GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

ans, aapJ, aapQ, aapM, aapP

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase CEV31_RS14335 CEV31_RS18295
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ CEV31_RS09895
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CEV31_RS09900 CEV31_RS19045
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) CEV31_RS09905 CEV31_RS08815
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CEV31_RS09910 CEV31_RS19030
Alternative steps:
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ CEV31_RS09375
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) CEV31_RS19045 CEV31_RS13485
aatP aspartate/asparagine ABC transporter, ATPase component CEV31_RS19030 CEV31_RS09910
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) CEV31_RS19045 CEV31_RS17385
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP CEV31_RS18290 CEV31_RS20665
bgtA aspartate ABC transporter, ATPase component BgtA CEV31_RS17400 CEV31_RS19030
bgtB' aspartate ABC transporter, permease component 1 (BgtB) CEV31_RS09900
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA CEV31_RS09895
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) CEV31_RS09900
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) CEV31_RS09905
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) CEV31_RS09910 CEV31_RS19030
dauA dicarboxylic acid transporter DauA CEV31_RS13165
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ CEV31_RS19030 CEV31_RS09910
glt aspartate:proton symporter Glt CEV31_RS14880
natF aspartate ABC transporter, substrate-binding component NatF CEV31_RS09895
natG aspartate ABC transporter, permease component 1 (NatG) CEV31_RS19045 CEV31_RS18470
natH aspartate ABC transporter, permease component 2 (NatH) CEV31_RS09905 CEV31_RS19045
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A CEV31_RS01760
peb1B aspartate ABC transporter, permease component 1 (Peb1B) CEV31_RS17385 CEV31_RS20530
peb1C aspartate ABC transporter, ATPase component Peb1C CEV31_RS19030 CEV31_RS09910
peb1D aspartate ABC transporter, permease component 2 (Peb1D) CEV31_RS17390 CEV31_RS17385
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 24 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:

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