SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,429) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 21,642 71,681 37
Proteins 18,867 62,944 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 0.0001541 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic 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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.784 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 0.9813 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 1.642e-12 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 8.507e-10 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.352e-09 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 8.47e-08 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 8.011e-06 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0002423 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.3209 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.521 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2505 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.001871 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03083 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.008104 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.03235 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3057 Moderately Informative Inherited
Biological Process (BP) system process 0.08781 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.01367 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.284 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4696 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.9148 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.845 Moderately Informative Inherited
Biological Process (BP) cellular amide metabolic process 2.591e-11 Informative Direct
Biological Process (BP) fatty acid metabolic process 5.059e-11 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 1.968e-09 Informative Direct
Biological Process (BP) synaptic transmission 3.848e-05 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.000238 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.0003187 Informative Direct
Biological Process (BP) hexose metabolic process 0.0003714 Informative Direct
Biological Process (BP) secretion 0.0007669 Informative Direct
Biological Process (BP) protein oligomerization 0.00107 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.4959 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.01988 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.2178 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.002555 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.07986 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.6797 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.003212 Informative Inherited
Biological Process (BP) purine nucleotide metabolic process 0.315 Informative Inherited
Biological Process (BP) nucleobase metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 5.543e-09 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 1.125e-08 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 2.928e-08 Highly Informative Direct
Biological Process (BP) monosaccharide biosynthetic process 1.94e-07 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 1.413e-06 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 3.821e-06 Highly Informative Direct
Biological Process (BP) protein tetramerization 4.147e-06 Highly Informative Direct
Biological Process (BP) glutathione metabolic process 5.705e-06 Highly Informative Direct
Biological Process (BP) signal release 6.053e-06 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0001262 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.000146 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0005284 Highly Informative Direct
Biological Process (BP) nonribosomal peptide biosynthetic process 0.1993 Highly Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0.02799 Highly Informative Inherited
Molecular Function (MF) binding 0.9186 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 3.478e-06 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 6.291e-05 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 8.707e-05 Moderately Informative Direct
Molecular Function (MF) protein binding 0.937 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.8158 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.3463 Moderately Informative Inherited
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 3.496e-09 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 8.469e-06 Informative Direct
Molecular Function (MF) protein dimerization activity 1.834e-05 Informative Direct
Molecular Function (MF) nucleotide binding 0.8117 Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 1 Informative Inherited
Molecular Function (MF) sulfur compound binding 0 Highly Informative Direct
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) magnesium ion binding 1.308e-07 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 2.114e-07 Highly Informative Direct
Molecular Function (MF) peptide binding 1 Highly Informative Inherited
Molecular Function (MF) modified amino acid binding 0.03282 Highly Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0.4275 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.9672 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.009626 Least Informative Inherited
Cellular Component (CC) membrane 0.2418 Least Informative Inherited
Cellular Component (CC) organelle membrane 2.606e-07 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 4.662e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0009558 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.001811 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 0.03986 Moderately Informative Inherited
Cellular Component (CC) synapse 7.124e-10 Informative Direct
Cellular Component (CC) coated vesicle 1.843e-05 Informative Direct
Cellular Component (CC) clathrin-coated vesicle 4.007e-10 Highly Informative Direct
Cellular Component (CC) vesicle membrane 5.841e-05 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0.0006377 Highly Informative Direct

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-N1.332e-05InformativeDirect
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 carboxylase3.482e-15Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase3.972e-12Highly InformativeDirect
Enzyme Commission (EC)Methylcrotonoyl-CoA carboxylase1.397e-05Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylformylglycinamidine cyclo-ligase1.747e-05Highly 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 the central nervous system0.0996Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.15Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis2.416e-05Moderately InformativeDirect
Phenotypic Abnormality (PA)Hyperammonemia2.986e-05InformativeDirect
Phenotypic Abnormality (PA)Coma0.0002043InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0004219InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.5619Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.2421Moderately InformativeInherited
Mammalian Phenotype (MP)increased synaptic depression2.721e-07Highly 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)clear6.767e-06Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)nutrient utilization0.3009Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0007457InformativeDirect

Document: YP 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)plant cell0.08332Least InformativeInherited
Plant ANatomical entity (PAN)guard cell0.0002087Moderately 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--D-amino-acid ligases (peptide synthases)0InformativeDirect
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 formyltransferase4.844e-12Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (ammonia)7.476e-06Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase5.224e-05Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)1Highly InformativeInherited
Enzyme Commission (EC)Cyclo-ligases1Highly InformativeInherited
Enzyme Commission (EC)Ligases that form carbon-carbon bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)vitamins7.906e-05Least InformativeDirect
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited

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 processCell shape0InformativeDirect
Biological processPurine biosynthesis0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processFatty acid metabolism1.874e-07InformativeDirect
Biological processLipid biosynthesis0.00398InformativeInherited
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm2.4e-13Least InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least 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 metabolism9.13e-15Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.8858Moderately 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 degradation1.392e-05InformativeDirect
UniPathway (UP)fatty acid biosynthesis0.06113InformativeInherited
UniPathway (UP)metabolic intermediate degradation0.2556InformativeInherited
UniPathway (UP)glutathione biosynthesis0Highly InformativeDirect
UniPathway (UP)L-leucine degradation3.718e-08Highly InformativeDirect
UniPathway (UP)propanoyl-CoA degradation1.695e-07Highly InformativeDirect
UniPathway (UP)malonyl-CoA biosynthesis1.769e-07Highly 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 Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]