L-arginine catabolism in Chromobacterium vaccinii MWU205

Best path

artJ, artM, artP, artQ, astA, astB, astC, astD, astE

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 (50 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	VL52_RS06115	VL52_RS17825
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	VL52_RS06125	VL52_RS17815
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	VL52_RS06130	VL52_RS19750
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	VL52_RS06120	VL52_RS17820
astA	arginine N-succinyltransferase	VL52_RS15520	VL52_RS15515
astB	N-succinylarginine dihydrolase	VL52_RS15505
astC	succinylornithine transaminase	VL52_RS15525	VL52_RS16645
astD	succinylglutamate semialdehyde dehydrogenase	VL52_RS15510	VL52_RS21455
astE	succinylglutamate desuccinylase	VL52_RS21985
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	VL52_RS21980	VL52_RS21315
aguA	agmatine deiminase	VL52_RS19625	VL52_RS10900
aguB	N-carbamoylputrescine hydrolase
arcA	arginine deiminase	VL52_RS02440
arcB	ornithine carbamoyltransferase	VL52_RS02435	VL52_RS21320
arcC	carbamate kinase	VL52_RS02430
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase	VL52_RS15120
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	VL52_RS15520	VL52_RS15515
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	VL52_RS15515	VL52_RS15520
aruH	L-arginine:pyruvate transaminase	VL52_RS16045
aruI	2-ketoarginine decarboxylase	VL52_RS18265
atoB	acetyl-CoA C-acetyltransferase	VL52_RS14225	VL52_RS21005
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	VL52_RS18885	VL52_RS09675
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	VL52_RS15500
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	VL52_RS15495
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	VL52_RS15490	VL52_RS08010
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	VL52_RS15485	VL52_RS03360
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1	VL52_RS03530
davD	glutarate semialdehyde dehydrogenase	VL52_RS20940	VL52_RS07105
davT	5-aminovalerate aminotransferase	VL52_RS20935	VL52_RS15525
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	VL52_RS18865	VL52_RS21030
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	VL52_RS10360	VL52_RS21015
gabD	succinate semialdehyde dehydrogenase	VL52_RS20535	VL52_RS20940
gabT	gamma-aminobutyrate transaminase	VL52_RS20935	VL52_RS07075
gbamidase	guanidinobutyramidase
gbuA	guanidinobutyrase
gcdG	succinyl-CoA:glutarate CoA-transferase	VL52_RS20890
gcdH	glutaryl-CoA dehydrogenase	VL52_RS20895	VL52_RS19965
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	VL52_RS07105	VL52_RS21455
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	VL52_RS05540
ocd	ornithine cyclodeaminase
odc	L-ornithine decarboxylase	VL52_RS08800	VL52_RS21315
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)	VL52_RS07075	VL52_RS18210
patD	gamma-aminobutyraldehyde dehydrogenase	VL52_RS07105	VL52_RS21455
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	VL52_RS09515
PRO3	pyrroline-5-carboxylate reductase	VL52_RS05330
puo	putrescine oxidase
put1	proline dehydrogenase	VL52_RS18890
putA	L-glutamate 5-semialdeyde dehydrogenase	VL52_RS18890	VL52_RS20940
puuA	glutamate-putrescine ligase	VL52_RS07080	VL52_RS11885
puuB	gamma-glutamylputrescine oxidase	VL52_RS11115
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	VL52_RS07105	VL52_RS21455
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	VL52_RS07085
rocA	1-pyrroline-5-carboxylate dehydrogenase	VL52_RS18890	VL52_RS20940
rocD	ornithine aminotransferase	VL52_RS15525	VL52_RS20935
rocE	L-arginine permease	VL52_RS10410	VL52_RS13800
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.