SUPERFAMILY 1.75 HMM library and genome assignments server


D-aminoacid aminotransferase-like PLP-dependent enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   D-aminoacid aminotransferase-like PLP-dependent enzymes [ 56751]
Superfamily:   D-aminoacid aminotransferase-like PLP-dependent enzymes [ 56752]
Families:   D-aminoacid aminotransferase-like PLP-dependent enzymes [ 56753] (3)


Superfamily statistics
Genomes (2,833) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,608 0 9
Proteins 7,578 0 9


Functional annotation
General category Metabolism
Detailed category Transferases

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 process1.617e-101.411e-11Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process0.0010480.004586Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular catabolic process1.553e-120Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process1.155e-076.128e-09Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process1.694e-053.01e-07Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process1.597e-087.077e-10Moderately InformativeDirect
Biological Process (BP)carboxylic acid catabolic process5.187e-093.964e-11InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.017120.03754InformativeInherited
Biological Process (BP)secondary metabolic process0.094160.08962InformativeInherited
Biological Process (BP)branched-chain amino acid metabolic process00Highly InformativeDirect
Biological Process (BP)toxin metabolic process6.496e-051.48e-07Highly InformativeDirect
Molecular Function (MF)binding0.12111Least InformativeInherited
Molecular Function (MF)anion binding2.427e-116.484e-09Moderately InformativeDirect
Molecular Function (MF)lyase activity0.25870.07855Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.00071622.2e-06InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)transaminase activity00Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity1.378e-053.807e-10Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly 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) nitrogen compound metabolic process 1.411e-11 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.004586 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 6.128e-09 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 3.01e-07 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 7.077e-10 Moderately Informative Direct
Biological Process (BP) regulation of hormone levels 0.0001275 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 3.964e-11 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.03754 Informative Inherited
Biological Process (BP) secondary metabolic process 0.08962 Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) toxin metabolic process 1.48e-07 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 6.484e-09 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.07855 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 2.2e-06 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) transaminase activity 0 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 3.807e-10 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.519 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02571 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)Lyases0.6132Least InformativeInherited
Enzyme Commission (EC)Transferring nitrogenous groups0InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases6.04e-09InformativeDirect

Document: EC annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0.6615Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0.009152Moderately InformativeInherited
Enzyme Commission (EC)Transferring nitrogenous groups0Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases7.139e-09Highly 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 processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processFolate biosynthesis2.545e-15Highly InformativeDirect
Cellular componentMitochondrion0.0004457Moderately InformativeDirect
DomainTransit peptide2.13e-09Moderately InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism4.535e-13Least InformativeDirect
UniPathway (UP)cofactor metabolism0.825Least InformativeInherited
UniPathway (UP)aromatic compound metabolism0.8799Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0.0006125Moderately InformativeDirect
UniPathway (UP)L-isoleucine biosynthesis0InformativeDirect
UniPathway (UP)pteridine biosynthesis7.298e-09InformativeDirect
UniPathway (UP)tetrahydrofolate metabolism6.501e-06InformativeDirect
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0Highly InformativeDirect
UniPathway (UP)tetrahydrofolate biosynthesis5.764e-12Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001544 SSF56752 Protein matches
Abstract

Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped [PubMed1644759] into subfamilies.

One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C terminus side of the pyridoxal-phosphate-lysine. The D-amino acid transferases (D-AAT), which are among the members of this entry, are required by bacteria to catalyse the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity [PubMed7626635, PubMed9163511].


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 4 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 D-aminoacid aminotransferase-like PLP-dependent enzymes 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 4 hidden Markov models representing the D-aminoacid aminotransferase-like PLP-dependent enzymes 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 ]