GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Marinomonas arctica 328

Best path

rhaP, rhaQ, rhaS, 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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP) DK187_RS16465 DK187_RS05065
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) DK187_RS16460 DK187_RS19180
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS DK187_RS16475
rhaT' L-rhamnose ABC transporter, ATPase component RhaT DK187_RS16470 DK187_RS04275
rhaM L-rhamnose mutarotase DK187_RS16455
rhaA L-rhamnose isomerase DK187_RS16490
rhaB L-rhamnulokinase DK187_RS16455
rhaD rhamnulose 1-phosphate aldolase DK187_RS16485
tpi triose-phosphate isomerase DK187_RS01615 DK187_RS05025
aldA lactaldehyde dehydrogenase DK187_RS16485 DK187_RS17920
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component DK187_RS19180
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component DK187_RS01090 DK187_RS16470
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase DK187_RS00285
LRA1 L-rhamnofuranose dehydrogenase DK187_RS09365 DK187_RS13080
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase DK187_RS15790
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase DK187_RS13080 DK187_RS06280
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase DK187_RS05505 DK187_RS19500
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 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