GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Collimonas arenae Ter10

Best path

rhaT, LRA1, LRA2, LRA3, LRA5, LRA6

Rules

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
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase CAter10_RS16300 CAter10_RS07600
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase CAter10_RS16170 CAter10_RS19065
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase CAter10_RS10670 CAter10_RS05885
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase CAter10_RS05890 CAter10_RS10000
Alternative steps:
aldA lactaldehyde dehydrogenase CAter10_RS21305 CAter10_RS08205
BPHYT_RS34240 L-rhamnose ABC transporter, permease component CAter10_RS06725 CAter10_RS12715
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component CAter10_RS12710 CAter10_RS05910
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase
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) CAter10_RS06725 CAter10_RS05915
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) CAter10_RS05915 CAter10_RS06725
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT CAter10_RS05910 CAter10_RS06720
tpi triose-phosphate isomerase CAter10_RS13300 CAter10_RS18070

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