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hitA/fbpA	HS_0783	no
HI0097
hitB/fbpB	HS_0782	no	HI0098
hitC/fbpC	HS_0781	no	HI0099

	no	no	HI1470
	no	no	HI1471
	no	no	HI1472

* These fragments represent the H. somnus 129Pt counterpart of tbpA2 from H. somnus strain 649 and tbpA from H. ovis.
Table S13. Genes involved in DNA uptake and transformation

Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
comA (comEC)	HS_1109	HD0427	HI0439
comB	HS_1110	HD0432	HI0438
comC	HS_1111	no	HI0437
comD	no	no	HI0436
comE	HS_1112	HD0434	HI0435
comF	HS_1490	HD0209	HI0434
comG	HS_1491	HD0378	HI0433
comJ	HS_1107	HD1760	HI0441
comL	HS_0366	HD0470	HI0177
tpc N. gonorrhoeae	no	no	no
tfoX(sxy)	HS_1715	HD1985	HI0601
crp	HS_0139	HD0738	HI0957
pilF2 involved in uptake but not binding of DNA	HS_1197	HD0318	HI0366
pulJ involved in DNA binding and uptake --related to type II secretion system	HS_0278	HD0440	HI0937
pulG related to type II secretion system	HS_0264	HD0182	HI0938
pilA	HS_0250	HD1123	HI0299
pilB	HS_1430	HD1124	HI0298
pilC	HS_0457	HD1125	HI0297
pilD	HS_0458	HD1126	HI0296
pilE pilin	no	no	no

Table S14. Hemolysins and toxins

Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
Hemolysins
possible hemolysin	HS_0237	HD1145	HI0301
possible hemolysin	HS_0737	HD0800	HI1658
bi-functional hemolysin (N-terminal) and outer membrane protein A homolog (C-terminal)	HS_0842	no	no
hhdB	no	HD1326	no
hhdA	no	HD1327	no
possible hemolysin	HS_1429	HD0770	HI0107
hemolysin accessory protein	no	HD1155	no
Cytotoxins
cdtA cytolethal distending toxin A	no	HD0902	no
cdtB cytolethal distending toxin B	no	HD0903	no
cdtC cytolethal distending toxin C	no	HD0904	no
RTX toxins
RTX toxins and related Ca2+-binding proteins ZP_00132930	no	no	no
RTX toxins and related Ca2+-binding proteins ZP_00132933.2	no	no	no
AAG40310.1\|AF314526_1 leukotoxin [Pasteurella trehalosi]	no	no	no
CAC80494.1\| pore-forming RTX-Toxin; EHEC-hemolysin [Escherichia coli]	no	no	no
CAA60041.1\| EHEC-hlyC [Escherichia coli]	no	no	no
P15377\|RT2A_ACTPL RTX-II toxin determinant A (APX-IIA) (Hemolysin IIA) (HLY-IIA) (Cytolysin IIA) (CLY-IIA)	no	no	no

Table S15. Restriction-modification system genes

Gene	H. somnus 129Pt	Flanked by mobile element?	Near DNA uptake sequence?	H. ducreyi 35000HP	H. influenzae Rd
Type I
hsdS	`HS_0556`	yes HS_0555	yes	no	no
`hsdR`	`HS_0559`	see above	yes	no	HI1285
`hsdS`	`HS_0560`	see above	yes	no	no
`hsdM`	`no`	NA	NA	no	HI0215 contains a frameshift
hsdS	no	NA	NA	no	HI0216
hsdR	no	NA	NA	no	HI0218 contains frameshift
hsdS	no	NA	NA	no	HI1286
hsdM	no	NA	NA		HI1287
`possible type I methyltransferase protein`	no	NA	NA	HD0914	no
Type II
hindIIR	no	NA	NA	no	HI0512
hindIIM	no	NA	NA	no	HI0513
type II restriction enzyme, putative	no	NA	NA	no	HI1040
hindVM	no	NA	NA	no	HI1041
hindIIIM	no	NA	NA	no	HI1392
hindIIIR	no	NA	NA	no	HI1393
Type III
type III restriction-modification system enzyme	no	NA	NA	HD1690	no
type III restriction-modification system methyltransferase, subunit	no	NA	NA	HD1691	no
type III restriction/modification system modification methylase	no	NA	NA	HD1692 HD1693	HI1056
Other
`possible antirestriction enzyme`	HS_1780	yes HS_0001 phage integrase	yes	HD0917	no
`bcgIA`	`HS_0430`	yes HS_0424 phage integrase	no	HD0293	no
`bcgIB`	`HS_0431`	see above	no	HD0294	no
`bcgIB`	`HS_0432` `C-terminal`	see above	no	no	no
`possible endonuclease involved in recombination`	`HS_0010`	yes HS_0001	yes	HD1795	HI0305

Table S16. Putative exopolysaccharide biosynthesis genes

Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
mrsA/glmM phosphoglucomutase/ phosphomannomutase (PGM)	HS_0730	HD0201	HI1463 HI1337
galU UDP-glucose pyrophosphorylase (UGP)	HS_1117	HD1431	HI0812
galE UDP-glucose epimerase (UGE)	HS_0789	HD0829	HI0351
pgi Glucose-6-phosphate isomerase (PGI)	HS_0938	HD0418	HI1576
manA phosphomannose isomerase (PMI)	HS_0605	HD0765	HI1710 N-terminal fragment
manB phosphomannomutase (PMM)	HS_1670	HD1507	HI0740
manB phosphomannomutase (PMM)	HS_1118	no	no
manC GDP-D-mannose-pyrophosphorylase (GMP)	no	no	no

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