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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 (2,396) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,788 9,104 2
Proteins 3,687 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 process0.00014571.16e-08Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.00097680.0002087Least InformativeDirect
Biological Process (BP)lipid biosynthetic process0.00012714.858e-07Moderately InformativeDirect
Biological Process (BP)cellular lipid metabolic process1.956e-053.649e-09Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process5.92e-062.131e-12Moderately InformativeDirect
Biological Process (BP)organic hydroxy compound metabolic process2.637e-071.948e-12Moderately InformativeDirect
Biological Process (BP)alcohol metabolic process3.463e-095.898e-12InformativeDirect
Biological Process (BP)isoprenoid metabolic process4.214e-100InformativeDirect
Biological Process (BP)organic hydroxy compound biosynthetic process2.564e-072.547e-11InformativeDirect
Biological Process (BP)isoprenoid biosynthetic process1.58e-087.487e-14Highly InformativeDirect
Biological Process (BP)alcohol biosynthetic process2.794e-111.434e-10Highly InformativeDirect
Molecular Function (MF)transferase activity3.728e-085.705e-08Least 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 1.16e-08 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0002087 Least Informative Direct
Biological Process (BP) protein metabolic process 0.9579 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) lipid biosynthetic process 4.858e-07 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 3.649e-09 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 2.131e-12 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 1.948e-12 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0117 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.001529 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.03324 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.06437 Moderately Informative Inherited
Biological Process (BP) alcohol metabolic process 5.898e-12 Informative Direct
Biological Process (BP) isoprenoid metabolic process 0 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 2.547e-11 Informative Direct
Biological Process (BP) protein glycosylation 6.542e-08 Highly Informative Direct
Biological Process (BP) isoprenoid biosynthetic process 7.487e-14 Highly Informative Direct
Biological Process (BP) alcohol biosynthetic process 1.434e-10 Highly Informative Direct
Molecular Function (MF) transferase activity 5.705e-08 Least Informative Direct
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 0 Informative Direct
Molecular Function (MF) prenyltransferase activity 0.0001251 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.2869 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0.0001007 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

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 reticulum4.005e-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 metabolism2.838e-13Least 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) · 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) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.