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PLP-dependent transferases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   PLP-dependent transferase-like [ 53382] (3)
Superfamily:   PLP-dependent transferases [ 53383] (9)
Families:   AAT-like [ 53384] (16)
  Beta-eliminating lyases [ 53397] (2)
  Pyridoxal-dependent decarboxylase [ 69565] (3)
  Cystathionine synthase-like [ 53402] (16)
  GABA-aminotransferase-like [ 53417] (16)
  Ornithine decarboxylase major domain [ 53444]
  Glycine dehydrogenase subunits (GDC-P) [ 142678] (2)
  SelA-like [ 142683]
  SepSecS-like [ 159704]


Superfamily statistics
Genomes (3,262) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 107,854 0 166
Proteins 105,575 0 166


Functional annotation
General category Metabolism
Detailed category Transferases

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.00000002923Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Transferring nitrogenous groups0InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.821InformativeInherited
Enzyme Commission (EC)Glutamate decarboxylase0Highly InformativeDirect
Enzyme Commission (EC)Molybdenum cofactor sulfurtransferase0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.174Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.5895Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system0.4279Moderately InformativeInherited
Phenotypic Abnormality (PA)Aciduria0.0007479InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.006107Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.5054Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.6997Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.3171Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4829Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal amino acid level0.0001799InformativeDirect
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.01917InformativeInherited
Mammalian Phenotype (MP)hypertension0.0003925Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism behavior variant0.445Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.5993Least InformativeInherited
Worm Phenotype (WP)movement variant0.3193Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.3455Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.4928Moderately InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.01126InformativeInherited
Worm Phenotype (WP)body posture variant0.03066InformativeInherited
Worm Phenotype (WP)defecation variant0.03473InformativeInherited
Worm Phenotype (WP)cell stress response variant0.04325InformativeInherited
Worm Phenotype (WP)velocity of movement variant0.04478InformativeInherited
Worm Phenotype (WP)locomotor coordination variant0.05501InformativeInherited
Worm Phenotype (WP)defecation contraction variant0.0000595Highly InformativeDirect
Worm Phenotype (WP)mutagen induced apoptosis variant0.0000876Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.005467Highly InformativeInherited
Worm Phenotype (WP)forward point velocity variant0.01127Highly InformativeInherited
Worm Phenotype (WP)body posture amplitude variant0.01221Highly InformativeInherited
Worm Phenotype (WP)path curvature variant0.06294Highly InformativeInherited

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.3964Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3985Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk0.3994Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.5126Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.0006928Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.002113Moderately InformativeInherited
Xenopus ANatomical entity (XAN)intestine0.00002153InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.1972InformativeInherited

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0.00000000003814Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0000000001375Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.9981Moderately InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases1Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Intramolecular transferases0InformativeDirect
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Transferring nitrogenous groups0Highly InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0.0000000008892Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.7283Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited
Enzyme Commission (EC)Acid--thiol ligases1Highly 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 processLipid metabolism1Moderately InformativeInherited
Biological processAntibiotic biosynthesis0.00000000000007863InformativeDirect
Biological processAntibiotic resistance0.000000000007181InformativeDirect
Biological processLipid biosynthesis1InformativeInherited
Biological processChlorophyll biosynthesis0Highly InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Biological processOne-carbon metabolism0Highly InformativeDirect
Biological processPorphyrin biosynthesis0Highly InformativeDirect
Biological processPyridine nucleotide biosynthesis0Highly InformativeDirect
Biological processSphingolipid metabolism0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.000000000000002402Highly InformativeDirect
Biological processHeme biosynthesis0.00000000000003036Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0.0000000000301Highly InformativeDirect
Biological processArginine metabolism0.000000001216Highly InformativeDirect
Biological processLipid A biosynthesis0.00005337Highly InformativeDirect
Biological processPhenylalanine catabolism0.0009955Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionIron-sulfur0.0004849Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionSelenium0Highly InformativeDirect
Molecular functionPyruvate0.000000003821Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.00000004138Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect
Post-translational modificationNitration0.0000007561InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015424 SSF53383 Protein matches
Abstract

This entry represents the major region of PLP-dependent transferases. This domain has a three layer alpha/beta/alpha sandwich topology, with mixed beta-sheets of 7 strands. The major region can be found in the following PLP-dependent transferase families:

  • Aspartate aminotransferase (AAT)-like enzymes, such as aromatic aminoacid aminotransferase AroAT, glutamine aminotransferase and kynureninase [PubMed17300176].
  • Beta-eliminating lyases, such as tyrosine phenol lyase and tryptophanase [PubMed16790938].
  • Pyridoxal-dependent decarboxylases, such as DOPA decarboxylase and glutamate decarboxylase beta (GadB) [PubMed15690345].
  • Cystathionine synthase-like enzymes, such as cystalysin, methionine gamma-lyase (MGL), and cysteine desulphurase (IscS) [PubMed17014820].
  • GABA-aminotransferase-like enzymes, such as ornithine aminotransferase and serine hydroxymethyltransferase [PubMed15848278].
  • Ornithine decarboxylase major domain [PubMed10666573].

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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 92 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 PLP-dependent transferases 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 92 hidden Markov models representing the PLP-dependent transferases 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]