L-citrulline catabolism in Dyella japonica UNC79MFTsu3.2

Best path

PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA

Also see fitness data for the top candidates

Rules

Overview: Citrulline can be catabolized via ornithine carbamoyltransferase in reverse (PMID:3129535). Genetic evidence suggests that some bacteria use a putative citrullinase (EC 3.5.1.20) to consume citrulline.

• all:
  • citrulline-transport, arcB, arcC and ornithine-degradation
  • or citrulline-transport, citrullinase and ornithine-degradation
  • Comment: Citrulline is coverted to ornithine by ornithine carbamoyltransferase (arcB) in reverse; the carbamoyltransferase reaction also yields carbamoyl-phosphate, which is consumed by carbamate kinase (arcC) in reverse. Alternatively, a putative citrullinase hydrolyzes citrulline; the product is probably ornithine.
• 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.
• 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.
• putrescine-degradation: putrescine-to-GABA and GABA-degradation
  • Comment: Gamma-aminobutyrate is a common intermediate.
• 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-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.
• citrulline-transport:
  • AO353_03055, AO353_03050, AO353_03045 and AO353_03040
  • or PS417_17590, PS417_17595, PS417_17600 and PS417_17605
  • Comment: Transporters were identified using query: transporter:citrulline:L-citrulline

51 steps (26 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
PS417_17590	ABC transporter for L-Citrulline, periplasmic substrate-binding component
PS417_17595	ABC transporter for L-Citrulline, permease component 1
PS417_17600	ABC transporter for L-Citrulline, permease component 2
PS417_17605	ABC transporter for L-Citrulline, ATPase component	N515DRAFT_1085	N515DRAFT_2216
citrullinase	putative citrullinase	N515DRAFT_1536
rocD	ornithine aminotransferase	N515DRAFT_3630	N515DRAFT_3308
PRO3	pyrroline-5-carboxylate reductase	N515DRAFT_1783
put1	proline dehydrogenase	N515DRAFT_4232	N515DRAFT_0956
putA	L-glutamate 5-semialdeyde dehydrogenase	N515DRAFT_4232	N515DRAFT_3729
Alternative steps:
AO353_03040	ABC transporter for L-Citrulline, ATPase component	N515DRAFT_1085	N515DRAFT_1562
AO353_03045	ABC transporter for L-Citrulline, permease component 2
AO353_03050	ABC transporter for L-Citrulline, permease component 1
AO353_03055	ABC transporter for L-Citrulline, periplasmic substrate-binding component
arcB	ornithine carbamoyltransferase	N515DRAFT_3763	N515DRAFT_1776
arcC	carbamate kinase
aruF	ornithine/arginine N-succinyltransferase subunit AruAI (AruF)
aruG	ornithine/arginine N-succinyltransferase subunit AruAII (AruG)
astC	succinylornithine transaminase	N515DRAFT_3308	N515DRAFT_1751
astD	succinylglutamate semialdehyde dehydrogenase	N515DRAFT_3729	N515DRAFT_4232
astE	succinylglutamate desuccinylase
atoB	acetyl-CoA C-acetyltransferase	N515DRAFT_0938	N515DRAFT_2688
davD	glutarate semialdehyde dehydrogenase	N515DRAFT_3729	N515DRAFT_2488
davT	5-aminovalerate aminotransferase	N515DRAFT_3308	N515DRAFT_1751
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	N515DRAFT_1164	N515DRAFT_0416
fadB	(S)-3-hydroxybutanoyl-CoA dehydrogenase	N515DRAFT_2687	N515DRAFT_0416
gabD	succinate semialdehyde dehydrogenase	N515DRAFT_2488	N515DRAFT_3729
gabT	gamma-aminobutyrate transaminase	N515DRAFT_3308	N515DRAFT_1751
gcdG	succinyl-CoA:glutarate CoA-transferase	N515DRAFT_3223
gcdH	glutaryl-CoA dehydrogenase	N515DRAFT_0484	N515DRAFT_0492
glaH	glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD	L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)
ocd	ornithine cyclodeaminase
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)	N515DRAFT_3308	N515DRAFT_1751
patD	gamma-aminobutyraldehyde dehydrogenase	N515DRAFT_3729	N515DRAFT_2488
prdA	D-proline reductase, prdA component
prdB	D-proline reductase, prdB component
prdC	D-proline reductase, electron transfer component PrdC
prdF	proline racemase	N515DRAFT_0959
puo	putrescine oxidase
puuA	glutamate-putrescine ligase	N515DRAFT_3024
puuB	gamma-glutamylputrescine oxidase	N515DRAFT_2697
puuC	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase	N515DRAFT_3729	N515DRAFT_0379
puuD	gamma-glutamyl-gamma-aminobutyrate hydrolase
rocA	1-pyrroline-5-carboxylate dehydrogenase	N515DRAFT_4232	N515DRAFT_3729

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.