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 (3,123) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 13,108 71,222 34
Proteins 13,014 71,169 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 process5.142e-068.428e-08Least InformativeDirect
Biological Process (BP)single-organism metabolic process9.69e-110Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process10.7805Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process10.574Least InformativeInherited
Biological Process (BP)response to stimulus0.3091Least 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 process0.092080.009494Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process6.847e-090Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00028513.426e-05Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.46230.7513Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.37410.6742Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.084240.2941Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.041550.04755Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00090240.01954Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.059110.04771Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.14620.747Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.018030.1124Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process0.061660.2094Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process3.604e-051.745e-05InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds2.504e-091.63e-08InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process1.86e-079.475e-07InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process1.282e-062.456e-05InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.0026530.007602InformativeInherited
Biological Process (BP)glycosyl compound biosynthetic process0.0012730.001332InformativeInherited
Biological Process (BP)nucleoside monophosphate metabolic process0.0052590.1136InformativeInherited
Biological Process (BP)single-organism behavior2.348e-050.001878InformativeInherited
Biological Process (BP)purine ribonucleotide metabolic process11InformativeInherited
Biological Process (BP)internal protein amino acid acetylation6.558e-091.929e-06Highly InformativeDirect
Biological Process (BP)locomotory behavior3.427e-072.248e-05Highly InformativeDirect
Biological Process (BP)aerobic respiration4.364e-136.344e-13Highly InformativeDirect
Biological Process (BP)nucleoside monophosphate biosynthetic process0.00064591.974e-05Highly InformativeDirect
Biological Process (BP)purine ribonucleotide biosynthetic process2.64e-052.689e-05Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.7840.6264Highly InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.13320.001101Moderately InformativeInherited
Molecular Function (MF)structural molecule activity0.00021880.001184Moderately InformativeInherited
Molecular Function (MF)hydro-lyase activity6.847e-160InformativeDirect
Molecular Function (MF)intramolecular transferase activity6.106e-056.65e-11Highly InformativeDirect
Cellular Component (CC)cytoplasmic part2.255e-062.092e-05Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.039250.7589Least 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 8.428e-08 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.7805 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.574 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.009494 Least Informative Inherited
Biological Process (BP) response to stimulus 1 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) 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 3.426e-05 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.08625 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.03238 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.01522 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.7513 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.6742 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.2941 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.01954 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.04755 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.04771 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.1262 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.9182 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.747 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1124 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2094 Moderately Informative Inherited
Biological Process (BP) protein complex assembly 0.0009257 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 1.745e-05 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 1.63e-08 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 9.475e-07 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 2.456e-05 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.007602 Informative Inherited
Biological Process (BP) secondary metabolic process 0.03318 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.1136 Informative Inherited
Biological Process (BP) glycosyl compound biosynthetic process 0.001332 Informative Inherited
Biological Process (BP) single-organism behavior 0.001878 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.8685 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 1 Informative Inherited
Biological Process (BP) internal protein amino acid acetylation 1.929e-06 Highly Informative Direct
Biological Process (BP) locomotory behavior 2.248e-05 Highly Informative Direct
Biological Process (BP) aerobic respiration 6.344e-13 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 1.974e-05 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 2.689e-05 Highly Informative Direct
Biological Process (BP) phenylpropanoid metabolic process 1.934e-06 Highly Informative Direct
Biological Process (BP) secondary metabolite biosynthetic process 0.0002271 Highly Informative Direct
Biological Process (BP) protein tetramerization 2.147e-09 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 3.776e-08 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.6264 Highly Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.001101 Moderately Informative Inherited
Molecular Function (MF) structural molecule activity 0.001184 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) intramolecular transferase activity 6.65e-11 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 2.092e-05 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.7589 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)Global developmental delay0InformativeDirect

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)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Intramolecular transferases (mutases)1InformativeInherited
Enzyme Commission (EC)Lyases acting on amides, amidines, etc0Highly InformativeDirect
Enzyme Commission (EC)Ammonia-lyases0.1881Highly 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 biosynthesis9.183e-06InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processHistidine metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationEye lens protein1.142e-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)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis8.434e-05Moderately InformativeDirect
UniPathway (UP)nitrogen metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)purine metabolism1Moderately InformativeInherited
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)tricarboxylic acid cycle0InformativeDirect
UniPathway (UP)phenylpropanoid biosynthesis0InformativeDirect
UniPathway (UP)L-histidine degradation0Highly InformativeDirect
UniPathway (UP)urea cycle4.918e-06Highly InformativeDirect
UniPathway (UP)AMP biosynthesis4.33e-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 ]