GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Phaeobacter inhibens BS107

Best path

rhaT, LRA1, LRA2, LRA3, LRA4, aldA

Also see fitness data for the top candidates

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 (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase PGA1_c27390 PGA1_c13170
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase PGA1_c31400 PGA1_c19370
aldA lactaldehyde dehydrogenase PGA1_c21070 PGA1_c32800
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component PGA1_c23080
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component PGA1_c23060 PGA1_c03960
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase PGA1_c27200 PGA1_c23360
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase PGA1_c31980 PGA1_c07730
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase PGA1_c04530 PGA1_c32200
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) PGA1_c28050 PGA1_262p00440
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) PGA1_c23080 PGA1_c28050
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT PGA1_c23060 PGA1_c26910
tpi triose-phosphate isomerase PGA1_c20650 PGA1_c17530

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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