L-arginine catabolism in Pseudomonas fluorescens FW300-N1B4

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD

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 (56 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	Pf1N1B4_3431	Pf1N1B4_1641
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	Pf1N1B4_3433	Pf1N1B4_4398
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	Pf1N1B4_3435	Pf1N1B4_1640
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	Pf1N1B4_3432	Pf1N1B4_4399
adiA	arginine decarboxylase (AdiA/SpeA)	Pf1N1B4_1296	Pf1N1B4_4600
aguA	agmatine deiminase	Pf1N1B4_1661	Pf1N1B4_4325
aguB	N-carbamoylputrescine hydrolase	Pf1N1B4_1662	Pf1N1B4_4326
puuA	glutamate-putrescine ligase	Pf1N1B4_4354	Pf1N1B4_2254
puuB	gamma-glutamylputrescine oxidase	Pf1N1B4_6047	Pf1N1B4_4356
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	Pf1N1B4_2132	Pf1N1B4_4355
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	Pf1N1B4_4353	Pf1N1B4_2255
gabT	gamma-aminobutyrate transaminase	Pf1N1B4_2257	Pf1N1B4_1733
gabD	succinate semialdehyde dehydrogenase	Pf1N1B4_1734	Pf1N1B4_5616
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	Pf1N1B4_615
arcB	ornithine carbamoyltransferase	Pf1N1B4_616	Pf1N1B4_762
arcC	carbamate kinase	Pf1N1B4_617
arg-monooxygenase	arginine 2-monooxygenase	Pf1N1B4_2505
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	Pf1N1B4_3442	Pf1N1B4_5856
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	Pf1N1B4_3443	Pf1N1B4_4797
aruH	L-arginine:pyruvate transaminase	Pf1N1B4_4996	Pf1N1B4_5070
aruI	2-ketoarginine decarboxylase	Pf1N1B4_696	Pf1N1B4_3661
astA	arginine N-succinyltransferase	Pf1N1B4_3443	Pf1N1B4_4797
astB	N-succinylarginine dihydrolase	Pf1N1B4_3445
astC	succinylornithine transaminase	Pf1N1B4_3440	Pf1N1B4_2980
astD	succinylglutamate semialdehyde dehydrogenase	Pf1N1B4_3444	Pf1N1B4_3024
astE	succinylglutamate desuccinylase	Pf1N1B4_3447
atoB	acetyl-CoA C-acetyltransferase	Pf1N1B4_4786	Pf1N1B4_5835
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)	Pf1N1B4_4805
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	Pf1N1B4_1382	Pf1N1B4_3218
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	Pf1N1B4_1381	Pf1N1B4_3217
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	Pf1N1B4_3216	Pf1N1B4_1380
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	Pf1N1B4_1379	Pf1N1B4_3215
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	Pf1N1B4_1378	Pf1N1B4_3214
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	Pf1N1B4_1734	Pf1N1B4_4931
davT	5-aminovalerate aminotransferase	Pf1N1B4_1733	Pf1N1B4_4910
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	Pf1N1B4_4788	Pf1N1B4_3903
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	Pf1N1B4_3903	Pf1N1B4_5134
gbamidase	guanidinobutyramidase	Pf1N1B4_2504
gbuA	guanidinobutyrase	Pf1N1B4_525	Pf1N1B4_4717
gcdG	succinyl-CoA:glutarate CoA-transferase	Pf1N1B4_1815	Pf1N1B4_5611
gcdH	glutaryl-CoA dehydrogenase	Pf1N1B4_1816	Pf1N1B4_3987
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	Pf1N1B4_2132	Pf1N1B4_4355
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	Pf1N1B4_4264
ocd	ornithine cyclodeaminase	Pf1N1B4_4977
odc	L-ornithine decarboxylase	Pf1N1B4_1136	Pf1N1B4_4600
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)	Pf1N1B4_2257	Pf1N1B4_1239
patD	gamma-aminobutyraldehyde dehydrogenase	Pf1N1B4_3024	Pf1N1B4_3029
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	Pf1N1B4_5964	Pf1N1B4_5975
PRO3	pyrroline-5-carboxylate reductase	Pf1N1B4_2341
puo	putrescine oxidase
put1	proline dehydrogenase	Pf1N1B4_1489
putA	L-glutamate 5-semialdeyde dehydrogenase	Pf1N1B4_1489	Pf1N1B4_1109
rocA	1-pyrroline-5-carboxylate dehydrogenase	Pf1N1B4_1489	Pf1N1B4_1109
rocD	ornithine aminotransferase	Pf1N1B4_2980	Pf1N1B4_4910
rocE	L-arginine permease	Pf1N1B4_801	Pf1N1B4_1580
rocF	arginase	Pf1N1B4_525	Pf1N1B4_4717
speB	agmatinase	Pf1N1B4_4717	Pf1N1B4_525

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.