GapMind for catabolism of small carbon sources

 

Finding step TM1750 for D-mannose catabolism in Pseudomonas simiae WCS417

4 candidates for TM1750: mannose ABC transporter, ATPase component 2

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med PS417_04045 peptide ABC transporter ATP-binding protein TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 42% 97% 273.5 Dipeptide transport ATP-binding protein DppF, 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 86% 565.1
med PS417_08080 ABC transporter ATP-binding protein TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 46% 95% 255.8 OppF aka STM1742, component of Oligopeptide porter (also takes up amino glycoside antibiotics such as kanamycin, streptomycin and neomycin as well as cell wall-derived peptides such as murein tripeptide). It transports substrate peptides of 2-5 amino acids with highest affinity for tripeptides. Also transports δ-aminolevulinic acid (ALA). [May be regulated by PTS Enzyme INtr-aspartokinase.] ATP-binding to OppDF may result in donation of peptide to OppBC and simultaneous release of OppA 49% 280.8
med PS417_12190 microcin ABC transporter ATP-binding protein TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 48% 76% 243.4 uncharacterized ABC transporter ATP-binding protein yejF 60% 594.3
med PS417_12165 microcin ABC transporter ATP-binding protein TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 47% 78% 229.6 uncharacterized ABC transporter ATP-binding protein yejF 57% 551.2

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 TM1750

Or cluster all characterized TM1750 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