Supplemental Material Carbohydrate utilization



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C. Nicotinate phosphoribosyltransferase pathway:



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

nadV

nicotinate phosphoribosyltransferase
HS_0002


HD1447

no

2.7.7.1

Nicotinamide-nucleotide adenylyltransferase

no

no

no

Table S10. LOS biosynthesis genes

Genes identified in H. influenzae 86-028NP (18)


Gene

H. influenzae

86-028NP



H. influenzae Rd

H. somnus 129Pt

H. ducreyi 35000HP

kdsB

3-deoxy-D-manno-octulosonate cytidylyltransferase



NTHI0068

HI0058

HS_0658

HD0334

lpxK

tetraacyldisaccharide-1-P 4'-kinase
NTHI0069

HI0059

HS_0656

HD0217

msbA

Lipid A ABC transporter, ATP-binding protein



NTHI0072

HI0060

HS_1021

HD1630

msbB

lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase



NTHI0296

HI0199

HS_1202

HD0404

lgtC

glycosyl transferase


repeats?

NTHI0365

GACA repeated 10 times in frame



HI0258

GACA repeated 22 times in frame just after start codon
HS_0636 lob2D

CAGT repeated 19 times in the middle of the CDS
HD1090

no repeats

orfM

Xanthosine triphosphate pyrophosphatase
NTHI0366

HI0260

HS_0125

HD1348

kdkA

3-deoxy-D-manno-octulosonic acid kinase,



NTHI0367

HI0260.1

no

HD1101

opsX/rfaC

ADP-heptose:LPS heptosyltransferase I
NTHI0368

HI0261

HS_1611

lipopolysaccharide heptosyltransferase-1
HD0445

lpt6

phosphorylethanolamine transferase



NTHI0383

HI0275

HS_0234

no

galE

UDP-glucose 4-epimerase



NTHI0471

HI0351

HS_0789

HD0829

lic3A

alpha-2,3-sialyltransferase




NTHI0472
CAAT repeated 18 times in frame

HI0352


no

no

possible acetyltransferase

NTHI0512
AGCA repeated 8 times in frame

HI0391
no repeats

HS_0553
no repeats

no

waaQ

ADP-heptose:LPS heptosyltransferase III



NTHI0649

HI0523


no

HD1202


lic2A

UDP galactose lipooligosaccharide galactosyltransferase



NTHI0677

CAAT repeated 14 times in frame
HI0550

CAAT repeated 21 times in middle of CDS
HS_0637 lob2A

TGAT repeated 36 times in 300 bases upstream of CDS start
Top hit is to lgtB HD0472

no repeats



kdtA

3-deoxy-d-manno-octulosonic-acid transferase
NTHI0772

HI0652

HS_1590

HD0454

lgtF

UDP-glucose--Lipooligosaccharide glucosyltransferase




NTHI0773

HI0653

HS_0291

HD1201

lpxH

UDP-2,3 diacylglucosamine hydrolase
NTHI0892

HI0735

HS_0498

HD1938

manB phosphomannomutase

NTHI0899

HI0740

HS_1670

HD1507

lex2B

UDP-glucose--lipooligosaccharide glucosyltransferase



NTHI0913

this is a family 25 glycosyltransferase
top hit is HI1697

a family 25 glycosyltransferase
HS_0638 lob1 glycosyltransferase, family 25

top hit is HD1721

a family 25 glycosyltransferase

lic2B

glycosyltransferase lpsA homolog



NTHI0926

HI0765

HS_0637 lob2A is the top hit

HD0472 lgtB is the top hit

galU

glucosephosphate uridylyltransferase



NTHI0976

HI0812

HS_1117

HD1431

lic3A2

CMP-neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
NTHI1034
CAAT repeated 18 times in frame

HI0352
32 CAAT repeats and an earlier start are 317 bases upstream of the gene start. The earlier start and repeats are out of frame with the NTHI1034 gene.

no

no

rmlB/rffG

DTDP-glucose 4,6-dehydratase
NTHI1037

HI0873

HS_0707

HD0687

lpxD

UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase
NTHI1082

HI0915

HS_0978

HD1189

predicted PE--lipooligosaccharide phosphorylethanolamine transferase

NTHI1180

HI1005

no

HD0371

lpxB

lipid-A-disaccharide synthetase
NTHI1220

HI1060

HS_1358

HD0846

lpxA

UDP-N-acetylglucosamine acetyltransferase
NTHI1222

HI1061

HS_1359

HD1187

predicted PE-lipooligosaccharide phosphorylethanolamine transferase

NTHI1224

HI1064

no

HD1598

rfaF

ADP-heptose--LPS heptosyltransferase II
NTHI1272

HI1105

HS_1612

HD0653

rfaD

ADP-L-glycero-D-mannoheptose-6-epimerase
NTHI1278

HI1114

HS_1613

HD1890

lpxC

UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase



NTHI1312

HI1144

HS_0364

HD0816

lpcA/gmhA phosphoheptose isomerase

NTHI1350

HI1181

HS_1238

HD1228

lgtA

N-acetylglucosamine glycosyltransferase
NTHI1474

HI1578

no

HD0466

kdsA

2-dehydro-3-deoxyphosphooctonate aldolase
NTHI1576

HI1557

HS_0946

HD0857

licD

lipopolysaccharide choline phosphotransferase
NTHI1594

HI1540

HS_1458

HS_0727 fragment
no

licC

CTP:phosphocholine cytidylyltransferase
NTHI1595

HI1539

HS_1459

no

licB

choline transporter
NTHI1596

HI1538

HS_1460

no

licA

phosphorylcholine kinase
NTHI1597
CAAT repeated 15 times in frame

HI1537
alternative start and CAAT repeated 17 times out of frame prior to the gene start

HS_1461
no repeats

C-terminal only HD1021

no repeats

htrB

lipid A biosynthesis lauroyl acyltransferase



NTHI1606

HI1527

HS_0575

HD1106

rfaE

ADP-heptose synthase
NTHI1607

HI1526

HS_0576

HD1182

mrsA Phosphomannomutase

NTHI1664

HI1337

HS_0730

HD0201

glycosyltransferase

NTHI1750
GACA repeated 14 times in frame

HI0258 is top hit

HS_0636 lob2D is top hit ~50% identity

HD1090?
no repeats

glycosyltransferase

NTHI1769
CCAA repeated 17 times out of frame

HI1386
CCAA repeated 16 times in 300 bases upstream of gene start

no

HD0375 is top hit

no repeats

neuA

acylneuraminate cytidylyltransferase
NTHI1891

HI1279

HS_0706

HD0685

Possible polysaccharide biosynthesis protein

NTHI1921

HI1244

no

HD1508

lsgF

lipopolysaccharide biosynthesis protein
NTHI2002

HI1695

no

HD0886

lsgE

lipopolysaccharide biosynthesis protein
NTHI2003

HI1696

no

HD0885

lsgD

lipopolysaccharide biosynthesis protein
NTHI2004

HI1697

no

HD0883

lsgC

lipopolysaccharide biosynthesis protein, putative
NTHI2005

HI1698

no


no

lsgB

lipopolysaccharide biosynthesis protein

beta-galactoside alpha-2,3-sialyltransferase


NTHI2006

HI1699

no

no

lsgA

lipopolysaccharide biosynthesis protein
NTHI2007

HI1700

HI0867


no

HD0882

rfe/mraY/wecA undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase

NTHI2025

HI1716

HS_0355

HD1844

B. Genes identified in H. influenzae Rd (20) that are not included above



Gene

H. influenzae Rd

H. somnus 129Pt

H. ducreyi 35000HP

kfiC

beta-UDP-GlcA glycosyltransferase
HI0868

no

HD0466

orfE

predicted glycosyltransferase
HI0869

no

no

orfO

possible glycosyltransferase
HI0870

no

no

orfY

N-acetylneuraminic acid synthase-like protein
HI0871

no

HD0466

rfbP

HI0872

no

no

Genes identified in H. somnus 129Pt and H. ducreyi 35000HP



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

glycosyl transferase, group 2 family protein

HS_0116

no

no

conserved hypothetical protein; possible glycosyltransferase

HS_0275

no

no

glmU

bifunctional protein: UDP-N-acetylglucosamine diphosphorylase; glucosamine-1-phosphate N-acetyltransferase
HS_0333

HD1511

HI0642

murZ/murA

UDP-N-acetylglucosamine 1-carboxyvinyltransferase
HS_1167

HD0253

HI1081

ftsI

peptidoglycan glycosyltransferase (peptidoglycan synthetase)
HS_0352

HD0241

HI1132

murG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase

HS_0358

HD0824

HI1138

malQ

4-alpha-glucanotransferase
HS_0890

no

HI1356

conserved hypothetical protein (probable glycosyltransferase)

no

HD0375

no

lbgB

D-glycero-D-manno-heptosyl transferase/alpha-1,6-DD-heptosyltransferase
no

HD1720

no

lob1

HS_0638

36 CAAT repeats just after start
HD1721

no CAAT repeats
no

lob2A

20 GA repeats in last third of the CDS (strain 738)
HS_0637

no more than 2 GA repeats in a row
HD0472 lgtB

HI0550 lic2A

22 CAAT repeats in the first third of the CDS

lob2B

no

HD0472 lgtB

no GA repeats
no

lob2C

HS_0636a

HD0466 lgtA

HI1578

lob2D

HS_0636

29 CAGT repeats in the middle of the CDS
HD1090

HI0258

22 ACAG repeats just after the start


Table S11. Secretion systems, pili and adhesins

A. Secretion systems

1. General secretory (Sec) pathway for translocation of proteins across the inner membrane into the periplasm



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

Sec translocase










secD

HS_1313

HD1752

HI0240

secE

HS_0194

HD1886

HI0716

secF

HS_1312

HD1753

HI0239

secG

HS_1311

HD1277

HI0445

secA

HS_0990

HD1788

HI0909

secB

HS_0156

HD0661

HI0743

yajC

HS_1314

HD1751

HI0241

secY(prlA)

HS_0080

HD1957

HI0798

Catalyze protein folding in periplasm










dsbA

thiol:disulfide interchange protein
HS_0308


HD0638


HI0846


dsbA-like protein

HS_0624

HD1729

HI0428

dsbC

thiol:disulfide interchange protein
HS_1475


HD1340



HI1213


Signal peptidases










lepB signal peptidase I

HS_1241

HD1607

HI0015

lspA lipoprotein signal peptidase

HS_0185


HD0063


HI1006

2. Mechanisms for transport across the outer membrane – terminal branches of the general secretory pathway



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

Autotransporters










H. influenzae igA1 protease

no

no

HI0990

S. flexneri

icsA/virG

no


no


no

tsh

no

no

no

possible large adhesin*

HS_0209

no

no

possible large adhesin*

HS_0383

no

no

possible large adhesin*

HS_0478

no

no

possible adhesin

HS_0589

no

no

possible adhesin

HS_0602

no

no

possible large adhesin*

HS_0790

no

no

possible large adhesin*

HS_1058

no

no

possible large adhesin*

HS_1085

no

no

possible large adhesin*

HS_1154

no

no

possible large adhesin*

HS_1234

no

no

possible large adhesin*

HS_1616

no

no

possible large adhesin*

HS_1632

No

HI1718

Hia

no

no

no

Hsf

no

no

no

DsrA

HS_1543

HD0769

no

NcaA

no

HD1920

no

Chaperone/usher pathway pap genes (E. coli) involved in the biogenesis of P pili











papC

no

HD0283

41% aa identity
no

papA


no

HD0281

32% aa identity
no

papD

no

HD0284

52% aa identity
no

papE

no

no

no

Type II secretion










pulC

no

no

no

pulD

no

no

no

pulE

no

no

no

pulF

no

no

no

pulG

no

no

no

pulH

no

no

no

pulI

no

no

no

pulJ

no

no

no

pulK

no

no

no

pulL

no

no

no

pulM

no

no

no

pulN

no

no

no

pulO

no

no

no

Type III secretion










LcrD family proteins










lcrD (Y. enterocolitica)

no

no

no

invA (S. typhimurium)

no

no

no

mxiA (virH) (Shigella sonnei)

no

no

no

sepA (E.coli)

no

no

no

hrcV (Erwinia amylovora)

no

no

no

flhA (E.coli K-12)

no

no

no

Bordetella bpeI system










bscI

no

no

no

bscJ

no

no

no

bscK

no

no

no

bscL

no

no

no

bscN

no

no

no

bscO

no

no

no

Yersinia type III system










yscC

no

no

no

yscD

no

no

no

yscF

no

no

no

yscG

no

no

no

yscH

no

no

no

yscI

no

no

no

yscJ

no

no

no

yscK

no

no

no

yscL

no

no

no

yscM

no

no

no

yscN

no

no

no

yscO

no

no

no

Shigella type III system










ipaA

no

no

no

ipaD

no

no

no

ipaC

no

no

no

ipaB

no

no

no

Salmonella type III system











leucine rich repeat secreted by SPI-1

no

no

no

secreted effector protein secreted by SPI-2

no

no

no

secreted effector protein secreted by SPI-1

no

no

no

invG

no

no

no

prgH

no

no

no

prgK

no

no

no

prgI

no

no

no

prgJ

no

no

no

E. coli type III system











sepZ

no

no

no

Type IV secretion










Agrobacterium tumefaciens vir system










virA

sensor kinase
no


no


no


virB1

type IV secretion system apparatus lytic transglycosylase
no

no

no

virB2

prepropilin
no

no

no

virB3

type IV secretion system apparatus component
no

no

no

virB4

type IV secretion sytem apparatus ATPase
no

no

no

virB5

type IV secretion system apparatus component
no

no

no

virB6

type IV secretion system apparatus component
no


no

no


virB7

type IV secretion system apparatus outer membrane lipoprotein precursor
no

no

no

virB8

type IV secretion system apparatus component
no

no

no

virB9

type IV secretion system apparatus outer membrane protein
no

no

no

virB10

type IV secretion apparatus inner membrane protein
no

no

no

virB11

type IV secretion apparatus ATPase
no


no


no



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