GapMind for catabolism of small carbon sources


Protein H281DRAFT_02705 in Paraburkholderia bryophila 376MFSha3.1

Annotation: FitnessBrowser__Burk376:H281DRAFT_02705

Length: 365 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsB med D-ribose-binding periplasmic protein; EC (characterized) 38% 98% 180.3 RbsB, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 37% 167.5
D-mannose catabolism HSERO_RS03635 lo ABC-type sugar transport system, periplasmic component protein (characterized, see rationale) 33% 92% 127.9 D-ribose-binding periplasmic protein; EC 38% 180.3
D-fructose catabolism frcB lo Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale) 31% 97% 121.3 D-ribose-binding periplasmic protein; EC 38% 180.3
sucrose catabolism frcB lo Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale) 31% 97% 121.3 D-ribose-binding periplasmic protein; EC 38% 180.3
L-arabinose catabolism araUsh lo Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale) 32% 78% 119.4 D-ribose-binding periplasmic protein; EC 38% 180.3

Sequence Analysis Tools

View H281DRAFT_02705 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