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 (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