L-arginine catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

artJ, artM, artP, artQ, astA, astB, astC, astD, astE

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 (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	H281DRAFT_06484	H281DRAFT_00224
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	H281DRAFT_06475	H281DRAFT_00222
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	H281DRAFT_06476	H281DRAFT_00221
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	H281DRAFT_06474	H281DRAFT_00223
astA	arginine N-succinyltransferase	H281DRAFT_06479	H281DRAFT_06480
astB	N-succinylarginine dihydrolase	H281DRAFT_06482
astC	succinylornithine transaminase	H281DRAFT_06478	H281DRAFT_04057
astD	succinylglutamate semialdehyde dehydrogenase	H281DRAFT_06481	H281DRAFT_00213
astE	succinylglutamate desuccinylase	H281DRAFT_06483
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	H281DRAFT_00160
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase	H281DRAFT_05434
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	H281DRAFT_04119	H281DRAFT_01493
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	H281DRAFT_06479	H281DRAFT_06480
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	H281DRAFT_06480	H281DRAFT_06479
aruH	L-arginine:pyruvate transaminase	H281DRAFT_02907	H281DRAFT_05564
aruI	2-ketoarginine decarboxylase	H281DRAFT_03007
atoB	acetyl-CoA C-acetyltransferase	H281DRAFT_00852	H281DRAFT_00857
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	H281DRAFT_02405	H281DRAFT_01194
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	H281DRAFT_04062	H281DRAFT_02378
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	H281DRAFT_04061	H281DRAFT_05513
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	H281DRAFT_04060	H281DRAFT_02383
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	H281DRAFT_04059	H281DRAFT_02384
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1	H281DRAFT_02180
davD	glutarate semialdehyde dehydrogenase	H281DRAFT_03178	H281DRAFT_03540
davT	5-aminovalerate aminotransferase	H281DRAFT_03179	H281DRAFT_06478
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	H281DRAFT_05725	H281DRAFT_02514
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	H281DRAFT_00361	H281DRAFT_04625
gabD	succinate semialdehyde dehydrogenase	H281DRAFT_01155	H281DRAFT_03540
gabT	gamma-aminobutyrate transaminase	H281DRAFT_01082	H281DRAFT_03179
gbamidase	guanidinobutyramidase
gbuA	guanidinobutyrase	H281DRAFT_00178
gcdG	succinyl-CoA:glutarate CoA-transferase	H281DRAFT_04444	H281DRAFT_01169
gcdH	glutaryl-CoA dehydrogenase	H281DRAFT_04737	H281DRAFT_01204
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	H281DRAFT_00993	H281DRAFT_03016
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	H281DRAFT_02167
ocd	ornithine cyclodeaminase
odc	L-ornithine decarboxylase	H281DRAFT_00160
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)	H281DRAFT_01082	H281DRAFT_06342
patD	gamma-aminobutyraldehyde dehydrogenase	H281DRAFT_02464	H281DRAFT_00993
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	H281DRAFT_01193
PRO3	pyrroline-5-carboxylate reductase	H281DRAFT_04679
puo	putrescine oxidase
put1	proline dehydrogenase	H281DRAFT_02404	H281DRAFT_06542
putA	L-glutamate 5-semialdeyde dehydrogenase	H281DRAFT_02404	H281DRAFT_03016
puuA	glutamate-putrescine ligase	H281DRAFT_01081	H281DRAFT_00452
puuB	gamma-glutamylputrescine oxidase	H281DRAFT_03219	H281DRAFT_06337
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	H281DRAFT_00993	H281DRAFT_03016
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	H281DRAFT_01080	H281DRAFT_03954
rocA	1-pyrroline-5-carboxylate dehydrogenase	H281DRAFT_02404	H281DRAFT_03016
rocD	ornithine aminotransferase	H281DRAFT_03179	H281DRAFT_06478
rocE	L-arginine permease	H281DRAFT_04042	H281DRAFT_01668
rocF	arginase	H281DRAFT_00178
speB	agmatinase	H281DRAFT_00178

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.