GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Dyella japonica UNC79MFTsu3.2

Best path

BPHYT_RS17540

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 (8 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter N515DRAFT_4366
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP N515DRAFT_1085 N515DRAFT_1562
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM)
aatP aspartate/asparagine ABC transporter, ATPase component N515DRAFT_1085 N515DRAFT_1562
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ)
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA N515DRAFT_1562 N515DRAFT_1821
bgtB' aspartate ABC transporter, permease component 1 (BgtB)
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) N515DRAFT_1562 N515DRAFT_1821
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt N515DRAFT_0013 N515DRAFT_1080
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG)
natH aspartate ABC transporter, permease component 2 (NatH)
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B)
peb1C aspartate ABC transporter, ATPase component Peb1C N515DRAFT_1085 N515DRAFT_1562
peb1D aspartate ABC transporter, permease component 2 (Peb1D)
SLC7A13 sodium-independent aspartate transporter
yveA aspartate:proton symporter YveA N515DRAFT_4366

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, 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