L-arginine catabolism in Halomonas titanicae BH1

Best path

artJ, artM, artP, artQ, adiA, aguA, aguB, 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 (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	HALTITAN_RS15235	HALTITAN_RS11445
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	HALTITAN_RS15240	HALTITAN_RS11435
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	HALTITAN_RS15250	HALTITAN_RS11450
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	HALTITAN_RS15245	HALTITAN_RS11440
adiA	arginine decarboxylase (AdiA/SpeA)	HALTITAN_RS23450
aguA	agmatine deiminase	HALTITAN_RS00720	HALTITAN_RS04665
aguB	N-carbamoylputrescine hydrolase	HALTITAN_RS04660	HALTITAN_RS00275
puuA	glutamate-putrescine ligase	HALTITAN_RS00675	HALTITAN_RS19480
puuB	gamma-glutamylputrescine oxidase	HALTITAN_RS00680	HALTITAN_RS01005
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	HALTITAN_RS00660	HALTITAN_RS00740
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	HALTITAN_RS00670	HALTITAN_RS11255
gabT	gamma-aminobutyrate transaminase	HALTITAN_RS00665	HALTITAN_RS00620
gabD	succinate semialdehyde dehydrogenase	HALTITAN_RS06075	HALTITAN_RS00625
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	HALTITAN_RS20140
arcB	ornithine carbamoyltransferase	HALTITAN_RS20135	HALTITAN_RS18565
arcC	carbamate kinase	HALTITAN_RS20130
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	HALTITAN_RS20110	HALTITAN_RS20115
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	HALTITAN_RS20115	HALTITAN_RS20110
aruH	L-arginine:pyruvate transaminase	HALTITAN_RS11460	HALTITAN_RS18070
aruI	2-ketoarginine decarboxylase	HALTITAN_RS13895
astA	arginine N-succinyltransferase	HALTITAN_RS20115	HALTITAN_RS20110
astB	N-succinylarginine dihydrolase	HALTITAN_RS20125
astC	succinylornithine transaminase	HALTITAN_RS20105	HALTITAN_RS07740
astD	succinylglutamate semialdehyde dehydrogenase	HALTITAN_RS20120	HALTITAN_RS00740
astE	succinylglutamate desuccinylase	HALTITAN_RS15255
atoB	acetyl-CoA C-acetyltransferase	HALTITAN_RS18010	HALTITAN_RS18730
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)	HALTITAN_RS02320	HALTITAN_RS05180
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)	HALTITAN_RS02310	HALTITAN_RS22540
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	HALTITAN_RS02305	HALTITAN_RS22535
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	HALTITAN_RS06075	HALTITAN_RS00625
davT	5-aminovalerate aminotransferase	HALTITAN_RS00620	HALTITAN_RS07740
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	HALTITAN_RS11900	HALTITAN_RS16865
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	HALTITAN_RS23950	HALTITAN_RS11895
gbamidase	guanidinobutyramidase	HALTITAN_RS04660	HALTITAN_RS17720
gbuA	guanidinobutyrase	HALTITAN_RS13885	HALTITAN_RS01450
gcdG	succinyl-CoA:glutarate CoA-transferase	HALTITAN_RS07755	HALTITAN_RS23045
gcdH	glutaryl-CoA dehydrogenase	HALTITAN_RS07760	HALTITAN_RS05155
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
kauB	4-guanidinobutyraldehyde dehydrogenase	HALTITAN_RS00660	HALTITAN_RS00740
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd	ornithine cyclodeaminase	HALTITAN_RS07445
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)	HALTITAN_RS00665	HALTITAN_RS12685
patD	gamma-aminobutyraldehyde dehydrogenase	HALTITAN_RS00660	HALTITAN_RS00740
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	HALTITAN_RS08850	HALTITAN_RS20345
PRO3	pyrroline-5-carboxylate reductase	HALTITAN_RS18100
puo	putrescine oxidase
put1	proline dehydrogenase	HALTITAN_RS10685	HALTITAN_RS10675
putA	L-glutamate 5-semialdeyde dehydrogenase	HALTITAN_RS10685	HALTITAN_RS10675
rocA	1-pyrroline-5-carboxylate dehydrogenase	HALTITAN_RS10685	HALTITAN_RS10675
rocD	ornithine aminotransferase	HALTITAN_RS01040	HALTITAN_RS07740
rocE	L-arginine permease	HALTITAN_RS15020
rocF	arginase	HALTITAN_RS01450	HALTITAN_RS13885
speB	agmatinase	HALTITAN_RS01450	HALTITAN_RS13885

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.