GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Streptacidiphilus oryzae TH49

Best path

BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, 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
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component BS73_RS15640
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component BS73_RS15635 BS73_RS32735
BPHYT_RS34240 ABC transporter for L-fucose, permease component BS73_RS15630 BS73_RS01760
fucU L-fucose mutarotase FucU BS73_RS29745
fdh L-fucose 1-dehydrogenase BS73_RS03870 BS73_RS15480
fuconolactonase L-fucono-1,5-lactonase BS73_RS03885 BS73_RS15475
fucD L-fuconate dehydratase BS73_RS15490 BS73_RS29945
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase BS73_RS15485 BS73_RS00110
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase BS73_RS30775 BS73_RS00400
Alternative steps:
aldA lactaldehyde dehydrogenase BS73_RS10620 BS73_RS23595
fucA L-fuculose-phosphate aldolase FucA BS73_RS08390
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK BS73_RS10625
fucO L-lactaldehyde reductase BS73_RS30995 BS73_RS27570
fucP L-fucose:H+ symporter FucP
HSERO_RS05250 ABC transporter for L-fucose, ATPase component BS73_RS01755 BS73_RS32735
HSERO_RS05255 ABC transporter for L-fucose, permease component BS73_RS01760 BS73_RS07055
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
SM_b21103 ABC transporter for L-fucose, substrate-binding component
SM_b21104 ABC transporter for L-fucose, permease component 1 BS73_RS03350
SM_b21105 ABC transporter for L-fucose, permease component 2 BS73_RS04625 BS73_RS31740
SM_b21106 ABC transporter for L-fucose, ATPase component BS73_RS18100 BS73_RS12870
tpi triose-phosphate isomerase BS73_RS12430 BS73_RS16890

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 24 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