GapMind for catabolism of small carbon sources

 

L-asparagine catabolism in Desulfovibrio vulgaris Miyazaki F

Best path

ans, dauA

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
ans asparaginase DvMF_0839
dauA dicarboxylic acid transporter DauA DvMF_1575 DvMF_2017
Alternative steps:
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ DvMF_3152
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DvMF_2786
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DvMF_2788 DvMF_3151
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
aatJ aspartate/asparagine ABC transporter, substrate-binding component AatJ DvMF_3152 DvMF_2787
aatM aspartate/asparagine ABC transporter, permease component 2 (AatM) DvMF_3153 DvMF_1343
aatP aspartate/asparagine ABC transporter, ATPase component DvMF_2788 DvMF_3151
aatQ aspartate/asparagine ABC transporter, permease component 1 (AatQ) DvMF_3153 DvMF_2786
acaP aspartate permease AcaP
agcS Probable asparagine:Na+ symporter AgcS
AGP1 L-asparagine permease AGP1
ansP L-asparagine permease AnsP
bgtA aspartate ABC transporter, ATPase component BgtA DvMF_3151 DvMF_2788
bgtB' aspartate ABC transporter, permease component 1 (BgtB) DvMF_3154 DvMF_2686
BPHYT_RS17540 aspartate:H+ (or asparagine) symporter
bztA aspartate/asparagine ABC transporter, substrate-binding component BztA DvMF_3152
bztB aspartate/asparagine ABC transporter, permease component 1 (BztB) DvMF_3153
bztC aspartate/asparagine ABC transporter, permease component 2 (BztC) DvMF_2786
bztD aspartate/asparagine ABC transporter, ATPase component (BztD) DvMF_2788 DvMF_3151
glnP L-asparagine ABC transporter, fused permease and substrate-binding components GlnP
glnQ L-asparagine ABC transporter, ATPase component GlnQ DvMF_1920 DvMF_0862
glt aspartate:proton symporter Glt
natF aspartate ABC transporter, substrate-binding component NatF DvMF_3152
natG aspartate ABC transporter, permease component 1 (NatG) DvMF_1343 DvMF_3153
natH aspartate ABC transporter, permease component 2 (NatH) DvMF_2786 DvMF_3154
peb1A aspartate ABC transporter, perisplasmic substrate-binding component Peb1A DvMF_3152
peb1B aspartate ABC transporter, permease component 1 (Peb1B) DvMF_2786 DvMF_1919
peb1C aspartate ABC transporter, ATPase component Peb1C DvMF_2788 DvMF_1920
peb1D aspartate ABC transporter, permease component 2 (Peb1D) DvMF_2786 DvMF_1919
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 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, 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