SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,212) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 104,693 241,075 166
Proteins 102,556 236,849 166


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 process00Least InformativeDirect
Biological Process (BP)biosynthetic process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)regulation of cellular process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process00Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)negative regulation of cellular process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.43540.04659Moderately InformativeInherited
Biological Process (BP)cellular protein modification process11Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.020140Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0079160.0002093Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.059660.1341Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.075620.1076Moderately InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.35470.4526Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process11Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process11Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process10.8915Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process11Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.0064330.002315Moderately InformativeInherited
Biological Process (BP)cellular biogenic amine metabolic process9.804e-070InformativeDirect
Biological Process (BP)aspartate family amino acid metabolic process3.803e-090.0002226InformativeDirect
Biological Process (BP)cellular amide metabolic process00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process6.167e-150InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process6.84e-057.124e-07InformativeDirect
Biological Process (BP)negative regulation of response to stimulus0.44661InformativeInherited
Biological Process (BP)cellular ketone metabolic process0.024810.004476InformativeInherited
Biological Process (BP)carboxylic acid catabolic process0.49490.001645InformativeInherited
Biological Process (BP)cellular modified amino acid metabolic process11InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.17070.2026InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.23351InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.87190.09431InformativeInherited
Biological Process (BP)vitamin metabolic process0.0036251.928e-05InformativeInherited
Biological Process (BP)phospholipid metabolic process0.037290.01915InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.031240InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.0073540.5431InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.13630.8879InformativeInherited
Biological Process (BP)alcohol metabolic process0.58451InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.22171InformativeInherited
Biological Process (BP)glutamate metabolic process4.708e-130Highly InformativeDirect
Biological Process (BP)amide biosynthetic process00Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.00011981.374e-06Highly InformativeDirect
Biological Process (BP)regulation of cellular response to stress0.044270.6996Highly InformativeInherited
Biological Process (BP)benzene-containing compound metabolic process0.0012441.185e-05Highly InformativeInherited
Biological Process (BP)L-methionine biosynthetic process0.46190.002829Highly InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.047510.03659Highly InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.00058070.1607Highly InformativeInherited
Biological Process (BP)sphingolipid biosynthetic process0.11437.99e-06Highly InformativeInherited
Biological Process (BP)ethanolamine-containing compound metabolic process0.056530.0005453Highly InformativeInherited
Biological Process (BP)serine family amino acid metabolic process0.023860.003692Highly InformativeInherited
Biological Process (BP)alcohol biosynthetic process0.08650.3196Highly InformativeInherited
Biological Process (BP)polyol metabolic process1.609e-080.003275Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding1.966e-142.032e-14Moderately InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.53396.102e-07InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.33057.371e-08InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups11InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups0.98960.8523InformativeInherited
Molecular Function (MF)transaminase activity00Highly InformativeDirect
Molecular Function (MF)C-acyltransferase activity00Highly InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity1.057e-130Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.0001371.189e-08Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity00Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)acetyltransferase activity0.24161Highly InformativeInherited
Molecular Function (MF)aldehyde-lyase activity0.20550.1776Highly InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.021570.001416Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.61491Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0022537.416e-11Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)mitochondrial part0.091862.917e-09Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.82031Moderately InformativeInherited
Cellular Component (CC)mitochondrial matrix3.919e-051.636e-12InformativeDirect
Cellular Component (CC)microbody0.0001860.0002445InformativeDirect

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 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0002093 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.6364 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.5837 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04659 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.764 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1076 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1341 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.4526 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.8915 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.002315 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) vitamin metabolic process 1.928e-05 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.0002226 Informative Direct
Biological Process (BP) cellular amide metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 7.124e-07 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) cellular ketone metabolic process 0.004476 Informative Inherited
Biological Process (BP) cation homeostasis 0.7742 Informative Inherited
Biological Process (BP) response to organonitrogen compound 0.09886 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.606 Informative Inherited
Biological Process (BP) single-organism behavior 0.4467 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.001645 Informative Inherited
Biological Process (BP) pigment metabolic process 0.356 Informative Inherited
Biological Process (BP) cell-cell signaling 0.4765 Informative Inherited
Biological Process (BP) transmission of nerve impulse 0.1758 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 1 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.2026 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) cellular component movement 1 Informative Inherited
Biological Process (BP) locomotion 1 Informative Inherited
Biological Process (BP) localization of cell 1 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.09431 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.5431 Informative Inherited
Biological Process (BP) steroid metabolic process 0.901 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.0824 Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.01915 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.8879 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) reproductive structure development 0.9776 Informative Inherited
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 1 Informative Inherited
Biological Process (BP) response to hypoxia 0.0006079 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0 Highly Informative Direct
Biological Process (BP) porphyrin-containing compound biosynthetic process 2.485e-05 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.0005458 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 7.99e-06 Highly Informative Direct
Biological Process (BP) heme metabolic process 2.486e-05 Highly Informative Direct
Biological Process (BP) ethanolamine-containing compound metabolic process 0.0005453 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 1.185e-05 Highly Informative Direct
Biological Process (BP) molybdopterin cofactor metabolic process 0 Highly Informative Direct
Biological Process (BP) amide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 1.374e-06 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.6996 Highly Informative Inherited
Biological Process (BP) L-methionine biosynthetic process 0.002829 Highly Informative Inherited
Biological Process (BP) transition metal ion homeostasis 0.006535 Highly Informative Inherited
Biological Process (BP) response to alkaloid 0.004922 Highly Informative Inherited
Biological Process (BP) adult behavior 0.0176 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 1 Highly Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.03659 Highly Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.001542 Highly Informative Inherited
Biological Process (BP) development of primary male sexual characteristics 0.05441 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.1607 Highly Informative Inherited
Biological Process (BP) cellular hormone metabolic process 0.1234 Highly Informative Inherited
Biological Process (BP) pigment biosynthetic process 0.005983 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.003692 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.3196 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.003275 Highly Informative Inherited
Biological Process (BP) gonad development 0.2913 Highly Informative Inherited
Biological Process (BP) ovulation cycle process 0.00833 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.02628 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.032e-14 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 6.102e-07 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 7.371e-08 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.2802 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0.8523 Informative Inherited
Molecular Function (MF) transaminase activity 0 Highly Informative Direct
Molecular Function (MF) C-acyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.0004627 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 1.189e-08 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 1 Highly Informative Inherited
Molecular Function (MF) aldehyde-lyase activity 0.1776 Highly Informative Inherited
Molecular Function (MF) carboxy-lyase activity 0.001416 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 7.416e-11 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 2.917e-09 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.6164 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.9842 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.02623 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.1472 Moderately Informative Inherited
Cellular Component (CC) mitochondrial matrix 1.636e-12 Informative Direct
Cellular Component (CC) microbody 0.0002445 Informative Direct
Cellular Component (CC) plastid 0.002478 Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.02415 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups2.923e-08Least 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 nervous system physiology0.8681Least InformativeInherited
Phenotypic Abnormality (PA)Behavioral abnormality0.3532InformativeInherited
Phenotypic Abnormality (PA)Abnormal emotion/affect behavior0.04051Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.2459Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.7868Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.694InformativeInherited
Mammalian Phenotype (MP)abnormal inhibitory postsynaptic currents0.0003375Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.8634Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.1159Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.3164Moderately InformativeInherited
Worm Phenotype (WP)copulation variant0.0007429InformativeDirect
Worm Phenotype (WP)cell stress response variant0.006383InformativeInherited
Worm Phenotype (WP)genotoxic induced apoptosis variant1.751e-06Highly InformativeDirect
Worm Phenotype (WP)defecation contraction variant1.474e-05Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.0001284Highly InformativeDirect
Worm Phenotype (WP)cell ionizing radiation response variant0.007378Highly InformativeInherited

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system7.976e-05Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.04437Least InformativeInherited
Xenopus ANatomical entity (XAN)intestine1.76e-06Moderately InformativeDirect

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 lyases4.62e-10Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups5.57e-07Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases8.252e-05Moderately InformativeDirect
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 transferases (mutases)0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.7731InformativeInherited
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 lyases1.579e-09Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.9064Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited
Enzyme Commission (EC)Acting on phosphates1Highly 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 resistance2.391e-10InformativeDirect
Biological processLipid biosynthesis1InformativeInherited
Biological processChlorophyll biosynthesis0Highly InformativeDirect
Biological processHeme 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 biosynthesis1.308e-12Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis3.376e-12Highly InformativeDirect
Biological processAntibiotic biosynthesis8.708e-11Highly InformativeDirect
Biological processArginine metabolism1.768e-09Highly InformativeDirect
Biological processLipid A biosynthesis0.0002064Highly InformativeDirect
Biological processPhenylalanine catabolism0.0009803Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionPyruvate3.988e-12Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.0001124Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect
Post-translational modificationNitration2.014e-06InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
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)heterocycle metabolism0Moderately InformativeDirect
UniPathway (UP)macrocycle metabolism0Moderately InformativeDirect
UniPathway (UP)pigment metabolism6.23e-05Moderately InformativeDirect
UniPathway (UP)antibiotic biosynthesis0.009418Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)energy metabolism1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)organic acid metabolism1Moderately InformativeInherited
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)protoporphyrin-IX biosynthesis0InformativeDirect
UniPathway (UP)plant hormone biosynthesis3.758e-09InformativeDirect
UniPathway (UP)pigment biosynthesis5.049e-05InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0.358InformativeInherited
UniPathway (UP)organic acid degradation0.6235InformativeInherited
UniPathway (UP)heterocycle biosynthesis0.9297InformativeInherited
UniPathway (UP)alanine metabolism1InformativeInherited
UniPathway (UP)UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis0Highly InformativeDirect
UniPathway (UP)biotin biosynthesis0Highly InformativeDirect
UniPathway (UP)hydrocarbon biosynthesis5.348e-13Highly InformativeDirect
UniPathway (UP)alkene metabolism5.348e-13Highly InformativeDirect
UniPathway (UP)alanine degradation7.264e-13Highly InformativeDirect
UniPathway (UP)2-deoxystreptamine biosynthesis6.136e-08Highly InformativeDirect
UniPathway (UP)catecholamine biosynthesis1.32e-06Highly InformativeDirect
UniPathway (UP)aminoglycoside antibiotic biosynthesis1.415e-06Highly InformativeDirect
UniPathway (UP)ectoine biosynthesis1.512e-05Highly InformativeDirect
UniPathway (UP)chlorophyll biosynthesis2.146e-05Highly InformativeDirect
UniPathway (UP)L-threonine degradation5.851e-05Highly InformativeDirect
UniPathway (UP)L-phenylalanine degradation0.0001202Highly InformativeDirect
UniPathway (UP)L-lysine biosynthesis via AAA pathway0.0001441Highly InformativeDirect
UniPathway (UP)organosulfur metabolism0.0009915Highly InformativeDirect
UniPathway (UP)nonprotein amino-acid degradation0.003423Highly InformativeInherited
UniPathway (UP)4-aminobutanoate metabolism0.01146Highly InformativeInherited

Document: UP 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

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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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]