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Conserved domains on  [gi|1915211780|dbj|BBV70456|]
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cold-shock protein [Enterobacter kobei]

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 ...
 1-73 2.47e-49

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 PRK14998:

Pssm-ID: 471952  Cd Length: 73  Bit Score: 149.43  E-value: 2.47e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIEAETVA 73
Cdd:PRK14998   1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAEAVA 73
 
Name Accession Description Interval E-value
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-73 2.47e-49

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 149.43  E-value: 2.47e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIEAETVA 73
Cdd:PRK14998   1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAEAVA 73
cspD TIGR02381
cold shock domain protein CspD; This model represents what appears to be a phylogenetically ...
 1-68 1.35e-45

cold shock domain protein CspD; This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD (SP|P24245) and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication. [DNA metabolism, DNA replication, recombination, and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 131434  Cd Length: 68  Bit Score: 139.60  E-value: 1.35e-45
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIE 68
Cdd:TIGR02381  1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHIVPIE 68
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 4.64e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 107.97  E-value: 4.64e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 5.24e-32

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 105.40  E-value: 5.24e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-62 5.39e-28

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: 95.34  E-value: 5.39e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAV 61
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-65 4.74e-18

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: 69.94  E-value: 4.74e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1915211780   3 MGTVKWFNnaKGFGFICPEGGGEDIFAHYSTIQMdGYRTLKAGQSVRFDVH--QGPKGNHASLIV 65
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
 
Name Accession Description Interval E-value
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-73 2.47e-49

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 149.43  E-value: 2.47e-49
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIEAETVA 73
Cdd:PRK14998   1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVIVPIEAEAVA 73
PRK09937 PRK09937
cold shock-like protein CspD;
1-70 1.57e-48

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 147.57  E-value: 1.57e-48
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIEAE 70
Cdd:PRK09937   1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPVEVE 70
cspD TIGR02381
cold shock domain protein CspD; This model represents what appears to be a phylogenetically ...
 1-68 1.35e-45

cold shock domain protein CspD; This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD (SP|P24245) and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication. [DNA metabolism, DNA replication, recombination, and repair, Cellular processes, Adaptations to atypical conditions]


Pssm-ID: 131434  Cd Length: 68  Bit Score: 139.60  E-value: 1.35e-45
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPIE 68
Cdd:TIGR02381  1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHIVPIE 68
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 4.64e-33

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 107.97  E-value: 4.64e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1915211780  1 MEMGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:COG1278    1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 5.24e-32

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 105.40  E-value: 5.24e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-62 5.39e-28

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: 95.34  E-value: 5.39e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
Cdd:cd04458    3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAV 61
cspE PRK09507
cold shock-like protein CspE;
4-67 8.39e-23

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 82.39  E-value: 8.39e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:PRK09507   6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIAL 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
4-67 2.81e-21

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 78.48  E-value: 2.81e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:PRK10354   7 GIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTSL 70
PRK09890 PRK09890
cold shock protein CspG; Provisional
 4-67 4.40e-19

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 72.88  E-value: 4.40e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASLIVPI 67
Cdd:PRK09890   7 GLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANVVTL 70
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-61 4.06e-18

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 70.48  E-value: 4.06e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHA 61
Cdd:PRK10943   6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAA 63
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-65 4.74e-18

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: 69.94  E-value: 4.74e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1915211780   3 MGTVKWFNnaKGFGFICPEGGGEDIFAHYSTIQMdGYRTLKAGQSVRFDVH--QGPKGNHASLIV 65
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 4-62 3.35e-04

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 35.26  E-value: 3.35e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 1915211780  4 GTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
Cdd:PRK15463   7 GIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAA 65
VacB COG0557
Exoribonuclease R [Transcription];
11-28 1.99e-03

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 34.70  E-value: 1.99e-03
                          10
                  ....*....|....*...
gi 1915211780  11 NAKGFGFICPEGGGEDIF 28
Cdd:COG0557    77 HRDGFGFVIPDDGEEDIF 94
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 4-28 9.11e-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: 9.11e-03
                         10        20
                 ....*....|....*....|....*
gi 1915211780  4 GTVKwfNNAKGFGFICPEGGGEDIF 28
Cdd:pfam08206  1 GTVR--GHKKGFGFLIPDDEEDDIF 23
 
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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