GapMind for catabolism of small carbon sources


Finding step adh for thymidine catabolism in Burkholderia phytofirmans PsJN

5 candidates for adh: acetaldehyde dehydrogenase (not acylating)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BPHYT_RS25810 aldehyde dehydrogenase acetaldehyde dehydrogenase (EC (characterized) 100% 100% 1584.7 Aldehyde dehydrogenase family 16 member A1 41% 521.9
hi BPHYT_RS00120 aldehyde dehydrogenase Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC (characterized) 78% 97% 792.3 Long-chain-aldehyde dehydrogenase; Aldehyde dehydrogenase 1; EC 72% 766.5
hi BPHYT_RS32650 aldehyde dehydrogenase Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC; EC; EC (characterized) 50% 88% 484.2 Δ1-piperideine-6-carboxylate dehydrogenase 53% 438.3
med BPHYT_RS07710 succinylglutamate-semialdehyde dehydrogenase aldehyde dehydrogenase (NAD+) (EC (characterized) 56% 98% 557 Succinylglutamic semialdehyde dehydrogenase (EC 60% 592.8
med BPHYT_RS22430 succinate-semialdehyde dehydrogenase aldehyde dehydrogenase (NAD+) (EC (characterized) 56% 92% 551.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 70% 693.7

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 adh

Or cluster all characterized adh 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