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Conserved domains on  [gi|194473720|ref|NP_001123995|]
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cold shock domain-containing protein E1 isoform 3 [Homo sapiens]

Protein Classification

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 2.30e-17

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.30e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194473720  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.78e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.78e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473720  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 753
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 ...
 72-136 6.69e-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: 6.69e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194473720   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 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 ...
 536-597 7.03e-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: 7.03e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 597
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 771-801 6.50e-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: 6.50e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 194473720  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 1.29e-11

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: 60.31  E-value: 1.29e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720   365 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
201-263 2.30e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.30e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194473720  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.78e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.78e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473720  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--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 2.88e-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: 68.01  E-value: 2.88e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473720   202 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 263
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
72-136 6.69e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.69e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194473720   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 136
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-597 7.03e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 7.03e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 597
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 73-136 7.35e-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: 7.35e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473720    73 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKI 136
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 536-596 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 194473720   536 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNK 596
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVK 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 201-262 3.48e-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: 3.48e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720 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 ...
 690-753 5.04e-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: 61.46  E-value: 5.04e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720   690 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDG-IELQAGDEVEFSVILNQRTGKCSACNVWRV 753
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 ...
 771-801 6.50e-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: 6.50e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 194473720  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 1.29e-11

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: 60.31  E-value: 1.29e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720   365 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
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 ...
 545-594 7.94e-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: 7.94e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 194473720 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 594
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
212-263 1.25e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.82  E-value: 1.25e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 194473720 212 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
545-594 7.84e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 7.84e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 194473720 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 594
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 83-135 1.11e-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: 43.72  E-value: 1.11e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 194473720  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAVKLVK 135
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
374-411 2.37e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 42.61  E-value: 2.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 194473720  374 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVV 411
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CspC COG1278
Cold shock protein, CspA family [Transcription];
83-136 8.12e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 41.33  E-value: 8.12e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 194473720  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAVKLVKI 136
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 374-427 9.91e-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: 41.03  E-value: 9.91e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 194473720 374 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 427
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 199-260 8.90e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720 199 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 260
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
374-413 4.39e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 36.33  E-value: 4.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 194473720 374 GFGFIKCVDRDVRMFFHFSEILDGNQLHIA--DEVEFTVVPD 413
Cdd:COG1278   14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
201-263 2.30e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.30e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194473720  201 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
689-753 1.78e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.81  E-value: 1.78e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194473720  689 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--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 2.88e-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: 68.01  E-value: 2.88e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473720   202 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 263
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
72-136 6.69e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.69e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194473720   72 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 136
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-597 7.03e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 7.03e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720  536 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 597
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 73-136 7.35e-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: 7.35e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194473720    73 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKI 136
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 536-596 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 194473720   536 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNK 596
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVK 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 201-262 3.48e-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: 3.48e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720 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 ...
 690-753 5.04e-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: 61.46  E-value: 5.04e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720   690 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDG-IELQAGDEVEFSVILNQRTGKCSACNVWRV 753
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 ...
 771-801 6.50e-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: 6.50e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 194473720  771 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 801
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 365-428 1.29e-11

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: 60.31  E-value: 1.29e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720   365 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 428
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 ...
 545-594 7.94e-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: 7.94e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 194473720 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 594
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
212-263 1.25e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.82  E-value: 1.25e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 194473720 212 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 263
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
545-594 7.84e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 7.84e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 194473720 545 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 594
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGD-KGPQAVNV 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 83-135 1.11e-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: 43.72  E-value: 1.11e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 194473720  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAVKLVK 135
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
374-411 2.37e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 42.61  E-value: 2.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 194473720  374 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVV 411
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CspC COG1278
Cold shock protein, CspA family [Transcription];
83-136 8.12e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 41.33  E-value: 8.12e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 194473720  83 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAVKLVKI 136
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 374-427 9.91e-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: 41.03  E-value: 9.91e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 194473720 374 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 427
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 199-260 8.90e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.90e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194473720 199 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 260
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
374-413 4.39e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 36.33  E-value: 4.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 194473720 374 GFGFIKCVDRDVRMFFHFSEILDGNQLHIA--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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