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Conserved domains on  [gi|500691605|ref|WP_011976082|]
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cold-shock protein [Sinorhizobium medicae]

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];
1-69 9.88e-30

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 9.88e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500691605  1 MNSGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsgKSSADNLRSA 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-69 9.88e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 9.88e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500691605  1 MNSGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsgKSSADNLRSA 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-57 2.18e-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: 88.40  E-value: 2.18e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 500691605  4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTK 57
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 4.79e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 84.99  E-value: 4.79e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500691605   4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsgKSSADNLR 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK--GPQAANVT 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 6.76e-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: 76.87  E-value: 6.76e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500691605    4 GTVKWFNstKGFGFIQPDDGATDVFVHASAVErAGMRSLVEGQKVTFDIVRDTKSGKSSADNLR 67
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVV 62
cspE PRK09507
cold shock-like protein CspE;
4-64 3.54e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 75.46  E-value: 3.54e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500691605  4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsGKSSAD 64
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAK-GPSAAN 65
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-69 9.88e-30

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 99.50  E-value: 9.88e-30
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500691605  1 MNSGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsgKSSADNLRSA 69
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 4-57 2.18e-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: 88.40  E-value: 2.18e-25
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 500691605  4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTK 57
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
4-67 4.79e-24

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 84.99  E-value: 4.79e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500691605   4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsgKSSADNLR 67
Cdd:pfam00313  3 GTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTK--GPQAANVT 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 4-67 6.76e-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: 76.87  E-value: 6.76e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500691605    4 GTVKWFNstKGFGFIQPDDGATDVFVHASAVErAGMRSLVEGQKVTFDIVRDTKSGKSSADNLR 67
Cdd:smart00357  2 GVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPEGGEKPEAENVV 62
cspE PRK09507
cold shock-like protein CspE;
4-64 3.54e-20

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 75.46  E-value: 3.54e-20
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500691605  4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKsGKSSAD 64
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAK-GPSAAN 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-52 1.94e-18

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 71.16  E-value: 1.94e-18
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 500691605  3 SGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDI 52
Cdd:PRK10354  6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTI 55
PRK09937 PRK09937
cold shock-like protein CspD;
1-62 7.43e-18

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 69.76  E-value: 7.43e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500691605  1 MNSGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKSGKSS 62
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHAS 62
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-52 2.97e-17

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 68.25  E-value: 2.97e-17
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 500691605  3 SGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDI 52
Cdd:PRK09890  6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSI 55
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-62 3.08e-17

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 68.15  E-value: 3.08e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500691605  1 MNSGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIVRDTKSGKSS 62
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHAS 62
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-64 3.42e-16

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 65.47  E-value: 3.42e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500691605  4 GTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTFDIvRDTKSGKSSAD 64
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEI-QDGQKGPAAVN 65
VacB COG0557
Exoribonuclease R [Transcription];
13-60 1.46e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 43.17  E-value: 1.46e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 500691605  13 KGFGFIQPDDGATDVFVHASaveraGMRSLVEGQKVTFDIVRDTKSGK 60
Cdd:COG0557   79 DGFGFVIPDDGEEDIFIPPR-----ELNGALHGDRVLVRVTKEDRRGR 121
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-50 3.86e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 39.88  E-value: 3.86e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 500691605  3 SGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTF 50
Cdd:PRK15463  6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEF 53
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-50 1.04e-03

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 33.92  E-value: 1.04e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 500691605  3 SGTVKWFNSTKGFGFIQPDDGATDVFVHASAVERAGMRSLVEGQKVTF 50
Cdd:PRK15464  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEF 53
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 13-37 1.24e-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: 33.28  E-value: 1.24e-03
                         10        20
                 ....*....|....*....|....*
gi 500691605  13 KGFGFIQPDDGATDVFVHASAVERA 37
Cdd:pfam08206  8 KGFGFLIPDDEEDDIFIPPNQMKKA 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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