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

From: The Viral MetaGenome Annotation Pipeline (VMGAP): An automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

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:0016887go:0005524
7 Source of Gene Ontology assignment PF00005PF00005
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
  1. Each lane contains the annotation for a single predicted peptide. Multiple values within a field are separated by the symbol “”.