SUPERFAMILY 1.75 HMM library and genome assignments server

Chorismate mutase II superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Chorismate mutase II [ 48599]
Superfamily:   Chorismate mutase II [ 48600] (4)
Families:   Dimeric chorismate mutase [ 48601] (3)
  Allosteric chorismate mutase [ 48604]
  monomeric chorismate mutase [ 140942]
  Secreted chorismate mutase-like [ 140945]


Superfamily statistics
Genomes (2,385) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,702 22,500 12
Proteins 3,695 22,491 12


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

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)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process0.25450.0002166Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.30170.002482Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.38260.0043Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.69030.01631Least InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.000006220Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000018510Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.035560.00000000009779Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.013190.000000004521Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.04110.00000002916Moderately InformativeInherited
Biological Process (BP)aromatic amino acid family biosynthetic process0.0000049560Highly InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)intramolecular transferase activity00Highly InformativeDirect

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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0002166 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.01631 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.002482 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.0043 Least Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.000000004521 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.00000000009779 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.00000002916 Moderately Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.03083 Informative Inherited
Biological Process (BP) aromatic amino acid family biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) intramolecular transferase activity 0 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.000001266Least InformativeDirect
Enzyme Commission (EC)Hydro-lyases0.00000000004325Moderately InformativeDirect
Enzyme Commission (EC)Transferring other groups0InformativeDirect
Enzyme Commission (EC)Chorismate mutase0Highly InformativeDirect
Enzyme Commission (EC)Prephenate dehydratase0Highly InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.00001926Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.4654Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.00000001498Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0000008473InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processAromatic amino acid biosynthesis0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.0000000389Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0.000118Least InformativeDirect
UniPathway (UP)amino-acid metabolism0.02501Least InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis8.993e-16Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.00024Moderately InformativeDirect
UniPathway (UP)aromatic amino-acid biosynthesis0.000000000000004885InformativeDirect
UniPathway (UP)prephenate biosynthesis0Highly InformativeDirect
UniPathway (UP)L-phenylalanine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-tyrosine biosynthesis0.00000000001307Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR002701 SSF48600 Protein matches
Abstract

Chorismate mutase, , catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [PubMed9642265, PubMed9497350]. Prephenate dehydratase (, , PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [PubMed9642265].


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) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · 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 7 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 Chorismate mutase II 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 7 hidden Markov models representing the Chorismate mutase II 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) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]