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 (3,056) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,639 25,925 8
Proteins 5,637 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 4.008e-06 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0002128 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.007989 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 5.293e-05 Moderately Informative Direct
Biological Process (BP) gene expression 0.0007384 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.06793 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.04305 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.04595 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.04857 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.07879 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.666 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 6.461e-07 Informative Direct
Biological Process (BP) protein catabolic process 0.0002944 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.0009506 Informative Direct
Biological Process (BP) proteolysis 0.008838 Informative Inherited
Biological Process (BP) transcription, DNA-dependent 0.03823 Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 2.822e-08 Highly Informative Direct
Biological Process (BP) protein ubiquitination 4.144e-08 Highly Informative Direct
Molecular Function (MF) structural molecule activity 2.711e-08 Moderately Informative Direct
Molecular Function (MF) structural constituent of ribosome 1.316e-11 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 3.748e-08 Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 4.523e-09 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 9.151e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.007293 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.765 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1276 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 5.674e-10 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 2.483e-06 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.1755 Moderately Informative Inherited
Cellular Component (CC) large ribosomal subunit 0 Informative Direct
Cellular Component (CC) mitochondrial matrix 1.465e-09 Informative Direct
Cellular Component (CC) ubiquitin ligase complex 1.001e-08 Informative Direct
Cellular Component (CC) mitochondrial ribosome 9.852e-05 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

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) ]

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) · Internal database links ]