GapMind for catabolism of small carbon sources

 

L-citrulline catabolism in Burkholderia vietnamiensis G4

Best path

AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE

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.

51 steps (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
AO353_03055 ABC transporter for L-Citrulline, periplasmic substrate-binding component WP_034192590.1 WP_011880970.1
AO353_03050 ABC transporter for L-Citrulline, permease component 1 WP_011885684.1 WP_011884017.1
AO353_03045 ABC transporter for L-Citrulline, permease component 2 WP_011884019.1 WP_011885685.1
AO353_03040 ABC transporter for L-Citrulline, ATPase component WP_011876052.1 WP_011884020.1
arcB ornithine carbamoyltransferase WP_011885816.1 WP_011882576.1
arcC carbamate kinase
aruF ornithine/arginine N-succinyltransferase subunit AruAI (AruF) WP_011884024.1 WP_011884025.1
aruG ornithine/arginine N-succinyltransferase subunit AruAII (AruG) WP_011884025.1 WP_011884024.1
astC succinylornithine transaminase WP_011884023.1 WP_011885755.1
astD succinylglutamate semialdehyde dehydrogenase WP_011884026.1 WP_011885694.1
astE succinylglutamate desuccinylase WP_011884034.1
Alternative steps:
atoB acetyl-CoA C-acetyltransferase WP_011884947.1 WP_011879792.1
citrullinase putative citrullinase
davD glutarate semialdehyde dehydrogenase WP_011880938.1 WP_011880486.1
davT 5-aminovalerate aminotransferase WP_011880937.1 WP_011884023.1
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase WP_011883164.1 WP_011881868.1
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase WP_011885989.1 WP_011886130.1
gabD succinate semialdehyde dehydrogenase WP_011882248.1 WP_011880486.1
gabT gamma-aminobutyrate transaminase WP_011886234.1 WP_011880937.1
gcdG succinyl-CoA:glutarate CoA-transferase WP_011884420.1 WP_011882039.1
gcdH glutaryl-CoA dehydrogenase WP_011883419.1 WP_011880846.1
glaH glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)
lhgD L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO) WP_011886286.1
ocd ornithine cyclodeaminase
odc L-ornithine decarboxylase WP_011885706.1 WP_011882700.1
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) WP_011886234.1 WP_011880484.1
patD gamma-aminobutyraldehyde dehydrogenase WP_011886229.1 WP_011880783.1
prdA D-proline reductase, prdA component
prdB D-proline reductase, prdB component
prdC D-proline reductase, electron transfer component PrdC
prdF proline racemase WP_034193876.1
PRO3 pyrroline-5-carboxylate reductase WP_011883327.1
PS417_17590 ABC transporter for L-Citrulline, periplasmic substrate-binding component WP_011876049.1 WP_011880970.1
PS417_17595 ABC transporter for L-Citrulline, permease component 1 WP_011885684.1 WP_011884017.1
PS417_17600 ABC transporter for L-Citrulline, permease component 2 WP_011884019.1 WP_011885685.1
PS417_17605 ABC transporter for L-Citrulline, ATPase component WP_011884020.1 WP_011876052.1
puo putrescine oxidase
put1 proline dehydrogenase WP_011882823.1 WP_011881406.1
putA L-glutamate 5-semialdeyde dehydrogenase WP_011882823.1 WP_011882088.1
puuA glutamate-putrescine ligase WP_011886233.1 WP_011885444.1
puuB gamma-glutamylputrescine oxidase WP_011886241.1 WP_043292303.1
puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase WP_011886229.1 WP_011880783.1
puuD gamma-glutamyl-gamma-aminobutyrate hydrolase WP_011886232.1 WP_011885445.1
rocA 1-pyrroline-5-carboxylate dehydrogenase WP_011882823.1 WP_011882088.1
rocD ornithine aminotransferase WP_011880937.1 WP_011884023.1

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory