SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (3,164) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 27,251 160,015 29
Proteins 26,199 154,647 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 biogenesis0.28821Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.8431Least InformativeInherited
Biological Process (BP)primary metabolic process0.93980.8576Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.51190.00001402Least InformativeInherited
Biological Process (BP)biosynthetic process0.19040.0000000005588Least InformativeInherited
Biological Process (BP)single-organism cellular process0.72110.1969Least InformativeInherited
Biological Process (BP)protein complex biogenesis0.00025310.001045Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.014040.2511Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0021170.02532Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.029690.002656Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.02350.07391Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0064830.000175Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.00032430.00001651InformativeDirect
Biological Process (BP)cellular metabolic compound salvage0.000091570.00001219InformativeDirect
Biological Process (BP)protein oligomerization0.0000054460.000004935InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.0059980.00008544InformativeInherited
Biological Process (BP)movement of cell or subcellular component0.024960.716InformativeInherited
Biological Process (BP)microtubule-based process0.000023060.009605InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0018390.02043InformativeInherited
Biological Process (BP)microtubule-based movement0.000024730.0002294Highly InformativeDirect
Biological Process (BP)serine family amino acid metabolic process0.00011220.00005383Highly InformativeDirect
Biological Process (BP)protein homotrimerization0.0000020730.000001682Highly InformativeDirect
Molecular Function (MF)transferase activity0.0000021160.00000000000002886Least InformativeDirect
Molecular Function (MF)lyase activity0.030760.09116Moderately InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups00InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0000022410.000001109InformativeDirect
Molecular Function (MF)carbonate dehydratase activity0.00009750.0000009987Highly InformativeDirect
Molecular Function (MF)O-acyltransferase activity0.000026150.000004679Highly InformativeDirect
Molecular Function (MF)acetyltransferase activity0.0018180.007914Highly InformativeInherited
Cellular Component (CC)membrane0.96961Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.820.08857Least InformativeInherited
Cellular Component (CC)macromolecular complex0.017450.02133Least InformativeInherited
Cellular Component (CC)non-membrane-bounded organelle0.0038080.7107Least InformativeInherited
Cellular Component (CC)intracellular organelle part0.020060.9946Least InformativeInherited
Cellular Component (CC)organelle envelope0.021860.0308Moderately InformativeInherited
Cellular Component (CC)mitochondrial part0.10250.2118Moderately InformativeInherited
Cellular Component (CC)cytoskeleton0.00000065870.005881Moderately InformativeInherited
Cellular Component (CC)membrane protein complex0.15930.146Moderately InformativeInherited
Cellular Component (CC)mitochondrial respiratory chain0.000018170.000002163InformativeDirect
Cellular Component (CC)microtubule cytoskeleton0.0000000030750.00004856InformativeDirect
Cellular Component (CC)inner mitochondrial membrane protein complex0.0002380.00003968InformativeDirect
Cellular Component (CC)oxidoreductase complex0.000047690.00007524InformativeDirect
Cellular Component (CC)respiratory chain complex0.0013090.0002329InformativeInherited
Cellular Component (CC)actin cytoskeleton0.0011660.002701InformativeInherited
Cellular Component (CC)mitochondrial respiratory chain complex I0.000000091520.00000001804Highly 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 0.0000000005588 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00001402 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.1969 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.8576 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.00000000005587 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.000175 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0.000005443 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0001869 Moderately Informative Direct
Biological Process (BP) protein complex biogenesis 0.001045 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.2511 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.02532 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.898 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.6217 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.002656 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.03325 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.4766 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) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6832 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.002996 Moderately Informative Inherited
Biological Process (BP) gene expression 0.5897 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.003877 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.1024 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.5072 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.07391 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.00001651 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.0000000000002665 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0.000424 Informative Direct
Biological Process (BP) phospholipid metabolic process 0.0005521 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.0000000000004789 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0.00001219 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00000001265 Informative Direct
Biological Process (BP) protein oligomerization 0.000004935 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.00008544 Informative Direct
Biological Process (BP) liposaccharide metabolic process 0.000000001879 Informative Direct
Biological Process (BP) central nervous system development 0.1585 Informative Inherited
Biological Process (BP) cell development 0.9586 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.716 Informative Inherited
Biological Process (BP) microtubule-based process 0.009605 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.003329 Informative Inherited
Biological Process (BP) regulation of cellular amide metabolic process 0.001755 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.02043 Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.0000006801 Highly Informative Direct
Biological Process (BP) translational initiation 0.0000005336 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.0002294 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.00005383 Highly Informative Direct
Biological Process (BP) glycolipid biosynthetic process 0.00004373 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.00000000008332 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.000194 Highly Informative Direct
Biological Process (BP) gliogenesis 0.0001605 Highly Informative Direct
Biological Process (BP) response to drug 0.0005059 Highly Informative Direct
Biological Process (BP) lipid A metabolic process 0.0000000000008098 Highly Informative Direct
Biological Process (BP) protein homotrimerization 0.000001682 Highly Informative Direct
Biological Process (BP) oligosaccharide biosynthetic process 0.08869 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000000002886 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0.09116 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.4991 Moderately Informative Inherited
Molecular Function (MF) molecular function regulator 0.01401 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.000001109 Informative Direct
Molecular Function (MF) RNA binding 0.004148 Informative Inherited
Molecular Function (MF) carbonate dehydratase activity 0.0000009987 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0000001603 Highly Informative Direct
Molecular Function (MF) translation factor activity, RNA binding 0.000000001707 Highly Informative Direct
Molecular Function (MF) O-acyltransferase activity 0.000004679 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.007914 Highly Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.08857 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) macromolecular complex 0.02133 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.7107 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9946 Least Informative Inherited
Cellular Component (CC) organelle envelope 0.0308 Moderately Informative Inherited
Cellular Component (CC) mitochondrial part 0.2118 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.005881 Moderately Informative Inherited
Cellular Component (CC) membrane protein complex 0.146 Moderately Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain 0.000002163 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.00004856 Informative Direct
Cellular Component (CC) inner mitochondrial membrane protein complex 0.00003968 Informative Direct
Cellular Component (CC) respiratory chain complex 0.0002329 Informative Direct
Cellular Component (CC) oxidoreductase complex 0.00007524 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.002701 Informative Inherited
Cellular Component (CC) mitochondrial respiratory chain complex I 0.00000001804 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 plant0.01482Least InformativeInherited
Plant ANatomical entity (PAN)root system0.04026Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.1162Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.2298Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.000006042InformativeDirect
Plant ANatomical entity (PAN)portion of vascular tissue0.00001815InformativeDirect
Plant ANatomical entity (PAN)fruit0.00003503InformativeDirect
Plant ANatomical entity (PAN)parenchyma cell0.00000000001302Highly InformativeDirect
Plant ANatomical entity (PAN)phloem0.000000004906Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0000434Highly 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 phosphorus-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 processLipid A biosynthesis0Highly InformativeDirect
Biological processLysine biosynthesis0Highly InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processCysteine biosynthesis0.0000004938Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPlastid1Moderately InformativeInherited
Cellular componentKinetochore0.0000008615Highly InformativeDirect
Cellular componentCentromere0.00004981Highly InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0.000000000002136Least 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 biosynthesis0.2263Moderately 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 metabolism0.0000000000006862InformativeDirect
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
UniPathway (UP)LPS lipid A biosynthesis0Highly InformativeDirect
UniPathway (UP)starch biosynthesis0.000009955Highly 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 ]