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Conserved domains on  [gi|1831505908|ref|NP_001367859|]
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CSD domain-containing protein [Caenorhabditis elegans]

Protein Classification

cold shock domain-containing protein( domain architecture ID 10448154)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
SCOP:  4001909

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
64-134 4.02e-25

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.62  E-value: 4.02e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVTGP 134
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG-----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
64-134 4.02e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.62  E-value: 4.02e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVTGP 134
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG-----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
65-133 1.77e-19

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: 79.54  E-value: 1.77e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831505908  65 QGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVTG 133
Cdd:cd04458     2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG-----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
65-132 2.87e-18

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 76.39  E-value: 2.87e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1831505908  65 QGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:COG1278     3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG-----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
64-132 1.96e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 66.60  E-value: 1.96e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISksdTEKFylRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:PRK09507    4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQ---TNGF--KTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
65-134 2.18e-13

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: 63.39  E-value: 2.18e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1831505908   65 QGKVKWYSvlRRYGFISRSDGEKDVFVHQTAISKsdtekfYLRTLADEEEVLFDLV--DGKNGPEAANVTGP 134
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG------GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
64-134 4.02e-25

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 94.62  E-value: 4.02e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVTGP 134
Cdd:pfam00313   1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDG-----FRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
65-133 1.77e-19

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: 79.54  E-value: 1.77e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831505908  65 QGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVTG 133
Cdd:cd04458     2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDG-----FRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
65-132 2.87e-18

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 76.39  E-value: 2.87e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1831505908  65 QGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:COG1278     3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSG-----FRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
64-132 1.96e-14

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 66.60  E-value: 1.96e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISksdTEKFylRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:PRK09507    4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQ---TNGF--KTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
65-134 2.18e-13

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: 63.39  E-value: 2.18e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1831505908   65 QGKVKWYSvlRRYGFISRSDGEKDVFVHQTAISKsdtekfYLRTLADEEEVLFDLV--DGKNGPEAANVTGP 134
Cdd:smart00357   1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG------GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
62-132 6.82e-13

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 62.39  E-value: 6.82e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1831505908  62 AGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:PRK10943    2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG-----FKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
60-131 8.11e-13

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 62.09  E-value: 8.11e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1831505908  60 LTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANV 131
Cdd:PRK09890    1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNE-----FRTLNENQKVEFSIEQGQRGPAAANV 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
60-132 1.51e-11

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 58.83  E-value: 1.51e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1831505908  60 LTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAANVT 132
Cdd:PRK10354    1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG-----YKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
64-131 7.21e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 42.97  E-value: 7.21e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1831505908  64 LQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEkfylrTLADEEEVLFDLVDGKNGPEAANV 131
Cdd:PRK15463    5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAE-----ELTTGLRVEFCRINGLRGPTAANV 67
PRK09937 PRK09937
cold shock-like protein CspD;
65-129 1.49e-04

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 39.33  E-value: 1.49e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1831505908  65 QGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAA 129
Cdd:PRK09937    3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-----YRTLKAGQSVQFDVHQGPKGNHAS 62
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
66-129 2.01e-04

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 38.88  E-value: 2.01e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1831505908  66 GKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDtekfyLRTLADEEEVLFDLVDGKNGPEAA 129
Cdd:PRK14998    4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-----YRTLKAGQSVRFDVHQGPKGNHAS 62
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
60-131 2.94e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 38.54  E-value: 2.94e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1831505908  60 LTAGLQGKVKWYSVLRRYGFISRSDGEKDVFVHQTAISKSDTEKFYLRTladeeEVLFDLVDGKNGPEAANV 131
Cdd:PRK15464    1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGL-----RVEFCRVNGLRGPTAANV 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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