GapMind for catabolism of small carbon sources

 

Finding step fruII-ABC for D-fructose catabolism in Tatumella morbirosei LMG 23360

4 candidates for fruII-ABC: fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
med HA49_RS07395 PTS fructose transporter subunit IIBC 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 (characterized) 47% 74% 427.6 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 76% 839.0
med HA49_RS02720 PTS transporter subunit EIIC 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 (characterized) 47% 72% 416.4 PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 66% 588.6
med HA49_RS21135 HPr family phosphocarrier protein 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 (characterized) 45% 72% 411 PTS family enzyme IIB'BC, fructose-specific, component of The tagatose-specific PTS transporter/kinase, TagIIA-TPr/TagIIB'BC (tagatose-1-P forming) 80% 732.6
lo HA49_RS06185 PTS fructose transporter subunit EIIC The fructose-specific PTS Enzyme IIABC FruA (characterized) 40% 52% 249.2 Fructose-like permease IIC component 2; PTS system fructose-like EIIC component 2 85% 605.9

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.

Definition of step fruII-ABC

Or cluster all characterized fruII-ABC proteins

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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