Table I. Online resources used during the reconstruction and curation process.

Resource	Link	Reference
Functional annotation, draft generation, and subcellular localization
RAVEN Toolbox	http://biomet-toolbox.org/	Agren et al. (2013)
BLAST	http://blast.ncbi.nlm.nih.gov/	Altschul et al. (1990)
Phylogeny.fr	http://phylogeny.lirmm.fr/	Dereeper et al. (2008)
Manual curation
KEGG	http://www.genome.jp/kegg/	Kanehisa et al. (2014)
EMBL-EBI	http://www.ebi.ac.uk/intenz/	McWilliam et al. (2013)
ExplorEnz	http://www.enzyme-database.org/	McDonald et al. (2007)
BIGG	http://bigg.ucsd.edu/	Schellenberger et al. (2010)
BRENDA	http://www.brenda-enzymes.org/	Scheer et al. (2011)
MetaCyc	http://metacyc.org/	Caspi et al. (2014)
SwissProt	http://web.expasy.org/blast/	UniProt Consortium (2015)
TransportDB	http://www.membranetransport.org/	Ren and Paulsen (2007)
SignalP 4.1 server	http://www.cbs.dtu.dk/services/SignalP/	Petersen et al. (2011)
ChloroP 1.1 server	http://www.cbs.dtu.dk/services/ChloroP/	Emanuelsson et al. (1999)
HECTAR	http://www.sb-roscoff.fr/hectar/	Gschloessl et al. (2008)
WoLF PSORT	http://www.genscript.com/psort/wolf_psort	Horton et al. (2007))
ChemAxon	http:// http://www.chemaxon.com/	ChemAxon
TCDB	http://www.tcdb.org/browse.php	Saier et al. (2014)
Conversion to mathematical model
SimPheny, version 3.3	http://systemsbiology.ucsd.edu/Downloads/SimphenyPerlApplication	Schilling et al. (2008)
COBRA Toolbox 2.0	http://sourceforge.net/projects/opencobra/files/	Schellenberger et al. (2011)
ESCHER	http://escher.github.io/	King et al. (2015)
COBRApy	https://github.com/opencobra/cobrapy/blob/master/INSTALL.md	Ebrahim et al. (2013)
Kaleidagraph 4.5	http://www.synergy.com/wordpress_650164087/kaleidagraph/free/	Synergy Software
Gurobi Optimizer	http://www.gurobi.com/	Gurobi