SUPERFAMILY 1.75 HMM library and genome assignments server

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Ribosomal protein S18 superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   DNA/RNA-binding 3-helical bundle [ 46688] (14)
Superfamily:   Ribosomal protein S18 [ 46911]
Families:   Ribosomal protein S18 [ 46912]


Superfamily statistics
Genomes (3,006) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,502 18,170 9
Proteins 3,501 18,169 9


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 0.00001555 Least Informative Direct
Biological Process (BP) protein metabolic process 0.00002072 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0006566 Least Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000000006329 Moderately Informative Direct
Biological Process (BP) gene expression 0.00000001617 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.000000000000001562 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 0 Informative Direct
Cellular Component (CC) cytoplasmic part 0.00000000000178 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.243 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.09043 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.04703 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.00000001225 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.0000005713 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.0007405 Moderately Informative Direct
Cellular Component (CC) mitochondrial matrix 0 Informative Direct
Cellular Component (CC) small ribosomal subunit 0 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentPlastid0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Molecular functionrRNA-binding0InformativeDirect
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001648 SSF46911 Protein matches
Abstract

Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA [PubMed9281425]. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.

The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [PubMed2647521], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein [PubMed9371771]. S18 belongs to a family of ribosomal proteins [PubMed2179947] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.


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) · Worm Phenotype (WP) · 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 2 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 S18 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 2 hidden Markov models representing the Ribosomal protein S18 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) · Worm Phenotype (WP) · UniProtKB KeyWords (KW) · Internal database links ]