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 (2,792) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,220 28,827 13
Proteins 12,204 28,817 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 process0.0041180.09118Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.025780Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.010330.6618Least InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process4.756e-075.271e-10Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.0028664.833e-09Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.015020.002003Moderately InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process3.199e-060.0007502InformativeDirect
Molecular Function (MF)lyase activity5.168e-050Moderately InformativeDirect
Molecular Function (MF)hydro-lyase activity1.078e-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 0.8888 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.09118 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.6618 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 4.833e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 5.271e-10 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.008061 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.01338 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.002003 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.9727 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.8601 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.9218 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.0692 Moderately Informative Inherited
Biological Process (BP) response to inorganic substance 2.796e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0001539 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 3.267e-07 Informative Direct
Biological Process (BP) carbohydrate catabolic process 5.349e-05 Informative Direct
Biological Process (BP) cation homeostasis 2.415e-06 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0007502 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.1324 Informative Inherited
Biological Process (BP) regulation of translation 1.818e-06 Highly Informative Direct
Biological Process (BP) aerobic respiration 1.111e-05 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 1.604e-12 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 8.262e-11 Highly Informative Direct
Molecular Function (MF) binding 0.3664 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.001726 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.002244 Moderately Informative Inherited
Molecular Function (MF) RNA binding 5.771e-10 Informative Direct
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) transition metal ion binding 2.976e-05 Informative Direct
Molecular Function (MF) metal cluster binding 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 0.008022 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.763 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.03409 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.6935 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 0.0001852 Informative Direct
Cellular Component (CC) plastid 0.001934 Informative Inherited
Cellular Component (CC) chloroplast stroma 1.464e-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 peptide1.153e-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)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)organic acid metabolism7.074e-06Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)organic acid biosynthesis1.59e-07InformativeDirect
UniPathway (UP)2-oxosuberate biosynthesis5.801e-13Highly InformativeDirect
UniPathway (UP)Entner-Doudoroff pathway1.128e-12Highly InformativeDirect
UniPathway (UP)L-lysine biosynthesis via AAA pathway2.03e-11Highly InformativeDirect
UniPathway (UP)glyoxylate and dicarboxylate metabolism1.501e-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 ]