GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Burkholderia phytofirmans PsJN

Best path

BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component BPHYT_RS34250
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component BPHYT_RS34245 BPHYT_RS28215
BPHYT_RS34240 ABC transporter for L-fucose, permease component BPHYT_RS34240 BPHYT_RS28210
fucU L-fucose mutarotase FucU BPHYT_RS22600 BPHYT_RS27230
fdh L-fucose 1-dehydrogenase BPHYT_RS34225 BPHYT_RS27200
fuconolactonase L-fucono-1,5-lactonase BPHYT_RS34220 BPHYT_RS27205
fucD L-fuconate dehydratase BPHYT_RS34230 BPHYT_RS20755
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BPHYT_RS34215 BPHYT_RS16940
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase BPHYT_RS34210 BPHYT_RS28740
Alternative steps:
aldA lactaldehyde dehydrogenase BPHYT_RS09875 BPHYT_RS09900
fucA L-fuculose-phosphate aldolase FucA BPHYT_RS29405
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase BPHYT_RS28580 BPHYT_RS31860
fucP L-fucose:H+ symporter FucP
HSERO_RS05250 ABC transporter for L-fucose, ATPase component BPHYT_RS20740 BPHYT_RS27185
HSERO_RS05255 ABC transporter for L-fucose, permease component BPHYT_RS20745 BPHYT_RS27190
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component BPHYT_RS20750 BPHYT_RS27195
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 BPHYT_RS27975 BPHYT_RS35665
SM_b21105 ABC transporter for L-fucose, permease component 2 BPHYT_RS35660 BPHYT_RS27970
SM_b21106 ABC transporter for L-fucose, ATPase component BPHYT_RS17470 BPHYT_RS35680
tpi triose-phosphate isomerase BPHYT_RS06610 BPHYT_RS16270

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 (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 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