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 (2,489) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 85,183 241,075 166
Proteins 83,327 236,849 166


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)multicellular organismal process11Least InformativeInherited
Biological Process (BP)developmental process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process1.891e-071.825e-13Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process00Moderately InformativeDirect
Biological Process (BP)single-organism developmental process11Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.38091Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.78530.08117Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.4210.02074Moderately InformativeInherited
Biological Process (BP)cellular protein modification process11Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0019790Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.0071220.0379Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.046350.2056Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process11Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process10.9315Moderately InformativeInherited
Biological Process (BP)organophosphate metabolic process11Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process11Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process11Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.0048717.146e-05Moderately InformativeInherited
Biological Process (BP)cellular biogenic amine metabolic process7.26e-060InformativeDirect
Biological Process (BP)vitamin metabolic process7.448e-051.102e-05InformativeDirect
Biological Process (BP)glutamine family amino acid metabolic process1.767e-143.131e-12InformativeDirect
Biological Process (BP)aspartate family amino acid metabolic process4.329e-102.162e-07InformativeDirect
Biological Process (BP)cellular amide metabolic process00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process2.949e-107.914e-12InformativeDirect
Biological Process (BP)carboxylic acid catabolic process2.145e-060InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process1.892e-052.022e-06InformativeDirect
Biological Process (BP)amine biosynthetic process0.28361.095e-05InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.5950.4652InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.5690.1674InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.24131InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.68840.03671InformativeInherited
Biological Process (BP)phospholipid metabolic process0.010460.005542InformativeInherited
Biological Process (BP)membrane lipid metabolic process0.0068960InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.014130.4742InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.053950.5288InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.049210.5853InformativeInherited
Biological Process (BP)alcohol metabolic process0.52521InformativeInherited
Biological Process (BP)dicarboxylic acid metabolic process00Highly InformativeDirect
Biological Process (BP)L-methionine biosynthetic process0.39010.005488Highly InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.039980.03716Highly InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.00028410.09205Highly InformativeInherited
Biological Process (BP)monocarboxylic acid catabolic process11Highly InformativeInherited
Biological Process (BP)membrane lipid biosynthetic process0.46485.917e-07Highly InformativeInherited
Biological Process (BP)ceramide metabolic process2.301e-060.329Highly InformativeInherited
Biological Process (BP)ethanolamine-containing compound metabolic process0.045610.004609Highly InformativeInherited
Biological Process (BP)diol metabolic process0.049594.725e-05Highly InformativeInherited
Biological Process (BP)serine family amino acid metabolic process0.020632.786e-05Highly InformativeInherited
Biological Process (BP)alcohol biosynthetic process0.040680.3876Highly InformativeInherited
Biological Process (BP)polyol metabolic process0.00045520.04872Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity1.359e-140Moderately InformativeDirect
Molecular Function (MF)anion binding4.069e-142.042e-13Moderately InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.73019.411e-06InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.21931.585e-07InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups11InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups11InformativeInherited
Molecular Function (MF)transaminase activity00Highly InformativeDirect
Molecular Function (MF)C-acyltransferase activity00Highly InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity7.537e-140Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity1.932e-053.427e-10Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity00Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)acetyltransferase activity0.18361Highly InformativeInherited
Molecular Function (MF)aldehyde-lyase activity0.027070.08055Highly InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.15780.008627Highly InformativeInherited
Cellular Component (CC)cytoplasmic part5.389e-050Least InformativeDirect
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.012830.03141Least InformativeInherited
Cellular Component (CC)mitochondrial part0.14561.502e-10Moderately InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.63041Moderately InformativeInherited

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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic 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) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.825e-13 Moderately Informative Direct
Biological Process (BP) small molecule 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) organic hydroxy compound metabolic process 7.146e-05 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.4043 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) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.9507 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.629 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9315 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) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.08117 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02074 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) heterocycle biosynthetic process 0.0379 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.2056 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 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 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 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 1.102e-05 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 3.131e-12 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 2.162e-07 Informative Direct
Biological Process (BP) amine biosynthetic process 1.095e-05 Informative Direct
Biological Process (BP) cellular amide metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 7.914e-12 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 2.022e-06 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.4196 Informative Inherited
Biological Process (BP) single-organism behavior 0.2284 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 1 Informative Inherited
Biological Process (BP) response to organic nitrogen 0.4347 Informative Inherited
Biological Process (BP) tetrapyrrole metabolic process 0.001253 Informative Inherited
Biological Process (BP) pigment metabolic process 0.577 Informative Inherited
Biological Process (BP) synaptic transmission 0.02055 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 1 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.4652 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.1674 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 1 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 0.03671 Informative Inherited
Biological Process (BP) steroid metabolic process 0.9314 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.05017 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.06802 Informative Inherited
Biological Process (BP) metal ion homeostasis 1 Informative Inherited
Biological Process (BP) phospholipid metabolic process 0.005542 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.4742 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.5288 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.5853 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) reproductive system development 0.8869 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) regulation of neurotransmitter levels 0.0008961 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.0004005 Highly Informative Direct
Biological Process (BP) porphyrin-containing compound biosynthetic process 0.0003192 Highly Informative Direct
Biological Process (BP) cellular iron ion homeostasis 0.0006572 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 2.786e-05 Highly Informative Direct
Biological Process (BP) aromatic amino acid family catabolic process 0.0002117 Highly Informative Direct
Biological Process (BP) nonribosomal peptide biosynthetic process 9.295e-05 Highly Informative Direct
Biological Process (BP) diol metabolic process 4.725e-05 Highly Informative Direct
Biological Process (BP) heme metabolic process 0.0008159 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 1.596e-05 Highly Informative Direct
Biological Process (BP) response to alkaloid 0.000449 Highly Informative Direct
Biological Process (BP) dicarboxylic acid metabolic process 0 Highly Informative Direct
Biological Process (BP) membrane lipid biosynthetic process 5.917e-07 Highly Informative Direct
Biological Process (BP) L-methionine biosynthetic process 0.005488 Highly Informative Inherited
Biological Process (BP) adult behavior 0.01046 Highly Informative Inherited
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.9583 Highly Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.03716 Highly Informative Inherited
Biological Process (BP) secondary metabolite biosynthetic process 1 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.09205 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.1873 Highly Informative Inherited
Biological Process (BP) monocarboxylic acid catabolic process 1 Highly Informative Inherited
Biological Process (BP) ceramide metabolic process 0.329 Highly Informative Inherited
Biological Process (BP) ethanolamine-containing compound metabolic process 0.004609 Highly Informative Inherited
Biological Process (BP) glutamine family amino acid catabolic process 0.1279 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.3876 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.04872 Highly Informative Inherited
Biological Process (BP) gonad development 0.2063 Highly Informative Inherited
Biological Process (BP) ovulation cycle process 0.006029 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.0192 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 2.042e-13 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 9.411e-06 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 1.585e-07 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.258 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 1 Informative Inherited
Molecular Function (MF) transaminase activity 0 Highly Informative Direct
Molecular Function (MF) C-acyltransferase activity 0 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 3.427e-10 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 0.08055 Highly Informative Inherited
Molecular Function (MF) carboxy-lyase activity 0.008627 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.03141 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 1.502e-10 Moderately Informative Direct
Cellular Component (CC) extracellular region 1 Moderately Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.6647 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.5882 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.01256 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.01354 Moderately Informative Inherited
Cellular Component (CC) plastid 0.001323 Informative Inherited
Cellular Component (CC) endoplasmic reticulum membrane 0.005065 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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.7484Least InformativeInherited
Disease Ontology (DO)brain disease0.3841Moderately InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the central nervous system0.7284Least InformativeInherited
Phenotypic Abnormality (PA)Behavioural/Psychiatric Abnormality0.332InformativeInherited
Phenotypic Abnormality (PA)Irritability0.0007881Highly InformativeDirect

Document: HP 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 system7.763e-05Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.04699Least InformativeInherited
Xenopus ANatomical entity (XAN)intestine1.733e-06Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)plant cell0.4816Least InformativeInherited
Plant ANatomical entity (PAN)guard cell0.0001007Moderately InformativeDirect

Document: AP 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 lyases2.89e-09Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups6.475e-07Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases4.163e-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-lyases0.8903InformativeInherited
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 lyases9.281e-10Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.8532Highly 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)blood and blood forming organs9.965e-06Least InformativeDirect
Drugbank ATC_code (DB)digestives, incl. enzymes0.0007812Moderately InformativeDirect
Drugbank ATC_code (DB)antidotes0.1852Moderately InformativeInherited
Drugbank ATC_code (DB)respiratory system0.2754Moderately InformativeInherited
Drugbank ATC_code (DB)other ophthalmologicals1Moderately InformativeInherited
Drugbank ATC_code (DB)other irrigating solutions2.316e-09InformativeDirect
Drugbank ATC_code (DB)glutamic acid hydrochloride9.426e-07InformativeDirect
Drugbank ATC_code (DB)mucolytics0.0003782Highly InformativeDirect
Drugbank ATC_code (DB)acetylcysteine0.0003782Highly InformativeDirect
Drugbank ATC_code (DB)acetylcysteine0.0003782Highly 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 resistance2.441e-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 processPyridoxine biosynthesis0Highly InformativeDirect
Biological processSphingolipid metabolism0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis1.161e-11Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis1.256e-11Highly InformativeDirect
Biological processAntibiotic biosynthesis4.488e-11Highly InformativeDirect
Biological processArginine metabolism1.853e-09Highly InformativeDirect
Biological processLipid A biosynthesis0.0002143Highly InformativeDirect
Biological processTyrosine catabolism0.0004674Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.000994Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

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)amino-acid degradation0.5992Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism0.9136Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)energy metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)protoporphyrin-IX biosynthesis0InformativeDirect
UniPathway (UP)heterocycle biosynthesis5.077e-10InformativeDirect
UniPathway (UP)hormone metabolism9.959e-09InformativeDirect
UniPathway (UP)pigment biosynthesis1.34e-08InformativeDirect
UniPathway (UP)histidine metabolism2.686e-06InformativeDirect
UniPathway (UP)putrescine metabolism3.465e-06InformativeDirect
UniPathway (UP)antibiotic biosynthesis0.0007444InformativeDirect
UniPathway (UP)tRNA modification0.07061InformativeInherited
UniPathway (UP)amine and polyamine degradation0.1036InformativeInherited
UniPathway (UP)amine and polyamine biosynthesis0.403InformativeInherited
UniPathway (UP)L-arginine degradation0.9345InformativeInherited
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)aminoacyl-tRNA biosynthesis0Highly InformativeDirect
UniPathway (UP)L-tryptophan degradation2.504e-13Highly InformativeDirect
UniPathway (UP)2-deoxystreptamine biosynthesis4.649e-10Highly InformativeDirect
UniPathway (UP)ectoine biosynthesis8.362e-09Highly InformativeDirect
UniPathway (UP)aminoglycoside antibiotic biosynthesis2.165e-08Highly InformativeDirect
UniPathway (UP)chlorophyll biosynthesis1.326e-05Highly InformativeDirect
UniPathway (UP)catecholamine biosynthesis1.649e-05Highly InformativeDirect
UniPathway (UP)L-arginine degradation via AST pathway9.132e-05Highly InformativeDirect
UniPathway (UP)organosulfur metabolism0.0001915Highly InformativeDirect
UniPathway (UP)plant hormone biosynthesis0.005602Highly InformativeInherited
UniPathway (UP)alanine metabolism1Highly InformativeInherited
UniPathway (UP)L-threonine degradation1Highly 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) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]