GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA


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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
rhaM L-rhamnose mutarotase CEV31_RS06785
rhaA L-rhamnose isomerase
rhaB L-rhamnulokinase
rhaD rhamnulose 1-phosphate aldolase CEV31_RS16855
tpi triose-phosphate isomerase CEV31_RS12005 CEV31_RS08925
aldA lactaldehyde dehydrogenase CEV31_RS01730 CEV31_RS16855
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component CEV31_RS09010 CEV31_RS19245
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component CEV31_RS08760 CEV31_RS19250
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase CEV31_RS17940 CEV31_RS09095
LRA1 L-rhamnofuranose dehydrogenase CEV31_RS19170 CEV31_RS03445
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase CEV31_RS18535 CEV31_RS15470
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase CEV31_RS10450
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase CEV31_RS08050 CEV31_RS00350
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase CEV31_RS06805 CEV31_RS17405
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) CEV31_RS19245 CEV31_RS20785
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) CEV31_RS18895 CEV31_RS20360
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT CEV31_RS17255 CEV31_RS19250

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 24 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