L-arginine catabolism in Azospirillum brasilense Sp245

Best path

braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, put1, putA

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 (48 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	AZOBR_RS08260
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	AZOBR_RS08235	AZOBR_RS03565
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	AZOBR_RS08240	AZOBR_RS32410
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	AZOBR_RS08245	AZOBR_RS32405
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	AZOBR_RS08250	AZOBR_RS19790
arcA	arginine deiminase	AZOBR_RS13255
arcB	ornithine carbamoyltransferase	AZOBR_RS13250	AZOBR_RS19030
arcC	carbamate kinase	AZOBR_RS13245
rocD	ornithine aminotransferase	AZOBR_RS19590	AZOBR_RS19630
PRO3	pyrroline-5-carboxylate reductase	AZOBR_RS06245
put1	proline dehydrogenase	AZOBR_RS23695
putA	L-glutamate 5-semialdeyde dehydrogenase	AZOBR_RS23695	AZOBR_RS29185
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	AZOBR_RS27535	AZOBR_RS00105
aguA	agmatine deiminase	AZOBR_RS08825
aguB	N-carbamoylputrescine hydrolase	AZOBR_RS08170	AZOBR_RS30770
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	AZOBR_RS27130	AZOBR_RS00685
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	AZOBR_RS00675	AZOBR_RS23520
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	AZOBR_RS00690	AZOBR_RS29615
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	AZOBR_RS00680	AZOBR_RS23520
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	AZOBR_RS24065	AZOBR_RS12970
aruI	2-ketoarginine decarboxylase	AZOBR_RS04230
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	AZOBR_RS19025	AZOBR_RS19590
astD	succinylglutamate semialdehyde dehydrogenase	AZOBR_RS09720	AZOBR_RS19635
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	AZOBR_RS30610	AZOBR_RS28180
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	AZOBR_RS09720	AZOBR_RS19635
davT	5-aminovalerate aminotransferase	AZOBR_RS19630	AZOBR_RS19025
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	AZOBR_RS01260	AZOBR_RS26485
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	AZOBR_RS20225	AZOBR_RS29225
gabD	succinate semialdehyde dehydrogenase	AZOBR_RS09720	AZOBR_RS19635
gabT	gamma-aminobutyrate transaminase	AZOBR_RS19630	AZOBR_RS03635
gbamidase	guanidinobutyramidase	AZOBR_RS30770
gbuA	guanidinobutyrase	AZOBR_RS30775	AZOBR_RS30430
gcdG	succinyl-CoA:glutarate CoA-transferase	AZOBR_RS19675	AZOBR_RS29180
gcdH	glutaryl-CoA dehydrogenase	AZOBR_RS19670	AZOBR_RS22310
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	AZOBR_RS09720	AZOBR_RS19635
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	AZOBR_RS33525
ocd	ornithine cyclodeaminase	AZOBR_RS03120
odc	L-ornithine decarboxylase	AZOBR_RS27535	AZOBR_RS00105
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)	AZOBR_RS03635	AZOBR_RS22505
patD	gamma-aminobutyraldehyde dehydrogenase	AZOBR_RS22315	AZOBR_RS19635
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	AZOBR_RS27830
puo	putrescine oxidase
puuA	glutamate-putrescine ligase	AZOBR_RS08850
puuB	gamma-glutamylputrescine oxidase	AZOBR_RS08855	AZOBR_RS25655
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	AZOBR_RS09720	AZOBR_RS19635
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	AZOBR_RS02010	AZOBR_RS00395
rocA	1-pyrroline-5-carboxylate dehydrogenase	AZOBR_RS23695	AZOBR_RS29185
rocE	L-arginine permease
rocF	arginase	AZOBR_RS19585	AZOBR_RS30775
speB	agmatinase	AZOBR_RS30775	AZOBR_RS30430

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.