GapMind for catabolism of small carbon sources

 

Finding step TM1747 for D-mannose catabolism in Pseudomonas simiae WCS417

2 candidates for TM1747: mannose ABC transporter, permease component 1

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo PS417_11135 peptide ABC transporter TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 93% 183 Dipeptide transport system permease protein dppB, component of Di- and tri-peptide transporter, DppBCDF with periplasmic substrate binding receptors, A1, A3, A5, A7 and A9, each with differing specificities for peptides 39% 234.2
lo PS417_12175 peptide ABC transporter permease TM1747, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 91% 167.2 YejB, component of The antimicrobial peptide (protamine, melittin, polymyxin B, human defensin (HBD)-1 and HBD-2 exporter, YejABEF (Eswarappa et al., 2008). Prefers N-formyl methionine peptides, such as Microcin C (of prokaryotic origin) to non formylated peptides (of eukaryotic origin) 61% 447.6

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 TM1747

Or cluster all characterized TM1747 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