GapMind for catabolism of small carbon sources

 

L-arginine catabolism in Burkholderia vietnamiensis G4

Best path

artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD

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.

71 steps (50 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
artJ L-arginine ABC transporter, periplasmic substrate-binding component ArtJ/HisJ/ArtI/AotJ/ArgT WP_011884036.1 WP_011882828.1
artM L-arginine ABC transporter, permease component 1 (ArtM/HisM/AotM) WP_011884019.1 WP_011885685.1
artP L-arginine ABC transporter, ATPase component ArtP/HisP/AotP/BgtA WP_011884020.1 WP_011885686.1
artQ L-arginine ABC transporter, permease component 2 (ArtQ/HisQ/AotQ) WP_011884017.1 WP_011885684.1
adiA arginine decarboxylase (AdiA/SpeA) WP_011882700.1 WP_011885706.1
speB agmatinase WP_011882472.1 WP_011880884.1
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
gabT gamma-aminobutyrate transaminase WP_011886234.1 WP_011880937.1
gabD succinate semialdehyde dehydrogenase WP_011882248.1 WP_011880486.1
Alternative steps:
AAP3 L-arginine transporter AAP3
aguA agmatine deiminase
aguB N-carbamoylputrescine hydrolase
arcA arginine deiminase
arcB ornithine carbamoyltransferase WP_011885816.1 WP_011882576.1
arcC carbamate kinase
arg-monooxygenase arginine 2-monooxygenase WP_011881730.1
aroD L-arginine oxidase
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
aruH L-arginine:pyruvate transaminase WP_011883647.1 WP_011882827.1
aruI 2-ketoarginine decarboxylase
astA arginine N-succinyltransferase WP_011884025.1 WP_011884024.1
astB N-succinylarginine dihydrolase WP_011884027.1
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
atoB acetyl-CoA C-acetyltransferase WP_011884947.1 WP_011879792.1
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 WP_043292326.1 WP_011882824.1
braD ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 1 (BraD) WP_011880725.1 WP_011885761.1
braE ABC transporter for glutamate, histidine, arginine, and other amino acids, permease component 2 (BraE) WP_011880724.1 WP_011885760.1
braF ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 1 (BraF) WP_011880723.1 WP_011881645.1
braG ABC transporter for glutamate, histidine, arginine, and other amino acids, ATPase component 2 (BraG) WP_011880722.1 WP_011885758.1
Can1 L-arginine transporter Can1
CAT1 L-arginine transporter CAT1 WP_011886294.1
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
gbamidase guanidinobutyramidase WP_011884876.1
gbuA guanidinobutyrase WP_011880884.1 WP_011882472.1
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)
kauB 4-guanidinobutyraldehyde dehydrogenase WP_011886229.1 WP_011880783.1
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
puo putrescine oxidase
put1 proline dehydrogenase WP_011882823.1 WP_011881406.1
putA L-glutamate 5-semialdeyde dehydrogenase WP_011882823.1 WP_011882088.1
rocA 1-pyrroline-5-carboxylate dehydrogenase WP_011882823.1 WP_011882088.1
rocD ornithine aminotransferase WP_011880937.1 WP_011884023.1
rocE L-arginine permease WP_011881451.1 WP_011881650.1
rocF arginase WP_011880884.1 WP_011882472.1

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.

Links

Downloads

Related tools

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