GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Klebsiella michiganensis M5al

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BWI76_RS08110
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BWI76_RS08105 BWI76_RS05950
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BWI76_RS08100 BWI76_RS18355
aatP aspartate/asparagine ABC transporter, ATPase component BWI76_RS08095 BWI76_RS08965
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) BWI76_RS18355 BWI76_RS07580
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BWI76_RS08095 BWI76_RS08965
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 BWI76_RS08095 BWI76_RS16795
bgtB' aspartate ABC transporter, permease component 1 (BgtB) BWI76_RS12840
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) BWI76_RS18355
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BWI76_RS08095 BWI76_RS08965
dauA dicarboxylic acid transporter DauA BWI76_RS17465
glt aspartate:proton symporter Glt BWI76_RS02105 BWI76_RS26760
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) BWI76_RS08105 BWI76_RS18355
natH aspartate ABC transporter, permease component 2 (NatH) BWI76_RS08100 BWI76_RS05945
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A BWI76_RS05960
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BWI76_RS18355 BWI76_RS10375
peb1C aspartate ABC transporter, ATPase component Peb1C BWI76_RS08095 BWI76_RS16795
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BWI76_RS08100 BWI76_RS10375
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 (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 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