GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Pseudomonas fluorescens FW300-N2E3

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ AO353_16290 AO353_08055
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) AO353_16285 AO353_16280
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) AO353_16280 AO353_04605
aatP aspartate/asparagine ABC transporter, ATPase component AO353_16275 AO353_04600
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AO353_04615
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AO353_04605 AO353_12325
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AO353_04600 AO353_16275
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AO353_04610
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA AO353_04600 AO353_12330
bgtB' aspartate ABC transporter, permease component 1 (BgtB) AO353_04610 AO353_21715
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA AO353_04615
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) AO353_04610
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) AO353_04605
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) AO353_04600 AO353_16275
dauA dicarboxylic acid transporter DauA AO353_10315
glt aspartate:proton symporter Glt AO353_10990 AO353_02800
natF aspartate ABC transporter, substrate-binding component NatF AO353_04615
natG aspartate ABC transporter, permease component 1 (NatG) AO353_04610 AO353_25590
natH aspartate ABC transporter, permease component 2 (NatH) AO353_04605 AO353_12325
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A AO353_11675
peb1B aspartate ABC transporter, permease component 1 (Peb1B) AO353_21720 AO353_11670
peb1C aspartate ABC transporter, ATPase component Peb1C AO353_04600 AO353_11610
peb1D aspartate ABC transporter, permease component 2 (Peb1D) AO353_12325 AO353_16280
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