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StatusReference proteome
Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 4,359
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000000366
Taxonomy420662 - Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1)
StrainATCC BAA-1232 / LMG 22953 / PM1
Last modifiedAugust 19, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="">more...</a>)</p> GCA_000015725.1 from ENA/EMBL full
Pan proteomei <p>A pan proteome is the full set of proteins thought to be expressed by a group of highly related organisms (e.g. multiple strains of the same bacterial species).<p><a href='/help/pan_proteomes' target='_top'>More...</a></p> This proteome is part of the Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1) pan proteome (fasta)
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:98.4%[S:97.4%,D:1%],F:0.3%,M:1.3%,n:688 burkholderiales_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Standard

Methylibium petroleiphilum strain PM1 (ATCC BAA-1232) is a motile phototrophic methylotrophic Gram-negative bacterium phylogenetically associated with the beta subdivision of the Proteobacteria and representing a new species within the Rubrivivax group (Comamonadaceae family). It is found in many gasoline-contaminated aquifers (freshwater, sewage, and activated sludge) and can grow in the dark under aerobic conditions or photosynthetically under anaerobic conditions. PM1 can also grow on carbon dioxide or on hydrogen. It was isolated by Dr. Scow in 1998 from a sewage treatment plant biofilter that was used for treating discharge from oil refineries in Los Angeles, California. Methylibium petroleiphilum is a model organism for the study of photosynthetic processes due to its genetic tractability. Strain PM1 is capable of degrading the gasoline additive methyl tert-butyl ether (MTBE) and its daughter product tert-butyl alcohol (TBA). Strain PM1 also degrades aromatic hydrocarbons (benzene, toluene, and xylene) and n-alkanes (C5 to C12) present in petroleum products. It is capable of aerobic growth on methanol, formate and succinate, but not on methylamine. Whole-genome analysis of PM1 revealed a 4-Mb circular chromosome and a 600-kb megaplasmid. Hydrocarbon (aromatic and alkane) degradation, metal resistance (arsenic, chromate, copper, cobalt, nickel, molybdenum, iron), and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements (including tandem repeat encoding phosphonate transport and cobalamin biosynthesis). It was suggested that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1 ability to degrade MTBE and alkanes. The genetic basis for MTBE and TBA conversion is not known, although different classes of monooxygenases have been proposed to play a role in metabolism or cometabolism of these compounds including P-450 monooxygenase and alkane monooxygenase (hydroxylase) systems. It is noteworthy that MTBE degrading strains (PM1, MG4 and 312), from diverse locations possess nearly identical megaplasmids. PM1 can serve as a model for other MTBE-degrading methylotrophs such that the knowledge gained from analysis of its genome, transcriptome, and proteome can be applied to PM1-like bacteria. An understanding of the MTBE degradation pathway and its regulation will allow for optimization of MTBE bioremediation and the ability to monitor this unique process in situ using molecular tools.

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationProteins
Plasmid RPME01584


  1. "Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1."
    Kane S.R., Chakicherla A.Y., Chain P.S.G., Schmidt R., Shin M.W., Legler T.C., Scow K.M., Larimer F.W., Lucas S.M., Richardson P.M., Hristova K.R.
    J. Bacteriol. 189:1931-1945(2007) [PubMed] [Europe PMC] [Abstract]
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