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Conserved domains on  [gi|51972214|ref|NP_001004317|]
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protein lin-28 homolog B isoform 1 [Homo sapiens]

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 ...
 31-101 1.47e-20

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: 82.24  E-value: 1.47e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 51972214  31 TGHCKWFNVRMGFGFIsminregSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTG 101
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
PTZ00368 super family cl31762
universal minicircle sequence binding protein (UMSBP); Provisional
 120-165 4.30e-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: 36.71  E-value: 4.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 51972214  120 QKRKPKGDR-CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 165
Cdd:PTZ00368  70 EAPPGSGPRsCYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 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 ...
 31-101 1.47e-20

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: 82.24  E-value: 1.47e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 51972214  31 TGHCKWFNVRMGFGFIsminregSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTG 101
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
31-102 2.47e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 79.21  E-value: 2.47e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 51972214    31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGP 102
Cdd:pfam00313   2 TGTVKWFNAKKGFGFIT-------PEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
31-100 1.19e-15

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.45  E-value: 1.19e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51972214  31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:COG1278   3 TGTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
31-100 2.93e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 60.37  E-value: 2.93e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51972214   31 TGHCKWFNVRMGFGFIsminregSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:PRK10354   6 TGIVKWFNADKGFGFI-------TPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 31-102 3.11e-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: 46.44  E-value: 3.11e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 51972214     31 TGHCKWFNvrMGFGFISminregsPLDIPVDVFVHQSKLFMeGFRSLKEGEPVEF--TFKKSSKGLESIRVTGP 102
Cdd:smart00357   1 TGVVKWFN--KGFGFIR-------PDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 120-165 4.30e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 36.71  E-value: 4.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 51972214  120 QKRKPKGDR-CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 165
Cdd:PTZ00368  70 EAPPGSGPRsCYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 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 ...
 31-101 1.47e-20

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: 82.24  E-value: 1.47e-20
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 51972214  31 TGHCKWFNVRMGFGFIsminregSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTG 101
Cdd:cd04458   2 TGTVKWFDDEKGFGFI-------TPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CSD pfam00313
'Cold-shock' DNA-binding domain;
31-102 2.47e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 79.21  E-value: 2.47e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 51972214    31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVTGP 102
Cdd:pfam00313   2 TGTVKWFNAKKGFGFIT-------PEDGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CspC COG1278
Cold shock protein, CspA family [Transcription];
31-100 1.19e-15

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 69.45  E-value: 1.19e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51972214  31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:COG1278   3 TGTVKWFNAEKGFGFIT-------PDDGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
31-100 2.93e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 60.37  E-value: 2.93e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51972214   31 TGHCKWFNVRMGFGFIsminregSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:PRK10354   6 TGIVKWFNADKGFGFI-------TPDDGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
cspE PRK09507
cold shock-like protein CspE;
32-100 6.96e-12

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 59.28  E-value: 6.96e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 51972214   32 GHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:PRK09507   6 GNVKWFNESKGFGFIT-------PEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 32-100 6.04e-10

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 53.92  E-value: 6.04e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 51972214   32 GHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKGLESIRVT 100
Cdd:PRK10943   6 GQVKWFNESKGFGFIT-------PADGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09890 PRK09890
cold shock protein CspG; Provisional
 31-93 9.11e-09

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 50.92  E-value: 9.11e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51972214   31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKG 93
Cdd:PRK09890   6 TGLVKWFNADKGFGFIT-------PDDGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG 61
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 31-93 1.51e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 50.43  E-value: 1.51e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 51972214   31 TGHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKG 93
Cdd:PRK14998   3 TGTVKWFNNAKGFGFIC-------PEGGGEDIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG 58
PRK09937 PRK09937
cold shock-like protein CspD;
32-93 5.28e-08

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 48.96  E-value: 5.28e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 51972214   32 GHCKWFNVRMGFGFISminregsPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKSSKG 93
Cdd:PRK09937   4 GTVKWFNNAKGFGFIC-------PEGGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG 58
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 31-102 3.11e-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: 46.44  E-value: 3.11e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 51972214     31 TGHCKWFNvrMGFGFISminregsPLDIPVDVFVHQSKLFMeGFRSLKEGEPVEF--TFKKSSKGLESIRVTGP 102
Cdd:smart00357   1 TGVVKWFN--KGFGFIR-------PDDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 120-165 4.30e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 36.71  E-value: 4.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 51972214  120 QKRKPKGDR-CYNCGGLDHHAKECSLPPQ----PKKCHYCQSIMHMVANCP 165
Cdd:PTZ00368  70 EAPPGSGPRsCYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP 120
 
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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