GapMind for catabolism of small carbon sources


Finding step ech for L-isoleucine catabolism in Magnetospirillum magneticum AMB-1

5 candidates for ech: 2-methyl-3-hydroxybutyryl-CoA hydro-lyase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi AMB_RS03265 enoyl-CoA hydratase trans-2,3-dehydroadipyl-CoA hydratase (EC (characterized) 70% 100% 362.8 BadK 57% 291.2
hi AMB_RS13070 enoyl-CoA hydratase 2,3-dehydroadipyl-CoA hydratase (EC (characterized) 48% 98% 231.1 mitochondrial enoyl-CoA hydratase 44% 201.1
med AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase Probable enoyl-CoA hydratase; EC (uncharacterized) 47% 99% 225.7 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 58% 294.3
med AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase paaB: phenylacetate degradation probable enoyl-CoA hydratase PaaB (EC (TIGR02280) 100% 384.8 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 58% 294.3
med AMB_RS13030 enoyl-CoA hydratase Probable enoyl-CoA hydratase echA12; EC (uncharacterized) 35% 89% 145.2 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 36% 142.5
lo AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha enoyl-CoA hydratase (EC (characterized) 37% 98% 448.7 6-carboxyhex-2-enoyl-CoA hydratase 46% 601.3

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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 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