SUPERFAMILY 1.75 HMM library and genome assignments server


Ribosomal protein L25-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Ribosomal protein L25-like [ 50714]
Superfamily:   Ribosomal protein L25-like [ 50715] (2)
Families:   Ribosomal protein L25-like [ 50716] (2)
  Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain [ 50719]


Superfamily statistics
Genomes (2,854) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,855 22,864 14
Proteins 4,844 22,855 14


Functional annotation
General category Information
Detailed category Translation

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 2.799e-09 Least Informative Direct
Biological Process (BP) protein metabolic process 4.902e-09 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 8.308e-07 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0002293 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0002734 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0002854 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0004867 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000496 Least Informative Direct
Biological Process (BP) cellular amino acid metabolic process 1.278e-10 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 6.327e-09 Moderately Informative Direct
Biological Process (BP) gene expression 1.274e-07 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 4.823e-05 Moderately Informative Direct
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) translation 7.377e-15 Informative Direct
Cellular Component (CC) cytoplasmic part 0.2164 Least Informative Inherited
Cellular Component (CC) cytosol 0.0007445 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Glutamate--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionATP-binding1.308e-08Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011035 SSF50715 Protein matches
Abstract

The bacterial ribosomal protein L25 is bound to 5S rRNA along with L5 and L18, forming a separate domain of the ribosome [PubMed10696113]. The solution structure of protein L25 uncomplexed with RNA shows two significantly disordered loops and a closed beta-barrel domain with a complex topology that has significant structural similarities to the N-terminal domain of the Thermus thermophilus ribosomal protein TL5, to the general stress protein CTC, and to the C-terminal anticodon-binding domain of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) [PubMed11418764, PubMed12737824]. GlnRS contains a duplication consisting of two L25-like beta-barrels domains with the swapping of N-terminal strands.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 4 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Ribosomal protein L25-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 4 hidden Markov models representing the Ribosomal protein L25-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]