GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Limnohabitans curvus MWH-C5

Best path

aatJ, aatQ, aatM, aatP

Rules

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

27 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ B9Z44_RS09140
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) B9Z44_RS09145
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) B9Z44_RS09150
aatP aspartate/asparagine ABC transporter, ATPase component B9Z44_RS09155 B9Z44_RS03630
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9Z44_RS09150
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9Z44_RS09155 B9Z44_RS03630
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA B9Z44_RS09155 B9Z44_RS03630
bgtB' aspartate ABC transporter, permease component 1 (BgtB) B9Z44_RS09150
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB)
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC)
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) B9Z44_RS09155 B9Z44_RS03630
dauA dicarboxylic acid transporter DauA B9Z44_RS04690
glt aspartate:proton symporter Glt B9Z44_RS08260
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) B9Z44_RS09145
natH aspartate ABC transporter, permease component 2 (NatH) B9Z44_RS09150
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) B9Z44_RS09150 B9Z44_RS09145
peb1C aspartate ABC transporter, ATPase component Peb1C B9Z44_RS09155 B9Z44_RS03630
peb1D aspartate ABC transporter, permease component 2 (Peb1D) B9Z44_RS09150
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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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