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Conserved domains on  [gi|1963666373|emb|CAD5356916|]
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cold shock protein; Qin prophage [Citrobacter freundii]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1-70 1.28e-38

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member PRK09890:

Pssm-ID: 471952  Cd Length: 70  Bit Score: 122.18  E-value: 1.28e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
 
Name Accession Description Interval E-value
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-70 1.28e-38

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 122.18  E-value: 1.28e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-70 3.14e-34

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 110.67  E-value: 3.14e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1963666373  6 TGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 9.38e-34

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 109.64  E-value: 9.38e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1963666373  5 MTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-67 2.80e-30

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: 100.73  E-value: 2.80e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1963666373  5 MTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNV 67
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 1.06e-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: 74.17  E-value: 1.06e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1963666373   6 TGLVKWFNpeKGFGFITPKDGSKDVFVHFSAIQShDFKTLNENQEVEFSVE--QGPKGPTAVNVVAV 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-70 1.28e-38

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 122.18  E-value: 1.28e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK09890   1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-70 6.09e-35

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 112.76  E-value: 6.09e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK10354   1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-70 3.14e-34

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 110.67  E-value: 3.14e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1963666373  6 TGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 9.38e-34

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 109.64  E-value: 9.38e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1963666373  5 MTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
3-70 9.01e-31

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 102.42  E-value: 9.01e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1963666373  3 NKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK09507   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 5-67 2.80e-30

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: 100.73  E-value: 2.80e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1963666373  5 MTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNV 67
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-70 2.10e-26

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 91.28  E-value: 2.10e-26
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1963666373  4 KMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK10943   3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK09937 PRK09937
cold shock-like protein CspD;
7-70 1.20e-20

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 76.69  E-value: 1.20e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1963666373  7 GLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-67 1.33e-20

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 76.48  E-value: 1.33e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNV 67
Cdd:PRK15463   1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 6-70 8.74e-20

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 74.70  E-value: 8.74e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1963666373  6 TGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNVVAV 70
Cdd:PRK14998   3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 1.06e-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: 74.17  E-value: 1.06e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1963666373   6 TGLVKWFNpeKGFGFITPKDGSKDVFVHFSAIQShDFKTLNENQEVEFSVE--QGPKGPTAVNVVAV 70
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 1-67 1.68e-16

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 66.28  E-value: 1.68e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1963666373  1 MSNKMTGLVKWFNPEKGFGFITPKDGSKDVFVHFSAIQSHDFKTLNENQEVEFSVEQGPKGPTAVNV 67
Cdd:PRK15464   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
16-33 1.98e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 34.31  E-value: 1.98e-03
                          10
                  ....*....|....*...
gi 1963666373  16 KGFGFITPKDGSKDVFVH 33
Cdd:COG0557    79 DGFGFVIPDDGEEDIFIP 96
 
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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