GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Pseudomonas fluorescens GW456-L13

Best path

HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, 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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS05250 ABC transporter for L-fucose, ATPase component PfGW456L13_3911 PfGW456L13_2121
HSERO_RS05255 ABC transporter for L-fucose, permease component PfGW456L13_3910 PfGW456L13_2122
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
tpi triose-phosphate isomerase PfGW456L13_5091 PfGW456L13_1066
aldA lactaldehyde dehydrogenase PfGW456L13_3932 PfGW456L13_2360
Alternative steps:
BPHYT_RS34240 ABC transporter for L-fucose, permease component PfGW456L13_2122
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component PfGW456L13_3911 PfGW456L13_2121
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fdh L-fucose 1-dehydrogenase PfGW456L13_2522 PfGW456L13_2058
fucD L-fuconate dehydratase PfGW456L13_3478 PfGW456L13_5042
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase PfGW456L13_3453 PfGW456L13_2119
fucO L-lactaldehyde reductase PfGW456L13_1214 PfGW456L13_3512
fuconolactonase L-fucono-1,5-lactonase
fucP L-fucose:H+ symporter FucP
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase PfGW456L13_3411 PfGW456L13_3396
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 PfGW456L13_3039 PfGW456L13_1897

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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