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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 (3,163) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 27,353 166,349 37
Proteins 23,884 146,434 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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0002488 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000001008 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4888 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.1454 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.6041 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.009629 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.00000002369 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.000005565 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.00000000000001422 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00008947 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00006739 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000002468 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.7452 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.2107 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.02765 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.9606 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.5278 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.1014 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.04619 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.006201 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.001824 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.7383 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.00344 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2093 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.1987 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.3172 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.01369 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.9532 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.7618 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.1489 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.8302 Moderately Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.00000005013 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000007745 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.0002012 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0.00005978 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0000000907 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.00003107 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.000001989 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.00000000000001763 Informative Direct
Biological Process (BP) protein oligomerization 0.003216 Informative Inherited
Biological Process (BP) response to metal ion 0.3527 Informative Inherited
Biological Process (BP) circulatory system development 0.3716 Informative Inherited
Biological Process (BP) secretion by cell 0.1016 Informative Inherited
Biological Process (BP) central nervous system development 0.2106 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.9696 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.5413 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.4216 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.8313 Informative Inherited
Biological Process (BP) regulation of neurotransmitter levels 0.0000004367 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000006592 Highly Informative Direct
Biological Process (BP) glutathione metabolic process 0.0000001687 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.000007714 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) nonribosomal peptide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) hexose biosynthetic process 0.000000007285 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0.00000001303 Highly Informative Direct
Biological Process (BP) camera-type eye development 0.000007782 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.00001573 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.004123 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.04048 Highly Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0.001075 Highly Informative Inherited
Molecular Function (MF) binding 0.6494 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0000004237 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) lyase activity 0.22 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.3329 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00001232 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.000000000008108 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.0000007912 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.00000003611 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.00000001761 Informative Direct
Molecular Function (MF) ribonucleotide binding 0 Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0000000000006142 Informative Direct
Molecular Function (MF) protein dimerization activity 0.0006703 Informative Direct
Molecular Function (MF) sulfur compound binding 0 Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.00001577 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00000000003996 Highly Informative Direct
Molecular Function (MF) vitamin binding 0.000007292 Highly Informative Direct
Molecular Function (MF) modified amino acid binding 0 Highly Informative Direct
Molecular Function (MF) peptide binding 1 Highly Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0.0283 Highly Informative Inherited
Molecular Function (MF) acid-amino acid ligase activity 1 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00000001174 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9957 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.6544 Moderately Informative Inherited
Cellular Component (CC) bounding membrane of organelle 0.5013 Moderately Informative Inherited
Cellular Component (CC) whole membrane 0.138 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.08595 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) cytoplasmic vesicle part 0.1787 Informative Inherited
Cellular Component (CC) exocytic vesicle 0.000000002784 Highly Informative Direct
Cellular Component (CC) presynapse 0.00000000001446 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.001896 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processLipid metabolism1Moderately InformativeInherited
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processFatty acid metabolism0.00000007459InformativeDirect
Biological processLipid biosynthesis0.002639InformativeInherited
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0.000000000004636Least InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionBiotin0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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) · UniProtKB KeyWords (KW) · Internal database links ]