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Overview

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> 3,711
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="http://www.uniprot.org/manual/proteomes%5Fmanual">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>UP000001036
Taxonomy498211 - Cellvibrio japonicus (strain Ueda107)
StrainUeda107
Last modifiedMarch 7, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000019225.1 from ENA/EMBL full
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:98.6%[S:98.4%,D:0.2%],F:0%,M:1.4%,n:913 cellvibrionales_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)

Cellvibrio japonicus (Strain Ueda107) is an aerobic Gram-negative saprophytic soil bacterium that was isolated from Japanese soil in 1952 and named Pseudomonas fluorescens subsp. cellulosa. Recent studies however demonstrated that C. japonicus is not a member of the genus Pseudomonas but is closely related to Cellvibrio mixtus, and hence the bacterium was renamed. C. japonicus represents an excellent system for studying the mechanism of plant cell wall degradation in a Gram-negative, non-cellulosomic saprophyte. It contains the complete repertoire of enzymes (glycoside hydrolases, lyases and esterases) required to degrade plant cell-wall and storage polysaccharides. It degrades all of the major plant cell wall polysaccharides including crystalline cellulose, mannan and xylan and is able to grow on media when these polysaccharides are the sole carbon and energy source. Unlike anaerobic plant cell wall degrading organisms, the C. japonicus enzymes that target polysaccharides, which are integral to the plant cell wall, are fully secreted into the culture media and do not assembly into large multienzyme cellulosome-like complexes. Approximately one third of these putative proteins are predicted to contain often multiple non-catalytic carbohydrate binding modules (CBMs). It increases catalytic activity by reducing the substrate accessibility problem. The variation in the portfolio of CBMs appended to these hydrolytic enzymes may impact upon the carbohydrate targeting of these biocatalysts and thus influence their substrate specificity. All the predicted plant cell-wall degrading enzymes contain signal peptides and are thus extra-cytoplasmic. The genome sequence of C. japonicus reveals a remarkable similarity between the plant cell-wall degrading apparatus of C. japonicus and that of the marine bacterium Saccharophagus degradans. Plant cell-wall degrading enzymes are widely used in the biotechnology sector for the production of detergents, paper, textiles, animal and human foods, however, the most important application of these biocatalysts is in the production of renewable biofuels. Therefore, the discovery of new and more efficient plant cell-wall degrading enzymes can potentially have numerous and important biotechnology applications.

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome3711

Publications

  1. "Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus."
    DeBoy R.T., Mongodin E.F., Fouts D.E., Tailford L.E., Khouri H., Emerson J.B., Mohamoud Y., Watkins K., Henrissat B., Gilbert H.J., Nelson K.E.
    J. Bacteriol. 190:5455-5463(2008) [PubMed] [Europe PMC] [Abstract]
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