GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Herbaspirillum seropedicae SmR1

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) HSERO_RS22215 HSERO_RS03645
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) HSERO_RS22210 HSERO_RS05325
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS HSERO_RS22225 HSERO_RS05095
rhaT' L-rhamnose ABC transporter, ATPase component RhaT HSERO_RS22220 HSERO_RS05250
rhaM L-rhamnose mutarotase HSERO_RS22205
rhaA L-rhamnose isomerase HSERO_RS22240
rhaB L-rhamnulokinase HSERO_RS22200
rhaD rhamnulose 1-phosphate aldolase HSERO_RS22235
tpi triose-phosphate isomerase HSERO_RS08805 HSERO_RS03345
aldA lactaldehyde dehydrogenase HSERO_RS22235 HSERO_RS09465
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component HSERO_RS22215 HSERO_RS05325
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component HSERO_RS22220 HSERO_RS05175
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase HSERO_RS00730
LRA1 L-rhamnofuranose dehydrogenase HSERO_RS02535 HSERO_RS05565
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase HSERO_RS19355 HSERO_RS15800
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase HSERO_RS01600
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase HSERO_RS06350 HSERO_RS02925
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase HSERO_RS06355 HSERO_RS17860
rhaT L-rhamnose:H+ symporter RhaT

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