GapMind for catabolism of small carbon sources

 

Definition of L-arginine catabolism

As rules and steps, or see full text

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.

Steps

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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