GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Bacteroides fluxus YIT 12057

Best path

rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO

Rules

Overview: Rhamnose utilization in GapMind is based on MetaCyc pathway I via L-rhamnulose 1-phosphate aldolase (link), pathway II via 2-keto-3-deoxy-L-rhamnonate aldolase (link), and pathway III via 2,4-diketo-3-deoxyrhamnonate hydrolase (link).

22 steps (9 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT HMPREF9446_RS15040
rhaM L-rhamnose mutarotase
rhaA L-rhamnose isomerase HMPREF9446_RS15035
rhaB L-rhamnulokinase HMPREF9446_RS15030 HMPREF9446_RS03585
rhaD rhamnulose 1-phosphate aldolase HMPREF9446_RS03005 HMPREF9446_RS15045
tpi triose-phosphate isomerase HMPREF9446_RS10880 HMPREF9446_RS04015
fucO L-lactaldehyde reductase HMPREF9446_RS03595
Alternative steps:
aldA lactaldehyde dehydrogenase
BPHYT_RS34240 L-rhamnose ABC transporter, permease component
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
LRA1 L-rhamnofuranose dehydrogenase HMPREF9446_RS05935 HMPREF9446_RS09995
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase HMPREF9446_RS05935 HMPREF9446_RS00960
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase HMPREF9446_RS09485
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP)
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ)
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT

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