GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Nocardiopsis baichengensis YIM 90130

Best path

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

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 (13 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 C892_RS0122410
fucA L-fuculose-phosphate aldolase FucA
tpi triose-phosphate isomerase C892_RS0126430 C892_RS0126425
aldA lactaldehyde dehydrogenase C892_RS0122405 C892_RS0112195
Alternative steps:
BPHYT_RS34240 ABC transporter for L-fucose, permease component C892_RS0117115 C892_RS0117110
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component C892_RS0117120 C892_RS0112255
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fdh L-fucose 1-dehydrogenase C892_RS0102880 C892_RS0125545
fucD L-fuconate dehydratase
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase C892_RS0113925 C892_RS0120415
fucO L-lactaldehyde reductase
fuconolactonase L-fucono-1,5-lactonase
HSERO_RS05250 ABC transporter for L-fucose, ATPase component C892_RS0109575 C892_RS0117120
HSERO_RS05255 ABC transporter for L-fucose, permease component C892_RS0117115 C892_RS0117110
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase C892_RS0124820 C892_RS0110605
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 C892_RS0103370 C892_RS0124910
SM_b21105 ABC transporter for L-fucose, permease component 2 C892_RS0110280 C892_RS0119340
SM_b21106 ABC transporter for L-fucose, ATPase component C892_RS0124950 C892_RS0124970

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 24 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:

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