GapMind for catabolism of small carbon sources


Definition of L-citrulline catabolism

As rules and steps, or see full text


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


AO353_03055: ABC transporter for L-Citrulline, periplasmic substrate-binding component

AO353_03050: ABC transporter for L-Citrulline, permease component 1

AO353_03045: ABC transporter for L-Citrulline, permease component 2

AO353_03040: ABC transporter for L-Citrulline, ATPase component

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

patA: putrescine aminotransferase (PatA/SpuC)

patD: gamma-aminobutyraldehyde dehydrogenase

puuA: glutamate-putrescine ligase

puuB: gamma-glutamylputrescine oxidase

puuC: gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

puuD: gamma-glutamyl-gamma-aminobutyrate hydrolase

puo: putrescine oxidase

gabT: gamma-aminobutyrate transaminase

gabD: succinate semialdehyde dehydrogenase

atoB: acetyl-CoA C-acetyltransferase

gcdH: glutaryl-CoA dehydrogenase

ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

fadB: (S)-3-hydroxybutanoyl-CoA dehydrogenase

glaH: glutarate 2-hydroxylase, succinate-releasing (GlaH or CsiD)

lhgD: L-2-hydroxyglutarate dehydrogenase or oxidase (LhgD or LhgO)

gcdG: succinyl-CoA:glutarate CoA-transferase

davT: 5-aminovalerate aminotransferase

davD: glutarate semialdehyde dehydrogenase

prdA: D-proline reductase, prdA component

prdB: D-proline reductase, prdB component

prdC: D-proline reductase, electron transfer component PrdC

put1: proline dehydrogenase

putA: L-glutamate 5-semialdeyde dehydrogenase

prdF: proline racemase

aruF: ornithine/arginine N-succinyltransferase subunit AruAI (AruF)

aruG: ornithine/arginine N-succinyltransferase subunit AruAII (AruG)

astC: succinylornithine transaminase

astD: succinylglutamate semialdehyde dehydrogenase

astE: succinylglutamate desuccinylase

rocD: ornithine aminotransferase

rocA: 1-pyrroline-5-carboxylate dehydrogenase

PRO3: pyrroline-5-carboxylate reductase

ocd: ornithine cyclodeaminase

odc: L-ornithine decarboxylase

orr: ornithine racemase

oraS: D-ornithine 4,5-aminomutase, alpha (S) subunit

oraE: D-ornithine 4,5-aminomutase, beta (E) subunit

ord: 2,4-diaminopentanoate dehydrogenase

ortA: 2-amino-4-oxopentanoate thiolase, alpha subunit

ortB: 2-amino-4-oxopentanoate thiolase, beta subunit

arcB: ornithine carbamoyltransferase

arcC: carbamate kinase

citrullinase: putative citrullinase



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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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