Table 2. Strain 195 genes identified in functionally enriched clusters and associated inferred annotations^* .

Locus Tag	Operon ID	Cluster No	Model Gene No	Primary Annotation	Revised Annotation in the Model	Suggested New Annotation from This Study	Subsystem
DET0509	106	2	113	hypothetical protein	putative bifunctional phosphoglucose/phosphomannose isomerase	Retain previous annotation	Central Carbon Metabolism
DET0742	160	2	192	triosephosphate isomerase	Retain previous annotation	Retain previous annotation	Central Carbon Metabolism
DET0369	84	2	57	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase	Retain previous annotation	Retain previous annotation	Lipid Metabolism
DET0371	84	2	58	1-deoxy-D-xylulose 5-phosphate reductoisomerase	Retain previous annotation	Retain previous annotation	Lipid Metabolism
DET0372	84	2	59	phosphatidate cytidylyltransferase	Retain previous annotation	Retain previous annotation	Lipid Metabolism
DET0417	91	2	79	amino acid ABC transporter; ATP-binding protein	putative glutamine transporter	putative methionine transporter	Transport
DET0418	91	2	80	amino acid ABC transporter; permease protein	putative glutamine transporter	putative methionine transporter	Transport
DET0518	108	2	118	translation initiation factor, putative,	methylthioribose-1-phosphate isomerase	Retain previous annotation	Amino Acid Metabolism
DET0591	125	2		hypothetical protein	hypothetical protein	putative carbohydrate esterase	Central Carbon Metabolism
DET0592	125	2		hypothetical protein	hypothetical protein	putative Maltose 6-phosphate glucosidase	Central Carbon Metabolism
DET0318	71	6	19	reductive dehalogenase, putative	tetrachloroethene reductive dehalogenase	Retain previous annotation	Energy Metabolism
DET0319	71	6	446	reductive dehalogenase anchoring protein, putative	tetrachloroethene reductive dehalogenase anchoring protein	Retain previous annotation	Energy Metabolism
DET0320	71	6		hypothetical protein	hypothetical protein	putative transcriptional regulator/activator	Non-metabolic
DET1558	326	8	523	reductive dehalogenase anchoring protein, putative	Retain previous annotation	Retain previous annotation	Energy Metabolism
DET1559	326	8	425	reductive dehalogenase, putative	Retain previous annotation	Retain previous annotation	Energy Metabolism
DET1500	310	8		hypothetical protein	hypothetical protein	putative transcriptional regulator/activator	Non-metabolic
DET1501	310	8		flavodoxin	flavodoxin	Retain previous annotation	Energy Metabolism

*A more detailed version of this table is presented in Table S16 in File S1, where rationales for each reannotation are described briefly.