GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Pedobacter sp. GW460-11-11-14-LB5

Best path

rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA

Also see fitness data for the top candidates

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT CA265_RS02625
rhaM L-rhamnose mutarotase CA265_RS13790
rhaA L-rhamnose isomerase CA265_RS02635
rhaB L-rhamnulokinase CA265_RS02640
rhaD rhamnulose 1-phosphate aldolase CA265_RS02630
tpi triose-phosphate isomerase CA265_RS10795 CA265_RS01880
aldA lactaldehyde dehydrogenase CA265_RS02630 CA265_RS14635
Alternative steps:
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
fucO L-lactaldehyde reductase CA265_RS24860
LRA1 L-rhamnofuranose dehydrogenase CA265_RS13715 CA265_RS15450
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase CA265_RS19875 CA265_RS04670
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase CA265_RS08355 CA265_RS15450
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase CA265_RS08350 CA265_RS15165
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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