Table 1. Survey of 19 GSM reconstruction procedures.

Variability of reference ID-databases, available annotations and metadata about reactions and heterogeneity of the methods used in each GSM reconstruction pipeline.

Species			Ref. database		Annotation of reactions					Methods and templates for reconstruction
Species	Group	Reference	Database used	Database crossreferences	Reactions	Unreferenced reactions	Literature or experimental justification	Confidence score	Gene association	Template model(s)	Orthology	Genome annotation	Gap-filling	Flux analysis	Manual curation
Synechocystis sp. PCC6803	Cyanobacteria	[27]	2	-	882	79	-	-	✓	3	-	✓	-	✓	✓
Synechocystis sp. PCC6803	Cyanobacteria	[28]	2	✓	1156	23	✓	-	✓	8	✓	✓	✓	✓	✓
Synechocystis sp. PCC6803	Cyanobacteria	[29]	1	✓	759	166	✓	✓	✓	9	✓	✓	-	✓	-
A. ferrooxi-dans ATCC 23270	Proteobacteria	[30]	3	-	615	4	✓	✓	✓	0	-	✓	-	✓	✓
Salmonella typhimurium LT2	Proteobacteria	[31]	2	-	2545	12	✓	✓	✓	2	-	-	-	✓	✓
Leptospira (4 strains)	Spirochaetes	[32]	2	✓	1017	52	-	-	NA	0	✓	✓	✓	✓	-
Staphylococcus aureus (64 strains)	Firmicutes	[24]	4	✓	1507	17	-	-	✓	15	✓	✓	✓	✓	✓
Enterococcus faecalis V583	Firmicutes	[33]	1	-	706	355	-	✓	✓	4	✓	-	-	✓	✓
Clostridium ljungdahlii	Firmicutes	[34]	3	✓	785	0	-	-	✓	4	✓	✓	✓	✓	✓
Lactobacillus planta-rum WCFS1	Firmicutes	[35]	1	-	761	371	✓	-	✓	0	✓	✓	-	✓	✓
Methanosarcina acetivorans	Euryarchaeotes	[36]	3	-	845	180	-	-	✓	2	-	✓	-	✓	✓
Pichia pastoris GS115	Ascomycetes	[37]	1	-	1202	NA	✓	-	✓	1	✓	-	✓	✓	✓
Saccharomyces cerevisiae	Ascomycetes	[38]	1	-	1412	NA	-	-	✓	2	-	✓	✓	✓	✓
Chlamydomonas reinhardtii	Green algae	[39]	2	✓	2190	632	✓	-	✓	2	✓	-	-	✓	✓
Chlamydomonas reinhardtii	Green algae	[40]	2	✓	2394	689	✓	✓	✓	1	✓	-	✓	✓	✓
Ectocarpus siliculosus	Brown algae	[41]	2	✓	1866	52	-	✓	✓	1	✓	✓	✓	✓	✓
Arabidopsis thaliana	Eudicots	[42]	2	-	1567	0	✓	-	✓	0	-	✓	✓	✓	✓
Zea mays	Monocots	[43]	2	-	8525	27	-	-	✓	1	✓	✓	✓	✓	✓
Homo sapiens	Primates	[44]	1	-	3742	20	✓	✓	✓	0	-	-	✓	✓	✓