| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| med | Sama_2636 | 4-aminobutyrate aminotransferase (RefSeq) | 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized) | 41% | 99% | 334 | gamma-aminobutyrate transaminase (EC 2.6.1.19) | 100% | 835.5 |
| lo | Sama_1628 | bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq) | 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized) | 35% | 96% | 216.5 | Succinylornithine transaminase (EC 2.6.1.81) | 65% | 534.3 |
| lo | Sama_3011 | bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq) | 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized) | 34% | 97% | 206.5 | Succinylornithine transaminase (EC 2.6.1.81) | 65% | 536.6 |
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.
Also see fitness data for the candidates
Or cluster all characterized lysN proteins
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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:
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