GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

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

Also see fitness data for the top candidates

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fucP L-fucose:H+ symporter FucP N515DRAFT_1222 N515DRAFT_1918
fucU L-fucose mutarotase FucU N515DRAFT_1223
fdh L-fucose 1-dehydrogenase N515DRAFT_1255 N515DRAFT_1583
fuconolactonase L-fucono-1,5-lactonase N515DRAFT_1254
fucD L-fuconate dehydratase N515DRAFT_1251
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase N515DRAFT_1253 N515DRAFT_0334
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase N515DRAFT_1252
Alternative steps:
aldA lactaldehyde dehydrogenase N515DRAFT_0379 N515DRAFT_3729
BPHYT_RS34240 ABC transporter for L-fucose, permease component N515DRAFT_2414
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component N515DRAFT_2413 N515DRAFT_3232
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
HSERO_RS05250 ABC transporter for L-fucose, ATPase component N515DRAFT_3232 N515DRAFT_2413
HSERO_RS05255 ABC transporter for L-fucose, permease component N515DRAFT_2415 N515DRAFT_3233
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 N515DRAFT_3134
SM_b21105 ABC transporter for L-fucose, permease component 2 N515DRAFT_3133
SM_b21106 ABC transporter for L-fucose, ATPase component N515DRAFT_4212 N515DRAFT_1562
tpi triose-phosphate isomerase N515DRAFT_1376 N515DRAFT_4291

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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