Database Authors
Ron Caspi1, Pedro Romero1, Peter D Karp1
1SRI International
Summary The primary data source for this dataset was the full genome sequence of Agrobacterium fabrum C58, derived from Genbank accessions AE008687, AE008688, AE008689, and AE008690 [Wood01].

This Pathway/Genome Database (PGDB) was created from the annotated genome using the PathoLogic [Karp11, Karp19] component of the Pathway Tools software and the MetaCyc reference database [Caspi20]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

We gratefully acknowledge the collaboration of researchers from the University of Washington, the University of Campinas, and DuPont.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
circular chromosome2,8332,7854802,841,490RefSeq:AE007869
linear chromosome1,8951,8761902,075,560RefSeq:AE007870
plasmid At54354300542,780RefSeq:AE007872
plasmid Ti19819800214,234RefSeq:AE007871
Total:5,4695,4026705,674,064
Ortholog data available?Yes
Database Contents
Genes5,469
Pathways357
Enzymatic Reactions1,949
Transport Reactions98
Polypeptides5,410
Protein Complexes166
Enzymes1,209
Transporters717
Compounds1,505
Transcription Units3,731
tRNAs57
Growth Media1
Protein Features6,699
GO Terms46,311
Gene Essentiality Datasets1
Database Version29.0 [History of Updates]
Synonyms Rhizobium radiobacter str. C58 (Cereon)
Rhizobium radiobacter str. C58 (Dupont)
Rhizobium radiobacter str. C58 (U. Washington)
Agrobacterium fabrum str. C58
Agrobacterium fabrum C58
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Rhizobiaceae
Rhizobium/Agrobacterium group
Agrobacterium
Agrobacterium tumefaciens complex
Agrobacterium fabrum
Agrobacterium fabrum C58
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0000707
NCBI-Taxonomy176299
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Pathogenicityplant
NCBI Genome Typereference
Copyright 2018, SRI International.

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

Wood01: Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li MJ, McClelland E, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao ZY, Dolan M, Chumley F, Tingey SV, Tomb JF, Gordon MP, Olson MV, Nester EW (2001). "The genome of the natural genetic engineer Agrobacterium tumefaciens C58." Science 294(5550);2317-23. PMID: 11743193

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of AgroCyc: Science 294:2317 2001.
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