GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Pontibacter ramchanderi LP43

Best path

fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase

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 BD749_RS13490 BD749_RS03265
fucU L-fucose mutarotase FucU BD749_RS13485
fdh L-fucose 1-dehydrogenase BD749_RS13460 BD749_RS04795
fuconolactonase L-fucono-1,5-lactonase BD749_RS13465
fucD L-fuconate dehydratase BD749_RS13480
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BD749_RS13475 BD749_RS14605
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase BD749_RS13470 BD749_RS13930
Alternative steps:
aldA lactaldehyde dehydrogenase BD749_RS10835 BD749_RS08950
BPHYT_RS34240 ABC transporter for L-fucose, permease component
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase
HSERO_RS05250 ABC transporter for L-fucose, ATPase component
HSERO_RS05255 ABC transporter for L-fucose, permease component
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
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 BD749_RS06110 BD749_RS06040
tpi triose-phosphate isomerase BD749_RS18150 BD749_RS06020

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