SUPERFAMILY 1.75 HMM library and genome assignments server

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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 27,353 217,936 37
Proteins 23,884 192,019 34


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

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 metabolism/homeostasis0.08893Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.1271Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.00000339Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0.08158Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.0000161InformativeDirect
Phenotypic Abnormality (PA)Reduced consciousness/confusion0.05652InformativeInherited
Phenotypic Abnormality (PA)Hyperammonemia0.0000006198Highly InformativeDirect
Phenotypic Abnormality (PA)Coma0.0005597Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.6706Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.3026Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)seizures0.00685InformativeInherited
Mammalian Phenotype (MP)abnormal emotion/affect behavior0.03796InformativeInherited
Mammalian Phenotype (MP)tonic-clonic seizures0.00004759Highly InformativeDirect
Mammalian Phenotype (MP)abnormal aggression-related behavior0.0001132Highly InformativeDirect
Mammalian Phenotype (MP)abnormal synaptic depression0.0002887Highly InformativeDirect
Mammalian Phenotype (MP)abnormal seizure response to inducing agent0.0009497Highly InformativeDirect
Mammalian Phenotype (MP)abnormal nervous system electrophysiology0.005447Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)pigmentation variant0.0004432InformativeDirect
Worm Phenotype (WP)clear0.00002484Highly 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 growth0.2089Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.2026Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0005757InformativeDirect
Yeast Phenotype (YP)prion formation0.0001133Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)post-embryonic stage0.2783Least InformativeInherited
Xenopus DEvelopment stage (XDE)climax stage0.1639Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)NF stage 620.0004185Highly 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)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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds1Moderately 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-donor0.3408InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases1InformativeInherited
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phosphoribosylamine--glycine ligase0Highly InformativeDirect
Enzyme Commission (EC)Carbamoyl-phosphate synthase (glutamine-hydrolyzing)0Highly InformativeDirect
Enzyme Commission (EC)Forming carbon-carbon bonds0Highly InformativeDirect
Enzyme Commission (EC)Phosphoribosylglycinamide formyltransferase0.000000000003951Highly InformativeDirect
Enzyme Commission (EC)Urea carboxylase0.00009204Highly InformativeDirect
Enzyme Commission (EC)In cyclic amides0.09838Highly InformativeInherited
Enzyme Commission (EC)Cyclo-ligases1Highly InformativeInherited

Document: EC annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · 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) ]

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 · 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) · Internal database links ]