Supplemental Material Carbohydrate utilization

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*Region 1 may be a decaying prophage that has had stretches of functional genes inserted into it.

Table S2. Pseudogenes in H. somnus 129Pt

Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
H. somnus 129Pt
tbpA transferrin-binding protein A, C-terminal region	HS_0097	no	HI0661 full length
tbpA transferrin-binding protein A, central fragment	HS_0098	no	HI0994 full length
tbpA transferrin-binding protein A, N-terminal region	HS_0102	no	HI1565 full length
transposase fragment	HS_0434	no	no
conserved hypothetical protein; possible transposase fragment	HS_0619a	no	no
lob2C glucosyltransferase; involved in LOS biosynthesis, N-terminal	HS_0636a	HD0466 lgtA full length	HI1578 full length
hgbA hemoglobin-binding protein, C-terminal	HS_0720	HD2025 full length	HI1567 full length
hgbA hemoglobin binding protein A, N-terminal	HS_0721	HD2025 full length	HI0712 full length HI0635? HI0661? HI1565?
conserved hypothetical protein, fragment	HS_1066a	no	no
IS1016 insertion sequence, C-terminal	HS_1462	no	HI1328.1
IS1016 insertion sequence, N-terminal	HS_1463	no	no
H+/gluconate symporter, N-terminal	HS_1522	no	HI0092 full length
H+/gluconate symporter, C-terminal	HS_1523	no	HI0092 full length
restriction-modification system methyltransferase, N-terminal	HS_1525	no	no
restriction-modification system methyltransferase, C-terminal	HS_1526	no	no

Table S3. IS elements excluding prophage transposases

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