L-arginine catabolism in Verminephrobacter eiseniae EF01-2

Best path

artJ, artM, artP, artQ, rocF, odc, patA, patD, 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 (44 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	VEIS_RS09425	VEIS_RS01670
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	VEIS_RS01680	VEIS_RS09420
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	VEIS_RS01685	VEIS_RS00920
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	VEIS_RS01675	VEIS_RS09415
rocF	arginase	VEIS_RS04750	VEIS_RS01665
odc	L-ornithine decarboxylase	VEIS_RS16955
patA	putrescine aminotransferase (PatA/SpuC)	VEIS_RS04035	VEIS_RS15550
patD	gamma-aminobutyraldehyde dehydrogenase	VEIS_RS16060	VEIS_RS09480
gabT	gamma-aminobutyrate transaminase	VEIS_RS04035	VEIS_RS15550
gabD	succinate semialdehyde dehydrogenase	VEIS_RS21865	VEIS_RS19570
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	VEIS_RS16955
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase	VEIS_RS13835
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	VEIS_RS09295	VEIS_RS07375
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	VEIS_RS14130	VEIS_RS13740
aruI	2-ketoarginine decarboxylase	VEIS_RS01690	VEIS_RS03860
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	VEIS_RS09290	VEIS_RS08300
astD	succinylglutamate semialdehyde dehydrogenase	VEIS_RS17310	VEIS_RS10490
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	VEIS_RS18480	VEIS_RS06505
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	VEIS_RS09140	VEIS_RS23840
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	VEIS_RS09145	VEIS_RS14585
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	VEIS_RS09150	VEIS_RS14580
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	VEIS_RS09155	VEIS_RS01440
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	VEIS_RS09160	VEIS_RS01435
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	VEIS_RS19570	VEIS_RS10490
davT	5-aminovalerate aminotransferase	VEIS_RS09290	VEIS_RS15235
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	VEIS_RS02240	VEIS_RS18720
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	VEIS_RS24060	VEIS_RS08750
gbamidase	guanidinobutyramidase
gbuA	guanidinobutyrase	VEIS_RS01665
gcdG	succinyl-CoA:glutarate CoA-transferase	VEIS_RS08450	VEIS_RS10765
gcdH	glutaryl-CoA dehydrogenase	VEIS_RS08445	VEIS_RS06515
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	VEIS_RS17310	VEIS_RS17035
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd	ornithine cyclodeaminase	VEIS_RS10510
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
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	VEIS_RS05135
PRO3	pyrroline-5-carboxylate reductase	VEIS_RS11395
puo	putrescine oxidase
put1	proline dehydrogenase	VEIS_RS21495	VEIS_RS03540
putA	L-glutamate 5-semialdeyde dehydrogenase	VEIS_RS21495	VEIS_RS22680
puuA	glutamate-putrescine ligase	VEIS_RS04040	VEIS_RS00570
puuB	gamma-glutamylputrescine oxidase	VEIS_RS04045	VEIS_RS00915
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	VEIS_RS17310	VEIS_RS17035
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	VEIS_RS00560
rocA	1-pyrroline-5-carboxylate dehydrogenase	VEIS_RS21495	VEIS_RS22680
rocD	ornithine aminotransferase	VEIS_RS15550	VEIS_RS15235
rocE	L-arginine permease	VEIS_RS13795
speB	agmatinase	VEIS_RS01665

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.