GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_4527 Pf1N1B4_5039
LRA2 L-rhamnono-gamma-lactonase
LRA3 L-rhamnonate dehydratase Pf1N1B4_5693 Pf1N1B4_3383
LRA4 2-keto-3-deoxy-L-rhamnonate aldolase Pf1N1B4_5694
aldA lactaldehyde dehydrogenase Pf1N1B4_5695 Pf1N1B4_171
Alternative steps:
BPHYT_RS34240 L-rhamnose ABC transporter, permease component Pf1N1B4_409
BPHYT_RS34245 L-rhamnose ABC transporter, ATPase component Pf1N1B4_4286 Pf1N1B4_6034
BPHYT_RS34250 L-rhamnose ABC transporter, substrate-binding component
Echvi_1617 L-rhamnose transporter
fucO L-lactaldehyde reductase Pf1N1B4_3270 Pf1N1B4_2542
LRA5 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase Pf1N1B4_5039 Pf1N1B4_451
LRA6 2,4-diketo-3-deoxyrhamnonate hydrolase Pf1N1B4_5706 Pf1N1B4_2275
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) Pf1N1B4_4287 Pf1N1B4_409
rhaQ L-rhamnose ABC transporter, permease component 2 (RhaQ) Pf1N1B4_409
rhaS L-rhamnose ABC transporter, substrate-binding component RhaS
rhaT' L-rhamnose ABC transporter, ATPase component RhaT Pf1N1B4_4286 Pf1N1B4_410
tpi triose-phosphate isomerase Pf1N1B4_1164 Pf1N1B4_2399

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 Aug 02 2021. The underlying query database was built on Aug 02 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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