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Conserved domains on  [gi|500670548|ref|WP_011970815|]
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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];
1-67 1.11e-25

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 89.10  E-value: 1.11e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500670548  1 MATGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENVSAL 67
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGfrTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 1.11e-25

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 89.10  E-value: 1.11e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500670548  1 MATGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENVSAL 67
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 ...
 3-64 2.41e-22

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: 80.70  E-value: 2.41e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENV 64
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGfrSLEEGDRVEFELEEGDK--GPQAVNV 63
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-67 3.06e-18

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 70.35  E-value: 3.06e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500670548   2 ATGTVKFFAQDKGFGFITPDSGGPDVFVHISAL---GFAgSLQDGQKVSYELGQdrKTGKSKAENVSAL 67
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIqgdGFR-SLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-67 5.48e-15

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: 61.85  E-value: 5.48e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500670548    3 TGTVKFFaqDKGFGFITPDSGGPDVFVHISAL-GFAGSLQDGQKVSYELGQDRKTGKSKAENVSAL 67
Cdd:smart00357  1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIqGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-67 4.12e-13

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 57.68  E-value: 4.12e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENVSAL 67
Cdd:PRK10354  6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGykSLDEGQKVSFTIESGAK--GPAAGNVTSL 70
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 1.11e-25

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 89.10  E-value: 1.11e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500670548  1 MATGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENVSAL 67
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 ...
 3-64 2.41e-22

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: 80.70  E-value: 2.41e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENV 64
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGfrSLEEGDRVEFELEEGDK--GPQAVNV 63
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-67 3.06e-18

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 70.35  E-value: 3.06e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500670548   2 ATGTVKFFAQDKGFGFITPDSGGPDVFVHISAL---GFAgSLQDGQKVSYELGQdrKTGKSKAENVSAL 67
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIqgdGFR-SLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-67 5.48e-15

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: 61.85  E-value: 5.48e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500670548    3 TGTVKFFaqDKGFGFITPDSGGPDVFVHISAL-GFAGSLQDGQKVSYELGQDRKTGKSKAENVSAL 67
Cdd:smart00357  1 TGVVKWF--NKGFGFIRPDDGGKDVFVHPSQIqGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-67 4.12e-13

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 57.68  E-value: 4.12e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtgKSKAENVSAL 67
Cdd:PRK10354  6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGykSLDEGQKVSFTIESGAK--GPAAGNVTSL 70
cspE PRK09507
cold shock-like protein CspE;
4-67 1.26e-12

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 56.20  E-value: 1.26e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500670548  4 GTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRKtGKSkAENVSAL 67
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGfkTLAEGQRVEFEITNGAK-GPS-AANVIAL 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-55 4.47e-12

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 54.77  E-value: 4.47e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRK 55
Cdd:PRK09890  6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEfrTLNENQKVEFSIEQGQR 60
PRK09937 PRK09937
cold shock-like protein CspD;
1-55 5.06e-11

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 52.43  E-value: 5.06e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 500670548  1 MATGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRK 55
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGyrTLKAGQSVQFDVHQGPK 57
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-55 8.73e-11

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 51.59  E-value: 8.73e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 500670548  1 MATGTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELGQDRK 55
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGyrTLKAGQSVRFDVHQGPK 57
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-67 1.97e-09

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 48.14  E-value: 1.97e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500670548  4 GTVKFFAQDKGFGFITPDSGGPDVFVHISALGFAG--SLQDGQKVSYELgQDRKTGKSkAENVSAL 67
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGfkTLAEGQNVEFEI-QDGQKGPA-AVNVTAI 69
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-34 4.14e-06

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 39.88  E-value: 4.14e-06
                        10        20        30
                ....*....|....*....|....*....|..
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISAL 34
Cdd:PRK15463  6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISAL 37
VacB COG0557
Exoribonuclease R [Transcription];
3-62 2.44e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 39.70  E-value: 2.44e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 500670548   3 TGTVKffAQDKGFGFITPDSGGPDVFVHISALGFAGslqDGQKVSYELGQDRKTGKSKAE 62
Cdd:COG0557   71 EGRVR--GHRDGFGFVIPDDGEEDIFIPPRELNGAL---HGDRVLVRVTKEDRRGRPEGR 125
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-34 5.55e-04

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 34.30  E-value: 5.55e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 500670548  3 TGTVKFFAQDKGFGFITPDSGGPDVFVHISAL 34
Cdd:PRK15464  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAF 37
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 4-37 5.99e-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: 34.05  E-value: 5.99e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 500670548   4 GTVKffAQDKGFGFITPDSGGPDVFVHISALGFA 37
Cdd:pfam08206  1 GTVR--GHKKGFGFLIPDDEEDDIFIPPNQMKKA 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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