GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Pseudomonas stutzeri RCH2

Best path

fucP, fucU, fucI, fucK, fucA, tpi, aldA

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 (10 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fucP L-fucose:H+ symporter FucP
fucU L-fucose mutarotase FucU
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucA L-fuculose-phosphate aldolase FucA
tpi triose-phosphate isomerase Psest_0975 Psest_0330
aldA lactaldehyde dehydrogenase Psest_0905 Psest_0375
Alternative steps:
BPHYT_RS34240 ABC transporter for L-fucose, permease component
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component Psest_1392
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fdh L-fucose 1-dehydrogenase Psest_2353 Psest_0357
fucD L-fuconate dehydratase Psest_0377
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase Psest_1716 Psest_3522
fucO L-lactaldehyde reductase Psest_0672 Psest_3782
fuconolactonase L-fucono-1,5-lactonase
HSERO_RS05250 ABC transporter for L-fucose, ATPase component Psest_1392
HSERO_RS05255 ABC transporter for L-fucose, permease component
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase Psest_3871
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 Psest_0871 Psest_1899

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