTVKWFDDEKGFGFITPDdGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
cspE PRK09507
cold shock-like protein CspE;
3-63 1.58e-23

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 83.93  E-value: 1.58e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  3 KGNVKWFNGEKGFGFIERE-GGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK09507   5 KGNVKWFNESKGFGFITPEdGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-63 1.69e-23

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 83.87  E-value: 1.69e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261024139  4 GNVKWFNGEKGFGFIE-REGGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK10354   7 GIVKWFNADKGFGFITpDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-63 7.06e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 79.81  E-value: 7.06e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261024139  4 GNVKWFNGEKGFGFIE-REGGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK09890   7 GLVKWFNADKGFGFITpDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
PRK09937 PRK09937
cold shock-like protein CspD;
1-61 1.09e-21

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 79.39  E-value: 1.09e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  1 MEKGNVKWFNGEKGFGFIEREGG-DDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQAS 61
Cdd:PRK09937   1 MEKGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-61 3.71e-20

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 75.47  E-value: 3.71e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  1 MEKGNVKWFNGEKGFGFIEREGG-DDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQAS 61
Cdd:PRK14998   1 METGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 3-63 1.42e-19

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 73.95  E-value: 1.42e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  3 KGNVKWFNGEKGFGFIE-REGGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK10943   5 KGQVKWFNESKGFGFITpADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-66 1.08e-16

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: 66.47  E-value: 1.08e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1261024139   3 KGNVKWFNgeKGFGFIEREGGD-DVFVHFSAIQGeGYKTLEEGQAVTFDLE--QGQRGPQASNVRKA 66
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 ...
 4-65 4.14e-11

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: 52.19  E-value: 4.14e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1261024139  4 GNVKWFNGEKGFGFIEREGGDDVFVHFSAIQGEGYkTLEEGQAVTFDLEQGQRGPQASNVRK 65
Cdd:NF038236   1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEGD-DIIEGDKVSFEVRKTPKGPRAYNIKK 61
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 4-63 5.01e-07

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.20  E-value: 5.01e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261024139  4 GNVKWFNGEKGFGFIE-REGGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK15463   7 GIVKTFDGKSGKGLITpSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 4-63 1.17e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 33.53  E-value: 1.17e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1261024139  4 GNVKWFNGEKGFGFI-EREGGDDVFVHFSAIQGEGYKTLEEGQAVTFDLEQGQRGPQASNV 63
Cdd:PRK15464   7 GIVKTFDRKSGKGFIiPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
 
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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