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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 (3,259) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 107,501 549,010 166
Proteins 105,233 541,156 166


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)biosynthetic process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process00Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)primary metabolic process0.20271Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular nitrogen 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)small molecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)cellular component assembly0.26731Moderately InformativeInherited
Biological Process (BP)cellular protein modification process11Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.086370.00001421Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.20340.000666Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.044250.0005662Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.014410Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.074540.03687Moderately InformativeInherited
Biological Process (BP)amide biosynthetic process0.00047370.08645Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.12930.03221Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process11Moderately InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.000000000030570.00000006922InformativeDirect
Biological Process (BP)dicarboxylic acid metabolic process00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.0000000000000031190InformativeDirect
Biological Process (BP)cellular modified amino acid metabolic process0.016490.02649InformativeInherited
Biological Process (BP)pteridine-containing compound metabolic process0.24980.01904InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.027221InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.065160.0003886InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.48830.03521InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.017170.002386InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.52551InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.49971InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.25480.02159InformativeInherited
Biological Process (BP)carboxylic acid catabolic process0.65520.03927InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.0015660.00005043InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.86620.5029InformativeInherited
Biological Process (BP)glutamine family amino acid metabolic process0.000006590.009826InformativeInherited
Biological Process (BP)alcohol metabolic process11InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.27180.5645InformativeInherited
Biological Process (BP)glutamate metabolic process0.000000000035820.00000000000004626Highly InformativeDirect
Biological Process (BP)biotin metabolic process00Highly InformativeDirect
Biological Process (BP)dicarboxylic acid biosynthetic process0.0000031450.0001643Highly InformativeDirect
Biological Process (BP)folic acid-containing compound metabolic process0.63360.509Highly InformativeInherited
Biological Process (BP)alcohol biosynthetic process0.14420.412Highly InformativeInherited
Biological Process (BP)L-methionine salvage11Highly InformativeInherited
Biological Process (BP)polyol metabolic process0.0000001240.03211Highly InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.072690.6522Highly InformativeInherited
Biological Process (BP)aldehyde catabolic process0.032360.004177Highly InformativeInherited
Biological Process (BP)glyoxylate metabolic process0.0025250.0001564Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)small molecule binding00Moderately InformativeDirect
Molecular Function (MF)anion binding00.00000000000001324Moderately InformativeDirect
Molecular Function (MF)isomerase activity11Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity11Moderately InformativeInherited
Molecular Function (MF)identical protein binding0.0001660.0000139InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.93120.1082InformativeInherited
Molecular Function (MF)carboxylic acid binding0.82340.09516InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups10.0009106InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups10.5367InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.81720.0000005743InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups11InformativeInherited
Molecular Function (MF)amino acid binding0.0000025690.00000001273Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-NH2 group of donors0.000021620.000000002962Highly InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity00Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring nitrogenous groups00Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.00000015880.0000000000001202Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity00Highly InformativeDirect
Molecular Function (MF)vitamin binding00Highly InformativeDirect
Molecular Function (MF)intramolecular transferase activity0.0075520.02802Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.024271Highly InformativeInherited
Molecular Function (MF)aldehyde-lyase activity0.038970.2411Highly InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.11720.0001967Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.38210.9655Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.0012770.0000000008491Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)mitochondrial part0.031510.00000000000617Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.96521Moderately InformativeInherited
Cellular Component (CC)microbody0.000012830.00004667InformativeDirect

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 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 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 catabolic process 0.0005662 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00001421 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000666 Moderately Informative Direct
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.6129 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.08645 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03221 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03687 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.0003886 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.00000006922 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0.0000003961 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00005043 Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0002016 Informative Direct
Biological Process (BP) protein oligomerization 0.012 Informative Inherited
Biological Process (BP) response to nitrogen compound 1 Informative Inherited
Biological Process (BP) behavior 0.755 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.02649 Informative Inherited
Biological Process (BP) pteridine-containing compound metabolic process 0.01904 Informative Inherited
Biological Process (BP) amine metabolic process 0.004057 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.03927 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.649 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 1 Informative Inherited
Biological Process (BP) cellular metabolic compound salvage 0.03521 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.002386 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) drug metabolic process 0.01548 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.5029 Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.02159 Informative Inherited
Biological Process (BP) pigment metabolic process 0.2328 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.009826 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.5645 Informative Inherited
Biological Process (BP) glutamate metabolic process 0.00000000000004626 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0 Highly Informative Direct
Biological Process (BP) heme biosynthetic process 0.0003298 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.00000001316 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.0006996 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 0.00002516 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.0001643 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0.0001564 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.000361 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.0000009903 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.6619 Highly Informative Inherited
Biological Process (BP) folic acid-containing compound metabolic process 0.509 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.412 Highly Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.001405 Highly Informative Inherited
Biological Process (BP) L-methionine salvage 1 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.03211 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.6522 Highly Informative Inherited
Biological Process (BP) aldehyde catabolic process 0.004177 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
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) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.00000000000001324 Moderately Informative Direct
Molecular Function (MF) isomerase activity 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.0009106 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000005743 Informative Direct
Molecular Function (MF) identical protein binding 0.0000139 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0.1082 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.09516 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.5367 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 1 Informative Inherited
Molecular Function (MF) amino acid binding 0.00000001273 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.000000002962 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring nitrogenous groups 0 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 0.0000000000001202 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.0001967 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0.02802 Highly Informative Inherited
Molecular Function (MF) acetyltransferase activity 1 Highly Informative Inherited
Molecular Function (MF) aldehyde-lyase activity 0.2411 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0000000008491 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9655 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.00000000000617 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.6298 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.9272 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.08569 Moderately Informative Inherited
Cellular Component (CC) microbody 0.00004667 Informative Direct
Cellular Component (CC) synapse 1 Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.09658 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 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) Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.006187Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.5054Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.7019Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.3185Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4839Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal amino acid level0.0001867InformativeDirect
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.01924InformativeInherited
Mammalian Phenotype (MP)hypertension0.0003914Highly 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 variant0.5891Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.5933Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.3187Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.3221Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.4864Moderately InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.01108InformativeInherited
Worm Phenotype (WP)body posture variant0.03027InformativeInherited
Worm Phenotype (WP)defecation variant0.03414InformativeInherited
Worm Phenotype (WP)cell stress response variant0.0428InformativeInherited
Worm Phenotype (WP)velocity of movement variant0.04463InformativeInherited
Worm Phenotype (WP)locomotor coordination variant0.05376InformativeInherited
Worm Phenotype (WP)defecation contraction variant0.00005884Highly InformativeDirect
Worm Phenotype (WP)mutagen induced apoptosis variant0.00008663Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.005422Highly InformativeInherited
Worm Phenotype (WP)forward point velocity variant0.0112Highly InformativeInherited
Worm Phenotype (WP)body posture amplitude variant0.01212Highly 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)anatomical cluster0.01194Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6296Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.6495Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.004665Moderately InformativeInherited
Xenopus ANatomical entity (XAN)intestine0.0001125InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.1117InformativeInherited
Xenopus ANatomical entity (XAN)somite0.08644Highly InformativeInherited

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 lyases0.00000000008851Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.0000000001259Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.941Moderately 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 lyases0.0000000007569Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.6973Highly 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 resistance0.0000000000592InformativeDirect
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 processHeme biosynthesis0.00000000000003277Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.00000000000003526Highly InformativeDirect
Biological processAntibiotic biosynthesis0.0000000000003168Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0.00000000003285Highly InformativeDirect
Biological processArginine metabolism0.000000001379Highly InformativeDirect
Biological processLipid A biosynthesis0.0002036Highly InformativeDirect
Biological processPhenylalanine catabolism0.0009313Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionIron-sulfur0.0002061Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionSelenium0Highly InformativeDirect
Molecular functionPyruvate0.000000004382Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.00000009055Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect
Post-translational modificationNitration0.000001427InformativeDirect

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)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)porphyrin-containing compound metabolism0Moderately InformativeDirect
UniPathway (UP)macrocycle metabolism0Moderately InformativeDirect
UniPathway (UP)antibiotic biosynthesis0.0015Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.5192Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)energy metabolism1Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)membrane lipid metabolism1Moderately InformativeInherited
UniPathway (UP)protoporphyrin-IX biosynthesis0InformativeDirect
UniPathway (UP)L-histidine biosynthesis0.0000000000006569InformativeDirect
UniPathway (UP)plant hormone metabolism0.000000000361InformativeDirect
UniPathway (UP)heterocycle biosynthesis0.000000001InformativeDirect
UniPathway (UP)pigment biosynthesis0.0000003642InformativeDirect
UniPathway (UP)organosulfur metabolism0.00000177InformativeDirect
UniPathway (UP)putrescine metabolism0.000007241InformativeDirect
UniPathway (UP)amine and polyamine degradation0.0961InformativeInherited
UniPathway (UP)tRNA modification0.1218InformativeInherited
UniPathway (UP)amine and polyamine biosynthesis0.4199InformativeInherited
UniPathway (UP)L-arginine degradation0.883InformativeInherited
UniPathway (UP)tryptophan metabolism1InformativeInherited
UniPathway (UP)nucleotide-sugar biosynthesis1InformativeInherited
UniPathway (UP)UDP-4-deoxy-4-formamido-beta-L-arabinose biosynthesis0Highly InformativeDirect
UniPathway (UP)biotin biosynthesis0Highly InformativeDirect
UniPathway (UP)L-serine biosynthesis0Highly InformativeDirect
UniPathway (UP)putrescine degradation0Highly InformativeDirect
UniPathway (UP)sphingolipid metabolism0Highly InformativeDirect
UniPathway (UP)hydrocarbon biosynthesis0Highly InformativeDirect
UniPathway (UP)alkene metabolism0Highly InformativeDirect
UniPathway (UP)aminoacyl-tRNA biosynthesis0Highly InformativeDirect
UniPathway (UP)L-tryptophan degradation0.0000000000004498Highly InformativeDirect
UniPathway (UP)alanine degradation0.0000000001939Highly InformativeDirect
UniPathway (UP)2-deoxystreptamine biosynthesis0.0000000006733Highly InformativeDirect
UniPathway (UP)ectoine biosynthesis0.00000001906Highly InformativeDirect
UniPathway (UP)aminoglycoside antibiotic biosynthesis0.0000001115Highly InformativeDirect
UniPathway (UP)catecholamine biosynthesis0.00002087Highly InformativeDirect
UniPathway (UP)chlorophyll biosynthesis0.0000634Highly InformativeDirect
UniPathway (UP)L-arginine degradation via AST pathway0.0002547Highly InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.01708Highly InformativeInherited
UniPathway (UP)L-threonine degradation0.8845Highly 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]