GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Acidovorax sp. GW101-3H11

Best path

rhaT, LRA1, LRA2, LRA3, LRA4, 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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase Ac3H11_2257 Ac3H11_2748
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase Ac3H11_3953 Ac3H11_600
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase Ac3H11_3372 Ac3H11_1482
aldA lactaldehyde dehydrogenase Ac3H11_1496 Ac3H11_4393
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component Ac3H11_1841
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component Ac3H11_607 Ac3H11_2881
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase Ac3H11_2497
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Ac3H11_2257 Ac3H11_2762
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase Ac3H11_4136 Ac3H11_1487
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase
rhaM L-rhamnose mutarotase
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) Ac3H11_2880 Ac3H11_3036
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) Ac3H11_1841
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT Ac3H11_609 Ac3H11_2881
tpi triose-phosphate isomerase Ac3H11_1454 Ac3H11_4404

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:

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