GapMind for catabolism of small carbon sources


L-fucose catabolism in Ruegeria conchae TW15

Best path

SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase


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).

23 steps (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21103 ABC transporter for L-fucose, substrate-binding component G7G_RS0110570
SM_b21104 ABC transporter for L-fucose, permease component 1 G7G_RS0110565
SM_b21105 ABC transporter for L-fucose, permease component 2 G7G_RS0110560 G7G_RS0115540
SM_b21106 ABC transporter for L-fucose, ATPase component G7G_RS0110555 G7G_RS0111275
fucU L-fucose mutarotase FucU G7G_RS0110545
fdh L-fucose 1-dehydrogenase G7G_RS0110580 G7G_RS0108780
fuconolactonase L-fucono-1,5-lactonase G7G_RS0110585 G7G_RS0115640
fucD L-fuconate dehydratase G7G_RS0110525
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase G7G_RS0110540 G7G_RS0114880
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase G7G_RS0110535 G7G_RS0100785
Alternative steps:
aldA lactaldehyde dehydrogenase G7G_RS0116915 G7G_RS0121155
BPHYT_RS34240 ABC transporter for L-fucose, permease component G7G_RS0100410
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component G7G_RS0100415 G7G_RS0100435
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase G7G_RS0120925
fucP L-fucose:H+ symporter FucP
HSERO_RS05250 ABC transporter for L-fucose, ATPase component G7G_RS0100435 G7G_RS0100415
HSERO_RS05255 ABC transporter for L-fucose, permease component G7G_RS0115755 G7G_RS0100410
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
tpi triose-phosphate isomerase G7G_RS0106540 G7G_RS0114345

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 Sep 24 2021. The underlying query database was built on Sep 17 2021.



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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