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 (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 2.631e-07 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.9446 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 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.8482 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.3637 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 2.967e-13 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 5.629e-13 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 4.7e-12 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 2.298e-08 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 1.036e-07 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 1.479e-07 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 4.077e-06 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 6.159e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.512 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.6532 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6715 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.002304 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03316 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.2417 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.4992 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3968 Moderately Informative Inherited
Biological Process (BP) system process 0.1528 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 0.009674 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.3694 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8098 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.8062 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.2161 Moderately Informative Inherited
Biological Process (BP) fatty acid metabolic process 3.054e-11 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 7.268e-11 Informative Direct
Biological Process (BP) amide biosynthetic process 3.995e-08 Informative Direct
Biological Process (BP) hexose metabolic process 4.075e-06 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 3.579e-05 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 4.327e-05 Informative Direct
Biological Process (BP) synaptic transmission 0.0001011 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0001898 Informative Direct
Biological Process (BP) peptide metabolic process 0.0007821 Informative Direct
Biological Process (BP) protein oligomerization 0.001339 Informative Inherited
Biological Process (BP) response to inorganic substance 0.004776 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.1723 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.3391 Informative Inherited
Biological Process (BP) secretion by cell 0.001301 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.08987 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.003191 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.07916 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.002021 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 7.937e-11 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 8.074e-11 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 3.853e-10 Highly Informative Direct
Biological Process (BP) acyl-CoA metabolic process 2.335e-09 Highly Informative Direct
Biological Process (BP) peptide biosynthetic process 1.946e-07 Highly Informative Direct
Biological Process (BP) glutathione metabolic process 2.867e-07 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 1.92e-06 Highly Informative Direct
Biological Process (BP) protein tetramerization 5.168e-06 Highly Informative Direct
Biological Process (BP) signal release 5.706e-06 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 1.205e-05 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0001397 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0003568 Highly Informative Direct
Biological Process (BP) response to cadmium ion 0.00071 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.002856 Highly Informative Inherited
Biological Process (BP) branched-chain amino acid metabolic process 0.03299 Highly Informative Inherited
Molecular Function (MF) binding 0.5868 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 7.605e-06 Moderately Informative Direct
Molecular Function (MF) cation binding 0.7886 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.2579 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) amide binding 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 3.958e-11 Informative Direct
Molecular Function (MF) transferase activity, transferring one-carbon groups 1.144e-10 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 1.079e-09 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 1.784e-07 Informative Direct
Molecular Function (MF) magnesium ion binding 2.923e-05 Informative Direct
Molecular Function (MF) protein dimerization activity 0.000148 Informative Direct
Molecular Function (MF) nucleotide binding 0.6439 Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 1 Informative Inherited
Molecular Function (MF) ATP binding 0 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 1.22e-09 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0.00019 Highly Informative Direct
Molecular Function (MF) peptide binding 1 Highly Informative Inherited
Molecular Function (MF) amino acid binding 0.4428 Highly Informative Inherited
Molecular Function (MF) monocarboxylic acid binding 0.3327 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.9894 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.06055 Least Informative Inherited
Cellular Component (CC) membrane 0.3978 Least Informative Inherited
Cellular Component (CC) organelle membrane 2.18e-06 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 3.443e-05 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.001774 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.001644 Moderately Informative Inherited
Cellular Component (CC) synapse part 1.265e-10 Informative Direct
Cellular Component (CC) coated vesicle 9.449e-06 Informative Direct
Cellular Component (CC) clathrin-coated vesicle 1.034e-10 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.01532 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-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 nervous system physiology0.08121Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1481Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis2.583e-05Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.1836Moderately InformativeInherited
Phenotypic Abnormality (PA)Hyperammonemia3.063e-05InformativeDirect
Phenotypic Abnormality (PA)Coma0.0002199InformativeDirect
Phenotypic Abnormality (PA)Lethargy0.0004204InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.5355Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.1998Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.03439InformativeInherited
Mammalian Phenotype (MP)abnormal social investigation2.297e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal aggression-related behavior4.12e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic depression0.0001247Highly 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)metabolism and growth0.09533Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.2375Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0006617InformativeDirect

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-donor0.1525InformativeInherited
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 formyltransferase5.216e-12Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (ammonia)1.391e-05Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase8.592e-05Highly 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 metabolism2.103e-07InformativeDirect
Biological processLipid biosynthesis0.00464InformativeInherited
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm2.809e-12Least InformativeDirect
Cellular componentCell junction0.04695Moderately InformativeInherited
Cellular componentSynapse0.0006875InformativeDirect
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)amino-acid metabolism0.06855Least InformativeInherited
UniPathway (UP)L-arginine metabolism0Moderately InformativeDirect
UniPathway (UP)heterocycle metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis1.386e-06Moderately InformativeDirect
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)cell wall biogenesis0InformativeDirect
UniPathway (UP)pyrimidine biosynthesis1InformativeInherited
UniPathway (UP)peptidoglycan biosynthesis0Highly 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 ]