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Conserved domains on  [gi|221330989|ref|NP_001137912|]
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upstream of N-ras, isoform B [Drosophila melanogaster]

Protein Classification

CSP_CDS and CSP domain-containing protein( domain architecture ID 11266085)

CSP_CDS and CSP domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 942-1006 1.02e-10

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: 58.38  E-value: 1.02e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 221330989    942 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 1006
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 347-395 2.93e-10

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: 56.87  E-value: 2.93e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 221330989   347 RGVVCSMKES--FGFIERADVVKEIFFHFSEAEGNV--ELRPGDDVEFTIQTR 395
Cdd:pfam00313    2 TGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfrSLQEGQKVEFEVVEG 54
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.06e-10

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: 56.84  E-value: 3.06e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 221330989    188 TGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKI 251
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 537-604 3.02e-09

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: 54.14  E-value: 3.02e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 221330989    537 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 604
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEG----GEKPEAENVVKL 64
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 790-834 2.61e-06

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: 45.70  E-value: 2.61e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 221330989   790 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 834
Cdd:pfam00313   11 KKGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
 
Name Accession Description Interval E-value
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 942-1006 1.02e-10

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: 58.38  E-value: 1.02e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 221330989    942 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 1006
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
347-395 2.93e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.87  E-value: 2.93e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 221330989   347 RGVVCSMKES--FGFIERADVVKEIFFHFSEAEGNV--ELRPGDDVEFTIQTR 395
Cdd:pfam00313    2 TGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfrSLQEGQKVEFEVVEG 54
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.06e-10

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: 56.84  E-value: 3.06e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 221330989    188 TGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKI 251
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
187-251 5.02e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.48  E-value: 5.02e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 221330989   187 ETGIIEKLL--HSYGFIQCCERQARLFFHFSQFSGNI-DHLKIGDPVEFEMTydRRTGKPIASQVSKI 251
Cdd:pfam00313    1 MTGTVKWFNakKGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 347-393 1.34e-09

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: 54.91  E-value: 1.34e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 221330989    347 RGVVCSMKESFGFIERADVVKEIFFHFSEAEGNVE-LRPGDDVEFTIQ 393
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKsLREGDEVEFKVV 48
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 537-604 3.02e-09

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: 54.14  E-value: 3.02e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 221330989    537 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 604
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEG----GEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 346-393 2.19e-08

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: 51.81  E-value: 2.19e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 221330989  346 YRGVVCSMKES--FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQ 393
Cdd:cd04458     1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISalEGDGFRSLEEGDRVEFELE 52
CSD pfam00313
'Cold-shock' DNA-binding domain;
944-1006 1.17e-07

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 49.55  E-value: 1.17e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 221330989   944 TVDSIKGqFGFLNFEVEDgKKLFFHMSEVQGNTV-ALHPGDTVEFSVVtnQRNGKSSACNVLKI 1006
Cdd:pfam00313    7 WFNAKKG-FGFITPEDGD-KDVFVHFSAIQGDGFrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 537-602 5.99e-07

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: 47.57  E-value: 5.99e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330989  537 QGTIASLKE--GFGFLRCVERQARLFFHFTEVL-DTSREIDINDEVEFTVIQEPGlaynnsRLQAIRIK 602
Cdd:cd04458     2 TGTVKWFDDekGFGFITPDDGGEDVFVHISALEgDGFRSLEEGDRVEFELEEGDK------GPQAVNVR 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 198-250 2.10e-06

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: 46.03  E-value: 2.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 221330989  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEmtYDRRTGKPIASQVSK 250
Cdd:cd04458    14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFE--LEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
790-834 2.61e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.61e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 221330989   790 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 834
Cdd:pfam00313   11 KKGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-588 2.97e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.97e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 221330989   536 EQGTIASLKE--GFGFLRCVERQARLFFHFTEV-LDTSREIDINDEVEFTVIQEPG 588
Cdd:pfam00313    1 MTGTVKWFNAkkGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 790-831 3.23e-06

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: 45.65  E-value: 3.23e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 221330989  790 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 831
Cdd:cd04458    11 EKGFGFITPDDGGEDVFVHISALeGDGFRSLEEGDRVEFELEE 53
CspC COG1278
Cold shock protein, CspA family [Transcription];
357-394 3.46e-06

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 45.57  E-value: 3.46e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 221330989  357 FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQT 394
Cdd:COG1278    15 FGFITPDDGGEDVFVHISalQRSGFRTLREGQRVEFEVEQ 54
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 783-829 3.60e-06

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: 45.28  E-value: 3.60e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 221330989    783 RGFIAVMKENFGFIETLSHDEEVFFHFSNYMGNPNWLELGQEVEYTL 829
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKV 47
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-251 1.85e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 43.26  E-value: 1.85e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 221330989  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEMTYDRRtgKPIASQVSKI 251
Cdd:COG1278    15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
535-602 2.98e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.18  E-value: 2.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 221330989  535 REQGTIASLKE--GFGFLRCVERQARLFFHFTEVLDTS-REIDINDEVEFTVIQEPGlaynnsRLQAIRIK 602
Cdd:COG1278     1 MATGTVKWFNAekGFGFITPDDGGEDVFVHISALQRSGfRTLREGQRVEFEVEQGDK------GPQAVNVR 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
793-831 5.87e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.02  E-value: 5.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 221330989  793 FGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 831
Cdd:COG1278    15 FGFITPDDGGEDVFVHISALqRSGFRTLREGQRVEFEVEQ 54
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 345-393 1.13e-03

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 1.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 221330989  345 KYRGVVCSMKES--FGFIERADVVKEIFFHFSEAEGN--VELRPGDDVEFTIQ 393
Cdd:PRK10943    3 KIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgfKTLAEGQNVEFEIQ 55
 
Name Accession Description Interval E-value
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 942-1006 1.02e-10

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: 58.38  E-value: 1.02e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 221330989    942 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 1006
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
347-395 2.93e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.87  E-value: 2.93e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 221330989   347 RGVVCSMKES--FGFIERADVVKEIFFHFSEAEGNV--ELRPGDDVEFTIQTR 395
Cdd:pfam00313    2 TGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfrSLQEGQKVEFEVVEG 54
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.06e-10

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: 56.84  E-value: 3.06e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 221330989    188 TGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKI 251
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
187-251 5.02e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.48  E-value: 5.02e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 221330989   187 ETGIIEKLL--HSYGFIQCCERQARLFFHFSQFSGNI-DHLKIGDPVEFEMTydRRTGKPIASQVSKI 251
Cdd:pfam00313    1 MTGTVKWFNakKGFGFITPEDGDKDVFVHFSAIQGDGfRSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 347-393 1.34e-09

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: 54.91  E-value: 1.34e-09
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*...
gi 221330989    347 RGVVCSMKESFGFIERADVVKEIFFHFSEAEGNVE-LRPGDDVEFTIQ 393
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKsLREGDEVEFKVV 48
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 537-604 3.02e-09

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: 54.14  E-value: 3.02e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 221330989    537 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 604
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEG----GEKPEAENVVKL 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 346-393 2.19e-08

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: 51.81  E-value: 2.19e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 221330989  346 YRGVVCSMKES--FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQ 393
Cdd:cd04458     1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISalEGDGFRSLEEGDRVEFELE 52
CSD pfam00313
'Cold-shock' DNA-binding domain;
944-1006 1.17e-07

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 49.55  E-value: 1.17e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 221330989   944 TVDSIKGqFGFLNFEVEDgKKLFFHMSEVQGNTV-ALHPGDTVEFSVVtnQRNGKSSACNVLKI 1006
Cdd:pfam00313    7 WFNAKKG-FGFITPEDGD-KDVFVHFSAIQGDGFrSLQEGQKVEFEVV--EGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 537-602 5.99e-07

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: 47.57  E-value: 5.99e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 221330989  537 QGTIASLKE--GFGFLRCVERQARLFFHFTEVL-DTSREIDINDEVEFTVIQEPGlaynnsRLQAIRIK 602
Cdd:cd04458     2 TGTVKWFDDekGFGFITPDDGGEDVFVHISALEgDGFRSLEEGDRVEFELEEGDK------GPQAVNVR 64
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 198-250 2.10e-06

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: 46.03  E-value: 2.10e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 221330989  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEmtYDRRTGKPIASQVSK 250
Cdd:cd04458    14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFE--LEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
790-834 2.61e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.61e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 221330989   790 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 834
Cdd:pfam00313   11 KKGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
536-588 2.97e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.97e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 221330989   536 EQGTIASLKE--GFGFLRCVERQARLFFHFTEV-LDTSREIDINDEVEFTVIQEPG 588
Cdd:pfam00313    1 MTGTVKWFNAkkGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 790-831 3.23e-06

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: 45.65  E-value: 3.23e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 221330989  790 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 831
Cdd:cd04458    11 EKGFGFITPDDGGEDVFVHISALeGDGFRSLEEGDRVEFELEE 53
CspC COG1278
Cold shock protein, CspA family [Transcription];
357-394 3.46e-06

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 45.57  E-value: 3.46e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 221330989  357 FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQT 394
Cdd:COG1278    15 FGFITPDDGGEDVFVHISalQRSGFRTLREGQRVEFEVEQ 54
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 783-829 3.60e-06

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: 45.28  E-value: 3.60e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 221330989    783 RGFIAVMKENFGFIETLSHDEEVFFHFSNYMGNPNWLELGQEVEYTL 829
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKV 47
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-251 1.85e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 43.26  E-value: 1.85e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 221330989  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEMTYDRRtgKPIASQVSKI 251
Cdd:COG1278    15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
535-602 2.98e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 40.18  E-value: 2.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 221330989  535 REQGTIASLKE--GFGFLRCVERQARLFFHFTEVLDTS-REIDINDEVEFTVIQEPGlaynnsRLQAIRIK 602
Cdd:COG1278     1 MATGTVKWFNAekGFGFITPDDGGEDVFVHISALQRSGfRTLREGQRVEFEVEQGDK------GPQAVNVR 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
793-831 5.87e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.02  E-value: 5.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 221330989  793 FGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 831
Cdd:COG1278    15 FGFITPDDGGEDVFVHISALqRSGFRTLREGQRVEFEVEQ 54
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 345-393 1.13e-03

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 1.13e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 221330989  345 KYRGVVCSMKES--FGFIERADVVKEIFFHFSEAEGN--VELRPGDDVEFTIQ 393
Cdd:PRK10943    3 KIKGQVKWFNESkgFGFITPADGSKDVFVHFSAIQGNgfKTLAEGQNVEFEIQ 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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