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Conserved domains on  [gi|446098513|ref|WP_000176368|]
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MULTISPECIES: cold-shock protein CspD [Bacillus]

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];
4-67 1.84e-31

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.84e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446098513  4 TGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:COG1278   3 TGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-67 1.84e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.84e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446098513  4 TGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:COG1278   3 TGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-67 4.44e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.39  E-value: 4.44e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513   3 LTGKVKWFNSEKGFGFIEVEGGN-DVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-66 5.92e-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: 94.95  E-value: 5.92e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446098513  4 TGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVK 66
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDdGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-67 1.08e-24

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 86.95  E-value: 1.08e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513  3 LTGKVKWFNSEKGFGFIEVEGGN-DVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK10354  5 MTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 1.64e-17

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: 68.39  E-value: 1.64e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446098513    4 TGKVKWFNseKGFGFIEVE-GGNDVFVHFSAITGdGFKSLDEGQEVSFEVE--DGNRGPQAKNVVKL 67
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 ...
 5-67 6.78e-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: 51.42  E-value: 6.78e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446098513  5 GKVKWFNSEKGFGFIEVEGGNDVFVHFSAITGDGfKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
4-67 1.84e-31

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 103.74  E-value: 1.84e-31
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446098513  4 TGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:COG1278   3 TGTVKWFNAEKGFGFITPDdGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-67 4.44e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.39  E-value: 4.44e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513   3 LTGKVKWFNSEKGFGFIEVEGGN-DVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDkDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-66 5.92e-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: 94.95  E-value: 5.92e-28
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446098513  4 TGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVK 66
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDdGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-67 1.08e-24

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 86.95  E-value: 1.08e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513  3 LTGKVKWFNSEKGFGFIEVEGGN-DVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK10354  5 MTGIVKWFNADKGFGFITPDDGSkDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
cspE PRK09507
cold shock-like protein CspE;
3-67 9.04e-23

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 82.01  E-value: 9.04e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513  3 LTGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK09507  4 IKGNVKWFNESKGFGFITPEdGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-67 3.94e-22

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 80.58  E-value: 3.94e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513  3 LTGKVKWFNSEKGFGFIEVE-GGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK09890  5 MTGLVKWFNADKGFGFITPDdGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 3-67 2.77e-20

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 75.49  E-value: 2.77e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446098513  3 LTGKVKWFNSEKGFGFIE-VEGGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK10943  4 IKGQVKWFNESKGFGFITpADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 1.64e-17

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: 68.39  E-value: 1.64e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446098513    4 TGKVKWFNseKGFGFIEVE-GGNDVFVHFSAITGdGFKSLDEGQEVSFEVE--DGNRGPQAKNVVKL 67
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDdGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK09937 PRK09937
cold shock-like protein CspD;
5-65 6.77e-17

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 67.45  E-value: 6.77e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446098513  5 GKVKWFNSEKGFGFIEVEGG-NDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVV 65
Cdd:PRK09937  4 GTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 4-67 1.29e-16

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 66.61  E-value: 1.29e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446098513  4 TGKVKWFNSEKGFGFIEVEGG-NDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:PRK14998  3 TGTVKWFNNAKGFGFICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
retron_eff_Se72 NF038236
retron Se72 family effector protein; Members of this family are cold shock domain-containing ...
 5-67 6.78e-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: 51.42  E-value: 6.78e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446098513  5 GKVKWFNSEKGFGFIEVEGGNDVFVHFSAITGDGfKSLDEGQEVSFEVEDGNRGPQAKNVVKL 67
Cdd:NF038236  1 GTVNAYDPFKGFGFIRREKGKDVFFFYDDINDEG-DDIIEGDKVSFEVRKTPKGPRAYNIKKV 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-64 1.95e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 40.65  E-value: 1.95e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446098513  3 LTGKVKWFNSEKGFGFIE-VEGGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNV 64
Cdd:PRK15463  5 MTGIVKTFDGKSGKGLITpSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-64 2.64e-05

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 37.77  E-value: 2.64e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446098513  3 LTGKVKWFNSEKGFGFI-EVEGGNDVFVHFSAITGDGFKSLDEGQEVSFEVEDGNRGPQAKNV 64
Cdd:PRK15464  5 MTGIVKTFDRKSGKGFIiPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 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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