GapMind for catabolism of small carbon sources


Finding step ech for L-lysine catabolism in Pseudomonas putida KT2440

5 candidates for ech: (S)-3-hydroxybutanoyl-CoA hydro-lyase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi PP_2217 enoyl-CoA hydratase Enoyl-CoA hydratase [valine degradation] (EC (characterized) 75% 100% 395.6 AcuK 56% 285.4
hi PP_3284 enoyl-CoA hydratase-isomerase Enoyl-CoA hydratase [valine degradation] (EC (characterized) 51% 97% 231.9 AcuK 46% 208.0
lo PP_2136 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase 3-hydroxybutyryl-CoA dehydrogenase (EC; 3-hydroxyacyl-CoA dehydrogenase (EC; short-chain-enoyl-CoA hydratase (EC (characterized) 33% 58% 197.2
lo PP_2047 3-hydroxyacyl-CoA dehydrogenase family protein 3-hydroxybutyryl-CoA dehydrogenase (EC; 3-hydroxyacyl-CoA dehydrogenase (EC; short-chain-enoyl-CoA hydratase (EC (characterized) 33% 59% 180.3 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 100% 819.7
lo PP_3726 Enoyl-CoA hydratase/isomerase family protein Crotonyl-CoA hydratase; EC (characterized) 34% 99% 153.3 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 41% 171.0

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 ech

Or cluster all characterized ech 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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