L-arginine catabolism in Cereibacter sphaeroides ATCC 17029

Best path

bgtB, artP, rocF, odc, 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 (42 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
bgtB	L-arginine ABC transporter, fused substrate-binding and permease components (BgtB/BgtAB)
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	RSPH17029_RS10165	RSPH17029_RS17510
rocF	arginase	RSPH17029_RS06535	RSPH17029_RS17500
odc	L-ornithine decarboxylase	RSPH17029_RS03580
puuA	glutamate-putrescine ligase	RSPH17029_RS10230	RSPH17029_RS01120
puuB	gamma-glutamylputrescine oxidase	RSPH17029_RS10235	RSPH17029_RS11565
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	RSPH17029_RS16005	RSPH17029_RS04350
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	RSPH17029_RS09530	RSPH17029_RS03635
gabT	gamma-aminobutyrate transaminase	RSPH17029_RS04315	RSPH17029_RS20165
gabD	succinate semialdehyde dehydrogenase	RSPH17029_RS13480	RSPH17029_RS16005
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)
aguA	agmatine deiminase
aguB	N-carbamoylputrescine hydrolase	RSPH17029_RS17110
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	RSPH17029_RS03670	RSPH17029_RS13430
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	RSPH17029_RS10170	RSPH17029_RS17495
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	RSPH17029_RS10180	RSPH17029_RS17505
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	RSPH17029_RS17505	RSPH17029_RS10175
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	RSPH17029_RS12225	RSPH17029_RS15545
aruI	2-ketoarginine decarboxylase	RSPH17029_RS06560
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	RSPH17029_RS03665	RSPH17029_RS04315
astD	succinylglutamate semialdehyde dehydrogenase	RSPH17029_RS13480	RSPH17029_RS16005
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	RSPH17029_RS12120	RSPH17029_RS19805
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)	RSPH17029_RS17970	RSPH17029_RS14875
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	RSPH17029_RS04845	RSPH17029_RS14870
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	RSPH17029_RS04855	RSPH17029_RS17980
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	RSPH17029_RS04835	RSPH17029_RS17985
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	RSPH17029_RS13480	RSPH17029_RS04350
davT	5-aminovalerate aminotransferase	RSPH17029_RS04315	RSPH17029_RS17535
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	RSPH17029_RS00050	RSPH17029_RS17990
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	RSPH17029_RS16015	RSPH17029_RS04435
gbamidase	guanidinobutyramidase	RSPH17029_RS17110	RSPH17029_RS15335
gbuA	guanidinobutyrase	RSPH17029_RS17500	RSPH17029_RS07860
gcdG	succinyl-CoA:glutarate CoA-transferase	RSPH17029_RS00595
gcdH	glutaryl-CoA dehydrogenase	RSPH17029_RS14905	RSPH17029_RS05935
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	RSPH17029_RS16005	RSPH17029_RS04350
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	RSPH17029_RS10685
ocd	ornithine cyclodeaminase
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)	RSPH17029_RS20165	RSPH17029_RS16010
patD	gamma-aminobutyraldehyde dehydrogenase	RSPH17029_RS16005	RSPH17029_RS04350
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	RSPH17029_RS15945
PRO3	pyrroline-5-carboxylate reductase	RSPH17029_RS15160
puo	putrescine oxidase
put1	proline dehydrogenase	RSPH17029_RS04265	RSPH17029_RS07235
putA	L-glutamate 5-semialdeyde dehydrogenase	RSPH17029_RS04265	RSPH17029_RS16005
rocA	1-pyrroline-5-carboxylate dehydrogenase	RSPH17029_RS04265	RSPH17029_RS16005
rocD	ornithine aminotransferase	RSPH17029_RS04315	RSPH17029_RS20165
rocE	L-arginine permease
speB	agmatinase	RSPH17029_RS07860	RSPH17029_RS17500

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 Apr 10 2024. The underlying query database was built on Sep 17 2021.