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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 “”.