GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Paraburkholderia phymatum STM815

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BPHY_RS13055 BPHY_RS23805
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BPHY_RS13050 BPHY_RS35860
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BPHY_RS13045 BPHY_RS05855
aatP aspartate/asparagine ABC transporter, ATPase component BPHY_RS13040 BPHY_RS27405
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BPHY_RS29405
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BPHY_RS13045 BPHY_RS27410
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BPHY_RS13040 BPHY_RS27405
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BPHY_RS13050 BPHY_RS25820
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA BPHY_RS13040 BPHY_RS27405
bgtB' aspartate ABC transporter, permease component 1 (BgtB) BPHY_RS07800
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter BPHY_RS13860 BPHY_RS28885
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA BPHY_RS29405
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) BPHY_RS13045 BPHY_RS13050
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) BPHY_RS13045
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BPHY_RS13040 BPHY_RS27405
dauA dicarboxylic acid transporter DauA
glt aspartate:proton symporter Glt BPHY_RS31785 BPHY_RS28230
natF aspartate ABC transporter, substrate-binding component NatF BPHY_RS29405
natG aspartate ABC transporter, permease component 1 (NatG) BPHY_RS35860 BPHY_RS13050
natH aspartate ABC transporter, permease component 2 (NatH) BPHY_RS13045 BPHY_RS16495
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BPHY_RS33255 BPHY_RS27410
peb1C aspartate ABC transporter, ATPase component Peb1C BPHY_RS13040 BPHY_RS33260
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BPHY_RS33255 BPHY_RS13045
SLC7A13 sodium-independent aspartate transporter
yveA aspartate:proton symporter YveA BPHY_RS28885 BPHY_RS13860

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