GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Desulfovibrio vulgaris Hildenborough

Best path

dauA

Rules

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

27 steps (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
dauA dicarboxylic acid transporter DauA DVU0279
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DVU2342
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DVU0967 DVU0751
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DVU0753 DVU2343
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DVU2341
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ DVU2342 DVU0752
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) DVU0967 DVU2340
aatP aspartate/asparagine ABC transporter, ATPase component DVU2343 DVU0753
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) DVU2341 DVU0751
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA DVU2343 DVU0753
bgtB' aspartate ABC transporter, permease component 1 (BgtB) DVU2340
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) DVU0751 DVU0676
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) DVU0751
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) DVU0753 DVU2343
glt aspartate:proton symporter Glt
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) DVU2341 DVU0967
natH aspartate ABC transporter, permease component 2 (NatH) DVU0751 DVU2340
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A DVU2342
peb1B aspartate ABC transporter, permease component 1 (Peb1B) DVU0751 DVU2341
peb1C aspartate ABC transporter, ATPase component Peb1C DVU0105 DVU0753
peb1D aspartate ABC transporter, permease component 2 (Peb1D) DVU0751
SLC7A13 sodium-independent aspartate transporter
yveA aspartate:proton symporter YveA

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 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, the preprint on GapMind for carbon sources, 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