Supplemental text

Haemophilus-specific protein, uncharacterized	HS_1408	no
no
Haemophilus-specific protein, uncharacterized	HS_1409	no	no
Haemophilus-specific protein, uncharacterized	HS_1410	no	no
hypothetical protein	HS_1411	no	no
Haemophilus -specific protein, uncharacterized	HS_1412	no	no
conserved hypothetical protein	HS_1413	no	no
hypothetical protein	HS_1414	no	no
conserved hypothetical protein; possible phage-related protein	HS_1415	no	no
Haemophilus -specific protein, uncharacterized	HS_1416	no	no
Haemophilus -specific protein, uncharacterized	HS_1417	no	no
Haemophilus -specific protein, uncharacterized	HS_1418	no	no
conserved hypothetical protein; possible phage recombinase	HS_1419	no	no
conserved hypothetical protein	HS_1420	no	no
conserved hypothetical protein	HS_1421	no	no
DNA-cytosine methyltransferase	HS_1422	no	no
Haemophilus -specific protein, uncharacterized	HS_1423	no	no
conserved hypothetical protein; possible transcriptional regulator	HS_1424	no	no
integrase	HS_1425	no	no

*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

IS Family/Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
IS1
insB	no	HD1970	no
insA	no	HD1971	no
IS150
	no	no	HI1721
IS200/IS605
	HS_0224	no	no
	HS_0486	no	no
	HS_0583	no	no
	HS_0666	no	no
	HS_0667	no	no
	HS_0668	no	no
	HS_0716	no	no
	HS_0717	no	no
	HS_1390	no	no
	HS_1391	no	no
IS1016
IS1016C2	HS_0642	no	no
	HS_0324	no	no
	HS_0434 fragment	no	no
	HS_1116	no	no
	HS_1462	no	no
	HS_1463	no	no
	HS_1679	no	no
	HS_1709	HD1616	HI1328.1
IS1016V6	no	no	HI1577
	no	no	HI1329
	similarity to above genes		HI1018
ISNCY
	HS_0445	HD0908	no
Other transposases
	HS_0224a	no	no
	HS_0619a	no	no
	no	HD0290	no
	no	HD0291	no
	no	HD0295	no
	no	HD1612	no
	no	HD1689	no
	no	HD1695	no
	no	HD1696	no

The genes in H. somnus 129Pt that were in the neighborhood of the complete IS1016 elements included iron transporter and pyrimidine metabolism genes (HS_0642), iron transporter genes (HS_0324), DNA, amino acid and carbohydrate metabolism genes (HS_1116), succinate-semialdehyde dehydrogenase (HS_1679) and DNA gyrase and helicase (HS_1709).
Table S4. Unique genes in H. somnus 129Pt, excluding genes annotated as hypothetical and conserved hypothetical.

Function	Locus Tag	Definition
Anion transport	HS_1426	sulfate transporter
Biosynthesis of cofactors, prosthetic groups, and carriers; Heme, porphyrin, and cobalamin	HS_1540	uroporphyrinogen decarboxylase
Biosynthesis of cofactors, prosthetic groups, and carriers; Menaquinone and ubiquinone	HS_0150	4-hydroxybenzoate synthetase (chorismate--pyruvate lyase)
	HS_0544	ubiquinone biosynthesis protein
	HS_0681	2-octaprenyl-6-methoxyphenol hydroxylase
	HS_0915	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Biosynthesis of cofactors, prosthetic groups, and carriers; Pyridoxine	HS_0925	4-hydroxythreonine-4-phosphate dehydrogenase
Biosynthesis of cofactors, prosthetic groups, and carriers; Thiamine	HS_0902	thiamine biosynthesis protein
Butanoate metabolism   Glutamate metabolism   Tyrosine metabolism	HS_0407	succinate-semialdehyde dehydrogenase (NAD(P)+)
Carbohydrate utilization	HS_0030	sugar ABC transporter, sugar-binding protein
	HS_0050	transcriptional regulator, possible sorbitol operon regulator
	HS_0054	ABC transporter, solute-binding, sugar transport
	HS_0437	PTS system, cellobiose-specific IIC component
	HS_0607	mannose-specific phosphotransferase system IID component
	HS_0607	mannose-specific phosphotransferase system IID component
	HS_0608	mannose-specific phosphotransferase system IIC component
	HS_0609	phosphotransferase system mannose/fructose-specific IIA component
	HS_0675	glucitol operon activator
	HS_0677	PTS system, glucitol/sorbitol-specific IIA component
	HS_0678	PTS system, glucitol/sorbitol-specific IIBC component
	HS_0679	PTS system, glucitol/sorbitol-specific IIC2 component
	HS_0765	ABC-type sugar-binding periplasmic protein
	HS_0843	conserved hypothetical protein; possible fructosamine kinase family enzyme
	HS_1142	PTS system, galactitol-specific IIC component
	HS_1143	PTS system, galactitol-specific IIB component
	HS_1144	PTS system, galactitol-specific IIA component
	HS_1145	tagatose 6-phosphate kinase
	HS_1146	tagatose 1,6-diphosphate aldolase
	HS_1250	mannitol operon repressor
	HS_1251	mannitol 1-phosphate 5-dehydrogenase
	HS_1330	beta-glucuronidase
	HS_1601	glucuronide permease
	HS_1602	glucuronate isomerase
Cation transport	HS_0343	calcium/proton antiporter
	HS_0375	potassium uptake protein; K+ transporter
	HS_0376	potassium uptake protein
	HS_0647	sodium-dependent transporter
	HS_0652	Na+/H+ antiporter
	HS_1078	possible sodium/calcium exchange protein
	HS_1101	ammonium transporter
	HS_1517	copper homeostasis protein
Cell envelope	HS_0625	membrane protein; possible tellurium resistance protein
	HS_1254	lytic murein transglycosylase A
	HS_1265	outer membrane protein precursor
Cellular processes; Adaptations to atypical conditions	HS_0633	stress response protein; tellurium resistance protein
	HS_0634	stress response protein; tellurium resistance protein
	HS_0635	stress response protein; tellurium resistance protein
Cellular processes; Cell division	HS_0441	cell filamentation-like protein
	HS_1346	chromosome partitioning-related protein
	HS_1719	chromosome partitioning-related protein
Citrate cycle (TCA cycle)   Glyoxylate and dicarboxylate metabolism	HS_0960	citrate synthase
	HS_1641	isocitrate dehydrogenase
Degradation of proteins, peptides, and glycopeptides	HS_0572	possible regulator of membrane protease activity
DNA replication, recombination, and repair	HS_1009	chromosome initiation inhibitor
	HS_1639	possible NTP pyrophosphohydrolase, MutT/Nudix family
DNA methylation	HS_1422	DNA-cytosine methyltransferase
Electron transport	HS_1156	possible 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase
	HS_1225	possible flavin:NADH reductase
	HS_1674	possible chaperone protein
Fatty acid and phospholipid metabolism	HS_0111	acyl carrier protein
	HS_0113	conserved hypothetical protein; possible 3-hydroxymyristoyl/3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
	HS_0164	possible fatty acid/phospholipid synthesis protein
Fermentation	HS_1681	NAD-dependent aldehyde dehydrogenase
	HS_1682	aldehyde dehydrogenase, possible succinate-semialdehyde dehydrogenase [NAD(P)]
Glutamate metabolism   Glutathione metabolism	HS_0287	glutamate--cysteine ligase
Glycerolipid metabolism	HS_0110	1-acyl-sn-glycerol-3-phosphate acyltransferase
Glycine, serine and threonine metabolism	HS_1718	D-serine dehydratase
Glycoconjugate degradation	HS_0435	alpha-L-fucosidase
Iron and heme metabolism	HS_0069	iron-regulated outer membrane protein
Inositol metabolism	HS_1576	dehydrogenase; possible myo-inositol 2-dehydrogenase
	HS_1577	myo-inositol catabolism protein
	HS_1587	conserved hypothetical protein; possible myo-inositol catabolism protein
LOS biosynthesis	HS_0116	glycosyl transferase, group 2 family protein
	HS_0275	conserved hypothetical protein; possible glycosyltransferase
	HS_0700	possible N-acylneuraminate cytidylyltransferase
Nitrogen metabolism   Tryptophan metabolism	HS_0801	tryptophanase
	HS_0810	glutamyl-tRNA reductase
Pentose phosphate pathway	HS_0379	gluconokinase (gluconate kinase)
Phage-related functions and prophages	HS_0424	phage integrase
	HS_0426	possible phage DNA-polymerase or DNA-primase
	HS_0519	phage integrase
	HS_0533	phage DNA primase-like protein
	HS_0555	phage integrase
	HS_0557	phage P1-related protein
	HS_0558	enterobacteria phage P1
	HS_1228	integrase
	HS_1335	conserved hypothetical protein; possible prophage CP4-57 regulatory protein
	HS_1337	integrase
	HS_1388	lysozyme, possible phage-related lysozyme
	HS_1400	conserved hypothetical protein; possible DNA methylase
	HS_1401	conserved hypothetical protein; possible replication protein P
	HS_1406	conserved hypothetical protein; possible repressor protein
	HS_1415	conserved hypothetical protein; possible phage-related protein
	HS_1425	integrase
Porphyrin and chlorophyll metabolism	HS_0044	hydroxymethylbilane synthase (porphobilinogen deaminase, PGB)
Purine metabolism	HS_0964	dGTP triphosphohydrolase
Regulatory functions	HS_0817	possible low molecular weight protein-tyrosine-phosphatase
Restriction and modification	HS_0560	type I restriction enzyme, specificity subunit
Transcription	HS_0422	transcriptional regulator
	HS_0757	NagC-like transcriptional regulator
Transport and binding proteins	HS_1233	membrane protein; possible multiple antibiotic resistance protein
	HS_1567	permease, possible drug/metabolite transporter superfamily
	HS_1586	permease, possible MFS superfamily
Transport and binding proteins; ABC Superfamily	HS_0849	ABC-type multidrug transport system, permease component
Transport and binding proteins; Carbohydrates, organic alcohols, and acids	HS_0924	possible 2-keto-3-deoxygluconate permease
Transposase	HS_0434	transposase fragment
	HS_0486	transposase
	HS_0583	transposase
	HS_0666	transposase
	HS_0667	transposase
	HS_0668	transposase
	HS_0716	transposase
	HS_0717	transposase
	HS_1463	IS1016 related transposase, possible protein V6
Unassigned	HS_0442	resolvase/integrase-like protein
	HS_0443	ParA-like protein
	HS_0632	serine/threonine kinase-like protein
	HS_0680	VisC protein, monooxygenase family
	HS_0808	possible SAM-dependent methyltransferase
	HS_0898	tetrathionate reductase, subunit C
	HS_1584	NAD-dependent aldehyde dehydrogenase
Unknown	HS_0019	permease, major facilitator superfamily
	HS_0100	conserved hypothetical protein; possible transcriptional regulator
	HS_0106	conserved hypothetical protein; possible dehydratase
	HS_0117	conserved hypothetical protein; possible acyltransferase
	HS_0119	conserved thioesterase
	HS_0121	conserved membrane protein
	HS_0277	conserved hypothetical protein; possible SAM-dependent methyltransferase
	HS_0297	conserved hypothetical protein; possible hydrolase
	HS_0380	conserved hypothetical protein; possible periplasmic-binding protein
	HS_0427	conserved hypothetical protein; possible virulence-associated protein E
	HS_0478	conserved hypothetical protein; possible cell-surface large adhesin
	HS_0589	conserved hypothetical protein; possible adhesin
	HS_0619a	conserved hypothetical protein; possible transposase fragment
	HS_0628	conserved hypothetical protein, with von Willebrand factor (vWF) domain
	HS_0630	conserved hypothetical protein, with von Willebrand factor (vWF) domain
	HS_0660	possible membrane protein
	HS_0686	conserved hypothetical protein; possible aphA-like regulator
	HS_0723	HugX protein
	HS_0766	conserved hypothetical protein; possible gluconolactonase precursor
	HS_1046	conserved hypothetical protein; possible permease
	HS_1183	conserved hypothetical protein; possible permease
	HS_1234	conserved hypothetical protein; possible large adhesin
	HS_1247	conserved hypothetical protein; possible autotransporter protein YapE
	HS_1424	conserved hypothetical protein; possible transcriptional regulator
	HS_1428	possible permease
	HS_1480	conserved hypothetical protein; possible permease
	HS_1543	conserved hypothetical protein; possible outer membrane protein
	HS_1583	conserved hypothetical protein; possible dehydrogenase
	HS_1615	conserved hypothetical protein; possible dehydrogenase
	HS_1616	conserved hypothetical protein; possible large adhesin
	HS_1675	conserved hypothetical protein; possible histone acetyltransferase

Table S5. Carbohydrate metabolism

A. Galactitol

Gene