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

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

Module Family ID Description
M1 PF13472a GDSL-like lipase/acylhydrolase family
PF00756a Putative esterase
M2 PF14200a,b Ricin-type β-trefoil lectin domain-like
PF00652a,b Ricin-type β-trefoil lectin domain
PF00754a F5/8 type C domain
PF00041a Fibronectin type III domain
PF02311 AraC-like ligand-binding domain
PF13483 Beta-lactamase superfamily domain
M3 PF03629a,b DUF303
PF00657a GDSL-like lipase/acylhydrolase
PF13472a GDSL-like lipase/acylhydrolase family
PF13229a Right-handed beta helix region
M4 PF14310a Fibronectin type III-like domain
PF07859 Alpha/beta hydrolase fold
PF00135 Carboxylesterase family
PF13802 Galactose mutarotase-like
M5 PF13186a,b DUF4008
PF05593 RHS repeat
PF07591 Pretoxin Hint domain
PF07238 PilZ domain
PF13403 Hint domain
  1. 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.
  2. aProtein families appearing in the gene clusters identified by mapping the PDMs to the phenotype-positive genomes.
  3. 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).
  4. 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.