GapMind for catabolism of small carbon sources


Definition of L-arginine catabolism

As rules and steps, or see full text


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.


artJ: L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT

artM: L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM)

artP: L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA

artQ: L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ)

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)

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)

braG: ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG)

rocE: L-arginine permease

AAP3: L-arginine transporter AAP3

CAT1: L-arginine transporter CAT1

Can1: L-arginine transporter Can1

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)

astA: arginine N-succinyltransferase

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

rocF: arginase

astB: N-succinylarginine dihydrolase

adiA: arginine decarboxylase (AdiA/SpeA)

speB: agmatinase

aguA: agmatine deiminase

aguB: N-carbamoylputrescine hydrolase

arcA: arginine deiminase

arcB: ornithine carbamoyltransferase

arcC: carbamate kinase

aroD: L-arginine oxidase

aruI: 2-ketoarginine decarboxylase

kauB: 4-guanidinobutyraldehyde dehydrogenase

gbuA: guanidinobutyrase

aruH: L-arginine:pyruvate transaminase

arg-monooxygenase: arginine 2-monooxygenase

gbamidase: guanidinobutyramidase



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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