L-arginine catabolism in Pseudomonas putida KT2440

Best path

artJ, artM, artP, artQ, adiA, speB, 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	PP_4486	PP_0282
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	PP_4484	PP_0280
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	PP_4483	PP_0283
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	PP_4485	PP_0281
adiA	arginine decarboxylase (AdiA/SpeA)	PP_0567	PP_4140
speB	agmatinase	PP_2196	PP_4523
puuA	glutamate-putrescine ligase	PP_5184	PP_5299
puuB	gamma-glutamylputrescine oxidase	PP_2448	PP_3146
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	PP_5278	PP_2589
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	PP_3598	PP_2179
gabT	gamma-aminobutyrate transaminase	PP_5182	PP_2180
gabD	succinate semialdehyde dehydrogenase	PP_0213	PP_3151
Alternative steps:
AAP3	L-arginine transporter AAP3
aguA	agmatine deiminase	PP_0266
aguB	N-carbamoylputrescine hydrolase	PP_0382
arcA	arginine deiminase	PP_1001
arcB	ornithine carbamoyltransferase	PP_1000	PP_1079
arcC	carbamate kinase	PP_0999
arg-monooxygenase	arginine 2-monooxygenase	PP_0383
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	PP_4480	PP_4479
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	PP_4479	PP_4480
aruH	L-arginine:pyruvate transaminase	PP_3721	PP_0858
aruI	2-ketoarginine decarboxylase	PP_3723	PP_1394
astA	arginine N-succinyltransferase	PP_4480	PP_4479
astB	N-succinylarginine dihydrolase	PP_4477
astC	succinylornithine transaminase	PP_4481	PP_0372
astD	succinylglutamate semialdehyde dehydrogenase	PP_4478	PP_5278
astE	succinylglutamate desuccinylase	PP_4475
atoB	acetyl-CoA C-acetyltransferase	PP_2215	PP_4636
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	PP_4867	PP_1141
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	PP_1140	PP_4866
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	PP_1139	PP_4865
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	PP_4864	PP_1138
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	PP_4863	PP_1137
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	PP_0213	PP_4422
davT	5-aminovalerate aminotransferase	PP_0214	PP_4108
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	PP_2217	PP_3284
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	PP_2136	PP_3755
gbamidase	guanidinobutyramidase	PP_0382	PP_3846
gbuA	guanidinobutyrase	PP_4523	PP_2196
gcdG	succinyl-CoA:glutarate CoA-transferase	PP_0159	PP_3001
gcdH	glutaryl-CoA dehydrogenase	PP_0158	PP_4064
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)	PP_2909
kauB	4-guanidinobutyraldehyde dehydrogenase	PP_5278	PP_2589
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	PP_2910
ocd	ornithine cyclodeaminase	PP_3533	PP_4431
odc	L-ornithine decarboxylase	PP_0864	PP_4140
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)	PP_5182	PP_2180
patD	gamma-aminobutyraldehyde dehydrogenase	PP_1481	PP_2801
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	PP_1258
PRO3	pyrroline-5-carboxylate reductase	PP_5095	PP_3778
puo	putrescine oxidase
put1	proline dehydrogenase	PP_4947
putA	L-glutamate 5-semialdeyde dehydrogenase	PP_4947	PP_2694
rocA	1-pyrroline-5-carboxylate dehydrogenase	PP_4947	PP_2694
rocD	ornithine aminotransferase	PP_0214	PP_4223
rocE	L-arginine permease	PP_3727	PP_0660
rocF	arginase	PP_4523	PP_2196

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.