GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Bradyrhizobium sp. BTAi1

Best path

rhaT, LRA1, LRA2, LRA3, LRA5, LRA6

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 BBTA_RS21880 BBTA_RS15285
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase BBTA_RS13750 BBTA_RS30415
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase BBTA_RS16605 BBTA_RS17885
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase BBTA_RS05710 BBTA_RS15180
Alternative steps:
aldA lactaldehyde dehydrogenase BBTA_RS18005 BBTA_RS22610
BPHYT_RS34240 L-rhamnose ABC transporter, permease component BBTA_RS12645 BBTA_RS12035
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component BBTA_RS09915 BBTA_RS36620
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase BBTA_RS13745
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) BBTA_RS36615 BBTA_RS31435
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) BBTA_RS36615
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS BBTA_RS31440
rhaT' L-rhamnose ABC transporter, ATPase component RhaT BBTA_RS28795 BBTA_RS09965
tpi triose-phosphate isomerase BBTA_RS20935 BBTA_RS02165

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 Apr 09 2024. 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