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 (2,843) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,669 38,497 9
Proteins 7,637 38,478 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 process0.00000000010380.00000000000692Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00000000018840.000000237Least InformativeDirect
Biological Process (BP)biosynthetic process0.00052330.002458Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.0000000000047660Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.0000038160.0000003161Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.000000000065970.000000000000007248Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.0000079610.0000001213Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.000000036580.000000001377Moderately InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.0000000036090.0000000000218InformativeDirect
Biological Process (BP)organonitrogen compound catabolic process0.00000000067490.0000000002061InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.011050.0259InformativeInherited
Biological Process (BP)secondary metabolic process0.052340.0212InformativeInherited
Biological Process (BP)branched-chain amino acid metabolic process00Highly InformativeDirect
Biological Process (BP)toxin metabolic process0.000015750.000000006206Highly InformativeDirect
Molecular Function (MF)transferase activity0.000000000000020640Least InformativeDirect
Molecular Function (MF)binding0.063671Least InformativeInherited
Molecular Function (MF)anion binding0.0000000000013650.0000000005837Moderately InformativeDirect
Molecular Function (MF)lyase activity0.29780.09129Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.00073730.000002052InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)transaminase activity00Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.000014360.0000000003555Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.4890.3555Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.25010.01878Least 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 0.00000000000692 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000237 Least Informative Direct
Biological Process (BP) biosynthetic process 0.002458 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) small molecule biosynthetic process 0.0000003161 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.000000000000007248 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0000001213 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000000001377 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.5752 Moderately Informative Inherited
Biological Process (BP) regulation of hormone levels 0.0001061 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0000000000218 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0.0000000002061 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0259 Informative Inherited
Biological Process (BP) secondary metabolic process 0.0212 Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) toxin metabolic process 0.000000006206 Highly Informative Direct
Biological Process (BP) secondary metabolite catabolic process 0.0003947 Highly Informative Direct
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.0000000005837 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.09129 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0.000002052 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 0.0000000003555 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.3555 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01878 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-lyases0.00000000604InformativeDirect

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)Lyases0.6824Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases0.01047Moderately InformativeInherited
Enzyme Commission (EC)Transferring nitrogenous groups0Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.0000000183Highly 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 biosynthesis0.000000000000003462Highly InformativeDirect
Cellular componentMitochondrion0.0004909Moderately InformativeDirect
DomainTransit peptide0.000000002557Moderately 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 metabolism0.0000000000001564Least InformativeDirect
UniPathway (UP)cofactor metabolism0.8561Least InformativeInherited
UniPathway (UP)aromatic compound metabolism0.9082Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0.0007186Moderately InformativeDirect
UniPathway (UP)L-isoleucine biosynthesis0InformativeDirect
UniPathway (UP)pteridine biosynthesis0.000000008961InformativeDirect
UniPathway (UP)tetrahydrofolate metabolism0.000008042InformativeDirect
UniPathway (UP)L-leucine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0Highly InformativeDirect
UniPathway (UP)tetrahydrofolate biosynthesis0.000000000007603Highly 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 ]