GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Best path

HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, 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
HSERO_RS05250 ABC transporter for L-fucose, ATPase component HTA01S_RS05330 HTA01S_RS08955
HSERO_RS05255 ABC transporter for L-fucose, permease component HTA01S_RS05335 HTA01S_RS08960
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component HTA01S_RS05340
fucU L-fucose mutarotase FucU HTA01S_RS01645 HTA01S_RS05370
fdh L-fucose 1-dehydrogenase HTA01S_RS05365 HTA01S_RS17590
fuconolactonase L-fucono-1,5-lactonase HTA01S_RS05355
fucD L-fuconate dehydratase HTA01S_RS05350 HTA01S_RS13455
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase HTA01S_RS05325 HTA01S_RS17590
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase HTA01S_RS05345 HTA01S_RS09135
Alternative steps:
aldA lactaldehyde dehydrogenase HTA01S_RS10225 HTA01S_RS03325
BPHYT_RS34240 ABC transporter for L-fucose, permease component HTA01S_RS10205 HTA01S_RS11580
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component HTA01S_RS16385 HTA01S_RS10210
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA HTA01S_RS02530
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase HTA01S_RS08210
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
SM_b21105 ABC transporter for L-fucose, permease component 2
SM_b21106 ABC transporter for L-fucose, ATPase component HTA01S_RS19170 HTA01S_RS13320
tpi triose-phosphate isomerase HTA01S_RS22235

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