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 (2,429) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 21,050 69,211 29
Proteins 20,200 67,786 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 component organization or biogenesis0.74781Least InformativeInherited
Biological Process (BP)biosynthetic process0.086692.221e-08Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.83741Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.042960.2065Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.12090.1303Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.007668.256e-09Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.019891.558e-05Moderately InformativeInherited
Biological Process (BP)protein oligomerization0.10320.01668InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0019291.25e-05InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.010315.548e-12InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.0036272.569e-07InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.007191.823e-09InformativeInherited
Biological Process (BP)cellular component movement0.00049660.1829InformativeInherited
Biological Process (BP)microtubule-based process3.404e-050.01843InformativeInherited
Biological Process (BP)microtubule-based movement9.498e-092.735e-05Highly InformativeDirect
Biological Process (BP)photorespiration7.738e-064.559e-12Highly InformativeDirect
Biological Process (BP)protein homooligomerization0.0022660.0001674Highly InformativeInherited
Biological Process (BP)cellular glucan metabolic process6.747e-050.001249Highly InformativeInherited
Molecular Function (MF)transferase activity6.968e-052.577e-12Least InformativeDirect
Molecular Function (MF)lyase activity0.00075590.01317Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups1.997e-110InformativeDirect
Molecular Function (MF)carbon-oxygen lyase activity7.365e-085.417e-07InformativeDirect
Molecular Function (MF)carbonate dehydratase activity0.00018856.575e-06Highly InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.0077230.01023Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.050420.1689Highly InformativeInherited
Cellular Component (CC)intracellular organelle part0.012570.935Least InformativeInherited
Cellular Component (CC)intracellular non-membrane-bounded organelle0.0025030.6788Least InformativeInherited
Cellular Component (CC)protein complex0.00063870.001693Least InformativeInherited
Cellular Component (CC)cytoskeleton1.792e-060.005816Moderately InformativeInherited
Cellular Component (CC)microtubule cytoskeleton4.393e-093.934e-05InformativeDirect
Cellular Component (CC)actin cytoskeleton0.0032040.002416InformativeInherited
Cellular Component (CC)microtubule associated complex7.928e-089.672e-07Highly 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 2.221e-08 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1411 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 8.256e-09 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 1.558e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.1303 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.2065 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.5472 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.9532 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7093 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.08595 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.03079 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.02409 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.03749 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.5846 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 cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.2519 Moderately Informative Inherited
Biological Process (BP) gene expression 0.1942 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.3662 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 5.548e-12 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 2.569e-07 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 1.25e-05 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 1.823e-09 Informative Direct
Biological Process (BP) protein oligomerization 0.01668 Informative Inherited
Biological Process (BP) central nervous system development 0.09368 Informative Inherited
Biological Process (BP) cellular component movement 0.1829 Informative Inherited
Biological Process (BP) microtubule-based process 0.01843 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.001863 Informative Inherited
Biological Process (BP) translational initiation 5.176e-09 Highly Informative Direct
Biological Process (BP) regulation of translation 3.586e-05 Highly Informative Direct
Biological Process (BP) microtubule-based movement 2.735e-05 Highly Informative Direct
Biological Process (BP) response to heat 0.0002296 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0001367 Highly Informative Direct
Biological Process (BP) photorespiration 4.559e-12 Highly Informative Direct
Biological Process (BP) glial cell differentiation 1.838e-05 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0004978 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0001674 Highly Informative Direct
Biological Process (BP) cellular glucan metabolic process 0.001249 Highly Informative Inherited
Molecular Function (MF) transferase activity 2.577e-12 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.006153 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.01317 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) organic cyclic compound binding 0.5803 Moderately Informative Inherited
Molecular Function (MF) heterocyclic compound binding 0.5531 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0007182 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 3.07e-15 Informative Direct
Molecular Function (MF) carbon-oxygen lyase activity 5.417e-07 Informative Direct
Molecular Function (MF) GTPase regulator activity 2.249e-05 Informative Direct
Molecular Function (MF) carbonate dehydratase activity 6.575e-06 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 1.413e-07 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 1.036e-07 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.1689 Highly Informative Inherited
Molecular Function (MF) O-acyltransferase activity 0.01023 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.02306 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.935 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.6788 Least Informative Inherited
Cellular Component (CC) protein complex 0.001693 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.218 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.005816 Moderately Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 3.934e-05 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.002416 Informative Inherited
Cellular Component (CC) microtubule associated complex 9.672e-07 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) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)plant cell0.005506Least InformativeInherited
Plant ANatomical entity (PAN)root0.1775Least InformativeInherited
Plant ANatomical entity (PAN)guard cell6.727e-06Moderately InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue1.381e-05InformativeDirect
Plant ANatomical entity (PAN)fruit3.229e-05InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue3.761e-05InformativeDirect
Plant ANatomical entity (PAN)stele3.928e-05InformativeDirect
Plant ANatomical entity (PAN)leaf mesophyll1.337e-11Highly InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell1.594e-11Highly InformativeDirect
Plant ANatomical entity (PAN)phloem4.163e-09Highly InformativeDirect
Plant ANatomical entity (PAN)root stele3.883e-05Highly InformativeDirect

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 processGlycogen metabolism0Highly InformativeDirect
Biological processLipid A biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processCysteine biosynthesis2.36e-07Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
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 biosynthesis0.2827Moderately 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 metabolism9.264e-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 ]