L-arginine catabolism in Pseudomonas fluorescens FW300-N2E3

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 (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	AO353_03055	AO353_11995
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	AO353_03045	AO353_27980
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	AO353_03040	AO353_12000
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	AO353_03050	AO353_27975
adiA	arginine decarboxylase (AdiA/SpeA)	AO353_13720	AO353_23560
aguA	agmatine deiminase	AO353_11915	AO353_28745
aguB	N-carbamoylputrescine hydrolase	AO353_11910	AO353_28740
puuA	glutamate-putrescine ligase	AO353_08595	AO353_29300
puuB	gamma-glutamylputrescine oxidase	AO353_20720	AO353_29290
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	AO353_09195	AO353_29295
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	AO353_29305
gabT	gamma-aminobutyrate transaminase	AO353_08585	AO353_15040
gabD	succinate semialdehyde dehydrogenase	AO353_11505	AO353_28230
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	AO353_03470
arcB	ornithine carbamoyltransferase	AO353_03475	AO353_04155
arcC	carbamate kinase	AO353_03480
arg-monooxygenase	arginine 2-monooxygenase	AO353_07420
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	AO353_03020	AO353_27915
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	AO353_03015	AO353_25630
aruH	L-arginine:pyruvate transaminase	AO353_24850	AO353_26890
aruI	2-ketoarginine decarboxylase	AO353_24845	AO353_03865
astA	arginine N-succinyltransferase	AO353_03015	AO353_25630
astB	N-succinylarginine dihydrolase	AO353_03005
astC	succinylornithine transaminase	AO353_03025	AO353_10500
astD	succinylglutamate semialdehyde dehydrogenase	AO353_03010	AO353_09195
astE	succinylglutamate desuccinylase	AO353_02995
atoB	acetyl-CoA C-acetyltransferase	AO353_25685	AO353_27945
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)	AO353_25590
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	AO353_13340	AO353_17125
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	AO353_13345	AO353_17120
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	AO353_17115	AO353_13350
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	AO353_13355	AO353_17110
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	AO353_13360	AO353_17105
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	AO353_11505	AO353_28230
davT	5-aminovalerate aminotransferase	AO353_11510	AO353_28215
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	AO353_25675	AO353_00510
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	AO353_00510	AO353_27535
gbamidase	guanidinobutyramidase	AO353_07425	AO353_28330
gbuA	guanidinobutyrase	AO353_18400
gcdG	succinyl-CoA:glutarate CoA-transferase	AO353_11105	AO353_23060
gcdH	glutaryl-CoA dehydrogenase	AO353_11100	AO353_20350
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	AO353_09195	AO353_29295
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd	ornithine cyclodeaminase	AO353_25185
odc	L-ornithine decarboxylase	AO353_05445	AO353_23560
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)	AO353_08585	AO353_15040
patD	gamma-aminobutyraldehyde dehydrogenase	AO353_04290	AO353_04265
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	AO353_14925	AO353_14880
PRO3	pyrroline-5-carboxylate reductase	AO353_08165
puo	putrescine oxidase
put1	proline dehydrogenase	AO353_12810
putA	L-glutamate 5-semialdeyde dehydrogenase	AO353_12810	AO353_05300
rocA	1-pyrroline-5-carboxylate dehydrogenase	AO353_12810	AO353_05300
rocD	ornithine aminotransferase	AO353_15640	AO353_28215
rocE	L-arginine permease	AO353_24825	AO353_05930
rocF	arginase	AO353_18400
speB	agmatinase	AO353_18400

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.