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PreATP-grasp domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   PreATP-grasp domain [ 52439]
Superfamily:   PreATP-grasp domain [ 52440] (8)
Families:   BC N-terminal domain-like [ 52441] (6)
  D-Alanine ligase N-terminal domain [ 52452] (2)
  Lysine biosynthesis enzyme LysX, N-terminal domain [ 102284]
  Prokaryotic glutathione synthetase, N-terminal domain [ 52457]
  Eukaryotic glutathione synthetase, substrate-binding domain [ 52460]
  Synapsin domain [ 52463] (2)
  Glutathionylspermidine synthase substrate-binding domain-like [ 142119]
  PurP N-terminal domain-like [ 159526]


Superfamily statistics
Genomes (3,154) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,203 156,521 37
Proteins 23,750 138,450 34


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.000000265 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.9456 Least Informative Inherited
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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) localization 0.995 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.8493 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.364 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0000000000002343 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0000000000006197 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00000000001291 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.00000002309 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000001487 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.000001071 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00000432 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00006122 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.5242 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.6648 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6759 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1842 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.003495 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.04374 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2429 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.558 Moderately Informative Inherited
Biological Process (BP) system process 0.09039 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.3622 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8112 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.8069 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1025 Moderately Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.00000000003648 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.00000000007219 Informative Direct
Biological Process (BP) amide biosynthetic process 0.0000001541 Informative Direct
Biological Process (BP) hexose metabolic process 0.000004076 Informative Direct
Biological Process (BP) synaptic transmission 0.00002371 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00003534 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.00003737 Informative Direct
Biological Process (BP) secretion by cell 0.00005601 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0001884 Informative Direct
Biological Process (BP) peptide metabolic process 0.000812 Informative Direct
Biological Process (BP) protein oligomerization 0.001393 Informative Inherited
Biological Process (BP) response to inorganic substance 0.004875 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.1716 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.3228 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.09379 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.003255 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.08238 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.002238 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 0.00000000008036 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0.00000000008231 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.0000000002888 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 0.000000002415 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 0.000000013 Highly Informative Direct
Biological Process (BP) signal release 0.00000005226 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0.0000001292 Highly Informative Direct
Biological Process (BP) peptide biosynthetic process 0.0000002112 Highly Informative Direct
Biological Process (BP) glutathione metabolic process 0.0000002752 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.000005366 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0001443 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0003565 Highly Informative Direct
Biological Process (BP) response to cadmium ion 0.0006878 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.00287 Highly Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0.0337 Highly Informative Inherited
Molecular Function (MF) binding 0.6016 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.000008062 Moderately Informative Direct
Molecular Function (MF) cation binding 0.7839 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.2578 Moderately Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.00000000004246 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.0000000001284 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000000000918 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000001762 Informative Direct
Molecular Function (MF) magnesium ion binding 0.0000303 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0001503 Informative Direct
Molecular Function (MF) nucleotide binding 0.6396 Informative Inherited
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.000000001204 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.0001799 Highly Informative Direct
Molecular Function (MF) peptide binding 1 Highly Informative Inherited
Molecular Function (MF) amino acid binding 0.44 Highly Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0.3171 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8652 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01385 Least Informative Inherited
Cellular Component (CC) membrane 0.2591 Least Informative Inherited
Cellular Component (CC) organelle membrane 0.0000001717 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.00003865 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0007111 Moderately Informative Direct
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) organelle envelope 0.002 Moderately Informative Inherited
Cellular Component (CC) synapse part 0.00000000002059 Informative Direct
Cellular Component (CC) coated vesicle 0.000003945 Informative Direct
Cellular Component (CC) neuron projection 0.2704 Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0.000000000007594 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.001288 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Least InformativeInherited
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N0.00001332InformativeDirect
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Cyclo-ligases1InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases1InformativeInherited
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzin0Highly InformativeDirect
Enzyme Commission (EC)Glutathione synthase0Highly InformativeDirect
Enzyme Commission (EC)5-(carboxyamino)imidazole ribonucleotide synthase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylaminoimidazole carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate carboxylase0.000000000000003482Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0.000000000003972Highly InformativeDirect
Enzyme Commission (EC)Methylcrotonoyl-CoA carboxylase0.00001397Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylformylglycinamidine cyclo-ligase0.00001747Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.08113Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1482Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.00002548Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.1835Moderately InformativeInherited
Phenotypic Abnormality (PA)Hyperammonemia0.00003018InformativeDirect
Phenotypic Abnormality (PA)Coma0.0002173InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0004168InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.5406Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.2012Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.03508InformativeInherited
Mammalian Phenotype (MP)abnormal social investigation0.00002748Highly InformativeDirect
Mammalian Phenotype (MP)abnormal aggression-related behavior0.00004583Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic depression0.000121Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)pigmentation variant0.0001002InformativeDirect
Worm Phenotype (WP)clear0.000006767Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.09579Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.2372Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0006591InformativeDirect
Yeast Phenotype (YP)prion formation0.0001102Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acid--amino-acid ligases (peptide synthases)0InformativeDirect
Enzyme Commission (EC)Carbon--nitrogen ligases with glutamine as amido-N-donor0.1599InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases1InformativeInherited
Enzyme Commission (EC)Carboxy-lyases1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phosphoribosylaminoimidazole carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Biotin carboxylase0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0.000000000005224Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (ammonia)0.00001453Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00008895Highly InformativeDirect
Enzyme Commission (EC)Cyclo-ligases1Highly InformativeInherited
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1Highly 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 processCell shape0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processFatty acid metabolism0.0000002027InformativeDirect
Biological processLipid biosynthesis0.004567InformativeInherited
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0.000000000002782Least InformativeDirect
Cellular componentCell junction0.0472Moderately InformativeInherited
Cellular componentSynapse0.0006985InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionBiotin0Highly InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)cell wall metabolism0Moderately InformativeDirect
UniPathway (UP)purine metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)energy metabolism0.00000000000000926Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.8771Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)lipid biosynthesis1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)IMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.00001339InformativeDirect
UniPathway (UP)fatty acid biosynthesis0.07484InformativeInherited
UniPathway (UP)metabolic intermediate degradation0.2538InformativeInherited
UniPathway (UP)oligopeptide biosynthesis0Highly InformativeDirect
UniPathway (UP)L-leucine degradation0.00000003577Highly InformativeDirect
UniPathway (UP)malonyl-CoA biosynthesis0.0000001536Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation0.0000002097Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 22 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 PreATP-grasp domain 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 22 hidden Markov models representing the PreATP-grasp domain 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 · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]