Database Authors
Ron Caspi1
1SRI International
Summary Aurantimonas manganoxydans SI85-9A1 is a marine α-proteobacterium isolated from Saanich Inlet, Canada, from the interface between the bottom anoxic water and the overlying oxygenated water [Tebo85, Anderson09]. The organism, which belongs to the Rhizobiales order, oxidizes Mn(II) and contains an active RubisCO enzyme [Caspi96, Dick08].

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.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome3,6653,6075804,285,343RefSeq:CH672387
Genes without a physical map position:1
Ortholog data available?Yes
Database Contents
Genes3,666
Pathways359
Enzymatic Reactions1,659
Transport Reactions107
Polypeptides3,611
Protein Complexes136
Enzymes1,032
Transporters321
Compounds1,208
Transcription Units2,604
tRNAs49
Protein Features4,783
GO Terms30,709
Database Version29.0
Synonyms Aurantimonas manganoxydans SI85-9A1
Rhizobiales bacterium SI85-9A1
manganese-oxidizing bacterium SI85-9A1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Aurantimonadaceae
Aurantimonas
Aurantimonas manganoxydans
Aurantimonas manganoxydans SI85-9A1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
GOLD0006098
NCBI-Taxonomy287752
Copyright SRI International 2008-2011.

References

Anderson09: Anderson CR, Dick GJ, Chu ML, Cho JC, Davis RE, Brauer SL, Tebo BM (2009). "Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) oxidizing representatives of a globally distributed clade of alpha-Proteobacteria from the order Rhizobiales." Geomicrobiol J 26(3);189-198. PMID: 19768133

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

Caspi96: Caspi R, Haygood MG, Tebo BM (1996). "Unusual ribulose-1,5-bisphosphate carboxylase/oxygenase genes from a marine manganese-oxidizing bacterium." Microbiology 142 ( Pt 9);2549-59. PMID: 8828223

Dick08: Dick GJ, Podell S, Johnson HA, Rivera-Espinoza Y, Bernier-Latmani R, McCarthy JK, Torpey JW, Clement BG, Gaasterland T, Tebo BM (2008). "Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1." Appl Environ Microbiol 74(9);2646-58. PMID: 18344346

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

Tebo85: Tebo BM, Emerson S (1985). "Effect of Oxygen Tension, Mn(II) Concentration, and Temperature on the Microbially Catalyzed Mn(II) Oxidation Rate in a Marine Fjord." Appl Environ Microbiol 50(5);1268-73. PMID: 16346931

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