GapMind for catabolism of small carbon sources

 

Finding step peb1B for L-aspartate catabolism in Desulfovibrio vulgaris Miyazaki F

2 candidates for peb1B: aspartate ABC transporter, permease component 1 (Peb1B)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq) PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 91% 132.5 NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB 39% 155.2
lo DvMF_1919 polar amino acid ABC transporter, inner membrane subunit (RefSeq) PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 80% 129 Glutamine transport system permease protein GlnP aka B0810, component of Three component ABC L-glutamine porter. The basal ATPase activity (ATP hydrolysis in the absence of substrate) is mainly caused by the docking of the closed-unliganded state of GlnH onto the transporter domain of GlnPQ. Unlike glutamine, arginine binds both GlnH domains, but does not trigger their closing. Comparison of the ATPase activity in nanodiscs with glutamine transport in proteoliposomes suggested that the stoichiometry of ATP per substrate is close to two 54% 232.6

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step peb1B

Or cluster all characterized peb1B proteins

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