GapMind for Amino acid biosynthesis


Finding step ilvE for L-isoleucine biosynthesis in Desulfovibrio vulgaris Hildenborough

4 candidates for ilvE: isoleucine transaminase

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi DVU3197 branched-chain amino acid aminotransferase Branched-chain amino acid aminotransferase (EC (characterized) 56% 100% 369
hi DVU3197 branched-chain amino acid aminotransferase ilvE: branched-chain amino acid aminotransferase (EC (TIGR01122) 99% 440.4
med DVU2364 aminotransferase, classes I and II branched-chain-amino-acid transaminase (EC (characterized) 41% 95% 310.1 2-aminoadipate transaminase (EC 45% 321.6
lo DVU2953 transcriptional regulator, GntR family branched-chain-amino-acid transaminase (EC (characterized) 34% 88% 223.8 kynurenine-oxoglutarate transaminase (EC 34% 227.6
lo DVU0030 transcriptional regulator, GntR family Branched-chain-amino-acid transaminase (EC (characterized) 30% 93% 164.5 uncharacterized HTH-type transcriptional regulator yjiR 36% 283.9

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

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 ilvE

Or cluster all characterized ilvE proteins

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.

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