Supplemental text

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

Q. Glycine degradation

Gene	H. somnus 129Pt	H. ducreyi 35000HP	H. influenzae Rd
gcv system
gcvP