GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Dyella japonica UNC79MFTsu3.2

Best path

rhaT, LRA1, LRA2, LRA3, LRA5, LRA6

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
LRA1 L-rhamnofuranose dehydrogenase N515DRAFT_1006 N515DRAFT_1583
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase N515DRAFT_1231
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase N515DRAFT_2873 N515DRAFT_1253
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase N515DRAFT_1252
Alternative steps:
aldA lactaldehyde dehydrogenase N515DRAFT_0379 N515DRAFT_3729
BPHYT_RS34240 L-rhamnose ABC transporter, permease component N515DRAFT_2414
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component N515DRAFT_2413 N515DRAFT_3232
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase N515DRAFT_2292
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase
rhaM L-rhamnose mutarotase
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) N515DRAFT_2415 N515DRAFT_2414
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) N515DRAFT_2415
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT N515DRAFT_3232 N515DRAFT_2413
tpi triose-phosphate isomerase N515DRAFT_1376 N515DRAFT_4291

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