Table 1.

Functional assignment criteria

Source	Known Protein	Putative	Hypothetical
Blastp (Mycoplasma DB)	Evalue < e-20	Evalue between	Evalue
		>e-20 and <e-4	> e-4 or No match
Blastp (Swissprot DB)	Evalue < e-20	Evalue between	Evalue
		>e-20 and <e-4	> e-4 or No match
HAMAP families	Confident protein family match	No confident protein family match	N/A
Interpro domains	If no HAMAP family match. Support evidence from at least one InterPro member database		Support evidence from one or none Interpro member database

Description of the criteria used to assign the genes products into the 3 following categories: Known Protein (known function: significant e-value and supported by confident protein family and functional domains), Putative protein (unclear function: twilight zone e-value but supported by functional domains) and Hypothetical protein (unknown function: non-significant e-value or no match in databases).