GapMind for catabolism of small carbon sources


L-rhamnose catabolism in Algoriphagus machipongonensis PR1

Best path

Echvi_1617, 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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1617 L-rhamnose transporter ALPR1_RS05650
rhaM L-rhamnose mutarotase ALPR1_RS09260
rhaA L-rhamnose isomerase ALPR1_RS05660
rhaB L-rhamnulokinase ALPR1_RS05635
rhaD rhamnulose 1-phosphate aldolase ALPR1_RS05645 ALPR1_RS05690
tpi triose-phosphate isomerase ALPR1_RS03020 ALPR1_RS05050
aldA lactaldehyde dehydrogenase ALPR1_RS05645 ALPR1_RS05690
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
fucO L-lactaldehyde reductase
LRA1 L-rhamnofuranose dehydrogenase ALPR1_RS18920 ALPR1_RS17925
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase ALPR1_RS11090
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase ALPR1_RS17925 ALPR1_RS06100
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase ALPR1_RS13845 ALPR1_RS13065
rhaP L-rhamnose ABC transporter, permease component 1 (RhaP)
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ)
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT L-rhamnose:H+ symporter RhaT
rhaT' L-rhamnose ABC transporter, ATPase component 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