GapMind for catabolism of small carbon sources

 

Finding step dctA for acetate catabolism in Cupriavidus basilensis 4G11

4 candidates for dctA: organic acid/proton symporter DctA

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med RR42_RS26105 C4-dicarboxylate transporter Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 71% 99% 613.2 aerobic C4-dicarboxylate transport protein 71% 604.4
med RR42_RS01695 C4-dicarboxylate transporter Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 61% 96% 516.2 C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) 63% 534.6
med RR42_RS33745 C4-dicarboxylate transporter Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 57% 98% 491.9 Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate 58% 493.4
med RR42_RS19790 C4-dicarboxylate ABC transporter Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 53% 98% 444.9 Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate 54% 459.1

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 dctA

Or cluster all characterized dctA 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