Table 2. Description of the contents of the evidence file generated by the VMGAP.

1	2	3	4	5	6	7	8	9
ID	CDD_RPS	Subject definition	% cov	% ident	e-value		% ident
ID	ALL GROUP_PEP	Subject ID	Subject definition	Query length	Subject length	% cov	% ident	e-value
ID	ACLAME_PEP	Subject ID	Subject definition	Query length	Subject length	% cov	% ident	e-value
ID	SANGER_PEP	Subject ID	Subject definition	Query length	Subject length	% cov	% ident	e-value
ID	ENV_NT	Subject ID	Subject definition	Query length	Subject length	% cov	% ident	e-value
ID	ENV_NR	Subject ID	Subject definition	Query length	Subject length	% cov	HMM description	e-value
ID	FRAG_HMM	HMM begin	HMM end	% cov	Total    e-value	HMM accession	HMM description	HMM length
ID	PFAM/TIGRFAM_HMM	HMM begin	HMM end	% cov	Total    e-value	HMM accession		HMM length
ID	PRIAM	EC Number	e-value				HMM description
ID	ACLAME_HMM	HMM begin	HMM end	% cov	Total    e-value	HMM accession		HMM length
ID	PEPSTATS	Molecular weight	Isoelectric point
ID	TMHMM	Number predicted helixes
ID	SIGNALP	signal pep	cleavage site position

Fields 1 and 2 correspond to the protein identifier and a flag specific for each analysis, respectively. % cov, percent coverage; % ident, percent identity; CDD_RPS, RPS-Blast vs. CDD DB; ALLGROUP_PEP, Blastp vs. protein NR DB; ACLAME_PEP, Blastp vs. ACLAME protein DB; SANGER_PEP, Blastp vs. in-house viral metagenomic DB; ENV_NT, Tblastn vs. ENV_NT DB; ENV_NR, Blastp vs. ENV_NR DB; FRAG_HMM, HMM searches vs. local PFAM/TIGRFAM HMM DB; PFAM/TIGRFAM_HMM, HMM searches vs. global PFAM/TIGRFAM HMM DB; PRIAM, RPS-Blast vs. PRIAM profile DB; ACLAME_HMM, HMM searches vs. global ACLAME HMM DB; PEPSTATS, peptide statistics; TMHMM, transmembrane domain searches; SIGNALP, signal peptide searches.