GapMind for catabolism of small carbon sources

 

Finding step gntB for D-gluconate catabolism in Marivita geojedonensis DPG-138

4 candidates for gntB: gluconate TRAP transporter, large permease component

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med MGEO_RS11590 TRAP transporter large permease D-gluconate TRAP transporter, large permease component (characterized) 41% 98% 337 Sialic acid TRAP transporter large permease protein SiaM 41% 328.6
lo MGEO_RS04955 TRAP transporter large permease TRAP-type large permease component (characterized, see rationale) 37% 100% 303.9 Sialic acid TRAP transporter large permease protein SiaM 40% 338.6
lo MGEO_RS06865 TRAP transporter large permease TRAP-type large permease component (characterized, see rationale) 33% 99% 238.8 C4-dicarboxylate TRAP transporter large permease protein DctM 32% 243.8
lo MGEO_RS05370 TRAP transporter large permease Large component of TRAP-type D-gluconate transporter (characterized) 32% 96% 216.9 C4-dicarboxylate TRAP transporter large permease protein DctM 35% 258.5

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.

Definition of step gntB

Or cluster all characterized gntB proteins

This GapMind analysis is from Sep 24 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