Annotation: FitnessBrowser__Burk376:H281DRAFT_02331
Length: 520 amino acids
Source: Burk376 in FitnessBrowser
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
D-galactose catabolism | BPHYT_RS16930 | hi | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 56% | 96% | 545.4 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 52% | 501.9 |
L-arabinose catabolism | araG | hi | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) | 52% | 98% | 501.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 46% | 422.2 |
xylitol catabolism | PS417_12065 | lo | D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 99% | 356.3 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 52% | 501.9 |
View H281DRAFT_02331 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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MTSSHTATSLGGADAPLQTPSPVPASTEPYLQLDGITVRFPGVLALDQVSLEVRRGEVHG LMGENGAGKSTLLKVLSGVNQPAAGTLSLDGVEQQFTTTKAAIAAGVAIIYQELHLVPEL TVAENLMLGALPNRFGVLDEKALVARAVRELERLGEKIDPSQQVKNLSIGQRQMIEIGKA LMRDARVIAFDEPTSSLSSRETTQLFRIIRALRAEGRAIIYVTHRMDEVYELCDRVTVFR DGRRIDTFDAGAGLDRDRLISCMVGRSIADVYGYRTRDVGDVQLDVKGLMGPGLREPATF SARKGEIVGFFGLVGAGRSELMKLIYGAVKPTAGDITLKGKQVRFATPRDAVRAGVALCP EDRKQEGIVSIASVSDNLNISCRRHFSRFNVLNGRKEAQTAKEFIGKLAIKTRNGETPIG TLSGGNQQKVILSRWLAEDIDVFLMDEPTRGIDVGARSEIYGLLYGLADAGRTVIVVSSD LAEVIGVTDRVIVMKEGRLVGDLPKAQATPDALIKLALPR
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