GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Paraburkholderia atlantica CCGE1002

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BC1002_RS13140 BC1002_RS22510
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BC1002_RS13135 BC1002_RS16325
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BC1002_RS13130 BC1002_RS39380
aatP aspartate/asparagine ABC transporter, ATPase component BC1002_RS13125 BC1002_RS02010
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) BC1002_RS13130 BC1002_RS18870
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BC1002_RS13125 BC1002_RS02010
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BC1002_RS13135
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA BC1002_RS13125 BC1002_RS02010
bgtB' aspartate ABC transporter, permease component 1 (BgtB)
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter BC1002_RS13930
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) BC1002_RS13130
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) BC1002_RS13130
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BC1002_RS13125 BC1002_RS03950
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt BC1002_RS29195 BC1002_RS32910
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) BC1002_RS16325 BC1002_RS02005
natH aspartate ABC transporter, permease component 2 (NatH) BC1002_RS13130 BC1002_RS02005
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BC1002_RS02005 BC1002_RS06450
peb1C aspartate ABC transporter, ATPase component Peb1C BC1002_RS13125 BC1002_RS02010
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BC1002_RS02005 BC1002_RS18385
SLC7A13 sodium-independent aspartate transporter
yveA aspartate:proton symporter YveA BC1002_RS13930

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