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Conserved domains on  [gi|563926973|ref|WP_023809797|]
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MULTISPECIES: cold-shock protein [Mesorhizobium]

Protein Classification

cold-shock protein( domain architecture ID 10003418)

cold-shock protein (Csp) such as bacterial CspA and CspB involved in cold stress response

CATH:  2.40.50.140
Gene Ontology:  GO:0003676
PubMed:  9371456|12530521

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-68 1.39e-29

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.11  E-value: 1.39e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 563926973  1 MNTGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGReSAANLQLI 68
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGP-QAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-68 1.39e-29

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.11  E-value: 1.39e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 563926973  1 MNTGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGReSAANLQLI 68
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGP-QAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-67 6.15e-25

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: 87.25  E-value: 6.15e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGREsAANLQL 67
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQ-AVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-68 8.32e-23

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 81.90  E-value: 8.32e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 563926973   3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGREsAANLQLI 68
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQ-AANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
4-68 3.22e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 75.46  E-value: 3.22e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  4 GTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGrESAANLQLI 68
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVIAL 69
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-68 1.05e-13

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: 58.76  E-value: 1.05e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 563926973    3 TGTVKFYNgqKGFGFIQPTDGGKDVFVHVSALErAGFPGLAEGQKLQFELERDTK-GRESAANLQLI 68
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGgEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-68 1.39e-29

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.11  E-value: 1.39e-29
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 563926973  1 MNTGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGReSAANLQLI 68
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGP-QAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-67 6.15e-25

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: 87.25  E-value: 6.15e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGREsAANLQL 67
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQ-AVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
3-68 8.32e-23

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 81.90  E-value: 8.32e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 563926973   3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGREsAANLQLI 68
Cdd:pfam00313  2 TGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQ-AANVTKP 66
cspE PRK09507
cold shock-like protein CspE;
4-68 3.22e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 75.46  E-value: 3.22e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  4 GTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGrESAANLQLI 68
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG-PSAANVIAL 69
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-65 6.81e-19

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 72.32  E-value: 6.81e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGrESAANL 65
Cdd:PRK10354  6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG-PAAGNV 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-65 4.58e-17

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 67.48  E-value: 4.58e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGrESAANL 65
Cdd:PRK09890  6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG-PAAANV 67
PRK09937 PRK09937
cold shock-like protein CspD;
1-62 1.82e-15

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 63.60  E-value: 1.82e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 563926973  1 MNTGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGRESA 62
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-58 2.09e-15

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 63.55  E-value: 2.09e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  4 GTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKG 58
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG 60
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-62 1.29e-14

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 61.60  E-value: 1.29e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 563926973  1 MNTGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGRESA 62
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-68 1.05e-13

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: 58.76  E-value: 1.05e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 563926973    3 TGTVKFYNgqKGFGFIQPTDGGKDVFVHVSALErAGFPGLAEGQKLQFELERDTK-GRESAANLQLI 68
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGgEKPEAENVVKL 64
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-67 6.21e-10

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 49.51  E-value: 6.21e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSALERAGFPGLAEGQKLQFELERDTKGrESAANLQL 67
Cdd:PRK15463  6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRG-PTAANVYL 69
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-34 2.32e-05

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 37.77  E-value: 2.32e-05
                        10        20        30
                ....*....|....*....|....*....|..
gi 563926973  3 TGTVKFYNGQKGFGFIQPTDGGKDVFVHVSAL 34
Cdd:PRK15464  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAF 37
VacB COG0557
Exoribonuclease R [Transcription];
3-38 2.30e-04

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 37.01  E-value: 2.30e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 563926973   3 TGTVKFYngQKGFGFIQPTDGGKDVFVHVSALERAG 38
Cdd:COG0557   71 EGRVRGH--RDGFGFVIPDDGEEDIFIPPRELNGAL 104
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 4-37 3.48e-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: 32.12  E-value: 3.48e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 563926973   4 GTVKFYngQKGFGFIQPTDGGKDVFVHVSALERA 37
Cdd:pfam08206  1 GTVRGH--KKGFGFLIPDDEEDDIFIPPNQMKKA 32
 
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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