GapMind for catabolism of small carbon sources


L-fucose catabolism in Sinorhizobium meliloti 1021

Best path

SM_b21103, SM_b21104, SM_b21105, SM_b21106, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21103 ABC transporter for L-fucose, substrate-binding component SM_b21103
SM_b21104 ABC transporter for L-fucose, permease component 1 SM_b21104 SM_b21220
SM_b21105 ABC transporter for L-fucose, permease component 2 SM_b21105 SMa1341
SM_b21106 ABC transporter for L-fucose, ATPase component SM_b21106 SM_b20235
fucU L-fucose mutarotase FucU SM_b21108 SMc02173
fdh L-fucose 1-dehydrogenase SM_b21109 SMa1403
fuconolactonase L-fucono-1,5-lactonase SM_b21101
fucD L-fuconate dehydratase SM_b21113 SMc02776
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase SM_b21111 SMc01635
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase SM_b21112 SMc04240
Alternative steps:
aldA lactaldehyde dehydrogenase SMc02322 SMa2213
BPHYT_RS34240 ABC transporter for L-fucose, permease component SM_b20352 SM_b21375
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component SM_b21344 SM_b20673
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA SMc01621 SM_b20490
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase SMc01582 SMa0263
fucP L-fucose:H+ symporter FucP
HSERO_RS05250 ABC transporter for L-fucose, ATPase component SMc02337 SM_b20855
HSERO_RS05255 ABC transporter for L-fucose, permease component SM_b21375 SM_b21423
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component SMc02774
tpi triose-phosphate isomerase SMc01023 SMc01614

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.



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:

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