GapMind for catabolism of small carbon sources

 

Definition of L-rhamnose catabolism

As rules and steps, or see full text

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).

Steps

rhaT: L-rhamnose:H+ symporter RhaT

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 ABC transporter, ATPase component RhaT

Echvi_1617: L-rhamnose transporter

BPHYT_RS34250: L-rhamnose ABC transporter, substrate-binding component

BPHYT_RS34245: L-rhamnose ABC transporter, ATPase component

BPHYT_RS34240: L-rhamnose ABC transporter, permease component

rhaM: L-rhamnose mutarotase

rhaA: L-rhamnose isomerase

rhaB: L-rhamnulokinase

rhaD: rhamnulose 1-phosphate aldolase

tpi: triose-phosphate isomerase

aldA: lactaldehyde dehydrogenase

fucO: L-lactaldehyde reductase

LRA1: L-rhamnofuranose dehydrogenase

LRA2: L-rhamnono-gamma-lactonase

LRA3: L-rhamnonate dehydratase

LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase

LRA5: 2-keto-3-deoxy-L-rhamnonate 4-dehydrogenase

LRA6: 2,4-diketo-3-deoxyrhamnonate hydrolase

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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