Table 3. Genome contents of several protein families from the Pfam database involved in membrane transport, along with the number of these predicted to have been acquired via LGT according to BLAST at the level of Order, BLAST at the level of Family, or at least one compositional method (AlienHunter, IslandPath-DIMOB and SIGI-HMM).

Organism	MFS-1 major facilitator transporter superfamily: PF00083, PF07690, PF05977	Periplasmic-binding proteins: PF00532, PF00497, PF01094, PF01547	Carbohydrate-selective porins: PF04966	Major intrinsic proteins: PF00230	Total
Methylocella silvestris
Total genes	25	17	1	1	44
LGT Order level BLAST	2	0	0	0	2
LGT Family level BLAST	14	2	0	1	17
LGT Compositional	4	3	0	0	7
Methylocapsa acidiphila
Total genes	14	10	1	1	26
LGT Order level BLAST	0	0	0	0	0
LGT Family level BLAST	4	0	0	0	4
LGT Compositional	2	2	0	0	4
Beijerinckia indica
Total genes	43	24	5	3	75*
LGT Order level BLAST	18	3	1	2	24*
LGT Family level BLAST	26	10	5	2	43*
LGT Compositional	9	1	0	0	10

Abbreviation: LGT, lateral gene transfer.

An asterisk in the ‘Total' column indicates that the number of transporters, or the proportion of predicted LGT, is significantly higher in B. indica than in M. acidiphila, calculated with a Z-ratio test of proportions and a Bonferroni correction for three comparisons (P=0.05). There were no significant differences between M. silvestris and M. acidiphila.