L-arginine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE

Also see fitness data for the top candidates

Rules

Overview: Arginine utilization in GapMind is based on MetaCyc pathways L-arginine degradation I via arginase (link); II via arginine succinyltransferase (link), III via arginine decarboxylase and agmatinase (link), IV via arginine decarboxylase and agmatine deiminase (link), V via arginine deiminase (link), VI (arginase 2, link), VII (arginase 3, link), VIII via arginase oxidase (link), IX via arginine:pyruvate transaminase (link), X via arginine monooxygenase (link), XIII via proline (link), and XIV via D-ornithine (link). Common intermediates are L-ornithine or L-proline. GapMind does not include pathways XI (link), which is poorly understood, or XII (link), which is not reported in prokaryotes.

• all:
  • arginine-transport, rocF and ornithine-degradation
  • or arginine-transport, arginine-succinyltransferase, astB, astC, astD and astE
  • or arginine-transport, adiA, speB and putrescine-degradation
  • or arginine-transport, adiA, aguA, aguB and putrescine-degradation
  • or arginine-transport, arcA, arcB, arcC and ornithine-degradation
  • or arginine-transport, aroD, aruI, kauB, gbuA and GABA-degradation
  • or arginine-transport, aruH, aruI, kauB, gbuA and GABA-degradation
  • or arginine-transport, arg-monooxygenase, gbamidase, kauB, gbuA and GABA-degradation
  • Comment: Pathways I, VI, or VII begin with rocF (arginase), which forms ornithine and urea. (The urea might not be utilized, so urease is not described here.) They differ in how the ornithine is catabolized. Pathway II begins with arginine succinyltransferase and ends with succinate and glutamate. The succinate would then be activated to succinyl-CoA to restart the cycle, or the glutamate might be oxidized to succinyl-CoA; these steps are not included here. Pathway III begins with decarboxylation to agmatine by adiA, followed by hydrolysis to putrescine and urea. Pathway IV begins with adiA and agmatine deiminase (aguA), which yields N-carbamoylputrescine; this is hydrolyzed to putrescine and urea. Pathway V begins with arginine deiminase (arcA), forming citrulline, and and a carbamoyltransferase forms carbamoyl-phosphate and ornithine. The carbamoyl-phosphate is consumed by carbamate kinase (in reverse, forming ammonia and CO2 and ATP). Pathway VIII begins with arginine oxidase aroD, which forms 5-guanidino-2-oxopentanoate (2-ketoarginine); this is converted to gamma-aminobutyrate (GABA). Pathway IX is similar to pathway VIII but the transaminase aruH forms the 5-guanidino-2-oxopentanoate. Pathway X involves arginine 2-monooxygenase (decarboxylating), forming 4-guanidinobutyramide, and an amidase, forming 4-guanidinobutyrate, which is consumed as in pathway VIII or IX.
• ornithine-degradation:
  • aruF, aruG, astC, astD and astE
  • or rocD and rocA
  • or rocD, PRO3 and proline-degradation
  • or ocd and proline-degradation
  • or odc and putrescine-degradation
  • or orr, oraS, oraE, ord, ortA and ortB
  • Comment: Ornithine is a common intermediate. It can be succinylated by aruFG and then catabolized by the later steps of the arginine succinyltransferase pathway, via aminotransferase, dehydrogenase, and desuccinylase reactions (see PMC179677 and PMID:7523119). Or as part of L-arginine degradation I, the aminotransferase rocD converts ornithine to glutamate 5-semialdehyde, which spontaneously converts to 1-pyrroline-5-carboxylate. A dehydrogenase converts this to glutamate. Or 1-pyrroline-5-carboxylate can be reduced to proline by PRO3, as in L-arginine degradation VI. Alternatively, ornithine can be converted directly to proline by ornithine cyclodeaminase (ocd). Or ornithine can be decarboxylated to putrescine by odc (link). Or ornithine can be catabolized via D-ornithine, as in L-arginine degradation XIV. A racemase converts L-ornithine to D-ornithine; an aminomutase forms (2R,4S) 2,4-diaminopentanoate; a dehydrogenase forms (2R)-2-amino-4-oxopentanoate, and a thiolase cleaves it to D-alanine and acetyl-CoA. D-alanine could be oxidized to pyruvate or perhaps secreted; this is not described here.
• arginine-succinyltransferase:
  • aruF and aruG
  • or astA
• proline-degradation:
  • put1 and putA
  • or prdF, D-proline-reductase and 5-aminovalerate-degradation
  • Comment: In pathway I, proline dehydrogenase (put1) forms (S)-1-pyrroline-5-carboxylate, which spontaneously hydrates to L-glutamate 5-semialdehyde, and a dehydrogenase (putA) to glutamate. Glutamate can be transaminated to 2-oxoglutarate, which is an intermediate in central metabolism (not represented). In pathway II, proline racemase (prdF) forms D-proline, and a reductase forms 5-aminovalerate.
• D-proline-reductase: prdA, prdB and prdC
  • Comment: D-proline reductase includes components PrdA and PrdB and electron transfer protein PrdC
• 5-aminovalerate-degradation: davT, davD and glutarate-degradation
  • Comment: 5-aminovalerate is an intermediate in L-lysine degradation (link, link). It is transaminated to glutarate semialdehyde and oxidized to glutarate. (A fermentative pathway via 5-hydroxyvalerate has also been reported, but does not seem to be fully linked to sequence; see pathway 5 of PMID:11759672.)
• glutarate-degradation:
  • glaH and lhgD
  • or gcdG and glutaryl-CoA-degradation
  • Comment: Glutarate is an intermediate in L-lysine degradation. As part of MetaCyc pathway L-lysine degradation I (link), gluratate is hydroxylated to L-2-hydroxyglutarate (also known as (S)-2-hydroxyglutarate) by a 2-oxoglutarate-dependent oxidase. This reaction releases succinate (a TCA cycle intermediate) and CO2. A dehydrogenase then oxidizes to L-2-hydroxyglutarate to regenerate 2-oxoglutarate. Alternatively, as part of pathway IV (link), glutarate can be activated to glutaryl-CoA by a CoA-transferase. Glutaryl-CoA degradation (link) involves glutaryl-CoA dehydrogenase (decarboxylating) to crotonyl-CoA (trans-but-2-enoyl-CoA), hydration to (S)-hydroxybutanoyl-CoA, oxidization to acetoacetyl-CoA, and cleavage by a C-acetyltransferase to two acetyl-CoA.
• glutaryl-CoA-degradation: gcdH, ech, fadB and atoB
  • Comment: In MetaCyc pathway glutaryl-CoA degradation (link), glutaryl-CoA is oxidized to (E)-glutaconyl-CoA and oxidatively decarboxylated to crotonyl-CoA (both by the same enzyme), hydrated to 3-hydroxybutanoyl-CoA, oxidized to acetoacetyl-CoA, and cleaved to two acetyl-CoA.
• GABA-degradation: gabT and gabD
  • Comment: GABA (4-aminobutanoate) is consumed by an aminotransferase (known as gabT or puuE), which forms succinate semialdehyde, and dehydrogenase gabD, which forms succinate.
• putrescine-degradation: putrescine-to-GABA and GABA-degradation
  • Comment: Gamma-aminobutyrate is a common intermediate.
• putrescine-to-GABA:
  • patA and patD
  • or puuA, puuB, puuC and puuD
  • or puo and patD
  • Comment: In pathway I or pathway V, putrescine aminotransferase (patA or spuC) forms 4-aminobutanal, and dehydrogenase patD forms GABA. In pathway II, putrescine is converted to GABA with glutamylated intermedates: puuA forms gamma-glutamyl-putrescine, an oxidase forms 4-(gamma-glutaminylamino)butanal, a dehydrogenase forms 4-(gamma-glutamylamino)butanoate, and a hydrolase releases glutamate and GABA. As part of pathway IV, putrescine oxidase (puo) forms 4-aminobutanal, which is probably converted to GABA by dehydrogenase patD.
• arginine-transport:
  • artJ, artM, artP and artQ
  • or bgtB and artP
  • or braC, braD, braE, braF and braG
  • or rocE
  • or AAP3
  • or CAT1
  • or Can1
  • Comment: Transporters were identified using: query: transporter:arginine:L-arginine:arg.

71 steps (55 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	Pf6N2E2_5660	Pf6N2E2_3856
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	Pf6N2E2_5662	Pf6N2E2_3858
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	Pf6N2E2_5663	Pf6N2E2_3855
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	Pf6N2E2_5661	Pf6N2E2_3857
arcA	arginine deiminase	Pf6N2E2_2908
arcB	ornithine carbamoyltransferase	Pf6N2E2_2909	Pf6N2E2_5579
arcC	carbamate kinase	Pf6N2E2_2910
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	Pf6N2E2_5666	Pf6N2E2_2180
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	Pf6N2E2_5667	Pf6N2E2_2181
astC	succinylornithine transaminase	Pf6N2E2_5665	Pf6N2E2_5326
astD	succinylglutamate semialdehyde dehydrogenase	Pf6N2E2_5668	Pf6N2E2_1370
astE	succinylglutamate desuccinylase	Pf6N2E2_5671
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	Pf6N2E2_3504
aguA	agmatine deiminase	Pf6N2E2_3876
aguB	N-carbamoylputrescine hydrolase	Pf6N2E2_4777
arg-monooxygenase	arginine 2-monooxygenase	Pf6N2E2_4778
aroD	L-arginine oxidase
aruH	L-arginine:pyruvate transaminase	Pf6N2E2_462	Pf6N2E2_3173
aruI	2-ketoarginine decarboxylase	Pf6N2E2_5475	Pf6N2E2_5839
astA	arginine N-succinyltransferase	Pf6N2E2_5667	Pf6N2E2_2181
astB	N-succinylarginine dihydrolase	Pf6N2E2_5669
atoB	acetyl-CoA C-acetyltransferase	Pf6N2E2_2113	Pf6N2E2_1145
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)	Pf6N2E2_1799
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	Pf6N2E2_3580	Pf6N2E2_2921
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	Pf6N2E2_3579	Pf6N2E2_2923
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	Pf6N2E2_2924	Pf6N2E2_3578
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	Pf6N2E2_3577	Pf6N2E2_2925
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	Pf6N2E2_3576	Pf6N2E2_2926
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	Pf6N2E2_4014	Pf6N2E2_368
davT	5-aminovalerate aminotransferase	Pf6N2E2_4013	Pf6N2E2_373
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	Pf6N2E2_1147	Pf6N2E2_1834
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	Pf6N2E2_2290	Pf6N2E2_1922
gabD	succinate semialdehyde dehydrogenase	Pf6N2E2_4014	Pf6N2E2_1919
gabT	gamma-aminobutyrate transaminase	Pf6N2E2_4512	Pf6N2E2_4013
gbamidase	guanidinobutyramidase	Pf6N2E2_4777
gbuA	guanidinobutyrase	Pf6N2E2_2655
gcdG	succinyl-CoA:glutarate CoA-transferase	Pf6N2E2_4035	Pf6N2E2_3139
gcdH	glutaryl-CoA dehydrogenase	Pf6N2E2_4036	Pf6N2E2_2191
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	Pf6N2E2_4383	Pf6N2E2_1381
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	Pf6N2E2_261
ocd	ornithine cyclodeaminase
odc	L-ornithine decarboxylase	Pf6N2E2_3334
oraE	D-ornithine 4,5-aminomutase, beta (E) subunit
oraS	D-ornithine 4,5-aminomutase, alpha (S) subunit
ord	2,4-diaminopentanoate dehydrogenase
orr	ornithine racemase
ortA	2-amino-4-oxopentanoate thiolase, alpha subunit
ortB	2-amino-4-oxopentanoate thiolase, beta subunit
patA	putrescine aminotransferase (PatA/SpuC)	Pf6N2E2_4512	Pf6N2E2_1742
patD	gamma-aminobutyraldehyde dehydrogenase	Pf6N2E2_3131	Pf6N2E2_3126
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	Pf6N2E2_681	Pf6N2E2_671
PRO3	pyrroline-5-carboxylate reductase	Pf6N2E2_4600
puo	putrescine oxidase
put1	proline dehydrogenase	Pf6N2E2_3685
putA	L-glutamate 5-semialdeyde dehydrogenase	Pf6N2E2_3685	Pf6N2E2_3298
puuA	glutamate-putrescine ligase	Pf6N2E2_4509	Pf6N2E2_4511
puuB	gamma-glutamylputrescine oxidase	Pf6N2E2_80	Pf6N2E2_4388
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	Pf6N2E2_4383	Pf6N2E2_1381
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	Pf6N2E2_4510
rocA	1-pyrroline-5-carboxylate dehydrogenase	Pf6N2E2_3685	Pf6N2E2_3298
rocD	ornithine aminotransferase	Pf6N2E2_5326	Pf6N2E2_373
rocE	L-arginine permease	Pf6N2E2_4959	Pf6N2E2_5459
rocF	arginase	Pf6N2E2_2655
speB	agmatinase	Pf6N2E2_2655

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.