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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 (3,255) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 107,250 549,010 166
Proteins 104,991 541,156 166


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)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)primary metabolic process0.23131Least 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)cofactor metabolic process0.014270Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.12071Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular protein modification process11Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.16660.0002304Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.008180.000006341Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.16980.00001107Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)amide biosynthetic process0.0004070.0579Moderately InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.0000000000440.00000005345InformativeDirect
Biological Process (BP)dicarboxylic acid metabolic process00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.0000000000000059440InformativeDirect
Biological Process (BP)organonitrogen compound catabolic process0.00046260.00000000004955InformativeDirect
Biological Process (BP)cellular modified amino acid metabolic process0.021750.04063InformativeInherited
Biological Process (BP)pteridine-containing compound metabolic process0.54770.1577InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0083950.000276InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.015491InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.10840.001465InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.93530.2773InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.21990.4906InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.44891InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.30380.01611InformativeInherited
Biological Process (BP)carboxylic acid catabolic process0.69480.01507InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.0014950.00002883InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.89790.6428InformativeInherited
Biological Process (BP)glutamine family amino acid metabolic process0.0000053340.00976InformativeInherited
Biological Process (BP)alcohol metabolic process11InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.51511InformativeInherited
Biological Process (BP)glutamate metabolic process0.000000000041120.0000000000004796Highly InformativeDirect
Biological Process (BP)biotin metabolic process00Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.00092290.00000003015Highly InformativeDirect
Biological Process (BP)dicarboxylic acid biosynthetic process0.0000049120.0005218Highly InformativeDirect
Biological Process (BP)folic acid-containing compound metabolic process0.64630.5606Highly InformativeInherited
Biological Process (BP)L-methionine salvage11Highly InformativeInherited
Biological Process (BP)alcohol biosynthetic process0.19450.264Highly InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.053220.663Highly InformativeInherited
Biological Process (BP)aldehyde catabolic process0.039390.004033Highly InformativeInherited
Biological Process (BP)glyoxylate metabolic process0.011350.001237Highly InformativeInherited
Biological Process (BP)polyol metabolic process0.00000013460.1614Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding00Moderately InformativeDirect
Molecular Function (MF)protein binding11Moderately InformativeInherited
Molecular Function (MF)isomerase activity11Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity11Moderately InformativeInherited
Molecular Function (MF)small molecule binding10.9023Moderately InformativeInherited
Molecular Function (MF)identical protein binding0.00034370.0001243InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.93850.1186InformativeInherited
Molecular Function (MF)carboxylic acid binding0.93480.119InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups10.001105InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.79130.0000004727InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups10.5871InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups11InformativeInherited
Molecular Function (MF)amino acid binding0.000021010.0000005952Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-NH2 group of donors0.000018910.0000001286Highly InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity00Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring nitrogenous groups00Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.00000017130.0000000000001472Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity00Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)intramolecular transferase activity0.0078090.02802Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.018241Highly InformativeInherited
Molecular Function (MF)aldehyde-lyase activity0.0240.1653Highly InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.17660.0006303Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.00036970.00000000003966Least InformativeDirect
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.17480.8563Least InformativeInherited
Cellular Component (CC)mitochondrial part0.025180.000000000002921Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.89021Moderately InformativeInherited
Cellular Component (CC)microbody0.000011230.00002888InformativeDirect

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) 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) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary 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 0.000006341 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00001107 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0002304 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) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 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) carbohydrate 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 0.0579 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.00000005345 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0.000207 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00002883 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) organonitrogen compound catabolic process 0.00000000004955 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.000276 Informative Direct
Biological Process (BP) protein oligomerization 0.008506 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.7895 Informative Inherited
Biological Process (BP) response to nitrogen compound 1 Informative Inherited
Biological Process (BP) behavior 0.6603 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.04063 Informative Inherited
Biological Process (BP) pteridine-containing compound metabolic process 0.1577 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.01507 Informative Inherited
Biological Process (BP) pigment metabolic process 0.2389 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.001465 Informative Inherited
Biological Process (BP) cellular metabolic compound salvage 0.2773 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.4906 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) drug metabolic process 0.01952 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.6428 Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.01611 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 1 Informative Inherited
Biological Process (BP) amine metabolic process 0.9443 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.00976 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.000412 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.0000000000004796 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0 Highly Informative Direct
Biological Process (BP) heme biosynthetic process 0.0004742 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.00000003015 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 0.00001369 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.0005218 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.0006756 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.00007629 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.5123 Highly Informative Inherited
Biological Process (BP) folic acid-containing compound metabolic process 0.5606 Highly Informative Inherited
Biological Process (BP) L-methionine salvage 1 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.264 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.663 Highly Informative Inherited
Biological Process (BP) aldehyde catabolic process 0.004033 Highly Informative Inherited
Biological Process (BP) glyoxylate metabolic process 0.001237 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.1614 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) anion binding 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.9023 Moderately Informative Inherited
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0.0000004727 Informative Direct
Molecular Function (MF) identical protein binding 0.0001243 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0.1186 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.119 Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.001105 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.5871 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 1 Informative Inherited
Molecular Function (MF) amino acid binding 0.0000005952 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.0000001286 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 0.0000000000001472 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.0006303 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) intramolecular transferase activity 0.02802 Highly Informative Inherited
Molecular Function (MF) acetyltransferase activity 1 Highly Informative Inherited
Molecular Function (MF) aldehyde-lyase activity 0.1653 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00000000003966 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.8563 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.000000000002921 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.7939 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 1 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.09548 Moderately Informative Inherited
Cellular Component (CC) transferase complex 0.4916 Moderately Informative Inherited
Cellular Component (CC) microbody 0.00002888 Informative Direct
Cellular Component (CC) synapse 1 Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.06015 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 homeostasis0.004434Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.5146Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.676Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.3159Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4776Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal amino acid level0.000201InformativeDirect
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.02009InformativeInherited
Mammalian Phenotype (MP)hypertension0.0004151Highly 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 variant0.5368Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.6419Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.2358Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.2889Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.4632Moderately InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.00484InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.01101InformativeInherited
Worm Phenotype (WP)cell stress response variant0.01982InformativeInherited
Worm Phenotype (WP)body posture variant0.0272InformativeInherited
Worm Phenotype (WP)defecation variant0.02953InformativeInherited
Worm Phenotype (WP)velocity of movement variant0.04599InformativeInherited
Worm Phenotype (WP)locomotor coordination variant0.05391InformativeInherited
Worm Phenotype (WP)mutagen induced apoptosis variant0.00004769Highly InformativeDirect
Worm Phenotype (WP)defecation contraction variant0.00005291Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.00457Highly InformativeInherited
Worm Phenotype (WP)forward point velocity variant0.01005Highly InformativeInherited
Worm Phenotype (WP)body posture amplitude variant0.0109Highly InformativeInherited
Worm Phenotype (WP)backward point velocity variant0.0111Highly InformativeInherited
Worm Phenotype (WP)roaming variant0.02325Highly InformativeInherited
Worm Phenotype (WP)foraging hyperactive0.03866Highly InformativeInherited
Worm Phenotype (WP)path curvature variant0.06278Highly 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 cluster0.01215Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.6151Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.638Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.004553Moderately InformativeInherited
Xenopus ANatomical entity (XAN)intestine0.0001175InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.08778InformativeInherited
Xenopus ANatomical entity (XAN)somite0.06555Highly 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 lyases0.0000000002369Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.000000006308Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.134Moderately 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 lyases0.0000000007614Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.6977Highly 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

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0Least InformativeDirect
Drugbank ATC_code (DB)blood and blood forming organs0.1553Least InformativeInherited
Drugbank ATC_code (DB)nervous system1Least InformativeInherited
Drugbank ATC_code (DB)antidepressants0.3143Moderately InformativeInherited
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)pyridoxal phosphate0InformativeDirect
Drugbank ATC_code (DB)irrigating solutions0.00001021InformativeDirect
Drugbank ATC_code (DB)other irrigating solutions0.000002376Highly InformativeDirect
Drugbank ATC_code (DB)phenelzine0.00001867Highly InformativeDirect

Document: DB 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 resistance0.00000000005988InformativeDirect
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 biosynthesis0.00000000000003637Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.00000000000003817Highly InformativeDirect
Biological processAntibiotic biosynthesis0.0000000000003434Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0.00000000003599Highly InformativeDirect
Biological processArginine metabolism0.00000000148Highly InformativeDirect
Biological processLipid A biosynthesis0.00021Highly InformativeDirect
Biological processPhenylalanine catabolism0.0009507Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular function2Fe-2S0InformativeDirect
Molecular functionIron-sulfur0.0001801InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionPyruvate0.000000000001149Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.00000508Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect
Post-translational modificationNitration0.000001441InformativeDirect

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 biosynthesis0.001539Moderately InformativeInherited
UniPathway (UP)amino-acid degradation0.5276Moderately 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 biosynthesis0.0000000000009365InformativeDirect
UniPathway (UP)plant hormone metabolism0.0000000002171InformativeDirect
UniPathway (UP)heterocycle biosynthesis0.000000001018InformativeDirect
UniPathway (UP)pigment biosynthesis0.0000003335InformativeDirect
UniPathway (UP)organosulfur metabolism0.000006772InformativeDirect
UniPathway (UP)putrescine metabolism0.000007525InformativeDirect
UniPathway (UP)amine and polyamine degradation0.09807InformativeInherited
UniPathway (UP)tRNA modification0.1363InformativeInherited
UniPathway (UP)amine and polyamine biosynthesis0.4225InformativeInherited
UniPathway (UP)L-arginine degradation0.9012InformativeInherited
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 degradation0.0000000000004543Highly InformativeDirect
UniPathway (UP)alanine degradation0.0000000001283Highly InformativeDirect
UniPathway (UP)2-deoxystreptamine biosynthesis0.0000000006873Highly InformativeDirect
UniPathway (UP)ectoine biosynthesis0.0000000196Highly InformativeDirect
UniPathway (UP)aminoglycoside antibiotic biosynthesis0.0000001117Highly InformativeDirect
UniPathway (UP)catecholamine biosynthesis0.00002121Highly InformativeDirect
UniPathway (UP)chlorophyll biosynthesis0.00006525Highly InformativeDirect
UniPathway (UP)L-arginine degradation via AST pathway0.000264Highly InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.01399Highly InformativeInherited
UniPathway (UP)L-threonine degradation0.8862Highly 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]