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Pto DC3000 - Genome Properties

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Sequencing and annotation of the genome and two plasmids (pDC3000A and pDC3000B) was completed by The Institute for Genome Research (TIGR) in March, 2003 and published in Buell et al. 2003. Please note that these analyses do not reflect changes in the annotation since its original deposition

General features:

Size (bp)6,397,126 bp73,661 bp67,473 bp
G+C percentage58.4%55.1%56.1%
Number of ORFs5,6157177
Percent Coding86.8%81.9%84.7%
Average ORF length988 nt849 nt742 nt
No. ORFs encoding:
protein with a known function3,402 (61%)52 (73%)46 (60%)
hypothetical protein610 (11%)10 (14%)16 (21%)
conserved hypothetical protein961 (17%)8 (11%)12 (16%)
protein of unknown function642 (11%)1 (1%)3 (4%)

Genome publication and supporting information:

Buell, et al. 2003. The complete sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci 100:10181-10186. Supporting materials contain the following information:

supporting Table 2 - DC3000 factors implicated in virulence and putative homologs in pathogenic bacteria
supporting Table 3 - DC3000 genes disrupted by IS elements or phage genes
supporting Table 4 - IS elements present in DC3000
supporting Table 5 - phage and bacteriocin regions in DC3000
supporting Table 6 - genes with unknown function unique to DC3000
supporting Fig 4 - functional classification of annotated ORFs in DC3000
supporting Fig 5 - distribution of ORFs in paralogous families in DC3000
supporting Fig 6 - virulence determinants in DC3000 and their distribution in other bacterial pathogens

Additional features of the original genome sequence and annotation are available at the following sites:

TIGR-CMR Pseudomonas syringae DC3000

CAZy - Database of carbohydrate active enzymes in DC3000

DNA Structural Atlas - plots of structural features in the DC3000 chromosome generated by the Center for Biological Sequence Analysis at the Technical University of Denmark

Transporter Protein Analysis Database - TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available