GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Klebsiella michiganensis M5al

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) BWI76_RS00655 BWI76_RS14865
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) BWI76_RS00650 BWI76_RS14865
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS BWI76_RS00665 BWI76_RS24645
rhaT' L-rhamnose ABC transporter, ATPase component RhaT BWI76_RS00660 BWI76_RS07240
rhaM L-rhamnose mutarotase BWI76_RS00640
rhaA L-rhamnose isomerase BWI76_RS00675
rhaB L-rhamnulokinase BWI76_RS00680
rhaD rhamnulose 1-phosphate aldolase BWI76_RS00670
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
aldA lactaldehyde dehydrogenase BWI76_RS13210 BWI76_RS10695
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component BWI76_RS14605 BWI76_RS00280
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component BWI76_RS14860 BWI76_RS00275
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase BWI76_RS00645 BWI76_RS22480
LRA1 L-rhamnofuranose dehydrogenase BWI76_RS23430 BWI76_RS07640
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase BWI76_RS19990 BWI76_RS24840
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase BWI76_RS19980 BWI76_RS24830
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BWI76_RS11090 BWI76_RS23705
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase BWI76_RS03870 BWI76_RS05690
rhaT L-rhamnose:H+ symporter RhaT BWI76_RS00700

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