Annotation: FitnessBrowser__Phaeo:GFF1398
Length: 695 amino acids
Source: Phaeo in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
D-maltose catabolism | malK_Ss | lo | MalK, component of Maltose and maltooligosaccharide porter (characterized) | 36% | 99% | 371.3 | Uncharacterized ABC transporter ATP-binding protein Rv1281c/MT1318, component of The glutathione transporter, OppA (Dasgupta et al., 2010). OppA binds glutathione and the nanopeptide, bradykinin. Also regulates cytokine release, apoptosis and the innate immune response of macrophages infected with M. tuberculosis | 39% | 397.5 |
View GFF1398 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MNKLAEYDGPILEIDKLSISFFTRLREIPAVMDFSVSVMPGEAVGLVGESGCGKSTVALG VMQDLGKNGRIVGGSIKFKGRDLAEMSAEELRDVRGNEIAMIYQEPMASLNPAMKIGKQL MEVPMIHEGVSKEEAYRRALEVVTDVRLPDPERMLNSFPHQLSGGQQQRIVIAMALMSKP ALLILDEPTTALDVTVEAAVVELVKDLGKKYGTSMLFISHNLGLVLETCDRLCVMYSGEA VERGSIHDVFDEMQHPYTQALFRSIPLPGADKNARPLVAIPGNFPLPHERPSGCNFGPRC DYFEAGRCDAQDIPMVPVQGNDRHHTRCLRHDEIDWAAPITVGEQKEKPEVGEVVLKIDN LRKYYEVSANALFDSGARKVVKANETLSFEARESETLAIVGESGCGKSTFAKVLMGLETA TDGEIQLDGKNIEATPIEHRDTRTVSDVQMVFQNPFDTLNPSMTVGRQIVRALEIFGIGD STAARRERMLELLDLVKLPRAFADRMPRQLSGGQKQRVGIARAFAGGARIVVADEPVSAL DVSVQAAVTDLLMEIQRKEKTTLLFISHDLSIVRYLSDRVMVMYLGHVVELGTTDQVFAP PYHPYTEALLSAVPIADTSVEKRHIVLEGDIPSAMNPPPGCPFQTRCRWKSKVADGLCER EVPPVRTLDGGHQVKCHLSDADLTEMEPVIKIAAE
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