GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Pseudomonas fluorescens FW300-N1B4

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase Pf1N1B4_2023 Pf1N1B4_6037
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ Pf1N1B4_771 Pf1N1B4_2375
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) Pf1N1B4_772 Pf1N1B4_773
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) Pf1N1B4_773 Pf1N1B4_915
aatP aspartate/asparagine ABC transporter, ATPase component Pf1N1B4_774 Pf1N1B4_914
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf1N1B4_917
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf1N1B4_915 Pf1N1B4_4805
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf1N1B4_914 Pf1N1B4_774
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf1N1B4_916 Pf1N1B4_772
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS Pf1N1B4_2024
AGP1 L-asparagine permease AGP1 Pf1N1B4_3559
ansP L-asparagine permease AnsP Pf1N1B4_801 Pf1N1B4_3559
bgtA aspartate ABC transporter, ATPase component BgtA Pf1N1B4_914 Pf1N1B4_774
bgtB' aspartate ABC transporter, permease component 1 (BgtB) Pf1N1B4_916 Pf1N1B4_1643
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA Pf1N1B4_917
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) Pf1N1B4_916
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) Pf1N1B4_915
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) Pf1N1B4_914 Pf1N1B4_774
dauA dicarboxylic acid transporter DauA Pf1N1B4_2936 Pf1N1B4_1905
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ Pf1N1B4_774 Pf1N1B4_3435
glt aspartate:proton symporter Glt Pf1N1B4_1888 Pf1N1B4_3487
natF aspartate ABC transporter, substrate-binding component NatF Pf1N1B4_917
natG aspartate ABC transporter, permease component 1 (NatG) Pf1N1B4_916 Pf1N1B4_4805
natH aspartate ABC transporter, permease component 2 (NatH) Pf1N1B4_915 Pf1N1B4_773
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A
peb1B aspartate ABC transporter, permease component 1 (Peb1B) Pf1N1B4_5643 Pf1N1B4_1694
peb1C aspartate ABC transporter, ATPase component Peb1C Pf1N1B4_914 Pf1N1B4_4804
peb1D aspartate ABC transporter, permease component 2 (Peb1D) Pf1N1B4_773 Pf1N1B4_2211
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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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