L-fucose catabolism in Burkholderia phytofirmans PsJN

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).

all:

fucose-transport, fucU, fucI, fucK, fucA, tpi and lactaldehyde-conversion
or fucose-transport, fucU, fdh, fuconolactonase, fucD, fucDH and KDF-hydrolase
Comment: In the L-fucuolose pathway, mutarotase fucU converts the beta-pyranose to the alpha-pyranose form, isomerase fucI produces L-fuculose, kinase fucK forms L-fuculose 1-phosphate, and aldolase fucA produces glycerone phosphate and (S)-lactaldehyde. Lactaldehyde might be oxidized to lactate and secreted (or oxidized to pyruvate), or, it might be reduced to propane-1,2-diol and secreted; tpi converts glycerone-phosphate to glyceraldehyde 3-phosphate. In the oxidative pathway, mutarotase fucU forms the beta-pyranose form, fucose dehydrogenase (fdh) forms L-fucono-1,5-lactone, a lactonase forms L-fuconate, dehydratase fucD forms 2-keto-3-deoxy-L-fuconate, dehydrogenase fucDH forms 2,4-diketo-3-deoxy-L-fuconate (KDF, also known as 2,4-diketo-3-deoxy-L-rhamnonate), and a hydrolase forms lactate and pyruvate. The lactate could be secreted or oxidized to pyruvate.

lactaldehyde-conversion:

aldA
or fucO
Comment: Lactaldehyde can be oxidized to lactate (aldA) or reduced to propanediol (fucO). Either of these can be excreted.

fucose-transport:

fucP
or SM_b21103, SM_b21104, SM_b21105 and SM_b21106
or BPHYT_RS34250, BPHYT_RS34245 and BPHYT_RS34240
or HSERO_RS05250, HSERO_RS05255 and HSERO_RS05260
Comment: Transporters were identified using query: transporter:L-fucose:L-fucopyranose:CPD-10329:CPD0-1107:CPD-15619

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources