GapMind for catabolism of small carbon sources

 

Finding step dctM for succinate catabolism in Marinomonas arctica 328

5 candidates for dctM: succinate TRAP transporter, large permease protein DctM

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi DK187_RS05080 TRAP transporter large permease subunit C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 43% 97% 328.9 Sialic acid TRAP transporter large permease protein SiaM 38% 298.1
med DK187_RS02430 TRAP transporter large permease C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 41% 100% 354 Sialic acid TRAP transporter large permease protein SiaM 43% 354.8
med DK187_RS09250 TRAP transporter large permease subunit dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) 48% 79% 328.2 Large component of TRAP-type D-gluconate transporter 39% 194.1
lo DK187_RS15800 TRAP transporter large permease C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 40% 100% 325.5 Sialic acid TRAP transporter large permease protein SiaM 41% 349.7
lo DK187_RS09745 TRAP transporter large permease C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 38% 99% 322.8 Sialic acid TRAP transporter large permease protein SiaM 40% 330.5

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 dctM

Or cluster all characterized dctM 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