GapMind for catabolism of small carbon sources

 

Protein BWI76_RS10670 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS10670

Length: 358 amino acids

Source: Koxy in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism manP lo protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 44% 51% 268.9 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
D-fructose catabolism fruA lo Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale) 42% 57% 263.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
sucrose catabolism fruA lo Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale) 42% 57% 263.1 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
D-fructose catabolism fruII-ABC lo The fructose-specific PTS Enzyme IIABC FruA (characterized) 41% 52% 260 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
sucrose catabolism fruII-ABC lo The fructose-specific PTS Enzyme IIABC FruA (characterized) 41% 52% 260 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
D-fructose catabolism fruII-C lo Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 38% 90% 244.6 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1
sucrose catabolism fruII-C lo Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized) 38% 90% 244.6 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 86% 617.1

Sequence Analysis Tools

View BWI76_RS10670 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...

Sequence

MNELVQILKNTRQHLMTGVSHMIPFVVSGGILLAVSVMLYGKGAVPDAATDPNLKKLFDI
GVAGLTLMVPFLAAYIGYSISDRAALAPCAIGAWVGNSFGAGFFGALIAGIIGGLVVYYL
KKIPVHKVLRSVMPIFVIPIIGTFITAGIMMWGLGEPIGALTASLTGWLQGMREGSIVIL
AIIMGLMLAFDMGGPVNKVAYAFMLICVSQGVYSVVAIAAVGIAVPPLGMGLATLIGRKY
FSAEERETGKAALVMGCVGVTEGAIPFAAADPLRVIPANMIGAAAGCVTAALLGAQCYAG
WGGLIVLPVVEGKGGFIAGLAVGAIVSAACVILLKALAKKKTSDAKADDEMDLDFEIN

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

Links

Downloads

Related tools

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