SUPERFAMILY 1.75 HMM library and genome assignments server


Trimeric LpxA-like enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Single-stranded left-handed beta-helix [ 51160] (4)
Superfamily:   Trimeric LpxA-like enzymes [ 51161] (8)
Families:   UDP N-acetylglucosamine acyltransferase [ 51162]
  Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD [ 51165]
  Galactoside acetyltransferase-like [ 51168] (3)
  GlmU C-terminal domain-like [ 51171] (3)
  gamma-carbonic anhydrase-like [ 51174] (3)
  Serine acetyltransferase [ 110309]
  YdcK-like [ 141583]
  PglD-like [ 159280]


Superfamily statistics
Genomes (3,157) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,129 153,614 29
Proteins 26,127 150,595 29


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular macromolecule metabolic process0.83181Least InformativeInherited
Biological Process (BP)biosynthetic process0.064288.92e-08Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.38451Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.99370.3755Least InformativeInherited
Biological Process (BP)organelle organization0.19681Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.00011830.04176Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.12270.007495Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0015533.022e-09Moderately InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.00040892.155e-12InformativeDirect
Biological Process (BP)microtubule-based process4.709e-092.931e-05InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.00011334.707e-08InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.0033312.757e-07InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0032871.248e-05InformativeInherited
Biological Process (BP)cell cycle process0.0031270.2678InformativeInherited
Biological Process (BP)mitotic cell cycle0.00019320.03621InformativeInherited
Biological Process (BP)cytoskeleton organization0.0039560.2729InformativeInherited
Biological Process (BP)spindle organization2.679e-054.704e-05Highly InformativeDirect
Biological Process (BP)photorespiration1.095e-054.55e-12Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.0026770.002433Highly InformativeInherited
Molecular Function (MF)transferase activity7.933e-052.781e-12Least InformativeDirect
Molecular Function (MF)lyase activity0.010410.104Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups3.034e-130InformativeDirect
Molecular Function (MF)hydro-lyase activity4.447e-062.608e-05InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.013680.00295Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.096690.1953Highly InformativeInherited
Cellular Component (CC)protein complex7.951e-050.0006819Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0020640.7142Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle8.172e-050.3227Least InformativeInherited
Cellular Component (CC)cytoskeleton2.438e-090.000217Moderately InformativeDirect
Cellular Component (CC)actin cytoskeleton9.262e-054.659e-05InformativeDirect
Cellular Component (CC)microtubule cytoskeleton6.075e-131.893e-07InformativeDirect
Cellular Component (CC)microtubule associated complex2.671e-121.311e-10Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biosynthetic process 8.92e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.3755 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 3.022e-09 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0007884 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 5.837e-05 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.06147 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.3862 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.1493 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.04811 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8567 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.6115 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.1724 Moderately Informative Inherited
Biological Process (BP) system process 0.6845 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8427 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1657 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.06328 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.04176 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.007495 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.3845 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2748 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 2.155e-12 Informative Direct
Biological Process (BP) microtubule-based process 2.931e-05 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.0003312 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 4.707e-08 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 1.248e-05 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 2.757e-07 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.00061 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.004039 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.0047 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.001114 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.009929 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.04 Informative Inherited
Biological Process (BP) central nervous system development 0.144 Informative Inherited
Biological Process (BP) cell cycle process 0.2678 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.03621 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.2729 Informative Inherited
Biological Process (BP) cellular component movement 0.4834 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.00454 Informative Inherited
Biological Process (BP) translation 0.001164 Informative Inherited
Biological Process (BP) translational initiation 7.497e-08 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001178 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0004058 Highly Informative Direct
Biological Process (BP) spindle organization 4.704e-05 Highly Informative Direct
Biological Process (BP) response to heat 0.0004635 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0002382 Highly Informative Direct
Biological Process (BP) photorespiration 4.55e-12 Highly Informative Direct
Biological Process (BP) glial cell differentiation 5.365e-05 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 1.828e-08 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0001999 Highly Informative Direct
Biological Process (BP) response to drug 0.003078 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.002433 Highly Informative Inherited
Biological Process (BP) regulation of membrane potential 0.001256 Highly Informative Inherited
Molecular Function (MF) transferase activity 2.781e-12 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.008369 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.104 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.416 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 1.119e-14 Informative Direct
Molecular Function (MF) hydro-lyase activity 2.608e-05 Informative Direct
Molecular Function (MF) GTPase regulator activity 4.167e-05 Informative Direct
Molecular Function (MF) RNA binding 0.001446 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 3.527e-07 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 9.25e-08 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.1953 Highly Informative Inherited
Molecular Function (MF) O-acyltransferase activity 0.00295 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.01553 Highly Informative Inherited
Cellular Component (CC) protein complex 0.0006819 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7142 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.3227 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4097 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.000217 Moderately Informative Direct
Cellular Component (CC) actin cytoskeleton 4.659e-05 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 1.893e-07 Informative Direct
Cellular Component (CC) microtubule associated complex 1.311e-10 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)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0.01476Least InformativeInherited
Plant ANatomical entity (PAN)root system0.04008Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.1159Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.2297Least InformativeInherited
Plant ANatomical entity (PAN)vascular system1.829e-10InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue6.024e-06InformativeDirect
Plant ANatomical entity (PAN)fruit3.454e-05InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell1.298e-11Highly InformativeDirect
Plant ANatomical entity (PAN)phloem3.4e-09Highly InformativeDirect
Plant ANatomical entity (PAN)root stele4.112e-05Highly InformativeDirect
Plant ANatomical entity (PAN)mesophyll1Highly InformativeInherited

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately 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 processCarbohydrate metabolism0Moderately InformativeDirect
Biological processLipid metabolism0Moderately InformativeDirect
Biological processCell shape0InformativeDirect
Biological processLipid biosynthesis0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processDiaminopimelate biosynthesis0Highly InformativeDirect
Biological processGlycogen biosynthesis0Highly InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processCysteine biosynthesis2.99e-07Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore2.521e-07Highly InformativeDirect
Cellular componentCentromere2.083e-05Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)biopolymer biosynthesis0Moderately InformativeDirect
UniPathway (UP)lipid biosynthesis0Moderately InformativeDirect
UniPathway (UP)glycan metabolism0Moderately InformativeDirect
UniPathway (UP)nucleotide metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0.2472Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)lipopolysaccharide biosynthesis0InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0InformativeDirect
UniPathway (UP)L-lysine biosynthesis0InformativeDirect
UniPathway (UP)carnitine metabolism8.011e-13InformativeDirect
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)L-lysine biosynthesis via DAP pathway0Highly InformativeDirect
UniPathway (UP)UDP-N-acetyl-alpha-D-glucosamine biosynthesis0Highly InformativeDirect
UniPathway (UP)glycogen biosynthesis0Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR011004 SSF51161 Protein matches
Abstract

This domain is characterised by trimeric LpxA-like enzymes that display a single-stranded left-handed beta-helix fold, composed of tandem repeats of a hexapeptide, as represented by the Bacterial transferase hexapeptide repeat, where the hexapeptide repeats correspond to individual strands. Many bacterial transferases contain this domain. The structures of several proteins with this domain have been determined, including UDP N-acetylglucosamine acyltransferase (LpxA, ) from Escherichia coli, the first enzyme in the lipid A biosynthetic pathway [PubMed7481807]; galactoside acetyltransferase (GAT, LacA, ) from E. coli, a gene product of the lac operon that may assist cellular detoxification [PubMed11937062]; gamma-class Archaeon carbonic anhydrase , a zinc-containing enzyme that catalyses the reversible hydration of carbon dioxide [PubMed10924115]; tetrahydrodipicolinate-N-succinlytransferase (DapD) from Mycobacterium bovis, an enzyme from the lysine biosynthetic pathway that contains an extra N-terminal 3-helical domain [PubMed11910040]; and the C-terminal domain of N-acetylglucosamine 1-phosphate uridyltransferase (GlmU, ) from E. coli, a trimeric bifunctional enzyme that catalyses the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine, an essential precursor for many biomolecules [PubMed11329257].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 18 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 Trimeric LpxA-like enzymes 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 18 hidden Markov models representing the Trimeric LpxA-like enzymes 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]