Table 3 Pseudogenes shared between Paratyphi A and Typhi

i^

0062a

n/a

-

putative viral protein

-

i^

0255a

n/a

-

putative uncharacterized protein

-

i

1103

1362

-

Pertussis toxin subunit S1 related protein

1.22%

i^

1699a

0971

sopD2

*secreted effector protein SopD homolog

1.73%

i^

2014

0610

silA

*putative inner membrane proton/cation antiporter

1.08%

i^

2014a

0609a

cusS

*putative copper-ion sensor protein

0.18%

i^

3229

4202

-

putative phosphosugar-binding protein

0.14%

i

3640

3800

cdh

CDP-diacylglycerol pyrophosphatase

2.32%

i^

3888

4728a

-

putative uncharacterized protein

1.35%

i

30 transposase/phage genes and gene remnants, details available in Additional file 1

ii

0097

0113

-

*putative secreted protein

0.25%

ii

0431b

2631

-

putative IS transposase

0.24%

ii

0754a

2275

sopA

*secreted effector protein

0.23%

ii

3228

4203

-

putative L-asparaginase

0.14%

ii

3365a

4037

sugR

putative uncharacterized protein (SPI-3)

0.14%

iii

0192a

0218

fhuA

*ferrichrome-iron receptor precursor

23.95%

iii

0317a

2775

-

putative anaerobic dimethylsulfoxide reductase component

1.79%

iii

0329a

2762

sivH

*putative invasin (CS54)

1.17%

iii

0331a

2758

ratB

*putative lipoprotein (CS54)

1.67%

iii

0331b

2755

shdA

*putative uncharacterized protein (CS54)

2.11%

iii

0621a

2422

mglA

*galactoside transport ATP-binding protein

1.09%

iii

0720a

2311

wcaK

*putative extracellular polysaccharide biosynthesis protein

1.82%

iii

0756a

2268

yeeC

penicillin-binding protein

2.19%

iii

0850a

2166

fliB

lysine-N-methylase

3.11%

iii

0943a

1995

-

transposase

4.77%

iii

1014a

1913

hyaA

hydrogenase-1 small subunit

0.33%

iii

1220a

1508

-

*putative transport protein

1.31%

iii

1367a

1739

-

putative ribokinase (SPI-2)

1.42%

iii

1531a

1244

fhuE

*FhuE receptor precursor

0.96%

iii

1642a

1104

-

*putative secreted protein

1.54%

iii

1820a

0833

slrP

*secreted effector protein

1.95%

iii

2045a

0569

ybbW

*putative allantoin transporter

1.19%

iii

2301a

0333

safE

*probable lipoprotein (SPI-6 fimbrial cluster)

1.52%

iii

3388a

4007

-

putative cytoplasmic protein

1.12%

iii

3636a

3805

-

*putative permease of the Na+:galactoside symporter family

2.42%

iii

3828b

4503

dmsA

anaerobic dimethyl sulfoxide reductase chain A

0.22%

iii

3998a

4839

sefD

*putative fimbrial protein (SPI-10)

0.18%

iii, iv¹

1197a

1486

narW

respiratory nitrate reductase 2 delta chain

1.74%

iii, iv²

2900a

3421

yhaO

*putative transport system protein

0.58%

iv³

0708

2328

wcaA

putative uncharacterized protein

1.35%