L-arginine catabolism in Halomonas salina B6

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 (47 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	BN1003_RS05855	BN1003_RS11755
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	BN1003_RS05860	BN1003_RS01405
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	BN1003_RS05870	BN1003_RS01390
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	BN1003_RS05865	BN1003_RS01400
adiA	arginine decarboxylase (AdiA/SpeA)	BN1003_RS03960
aguA	agmatine deiminase	BN1003_RS17580
aguB	N-carbamoylputrescine hydrolase	BN1003_RS17585
puuA	glutamate-putrescine ligase	BN1003_RS17985	BN1003_RS18035
puuB	gamma-glutamylputrescine oxidase	BN1003_RS18025	BN1003_RS18060
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	BN1003_RS17970	BN1003_RS18195
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	BN1003_RS17980	BN1003_RS10510
gabT	gamma-aminobutyrate transaminase	BN1003_RS17975	BN1003_RS11280
gabD	succinate semialdehyde dehydrogenase	BN1003_RS12190	BN1003_RS11285
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	BN1003_RS05590
arcB	ornithine carbamoyltransferase	BN1003_RS05595	BN1003_RS16210
arcC	carbamate kinase	BN1003_RS05600
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	BN1003_RS05025
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	BN1003_RS05025
aruH	L-arginine:pyruvate transaminase	BN1003_RS01385	BN1003_RS03740
aruI	2-ketoarginine decarboxylase	BN1003_RS01370
astA	arginine N-succinyltransferase	BN1003_RS05025
astB	N-succinylarginine dihydrolase	BN1003_RS05040
astC	succinylornithine transaminase	BN1003_RS05020	BN1003_RS11780
astD	succinylglutamate semialdehyde dehydrogenase	BN1003_RS05035	BN1003_RS13545
astE	succinylglutamate desuccinylase	BN1003_RS05875
atoB	acetyl-CoA C-acetyltransferase	BN1003_RS03690	BN1003_RS11730
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
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	BN1003_RS13575	BN1003_RS09910
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	BN1003_RS13580	BN1003_RS09895
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	BN1003_RS13585	BN1003_RS07375
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	BN1003_RS12190	BN1003_RS11285
davT	5-aminovalerate aminotransferase	BN1003_RS11280	BN1003_RS05020
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	BN1003_RS10785	BN1003_RS18225
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	BN1003_RS18750	BN1003_RS10780
gbamidase	guanidinobutyramidase	BN1003_RS18485	BN1003_RS17585
gbuA	guanidinobutyrase
gcdG	succinyl-CoA:glutarate CoA-transferase	BN1003_RS15925	BN1003_RS09100
gcdH	glutaryl-CoA dehydrogenase	BN1003_RS15930	BN1003_RS16630
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)	BN1003_RS05775
kauB	4-guanidinobutyraldehyde dehydrogenase	BN1003_RS17970	BN1003_RS18195
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	BN1003_RS05780	BN1003_RS14825
ocd	ornithine cyclodeaminase	BN1003_RS16460
odc	L-ornithine decarboxylase
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)	BN1003_RS17975	BN1003_RS06525
patD	gamma-aminobutyraldehyde dehydrogenase	BN1003_RS17970	BN1003_RS18195
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	BN1003_RS03785
puo	putrescine oxidase
put1	proline dehydrogenase	BN1003_RS02080	BN1003_RS18365
putA	L-glutamate 5-semialdeyde dehydrogenase	BN1003_RS02080	BN1003_RS18365
rocA	1-pyrroline-5-carboxylate dehydrogenase	BN1003_RS02080	BN1003_RS18365
rocD	ornithine aminotransferase	BN1003_RS11280	BN1003_RS17975
rocE	L-arginine permease
rocF	arginase
speB	agmatinase

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.