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Conserved domains on  [gi|490278429|ref|WP_004174375|]
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MULTISPECIES: cold-shock protein [Nitrosomonadaceae]

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 4.92e-39

Cold shock protein, CspA family [Transcription];


:

Pssm-ID: 440889  Cd Length: 67  Bit Score: 123.00  E-value: 4.92e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490278429  1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQSA 67
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 4.92e-39

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 123.00  E-value: 4.92e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490278429  1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQSA 67
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-65 1.54e-34

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 111.57  E-value: 1.54e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429   2 ATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQ 65
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVT 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-65 2.21e-33

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: 108.43  E-value: 2.21e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQ 65
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVR 64
cspD TIGR02381
cold shock domain protein CspD; This model represents what appears to be a phylogenetically ...
 1-64 1.34e-31

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: 104.16  E-value: 1.34e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429   1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:TIGR02381  1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHI 64
cspE PRK09507
cold shock-like protein CspE;
4-66 2.06e-27

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 93.56  E-value: 2.06e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490278429  4 GTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQS 66
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIA 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-65 7.18e-22

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: 79.57  E-value: 7.18e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490278429    3 TGTVKWFNdsKGFGFITPDDGSEDLFAHFSAINMsGFKTLKEGQKVSFEVT--QGPKGKQASNIQ 65
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
 
Name Accession Description Interval E-value
CspC COG1278
Cold shock protein, CspA family [Transcription];
1-67 4.92e-39

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 123.00  E-value: 4.92e-39
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490278429  1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQSA 67
Cdd:COG1278   1 MATGTVKWFNAEKGFGFITPDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CSD pfam00313
'Cold-shock' DNA-binding domain;
2-65 1.54e-34

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 111.57  E-value: 1.54e-34
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429   2 ATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQ 65
Cdd:pfam00313  1 MTGTVKWFNAKKGFGFITPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVT 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 3-65 2.21e-33

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: 108.43  E-value: 2.21e-33
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQ 65
Cdd:cd04458   2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVR 64
cspD TIGR02381
cold shock domain protein CspD; This model represents what appears to be a phylogenetically ...
 1-64 1.34e-31

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: 104.16  E-value: 1.34e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429   1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:TIGR02381  1 MAIGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGPKGAHATHI 64
cspE PRK09507
cold shock-like protein CspE;
4-66 2.06e-27

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 93.56  E-value: 2.06e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490278429  4 GTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQS 66
Cdd:PRK09507  6 GNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVIA 68
PRK09937 PRK09937
cold shock-like protein CspD;
1-64 2.33e-27

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 93.64  E-value: 2.33e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429  1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:PRK09937  1 MEKGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKGNHASVI 64
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 1-64 7.78e-27

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 92.42  E-value: 7.78e-27
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429  1 MATGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:PRK14998  1 METGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKGNHASVI 64
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
3-66 3.80e-25

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 88.11  E-value: 3.80e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQS 66
Cdd:PRK10354  6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVTS 69
PRK09890 PRK09890
cold shock protein CspG; Provisional
 3-64 6.38e-24

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 84.82  E-value: 6.38e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:PRK09890  6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRGPAAANV 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 3-65 7.18e-22

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: 79.57  E-value: 7.18e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490278429    3 TGTVKWFNdsKGFGFITPDDGSEDLFAHFSAINMsGFKTLKEGQKVSFEVT--QGPKGKQASNIQ 65
Cdd:smart00357  1 TGVVKWFN--KGFGFIRPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFKVVspEGGEKPEAENVV 62
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 4-66 2.46e-21

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 78.19  E-value: 2.46e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490278429  4 GTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNIQS 66
Cdd:PRK10943  6 GQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVTA 68
PRK15463 PRK15463
cold shock-like protein CspF; Provisional
 3-64 2.09e-10

cold shock-like protein CspF; Provisional


Pssm-ID: 185360  Cd Length: 70  Bit Score: 50.67  E-value: 2.09e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:PRK15463  6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRDAEELTTGLRVEFCRINGLRGPTAANV 67
PRK15464 PRK15464
cold shock-like protein CspH; Provisional
 3-64 9.16e-07

cold shock-like protein CspH; Provisional


Pssm-ID: 185361  Cd Length: 70  Bit Score: 41.62  E-value: 9.16e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490278429  3 TGTVKWFNDSKGFGFITPDDGSEDLFAHFSAINMSGFKTLKEGQKVSFEVTQGPKGKQASNI 64
Cdd:PRK15464  6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAANV 67
VacB COG0557
Exoribonuclease R [Transcription];
11-28 1.74e-04

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 37.39  E-value: 1.74e-04
                         10
                 ....*....|....*...
gi 490278429  11 DSKGFGFITPDDGSEDLF 28
Cdd:COG0557   77 HRDGFGFVIPDDGEEDIF 94
OB_RNB pfam08206
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ...
 12-36 3.29e-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: 3.29e-03
                         10        20
                 ....*....|....*....|....*
gi 490278429  12 SKGFGFITPDDGSEDLFAHFSAINM 36
Cdd:pfam08206  7 KKGFGFLIPDDEEDDIFIPPNQMKK 31
CSD2 pfam17876
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ...
 17-61 4.52e-03

Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.


Pssm-ID: 465546 [Multi-domain]  Cd Length: 74  Bit Score: 31.98  E-value: 4.52e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 490278429  17 FITPDDG--SEDLFahfsaINMSGFKTLKEGQKVSFEVTQGPKGKQA 61
Cdd:pfam17876  1 FVVPDDKriPQDIF-----IPKEDLKGAKDGDKVVVEITEYPDGKNP 42
 
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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