GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

Echvi_1617, 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
Echvi_1617 L-rhamnose transporter Echvi_1617
rhaM L-rhamnose mutarotase Echvi_1620
rhaA L-rhamnose isomerase Echvi_1573
rhaB L-rhamnulokinase Echvi_1574
rhaD rhamnulose 1-phosphate aldolase Echvi_1572
tpi triose-phosphate isomerase Echvi_1196 Echvi_0337
aldA lactaldehyde dehydrogenase Echvi_1572 Echvi_0481
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component Echvi_1280
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component Echvi_1282
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
fucO L-lactaldehyde reductase Echvi_0924
LRA1 L-rhamnofuranose dehydrogenase Echvi_4610 Echvi_1862
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase Echvi_3632
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Echvi_0507 Echvi_4610
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase Echvi_2939 Echvi_2930
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP)
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) Echvi_1280
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT L-rhamnose:H+ symporter RhaT Echvi_1690
rhaT' L-rhamnose ABC transporter, ATPase component RhaT Echvi_1282

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