GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Escherichia coli BW25113

Best path

rhaT, rhaM, rhaA, rhaB, rhaD, tpi, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT b3907
rhaM L-rhamnose mutarotase b3901
rhaA L-rhamnose isomerase b3903
rhaB L-rhamnulokinase b3904 b2803
rhaD rhamnulose 1-phosphate aldolase b3902
tpi triose-phosphate isomerase b3919 b2926
aldA lactaldehyde dehydrogenase b1415 b1300
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component b3750 b2546
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component b3749 b2149
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase b2799 b3589
LRA1 L-rhamnofuranose dehydrogenase b2842 b2774
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase b2247 b3128
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase b2245 b3126
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase b1093 b1774
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase b1180
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) b3750 b4086
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) b4460 b1515
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS b1516
rhaT' L-rhamnose ABC transporter, ATPase component RhaT b3749 b2149

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