Annotation: FitnessBrowser__Smeli:SMa0819
Length: 353 amino acids
Source: Smeli in FitnessBrowser
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| D-lactate catabolism | lctC | lo | lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized) | 38% | 78% | 233 | caffeoyl-CoA reductase (subunit 1/3) (EC 1.3.1.108) | 43% | 278.5 |
| L-threonine catabolism | lctC | lo | lactate dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.110) (characterized) | 38% | 78% | 233 | caffeoyl-CoA reductase (subunit 1/3) (EC 1.3.1.108) | 43% | 278.5 |
| L-lysine catabolism | etfA | lo | butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized) | 40% | 96% | 231.1 | caffeoyl-CoA reductase (subunit 1/3) (EC 1.3.1.108) | 43% | 278.5 |
View SMa0819 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
Fitness BLAST: loading...
MKKGLPKQFQDYRNVWVFIELEHGQVHPVSIELLGEGRKLADKLGVHLAGVVIGPPGGQG TANAIADAFAYGADLSYLVESPLLAHYRNEPFTKALTDLVLANKPEILLLGATTLGRDLA GSVATTLKTGLTADCTELNVDSDGSLAATRPTFGGSLLCTIYTLKCRPQMATVRPSVMAT PQRVNRPTGSIIRHDLKMLEEEIATKVLAFFSDCDSTIANLAYADVVVAGGLGLGAVQNL QLLKDLARTLGGDFGCSRPLVQKGWMPFDRQIGQTGNTIRPKLYIAAGISGAVQHRVGVE GSDLIVAINTDPNAPIFDFAHLGVVADAISFLPALTEVFTKRLEPRNLEKFVQ
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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