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Conserved domains on  [gi|24660935|ref|NP_648226|]
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upstream of N-ras, isoform A [Drosophila melanogaster]

Protein Classification

S1 RNA-binding domain-containing protein; eukaryotic translation initiation factor 1A( domain architecture ID 11266078)

S1 RNA-binding domain-containing protein similar to Staphylococcus aureus conserved virulence factor B (CvfB), which helps regulate proteins of the agr locus and facilitates production of factors thru an agr-independent pathway| eukaryotic translation initiation factor 1A (eIF1A) may be required for maximal rate of protein biosynthesis; it enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits

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 ...
 347-414 2.07e-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: 2.07e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24660935     347 RGVVCSMKESFGFIERADVVKEIFFHFSEAEGNVE-LRPGDDVEFTIQTRSSasvppQGREFACNITRL 414
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKsLREGDEVEFKVVSPEG-----GEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 924-988 1.07e-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: 57.99  E-value: 1.07e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24660935     924 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 988
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.10e-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: 3.10e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24660935     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 ...
 519-586 3.21e-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: 53.76  E-value: 3.21e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660935     519 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 586
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 ...
 772-816 2.59e-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: 2.59e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 24660935    772 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 816
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 ...
 347-414 2.07e-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: 2.07e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24660935     347 RGVVCSMKESFGFIERADVVKEIFFHFSEAEGNVE-LRPGDDVEFTIQTRSSasvppQGREFACNITRL 414
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKsLREGDEVEFKVVSPEG-----GEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
347-414 5.80e-11

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 58.79  E-value: 5.80e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24660935    347 RGVVCSMKES--FGFIERADVVKEIFFHFSEAEGNV--ELRPGDDVEFTIQTRssasvppQGREFACNITRL 414
Cdd:pfam00313    2 TGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfrSLQEGQKVEFEVVEG-------TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 924-988 1.07e-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: 57.99  E-value: 1.07e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24660935     924 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 988
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.10e-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: 3.10e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24660935     188 TGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKI 251
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
187-251 5.18e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.10  E-value: 5.18e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660935    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 ...
 519-586 3.21e-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: 53.76  E-value: 3.21e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660935     519 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 586
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 2.59e-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: 51.43  E-value: 2.59e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24660935  346 YRGVVCSMKES--FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQ 393
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISalEGDGFRSLEEGDRVEFELE 52
CSD pfam00313
'Cold-shock' DNA-binding domain;
926-988 1.22e-07

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 49.55  E-value: 1.22e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24660935    926 TVDSIKGqFGFLNFEVEDgKKLFFHMSEVQGNTV-ALHPGDTVEFSVVtnQRNGKSSACNVLKI 988
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 ...
 519-584 7.02e-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: 47.19  E-value: 7.02e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24660935  519 QGTIASLKE--GFGFLRCVERQARLFFHFTEVL-DTSREIDINDEVEFTVIQEPGlaynnsRLQAIRIK 584
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 2.39e-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: 2.39e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24660935  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEmtYDRRTGKPIASQVSK 250
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFE--LEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
772-816 2.59e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.59e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 24660935    772 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 816
Cdd:pfam00313   11 KKGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
518-570 3.03e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 3.03e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 24660935    518 EQGTIASLKE--GFGFLRCVERQARLFFHFTEV-LDTSREIDINDEVEFTVIQEPG 570
Cdd:pfam00313    1 MTGTVKWFNAkkGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 765-811 3.64e-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: 3.64e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 24660935     765 RGFIAVMKENFGFIETLSHDEEVFFHFSNYMGNPNWLELGQEVEYTL 811
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKV 47
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 772-813 3.68e-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: 45.26  E-value: 3.68e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 24660935  772 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 813
Cdd:cd04458   11 EKGFGFITPDDGGEDVFVHISALeGDGFRSLEEGDRVEFELEE 53
CspC COG1278
Cold shock protein, CspA family [Transcription];
357-394 3.71e-06

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 45.19  E-value: 3.71e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 24660935  357 FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQT 394
Cdd:COG1278   15 FGFITPDDGGEDVFVHISalQRSGFRTLREGQRVEFEVEQ 54
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-251 1.99e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 43.26  E-value: 1.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24660935  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEMTYDRRtgKPIASQVSKI 251
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
517-584 3.17e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.79  E-value: 3.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24660935  517 REQGTIASLKE--GFGFLRCVERQARLFFHFTEVLDTS-REIDINDEVEFTVIQEPGlaynnsRLQAIRIK 584
Cdd:COG1278    1 MATGTVKWFNAekGFGFITPDDGGEDVFVHISALQRSGfRTLREGQRVEFEVEQGDK------GPQAVNVR 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
775-813 6.05e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.02  E-value: 6.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 24660935  775 FGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 813
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALqRSGFRTLREGQRVEFEVEQ 54
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 345-393 1.09e-03

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 1.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 24660935   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 ...
 347-414 2.07e-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: 2.07e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24660935     347 RGVVCSMKESFGFIERADVVKEIFFHFSEAEGNVE-LRPGDDVEFTIQTRSSasvppQGREFACNITRL 414
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKsLREGDEVEFKVVSPEG-----GEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
347-414 5.80e-11

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 58.79  E-value: 5.80e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24660935    347 RGVVCSMKES--FGFIERADVVKEIFFHFSEAEGNV--ELRPGDDVEFTIQTRssasvppQGREFACNITRL 414
Cdd:pfam00313    2 TGTVKWFNAKkgFGFITPEDGDKDVFVHFSAIQGDGfrSLQEGQKVEFEVVEG-------TKGPQAANVTKP 66
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 924-988 1.07e-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: 57.99  E-value: 1.07e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24660935     924 RATVDSIKGQFGFLnfEVEDGKK-LFFHMSEVQGNTVALHPGDTVEFSVVTNQRNGKSSACNVLKI 988
Cdd:smart00357    1 TGVVKWFNKGFGFI--RPDDGGKdVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 188-251 3.10e-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: 3.10e-10
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24660935     188 TGIIEKLLHSYGFIQCCERQARLFFHFSQFSGNIDHLKIGDPVEFEMTYDRRTGKPIASQVSKI 251
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
CSD pfam00313
'Cold-shock' DNA-binding domain;
187-251 5.18e-10

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 56.10  E-value: 5.18e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660935    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 ...
 519-586 3.21e-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: 53.76  E-value: 3.21e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24660935     519 QGTIASLKEGFGFLRCVERQARLFFHFTEVLDTSREIDINDEVEFTVIQEPGlaynNSRLQAIRIKHL 586
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 2.59e-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: 51.43  E-value: 2.59e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24660935  346 YRGVVCSMKES--FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQ 393
Cdd:cd04458    1 VTGTVKWFDDEkgFGFITPDDGGEDVFVHISalEGDGFRSLEEGDRVEFELE 52
CSD pfam00313
'Cold-shock' DNA-binding domain;
926-988 1.22e-07

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 49.55  E-value: 1.22e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24660935    926 TVDSIKGqFGFLNFEVEDgKKLFFHMSEVQGNTV-ALHPGDTVEFSVVtnQRNGKSSACNVLKI 988
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 ...
 519-584 7.02e-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: 47.19  E-value: 7.02e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24660935  519 QGTIASLKE--GFGFLRCVERQARLFFHFTEVL-DTSREIDINDEVEFTVIQEPGlaynnsRLQAIRIK 584
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 2.39e-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: 2.39e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24660935  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEmtYDRRTGKPIASQVSK 250
Cdd:cd04458   14 FGFITPDDGGEDVFVHISALEGDgFRSLEEGDRVEFE--LEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
772-816 2.59e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 2.59e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 24660935    772 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLARNGN 816
Cdd:pfam00313   11 KKGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSD pfam00313
'Cold-shock' DNA-binding domain;
518-570 3.03e-06

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 45.70  E-value: 3.03e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 24660935    518 EQGTIASLKE--GFGFLRCVERQARLFFHFTEV-LDTSREIDINDEVEFTVIQEPG 570
Cdd:pfam00313    1 MTGTVKWFNAkkGFGFITPEDGDKDVFVHFSAIqGDGFRSLQEGQKVEFEVVEGTK 56
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 765-811 3.64e-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: 3.64e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 24660935     765 RGFIAVMKENFGFIETLSHDEEVFFHFSNYMGNPNWLELGQEVEYTL 811
Cdd:smart00357    1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKV 47
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 772-813 3.68e-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: 45.26  E-value: 3.68e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 24660935  772 KENFGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 813
Cdd:cd04458   11 EKGFGFITPDDGGEDVFVHISALeGDGFRSLEEGDRVEFELEE 53
CspC COG1278
Cold shock protein, CspA family [Transcription];
357-394 3.71e-06

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 45.19  E-value: 3.71e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 24660935  357 FGFIERADVVKEIFFHFS--EAEGNVELRPGDDVEFTIQT 394
Cdd:COG1278   15 FGFITPDDGGEDVFVHISalQRSGFRTLREGQRVEFEVEQ 54
CspC COG1278
Cold shock protein, CspA family [Transcription];
198-251 1.99e-05

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 43.26  E-value: 1.99e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24660935  198 YGFIQCCERQARLFFHFSQFSGN-IDHLKIGDPVEFEMTYDRRtgKPIASQVSKI 251
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALQRSgFRTLREGQRVEFEVEQGDK--GPQAVNVRVL 67
CspC COG1278
Cold shock protein, CspA family [Transcription];
517-584 3.17e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.79  E-value: 3.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24660935  517 REQGTIASLKE--GFGFLRCVERQARLFFHFTEVLDTS-REIDINDEVEFTVIQEPGlaynnsRLQAIRIK 584
Cdd:COG1278    1 MATGTVKWFNAekGFGFITPDDGGEDVFVHISALQRSGfRTLREGQRVEFEVEQGDK------GPQAVNVR 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
775-813 6.05e-04

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 39.02  E-value: 6.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 24660935  775 FGFIETLSHDEEVFFHFSNY-MGNPNWLELGQEVEYTLAR 813
Cdd:COG1278   15 FGFITPDDGGEDVFVHISALqRSGFRTLREGQRVEFEVEQ 54
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 345-393 1.09e-03

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 38.51  E-value: 1.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 24660935   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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