GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Pseudomonas simiae WCS417

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase PS417_18410 PS417_28140
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ PS417_05560 PS417_26550
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) PS417_05555 PS417_01810
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) PS417_05550 PS417_04910
aatP aspartate/asparagine ABC transporter, ATPase component PS417_05545 PS417_04915
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PS417_23345 PS417_04900
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PS417_04910 PS417_01810
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PS417_04915 PS417_26115
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PS417_04905
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS PS417_28135
AGP1 L-asparagine permease AGP1 PS417_23700 PS417_22235
ansP L-asparagine permease AnsP PS417_05405 PS417_01755
bgtA aspartate ABC transporter, ATPase component BgtA PS417_04915 PS417_26115
bgtB' aspartate ABC transporter, permease component 1 (BgtB) PS417_04905 PS417_18935
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter PS417_14300
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA PS417_23345 PS417_04900
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) PS417_04905
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) PS417_04910
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) PS417_04915 PS417_26115
dauA dicarboxylic acid transporter DauA PS417_00130
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ PS417_01815 PS417_15490
glt aspartate:proton symporter Glt PS417_19045 PS417_00470
natF aspartate ABC transporter, substrate-binding component NatF PS417_23345 PS417_04900
natG aspartate ABC transporter, permease component 1 (NatG) PS417_04905 PS417_21785
natH aspartate ABC transporter, permease component 2 (NatH) PS417_04910 PS417_01810
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) PS417_12105 PS417_01100
peb1C aspartate ABC transporter, ATPase component Peb1C PS417_04915 PS417_01815
peb1D aspartate ABC transporter, permease component 2 (Peb1D) PS417_05550 PS417_01100
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA PS417_14300

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 (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 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