GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Pseudomonas fluorescens FW300-N2E2

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase Pf6N2E2_1323 Pf6N2E2_5209
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase Pf6N2E2_1104 Pf6N2E2_860
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase Pf6N2E2_1314 Pf6N2E2_1103
aldA lactaldehyde dehydrogenase Pf6N2E2_1102 Pf6N2E2_1751
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component Pf6N2E2_5970 Pf6N2E2_163
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component Pf6N2E2_162 Pf6N2E2_523
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase Pf6N2E2_1297 Pf6N2E2_2802
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Pf6N2E2_1375 Pf6N2E2_1004
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase Pf6N2E2_1662 Pf6N2E2_865
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) Pf6N2E2_524 Pf6N2E2_5970
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) Pf6N2E2_5970
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT Pf6N2E2_523 Pf6N2E2_1456
tpi triose-phosphate isomerase Pf6N2E2_3356 Pf6N2E2_4657

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 (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 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