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Conserved domains on  [gi|78042603|ref|NP_001026942|]
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protein lin-28 homolog B [Mus musculus]

Protein Classification

CSP_CDS and PTZ00368 domain-containing protein( domain architecture ID 12938555)

CSP_CDS and PTZ00368 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 ...
 29-99 5.13e-21

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: 83.78  E-value: 5.13e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 78042603  29 TGHCKWFNVRMGFGFIsmisregNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVTG 99
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 151-187 1.95e-03

universal minicircle sequence binding protein (UMSBP); Provisional


The actual alignment was detected with superfamily member PTZ00368:

Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.86  E-value: 1.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 78042603  151 CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 187
Cdd:PTZ00368  80 CYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 120
 
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 ...
 29-99 5.13e-21

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: 83.78  E-value: 5.13e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 78042603  29 TGHCKWFNVRMGFGFIsmisregNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVTG 99
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
29-100 3.75e-20

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 81.52  E-value: 3.75e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 78042603    29 TGHCKWFNVRMGFGFIsmisregNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVTGP 100
Cdd:pfam00313   2 TGTVKWFNAKKGFGFI-------TPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
29-98 3.21e-16

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 70.99  E-value: 3.21e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78042603  29 TGHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:COG1278   3 TGTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
30-98 4.79e-12

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 60.05  E-value: 4.79e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 78042603   30 GHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:PRK09507   6 GNVKWFNESKGFGFIT-------PEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 29-100 1.02e-07

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: 47.98  E-value: 1.02e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 78042603     29 TGHCKWFNvrMGFGFIsmisregNPLDIPVDVFVHQSKLFMeGFRSLKEGEPVEF--TFKKSPKGLESIRVTGP 100
Cdd:smart00357   1 TGVVKWFN--KGFGFI-------RPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 151-187 1.95e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.86  E-value: 1.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 78042603  151 CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 187
Cdd:PTZ00368  80 CYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 120
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 149-190 2.27e-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: 38.29  E-value: 2.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 78042603 149 PRCYNCGGLDHHAKEC--------------SLP-PQPKKCHYCQSIMHMVANC-PHKL 190
Cdd:COG5082  61 PVCFNCGQNGHLRRDCphsicyncswdghrSNHcPKPKKCYNCGETGHLSRDCnPSKD 118
 
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 ...
 29-99 5.13e-21

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: 83.78  E-value: 5.13e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 78042603  29 TGHCKWFNVRMGFGFIsmisregNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVTG 99
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
29-100 3.75e-20

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 81.52  E-value: 3.75e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 78042603    29 TGHCKWFNVRMGFGFIsmisregNPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVTGP 100
Cdd:pfam00313   2 TGTVKWFNAKKGFGFI-------TPEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
29-98 3.21e-16

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 70.99  E-value: 3.21e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78042603  29 TGHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:COG1278   3 TGTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
cspE PRK09507
cold shock-like protein CspE;
30-98 4.79e-12

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 60.05  E-value: 4.79e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 78042603   30 GHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:PRK09507   6 GNVKWFNESKGFGFIT-------PEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
29-98 5.98e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 59.99  E-value: 5.98e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78042603   29 TGHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:PRK10354   6 TGIVKWFNADKGFGFIT-------PDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 30-98 2.81e-10

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 55.07  E-value: 2.81e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 78042603   30 GHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKGLESIRVT 98
Cdd:PRK10943   6 GQVKWFNESKGFGFIT-------PADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 29-91 3.69e-10

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 55.06  E-value: 3.69e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 78042603   29 TGHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKG 91
Cdd:PRK14998   3 TGTVKWFNNAKGFGFIC-------PEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG 58
PRK09937 PRK09937
cold shock-like protein CspD;
30-91 3.56e-09

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 52.43  E-value: 3.56e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 78042603   30 GHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKG 91
Cdd:PRK09937   4 GTVKWFNNAKGFGFIC-------PEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG 58
PRK09890 PRK09890
cold shock protein CspG; Provisional
 29-91 1.60e-08

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 50.53  E-value: 1.60e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 78042603   29 TGHCKWFNVRMGFGFISmisregnPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSPKG 91
Cdd:PRK09890   6 TGLVKWFNADKGFGFIT-------PDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG 61
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 29-100 1.02e-07

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: 47.98  E-value: 1.02e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 78042603     29 TGHCKWFNvrMGFGFIsmisregNPLDIPVDVFVHQSKLFMeGFRSLKEGEPVEF--TFKKSPKGLESIRVTGP 100
Cdd:smart00357   1 TGVVKWFN--KGFGFI-------RPDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 151-187 1.95e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.86  E-value: 1.95e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 78042603  151 CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 187
Cdd:PTZ00368  80 CYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 120
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 149-190 2.27e-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: 38.29  E-value: 2.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 78042603 149 PRCYNCGGLDHHAKEC--------------SLP-PQPKKCHYCQSIMHMVANC-PHKL 190
Cdd:COG5082  61 PVCFNCGQNGHLRRDCphsicyncswdghrSNHcPKPKKCYNCGETGHLSRDCnPSKD 118
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 151-189 9.92e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 35.94  E-value: 9.92e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 78042603  151 CYNCGGLDHHAKEC----SLPPQPKKCHYCQSIMHMVANCPHK 189
Cdd:PTZ00368 106 CYNCGGEGHISRDCpnagKRPGGDKTCYNCGQTGHLSRDCPDK 148
 
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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