GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Azospirillum brasilense Sp245

Best path

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase AZOBR_RS09410 AZOBR_RS02035
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase AZOBR_RS31430 AZOBR_RS26635
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase AZOBR_RS08390 AZOBR_RS24695
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase AZOBR_RS15905 AZOBR_RS26375
Alternative steps:
aldA lactaldehyde dehydrogenase AZOBR_RS29185 AZOBR_RS19635
BPHYT_RS34240 L-rhamnose ABC transporter, permease component AZOBR_RS27940
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component AZOBR_RS31210 AZOBR_RS31245
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase AZOBR_RS32240 AZOBR_RS28580
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
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) AZOBR_RS27940 AZOBR_RS31200
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) AZOBR_RS27940
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT AZOBR_RS31245 AZOBR_RS31210
tpi triose-phosphate isomerase AZOBR_RS03885 AZOBR_RS30960

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:

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