GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Paraburkholderia bryophila 376MFSha3.1

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase H281DRAFT_00783 H281DRAFT_04915
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ H281DRAFT_04270 H281DRAFT_02625
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) H281DRAFT_04269 H281DRAFT_03349
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) H281DRAFT_04268 H281DRAFT_02563
aatP aspartate/asparagine ABC transporter, ATPase component H281DRAFT_04267 H281DRAFT_02565
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) H281DRAFT_05402 H281DRAFT_04268
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H281DRAFT_04267 H281DRAFT_02565
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H281DRAFT_03349 H281DRAFT_04269
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1 H281DRAFT_04042
ansP L-asparagine permease AnsP H281DRAFT_04042 H281DRAFT_01668
bgtA aspartate ABC transporter, ATPase component BgtA H281DRAFT_04267 H281DRAFT_02573
bgtB' aspartate ABC transporter, permease component 1 (BgtB) H281DRAFT_00383
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter H281DRAFT_05687
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) H281DRAFT_04268
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) H281DRAFT_04267 H281DRAFT_02565
dauA dicarboxylic acid transporter DauA H281DRAFT_01715
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ H281DRAFT_04267 H281DRAFT_03348
glt aspartate:proton symporter Glt H281DRAFT_02039 H281DRAFT_01363
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) H281DRAFT_05872 H281DRAFT_04269
natH aspartate ABC transporter, permease component 2 (NatH) H281DRAFT_03349 H281DRAFT_04268
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) H281DRAFT_05872 H281DRAFT_00741
peb1C aspartate ABC transporter, ATPase component Peb1C H281DRAFT_04267 H281DRAFT_02565
peb1D aspartate ABC transporter, permease component 2 (Peb1D) H281DRAFT_05872 H281DRAFT_05299
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA H281DRAFT_05687

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