GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Klebsiella michiganensis M5al

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fucP L-fucose:H+ symporter FucP BWI76_RS22920 BWI76_RS23685
fucU L-fucose mutarotase FucU BWI76_RS22935
fucI L-fucose isomerase FucI BWI76_RS22925
fucK L-fuculose kinase FucK BWI76_RS22930 BWI76_RS00680
fucA L-fuculose-phosphate aldolase FucA BWI76_RS22915
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
aldA lactaldehyde dehydrogenase BWI76_RS13210 BWI76_RS10695
Alternative steps:
BPHYT_RS34240 ABC transporter for L-fucose, permease component BWI76_RS14605 BWI76_RS00280
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component BWI76_RS14860 BWI76_RS00275
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fdh L-fucose 1-dehydrogenase BWI76_RS01745 BWI76_RS16075
fucD L-fuconate dehydratase BWI76_RS24840 BWI76_RS13570
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BWI76_RS11090 BWI76_RS07640
fucO L-lactaldehyde reductase BWI76_RS00645 BWI76_RS22480
fuconolactonase L-fucono-1,5-lactonase
HSERO_RS05250 ABC transporter for L-fucose, ATPase component BWI76_RS14860 BWI76_RS07240
HSERO_RS05255 ABC transporter for L-fucose, permease component BWI76_RS14865 BWI76_RS00280
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase BWI76_RS03870 BWI76_RS05690
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 BWI76_RS06705 BWI76_RS03240
SM_b21106 ABC transporter for L-fucose, ATPase component BWI76_RS17830 BWI76_RS03270

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