GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Brucella inopinata BO1

Best path

SM_b21103, SM_b21104, SM_b21105, SM_b21106, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21103 ABC transporter for L-fucose, substrate-binding component BIBO1_RS12760
SM_b21104 ABC transporter for L-fucose, permease component 1 BIBO1_RS12765 BIBO1_RS14920
SM_b21105 ABC transporter for L-fucose, permease component 2 BIBO1_RS12770 BIBO1_RS16195
SM_b21106 ABC transporter for L-fucose, ATPase component BIBO1_RS12775 BIBO1_RS17945
fucU L-fucose mutarotase FucU BIBO1_RS12785 BIBO1_RS09790
fdh L-fucose 1-dehydrogenase BIBO1_RS12790 BIBO1_RS10840
fuconolactonase L-fucono-1,5-lactonase BIBO1_RS12750
fucD L-fuconate dehydratase BIBO1_RS12810 BIBO1_RS12780
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BIBO1_RS12800 BIBO1_RS08590
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase BIBO1_RS12805 BIBO1_RS19775
Alternative steps:
aldA lactaldehyde dehydrogenase BIBO1_RS19460 BIBO1_RS14100
BPHYT_RS34240 ABC transporter for L-fucose, permease component BIBO1_RS11585 BIBO1_RS18545
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component BIBO1_RS14060 BIBO1_RS15040
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA BIBO1_RS19585
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase BIBO1_RS16890
fucP L-fucose:H+ symporter FucP BIBO1_RS15725
HSERO_RS05250 ABC transporter for L-fucose, ATPase component BIBO1_RS15355 BIBO1_RS19475
HSERO_RS05255 ABC transporter for L-fucose, permease component BIBO1_RS18545 BIBO1_RS11585
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
tpi triose-phosphate isomerase BIBO1_RS08660 BIBO1_RS18585

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