Table 1 Required genes for mycobacterial in vivo growth that contain non-synonymous SNPs in Pasteur 1173P2 and Danish 1331

1

Rv0101

nrp

Peptide synthetase Nrp

L1365M

 + 

 + 

2

Rv0169

mce1A

Mce family protein Mce1A

S313A, P359S

 + 

 + 

3

Rv0170

mce1B

Mce family protein Mce1B

I179T

 + 

 + 

4

Rv0171

mce1C

Mce family protein Mce1C

E212D

 + 

 + 

5

Rv0176

-

Mce associated transmembrane protein

N285S, S291A

 + 

 + 

6

Rv0218

-

Transmembrane protein

C316R, D413N

 + 

 + 

7

Rv0490

senX3

Two component sensor histidine kinase SenX3

F109S

 + 

 + 

8

Rv0636

hadB

(3R)-hydroxyacyl-ACP dehydratase subunit HadB

T54A

 + 

 + 

9

Rv0643c

mmaA3

Methoxy mycolic acid synthase MmaA3

G98D

 + 

 + 

10

Rv1028c

kdpD

Sensor protein KdpD

N776D, P368S, G295D, P83S

 + 

 + 

11

Rv1109c

-

Hypothetical protein

A147T

 + 

 + 

12

Rv1128c

-

Hypothetical protein

E270G

 + 

 + 

13

Rv1204c

-

Hypothetical protein

L484I

 + 

 + 

14

Rv1224

tatB

Sec-independent protein translocase protein TatB

W8G

 + 

 + 

15

Rv1244

lpqZ

Lipoprotein LpqZ

Q242K

 + 

 + 

16

Rv1338

murI

Glutamate racemase

R154L

 + 

 + 

17

Rv1371

-

Membrane protein

I368V

 + 

 + 

18

Rv1460

-

Transcriptional regulator

I198F, A266V

 + 

 + 

19

Rv1640c

lysX

Bifunctional lysine-tRNA ligase/phosphatidylglycerol lysyltransferase

D944G, D769E

 + 

 + 

20

Rv2048c

pks12

Polyketide synthase

A4047S, P3095L, S2964R H2147Q, G1865S

 + 

 + 

21

Rv2072c

cobL

Precorrin-6Y C(5,15)-methyltransferase

L205P

 + 

 + 

22

Rv2275

-

Cyclo(L-tyrosyl-L-tyrosyl) synthase

E261A

 + 

 + 

23

Rv2359

zur

Zinc uptake regulation protein

H64R

 + 

 + 

24

Rv2374c

hrcA

Heat-inducible transcription repressor HrcA

R79Q

 + 

-

25

Rv2388c

hemN

Oxygen-independent coproporphyrinogen III oxidase

A184T

 + 

 + 

26

Rv2483c

plsC

Bifunctional L-3 phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase

C189G

 + 

 + 

27

Rv2502c

accD1

Acetyl/propionyl-CoA carboxylase subunit beta

F343L, G77S

 + 

 + 

27

Rv2692

ceoC

TRK system potassium uptake protein CeoC

I133V

 + 

 + 

29

Rv2696c

-

Hypothetical protein

D164N

 + 

 + 

30

Rv2702

ppgK

Polyphosphate glucokinase

I203T

 + 

 + 

31

Rv2813

-

Hypothetical protein

I76V

 + 

 + 

32

Rv2845c

proS

Proline–tRNA ligase

A232T, H177R

 + 

 + 

33

Rv2936

drrA

Daunorubicin ABC transporter ATP-binding protein DrrA

H309D

 + 

 + 

34

Rv2981c

ddlA

D-alanine–D-alanine ligase

T365A

 + 

 + 

35

Rv3042c

serB2

Phosphoserine phosphatase SerB

G116E, A70S

 + 

 + 

36

Rv3061c

fadE22

Acyl-CoA dehydrogenase FadE22

S497C, K488E

 + 

 + 

37

Rv3087

-

Diacylglycerol O-acyltransferase

L447V

 + 

 + 

38

Rv3114

-

Hypothetical protein

S11P

 + 

 + 

39

Rv3277

-

Transmembrane protein

S272L

 + 

 + 

40

Rv3335c

-

Integral membrane protein

A86V

 + 

 + 

41

Rv3371

-

Diacylglycerol O-acyltransferase

R339G, I368V

 + 

 + 

42

Rv3497c

mce4C

Mce family protein Mce4C

T46P

 + 

 + 

43

Rv3551

-

CoA-transferase subunit alpha

A7S

 + 

 + 

44

Rv3563

fadE32

Acyl-CoA dehydrogenase FadE32

Q105R, W275S

 + 

 + 

45

Rv3616c

espA

ESX-1 secretion-associated protein EspA

T192I, A4V

 + 

 + 

46

Rv3805c

aftB

Terminalbeta-(1- > 2)-arabinofuranosyltransferase

I327V

 + 

 + 

47

Rv3868

eccA1

ESX-1 secretion system protein EccA1

A243V

 + 

 + 

48

Rv3910

-

Peptidoglycan biosynthesis protein

V480A

 + 

 +