GapMind for catabolism of small carbon sources


Finding step BPHYT_RS34240 for L-fucose catabolism in Herbaspirillum seropedicae SmR1

2 candidates for BPHYT_RS34240: ABC transporter for L-fucose, permease component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo HSERO_RS22215 branched-chain amino acid ABC transporter permease Monosaccharide-transporting ATPase; EC; Flags: Precursor (characterized, see rationale) 34% 88% 159.1 RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) 54% 320.5
lo HSERO_RS05325 ribose ABC transporter permease Monosaccharide-transporting ATPase; EC; Flags: Precursor (characterized, see rationale) 33% 92% 151 Ribose import permease protein RbsC 49% 282.7

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 BPHYT_RS34240

Or cluster all characterized BPHYT_RS34240 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