L-arginine catabolism in Pseudomonas benzenivorans DSM 8628

Best path

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

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 (50 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	BLS63_RS24440	BLS63_RS01130
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	BLS63_RS26105	BLS63_RS24450
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	BLS63_RS26115	BLS63_RS24435
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	BLS63_RS26100	BLS63_RS24445
adiA	arginine decarboxylase (AdiA/SpeA)	BLS63_RS04420	BLS63_RS11675
aguA	agmatine deiminase	BLS63_RS16690
aguB	N-carbamoylputrescine hydrolase	BLS63_RS16685
puuA	glutamate-putrescine ligase	BLS63_RS16675	BLS63_RS16665
puuB	gamma-glutamylputrescine oxidase	BLS63_RS17215	BLS63_RS19080
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	BLS63_RS19060	BLS63_RS08515
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	BLS63_RS16670
gabT	gamma-aminobutyrate transaminase	BLS63_RS08505	BLS63_RS16660
gabD	succinate semialdehyde dehydrogenase	BLS63_RS26230	BLS63_RS15725
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	BLS63_RS10645
arcB	ornithine carbamoyltransferase	BLS63_RS10650	BLS63_RS23235
arcC	carbamate kinase	BLS63_RS10655
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	BLS63_RS19260	BLS63_RS19265
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	BLS63_RS19265	BLS63_RS19260
aruH	L-arginine:pyruvate transaminase	BLS63_RS09835	BLS63_RS08895
aruI	2-ketoarginine decarboxylase	BLS63_RS23590	BLS63_RS01110
astA	arginine N-succinyltransferase	BLS63_RS19265	BLS63_RS19260
astB	N-succinylarginine dihydrolase	BLS63_RS19275
astC	succinylornithine transaminase	BLS63_RS19255	BLS63_RS01095
astD	succinylglutamate semialdehyde dehydrogenase	BLS63_RS19270	BLS63_RS15725
astE	succinylglutamate desuccinylase	BLS63_RS19285
atoB	acetyl-CoA C-acetyltransferase	BLS63_RS22810	BLS63_RS21120
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	BLS63_RS23775	BLS63_RS09655
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	BLS63_RS23780	BLS63_RS09650
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	BLS63_RS09645	BLS63_RS23785
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	BLS63_RS09640	BLS63_RS23790
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	BLS63_RS23795	BLS63_RS09635
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	BLS63_RS26230	BLS63_RS15725
davT	5-aminovalerate aminotransferase	BLS63_RS01095	BLS63_RS26240
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	BLS63_RS21705	BLS63_RS07890
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	BLS63_RS07890	BLS63_RS21115
gbamidase	guanidinobutyramidase
gbuA	guanidinobutyrase	BLS63_RS23615	BLS63_RS15905
gcdG	succinyl-CoA:glutarate CoA-transferase	BLS63_RS14580	BLS63_RS17670
gcdH	glutaryl-CoA dehydrogenase	BLS63_RS14585	BLS63_RS24330
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	BLS63_RS19060	BLS63_RS08515
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	BLS63_RS24405
ocd	ornithine cyclodeaminase
odc	L-ornithine decarboxylase	BLS63_RS22540	BLS63_RS01145
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)	BLS63_RS16660	BLS63_RS08505
patD	gamma-aminobutyraldehyde dehydrogenase	BLS63_RS09095	BLS63_RS09120
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase
PRO3	pyrroline-5-carboxylate reductase	BLS63_RS16225
puo	putrescine oxidase
put1	proline dehydrogenase	BLS63_RS22035
putA	L-glutamate 5-semialdeyde dehydrogenase	BLS63_RS22035	BLS63_RS03170
rocA	1-pyrroline-5-carboxylate dehydrogenase	BLS63_RS22035	BLS63_RS03170
rocD	ornithine aminotransferase	BLS63_RS07545	BLS63_RS01095
rocE	L-arginine permease
rocF	arginase	BLS63_RS23615	BLS63_RS22150
speB	agmatinase	BLS63_RS15905	BLS63_RS22150

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 24 2021. The underlying query database was built on Sep 17 2021.