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 (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