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YjgF-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Bacillus chorismate mutase-like [ 55297] (9)
Superfamily:   YjgF-like [ 55298] (2)
Families:   YjgF/L-PSP [ 55299] (11)
  Chorismate mutase [ 55304]


Superfamily statistics
Genomes (2,730) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 9,479 60,011 21
Proteins 8,975 57,843 21


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.60141Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.000069230.029Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.026590.6681Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.038370.2055Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.024810.257Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.092260.01219Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.0002020.1253Moderately InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.0000160.0000005018InformativeDirect
Biological Process (BP)negative regulation of cellular protein metabolic process0.0000026910.0004878InformativeDirect
Biological Process (BP)regulation of cellular amide metabolic process0.000000050380.0000001919InformativeDirect
Biological Process (BP)negative regulation of macromolecule biosynthetic process0.00060220.02964InformativeInherited
Biological Process (BP)negative regulation of gene expression0.00000010180.003456InformativeInherited
Biological Process (BP)negative regulation of cellular biosynthetic process0.0000026910.01725InformativeInherited
Biological Process (BP)negative regulation of translation0.00000036560.000006575Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.14630.1254Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.00063850.001672Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.0000000050740.0000001166InformativeDirect
Molecular Function (MF)endoribonuclease activity0.00000000000049280.000000000005098Highly InformativeDirect
Molecular Function (MF)deaminase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.90041Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.96111Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.26861Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.0041620.2555Moderately InformativeInherited
Cellular Component (CC)microbody0.0000030730.000006169InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.029 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6681 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.2055 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.257 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01219 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1253 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000005018 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0004878 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0000001919 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.02964 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.003456 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.01725 Informative Inherited
Biological Process (BP) negative regulation of translation 0.000006575 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.1254 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.001672 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.0000001166 Informative Direct
Molecular Function (MF) endoribonuclease activity 0.000000000005098 Highly Informative Direct
Molecular Function (MF) deaminase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2555 Moderately Informative Inherited
Cellular Component (CC) microbody 0.000006169 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.0333Moderately InformativeInherited
Biological processDetoxification0.000000000007556Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00003636Highly InformativeDirect
Cellular componentMitochondrion0.00001908Moderately InformativeDirect
Cellular componentPeroxisome0.00000001341InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013813 SSF55298 Protein matches
Abstract

This entry represents the beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets.

Chorismate mutase (CM, ) is an enzyme of the aromatic amino acid biosynthetic pathway that catalyses the reaction at the branch point of the pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. The structure of chorismate mutase enzymes from Bacillus subtilis [PubMed10818343] and Thermus thermophilus have been solved and were shown to have a catalytic homotrimer, with the active sites being located at the subunit interfaces, where residues from two subunits contribute to each site.

The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes. Members include not only the conserved bacterial protein YjgF that displays a homotrimeric structure [PubMed10595546], but also the regulatory protein YabJ from B. subtilis that is required for adenine-mediated repression of purine biosynthetic genes [PubMed10557275], the yeast growth inhibitor YER057cp that appears to play a role in the regulation of metabolic pathways and cell differentiation [PubMed11442631], and the mammalian 14.5 kDa translational inhibitor protein L-PSP (liver perchloric acid-soluble protein) with endoribonucleolytic activity that directly affects mRNA translation and can induce disaggregation of the reticulocyte polysomes into 80 S ribosomes [PubMed10400702].


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-quality) · Gene Ontology (high-coverage) · 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 18 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 YjgF-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 18 hidden Markov models representing the YjgF-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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]