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Conserved domains on  [gi|16128606|ref|NP_415156|]
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transcription antiterminator and regulator of RNA stability CspE [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

S1 domain-containing protein; eukaryotic translation initiation factor 1A( domain architecture ID 10793280)

S1 domain-containing protein may bind RNA| eukaryotic translation initiation factor 1A (eIF1A) may be required for maximal rate of protein biosynthesis; it enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cspE PRK09507
cold shock-like protein CspE;
1-69 1.34e-43

cold shock-like protein CspE;


:

Pssm-ID: 169931  Cd Length: 69  Bit Score: 134.78  E-value: 1.34e-43
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128606   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK09507  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
 
Name Accession Description Interval E-value
cspE PRK09507
cold shock-like protein CspE;
1-69 1.34e-43

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 134.78  E-value: 1.34e-43
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128606   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK09507  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 8.00e-36

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 114.65  E-value: 8.00e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128606    5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-69 5.43e-35

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 112.60  E-value: 5.43e-35
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128606  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:COG1278  3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-66 1.21e-31

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: 104.20  E-value: 1.21e-31
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16128606  4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:cd04458  1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-69 3.90e-22

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: 80.34  E-value: 3.90e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128606     5 KGNVKWFNesKGFGFITPEDGSKDVFVHFSAIQTnGFKTLAEGQRVEFEIT--NGAKGPSAANVIAL 69
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
cspE PRK09507
cold shock-like protein CspE;
1-69 1.34e-43

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 134.78  E-value: 1.34e-43
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128606   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK09507  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 8.00e-36

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 114.65  E-value: 8.00e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128606    5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-69 5.43e-35

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 112.60  E-value: 5.43e-35
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128606  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:COG1278  3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 1-69 6.91e-33

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 107.46  E-value: 6.91e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128606   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK10943  1 MAKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-69 8.20e-32

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 105.06  E-value: 8.20e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128606   3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK10354  4 KMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-66 1.21e-31

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: 104.20  E-value: 1.21e-31
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16128606  4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:cd04458  1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
PRK09890 PRK09890
cold shock protein CspG; Provisional
 2-69 2.28e-30

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 101.38  E-value: 2.28e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16128606   2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK09890  3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK09937 PRK09937
cold shock-like protein CspD;
5-67 2.28e-22

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 81.32  E-value: 2.28e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16128606   5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
Cdd:PRK09937  3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIV 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-69 3.90e-22

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: 80.34  E-value: 3.90e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128606     5 KGNVKWFNesKGFGFITPEDGSKDVFVHFSAIQTnGFKTLAEGQRVEFEIT--NGAKGPSAANVIAL 69
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVVKL 64
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 6-69 1.93e-20

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 76.24  E-value: 1.93e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128606   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
Cdd:PRK14998  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPI 67
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-66 1.71e-17

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 68.77  E-value: 1.71e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128606   1 MS-KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:PRK15463  1 MSrKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-66 1.36e-13

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 58.96  E-value: 1.36e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16128606   3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:PRK15464  4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
14-60 1.53e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 40.48  E-value: 1.53e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 16128606  14 SKGFGFITPEDGSKDVFVHFSaiQTNGfktLAEGQRVEFEITNGAKG 60
Cdd:COG0557  78 RDGFGFVIPDDGEEDIFIPPR--ELNG---ALHGDRVLVRVTKEDRR 119
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 14-60 2.23e-04

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: 35.21  E-value: 2.23e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 16128606   14 SKGFGFITPEDGSKDVFVHFsaiqtNGFKTLAEGQRVEFEITNGAKG 60
Cdd:pfam08206  7 KKGFGFLIPDDEEDDIFIPP-----NQMKKAMHGDRVLVRITKGDRR 48
 
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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