GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Photobacterium gaetbulicola Gung47

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
glt aspartate:proton symporter Glt H744_RS22180 H744_RS25105
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ H744_RS20715 H744_RS06585
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H744_RS20725 H744_RS06575
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H744_RS20730 H744_RS06570
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H744_RS20720 H744_RS06580
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) H744_RS06575 H744_RS20725
aatP aspartate/asparagine ABC transporter, ATPase component H744_RS20730 H744_RS06570
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) H744_RS04745 H744_RS06575
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA H744_RS06570 H744_RS20730
bgtB' aspartate ABC transporter, permease component 1 (BgtB) H744_RS06580 H744_RS20720
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA H744_RS20715 H744_RS06585
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) H744_RS20720 H744_RS06580
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) H744_RS06575 H744_RS20725
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) H744_RS20730 H744_RS06570
dauA dicarboxylic acid transporter DauA H744_RS13655
natF aspartate ABC transporter, substrate-binding component NatF H744_RS20715 H744_RS06585
natG aspartate ABC transporter, permease component 1 (NatG) H744_RS20720 H744_RS04745
natH aspartate ABC transporter, permease component 2 (NatH) H744_RS20725 H744_RS06575
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) H744_RS04735 H744_RS10300
peb1C aspartate ABC transporter, ATPase component Peb1C H744_RS20730 H744_RS06570
peb1D aspartate ABC transporter, permease component 2 (Peb1D) H744_RS04735 H744_RS20725
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