GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Tistlia consotensis USBA 355

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
fucP L-fucose:H+ symporter FucP
fucU L-fucose mutarotase FucU
fdh L-fucose 1-dehydrogenase B9O00_RS13755 B9O00_RS14420
fuconolactonase L-fucono-1,5-lactonase B9O00_RS13760
fucD L-fuconate dehydratase B9O00_RS01575 B9O00_RS27415
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase B9O00_RS31075 B9O00_RS11105
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase B9O00_RS01570 B9O00_RS15580
Alternative steps:
aldA lactaldehyde dehydrogenase B9O00_RS10030 B9O00_RS15630
BPHYT_RS34240 ABC transporter for L-fucose, permease component B9O00_RS01465 B9O00_RS13730
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component B9O00_RS21270 B9O00_RS23655
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA B9O00_RS11655 B9O00_RS18550
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase B9O00_RS06960 B9O00_RS11945
HSERO_RS05250 ABC transporter for L-fucose, ATPase component B9O00_RS28465 B9O00_RS21320
HSERO_RS05255 ABC transporter for L-fucose, permease component B9O00_RS01465 B9O00_RS13775
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 B9O00_RS20755 B9O00_RS15885
SM_b21105 ABC transporter for L-fucose, permease component 2 B9O00_RS20760 B9O00_RS16335
SM_b21106 ABC transporter for L-fucose, ATPase component B9O00_RS31080 B9O00_RS01280
tpi triose-phosphate isomerase B9O00_RS25305 B9O00_RS28505

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 Apr 09 2024. 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