GapMind for catabolism of small carbon sources

 

Finding step BPHYT_RS16930 for D-galactose catabolism in Pseudomonas simiae WCS417

5 candidates for BPHYT_RS16930: galactose ABC transporter, ATPase component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PS417_11030 L-arabinose transporter ATP-binding protein Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 86% 96% 825.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 60% 582.8
hi PS417_21330 L-arabinose transporter ATP-binding protein Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 85% 97% 815.8 L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 61% 586.6
hi PS417_18400 sugar ABC transporter ATPase Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 42% 97% 367.1 D-allose import ATP-binding protein AlsA; EC 7.5.2.8 40% 352.8
med PS417_11890 D-ribose transporter ATP-binding protein Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 42% 98% 399.1 Inositol transport system ATP-binding protein 100% 1003.4
lo PS417_17730 ribonucleotide-diphosphate reductase subunit alpha Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 39% 97% 364 Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 44% 409.5

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_RS16930

Or cluster all characterized BPHYT_RS16930 proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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