GapMind for catabolism of small carbon sources

 

Definition of L-asparagine catabolism

As rules and steps, or see full text

Rules

Overview: Asparagine catabolism in GapMind is based on asparaginase, which forms ammonia and aspartate. The asparaginase may be secreted or cytoplasmic. Asparatate can be transaminated to oxaloacetate, which is an intermediate in central metabolism.

Steps

bztA: aspartate/asparagine ABC transporter, substrate-binding component BztA

bztB: aspartate/asparagine ABC transporter, permease component 1 (BztB)

bztC: aspartate/asparagine ABC transporter, permease component 2 (BztC)

bztD: aspartate/asparagine ABC transporter, ATPase component (BztD)

aatJ: aspartate/asparagine ABC transporter, substrate-binding component AatJ

aatQ: aspartate/asparagine ABC transporter, permease component 1 (AatQ)

aatM: aspartate/asparagine ABC transporter, permease component 2 (AatM)

aatP: aspartate/asparagine ABC transporter, ATPase component

glnQ: L-asparagine ABC transporter, ATPase component GlnQ

glnP: L-asparagine ABC transporter, fused permease and substrate-binding components GlnP

aapJ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ

aapQ: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)

aapM: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)

aapP: ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP

ansP: L-asparagine permease AnsP

AGP1: L-asparagine permease AGP1

yhiT: probable L-asparagine transporter YhiT

agcS: Probable asparagine:Na+ symporter AgcS

peb1A: aspartate ABC transporter, perisplasmic substrate-binding component Peb1A

peb1B: aspartate ABC transporter, permease component 1 (Peb1B)

peb1C: aspartate ABC transporter, ATPase component Peb1C

peb1D: aspartate ABC transporter, permease component 2 (Peb1D)

natF: aspartate ABC transporter, substrate-binding component NatF

bgtB': aspartate ABC transporter, permease component 1 (BgtB)

natH: aspartate ABC transporter, permease component 2 (NatH)

bgtA: aspartate ABC transporter, ATPase component BgtA

natG: aspartate ABC transporter, permease component 1 (NatG)

glt: aspartate:proton symporter Glt

acaP: aspartate permease AcaP

SLC7A13: sodium-independent aspartate transporter

BPHYT_RS17540: aspartate:H+ (or asparagine) symporter

yveA: aspartate:proton symporter YveA

dauA: dicarboxylic acid transporter DauA

ans: asparaginase

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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