GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Dinoroseobacter shibae DFL-12

Best path

rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA

Also see fitness data for the top candidates


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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) Dshi_2432 Dshi_0529
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) Dshi_2431 Dshi_2432
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS Dshi_2434
rhaT' L-rhamnose ABC transporter, ATPase component RhaT Dshi_2433 Dshi_0530
rhaM L-rhamnose mutarotase Dshi_2430
rhaA L-rhamnose isomerase Dshi_2437
rhaB L-rhamnulokinase Dshi_2429
rhaD rhamnulose 1-phosphate aldolase Dshi_2436
tpi triose-phosphate isomerase Dshi_2078 Dshi_2155
aldA lactaldehyde dehydrogenase Dshi_2436 Dshi_1095
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component Dshi_2432 Dshi_1424
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component Dshi_2433 Dshi_0530
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase
LRA1 L-rhamnofuranose dehydrogenase Dshi_0553 Dshi_2182
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase Dshi_2447 Dshi_2038
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase Dshi_1647 Dshi_2586
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Dshi_2036 Dshi_2182
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase Dshi_2542 Dshi_0967
rhaT L-rhamnose:H+ symporter 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.



Related tools

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 paper from 2022 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