Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Table 3 Protein families of the modules M1 to M5 with potential functions in plant biomass degradation

Module	Family ID	Description
M1	PF13472^a	GDSL-like lipase/acylhydrolase family
M1	PF00756^a	Putative esterase
M2	PF14200^a,b	Ricin-type β-trefoil lectin domain-like
	PF00652^a,b	Ricin-type β-trefoil lectin domain
	PF00754^a	F5/8 type C domain
	PF00041^a	Fibronectin type III domain
	PF02311	AraC-like ligand-binding domain
	PF13483	Beta-lactamase superfamily domain
M3	PF03629^a,b	DUF303
	PF00657^a	GDSL-like lipase/acylhydrolase
	PF13472^a	GDSL-like lipase/acylhydrolase family
	PF13229^a	Right-handed beta helix region
M4	PF14310^a	Fibronectin type III-like domain
	PF07859	Alpha/beta hydrolase fold
	PF00135	Carboxylesterase family
	PF13802	Galactose mutarotase-like
M5	PF13186^a,b	DUF4008
	PF05593	RHS repeat
	PF07591	Pretoxin Hint domain
	PF07238	PilZ domain
	PF13403	Hint domain

DUF, domain of unknown function; GDSL, a motif in the amino acid sequences of the members of this protein family; PDM, plant biomass degradation module.
^aProtein families appearing in the gene clusters identified by mapping the PDMs to the phenotype-positive genomes.
^bSome potential functions of the families PF14200, PF00652, PF03629, and PF13186 are discussed in the context of the respective PDMs (see Results section; see Additional file 2: Section 1).
The table lists protein families of the plant biomass degradation modules (PDMs) that had no commonly known functions in plant biomass degradation. Every second family (55%) occurred in the gene clusters that were identified based on the PDMs. Note that family PF13472 was part of M1 and M3.

ISSN: 2731-3654