Annotation: FitnessBrowser__Miya:8501897
Length: 455 amino acids
Source: Miya in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
L-lysine biosynthesis | hcs | med | Homocitrate synthase; EC 2.3.3.14 (uncharacterized) | 39% | 93% | 218.8 | 2-phosphonomethylmalate synthase (EC 2.3.3.19) | 35% | 183.0 |
L-isoleucine biosynthesis | cimA | lo | Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized) | 38% | 72% | 204.5 | homocitrate synthase (EC 2.3.3.14) | 35% | 195.7 |
L-leucine biosynthesis | leuA | lo | 2-isopropylmalate synthase 2; EC 2.3.3.13; Alpha-IPM synthase 2; Alpha-isopropylmalate synthase 2 (uncharacterized) | 33% | 93% | 194.9 | homocitrate synthase (EC 2.3.3.14) | 35% | 195.7 |
View 8501897 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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MLLDTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWAGREDLTDMLALSARVAP GLAAAAWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAEAR MLGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRALRA ELEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGVAR LEELAAALVVRGRARFELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHAHGVR RDPSLFEPFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRDLSAT LRRPLTPAELAEVAGLGKHHAPPMQTDIPGHAPTARPTARPVPANGIPPQSGPESAPVVS GMPATDRAATGPHRHPDHTGAHRRGPVPTASGREA
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