GapMind for catabolism of small carbon sources


Protein BPHYT_RS19720 in Burkholderia phytofirmans PsJN

Annotation: FitnessBrowser__BFirm:BPHYT_RS19720

Length: 515 amino acids

Source: BFirm in FitnessBrowser

Candidate for 6 steps in catabolism of small carbon sources

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 (characterized, see rationale) 57% 96% 547.4 L-arabinose ABC transporter, ATP-binding protein AraG; EC 52% 497.7
L-arabinose catabolism araG hi L-arabinose ABC transporter, ATP-binding protein AraG; EC (characterized) 52% 99% 497.7 ribose transport, ATP-binding protein RbsA; EC 45% 411.0
myo-inositol catabolism PS417_11890 med m-Inositol ABC transporter, ATPase component (itaA) (characterized) 43% 99% 410.2 L-arabinose ABC transporter, ATP-binding protein AraG; EC 52% 497.7
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC (characterized, see rationale) 44% 96% 409.1 L-arabinose ABC transporter, ATP-binding protein AraG; EC 52% 497.7
L-rhamnose catabolism rhaT' med RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 40% 97% 386 L-arabinose ABC transporter, ATP-binding protein AraG; EC 52% 497.7
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) 39% 99% 353.6 L-arabinose ABC transporter, ATP-binding protein AraG; EC 52% 497.7

Sequence Analysis Tools

View BPHYT_RS19720 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

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This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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