GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Desulfoscipio geothermicus DSM 3669

Best path

glt

Rules

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

27 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glt aspartate:proton symporter Glt
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) BM299_RS18040
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BM299_RS08585 BM299_RS18035
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) BM299_RS18040 BM299_RS05465
aatP aspartate/asparagine ABC transporter, ATPase component BM299_RS00225 BM299_RS18035
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BM299_RS00230 BM299_RS18040
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA BM299_RS05470 BM299_RS00225
bgtB' aspartate ABC transporter, permease component 1 (BgtB)
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) BM299_RS08585 BM299_RS18035
dauA dicarboxylic acid transporter DauA
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) BM299_RS18040 BM299_RS00230
natH aspartate ABC transporter, permease component 2 (NatH) BM299_RS18040 BM299_RS05465
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BM299_RS05465 BM299_RS18040
peb1C aspartate ABC transporter, ATPase component Peb1C BM299_RS18035 BM299_RS00225
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BM299_RS18040
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 Apr 09 2024. 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:

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