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Conserved domains on  [gi|16128955|ref|NP_415509|]
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CspA family protein CspH [Escherichia coli str. K-12 substr. MG1655]

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 1.45e-44

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 PRK15464:

Pssm-ID: 471952  Cd Length: 70  Bit Score: 137.15  E-value: 1.45e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
Cdd:PRK15464  1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
 
Name Accession Description Interval E-value
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 1-70 1.45e-44

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 137.15  E-value: 1.45e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
Cdd:PRK15464  1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 6.47e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.01  E-value: 6.47e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16128955    5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 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 ...
 5-69 8.18e-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: 71.84  E-value: 8.18e-19
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128955  5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYL 69
Cdd:cd04458  1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-69 4.70e-18

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.84  E-value: 4.70e-18
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128955  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYL 69
Cdd:COG1278  3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 2.11e-12

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: 55.68  E-value: 2.11e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128955     6 TGIVKTFDRksGKGFIIPSDGRKEVQVHISAFTPRdAEVLIPGLRVEFCRV--NGLRGPTAANVYLS 70
Cdd:smart00357  1 TGVVKWFNK--GFGFIRPDDGGKDVFVHPSQIQGG-LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 1-70 1.45e-44

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 137.15  E-value: 1.45e-44
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
Cdd:PRK15464  1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-70 2.58e-41

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 128.87  E-value: 2.58e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 70
Cdd:PRK15463  1 MSRKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANVYLS 70
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-70 6.47e-30

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 100.01  E-value: 6.47e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16128955    5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYLS 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 ...
 5-69 8.18e-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: 71.84  E-value: 8.18e-19
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128955  5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYL 69
Cdd:cd04458  1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
6-69 4.70e-18

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.84  E-value: 4.70e-18
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128955  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVYL 69
Cdd:COG1278  3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRV 66
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
1-67 1.38e-17

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 68.85  E-value: 1.38e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
Cdd:PRK10354  1 MSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNV 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 1-67 9.97e-16

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 64.40  E-value: 9.97e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128955   1 MSRKMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
Cdd:PRK09890  1 MSNKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
cspE PRK09507
cold shock-like protein CspE;
4-67 2.36e-15

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 63.52  E-value: 2.36e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128955   4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
Cdd:PRK09507  3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 6-70 2.11e-12

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: 55.68  E-value: 2.11e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128955     6 TGIVKTFDRksGKGFIIPSDGRKEVQVHISAFTPRdAEVLIPGLRVEFCRV--NGLRGPTAANVYLS 70
Cdd:smart00357  1 TGVVKWFNK--GFGFIRPDDGGKDVFVHPSQIQGG-LKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-68 5.36e-12

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 54.69  E-value: 5.36e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128955   4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANVY 68
Cdd:PRK10943  3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 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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