SUPERFAMILY 1.75 HMM library and genome assignments server

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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 (2,861) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,874 25,956 14
Proteins 4,863 25,917 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 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000000002106 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000000009815 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00000000009142 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000008373 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000002258 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.0000002851 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000007396 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002635 Least Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.0000000004818 Moderately Informative Direct
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Cellular Component (CC) protein complex 0.01174 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4641 Least Informative Inherited

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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Molecular functionNucleotide-binding0.0004646Least InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect
Post-translational modificationrRNA-binding0InformativeDirect
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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]