Annotation: FitnessBrowser__pseudo3_N2E3:AO353_24260
Length: 309 amino acids
Source: pseudo3_N2E3 in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-lysine biosynthesis | hcs | med | Putative homocitrate synthase; EC 2.3.3.14 (uncharacterized) | 40% | 82% | 211.5 | 2-isopropylmalate synthase (EC 2.3.3.13) | 34% | 180.3 |
L-leucine biosynthesis | leuA | lo | 2-isopropylmalate synthase (EC 2.3.3.13) (characterized) | 34% | 59% | 180.3 | Probable homocitrate synthase AksA; (R)-homo(2)citrate synthase; (R)-homo(3)citrate synthase; EC 2.3.3.14; EC 2.3.3.- | 36% | 169.1 |
L-isoleucine biosynthesis | cimA | lo | Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized) | 34% | 62% | 170.6 | 2-isopropylmalate synthase (EC 2.3.3.13) | 34% | 180.3 |
View AO353_24260 at FitnessBrowser
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Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MTFITLVDSTLREGNQAPGVKLTTKSTLTIAYALADAGIDFIEAGHPYASKQEFDRVTAL VKSKIAKNILAHSRAHQDDIDAVAATGANWIGIFAGINETSQKYRIRKSKAQIQDLIKRS VLYAKSLGLKVRYTIEDASRTPSDDLIETFKIAKAAGADRICYADSLGVCDPFKVQATIK LIRQSLSDIDLEVHFHDDRGLAMANTLASIEAGATFISCTVNGIGERCGITETCLLITNL HFNSILCSGKASKVLKLSSIVSKELGDAFDRRRPIIGEYSFVHTAKLHVTANSRNKNCYH WIDPAYLSE
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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