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Conserved domains on  [gi|21450287|ref|NP_659150|]
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cold shock domain-containing protein E1 isoform 1 [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;
186-248 1.63e-17

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.63e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450287   186 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 248
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
674-738 1.66e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.66e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21450287   674 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 738
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
26-90 3.88e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.88e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21450287    26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 90
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 ...
 521-581 7.10e-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: 7.10e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287   521 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 581
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 350-413 3.44e-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: 3.44e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287    350 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 413
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 ...
 756-786 7.18e-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: 7.18e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 21450287   756 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 786
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
186-248 1.63e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.63e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450287   186 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 248
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
674-738 1.66e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.66e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21450287   674 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 738
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 187-248 2.24e-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: 2.24e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287    187 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 248
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
26-90 3.88e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.88e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21450287    26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 90
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 27-90 5.99e-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: 66.85  E-value: 5.99e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287     27 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAIKLVKI 90
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
521-581 7.10e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 7.10e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287   521 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 581
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 521-582 1.94e-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: 1.94e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21450287    521 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 582
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 675-738 2.22e-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: 2.22e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287    675 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 738
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 ...
 186-247 2.73e-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: 62.21  E-value: 2.73e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287 186 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 247
Cdd:cd04458   1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 350-413 3.44e-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: 3.44e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287    350 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 413
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 ...
 756-786 7.18e-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: 7.18e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 21450287   756 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 786
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 530-579 6.16e-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: 58.36  E-value: 6.16e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21450287 530 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 579
Cdd:cd04458  14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
197-248 1.03e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 55.20  E-value: 1.03e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 21450287 197 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 248
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
530-579 6.32e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 6.32e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21450287 530 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 579
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
359-396 8.13e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 44.16  E-value: 8.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 21450287   359 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 396
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 37-89 1.92e-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: 42.95  E-value: 1.92e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21450287  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAIKLVK 89
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 ...
 359-412 4.48e-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: 41.80  E-value: 4.48e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21450287 359 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 412
Cdd:cd04458  13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
37-90 1.46e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.56  E-value: 1.46e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 21450287  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAIKLVKI 90
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 184-245 8.31e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287  184 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 245
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
359-398 9.20e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 38.25  E-value: 9.20e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 21450287 359 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 398
Cdd:COG1278  14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
186-248 1.63e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 77.28  E-value: 1.63e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21450287   186 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 248
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
674-738 1.66e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.66e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21450287   674 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGV--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 738
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 187-248 2.24e-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: 2.24e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287    187 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 248
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
26-90 3.88e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 67.65  E-value: 3.88e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21450287    26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAIKLVKI 90
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 27-90 5.99e-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: 66.85  E-value: 5.99e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287     27 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAIKLVKI 90
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
521-581 7.10e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 7.10e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21450287   521 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNK 581
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTK 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 521-582 1.94e-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: 1.94e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21450287    521 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNKA 582
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 675-738 2.22e-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: 2.22e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287    675 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDGVE-LQAGDEVEFSVILNQRTGKCSACNVWRV 738
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 ...
 186-247 2.73e-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: 62.21  E-value: 2.73e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287 186 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 247
Cdd:cd04458   1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 350-413 3.44e-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: 3.44e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287    350 MGVIAAMRDGFGFIKCVDRDARMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 413
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 ...
 756-786 7.18e-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: 7.18e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 21450287   756 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 786
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 530-579 6.16e-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: 58.36  E-value: 6.16e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21450287 530 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 579
Cdd:cd04458  14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
197-248 1.03e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 55.20  E-value: 1.03e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 21450287 197 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 248
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
530-579 6.32e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 6.32e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 21450287 530 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 579
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
359-396 8.13e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 44.16  E-value: 8.13e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 21450287   359 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVV 396
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 37-89 1.92e-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: 42.95  E-value: 1.92e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21450287  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAIKLVK 89
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 ...
 359-412 4.48e-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: 41.80  E-value: 4.48e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21450287 359 GFGFIKCVDRDARMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 412
Cdd:cd04458  13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
37-90 1.46e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.56  E-value: 1.46e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 21450287  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAIKLVKI 90
Cdd:COG1278  15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 184-245 8.31e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21450287  184 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 245
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
359-398 9.20e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 38.25  E-value: 9.20e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 21450287 359 GFGFIKCVDRDARMFFHFSEILDGNQLHIA--DEVEFTVVPD 398
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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