GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Dinoroseobacter shibae DFL-12

Best path

bztA, bztB, bztC, bztD

Also see fitness data for the top candidates

Rules

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

27 steps (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA Dshi_0318
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) Dshi_0319
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) Dshi_0320
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) Dshi_0321 Dshi_2221
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) Dshi_0320 Dshi_0319
aatP aspartate/asparagine ABC transporter, ATPase component Dshi_0321 Dshi_2221
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) Dshi_0319
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA Dshi_0321 Dshi_2221
bgtB' aspartate ABC transporter, permease component 1 (BgtB) Dshi_0319
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt
natF aspartate ABC transporter, substrate-binding component NatF Dshi_0318
natG aspartate ABC transporter, permease component 1 (NatG) Dshi_0319
natH aspartate ABC transporter, permease component 2 (NatH) Dshi_0320
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B)
peb1C aspartate ABC transporter, ATPase component Peb1C Dshi_0321 Dshi_2221
peb1D aspartate ABC transporter, permease component 2 (Peb1D)
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, 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