L-arginine catabolism in Oceanisphaera arctica V1-41

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 (51 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	UN63_RS13380	UN63_RS02420
artM	L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)	UN63_RS03175	UN63_RS13370
artP	L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA	UN63_RS03190	UN63_RS13385
artQ	L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)	UN63_RS13375	UN63_RS03180
adiA	arginine decarboxylase (AdiA/SpeA)	UN63_RS01430	UN63_RS14765
aguA	agmatine deiminase	UN63_RS03760
aguB	N-carbamoylputrescine hydrolase	UN63_RS03755
puuA	glutamate-putrescine ligase	UN63_RS03990	UN63_RS03995
puuB	gamma-glutamylputrescine oxidase	UN63_RS14970	UN63_RS04000
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	UN63_RS09060	UN63_RS14965
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase	UN63_RS09905	UN63_RS07980
gabT	gamma-aminobutyrate transaminase	UN63_RS03985	UN63_RS03445
gabD	succinate semialdehyde dehydrogenase	UN63_RS08090	UN63_RS03450
Alternative steps:
AAP3	L-arginine transporter AAP3
arcA	arginine deiminase	UN63_RS14305
arcB	ornithine carbamoyltransferase	UN63_RS13060	UN63_RS14300
arcC	carbamate kinase	UN63_RS14295
arg-monooxygenase	arginine 2-monooxygenase
aroD	L-arginine oxidase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)	UN63_RS03530
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)	UN63_RS03530
aruH	L-arginine:pyruvate transaminase
aruI	2-ketoarginine decarboxylase	UN63_RS06885
astA	arginine N-succinyltransferase	UN63_RS03530
astB	N-succinylarginine dihydrolase	UN63_RS04100
astC	succinylornithine transaminase	UN63_RS03535	UN63_RS03445
astD	succinylglutamate semialdehyde dehydrogenase	UN63_RS03525	UN63_RS09060
astE	succinylglutamate desuccinylase	UN63_RS04150
atoB	acetyl-CoA C-acetyltransferase	UN63_RS04220	UN63_RS09000
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	UN63_RS11720
braD	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD)	UN63_RS11725
braE	ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE)	UN63_RS11730
braF	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF)	UN63_RS11735	UN63_RS11740
braG	ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)	UN63_RS11740	UN63_RS06410
Can1	L-arginine transporter Can1
CAT1	L-arginine transporter CAT1
davD	glutarate semialdehyde dehydrogenase	UN63_RS08090	UN63_RS03450
davT	5-aminovalerate aminotransferase	UN63_RS03445	UN63_RS03535
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	UN63_RS10750	UN63_RS14495
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	UN63_RS14495	UN63_RS01710
gbamidase	guanidinobutyramidase	UN63_RS03755
gbuA	guanidinobutyrase	UN63_RS16495
gcdG	succinyl-CoA:glutarate CoA-transferase
gcdH	glutaryl-CoA dehydrogenase	UN63_RS13340	UN63_RS08990
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)	UN63_RS15945
kauB	4-guanidinobutyraldehyde dehydrogenase	UN63_RS09060	UN63_RS14965
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)	UN63_RS15950
ocd	ornithine cyclodeaminase	UN63_RS12655
odc	L-ornithine decarboxylase	UN63_RS14765
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)	UN63_RS03985	UN63_RS05125
patD	gamma-aminobutyraldehyde dehydrogenase	UN63_RS14965	UN63_RS09060
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	UN63_RS09040
PRO3	pyrroline-5-carboxylate reductase	UN63_RS05200
puo	putrescine oxidase
put1	proline dehydrogenase	UN63_RS01445	UN63_RS05380 with UN63_RS06480
putA	L-glutamate 5-semialdeyde dehydrogenase	UN63_RS01445	UN63_RS05380 with UN63_RS06480
rocA	1-pyrroline-5-carboxylate dehydrogenase	UN63_RS01445	UN63_RS05380 with UN63_RS06480
rocD	ornithine aminotransferase	UN63_RS03445	UN63_RS03985
rocE	L-arginine permease
rocF	arginase
speB	agmatinase	UN63_RS16495

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.