GapMind for catabolism of small carbon sources

 

L-aspartate catabolism in Cereibacter sphaeroides ATCC 17029

Best path

bztA, bztB, bztC, bztD

Rules

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

27 steps (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA RSPH17029_RS02000 RSPH17029_RS18145
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) RSPH17029_RS02005 RSPH17029_RS18140
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) RSPH17029_RS02010 RSPH17029_RS18135
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) RSPH17029_RS02015 RSPH17029_RS18130
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ RSPH17029_RS18145 RSPH17029_RS02000
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) RSPH17029_RS18135 RSPH17029_RS02010
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RSPH17029_RS02015 RSPH17029_RS18130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RSPH17029_RS18140 RSPH17029_RS02005
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) RSPH17029_RS15650 RSPH17029_RS02010
aatP aspartate/asparagine ABC transporter, ATPase component RSPH17029_RS02015 RSPH17029_RS18130
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) RSPH17029_RS17505 RSPH17029_RS18140
acaP aspartate permease AcaP
bgtA aspartate ABC transporter, ATPase component BgtA RSPH17029_RS02015 RSPH17029_RS18130
bgtB' aspartate ABC transporter, permease component 1 (BgtB) RSPH17029_RS18140 RSPH17029_RS02005
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
dauA dicarboxylic acid transporter DauA RSPH17029_RS11255
glt aspartate:proton symporter Glt
natF aspartate ABC transporter, substrate-binding component NatF RSPH17029_RS02000 RSPH17029_RS18145
natG aspartate ABC transporter, permease component 1 (NatG) RSPH17029_RS02005 RSPH17029_RS18140
natH aspartate ABC transporter, permease component 2 (NatH) RSPH17029_RS02010 RSPH17029_RS18135
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) RSPH17029_RS17505 RSPH17029_RS18140
peb1C aspartate ABC transporter, ATPase component Peb1C RSPH17029_RS02015 RSPH17029_RS18130
peb1D aspartate ABC transporter, permease component 2 (Peb1D) RSPH17029_RS15650
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 10 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