L-arginine catabolism in Thermovenabulum gondwanense R270

Best path

rocE, arcA, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB

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 (42 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
rocE	L-arginine permease
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	ATZ99_RS01860	ATZ99_RS09495
arcC	carbamate kinase	ATZ99_RS05315
rocD	ornithine aminotransferase	ATZ99_RS04550	ATZ99_RS11410
PRO3	pyrroline-5-carboxylate reductase	ATZ99_RS08680
prdF	proline racemase	ATZ99_RS05955
prdA	D-proline reductase, prdA component	ATZ99_RS05925
prdB	D-proline reductase, prdB component	ATZ99_RS11620	ATZ99_RS10580
prdC	D-proline reductase, electron transfer component PrdC	ATZ99_RS05920	ATZ99_RS09305
davT	5-aminovalerate aminotransferase	ATZ99_RS11410	ATZ99_RS04550
davD	glutarate semialdehyde dehydrogenase
gcdG	succinyl-CoA:glutarate CoA-transferase	ATZ99_RS05180
gcdH	glutaryl-CoA dehydrogenase	ATZ99_RS09730
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	ATZ99_RS09725
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	ATZ99_RS09735	ATZ99_RS08105
atoB	acetyl-CoA C-acetyltransferase	ATZ99_RS10405	ATZ99_RS09740
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	ATZ99_RS06595	ATZ99_RS02740
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	ATZ99_RS01745	ATZ99_RS10675
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	ATZ99_RS01740	ATZ99_RS10670
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	ATZ99_RS10665	ATZ99_RS01735
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	ATZ99_RS10670	ATZ99_RS01740
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	ATZ99_RS09760	ATZ99_RS06170
aruI	2-ketoarginine decarboxylase	ATZ99_RS01925
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	ATZ99_RS04550	ATZ99_RS11410
astD	succinylglutamate semialdehyde dehydrogenase
astE	succinylglutamate desuccinylase
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	ATZ99_RS04375
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	ATZ99_RS08565	ATZ99_RS04370
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	ATZ99_RS04365	ATZ99_RS08560
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	ATZ99_RS04360	ATZ99_RS08555
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	ATZ99_RS04355	ATZ99_RS08550
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
gabD	succinate semialdehyde dehydrogenase	ATZ99_RS10955
gabT	gamma-aminobutyrate transaminase	ATZ99_RS10390	ATZ99_RS00645
gbamidase	guanidinobutyramidase	ATZ99_RS03690
gbuA	guanidinobutyrase	ATZ99_RS09910
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	ATZ99_RS07550
ocd	ornithine cyclodeaminase	ATZ99_RS03005
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	ATZ99_RS10260
ortA	2-amino-4-oxopentanoate thiolase, alpha subunit	ATZ99_RS03560
ortB	2-amino-4-oxopentanoate thiolase, beta subunit	ATZ99_RS03555
patA	putrescine aminotransferase (PatA/SpuC)	ATZ99_RS04550	ATZ99_RS00645
patD	gamma-aminobutyraldehyde dehydrogenase
puo	putrescine oxidase
put1	proline dehydrogenase	ATZ99_RS04510	ATZ99_RS03030
putA	L-glutamate 5-semialdeyde dehydrogenase
puuA	glutamate-putrescine ligase	ATZ99_RS06650
puuB	gamma-glutamylputrescine oxidase
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	ATZ99_RS04435
rocA	1-pyrroline-5-carboxylate dehydrogenase
rocF	arginase	ATZ99_RS09910
speB	agmatinase	ATZ99_RS09910

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.