L-arginine catabolism in Amycolatopsis halophila YIM 93223

Best path

rocE, arg-monooxygenase, gbamidase, kauB, gbuA, 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
rocE	L-arginine permease
arg-monooxygenase	arginine 2-monooxygenase	AMYHA_RS23880
gbamidase	guanidinobutyramidase	AMYHA_RS23875
kauB	4-guanidinobutyraldehyde dehydrogenase	AMYHA_RS12585	AMYHA_RS25345
gbuA	guanidinobutyrase	AMYHA_RS23885
gabT	gamma-aminobutyrate transaminase	AMYHA_RS13090	AMYHA_RS09750
gabD	succinate semialdehyde dehydrogenase	AMYHA_RS09755	AMYHA_RS16465
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	AMYHA_RS05040
aguA	agmatine deiminase	AMYHA_RS23905
aguB	N-carbamoylputrescine hydrolase	AMYHA_RS23910
arcA	arginine deiminase	AMYHA_RS02430
arcB	ornithine carbamoyltransferase	AMYHA_RS15985	AMYHA_RS11270
arcC	carbamate kinase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	AMYHA_RS03540
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	AMYHA_RS03535	AMYHA_RS18270
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	AMYHA_RS03530	AMYHA_RS18260
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	AMYHA_RS03535	AMYHA_RS22135
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	AMYHA_RS01030	AMYHA_RS01585
aruI	2-ketoarginine decarboxylase	AMYHA_RS20650	AMYHA_RS20285
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	AMYHA_RS15990	AMYHA_RS17620
astD	succinylglutamate semialdehyde dehydrogenase	AMYHA_RS13095	AMYHA_RS08895
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	AMYHA_RS06490	AMYHA_RS10330
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)	AMYHA_RS16255	AMYHA_RS04370
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	AMYHA_RS10525	AMYHA_RS20915
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	AMYHA_RS05545	AMYHA_RS10540
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	AMYHA_RS20895	AMYHA_RS10515
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	AMYHA_RS09755	AMYHA_RS13095
davT	5-aminovalerate aminotransferase	AMYHA_RS07330	AMYHA_RS09750
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	AMYHA_RS20710	AMYHA_RS24905
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	AMYHA_RS03760	AMYHA_RS17210
gcdG	succinyl-CoA:glutarate CoA-transferase	AMYHA_RS12685	AMYHA_RS16450
gcdH	glutaryl-CoA dehydrogenase	AMYHA_RS24060	AMYHA_RS09585
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	AMYHA_RS02030
ocd	ornithine cyclodeaminase
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)	AMYHA_RS13090	AMYHA_RS15990
patD	gamma-aminobutyraldehyde dehydrogenase	AMYHA_RS23925	AMYHA_RS20335
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	AMYHA_RS01435
puo	putrescine oxidase	AMYHA_RS13775	AMYHA_RS23045
put1	proline dehydrogenase
putA	L-glutamate 5-semialdeyde dehydrogenase	AMYHA_RS10060	AMYHA_RS09435
puuA	glutamate-putrescine ligase	AMYHA_RS20005	AMYHA_RS24480
puuB	gamma-glutamylputrescine oxidase	AMYHA_RS23075
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	AMYHA_RS13095	AMYHA_RS08895
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	AMYHA_RS20010	AMYHA_RS23110
rocA	1-pyrroline-5-carboxylate dehydrogenase	AMYHA_RS09435	AMYHA_RS10060
rocD	ornithine aminotransferase	AMYHA_RS17620	AMYHA_RS15990
rocF	arginase	AMYHA_RS23885	AMYHA_RS17685
speB	agmatinase	AMYHA_RS23885

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.