Fig 1.
Graphical representation of the proteins (denoted P1, P2, P3, P4, P5) which can serve as markers for the bacterial (denoted B1, B2, B3, B4) group of interest consisting of B1 and B2: (A) shows that P1, P2 can serve as a minimal set of markers for the group of interest; (B) P1 only can serve as a marker for the group of interest; and (C) there are no markers for the group of interest.
Fig 2.
Software structure and output.
Table 1.
Hitting sets (marker proteins) of 17 microorganism groups.
HS, hitting set. Min., minimal. Greedy and random refer to the algorithm type. Phen., phenotypic. Tax., taxonomic. AIEC, adherent-invasive E. coli. EPEC, enteropathogenic E. coli. UPEC, uropathogenic E. coli. STEC, Shiga toxin-producing E. coli. NMEC, neonatal meningitis-associated E. coli. ExPEC, extra-intestinal pathogenic E. coli. ETEC, enterotoxigenic E. coli. EIEC, enteroinvasive E. coli. EHEC, enterohemorrhagic E. coli. EAEC, enteroaggregative E. coli. APEC, avian pathogenic E. coli. EAHEC, enteroaggregative hemorrhagic E. coli.
Fig 3.
Maximum-likelihood phylogenetic tree of the NusG protein.
All archaeal NusG sequences were taken from the GenBank database, along with their most similar bacterial and eukaryotic homologs for a total of 500 protein sequences. The bootstrap consensus tree inferred from 100 replicates was taken to represent the evolutionary history of the taxa analyzed. Branches were merged at the domain level.