GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Sinorhizobium fredii NGR234

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
HSERO_RS05250 ABC transporter for L-fucose, ATPase component NGR_RS19930 NGR_RS09875
HSERO_RS05255 ABC transporter for L-fucose, permease component NGR_RS19925 NGR_RS10590
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component NGR_RS27955
fucU L-fucose mutarotase FucU NGR_RS11910 NGR_RS06140
fdh L-fucose 1-dehydrogenase NGR_RS14565 NGR_RS14570
fuconolactonase L-fucono-1,5-lactonase NGR_RS27975
fucD L-fuconate dehydratase NGR_RS10410 NGR_RS27945
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase NGR_RS26075 NGR_RS07185
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase NGR_RS05215 NGR_RS02045
Alternative steps:
aldA lactaldehyde dehydrogenase NGR_RS12570 NGR_RS30435
BPHYT_RS34240 ABC transporter for L-fucose, permease component NGR_RS00535 NGR_RS00530
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component NGR_RS19930 NGR_RS07170
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA NGR_RS05520 NGR_RS14385
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK NGR_RS25880
fucO L-lactaldehyde reductase NGR_RS21905 NGR_RS14365
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 NGR_RS09950 NGR_RS30985
SM_b21105 ABC transporter for L-fucose, permease component 2 NGR_RS08910 NGR_RS09945
SM_b21106 ABC transporter for L-fucose, ATPase component NGR_RS05345 NGR_RS09720
tpi triose-phosphate isomerase NGR_RS17645 NGR_RS14620

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.

Links

Downloads

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