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

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