SUPERFAMILY 1.75 HMM library and genome assignments server


LeuD/IlvD-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   The "swivelling" beta/beta/alpha domain [ 52008] (10)
Superfamily:   LeuD/IlvD-like [ 52016] (3)
Families:   LeuD-like [ 52017] (4)
  IlvD/EDD C-terminal domain-like [ 141976]
  AF0055-like [ 141979]


Superfamily statistics
Genomes (2,837) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 12,288 65,727 13
Proteins 12,268 65,713 13


Functional annotation
General category Metabolism
Detailed category Energy

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)biosynthetic process0.0042520.1096Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.02530Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.010460.7029Least InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process1.019e-065.232e-10Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.00286.844e-09Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.014980.002414Moderately InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process4.6e-060.0007385InformativeDirect
Molecular Function (MF)lyase activity5.217e-050Moderately InformativeDirect
Molecular Function (MF)hydro-lyase activity1.766e-070InformativeDirect

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) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9237 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1096 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7029 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 6.844e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 5.232e-10 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.008358 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01494 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.002414 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.9899 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.09293 Moderately Informative Inherited
Biological Process (BP) response to inorganic substance 5.269e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0002388 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 1.356e-07 Informative Direct
Biological Process (BP) carbohydrate catabolic process 6.177e-05 Informative Direct
Biological Process (BP) metal ion homeostasis 8.755e-07 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0007385 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.1269 Informative Inherited
Biological Process (BP) regulation of translation 2.816e-06 Highly Informative Direct
Biological Process (BP) aerobic respiration 5.763e-06 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 1.184e-12 Highly Informative Direct
Biological Process (BP) iron ion homeostasis 3.294e-12 Highly Informative Direct
Molecular Function (MF) binding 0.4644 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0007611 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.002324 Moderately Informative Inherited
Molecular Function (MF) RNA binding 4.299e-10 Informative Direct
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) transition metal ion binding 6.478e-06 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.002746 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.6717 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.04426 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.9558 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.0002377 Informative Direct
Cellular Component (CC) plastid 0.002049 Informative Inherited
Cellular Component (CC) chloroplast stroma 1.807e-05 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Aconitate hydratase0Highly InformativeDirect
Enzyme Commission (EC)2-methylisocitrate dehydratase0.0002439Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)surface structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)immune system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skin0InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect
Xenopus ANatomical entity (XAN)endocrine system0InformativeDirect
Xenopus ANatomical entity (XAN)tail0InformativeDirect
Xenopus ANatomical entity (XAN)oviduct0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect

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 processTricarboxylic acid cycle0InformativeDirect
Biological processBranched-chain amino acid biosynthesis0Highly InformativeDirect
DomainTransit peptide1.389e-06Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular function4Fe-4S0InformativeDirect
Molecular functionIron-sulfur0InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism0.917Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)L-isoleucine biosynthesis0InformativeDirect
UniPathway (UP)tricarboxylic acid cycle6.755e-16InformativeDirect
UniPathway (UP)organic acid biosynthesis0.007397InformativeInherited
UniPathway (UP)L-lysine biosynthesis1InformativeInherited
UniPathway (UP)L-lysine biosynthesis via AAA pathway0Highly InformativeDirect
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0Highly InformativeDirect
UniPathway (UP)2-oxosuberate biosynthesis3.878e-08Highly InformativeDirect
UniPathway (UP)glyoxylate and dicarboxylate metabolism1.932e-07Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR015928 SSF52016 Protein matches
Abstract

This entry represents the 'swivel' domain found at the C-terminal of eukaryotic mAcn, cAcn/IPR1 and IRP2, and bacterial AcnA, but in the N-terminal region following the HEAT-like domain in bacterial AcnB. This domain has a three layer beta/beta/alpha structure, and in cytosolic Acn is known to rotate between the cAcn and IRP1 forms of the enzyme. This domain is also found in the small subunit of isopropylmalate dehydratase (LeuD).

More information about these proteins can be found at Protein of the Month: Aconitase.


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) · Disease Ontology (DO) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · 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 6 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 LeuD/IlvD-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 6 hidden Markov models representing the LeuD/IlvD-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) · Enzyme Commission (EC) · Disease Ontology (DO) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]