GapMind for catabolism of small carbon sources


L-fucose catabolism in Herbaspirillum seropedicae SmR1

Best path

HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase

Also see fitness data for the top candidates


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 HSERO_RS05250 HSERO_RS11485
HSERO_RS05255 ABC transporter for L-fucose, permease component HSERO_RS05255 HSERO_RS11490
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component HSERO_RS05260
fucU L-fucose mutarotase FucU HSERO_RS05110 HSERO_RS05245
fdh L-fucose 1-dehydrogenase HSERO_RS05240 HSERO_RS04830
fuconolactonase L-fucono-1,5-lactonase HSERO_RS05265 HSERO_RS22485
fucD L-fuconate dehydratase HSERO_RS05235 HSERO_RS19355
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase HSERO_RS19365 HSERO_RS17460
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase HSERO_RS06355 HSERO_RS17860
Alternative steps:
aldA lactaldehyde dehydrogenase HSERO_RS22235 HSERO_RS09465
BPHYT_RS34240 ABC transporter for L-fucose, permease component HSERO_RS22215 HSERO_RS05325
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component HSERO_RS22220 HSERO_RS05175
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA HSERO_RS21150
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase HSERO_RS00730
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 HSERO_RS01340 HSERO_RS16725
SM_b21105 ABC transporter for L-fucose, permease component 2 HSERO_RS16730 HSERO_RS02200
SM_b21106 ABC transporter for L-fucose, ATPase component HSERO_RS16715 HSERO_RS18940
tpi triose-phosphate isomerase HSERO_RS08805 HSERO_RS03345

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:

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