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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> 5,353
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>UP000001596
Taxonomy311402 - Agrobacterium vitis (strain S4 / ATCC BAA-846)
StrainS4 / ATCC BAA-846
Last modifiedJanuary 15, 2020
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000016285.1 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 Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain S4)) pan proteome (fasta)
BuscoC:98.5%[S:98.3%,D:0.3%],F:1.3%,M:0.1%,n:686
CompletenessStandard

Agrobacterium are Gram-negative, motile, soil-dwelling plant pathogens with the species name given based on the disease phenotype associated with the bacteria. They invade the crown, roots and stems of a great variety of plants via wounds causing tumors. The diseases are crown gall, hairy root, and cane gall. Some strains possess a wide host range, whereas other possess a very limited host range. The tumor is correlated with the presence of a large tumor-inducing plasmid (Ti plasmid) in the bacteria. Thus A.tumefaciens causes crown gall on many dicotyledonous plants; A.rubi causes crown gall on raspberries; A.vitis gall formation on grapes; A.rhizogenes causes hairy roots; A.radiobacter is avirulent. However the ability to cause disease is associated with transmissible plasmids, and this grouping is easily disrupted when plasmids move from one strain to another. More recently Agrobacterium have been classified into 3 biovars based on physiological and biochemical phenotypes without consideration of disease; the 2 classification systems are not compatible. There is now a fully sequenced representative of each biovar publicly available.

Crown galls are formed when Agrobacterium with a a tumor-inducing Ti plasmid infects a wounded plant. A portion of the Ti-plasmid DNA (T-DNA) is transferred from the bacterial plasmid into the host plant cell where the T-DNA is integrated into host plant chromosomal DNA by an illegitimate recombination process. Some of the transferred genes encode enzymes responsible for the synthesis of plant hormones that cannot be controlled by the plant, causing abnormal cell divisions that produce a plant gall. Other transferred genes encode biosynthetic enzymes capable of transforming plant metabolites into a class of compounds called opines that are not catabolizable by the host plant, but are catabolizable by the tumor-inducing bacterial strain. A.vitis strain S4 is a virulent biovar III strain isolated from the Vitis vinifera (grape) cv. Izsaki Sarfeher crown gall in Kecskemet/Orgavony, Hungary in 1981. It produces the opine vitopine. A.vitis strains not only cause galls on grapevines but also necrosis on grapevine roots and a hypersensitive response on nonhost plants (adapted from PubMed 11524123 and 19251847).

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

Component nameGenome Accession(s)
Component representationProteins
Chromosome 13224
Chromosome 21054
Plasmid pAtS4b107
Plasmid pAtS4c170
Plasmid pTiS4196
Plasmid pAtS4e522
Plasmid pAtS4a80
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Main funding by: National Institutes of Health

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