GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Cupriavidus basilensis 4G11

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase RR42_RS26140 RR42_RS12610
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ RR42_RS02575 RR42_RS04390
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) RR42_RS02580 RR42_RS31740
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) RR42_RS02585 RR42_RS04400
aatP aspartate/asparagine ABC transporter, ATPase component RR42_RS02590 RR42_RS16370
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) RR42_RS27120 RR42_RS09485
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RR42_RS16370 RR42_RS02590
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) RR42_RS31740 RR42_RS16450
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1 RR42_RS33495
ansP L-asparagine permease AnsP RR42_RS28305 RR42_RS33495
bgtA aspartate ABC transporter, ATPase component BgtA RR42_RS16370 RR42_RS16445
bgtB' aspartate ABC transporter, permease component 1 (BgtB) RR42_RS02580 RR42_RS09485
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter RR42_RS36375
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) RR42_RS02585
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) RR42_RS04400
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) RR42_RS16370 RR42_RS02590
dauA dicarboxylic acid transporter DauA RR42_RS16025
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ RR42_RS31735 RR42_RS07815
glt aspartate:proton symporter Glt RR42_RS03990 RR42_RS26130
natF aspartate ABC transporter, substrate-binding component NatF
natG aspartate ABC transporter, permease component 1 (NatG) RR42_RS02580 RR42_RS31740
natH aspartate ABC transporter, permease component 2 (NatH) RR42_RS02585 RR42_RS09485
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) RR42_RS04400 RR42_RS09485
peb1C aspartate ABC transporter, ATPase component Peb1C RR42_RS16370 RR42_RS02590
peb1D aspartate ABC transporter, permease component 2 (Peb1D) RR42_RS02585 RR42_RS27120
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA RR42_RS36375

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