GapMind for catabolism of small carbon sources

 

Finding step aatP for L-asparagine catabolism in Herbaspirillum seropedicae SmR1

4 candidates for aatP: aspartate/asparagine ABC transporter, ATPase component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi HSERO_RS19240 arginine ABC transporter ATP-binding protein ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 77% 100% 380.2 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 58% 291.2
hi HSERO_RS17555 arginine ABC transporter ATP-binding protein ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 72% 100% 359.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 61% 290.8
med HSERO_RS00320 peptide ABC transporter ATP-binding protein ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 55% 99% 259.6 Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity 61% 299.3
med HSERO_RS05835 arginine ABC transporter ATP-binding protein Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 54% 100% 255.4 TcyC (YckI), component of Uptake system for L-cystine 54% 266.9

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 aatP

Or cluster all characterized aatP 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, 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