NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|215765074|dbj|BAG86771|]
View 

unnamed protein product [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RPS31 super family cl27771
Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal ...
 62-120 5.87e-19

Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal subunits. It seems that linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits.


The actual alignment was detected with superfamily member pfam17067:

Pssm-ID: 332592  Cd Length: 99  Bit Score: 76.06  E-value: 5.87e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 215765074   62 VYCGRGDKKTKRGKRFNHSYGNtchlltavcssqARPRNKKKGTGPARLFAPPAPPRKD 120
Cdd:pfam17067  53 VYCGRGDRKTAKGKRFNHSFGN------------ARPRNKSKGRGPERVPVPPAPPRKD 99
 
Name Accession Description Interval E-value
RPS31 pfam17067
Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal ...
 62-120 5.87e-19

Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal subunits. It seems that linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits.


Pssm-ID: 293672  Cd Length: 99  Bit Score: 76.06  E-value: 5.87e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 215765074   62 VYCGRGDKKTKRGKRFNHSYGNtchlltavcssqARPRNKKKGTGPARLFAPPAPPRKD 120
Cdd:pfam17067  53 VYCGRGDRKTAKGKRFNHSFGN------------ARPRNKSKGRGPERVPVPPAPPRKD 99
ribo_THX TIGR04560
ribosomal small subunit protein bTHX; Members of this protein are the lineage-specific ...
 65-101 3.15e-07

ribosomal small subunit protein bTHX; Members of this protein are the lineage-specific bacterial ribosomal small subunit proteint bTHX (previously THX), originally shown to exist in the genus Thermus. The protein is conserved for the first 26 amino acids, past which some members continue with additional sequence, often repetitive or low-complexity. This model also finds eukaryotic organelle forms, which have additional N-terminal transit peptides. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 275353  Cd Length: 26  Bit Score: 43.96  E-value: 3.15e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 215765074   65 GRGDKKTKRGKRFNHSYGNTchlltavcssqaRPRNK 101
Cdd:TIGR04560   2 GKGDKKTKRGKISRGSYGKR------------RPRKK 26
 
Name Accession Description Interval E-value
RPS31 pfam17067
Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal ...
 62-120 5.87e-19

Ribosomal protein S31e; RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal subunits. It seems that linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits.


Pssm-ID: 293672  Cd Length: 99  Bit Score: 76.06  E-value: 5.87e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 215765074   62 VYCGRGDKKTKRGKRFNHSYGNtchlltavcssqARPRNKKKGTGPARLFAPPAPPRKD 120
Cdd:pfam17067  53 VYCGRGDRKTAKGKRFNHSFGN------------ARPRNKSKGRGPERVPVPPAPPRKD 99
ribo_THX TIGR04560
ribosomal small subunit protein bTHX; Members of this protein are the lineage-specific ...
 65-101 3.15e-07

ribosomal small subunit protein bTHX; Members of this protein are the lineage-specific bacterial ribosomal small subunit proteint bTHX (previously THX), originally shown to exist in the genus Thermus. The protein is conserved for the first 26 amino acids, past which some members continue with additional sequence, often repetitive or low-complexity. This model also finds eukaryotic organelle forms, which have additional N-terminal transit peptides. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 275353  Cd Length: 26  Bit Score: 43.96  E-value: 3.15e-07
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 215765074   65 GRGDKKTKRGKRFNHSYGNTchlltavcssqaRPRNK 101
Cdd:TIGR04560   2 GKGDKKTKRGKISRGSYGKR------------RPRKK 26
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH