Supplemental Material Carbohydrate utilization



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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


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