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Conserved domains on  [gi|41055233|ref|NP_957385|]
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protein lin-28 homolog A [Danio rerio]

Protein Classification

CSP_CDS and AIR1 domain-containing protein( domain architecture ID 12938576)

CSP_CDS and AIR1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 36-105 1.48e-19

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: 78.39  E-value: 1.48e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055233  36 GVCKWFNVRMGFGFLSMTHREGicldspvDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVTG 105
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGE-------DVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 119-172 5.94e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


The actual alignment was detected with superfamily member COG5082:

Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 36.37  E-value: 5.94e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 41055233 119 KGTQKRRSKGDRCFNCGGPNHHAKECqlpPQPKKCHFCQSISHMVANCPIKAQQ 172
Cdd:COG5082  69 NGHLRRDCPHSICYNCSWDGHRSNHC---PKPKKCYNCGETGHLSRDCNPSKDQ 119
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 36-105 1.48e-19

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: 78.39  E-value: 1.48e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055233  36 GVCKWFNVRMGFGFLSMTHREGicldspvDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVTG 105
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGE-------DVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
36-106 5.08e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 5.08e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41055233    36 GVCKWFNVRMGFGFLsmthregICLDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVTGP 106
Cdd:pfam00313   3 GTVKWFNAKKGFGFI-------TPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
36-104 2.67e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.83  E-value: 2.67e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055233  36 GVCKWFNVRMGFGFLSmthregiCLDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:COG1278   4 GTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
35-104 7.26e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 58.45  E-value: 7.26e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055233   35 SGVCKWFNVRMGFGFLSMThregiclDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPD-------DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 36-106 6.66e-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: 52.99  E-value: 6.66e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055233     36 GVCKWFNvrMGFGFLsmthregICLDSPVDVFVHQSKLHMeGFRSLKEGEAVEF--TFKRSSKGLESLQVTGP 106
Cdd:smart00357   2 GVVKWFN--KGFGFI-------RPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 119-172 5.94e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 36.37  E-value: 5.94e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 41055233 119 KGTQKRRSKGDRCFNCGGPNHHAKECqlpPQPKKCHFCQSISHMVANCPIKAQQ 172
Cdd:COG5082  69 NGHLRRDCPHSICYNCSWDGHRSNHC---PKPKKCYNCGETGHLSRDCNPSKDQ 119
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 126-167 7.08e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 35.55  E-value: 7.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 41055233  126 SKGDRCFNCGGPNHHAKEC---QLPPQPKKCHFCQSISHMVANCP 167
Cdd:PTZ00368  25 AKARPCYKCGEPGHLSRECpsaPGGRGERSCYNCGKTGHLSRECP 69
 
Name Accession Description Interval E-value
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 36-105 1.48e-19

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: 78.39  E-value: 1.48e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055233  36 GVCKWFNVRMGFGFLSMTHREGicldspvDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVTG 105
Cdd:cd04458   3 GTVKWFDDEKGFGFITPDDGGE-------DVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
36-106 5.08e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 5.08e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 41055233    36 GVCKWFNVRMGFGFLsmthregICLDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVTGP 106
Cdd:pfam00313   3 GTVKWFNAKKGFGFI-------TPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
36-104 2.67e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.83  E-value: 2.67e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055233  36 GVCKWFNVRMGFGFLSmthregiCLDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:COG1278   4 GTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
35-104 7.26e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 58.45  E-value: 7.26e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 41055233   35 SGVCKWFNVRMGFGFLSMThregiclDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:PRK10354   6 TGIVKWFNADKGFGFITPD-------DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
cspE PRK09507
cold shock-like protein CspE;
36-104 4.06e-11

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 56.58  E-value: 4.06e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055233   36 GVCKWFNVRMGFGFLSMThregiclDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:PRK09507   6 GNVKWFNESKGFGFITPE-------DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 36-106 6.66e-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: 52.99  E-value: 6.66e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055233     36 GVCKWFNvrMGFGFLsmthregICLDSPVDVFVHQSKLHMeGFRSLKEGEAVEF--TFKRSSKGLESLQVTGP 106
Cdd:smart00357   2 GVVKWFN--KGFGFI-------RPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 36-104 2.84e-09

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 51.61  E-value: 2.84e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 41055233   36 GVCKWFNVRMGFGFLSMThregiclDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKGLESLQVT 104
Cdd:PRK10943   6 GQVKWFNESKGFGFITPA-------DGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
36-97 9.94e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 50.11  E-value: 9.94e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055233   36 GVCKWFNVRMGFGFlsmthregICLDSP-VDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKG 97
Cdd:PRK09937   4 GTVKWFNNAKGFGF--------ICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG 58
PRK09890 PRK09890
cold shock protein CspG; Provisional
 35-97 1.25e-08

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 49.76  E-value: 1.25e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 41055233   35 SGVCKWFNVRMGFGFLSMThregiclDSPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKG 97
Cdd:PRK09890   6 TGLVKWFNADKGFGFITPD-------DGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG 61
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 35-97 3.49e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 48.89  E-value: 3.49e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 41055233   35 SGVCKWFNVRMGFGFlsmthregICLDSP-VDVFVHQSKLHMEGFRSLKEGEAVEFTFKRSSKG 97
Cdd:PRK14998   3 TGTVKWFNNAKGFGF--------ICPEGGgEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG 58
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 119-172 5.94e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 36.37  E-value: 5.94e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 41055233 119 KGTQKRRSKGDRCFNCGGPNHHAKECqlpPQPKKCHFCQSISHMVANCPIKAQQ 172
Cdd:COG5082  69 NGHLRRDCPHSICYNCSWDGHRSNHC---PKPKKCYNCGETGHLSRDCNPSKDQ 119
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 126-167 7.08e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 35.55  E-value: 7.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 41055233  126 SKGDRCFNCGGPNHHAKEC---QLPPQPKKCHFCQSISHMVANCP 167
Cdd:PTZ00368  25 AKARPCYKCGEPGHLSRECpsaPGGRGERSCYNCGKTGHLSRECP 69
 
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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