SUPERFAMILY 1.75 HMM library and genome assignments server


L-aspartase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   L-aspartase-like [ 48556]
Superfamily:   L-aspartase-like [ 48557] (2)
Families:   L-aspartase/fumarase [ 48558] (5)
  HAL/PAL-like [ 48572] (2)


Superfamily statistics
Genomes (3,081) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 12,722 31,038 34
Proteins 12,646 31,005 34


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)nitrogen compound metabolic process8.833e-062.582e-06Least InformativeDirect
Biological Process (BP)single-organism metabolic process2.104e-100Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process10.9715Least InformativeInherited
Biological Process (BP)response to stimulus0.22550.8709Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.071240.04758Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process4.691e-090Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00015172.927e-05Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.43050.6039Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.47310.6264Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.065350.1282Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.031520.1215Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00049120.02353Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.044180.1087Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.13670.6724Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.10830.2174Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.036980.148Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process1.805e-096.54e-09InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds1.93e-098.637e-09InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process1.443e-078.17e-07InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process6.168e-071.493e-06InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.0022710.005402InformativeInherited
Biological Process (BP)glycosyl compound biosynthetic process0.0011350.0004343InformativeInherited
Biological Process (BP)nucleoside monophosphate metabolic process0.0021370.05825InformativeInherited
Biological Process (BP)single-organism behavior1.657e-050.001055InformativeInherited
Biological Process (BP)purine ribonucleotide metabolic process0.85690.972InformativeInherited
Biological Process (BP)internal protein amino acid acetylation3.741e-091.278e-06Highly InformativeDirect
Biological Process (BP)locomotory behavior2.175e-071.291e-05Highly InformativeDirect
Biological Process (BP)aerobic respiration3.875e-133.47e-13Highly InformativeDirect
Biological Process (BP)nucleoside monophosphate biosynthetic process0.00070382.103e-05Highly InformativeDirect
Biological Process (BP)purine ribonucleotide biosynthetic process2.031e-052.253e-05Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.77950.6339Highly InformativeInherited
Molecular Function (MF)structural molecule activity0.00015920.0006769Moderately InformativeDirect
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.12530.01101Moderately InformativeInherited
Molecular Function (MF)hydro-lyase activity00InformativeDirect
Molecular Function (MF)intramolecular transferase activity5.44e-057.23e-08Highly InformativeDirect
Cellular Component (CC)cytoplasmic part7.388e-064.611e-06Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.052710.4342Least InformativeInherited

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) nitrogen compound metabolic process 2.582e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.9715 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8709 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.04758 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 2.927e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6039 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.6264 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1282 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.1215 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.02353 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1087 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.09094 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.8773 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6724 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2174 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.148 Moderately Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 6.54e-09 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 8.637e-09 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 8.17e-07 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 1.493e-06 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.0004343 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.005402 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.05825 Informative Inherited
Biological Process (BP) single-organism behavior 0.001055 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.867 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.972 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 1.278e-06 Highly Informative Direct
Biological Process (BP) locomotory behavior 1.291e-05 Highly Informative Direct
Biological Process (BP) aerobic respiration 3.47e-13 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 2.103e-05 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 2.253e-05 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 1.746e-08 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.6339 Highly Informative Inherited
Molecular Function (MF) structural molecule activity 0.0006769 Moderately Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.01101 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) intramolecular transferase activity 7.23e-08 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 4.611e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.4342 Least Informative Inherited

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)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc1.741e-12Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of brain morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Intellectual disability0InformativeDirect
Phenotypic Abnormality (PA)Seizures0InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental delay0InformativeDirect
Phenotypic Abnormality (PA)Global developmental delay0Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect

Document: WP 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)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

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

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 lyases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Intramolecular transferases (mutases)1InformativeInherited
Enzyme Commission (EC)Lyases acting on amides, amidines, etc0Highly InformativeDirect
Enzyme Commission (EC)Ammonia-lyases0.1533Highly InformativeInherited
Enzyme Commission (EC)Intramolecular lyases1Highly InformativeInherited

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 processPurine biosynthesis9.969e-06InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processHistidine metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationEye lens protein1.16e-06Highly 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)L-arginine metabolism0Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism0.09216Moderately InformativeInherited
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)urea cycle6.085e-05Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR008948 SSF48557 Protein matches
Abstract

The enzyme L-aspartate ammonia-lyase (aspartase) catalyses the reversible deamination of the amino acid L-aspartic acid, using a carbanion mechanism to produce fumaric acid and ammonium ion. Aspartases from different organisms show high sequence homology, and this homology extends to functionally related enzymes such as the class II fumarases, the argininosuccinate and adenylosuccinate lyases. The high-resolution structure of aspartase reveals a monomer that is composed of three domains oriented in an elongated S-shape [PubMed9230045]. The central domain, comprised of five-helices, provides the subunit contacts in the functionally active tetramer. The active sites are located in clefts between the subunits and structural and mutagenic studies have identified several of the active site functional groups. A separate regulatory site has been identified. The substrate, aspartic acid, can also play the role of an activator, binding at this site along with a required divalent metal ion.


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) · Human Phenotype (HP) · Worm Phenotype (WP) · 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 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 L-aspartase-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 L-aspartase-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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]