GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Sinorhizobium meliloti 1021

Best path

aapJ, aapQ, aapM, aapP

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ SMc02118 SMc00676
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) SMc02119 SMc03865
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) SMc02120 SMc03865
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SMc02121 SMc03135
Alternative steps:
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) SMc03133 SMc02120
aatP aspartate/asparagine ABC transporter, ATPase component SMc02121 SMc03135
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) SMc03865 SMa0079
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA SMc03135 SMa0083
bgtB' aspartate ABC transporter, permease component 1 (BgtB) SMc02119 SMa2197
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA SMc02118 SMc00676
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) SMc02119 SMc03133
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) SMc02120 SMc00139
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) SMc02121 SMc03135
dauA dicarboxylic acid transporter DauA SMc00476
glt aspartate:proton symporter Glt SM_b20611
natF aspartate ABC transporter, substrate-binding component NatF SMc02118 SMc00676
natG aspartate ABC transporter, permease component 1 (NatG) SMc03865 SM_b21136
natH aspartate ABC transporter, permease component 2 (NatH) SMc02120 SMc03865
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) SMc03893 SM_b21136
peb1C aspartate ABC transporter, ATPase component Peb1C SMc02121 SMa0083
peb1D aspartate ABC transporter, permease component 2 (Peb1D) SM_b21137 SMc02120
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