GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Burkholderia phytofirmans PsJN

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase BPHYT_RS08815 BPHYT_RS07040
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ BPHYT_RS16700 BPHYT_RS29570
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) BPHYT_RS16695 BPHYT_RS34465
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) BPHYT_RS16690 BPHYT_RS34460
aatP aspartate/asparagine ABC transporter, ATPase component BPHYT_RS16685 BPHYT_RS34455
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BPHYT_RS24645 BPHYT_RS34460
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BPHYT_RS16685 BPHYT_RS34455
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BPHYT_RS21915 BPHYT_RS16695
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1 BPHYT_RS15500
ansP L-asparagine permease AnsP BPHYT_RS15500 BPHYT_RS21680
bgtA aspartate ABC transporter, ATPase component BgtA BPHYT_RS34455 BPHYT_RS16685
bgtB' aspartate ABC transporter, permease component 1 (BgtB) BPHYT_RS13290 BPHYT_RS34465
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter BPHYT_RS17540
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) BPHYT_RS16690 BPHYT_RS13290
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) BPHYT_RS16685 BPHYT_RS34455
dauA dicarboxylic acid transporter DauA
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ BPHYT_RS34455 BPHYT_RS16685
glt aspartate:proton symporter Glt BPHYT_RS33330 BPHYT_RS02510
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) BPHYT_RS16695 BPHYT_RS34465
natH aspartate ABC transporter, permease component 2 (NatH) BPHYT_RS16690 BPHYT_RS21915
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) BPHYT_RS08555 BPHYT_RS21915
peb1C aspartate ABC transporter, ATPase component Peb1C BPHYT_RS16685 BPHYT_RS34455
peb1D aspartate ABC transporter, permease component 2 (Peb1D) BPHYT_RS24045 BPHYT_RS16690
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA BPHYT_RS17540

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 paper from 2022 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