GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Phaeobacter inhibens BS107

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 (14 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 PGA1_c16250
tpi triose-phosphate isomerase PGA1_c20650 PGA1_c17530
aldA lactaldehyde dehydrogenase PGA1_c21070 PGA1_c32800
Alternative steps:
BPHYT_RS34240 ABC transporter for L-fucose, permease component PGA1_c23080
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component PGA1_c23060 PGA1_c03960
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fdh L-fucose 1-dehydrogenase PGA1_c23480
fucD L-fuconate dehydratase
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase PGA1_c27390 PGA1_c13170
fucO L-lactaldehyde reductase PGA1_c27200 PGA1_c23360
fuconolactonase L-fucono-1,5-lactonase
HSERO_RS05250 ABC transporter for L-fucose, ATPase component PGA1_c23060 PGA1_c26910
HSERO_RS05255 ABC transporter for L-fucose, permease component PGA1_c23080 PGA1_c28050
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase PGA1_c04530 PGA1_c32200
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 PGA1_c16700 PGA1_c07410
SM_b21105 ABC transporter for L-fucose, permease component 2 PGA1_c16690
SM_b21106 ABC transporter for L-fucose, ATPase component PGA1_c07440 PGA1_c16680

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