GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

ans, aatJ, aatQ, aatM, aatP

Also see fitness data for the top candidates

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.

34 steps (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase Pf6N2E2_4087 Pf6N2E2_2102
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ Pf6N2E2_5570
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) Pf6N2E2_5569 Pf6N2E2_5568
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) Pf6N2E2_5568 Pf6N2E2_5404
aatP aspartate/asparagine ABC transporter, ATPase component Pf6N2E2_5567 Pf6N2E2_5405
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf6N2E2_5402
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf6N2E2_5404 Pf6N2E2_1799
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf6N2E2_5405 Pf6N2E2_5567
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf6N2E2_5403
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS Pf6N2E2_4086
AGP1 L-asparagine permease AGP1 Pf6N2E2_5633
ansP L-asparagine permease AnsP Pf6N2E2_5459 Pf6N2E2_5633
bgtA aspartate ABC transporter, ATPase component BgtA Pf6N2E2_5405 Pf6N2E2_5567
bgtB' aspartate ABC transporter, permease component 1 (BgtB) Pf6N2E2_5403 Pf6N2E2_4281
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA Pf6N2E2_5402
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) Pf6N2E2_5403
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) Pf6N2E2_5404 Pf6N2E2_3404
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) Pf6N2E2_5405 Pf6N2E2_5567
dauA dicarboxylic acid transporter DauA Pf6N2E2_5239 Pf6N2E2_4131
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ Pf6N2E2_5567 Pf6N2E2_1800
glt aspartate:proton symporter Glt Pf6N2E2_2249 Pf6N2E2_4148
natF aspartate ABC transporter, substrate-binding component NatF Pf6N2E2_5402
natG aspartate ABC transporter, permease component 1 (NatG) Pf6N2E2_5403 Pf6N2E2_1799
natH aspartate ABC transporter, permease component 2 (NatH) Pf6N2E2_5404 Pf6N2E2_5568
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) Pf6N2E2_2051 Pf6N2E2_3920
peb1C aspartate ABC transporter, ATPase component Peb1C Pf6N2E2_5405 Pf6N2E2_1800
peb1D aspartate ABC transporter, permease component 2 (Peb1D) Pf6N2E2_2052 Pf6N2E2_5568
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
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 17 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 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, the preprint on GapMind for carbon sources, 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