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Conserved domains on  [gi|1768622360|gb|KAB8170257|]
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transcription antiterminator/RNA stability regulator CspE [Raoultella ornithinolytica]

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 3.29e-43

cold shock-like protein CspE;


:

Pssm-ID: 169931  Cd Length: 69  Bit Score: 133.62  E-value: 3.29e-43
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1768622360  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:PRK09507   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
 
Name Accession Description Interval E-value
cspE PRK09507
cold shock-like protein CspE;
1-69 3.29e-43

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 133.62  E-value: 3.29e-43
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1768622360  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:PRK09507   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 8.36e-36

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 114.65  E-value: 8.36e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1768622360  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-69 1.15e-34

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 111.82  E-value: 1.15e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1768622360  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 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 1.01e-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: 104.58  E-value: 1.01e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1768622360  4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-66 1.11e-21

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: 79.18  E-value: 1.11e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1768622360   5 KGNVKWFNesKGFGFITPEDGSKDVFVHFSAIQSnGFKTLAEGQRVEFEIT--NGAKGPSAANV 66
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENV 61
 
Name Accession Description Interval E-value
cspE PRK09507
cold shock-like protein CspE;
1-69 3.29e-43

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 133.62  E-value: 3.29e-43
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1768622360  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:PRK09507   1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
CSD pfam00313
'Cold-shock' DNA-binding domain;
5-69 8.36e-36

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 114.65  E-value: 8.36e-36
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1768622360  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
5-69 1.15e-34

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 111.82  E-value: 1.15e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1768622360  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:COG1278    3 TGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 1-69 2.00e-32

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 106.31  E-value: 2.00e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1768622360  1 MSKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 69
Cdd:PRK10943   1 MAKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTAI 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-69 4.01e-32

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 105.83  E-value: 4.01e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1768622360  3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANVNAI 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 1.01e-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: 104.58  E-value: 1.01e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1768622360  4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:cd04458    1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNV 63
PRK09890 PRK09890
cold shock protein CspG; Provisional
 2-66 2.88e-29

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 98.68  E-value: 2.88e-29
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1768622360  2 SKIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:PRK09890   3 NKMTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 5-66 1.11e-21

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: 79.18  E-value: 1.11e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1768622360   5 KGNVKWFNesKGFGFITPEDGSKDVFVHFSAIQSnGFKTLAEGQRVEFEIT--NGAKGPSAANV 66
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENV 61
PRK09937 PRK09937
cold shock-like protein CspD;
5-64 1.35e-21

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 79.39  E-value: 1.35e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1768622360  5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAA 64
Cdd:PRK09937   3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 6-64 1.39e-19

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 73.93  E-value: 1.39e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1768622360  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAA 64
Cdd:PRK14998   4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 1-66 2.46e-17

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 68.39  E-value: 2.46e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1768622360  1 MS-KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:PRK15463   1 MSrKMTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-66 1.20e-13

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 58.96  E-value: 1.20e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1768622360  3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQSNGFKTLAEGQRVEFEITNGAKGPSAANV 66
Cdd:PRK15464   4 KMTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
14-60 1.02e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 40.86  E-value: 1.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1768622360  14 SKGFGFITPEDGSKDVFVHfsaiqSNGFKTLAEGQRVEFEITNGAKG 60
Cdd:COG0557    78 RDGFGFVIPDDGEEDIFIP-----PRELNGALHGDRVLVRVTKEDRR 119
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 14-60 1.16e-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: 35.59  E-value: 1.16e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1768622360 14 SKGFGFITPEDGSKDVFvhfsaIQSNGFKTLAEGQRVEFEITNGAKG 60
Cdd:pfam08206  7 KKGFGFLIPDDEEDDIF-----IPPNQMKKAMHGDRVLVRITKGDRR 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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