GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Pseudomonas benzenivorans DSM 8628

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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BLS63_RS18555
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BLS63_RS18550 BLS63_RS18545
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BLS63_RS18545 BLS63_RS08610
aatP aspartate/asparagine ABC transporter, ATPase component BLS63_RS18540 BLS63_RS08615
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLS63_RS08600
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLS63_RS08610 BLS63_RS18545
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLS63_RS08615 BLS63_RS23600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLS63_RS08605 BLS63_RS11280
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA BLS63_RS08615 BLS63_RS18540
bgtB' aspartate ABC transporter, permease component 1 (BgtB) BLS63_RS08605 BLS63_RS01120
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA BLS63_RS08600
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) BLS63_RS08605
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) BLS63_RS08610 BLS63_RS18545
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BLS63_RS08615 BLS63_RS23600
dauA dicarboxylic acid transporter DauA BLS63_RS23090 BLS63_RS15055
glt aspartate:proton symporter Glt BLS63_RS18495 BLS63_RS07270
natF aspartate ABC transporter, substrate-binding component NatF BLS63_RS08600
natG aspartate ABC transporter, permease component 1 (NatG) BLS63_RS08605 BLS63_RS18550
natH aspartate ABC transporter, permease component 2 (NatH) BLS63_RS08610 BLS63_RS11280
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BLS63_RS18550
peb1C aspartate ABC transporter, ATPase component Peb1C BLS63_RS08615 BLS63_RS23600
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BLS63_RS18545 BLS63_RS11280
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 24 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:

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