SUPERFAMILY 1.75 HMM library and genome assignments server

ClpS-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   ClpS-like [ 54735]
Superfamily:   ClpS-like [ 54736] (2)
Families:   Ribosomal protein L7/12, C-terminal domain [ 54737]
  Adaptor protein ClpS (YljA) [ 82641]


Superfamily statistics
Genomes (3,057) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,646 25,925 8
Proteins 5,644 25,923 8


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) cellular macromolecule metabolic process 0.000003045 Least Informative Direct
Biological Process (BP) protein metabolic process 0.000227 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.007082 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.00005221 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.08535 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06576 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.04726 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.08982 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.05088 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.6722 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.05369 Moderately Informative Inherited
Biological Process (BP) gene expression 0.001057 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0.0000006668 Informative Direct
Biological Process (BP) protein catabolic process 0.0003003 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000998 Informative Direct
Biological Process (BP) proteolysis 0.008971 Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.03211 Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.00000003252 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0.00000004387 Highly Informative Direct
Molecular Function (MF) transferase activity 0.02286 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0.00000002694 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 0.00000000001309 Informative Direct
Molecular Function (MF) ubiquitin-protein transferase activity 0.000000004274 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.0000001551 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.6642 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1386 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.006359 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 0.0000000005392 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.0000008922 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.000002679 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.1088 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.000000002898 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 0.00000001808 Informative Direct
Cellular Component (CC) mitochondrial ribosome 0.00009818 Highly Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationRibonucleoprotein0Moderately InformativeDirect
Post-translational modificationRibosomal protein0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR014719 SSF54736 Protein matches
Abstract

This entry represents a domain found at the C-terminus of ribosomal proteins L7 and L12, and also in the adaptor protein ClpS, forming an alpha/beta sandwich [PubMed12235156].

The L7 and L12 ribosomal proteins are part of the large 50S ribosomal subunit, and occur in four copies organised as two dimers. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post-translational modification of the addition of an acetyl group to the N terminus of L7 [PubMed10488095].

ClpS is an adaptor protein that influences protein degradation through its binding to the N-terminal domain of the chaperone ClpA in the ClpAP chaperone-protease pair. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins [PubMed11931773].


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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 ClpS-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 ClpS-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) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]