Table 3. Explanation of the annotation file generated by the VMGAP.

Column	Description	Example
1	Unique peptide ID	JCVI_PEP_metagenomic.orf.112038372243 2.1
2	Protein common name tag	common_name
3	Functional description (s)	phosphonate C-P lyase system protein PhnL, putative
4	Source of functional description assignment	AllGroup High:rf|YP_001889651.1
5	GO tag	GO
6	Gene Ontology ID (s)	go:0016887||go:0005524
7	Source of Gene Ontology assignment	PF00005||PF00005
8	EC tag	EC
9	Enzyme Commission number ID (s)	3.6.3.28
10	Source of Enzyme Commission ID	PRIAM
11	Hits against ENV_NT DB tag	ENV_NT
12	ENV_NT DB libraries hit with e-values ≤1 × 10-3	Hydrothermal vent metagenome FOSS10958.y2,    whole genome shotgun sequence ||     Lake Washington Formate SIP Enrichment Freshwater Metagenome ||     Human Gut Metagenome (healthy human sample In-M, Infant, Female)
13	Best hit e-value per environmental library	6.65676e-54 || 2.14066e-44 || 1.34265e-46
14	Number of hits with e-value ≤1 × 10-3 per environmental DB library	1 || 1 || 4
15	HMM DB tag	PFAM/TIGRFAM_HMM
16	PFAM/TIGRFAM HMM hit above trusted cutoff	PF000005
17	Signalp tag	SIGNALP
18	Presence (Y) or absence (N) of predicted signal peptide	Y
19	Cleavage site position	16
20	Transmembrane domain tag	TMHMM
21	Number of predicted transmembrane domains	2
22	Protein statistics tag	PEPSTATS
23	Molecular weight	17369.86
24	Isoelectric point	9.9423

Each lane contains the annotation for a single predicted peptide. Multiple values within a field are separated by the symbol “||”.