GapMind for catabolism of small carbon sources

 

L-fucose catabolism in Phyllobacterium brassicacearum STM 196

Best path

SM_b21103, SM_b21104, SM_b21105, SM_b21106, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
SM_b21103 ABC transporter for L-fucose, substrate-binding component CU102_RS28910
SM_b21104 ABC transporter for L-fucose, permease component 1 CU102_RS28905 CU102_RS19480
SM_b21105 ABC transporter for L-fucose, permease component 2 CU102_RS28900 CU102_RS19475
SM_b21106 ABC transporter for L-fucose, ATPase component CU102_RS28895 CU102_RS11585
fucU L-fucose mutarotase FucU CU102_RS28885 CU102_RS21590
fdh L-fucose 1-dehydrogenase CU102_RS28880 CU102_RS20255
fuconolactonase L-fucono-1,5-lactonase CU102_RS28920
fucD L-fuconate dehydratase CU102_RS28860 CU102_RS23320
fucDH 2-keto-3-deoxy-L-fuconate 4-dehydrogenase CU102_RS28870 CU102_RS05200
KDF-hydrolase 2,4-diketo-3-deoxy-L-fuconate hydrolase CU102_RS28865 CU102_RS18365
Alternative steps:
aldA lactaldehyde dehydrogenase CU102_RS25585 CU102_RS00695
BPHYT_RS34240 ABC transporter for L-fucose, permease component CU102_RS04470 CU102_RS09585
BPHYT_RS34245 ABC transporter for L-fucose, ATPase component CU102_RS25520 CU102_RS25570
BPHYT_RS34250 ABC transporter for L-fucose, substrate-binding component
fucA L-fuculose-phosphate aldolase FucA
fucI L-fucose isomerase FucI
fucK L-fuculose kinase FucK
fucO L-lactaldehyde reductase CU102_RS29015
fucP L-fucose:H+ symporter FucP
HSERO_RS05250 ABC transporter for L-fucose, ATPase component CU102_RS28785 CU102_RS04475
HSERO_RS05255 ABC transporter for L-fucose, permease component CU102_RS09585 CU102_RS28780
HSERO_RS05260 ABC transporter for L-fucose, substrate-binding component
tpi triose-phosphate isomerase CU102_RS08140 CU102_RS09220

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