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 (3,158) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,161 153,614 29
Proteins 26,152 150,595 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 process0.85670.9338Least InformativeInherited
Biological Process (BP)single-organism cellular process0.60320.5461Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.5030.0005011Least InformativeInherited
Biological Process (BP)biosynthetic process0.081080.0000001377Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.281Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular component biogenesis0.26520.2923Moderately InformativeInherited
Biological Process (BP)single-organism organelle organization0.05240.993Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.00011540.08507Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.1330.008023Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.0020730.0000000007223Moderately InformativeInherited
Biological Process (BP)polysaccharide metabolic process0.0004610.0000000000002404InformativeDirect
Biological Process (BP)microtubule-based process0.0000000055380.00003546InformativeDirect
Biological Process (BP)carbohydrate biosynthetic process0.000095240.00000000505InformativeDirect
Biological Process (BP)protein oligomerization0.017970.006266InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.004070.00000004734InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.0039360.00002038InformativeInherited
Biological Process (BP)cell cycle process0.0036380.3238InformativeInherited
Biological Process (BP)mitotic cell cycle0.00057570.09323InformativeInherited
Biological Process (BP)cytoskeleton organization0.0042820.2901InformativeInherited
Biological Process (BP)spindle organization0.000048330.0001058Highly InformativeDirect
Biological Process (BP)photorespiration0.000011480.000000000005178Highly InformativeDirect
Biological Process (BP)protein homooligomerization0.00026150.0002286Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.0030090.002586Highly InformativeInherited
Molecular Function (MF)transferase activity0.000083310.000000000006887Least InformativeDirect
Molecular Function (MF)lyase activity0.015150.1444Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups0.000000000000023110InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0000090120.00003962InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.0030540.0004066Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.061160.1241Highly InformativeInherited
Cellular Component (CC)protein complex0.000098580.0008764Least InformativeDirect
Cellular Component (CC)intracellular organelle part0.0024620.7205Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.00017070.412Least InformativeInherited
Cellular Component (CC)cytoskeleton0.0000000035240.0003991Moderately InformativeDirect
Cellular Component (CC)actin cytoskeleton0.000078650.00003365InformativeDirect
Cellular Component (CC)microtubule cytoskeleton0.00000000000067970.0000002753InformativeDirect
Cellular Component (CC)microtubule associated complex0.00000000000180.00000000007544Highly 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 0.0000001377 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0005011 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.9338 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5461 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 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 0.0000000007223 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.00002492 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.2868 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.006616 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2923 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.05772 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.1724 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8983 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.6605 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.3121 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.9763 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.1623 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.002742 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8865 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.1945 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.0792 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.4222 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.993 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.08507 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.008023 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.5828 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.3669 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.0000000000002404 Informative Direct
Biological Process (BP) microtubule-based process 0.00003546 Informative Direct
Biological Process (BP) regulation of nucleoside metabolic process 0.0004335 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00000000505 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00002038 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00000004734 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0006255 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.0004089 Informative Direct
Biological Process (BP) protein oligomerization 0.006266 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.07154 Informative Inherited
Biological Process (BP) regulation of cellular catabolic process 0.009383 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 0.001598 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.003856 Informative Inherited
Biological Process (BP) regulation of purine nucleotide metabolic process 0.001459 Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.007892 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.07454 Informative Inherited
Biological Process (BP) central nervous system development 0.1629 Informative Inherited
Biological Process (BP) cell cycle process 0.3238 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.09323 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.2901 Informative Inherited
Biological Process (BP) cellular component movement 0.5354 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.00524 Informative Inherited
Biological Process (BP) translational initiation 0.00000007566 Highly Informative Direct
Biological Process (BP) regulation of translation 0.0001335 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0003953 Highly Informative Direct
Biological Process (BP) spindle organization 0.0001058 Highly Informative Direct
Biological Process (BP) ensheathment of neurons 0.000002232 Highly Informative Direct
Biological Process (BP) response to heat 0.0005294 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.0002819 Highly Informative Direct
Biological Process (BP) photorespiration 0.000000000005178 Highly Informative Direct
Biological Process (BP) glial cell differentiation 0.00005751 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000000003143 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.000276 Highly Informative Direct
Biological Process (BP) positive regulation of GTPase activity 0.00006128 Highly Informative Direct
Biological Process (BP) protein homooligomerization 0.0002286 Highly Informative Direct
Biological Process (BP) response to drug 0.003228 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.002586 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000000000006887 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0.1444 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.5465 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 8.141e-16 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.00003962 Informative Direct
Molecular Function (MF) RNA binding 0.006244 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000004327 Highly Informative Direct
Molecular Function (MF) translation factor activity, nucleic acid binding 0.00000001797 Highly Informative Direct
Molecular Function (MF) O-acyltransferase activity 0.0004066 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.1241 Highly Informative Inherited
Molecular Function (MF) adenylyltransferase activity 0.02941 Highly Informative Inherited
Cellular Component (CC) protein complex 0.0008764 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.7205 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.412 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.4821 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0003991 Moderately Informative Direct
Cellular Component (CC) actin cytoskeleton 0.00003365 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.0000002753 Informative Direct
Cellular Component (CC) microtubule associated complex 0.00000000007544 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 system0.0000000001829InformativeDirect
Plant ANatomical entity (PAN)portion of ground tissue0.000006024InformativeDirect
Plant ANatomical entity (PAN)fruit0.00003454InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell0.00000000001298Highly InformativeDirect
Plant ANatomical entity (PAN)phloem0.0000000034Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.00004112Highly 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 biosynthesis0.0000002983Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore0.0000002503Highly InformativeDirect
Cellular componentCentromere0.00002121Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMetal-binding9.203e-16Least 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 biosynthesis0.2437Moderately 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 metabolism0.0000000000007922InformativeDirect
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 ]