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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 (2,728) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 9,463 60,011 21
Proteins 8,963 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 regulation0.60631Least InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.000072030.02914Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.028330.6543Moderately InformativeInherited
Biological Process (BP)regulation of protein metabolic process0.098260.01225Moderately InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.040390.2031Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.026380.2546Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.0002270.1201Moderately InformativeInherited
Biological Process (BP)posttranscriptional regulation of gene expression0.000027090.0000005813InformativeDirect
Biological Process (BP)regulation of cellular amide metabolic process0.000000092410.0000002221InformativeDirect
Biological Process (BP)negative regulation of protein metabolic process0.0016240.003772InformativeInherited
Biological Process (BP)negative regulation of macromolecule biosynthetic process0.00078340.03116InformativeInherited
Biological Process (BP)negative regulation of gene expression0.00000014220.003542InformativeInherited
Biological Process (BP)negative regulation of cellular biosynthetic process0.0000038620.01782InformativeInherited
Biological Process (BP)negative regulation of cellular amide metabolic process0.000000000080290.000001587Highly InformativeDirect
Molecular Function (MF)hydrolase activity0.15490.1311Least InformativeInherited
Molecular Function (MF)hydrolase activity, acting on ester bonds0.00067410.001761Moderately InformativeInherited
Molecular Function (MF)nuclease activity0.0000000062230.000000147InformativeDirect
Molecular Function (MF)endoribonuclease activity0.00000000000037070.000000000003919Highly InformativeDirect
Molecular Function (MF)deaminase activity00Highly InformativeDirect
Cellular Component (CC)intracellular organelle part0.27871Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.91391Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.97311Least InformativeInherited
Cellular Component (CC)mitochondrial part0.00008550.0002914Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen0.0042230.2492Moderately InformativeInherited
Cellular Component (CC)microbody0.0000036470.00000678InformativeDirect

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 0.02914 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.6543 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01225 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.2031 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.2546 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1201 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.0000005813 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0000002221 Informative Direct
Biological Process (BP) negative regulation of protein metabolic process 0.003772 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.03116 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.003542 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.01782 Informative Inherited
Biological Process (BP) negative regulation of cellular amide metabolic process 0.000001587 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.1311 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.001761 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0.000000147 Informative Direct
Molecular Function (MF) endoribonuclease activity 0.000000000003919 Highly Informative Direct
Molecular Function (MF) deaminase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0002914 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.2492 Moderately Informative Inherited
Cellular Component (CC) microbody 0.00000678 Informative Direct

Document: GO annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)toxin resistance0Highly InformativeDirect

Document: YP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.0000002809Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.00000001297Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.03375Moderately InformativeInherited
Biological processDetoxification0.0000000000075Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis0.00003634Highly InformativeDirect
Cellular componentMitochondrion0.00001886Moderately InformativeDirect
Cellular componentPeroxisome0.00000001379InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0.0009113Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-isoleucine biosynthesis0.000000003254InformativeDirect

Document: UP 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) · Yeast Phenotype (YP) · Enzyme Commission (EC) · 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 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) · Yeast Phenotype (YP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]