GapMind for catabolism of small carbon sources

 

Definition of L-arabinose catabolism

As rules and steps, or see full text

Rules

Overview: L-arabinose utilization in GapMind is based on MetaCyc pathways L-arabinose degradation I, via xylulose 5-phosphate (link); III, oxidation to 2-oxoglutarate (link); and IV, via glycolaldehyde (link). Pathway II via xylitol and xylulose is not represented in GapMind because it is not reported in prokaryotes (link).

Steps

gguA: L-arabinose ABC transporter, ATPase component GguA

gguB: L-arabinose ABC transporter, permease component GguB

chvE: L-arabinose ABC transporter, substrate-binding component ChvE

araF: L-arabinose ABC transporter, substrate-binding component AraF

araG: L-arabinose ABC transporter, ATPase component AraG

araH: L-arabinose ABC transporter, permease component AraH

araS: L-arabinose ABC transporter, substrate-binding component AraS

araT: L-arabinose ABC transporter, permease component 1 (AraT)

araU: L-arabinose ABC transporter, permease component 2 (AraU)

araV: L-arabinose ABC transporter, ATPase component AraV

xacG: L-arabinose ABC transporter, substrate-binding component XacG

xacH: L-arabinose ABC transporter, permease component 1 (XacH)

xacI: L-arabinose ABC transporter, permease component 2 (XacI)

xacJ: L-arabinose ABC transporter, ATPase component 1 (XacJ)

xacK: L-arabinose ABC transporter, ATPase component 2 (XacK)

xylFsa: L-arabinose ABC transporter, substrate-binding component XylF

xylGsa: L-arabinose ABC transporter, ATPase component XylG

xylHsa: L-arabinose ABC transporter, permease component XylH

araUsh: L-arabinose ABC transporter, substrate-binding component AraU(Sh)

araVsh: L-arabinose ABC transporter, ATPase component AraV(Sh)

araWsh: L-arabinose ABC transporter, permease component 1 AraW(Sh)

araZsh: L-arabinose ABC transporter, permease component 2 AraZ(Sh)

araE: L-arabinose:H+ symporter

BT0355: L-arabinose:Na+ symporter

Echvi_1880: L-arabinose:Na+ symporter

araA: L-arabinose isomerase

araB: ribulokinase

araD: L-ribulose-5-phosphate epimerase

xacB: L-arabinose 1-dehydrogenase

xacC: L-arabinono-1,4-lactonase

xacD: L-arabinonate dehydratase

xacE: 2-dehydro-3-deoxy-L-arabinonate dehydratase

xacF: alpha-ketoglutarate semialdehyde dehydrogenase

aldA: (glycol)aldehyde dehydrogenase

aldox-large: (glycol)aldehyde oxidoreductase, large subunit

aldox-med: (glycol)aldehyde oxidoreductase, medium subunit

aldox-small: (glycol)aldehyde oxidoreductase, small subunit

gyaR: glyoxylate reductase

glcB: malate synthase

KDG-aldolase: 2-dehydro-3-deoxy-L-arabinonate aldolase

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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