NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|893550521|ref|NP_001297622|]
View 

cold shock domain-containing protein E1 isoform 3 [Mus musculus]

Protein Classification

cold shock domain-containing protein; S1 RNA-binding domain-containing protein( domain architecture ID 11092092)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation| S1 RNA-binding domain-containing protein similar to Staphylococcus aureus conserved virulence factor B (CvfB), which helps regulate proteins of the agr locus and facilitates production of factors thru an agr-independent pathway

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
56-118 2.80e-17

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.51  E-value: 2.80e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 893550521   56 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 118
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
544-608 2.93e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 2.93e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 893550521  544 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 608
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 391-451 1.18e-13

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 pfam00313:

Pssm-ID: 471952  Cd Length: 66  Bit Score: 66.11  E-value: 1.18e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 893550521  391 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 451
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 626-656 4.12e-12

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


:

Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 4.12e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 893550521  626 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 656
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 220-283 5.37e-12

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: 61.08  E-value: 5.37e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521   220 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 283
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
56-118 2.80e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.51  E-value: 2.80e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 893550521   56 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 118
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
544-608 2.93e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 2.93e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 893550521  544 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 608
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 57-118 3.55e-14

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: 67.62  E-value: 3.55e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 893550521    57 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 118
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
391-451 1.18e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.11  E-value: 1.18e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 893550521  391 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 451
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 391-452 3.17e-12

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: 3.17e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 893550521   391 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 452
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 545-608 3.39e-12

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: 3.39e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521   545 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 608
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGG-KDVFVHPSQIQGGLKsLREGDEVEFKVVSPEGGEKPEAENVVKL 64
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 626-656 4.12e-12

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 4.12e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 893550521  626 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 656
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 56-117 4.29e-12

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: 61.44  E-value: 4.29e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521  56 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 117
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 220-283 5.37e-12

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: 61.08  E-value: 5.37e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521   220 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 283
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 400-449 9.60e-11

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: 57.59  E-value: 9.60e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 893550521 400 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 449
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
67-118 1.47e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.43  E-value: 1.47e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 893550521  67 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 118
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
400-449 8.68e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 46.73  E-value: 8.68e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 893550521 400 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 449
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
229-266 1.00e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 43.38  E-value: 1.00e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 893550521  229 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 266
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 229-282 5.92e-05

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: 41.41  E-value: 5.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 893550521 229 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 282
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 65-115 8.34e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 893550521  65 EAFGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 115
Cdd:PRK10943  15 KGFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
229-268 1.15e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 37.87  E-value: 1.15e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 893550521 229 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 268
Cdd:COG1278   14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
56-118 2.80e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.51  E-value: 2.80e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 893550521   56 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 118
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
544-608 2.93e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 2.93e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 893550521  544 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 608
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 57-118 3.55e-14

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: 67.62  E-value: 3.55e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 893550521    57 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 118
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
391-451 1.18e-13

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.11  E-value: 1.18e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 893550521  391 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 451
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 391-452 3.17e-12

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: 3.17e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 893550521   391 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 452
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 545-608 3.39e-12

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: 3.39e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521   545 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 608
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGG-KDVFVHPSQIQGGLKsLREGDEVEFKVVSPEGGEKPEAENVVKL 64
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 626-656 4.12e-12

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 4.12e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 893550521  626 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 656
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 56-117 4.29e-12

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: 61.44  E-value: 4.29e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521  56 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 117
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 220-283 5.37e-12

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: 61.08  E-value: 5.37e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 893550521   220 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 283
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 400-449 9.60e-11

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: 57.59  E-value: 9.60e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 893550521 400 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 449
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
67-118 1.47e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.43  E-value: 1.47e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 893550521  67 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 118
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
400-449 8.68e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 46.73  E-value: 8.68e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 893550521 400 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 449
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
229-266 1.00e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 43.38  E-value: 1.00e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 893550521  229 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 266
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 229-282 5.92e-05

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: 41.41  E-value: 5.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 893550521 229 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 282
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 65-115 8.34e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 893550521  65 EAFGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 115
Cdd:PRK10943  15 KGFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
229-268 1.15e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 37.87  E-value: 1.15e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 893550521 229 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 268
Cdd:COG1278   14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH