GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Herbaspirillum seropedicae SmR1

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ HSERO_RS17575 HSERO_RS19255
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) HSERO_RS17565 HSERO_RS19250
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) HSERO_RS17560 HSERO_RS19245
aatP aspartate/asparagine ABC transporter, ATPase component HSERO_RS19240 HSERO_RS17555
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) HSERO_RS07530 HSERO_RS23030
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HSERO_RS19240 HSERO_RS17555
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HSERO_RS19340 HSERO_RS17565
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA HSERO_RS00320 HSERO_RS05835
bgtB' aspartate ABC transporter, permease component 1 (BgtB) HSERO_RS17565 HSERO_RS23035
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) HSERO_RS17560
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) HSERO_RS07530
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) HSERO_RS17555 HSERO_RS19240
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt HSERO_RS19090 HSERO_RS13105
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) HSERO_RS21620 HSERO_RS11445
natH aspartate ABC transporter, permease component 2 (NatH) HSERO_RS17560 HSERO_RS11445
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A HSERO_RS10775
peb1B aspartate ABC transporter, permease component 1 (Peb1B) HSERO_RS10770 HSERO_RS07530
peb1C aspartate ABC transporter, ATPase component Peb1C HSERO_RS00320 HSERO_RS19240
peb1D aspartate ABC transporter, permease component 2 (Peb1D) HSERO_RS17560 HSERO_RS19245
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