GapMind for catabolism of small carbon sources


Finding step treV for trehalose catabolism in Herbaspirillum seropedicae SmR1

4 candidates for treV: trehalose ABC transporter, ATPase component TreV

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med HSERO_RS16715 sugar ABC transporter ATP-binding protein TreV, component of Trehalose porter (characterized) 48% 78% 245.4 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 57% 393.3
med HSERO_RS18940 sn-glycerol-3-phosphate ABC transporter ATP-binding protein TreV, component of Trehalose porter (characterized) 44% 87% 242.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 57% 389.8
med HSERO_RS02210 sugar ABC transporter ATP-binding protein TreV, component of Trehalose porter (characterized) 47% 82% 241.5 ABC transporter for D-Sorbitol, ATPase component 67% 491.5
med HSERO_RS17020 sugar ABC transporter ATP-binding protein TreV, component of Trehalose porter (characterized) 48% 75% 233 ABC-type maltose transporter (EC 49% 341.3

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Also see fitness data for the candidates

Definition of step treV

Or cluster all characterized treV 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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