glycine dehydrogenase (decarboxylating) 1.4.4.2
|
no
|
no
|
no
|
lpdA
dihydrolipoate dehydrogenase
|
HS_1093
|
HD1623
|
HI1231
|
gcvH
lipoyl protein
|
no
|
no
|
no
|
gcvT
aminomethyltransferase 2.1.2.10
|
no
|
no
|
no
|
R. Serine degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
L-serine to pyruvate
|
|
|
|
sdaB
L-serine deaminase 2 4.3.1.17
|
no
|
HD1142
|
HI0288
|
sdaA
L-serine deaminase 1
|
no
|
no
|
no
|
sdhY
L-serine deaminase 3
|
no
|
no
|
no
|
S. Alanine degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
L-alanine to pyruvate
|
|
|
|
alanine dehydrogenase
1.4.1.1
|
HS_0232
|
HD1663
|
HI1362
|
T. Proline degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
L-proline to L-glutamate
|
|
|
|
putA
proline dehydrogenase 1.5.99.8/Delta-1-pyrroline-5-carboxylate dehydrogenase 1.5.1.12
|
no
|
no
|
no
|
U. Phenylalanine degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
L-phenylalanine to L-tyrosine
|
|
|
|
phhA phenylalanine-4-hydroxylase
1.14.16.1
|
no
|
no
|
no
|
V. Tyrosine degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
phhC/tyrB
tyrosine aminotransferase 2.6.1.5
|
no
|
no
|
no
|
hppD
4-hydroxyphenylpyruvate dioxygenase 1.13.11.27
|
no
|
no
|
no
|
W.Tryptophan degradation
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
L-tryptophan to pyruvate
|
|
|
|
tnaA
tryptophanase
|
HS_0801
|
no
|
no
|
L-tryptophan to tryptamine
|
|
|
|
aromatic L-amino acid decarboxylase
|
no
|
no
|
no
|
L-tryptophan to indole-3-acetate
|
|
|
|
key enzyme: indolepyruvate carboxylase
|
no
|
no
|
no
|
L-tryptophan to anthranilate
|
|
|
|
tryptophan 2,3-dioxygenase 1.13.11.11
|
no
|
no
|
no
|
Table S7. Nucleotide metabolism
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
purA
adenylosuccinate synthetase
|
HS_1328
|
HD1807
|
HI1633
|
purB
adenylosuccinate lyase
|
HS_1593
|
HD1649
|
HI0639
|
purC
phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICAR synthetase)
|
HS_1364
|
HD0251N-terminal
HD0252 C-terminal
|
HI1726
|
purD
phosphoribosylamine--glycine ligase
|
HS_1626
|
HD1042 C-terminal
HD1043 N-terminal
|
HI0888
|
purE
phosphoribosylaminoimidazole carboxylase (AIR carboxylase)
|
HS_0672
|
HD1424
|
HI1615
|
purF
amidophosphoribosyltransferase
|
HS_0916
|
HD1210 C-terminal
HD1209 N-terminal
|
HI1207
|
purH
phosphoribosylaminoimidazolecarboxamide formyltransferase
|
HS_1625
|
HD1703 N-terminal
HD1702 N-terminal
|
HI0887
|
purK
phosphoribosylaminoimidazole carboxylase, ATPase subunit
|
HS_0839
|
HD1421 C-terminal
HD1423 N-terminal
|
HI1616
|
purL
phosphoribosylformylglycinamidine synthase
|
HS_1503
|
HD2008 N-terminal
HD2009 central region
HD2010 C-terminal
|
HI0752
|
purM
phosphoribosylformylglycinamidine cyclo-ligase
|
HS_1551
|
HD0561
|
HI1429
|
purN
phosphoribosylglycinamide formyltransferase
|
HS_0913
|
HD0548
|
HI1428
|
purR
purine nucleotide synthesis repressor
|
HS_1032
|
HD1641
|
HI1635
|
purT
phosphoribosylglycinamide formyltransferase 2
|
HS_0549
|
HD0548
|
no – but this enzyme is redundant with purN
|
purU
formyltetrahydrofolate deformylase
|
HS_0786
|
no
|
HI1588
|
guaA
GMP synthase, glutamine-hydrolyzing (glutamine amidotransferase)
|
HS_0421
|
HD1504
|
HI0222
|
guaB
IMP dehydrogenase (inosine-5'-monophosphate dehydrogenase)
|
HS_0420
|
HD1503
|
HI0221
|
guaC
GMP reductase [Escherichia coli]
|
no
|
no
|
no
|
adk
adenylate kinase
|
HS_0648
|
HD0826
|
HI0349
|
gmk
guanylate kinase
|
HS_1457
|
HD1830
|
HI1743
|
ndk
nucleoside-diphosphate kinase
|
HS_0387
|
HD1053
|
HI0876
|
nrdA
ribonucleoside diphosphate reductase 1, alpha subunit
|
HS_1196
|
HD1731
|
HI1659
|
nrdB
ribonucleoside-diphosphate reductase 1, beta subunit
|
HS_0961
|
HD1732
|
HI1660
|
nrdE
ribonucleoside-diphosphate reductase 2, alpha subunit
|
no
|
no
|
no
|
nrdF
ribonucleoside-diphosphate reductase 2, beta subunit
|
no
|
no
|
no
|
carA/pyrA
carbamoyl phosphate synthetase, glutamine amidotransferase small subunit
|
no
|
HD0235
|
no
|
carB
carbamoyl phosphate synthase, large subunit
|
no
|
HD0233
|
no
|
pyrB
aspartate carbamoyltransferase, catalytic subunit
|
no
|
no
|
no
|
pyrC
dihydro-orotase
|
no
|
no
|
no
|
pyrD
dihydroorotate dehydrogenase
|
no
|
HD1626
|
HI1401
|
pyrE
orotate phosphoribosyltransferase
|
no
|
HD1759
|
HI0272
|
pyrF
orotidine 5`-phosphate decarboxylase
|
no
|
HD1356
|
HI1224
|
pyrG
CTP synthase (UTP--ammonia ligase)
|
HS_0552
|
HD0373
|
HI1077
|
pyrH
uridylate kinase
|
HS_0987
|
HD1597
|
HI1065
|
pyrI
aspartate carbamoyltransferase, regulatory subunit
|
no
|
no
|
no
|
pyrR
pyrimidine operon regulatory protein / uracil phosphoribosyltransferase
|
HS_1561
|
HD1178
HD1181
|
HI0459
|
Table S8. Genes involved in TCA cycle, Embden-Meyerhof, pentose phosphate, Entner-Doudoroff, ubiquinone/menaquinone biosynthesis and fermentation pathways in H. somnus 129Pt, H. ducreyi 35000HP and H. influenzae Rd.
TCA cycle
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
aceE
pyruvate dehydrogenase E1 component
|
HS_1095
|
HD1625
|
HI1233
|
aceF
pyruvate dehydrogenase, E2 complex
|
HS_1094
|
HD1624
|
HI1232
|
lpdA
pyruvate dehydrogenase multienzyme complex, E3
|
HS_1093
|
HD1623
|
HI1231
|
gltA
citrate synthase
|
HS_0960
|
no
|
no
|
acnA
aconitase
|
no
|
no
|
no
|
acnB
aconitate hydratase2
|
HS_1270
|
no
|
no
|
icd
isocitrate dehydrogenase
|
no
|
no
|
no
|
sucA
alpha ketoglutarate dehydrogenase
|
HS_0959
|
HD1336
|
HI1662
|
sucB
alpha ketoglutarate dehydrogenase, dihydrolipoamide succinyltransferase component
|
HS_0958
|
HD1334
|
HI1661
|
sucC
succinyl-CoA synthetase beta chain
|
HS_0957
|
no
|
HI1196
|
sucD
succinyl-CoA synthetase alpha chain
|
HS_0956
|
no
|
HI1197
|
sdhA
succinate dehydrogenase flavoprotein subunit
|
no
|
no
|
no
|
sdhB
succinate dehydrogenase iron-sulfur protein
|
no
|
no
|
no
|
sdhC
succinate dehydrogenase cytochrome b-556 subunit
|
no
|
no
|
no
|
sdhD
succinate dehydrogenase hydrophobic membrane anchor protei
|
no
|
no
|
no
|
fumA
fumarase
|
no
|
no
|
no
|
fumB
fumarate hydratase class I, anaerobic
|
no
|
no
|
no
|
fumC
fumarate hydratase class II
|
HS_1102
|
HD1986
|
HI1398
|
mdh
malate dehydrogenase
|
HS_1055
|
HD0264
|
HI1210
|
malate dehydrogenase, FAD/NAD(P)-binding domain
|
no
|
HD0165
|
no
|
frdA
fumarate reductase, flavoprotein subunit
|
HS_1277
|
HD0030
|
HI0835
|
frdB
fumarate reductase, iron-sulfur protein
|
HS_1278
|
HD0032
|
HI0834
|
frdC
fumarate reductase 15 kDa hydrophobic protein
|
HS_1279
|
HD0033
|
HI0833
|
frdD
fumarate reductase, 13 kDa hydrophobic protein
|
HS_1280
|
HD0034
|
HI0832
|
Embden-Meyerhof
|
|
|
|
glk
hexokinase (glucokinase)
|
HS_0379
|
no
|
no
|
putative glucokinase from Streptomyces coelicolor A3
NP_624417
|
no
|
no
|
HI0144
|
glucokinase from Streptomyces coelicolor A3
NP_626383
|
HS_1041
ROK
|
no
|
HI0182
|
pfkA
6-phosphofructokinase I
|
HS_0485
|
HD0465
|
HI0982
|
pfkB
6-phosphofructokinase II
|
no
|
no
|
no
|
fruK
1-phosphofructokinase
|
no
|
no
|
HI0447
|
fba
fructose bisphosphate aldolase
|
HS_0206
|
HD0864
|
HI0524
|
pgi
glucose 6-phosphate isomerase
|
HS_0938
|
HD0418
|
HI1576
|
tpiA
triosephosphate isomerase
|
HS_1591
|
HD0762
|
HI0678
|
gap
glyceraldehyde 3-phosphate dehydrogenase
|
HS_1466
|
HD1291
|
HI0001
|
pgk
phosphoglycerate kinase
|
HS_0207
|
HD0865
|
HI0525
|
gpmA
phosphoglycerate mutase 1
|
HS_1445
|
HD1659
|
HI0757
|
gpmB
phosphoglycerate mutase 2
|
HS_1664
|
no
|
no
|
eno
enolase
|
HS_0561
|
HD0477
|
HI0932
|
pyk
pyruvate kinase II
|
HS_1086
|
HD0446
|
HI1573
|
ldhA
fermentative D-lactate dehydrogenase, NAD-dependent
|
no
|
no
|
HI0085
|
dld
D-lactate dehydrogenase, FAD protein, NADH independent
|
HS_0784
|
no
|
HI1649
|
lldD/lctD
L-lactate dehydrogenase
|
no
|
HD0084
|
HI1739.1
|
ptsG
PTS system, glucose-specific IIABC component
|
no
|
no
|
no
|
crr
PTS system, glucose-specific enzyme II, A component
|
HS_1096
|
HD0227
|
HI1711
|
Pentose Phosphate
|
|
|
|
zwf
glucose 6-phosphate 1-dehydrogenase
|
HS_1651
|
HD0838
|
HI0558
|
pgl
6-phosphogluconolactonase
|
HS_1652
|
HD0836
|
HI0556
|
gnd
6-phosphogluconate dehydrogenase, decarboxylating
|
HS_1654
|
HD0833
|
HI0553
|
rpiA
ribose 5-phosphate isomerase A, constitutive
|
HS_0123
|
HD0199
|
HI0464
|
rpiB
ribose 5-phosphate isomerase B, inducible
|
no
|
no
|
no
|
rpe
ribulose phosphate 3-epimerase
|
HS_0175
HS_0057
|
HD1929
|
HI0566
|
tktA
transketolase I
|
HS_0551
|
HD1723
|
HI1023
|
tktB
transketolase II
|
no
|
no
|
no
|
talA
transaldolase A
|
no
|
no
|
no
|
talB
transaldolase B
|
HS_0204
|
HD0310
|
HI1125
|
Entner-Doudoroff
|
|
|
|
edd
phosphogluconate dehydratase
|
HS_0342
|
no
|
HI0738
|
eda
oxaloacetate decarboxylase
|
HS_1603
|
no
|
HI0047
|
Ubiquinone biosynthesis
|
|
|
|
ubiA
4-hydroxybenzoate-octaprenyltransferase
|
HS_0159
|
HD1647
|
no
|
ubiB
NADPH:flavin oxidoreductase
|
HS_0544
|
HD0717
|
no
|
ubiC
chorismate lyase
|
HS_0150
|
no
|
no
|
ubiD
3-octaprenyl-4-hydroxybenzoate carboxy-lyase
|
HS_0474
|
HD0197
|
no
|
ubiE
ubiquinone/menaquinone biosynthesis methyltransferase
|
HS_0542
|
HD0719
|
no
|
ubiH
2-octaprenyl-6-methoxyphenol hydroxylase
|
HS_0681
|
HD0579
|
no
|
ubiX
3-octaprenyl-4-hydroxybenzoate carboxy-lyase
|
HS_0915
|
HD1360
|
no
|
ubiG
3-demethylubiquinone 3-methyltransferase / 2-octaprenyl-6-hydroxyphenol methylase
|
HS_1162
|
HD1750
|
no
|
ubiF
2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase
|
HS_1156
|
HD1874
|
no
|
menaquinone biosynthesis
|
|
|
|
menA
1,4-dihydroxy-2-naphthoate octaprenyltransferase
|
HS_0221
|
HD0683
|
HI0509
|
menB
dihydroxynaphthoic acid synthase
|
HS_0562
|
HD1925
|
HI0968
|
menC
o-succinylbenzoate-CoA synthase (OSB synthase)
|
HS_0563
|
HD1055
|
HI0969
|
menD
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
|
HS_0617
|
HD1853
|
HI0283
|
menE
O-succinylbenzoate-CoA synthase
|
HS_1207
|
HD1271
|
HI0194
|
menF
menaquinone-specific isochorismate
|
HS_0618
|
HD0621
|
HI0285
|
entC
isochorismate synthase, enterobactin specific
|
no
|
no
|
no
|
menG
S-adenosylmethionine:2-demethylmenaquinone methyltransferase
|
HS_0220
|
HD0166
|
HI0508
|
chorismate biosynthesis (shikimate pathway)
|
|
|
|
aroA
3-phosphoshikimate-1-carboxyvinyltransferase
|
HS_0613
|
HD1383
|
HI1589
|
aroB
3-dehydroquinate synthase
|
HS_1114
|
HD0422
|
HI0208
|
aroC
3-dehydroquinate dehydratase (chorismate synthase)
|
HS_1205
|
HD1274
|
HI0196
|
aroD
3-dehydroquinate dehydratase
|
no
|
no
|
no
|
aroE
5-enolpyruvoylshikimate-3-phosphate synthase
|
HS_0006
|
HD0415
|
HI0655
HI0607
|
aroF
3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase)/
chorismate synthase
|
no
|
HD0444
|
no
|
aroG
2-dehydro-3-deoxyphosphoheptonate aldolase// 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, phenylalanine repressible)
|
HS_0941
|
HD1475
|
HI1547
|
aroH
2-dehydro-3-deoxyphosphoheptonate aldolase
|
no
|
no
|
no
|
aroK
shikimate kinase I
|
HS_1113
|
HD0423
|
HI0207
|
aroL
shikimate kinase II
|
no
|
no
|
no
|
Fermentation
|
|
|
|
pyruvate to D-lactate
|
|
|
|
ldhA
D-lactate dehydrogenase
|
HS_0945
|
no
|
HI0085
|
dld
D-lactate dehydrogenase
|
HS_0784
|
no
|
HI1649
|
pyruvate to L-lactate
|
|
|
|
lldD
L-lactate dehydrogenase
|
no
|
HD0084
|
HI1739.1
|
pyruvate to formate and acetyl-CoA
|
|
|
|
pflB
formate acetyltransferase 1
|
HS_1136
|
HD0990
|
HI0180
|
acetyl-CoA to acetate
|
|
|
|
pta
phosphate acetyltransferase
|
HS_0802
|
HD1457
|
HI1203
|
ackA
acetate kinase A
|
HS_0803
|
HD1456
|
HI1204
|
acetyl-CoA to ethanol
|
|
|
|
adhE
acetaldehyde/alcohol dehydrogenase
|
no
|
no
|
no
|
Table S9. NAD biosynthesis and salvage
A. de novo pathway
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
nadA
quinolinate synthetease A
|
no
|
no
|
no
|
nadB
L-aspartate oxidase
|
no
|
no
|
no
|
nadC
quinolinate phosphoribosyl transferase
|
no
|
no
|
no
|
nadD
NAMN adenylyltransferase
|
no
|
no
|
no
|
nadE
NAD synthetase, prefers NH3 over glutamine
|
no
|
no
|
no
|
B. salvage pathway (from MetaCyc (8))
Gene
|
H. somnus 129Pt
|
H. ducreyi 35000HP
|
H. influenzae Rd
|
NAD salvage pathway II
|
|
|
|
nadR
bifunctional protein: NMN adenylyltransferase; ribosylnicotinamide
kinase
|
HS_0087
|
HD0274
C-terminal fragment
HD0275
N-terminal fragment
|
HI0763
|
NAD salvage pathway I
|
|
|
|
NAD(+) nucleosidase
3.2.2.5
|
no
|
no
|
no
|
nudC
NADH pyrophosphatase
|
no
|
no
|
possibly HI0432 conserved hypothetical protein
47% aa identity
|
pncA
nicotinamidase and pyrazinamidase
|
no
|
no
|
no
|
pncB
nicotinate phosphoribosyltransferase
|
no
|
no
|
no
|
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
|
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