Supplemental Material Carbohydrate utilization



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G. Arginine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

E. coli ast pathway (arginine degradation VI)










astA

arginine succinyltransferase



no

no

no

astB

succinylarginine dihydrolase



no

no

no

astC

acetylornithine delta-aminotransferase



no

no


no

astD

succinylglutamic semialdehyde dehydrogenase



no


no

no

astE

succinylglutamate desuccinylase



no

no

no

B. subtilis


arginase pathway (arginine degradation I, IX, XIII, XII)










rocF

arginase


no

no

no

rocD

ornithine aminotransferase



no

no

no

rocA

pyrroline-5 carboxylate dehydrogenase



no

no

no

Pseudomonas aeruginosa arginine deiminase (arginine degradation X and XI)










arcA

arginine deiminase



no

no

no

arcB

ornithine carbamoyltransferase, catabolic



no

HD0232


HI0596


arcC

carbamate kinase



no

no

HI0595


arginine degradation II and XII Deinococcus radiodurans , Sulfolobus solfataricus, E.coli










speA

arginine decarboxylase, biosynthetic

NP_417413


no

no

no

adiA

arginine decarboxylase, degradative

NP_418541


no



no

no


speB

agmatinase

NP_417412


no

no

no

speC

ornithine

decarboxylase, biosynthetic


HS_1573


no

HI0591


arginine degradation V










Arginine 2-monooxygenase 1.13.12.1

no

no

no

arginine degradation IV










Gamma-guanidinobutyraldehyde dehydrogenase 1.2.1.54

no

no

no

H. Cysteine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

tnaA

tryptophanase



HS_0801


no

no

metC

cystathionine beta-lyase



HS_0475


no

HI0122

I. Glutamate and Glutamine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

L-glutamate to fumarate










aspC

aspartate aminotransferase



HS_0838

HD1419


HI1617


aspA

aspartate ammonia-lyase



HS_0466

HD0564


HI0534


L-glutamate to alpha-ketoglutarate










gdhA

glutamate dehydrogenase, NADP-specific



HS_1339

no

HI0189


L-glutamate to (2S, 3S)-3-methylaspartate










glmE

glutamate mutase epsilon subunit 5.4.99.1



no

no

no

L-glutamate to L-glutamine










glnA

glutamine synthetase



HS_0418

HD0750


HI0865


L-glutamine to L-glutamate










glutaminase 3.5.1.2

no

no

no

gltB

glutamate synthase, large subunit



no

no

no

gltD

glutamate synthase, small subunit



no

no

no

J. Aspartate degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

L-aspartate to NAD










nadA

quinolinate synthetase, A protein



no

no

no

nadE

NAD synthetase, prefers NH3 over glutamine



no

no

no

nadB

quinolinate synthetase, B protein



no

no

no

nadC

quinolinate phosphoribosyltransferase



no

no

no

nadD

NAMN adenylyltransferase



no

no

no

L-aspartate to beta-alanine










panD

Aspartate 1-decarboxylase



no

no

no

K.. Asparagine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

Asparagine to aspartate










ansB

periplasmic L-asparaginase II



no

HD0372


no

ansA

cytoplasmic L-asparaginase I



no

no


no

L. Lysine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

lysine to cadaverine










ldcC

lysine decarboxylase 2, constitutive



HS_1007


no

no

cadA

lysine decarboxylase 1



HS_1007


no

no

cadB

cadaverine/lysine antiporter



HS_1006

no

no

M. Threonine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

threonine to glycine or aminoacetone










tdh

threonine dehydrogenase




no

no

no

threonine to homoserine, cystathione, o-succinyl-L-homoserine, propionate










ilvA

threonine deaminase (dehydratase)



HS_0183


no

HI0738.1


L-cysteine desulfhydrase

no

no

no

metB

2.5.1.48


cystathionine gamma-synthase

HS_1345

no

HI0086

2-oxobutanoate to propionate










pyruvate formate-lyase , formate acetyltransferase

HS_1136

HD0990

HI0180

ackA

HS_0803

HD1456

HI1204

N. Methionine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

metK see above

yes

yes

yes

DNA-cytosine methyltransferase

HS_1422

no

no

2.1.1.37

DNA (cytosine-5-)-methyltransferase

no

no

HI1041

3.3.1.1

adenosyl homocysteinase



no

no

no

4.2.1.22

serine sulfhydrolase



no

no

no

O. Leucine, Isoleucine and Valine degradation degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

Common pathway










ilvE

branched-chain amino acid transaminase



HS_0494

no

HI1193


bfmBAA

2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4



no

no

no

bfmBAB

2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4



no

no

no

2-methylacyl-CoA dehydrogenase

1.3.99.12

no

no

no

Leucine










3-methylcrotonyl-CoA carboxylase, beta subunit

6.4.1.4


no

no

no

3-methylglutaconyl-CoA hydratase 4.2.1.18

no

no

no

Isoleucine










3-hydroxyacyl-CoA dehydrogenase 1.1.1.178

no

no

no

Valine










3-hydroxyisobutyryl-CoA hydrolase 3.1.2.4

no

no

no

P. Histidine degradation



Gene

H. somnus 129Pt

H. ducreyi 35000HP

H. influenzae Rd

hutH

histidase (histidine ammonia lyase) 4.3.1.3



no

no

no

hutU

urocanase (urocanate hydratase) 4.2.1.49



no

no

no

hutI

imidazolonepropionase

3.5.2.7


no

no

no

hutF

formiminoglutamate deiminase

3.5.3.13


no

no

no



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