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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> 5,019
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>UP000000361
Taxonomy318586 - Paracoccus denitrificans (strain Pd 1222)
StrainPd 1222
Last modifiedMarch 7, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="">more...</a>)</p> GCA_000203895.1 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 Paracoccus denitrificans (strain Pd 1222) 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:97.2%,D:1.2%],F:0%,M:1.6%,n:833 rhodobacterales_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> Close to standard (high value)

Paracoccus denitrificans is a Gram-negative, non-motile coccoid soil bacterium from the alpha subdivision of the proteobacteria. Formerly known as Micrococcus denitrificans, it was first isolated in 1910 by M. Beijerinck, and renamed in 1969 to Paracoccus denitrificans by Davis. P. denitrificans is a model organism for the study of denitrification. Besides its intrinsic interest, denitrification also represents a source of atmosphere damaging compounds (nitric oxide and nitrous oxide), is a route for the loss of nitrogen fertilizer from agricultural soil, and has potential applications in the water treatment industry. P. denitrificans is a popular model for investigators with interests in a variety of aspects of microbial physiology. The organism grows well under aerobic conditions, expressing a respiratory chain very similar to that of the eukaryotic mitochondrion. P. denitrificans has been, and continues to be, the subject of many studies of the fundamental biochemical and bioenergetic properties of the aerobic electron transport chain. The evidence from 16S rRNA analysis indicates that the evolutionary precursor of the mitochondrion was a close relative of P. denitrificans (both fall in the alpha sub-group of the proteobacteria), justifying the use of P. denitrificans as a model for the mitochondrial respiratory chain. P. denitrificans has also been extensively studied for its ability to grow on C1 compounds such as methanol and methylamine, what it does by oxidation to carbon dioxide, then assimilation via the Calvin cycle. The organism can also grow as a chemolithoautotroph, using inorganic energy sources with carbon dioxide as the carbon source. P. denitrificans is now being exploited as a model organism for the study of poorly characterized sulfur compound transformations, because of its ability to use hydrogen and sulfur compounds, such as thiosulfate. Metabolic flexibility in this organism is reflected in an underlying flexibility of regulatory networks, which are currently only partially understood. Paracoccus is a biochemically versatile Genus, with a wide range of diverse degradative capabilities and potential applications in bioremediation. Strains have been isolated that utilize thiocyanate as an energy source, for the possible bioremediation of thiocyanate-contaminated wastewater from coke-oven factories. Strains that degrade halobenzoates under anaerobic denitrifying conditions, and that degrade sulfonates under anaerobic growth conditions have been described. Several strains of P. denitrificans have been isolated that grow chemolithoautotrophically using carbon disulfide or carbonyl sulfide as energy sources, and strains have been isolated from activated sludge that are capable of degrading quaternary carbon compounds such as dimethylmalonate under denitrifying conditions. Another strain isolated from activated sludge degrades a variety of methylated amines under both aerobic and anaerobic conditions. Some strains are capable of 'aerobic denitrification', the complete dissimilation of nitrate to dinitrogen (or nitrous oxide) under aerobic growth conditions. P. denitrificans also has the very unusual ability to oxidize ammonia to nitrite during growth on organic energy sources ('heterotrophic nitrification'). Coupled to denitrification, heterotrophic nitrification allows for the complete transformation of ammonia to dinitrogen by a single organism.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome 12767
Chromosome 21654
Plasmid pPD1222616
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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