SUPERFAMILY 1.75 HMM library and genome assignments server


Undecaprenyl diphosphate synthase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Undecaprenyl diphosphate synthase [ 64004]
Superfamily:   Undecaprenyl diphosphate synthase [ 64005]
Families:   Undecaprenyl diphosphate synthase [ 64006]


Superfamily statistics
Genomes (3,068) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,616 9,104 2
Proteins 4,515 9,032 2


Functional annotation
General category Metabolism
Detailed category Secondary metabolism

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)biosynthetic process0.039547.438e-06Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.15250.0174Least InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.00076928.721e-08Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process6.359e-050.0001693Moderately InformativeDirect
Biological Process (BP)organic hydroxy compound metabolic process5.378e-052.996e-08Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process0.004128.466e-06Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process0.0025754.39e-06Moderately InformativeInherited
Biological Process (BP)alcohol metabolic process5.597e-061.452e-08InformativeDirect
Biological Process (BP)isoprenoid metabolic process1.677e-068.486e-07InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process8.113e-056.643e-08InformativeDirect
Biological Process (BP)isoprenoid biosynthetic process1.001e-054.017e-10Highly InformativeDirect
Biological Process (BP)alcohol biosynthetic process2.609e-072.239e-08Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups00InformativeDirect

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 7.438e-06 Least Informative Direct
Biological Process (BP) protein metabolic process 0.5003 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.6687 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.0174 Least Informative Inherited
Biological Process (BP) lipid biosynthetic process 4.39e-06 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 8.721e-08 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 8.466e-06 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0001693 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 2.996e-08 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.002014 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.004694 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.01547 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 1.452e-08 Informative Direct
Biological Process (BP) isoprenoid metabolic process 8.486e-07 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 6.643e-08 Informative Direct
Biological Process (BP) protein glycosylation 2.013e-09 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 4.017e-10 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 2.239e-08 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.8479 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3236 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 7.521e-06 Moderately Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited

Document: EC 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) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Cellular componentEndoplasmic reticulum5.356e-07Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism1.249e-12Least InformativeDirect
UniPathway (UP)protein glycosylation0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001441 SSF64005 Protein matches
Abstract

Synonym(s): Di-trans-poly-cis-undecaprenyl-diphosphate synthase, Undecaprenyl pyrophosphate synthetase, Undecaprenyl pyrophosphate synthase, UPP synthetase

Di-trans-poly-cis-decaprenylcistransferase (UPP synthetase) generates undecaprenyl pyrophosphate (UPP) from isopentenyl pyrophosphate (IPP) [PubMed9882662]. This bacterial enzyme is also found in archaebacteria and in a number of uncharacterised proteins including some from yeasts.


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) · 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 2 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 Undecaprenyl diphosphate synthase 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 2 hidden Markov models representing the Undecaprenyl diphosphate synthase 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]