GapMind for catabolism of small carbon sources

 

Finding step gtsD for D-xylose catabolism in Pseudomonas fluorescens FW300-N1B4

4 candidates for gtsD: xylose ABC transporter, ATPase component GtsD

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med Pf1N1B4_593 Glucose ABC transporter, ATP-binding subunit (EC 3.6.3.-) ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 88% 100% 670.2 ABC transporter for D-Galactose and D-Glucose, ATPase component 96% 734.9
med Pf1N1B4_4847 Various polyols ABC transporter, ATP-binding component ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 98% 312.4 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 95% 686.8
med Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19) ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 47% 92% 308.5 Maltose-transporting ATPase (EC 3.6.3.19) 58% 380.6
lo Pf1N1B4_691 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1) ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 238.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9

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 gtsD

Or cluster all characterized gtsD proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 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