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Conserved domains on  [gi|568922620|ref|XP_006501461|]
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cold shock domain-containing protein E1 isoform X2 [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

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List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
201-263 1.42e-17

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568922620  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.42e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.42e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568922620  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 753
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
72-136 3.35e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.35e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568922620   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 136
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 536-596 6.31e-14

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: 66.88  E-value: 6.31e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 596
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 3.03e-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: 62.23  E-value: 3.03e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620   365 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 771-801 7.31e-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: 60.25  E-value: 7.31e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 568922620  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
201-263 1.42e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568922620  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.42e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.42e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568922620  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 753
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 202-263 1.89e-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: 68.39  E-value: 1.89e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620   202 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 263
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
72-136 3.35e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.35e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568922620   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 136
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 73-136 5.27e-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: 67.24  E-value: 5.27e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620    73 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAIKLVKI 136
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-596 6.31e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.31e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 596
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 536-597 1.74e-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: 63.00  E-value: 1.74e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568922620   536 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 597
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 690-753 1.92e-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: 62.62  E-value: 1.92e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620   690 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 753
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGG-KDVFVHPSQIQGGLKsLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 201-262 2.43e-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: 62.60  E-value: 2.43e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620 201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 262
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 3.03e-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: 62.23  E-value: 3.03e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620   365 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 771-801 7.31e-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: 60.25  E-value: 7.31e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 568922620  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 545-594 5.53e-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: 58.74  E-value: 5.53e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568922620 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 594
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
212-263 9.78e-10

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 55.20  E-value: 9.78e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568922620 212 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
545-594 5.90e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.50  E-value: 5.90e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568922620 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 594
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
374-411 7.66e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 44.16  E-value: 7.66e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568922620  374 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 411
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 83-135 1.74e-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: 42.95  E-value: 1.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568922620  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAIKLVK 135
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 374-427 4.14e-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: 42.18  E-value: 4.14e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 568922620 374 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 427
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
83-136 1.39e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.56  E-value: 1.39e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 568922620  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAIKLVKI 136
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 199-260 8.47e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620 199 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 260
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
374-413 8.84e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 38.25  E-value: 8.84e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568922620 374 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 413
Cdd:COG1278   14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
201-263 1.42e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568922620  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.42e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.42e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568922620  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 753
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 202-263 1.89e-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: 68.39  E-value: 1.89e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620   202 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 263
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
72-136 3.35e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.35e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568922620   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 136
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 73-136 5.27e-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: 67.24  E-value: 5.27e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620    73 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAIKLVKI 136
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-596 6.31e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.31e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568922620  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 596
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 536-597 1.74e-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: 63.00  E-value: 1.74e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568922620   536 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 597
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 690-753 1.92e-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: 62.62  E-value: 1.92e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620   690 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 753
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGG-KDVFVHPSQIQGGLKsLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 201-262 2.43e-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: 62.60  E-value: 2.43e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620 201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 262
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 3.03e-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: 62.23  E-value: 3.03e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620   365 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 771-801 7.31e-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: 60.25  E-value: 7.31e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 568922620  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 545-594 5.53e-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: 58.74  E-value: 5.53e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568922620 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 594
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
212-263 9.78e-10

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 55.20  E-value: 9.78e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 568922620 212 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
545-594 5.90e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.50  E-value: 5.90e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 568922620 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 594
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
374-411 7.66e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 44.16  E-value: 7.66e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568922620  374 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 411
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 83-135 1.74e-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: 42.95  E-value: 1.74e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568922620  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAIKLVK 135
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 374-427 4.14e-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: 42.18  E-value: 4.14e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 568922620 374 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 427
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
83-136 1.39e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.56  E-value: 1.39e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 568922620  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAIKLVKI 136
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 199-260 8.47e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568922620 199 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 260
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
374-413 8.84e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 38.25  E-value: 8.84e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 568922620 374 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 413
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.
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