L-arginine catabolism in Phaeobacter inhibens BS107

Best path

artJ, artM, artP, artQ, rocF, ocd, put1, putA

Also see fitness data for the top candidates

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
artJ	L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT	PGA1_262p02360	PGA1_c11570
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	PGA1_c11550	PGA1_262p02380
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	PGA1_262p02350	PGA1_c11580
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	PGA1_262p02370	PGA1_c11560
rocF	arginase	PGA1_c16370	PGA1_c19920
ocd	ornithine cyclodeaminase	PGA1_c16390
put1	proline dehydrogenase	PGA1_c11750	PGA1_c23300
putA	L-glutamate 5-semialdeyde dehydrogenase	PGA1_c11750	PGA1_c05130
Alternative steps:
AAP3	L-arginine transporter AAP3
adiA	arginine decarboxylase (AdiA/SpeA)	PGA1_c03800	PGA1_c14480
aguA	agmatine deiminase	PGA1_c26490
aguB	N-carbamoylputrescine hydrolase
arcA	arginine deiminase
arcB	ornithine carbamoyltransferase	PGA1_c24220	PGA1_c03060
arcC	carbamate kinase
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
aruH	L-arginine:pyruvate transaminase	PGA1_262p02330	PGA1_c21250
aruI	2-ketoarginine decarboxylase	PGA1_262p02320	PGA1_c19360
astA	arginine N-succinyltransferase
astB	N-succinylarginine dihydrolase
astC	succinylornithine transaminase	PGA1_c24230	PGA1_c28750
astD	succinylglutamate semialdehyde dehydrogenase	PGA1_c32120	PGA1_262p01460
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	PGA1_c03400	PGA1_c33180
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)	PGA1_c02590
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)	PGA1_c32620	PGA1_c02610
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	PGA1_c02620	PGA1_c32560
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	PGA1_c29650	PGA1_c23170
davT	5-aminovalerate aminotransferase	PGA1_c24230	PGA1_c28750
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	PGA1_c36500	PGA1_262p01980
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	PGA1_c04110	PGA1_c11320
gabD	succinate semialdehyde dehydrogenase	PGA1_c29650	PGA1_c23170
gabT	gamma-aminobutyrate transaminase	PGA1_c34400	PGA1_c09350
gbamidase	guanidinobutyramidase
gbuA	guanidinobutyrase	PGA1_c19920	PGA1_c00310
gcdG	succinyl-CoA:glutarate CoA-transferase	PGA1_c27870	PGA1_c12340
gcdH	glutaryl-CoA dehydrogenase	PGA1_c15710	PGA1_c10280
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	PGA1_c32250	PGA1_c21670
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
odc	L-ornithine decarboxylase	PGA1_c11650	PGA1_c03800
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	PGA1_c17610
ortA	2-amino-4-oxopentanoate thiolase, alpha subunit
ortB	2-amino-4-oxopentanoate thiolase, beta subunit
patA	putrescine aminotransferase (PatA/SpuC)	PGA1_c34400	PGA1_c09350
patD	gamma-aminobutyraldehyde dehydrogenase	PGA1_c21670	PGA1_c32250
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	PGA1_262p00280	PGA1_c05120
PRO3	pyrroline-5-carboxylate reductase	PGA1_c24700
puo	putrescine oxidase
puuA	glutamate-putrescine ligase	PGA1_c11520	PGA1_c11540
puuB	gamma-glutamylputrescine oxidase	PGA1_c11510	PGA1_78p00350
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	PGA1_c32250	PGA1_c21670
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	PGA1_c09920	PGA1_c28350
rocA	1-pyrroline-5-carboxylate dehydrogenase	PGA1_c11750	PGA1_c05130
rocD	ornithine aminotransferase	PGA1_c28770	PGA1_c09350
rocE	L-arginine permease
speB	agmatinase	PGA1_c19930	PGA1_c19920

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 17 2021. The underlying query database was built on Sep 17 2021.