GapMind for catabolism of small carbon sources

 

Definition of L-fucose catabolism

As rules and steps, or see full text

Rules

Overview: Fucose degradation in GapMind is based on the MetaCyc pathway via L-fuculose (link) or the oxidative pathway via 2,4-diketo-3-deoxy-L-fuconate (KDF) hydrolase (PMC6336799).

Steps

fucP: L-fucose:H+ symporter FucP

SM_b21103: ABC transporter for L-fucose, substrate-binding component

SM_b21104: ABC transporter for L-fucose, permease component 1

SM_b21105: ABC transporter for L-fucose, permease component 2

SM_b21106: ABC transporter for L-fucose, ATPase component

BPHYT_RS34250: ABC transporter for L-fucose, substrate-binding component

BPHYT_RS34245: ABC transporter for L-fucose, ATPase component

BPHYT_RS34240: ABC transporter for L-fucose, permease component

HSERO_RS05250: ABC transporter for L-fucose, ATPase component

HSERO_RS05255: ABC transporter for L-fucose, permease component

HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component

fucU: L-fucose mutarotase FucU

fucI: L-fucose isomerase FucI

fucK: L-fuculose kinase FucK

fucA: L-fuculose-phosphate aldolase FucA

aldA: lactaldehyde dehydrogenase

fucO: L-lactaldehyde reductase

tpi: triose-phosphate isomerase

fdh: L-fucose 1-dehydrogenase

fuconolactonase: L-fucono-1,5-lactonase

fucD: L-fuconate dehydratase

fucDH: 2-keto-3-deoxy-L-fuconate 4-dehydrogenase

KDF-hydrolase: 2,4-diketo-3-deoxy-L-fuconate hydrolase

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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