GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Pseudomonas fluorescens GW456-L13

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
rhaT L-rhamnose:H+ symporter RhaT
LRA1 L-rhamnofuranose dehydrogenase PfGW456L13_3499 PfGW456L13_4129
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase PfGW456L13_3930 PfGW456L13_3478
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase PfGW456L13_3931
aldA lactaldehyde dehydrogenase PfGW456L13_3932 PfGW456L13_2360
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component PfGW456L13_2122
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component PfGW456L13_3911 PfGW456L13_2121
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase PfGW456L13_1214 PfGW456L13_3512
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase PfGW456L13_2105 PfGW456L13_3426
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase PfGW456L13_3411 PfGW456L13_3396
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) PfGW456L13_2122 PfGW456L13_3910
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) PfGW456L13_2122
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT PfGW456L13_2121 PfGW456L13_3911
tpi triose-phosphate isomerase PfGW456L13_5091 PfGW456L13_1066

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:

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