GapMind for catabolism of small carbon sources

 

Finding step glpS for glycerol catabolism in Cupriavidus basilensis 4G11

5 candidates for glpS: glycerol ABC transporter, ATPase component 1 (GlpS)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi RR42_RS13790 ABC transporter ABC transporter for Glycerol, ATPase component 1 (characterized) 71% 98% 485 AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules 34% 204.9
med RR42_RS22875 ABC transporter ABC transporter for Glycerol, ATPase component 1 (characterized) 41% 70% 180.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 56% 290.0
lo RR42_RS18590 hypothetical protein GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 97% 187.6 AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules 54% 363.2
lo RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 99% 184.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 58% 390.6
lo RR42_RS27800 ABC transporter ATP-binding protein ABC transporter for Glycerol, ATPase component 1 (characterized) 40% 79% 171.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 49% 254.2

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 glpS

Or cluster all characterized glpS 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