Table 2.

Genes with a SNP with Fst >0.5 in the top 20 lists

Criterion	Gene	Locus tag	Figure	Category	Annotation	Residue function
Fst >0.6+ top 20 in different pairwise comparisons	hefC	HP0607	3(b)	Efflux pump	Inner membrane component of the multidrug HefABC efflux pump	Channel entrance
	frpB-4	HP1512	4(a)	TonB-dependent importer	Outer membrane nickel importer	Ligand binding
	flaA	HP0601	6(b)	Motility	Flagellin A of flagella, involved in immune system evasion	Glycosylation for host mimicry and more
	katA	HP0875	6(a)	Sensor	Catalase sensing and destroying H2O2	Channel entrance; Dimer-dimer interface
	hopI	HP1156		Outer membrane protein	Outer membrane protein HopI
	hopB/alpB	HP0913		Outer membrane protein	Hop family adhesin HopB/AlpB/Omp21.
	tlpD	HP0599	6(c)	Sensor	Chemotaxis sensor sensing and destroying HOCl	Active site
	exbB-2	HP1339	S3C	TonB-dependent importer	Energizer/motor in the inner membrane driven by proton	Channel entrance
Fst >0.6 two or more SNPs	hofC	HP0486		Outer membrane protein	Hof family protein implicated in adhesion and antibiotics diffusion
	porB	HP1111		Energy metabolism	Subunit of pyruvate:ferredoxin oxidoreductase, part of the microaerophilic metabolic pathway leading to acetyl~CoA	Subunit interaction
	gltA	HP0026	5(b)	Energy metabolism	Citrate synthase, the first enzyme in TCA cycle incorporating acetyl~CoA	Subunit interaction
	oppD	HP0250	5(a)	Importer	Oligopeptide ABC transporter, ATPase subunit	Cofactor binding
Fst >0.5	ompA-18	HP1125		Outer membrane protein	OmpA family peptidoglycan-associated lipoprotein	Ligand binding
	fixP	HP0147	S4C	Energy metabolism	Subunit of cytochrome c oxidase in aerobic respiration	Channel entrance
	hypC	HP0899			Hydrogenase expression/formation protein	(Synonymous change)
	hefD	HP0971	3(c)	Efflux pump	Outer membrane component of the HefABC multidrug efflux pump	Protein binding
	copA	HP1503	S2E	Exporter	Copper(I) exporter	Protein stability
	mscS-1	HP0284		Sensor	Mechano-sensor sensing tension in the membrane	Scaffolding in the periplasm
	metQ	HP1564	S2D	Importer	d-methionine ABC transporter, methionine-binding subunit	Ligand binding
	frpB-1	HP0876	S3A	TonB-dependent importer	Outer membrane haem importer	Ligand binding
	fecA-1	HP0686	S3B	TonB-dependent importer	Outer membrane iron(III) dicitrate importer	Ligand binding; Channel (plug)
	exbD-2	HP1340	S3C	TonB-dependent importer	Inner membrane energizer/motor driven by proton	Proton channel entrance
	hpaA	HP0797	S3F	Outer membrane protein	Neuraminyllactose-binding hemagglutinin	Subunit interaction
	omp	HP0358		Outer membrane protein	Putative outermembrane protein
	panD	HP0034	S4A (i)	Micronutrient synthesis	Vitamin B5 synthesis	Interaction between cleaved peptides
	bioD	HP0029		Micronutrient synthesis	Vitamin B7 synthesis
	tgt	HP0281	S4A (iii)	Micronutrient synthesis	Q-base synthesis; Q-base on tRNA affects translation accuracy	Active site
	rhoD	HP1223	S4B	Detox	Rhodanese detoxifying cyanide generated in microbiome
	rkiP	HP0218	S2B	Oncoprotein	Mimic of human RKIP tumour suppressor	Interaction with signal peptide
	hcpX	–	S2A	Effector	SLR family with repeated alpha-helix pairs	Human protein binding
	dsbI	HP0595	S3D	Secretion	S-S formation	Active site
	jag	HP1451		Secretion	Regulator of VirB11/Cag-alpha gate of Cag secretion system	Cofactor binding
	lpxE	HP0021	S2C	Membrane lipid modifier	Lipid A 1-phosphatase to hide it from the innate immune response	Substrate binding; active site
	cfaS	HP0416	S3E	Membrane lipid modifier	Cyclopropane-fatty-acyl-phospholipid synthase for acid protection	Substrate binding
	fur	HP1027	S4D	Transcription factor	Regulator of Fe/Ni import, redox balance and acid response	Cofactor binding