GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Pseudomonas fluorescens GW456-L13

Best path

aatJ, aatQ, aatM, aatP

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ PfGW456L13_4770 PfGW456L13_1042
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) PfGW456L13_4771 PfGW456L13_4772
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) PfGW456L13_4772 PfGW456L13_1700
aatP aspartate/asparagine ABC transporter, ATPase component PfGW456L13_4773 PfGW456L13_1701
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PfGW456L13_1698
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PfGW456L13_1700 PfGW456L13_4772
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PfGW456L13_1701 PfGW456L13_4773
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PfGW456L13_1699
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA PfGW456L13_1701 PfGW456L13_4773
bgtB' aspartate ABC transporter, permease component 1 (BgtB) PfGW456L13_1699 PfGW456L13_3607
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter PfGW456L13_3582
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA PfGW456L13_1698
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) PfGW456L13_1699
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) PfGW456L13_1700 PfGW456L13_3607
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) PfGW456L13_1701 PfGW456L13_4773
dauA dicarboxylic acid transporter DauA PfGW456L13_643
glt aspartate:proton symporter Glt PfGW456L13_578 PfGW456L13_2016
natF aspartate ABC transporter, substrate-binding component NatF PfGW456L13_1698
natG aspartate ABC transporter, permease component 1 (NatG) PfGW456L13_1699 PfGW456L13_4771
natH aspartate ABC transporter, permease component 2 (NatH) PfGW456L13_1700 PfGW456L13_4772
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A PfGW456L13_444
peb1B aspartate ABC transporter, permease component 1 (Peb1B) PfGW456L13_445 PfGW456L13_877
peb1C aspartate ABC transporter, ATPase component Peb1C PfGW456L13_1701 PfGW456L13_4773
peb1D aspartate ABC transporter, permease component 2 (Peb1D) PfGW456L13_4772 PfGW456L13_445
SLC7A13 sodium-independent aspartate transporter
yveA aspartate:proton symporter YveA PfGW456L13_3582

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