GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, 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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS05250 ABC transporter for L-fucose, ATPase component H281DRAFT_00426 H281DRAFT_03380
HSERO_RS05255 ABC transporter for L-fucose, permease component H281DRAFT_00427 H281DRAFT_03379
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component H281DRAFT_00428 H281DRAFT_03378
fucU L-fucose mutarotase FucU H281DRAFT_03204
fdh L-fucose 1-dehydrogenase H281DRAFT_03531 H281DRAFT_03377
fuconolactonase L-fucono-1,5-lactonase H281DRAFT_03530 H281DRAFT_01224
fucD L-fuconate dehydratase H281DRAFT_03532 H281DRAFT_00429
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase H281DRAFT_03529 H281DRAFT_06296
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase H281DRAFT_03528 H281DRAFT_02528
Alternative steps:
aldA lactaldehyde dehydrogenase H281DRAFT_00972 H281DRAFT_03016
BPHYT_RS34240 ABC transporter for L-fucose, permease component H281DRAFT_02703 H281DRAFT_01222
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component H281DRAFT_01223 H281DRAFT_01057
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA H281DRAFT_02706 H281DRAFT_01508
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase H281DRAFT_02547 H281DRAFT_05508
fucP L-fucose:H+ symporter FucP
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 H281DRAFT_05891
SM_b21105 ABC transporter for L-fucose, permease component 2 H281DRAFT_03745 H281DRAFT_05890
SM_b21106 ABC transporter for L-fucose, ATPase component H281DRAFT_05701 H281DRAFT_03749
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190

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