GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Pseudomonas putida KT2440

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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase PP_2453 PP_0495
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ PP_1071
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) PP_1070 PP_5023
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) PP_1069 PP_1299
aatP aspartate/asparagine ABC transporter, ATPase component PP_1068 PP_1300
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PP_1297
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PP_1299 PP_1069
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PP_1300 PP_3597
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PP_1298 PP_5023
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS PP_0496
AGP1 L-asparagine permease AGP1 PP_0284 PP_4495
ansP L-asparagine permease AnsP PP_1059 PP_5031
bgtA aspartate ABC transporter, ATPase component BgtA PP_1300 PP_3597
bgtB' aspartate ABC transporter, permease component 1 (BgtB) PP_1298 PP_4749
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter PP_1259
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA PP_1297
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) PP_1298 PP_1070
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) PP_1299 PP_1069
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) PP_1300 PP_3597
dauA dicarboxylic acid transporter DauA PP_0075
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ PP_5022 PP_1068
glt aspartate:proton symporter Glt PP_0137 PP_1188
natF aspartate ABC transporter, substrate-binding component NatF PP_1297
natG aspartate ABC transporter, permease component 1 (NatG) PP_1298 PP_5023
natH aspartate ABC transporter, permease component 2 (NatH) PP_1299 PP_5023
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A PP_0227
peb1B aspartate ABC transporter, permease component 1 (Peb1B) PP_0226 PP_1070
peb1C aspartate ABC transporter, ATPase component Peb1C PP_1300 PP_3597
peb1D aspartate ABC transporter, permease component 2 (Peb1D) PP_1069 PP_5023
SLC7A13 sodium-independent aspartate transporter
yhiT probable L-asparagine transporter YhiT
yveA aspartate:proton symporter YveA PP_1259

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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