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Conserved domains on  [gi|1402749|gb|AAC80239|]
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major cold-shock protein, partial [Escherichia coli]

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 ...
 1-46 8.36e-26

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 PRK10354:

Pssm-ID: 471952  Cd Length: 70  Bit Score: 88.49  E-value: 8.36e-26
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1402749    1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK10354 15 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 60
 
Name Accession Description Interval E-value
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-46 8.36e-26

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 88.49  E-value: 8.36e-26
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1402749    1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK10354 15 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 60
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-46 7.88e-23

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 81.01  E-value: 7.88e-23
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
gi 1402749   1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:COG1278 12 EKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK 57
CSD pfam00313
'Cold-shock' DNA-binding domain;
1-46 5.86e-22

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 78.82  E-value: 5.86e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1402749     1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:pfam00313 11 KKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK 56
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 1-46 8.45e-20

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: 73.38  E-value: 8.45e-20
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
gi 1402749   1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:cd04458 11 EKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDK 56
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 1-43 1.07e-14

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: 60.31  E-value: 1.07e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1402749      1 DKGFGFITPDDGSKDVFVHFSAIQnDGYKSLDEGQKVSFTIES 43
Cdd:smart00357  8 NKGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVS 49
 
Name Accession Description Interval E-value
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-46 8.36e-26

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 88.49  E-value: 8.36e-26
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1402749    1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK10354 15 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 60
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-46 7.88e-23

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 81.01  E-value: 7.88e-23
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
gi 1402749   1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:COG1278 12 EKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK 57
CSD pfam00313
'Cold-shock' DNA-binding domain;
1-46 5.86e-22

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 78.82  E-value: 5.86e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1402749     1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:pfam00313 11 KKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK 56
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-46 4.81e-20

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 74.03  E-value: 4.81e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 1402749    1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK09890 15 DKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQR 60
cspE PRK09507
cold shock-like protein CspE;
2-46 7.43e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 73.53  E-value: 7.43e-20
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 1402749    2 KGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK09507 15 KGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAK 59
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 1-46 8.45e-20

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: 73.38  E-value: 8.45e-20
                       10        20        30        40
               ....*....|....*....|....*....|....*....|....*.
gi 1402749   1 DKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:cd04458 11 EKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDK 56
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 2-46 1.04e-15

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 63.16  E-value: 1.04e-15
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 1402749    2 KGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK10943 15 KGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQK 59
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 1-43 1.07e-14

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: 60.31  E-value: 1.07e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1402749      1 DKGFGFITPDDGSKDVFVHFSAIQnDGYKSLDEGQKVSFTIES 43
Cdd:smart00357  8 NKGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVS 49
PRK09937 PRK09937
cold shock-like protein CspD;
2-46 5.29e-14

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 58.97  E-value: 5.29e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 1402749    2 KGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK09937 13 KGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPK 57
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 2-46 3.97e-13

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 56.60  E-value: 3.97e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 1402749    2 KGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAK 46
Cdd:PRK14998 13 KGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPK 57
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-39 2.01e-05

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 37.19  E-value: 2.01e-05
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 1402749    3 GFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSF 39
Cdd:PRK15463 17 GKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF 53
VacB COG0557
Exoribonuclease R [Transcription];
2-19 7.77e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 37.01  E-value: 7.77e-05
                        10
                ....*....|....*...
gi 1402749    2 KGFGFITPDDGSKDVFVH 19
Cdd:COG0557  79 DGFGFVIPDDGEEDIFIP 96
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 1-25 4.12e-03

Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.


Pssm-ID: 429863 [Multi-domain]  Cd Length: 58  Bit Score: 30.97  E-value: 4.12e-03
                         10        20
                 ....*....|....*....|....*
gi 1402749     1 DKGFGFITPDDGSKDVFVHFSAIQN 25
Cdd:pfam08206  7 KKGFGFLIPDDEEDDIFIPPNQMKK 31
 
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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