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Conserved domains on  [gi|397468003|ref|XP_003805687|]
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cold shock domain-containing protein E1 isoform X5 [Pan paniscus]

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;
155-217 2.18e-17

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.18e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 397468003  155 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 217
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
643-707 1.76e-14

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.42  E-value: 1.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 397468003  643 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 707
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 ...
 26-90 6.43e-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: 6.43e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 397468003   26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 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 ...
 490-551 6.75e-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: 6.75e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003  490 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 551
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 ...
 725-755 5.52e-12

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


:

Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 5.52e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 397468003  725 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 755
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 319-382 1.32e-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: 1.32e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003   319 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 382
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGlKSLREGDEVEFKVVSPE-GGEKPEAENVVKL 64
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
155-217 2.18e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.18e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 397468003  155 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 217
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
643-707 1.76e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.42  E-value: 1.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 397468003  643 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 707
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 156-217 2.96e-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: 2.96e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 397468003   156 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 217
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
26-90 6.43e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.43e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 397468003   26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 90
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
490-551 6.75e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.75e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003  490 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 551
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 27-90 7.49e-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: 7.49e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 397468003    27 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKI 90
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 490-550 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 397468003   490 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNK 550
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVK 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 155-216 3.58e-12

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 61.83  E-value: 3.58e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003 155 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 216
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 644-707 5.13e-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: 5.13e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003   644 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDG-IELQAGDEVEFSVILNQRTGKCSACNVWRV 707
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 ...
 725-755 5.52e-12

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


Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 5.52e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 397468003  725 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 755
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 319-382 1.32e-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: 1.32e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003   319 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 382
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 ...
 499-548 8.09e-11

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 57.97  E-value: 8.09e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 397468003 499 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 548
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
166-217 1.22e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.82  E-value: 1.22e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 397468003 166 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 217
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
499-548 7.60e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 7.60e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 397468003 499 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 548
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 ...
 37-89 1.12e-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: 1.12e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 397468003  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAVKLVK 89
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
328-365 2.25e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 42.61  E-value: 2.25e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 397468003  328 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVV 365
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CspC COG1278
Cold shock protein, CspA family [Transcription];
37-90 8.03e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 41.33  E-value: 8.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 397468003  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAVKLVKI 90
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 ...
 328-381 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 397468003 328 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 381
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 153-214 8.38e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003 153 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 214
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
328-367 4.35e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 36.33  E-value: 4.35e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 397468003 328 GFGFIKCVDRDVRMFFHFSEILDGNQLHIA--DEVEFTVVPD 367
Cdd:COG1278   14 GFGFITPDDGGEDVFVHISALQRSGFRTLRegQRVEFEVEQG 55
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
155-217 2.18e-17

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 2.18e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 397468003  155 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGDL-ETLQPGDDVEFTIKDRNGKEVATDVRLL 217
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
643-707 1.76e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 68.42  E-value: 1.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 397468003  643 RRATVECVKD--QFGFINYEVGDsKKLFFHVKEVQDGI--ELQAGDEVEFSVIlnQRTGKCSACNVWRV 707
Cdd:pfam00313   1 MTGTVKWFNAkkGFGFITPEDGD-KDVFVHFSAIQGDGfrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 156-217 2.96e-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: 2.96e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 397468003   156 QGVVCAMKEAFGFIERGDVVKEIFFHYSEFKGDLETLQPGDDVEFTI--KDRNGKEVATDVRLL 217
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVvsPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
26-90 6.43e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.43e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 397468003   26 ETGVIEKLLTS--YGFIQCSERQARLFFHCSQYNGNL-QDLKVGDDVEFEVSSdrRTGKPIAVKLVKI 90
Cdd:pfam00313   1 MTGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVE--GTKGPQAANVTKP 66
CSD pfam00313
'Cold-shock' DNA-binding domain;
490-551 6.75e-14

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 66.88  E-value: 6.75e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003  490 GYVATLKD--NFGFIETANHDKEIFFHYSEFSGDV-DSLELGDMVEYSLSKGkGNKVSAEKVNKT 551
Cdd:pfam00313   3 GTVKWFNAkkGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVVEG-TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 27-90 7.49e-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: 7.49e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 397468003    27 TGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVEFEVSSDRRTGKPIAVKLVKI 90
Cdd:smart00357   1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 490-550 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 397468003   490 GYVATLKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGN-KVSAEKVNK 550
Cdd:smart00357   2 GVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGeKPEAENVVK 63
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 155-216 3.58e-12

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 61.83  E-value: 3.58e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003 155 CQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRL 216
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 644-707 5.13e-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: 5.13e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003   644 RATVECVKDQFGFINYEVGDsKKLFFHVKEVQDG-IELQAGDEVEFSVILNQRTGKCSACNVWRV 707
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 ...
 725-755 5.52e-12

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


Pssm-ID: 463745  Cd Length: 33  Bit Score: 60.63  E-value: 5.52e-12
                          10        20        30
                  ....*....|....*....|....*....|.
gi 397468003  725 RLKNITLDDASAPRLMVLRQPRGPDNSMGFG 755
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 319-382 1.32e-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: 1.32e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003   319 MGVIAAMRDGFGFIKCVDRDVRMFFHFSEILDG-NQLHIADEVEFTVVPDMlSAQRNHAIRIKKL 382
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 ...
 499-548 8.09e-11

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 57.97  E-value: 8.09e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 397468003 499 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKGnKVSAEKV 548
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGDK-GPQAVNV 63
CspC COG1278
Cold shock protein, CspA family [Transcription];
166-217 1.22e-09

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 54.82  E-value: 1.22e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 397468003 166 FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDVRLL 217
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDKGPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
499-548 7.60e-07

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 47.11  E-value: 7.60e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 397468003 499 FGFIETANHDKEIFFHYSEFSGD-VDSLELGDMVEYSLSKGKgNKVSAEKV 548
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 ...
 37-89 1.12e-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: 1.12e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 397468003  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRrtGKPIAVKLVK 89
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFELEEGD--KGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
328-365 2.25e-05

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 42.61  E-value: 2.25e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 397468003  328 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVV 365
Cdd:pfam00313  13 GFGFITPEDGDKDVFVHFSAIQGDGFrsLQEGQKVEFEVV 52
CspC COG1278
Cold shock protein, CspA family [Transcription];
37-90 8.03e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 41.33  E-value: 8.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 397468003  37 YGFIQCSERQARLFFHCSQYNGN-LQDLKVGDDVEFEVSSDRRtgKPIAVKLVKI 90
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 ...
 328-381 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 397468003 328 GFGFIKCVDRDVRMFFHFSEILDGNQ--LHIADEVEFTVVPDmlsAQRNHAIRIKK 381
Cdd:cd04458   13 GFGFITPDDGGEDVFVHISALEGDGFrsLEEGDRVEFELEEG---DKGPQAVNVRL 65
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 153-214 8.38e-04

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 8.38e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 397468003 153 ARCQGVVCAMKEA--FGFIERGDVVKEIFFHYSEFKGD-LETLQPGDDVEFTIKDRNGKEVATDV 214
Cdd:PRK10943   2 AKIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgFKTLAEGQNVEFEIQDGQKGPAAVNV 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
328-367 4.35e-03

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 36.33  E-value: 4.35e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 397468003 328 GFGFIKCVDRDVRMFFHFSEILDGNQLHIA--DEVEFTVVPD 367
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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