GapMind for catabolism of small carbon sources

 

Finding step glt for L-asparagine catabolism in Pseudomonas stutzeri RCH2

2 candidates for glt: aspartate:proton symporter Glt

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi Psest_4075 Na+/H+-dicarboxylate symporters Sodium:dicarboxylate symporter (characterized, see rationale) 46% 94% 356.3 The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up 35% 257.7
med Psest_1386 Na+/H+-dicarboxylate symporters Sodium:dicarboxylate symporter (characterized, see rationale) 38% 91% 279.3 Neutral amino acid transporter B(0); ATB(0); Sodium-dependent neutral amino acid transporter type 2; Solute carrier family 1 member 5 35% 224.6

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 glt

Or cluster all characterized glt 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