L-arginine catabolism in Microvirga lotononidis WSM3557

Best path

braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA

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
braC	ABC transporter for glutamate, histidine, arginine, and other amino acids, substrate-binding component BraC	MICLODRAFT_RS30935	MICLODRAFT_RS25195
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	MICLODRAFT_RS30910	MICLODRAFT_RS10115
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	MICLODRAFT_RS30915	MICLODRAFT_RS24145
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	MICLODRAFT_RS30920	MICLODRAFT_RS24155
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	MICLODRAFT_RS30925	MICLODRAFT_RS27000
rocF	arginase	MICLODRAFT_RS17905	MICLODRAFT_RS06915
rocD	ornithine aminotransferase	MICLODRAFT_RS12055	MICLODRAFT_RS31980
PRO3	pyrroline-5-carboxylate reductase	MICLODRAFT_RS31785
put1	proline dehydrogenase	MICLODRAFT_RS28585
putA	L-glutamate 5-semialdeyde dehydrogenase	MICLODRAFT_RS28585	MICLODRAFT_RS27600
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	MICLODRAFT_RS18525	MICLODRAFT_RS05475
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase
arcA	arginine deiminase	MICLODRAFT_RS23840
arcB	ornithine carbamoyltransferase	MICLODRAFT_RS19480	MICLODRAFT_RS09740
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	MICLODRAFT_RS20275	MICLODRAFT_RS29840
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	MICLODRAFT_RS20260	MICLODRAFT_RS12815
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	MICLODRAFT_RS20255	MICLODRAFT_RS06130
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	MICLODRAFT_RS20080	MICLODRAFT_RS20265
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	MICLODRAFT_RS32165	MICLODRAFT_RS00200
aruI	2-ketoarginine decarboxylase	MICLODRAFT_RS13015	MICLODRAFT_RS17510
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	MICLODRAFT_RS19475	MICLODRAFT_RS12055
astD	succinylglutamate semialdehyde dehydrogenase	MICLODRAFT_RS25285	MICLODRAFT_RS27600
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	MICLODRAFT_RS27925	MICLODRAFT_RS10820
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	MICLODRAFT_RS20175	MICLODRAFT_RS31070
davT	5-aminovalerate aminotransferase	MICLODRAFT_RS19475	MICLODRAFT_RS12055
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	MICLODRAFT_RS07440	MICLODRAFT_RS11370
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	MICLODRAFT_RS27085	MICLODRAFT_RS11370
gabD	succinate semialdehyde dehydrogenase	MICLODRAFT_RS20175	MICLODRAFT_RS03140
gabT	gamma-aminobutyrate transaminase	MICLODRAFT_RS31980	MICLODRAFT_RS13930
gbamidase	guanidinobutyramidase	MICLODRAFT_RS00290	MICLODRAFT_RS15305
gbuA	guanidinobutyrase	MICLODRAFT_RS12060	MICLODRAFT_RS06855
gcdG	succinyl-CoA:glutarate CoA-transferase	MICLODRAFT_RS17755	MICLODRAFT_RS24795
gcdH	glutaryl-CoA dehydrogenase	MICLODRAFT_RS17745	MICLODRAFT_RS25365
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	MICLODRAFT_RS03140	MICLODRAFT_RS25285
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	MICLODRAFT_RS16815
ocd	ornithine cyclodeaminase	MICLODRAFT_RS06910	MICLODRAFT_RS25665
odc	L-ornithine decarboxylase	MICLODRAFT_RS18525
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)	MICLODRAFT_RS13930	MICLODRAFT_RS31980
patD	gamma-aminobutyraldehyde dehydrogenase	MICLODRAFT_RS03140	MICLODRAFT_RS13925
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	MICLODRAFT_RS26655
puo	putrescine oxidase
puuA	glutamate-putrescine ligase
puuB	gamma-glutamylputrescine oxidase	MICLODRAFT_RS11195	MICLODRAFT_RS19545
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	MICLODRAFT_RS03140	MICLODRAFT_RS25285
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	MICLODRAFT_RS35440	MICLODRAFT_RS28365
rocA	1-pyrroline-5-carboxylate dehydrogenase	MICLODRAFT_RS28585	MICLODRAFT_RS27600
rocE	L-arginine permease
speB	agmatinase	MICLODRAFT_RS12060	MICLODRAFT_RS06855

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.