GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Jannaschia aquimarina GSW-M26

Best path

fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase

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).

23 steps (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fucP L-fucose:H+ symporter FucP
fucU L-fucose mutarotase FucU jaqu_RS16155
fdh L-fucose 1-dehydrogenase jaqu_RS16200 jaqu_RS05220
fuconolactonase L-fucono-1,5-lactonase jaqu_RS16195
fucD L-fuconate dehydratase jaqu_RS15145
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase jaqu_RS15175 jaqu_RS17725
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase jaqu_RS15185 jaqu_RS16390
Alternative steps:
aldA lactaldehyde dehydrogenase jaqu_RS03630 jaqu_RS08505
BPHYT_RS34240 ABC transporter for L-fucose, permease component jaqu_RS12950 jaqu_RS12915
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component jaqu_RS16085 jaqu_RS12955
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA jaqu_RS12935 jaqu_RS07515
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase jaqu_RS03420
HSERO_RS05250 ABC transporter for L-fucose, ATPase component jaqu_RS16085 jaqu_RS12955
HSERO_RS05255 ABC transporter for L-fucose, permease component jaqu_RS12950 jaqu_RS12915
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 jaqu_RS15665 jaqu_RS18660
SM_b21105 ABC transporter for L-fucose, permease component 2 jaqu_RS16545 jaqu_RS03155
SM_b21106 ABC transporter for L-fucose, ATPase component jaqu_RS16150 jaqu_RS18640
tpi triose-phosphate isomerase jaqu_RS04910 jaqu_RS05175

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