GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) H281DRAFT_01222 H281DRAFT_01120
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) H281DRAFT_01221 H281DRAFT_02714
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS H281DRAFT_01220 H281DRAFT_01114
rhaT' L-rhamnose ABC transporter, ATPase component RhaT H281DRAFT_01223 H281DRAFT_03380
LRA1 L-rhamnofuranose dehydrogenase H281DRAFT_01227 H281DRAFT_06377
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase H281DRAFT_03532 H281DRAFT_01228
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase H281DRAFT_01230 H281DRAFT_03856
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase H281DRAFT_03528 H281DRAFT_02528
Alternative steps:
aldA lactaldehyde dehydrogenase H281DRAFT_00972 H281DRAFT_03016
BPHYT_RS34240 L-rhamnose ABC transporter, permease component H281DRAFT_02703 H281DRAFT_01222
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component H281DRAFT_01223 H281DRAFT_01057
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase H281DRAFT_02547 H281DRAFT_05508
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase H281DRAFT_05315 H281DRAFT_03252
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase
rhaM L-rhamnose mutarotase H281DRAFT_01225
rhaT L-rhamnose:H+ symporter RhaT
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190

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