Supplemental text



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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


*has autotransporter Hia-like and YadA-like domains at C-terminal

B. Pili


Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

Possible competence, pili, secretion system genes in H. somnus 129Pt










Competence










comA

competence protein A



HS_1109

HD0427

HI0439

comB

competence protein B



HS_1110

no

HI0438

comC

competence protein C



HS_1111

HD0432

HI0437

comD

competence protein D



no

no

HI0436

comE

competence protein E



HS_1112

HD0434


HI0435


Type 4 pili










pilA

pilin


HS_0250

HD1123

HI0299

pilB

nucleotide binding protein



HS_1430

HD1124

HI0298


pilC

inner membrane protein



HS_0457

HD1125

HI0297

pilD

prepilin peptidase and methylase



HS_0458

HD1126

HI0296

pilM

domains in common with cell division protein FtsA and rod-shape-determining protein MreB



no

no

no

pilN

cytoplasmic membrane protein



no

no

no

pilO

cytoplasmic membrane protein



no

no

no

pilP

possible lipoprotein



no

no

no

pilQ outer membrane protein

secretin – pilus extrudes through this



no

no

no

pilT

motor required for motility



no

no

no

minor pilin-like proteins










pilE

no

no

no

pilV

no

no

no

pilW

no

no

no

pilX

no

no

no

fimT (not essential)

no

no

no

fimU

no

no

no

H. influenzae type b pilus










hifA

no

no

no

hifY3

no

no

no

hifY1

no

no

no

hifY2

no

no

no

hifB

no

no

no

hifC

no

no

no

hifD

no

no

no

hifE

no

no

no

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