GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Synechococcus elongatus PCC 7942

Best path

natF, bgtB', natH, bgtA

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natF aspartate ABC transporter, substrate-binding component NatF Synpcc7942_0246
bgtB' aspartate ABC transporter, permease component 1 (BgtB) Synpcc7942_0247
natH aspartate ABC transporter, permease component 2 (NatH) Synpcc7942_0248
bgtA aspartate ABC transporter, ATPase component BgtA Synpcc7942_0249 Synpcc7942_1414
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Synpcc7942_0246
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Synpcc7942_0248
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Synpcc7942_0249 Synpcc7942_1680
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Synpcc7942_0247
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) Synpcc7942_0248 Synpcc7942_0247
aatP aspartate/asparagine ABC transporter, ATPase component Synpcc7942_0249 Synpcc7942_1414
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) Synpcc7942_0248
acaP aspartate permease AcaP
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA Synpcc7942_0246
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) Synpcc7942_0247
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) Synpcc7942_0248
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) Synpcc7942_0249 Synpcc7942_1680
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt
natG aspartate ABC transporter, permease component 1 (NatG) Synpcc7942_0248
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) Synpcc7942_0248 Synpcc7942_0247
peb1C aspartate ABC transporter, ATPase component Peb1C Synpcc7942_0249 Synpcc7942_1680
peb1D aspartate ABC transporter, permease component 2 (Peb1D) Synpcc7942_0248
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.

Links

Downloads

Related tools

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