GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Pseudomonas simiae WCS417

Best path

rhaT, LRA1, LRA2, LRA3, LRA4, 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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase PS417_17895 PS417_11520
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase PS417_04210 PS417_00165
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase PS417_17865
aldA lactaldehyde dehydrogenase PS417_17430 PS417_24810
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component PS417_12060 PS417_13640
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component PS417_13635 PS417_18400
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase PS417_06905 PS417_25740
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase PS417_11520 PS417_17720
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase PS417_18185 PS417_17835
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) PS417_12060 PS417_17725
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) PS417_17725 PS417_21325
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS PS417_18405
rhaT' L-rhamnose ABC transporter, ATPase component RhaT PS417_11890 PS417_11030
tpi triose-phosphate isomerase PS417_24000 PS417_26430

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