GapMind for catabolism of small carbon sources


Finding step fruA for sucrose catabolism in Klebsiella michiganensis M5al

4 candidates for fruA: fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BWI76_RS19725 PTS fructose transporter subunit EIIBC PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC (characterized) 89% 99% 974.5 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 47% 426.4
med BWI76_RS24865 PTS family enzyme IIB'BC, fructose-specific protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 2/2) (EC (characterized) 57% 97% 513.1 PTS family enzyme IIB'BC, fructose-specific, component of The tagatose-specific PTS transporter/kinase, TagIIA-TPr/TagIIB'BC (tagatose-1-P forming) 94% 888.3
lo BWI76_RS27570 phosphotransferase system, fructose-specific IIC component PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC (characterized) 47% 57% 302 Putative PTS enzyme-II fructose, component of The FrzABC PTS putative transporter (promotes bacterial fitness under stress conditions and promotes fimbrial (fim) gene expression indirectly (Rouquet et al., 2009). Might transport D-tagatose, D-psicose and/or D-sorbose, or a disaccharide of these (Rouquet et al. 2009); involved in environmental sensing, host adaptation and virulence 95% 694.9
lo BWI76_RS10670 PTS fructose transporter subunit IIC 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

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Also see fitness data for the candidates

Definition of step fruA

Or cluster all characterized fruA proteins

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