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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 (2,850) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 7,688 40,958 9
Proteins 7,656 40,888 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)biosynthetic process0.0000016390.000000009183Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000000000000038810Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000014810.000002549Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000000000001280.00000000000007621Least InformativeDirect
Biological Process (BP)primary metabolic process0.19780.5191Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular catabolic process0.00000024810.00000009912Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.00000025770.00000000008819Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.0000012120.0000002465Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process0.0000014590.0000001504Moderately InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.000014290.00001085InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.00097690.01451InformativeInherited
Biological Process (BP)branched-chain amino acid metabolic process0.000000074860.00000000007301Highly InformativeDirect
Molecular Function (MF)transferase activity0.0000000015710.0000000001072Least InformativeDirect
Molecular Function (MF)binding0.003860.4856Least InformativeInherited
Molecular Function (MF)small molecule binding0.0000000000020970.000000000005301Moderately InformativeDirect
Molecular Function (MF)anion binding0.00000000000032010.00000000008Moderately InformativeDirect
Molecular Function (MF)lyase activity0.039530.01032Moderately InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.0000040350.00000007441InformativeDirect
Molecular Function (MF)transferase activity, transferring nitrogenous groups00Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.000000011230.000000000002387Highly InformativeDirect
Molecular Function (MF)vitamin 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) biosynthetic process 0.000000009183 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000002549 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000000000007621 Least Informative Direct
Biological Process (BP) primary metabolic process 0.5191 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00000009912 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00000000008819 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0000002465 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0000001504 Moderately Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.00001085 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.01451 Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0.00000000007301 Highly Informative Direct
Molecular Function (MF) transferase activity 0.0000000001072 Least Informative Direct
Molecular Function (MF) binding 0.4856 Least Informative Inherited
Molecular Function (MF) small molecule binding 0.000000000005301 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000000008 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.01032 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0.00000007441 Informative Direct
Molecular Function (MF) transferase activity, transferring nitrogenous groups 0 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 0.000000000002387 Highly Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8195 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1705 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

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 biosynthesis0.000000000000006373Highly InformativeDirect
Cellular componentMitochondrion0.0001494Moderately InformativeDirect
DomainTransit peptide0.00000000002921Moderately InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]