GapMind for catabolism of small carbon sources

 

Definition of L-aspartate catabolism

As rules and steps, or see full text

Rules

Overview: Aspartate can be transaminated to oxaloacetate, which is an intermediate in central metabolism, so GapMind only represents uptake.

Steps

bztA: aspartate/asparagine ABC transporter, substrate-binding component BztA

bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB)

bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC)

bztD: aspartate/asparagine ABC transporter, ATPase component (BztD)

peb1A: aspartate ABC transporter, perisplasmic substrate-binding component Peb1A

peb1B: aspartate ABC transporter, permease component 1 (Peb1B)

peb1C: aspartate ABC transporter, ATPase component Peb1C

peb1D: aspartate ABC transporter, permease component 2 (Peb1D)

aatJ: aspartate/asparagine ABC transporter, substrate-binding component AatJ

aatQ: aspartate/asparagine ABC transporter, permease component 1 (AatQ)

aatM: aspartate/asparagine ABC transporter, permease component 2 (AatM)

aatP: aspartate/asparagine ABC transporter, ATPase component

natF: aspartate ABC transporter, substrate-binding component NatF

bgtB': aspartate ABC transporter, permease component 1 (BgtB)

natH: aspartate ABC transporter, permease component 2 (NatH)

bgtA: aspartate ABC transporter, ATPase component BgtA

natG: aspartate ABC transporter, permease component 1 (NatG)

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

glt: aspartate:proton symporter Glt

acaP: aspartate permease AcaP

SLC7A13: sodium-independent aspartate transporter

BPHYT_RS17540: aspartate:H+ (or asparagine) symporter

yveA: aspartate:proton symporter YveA

dauA: dicarboxylic acid transporter DauA

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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