GapMind for catabolism of small carbon sources


Finding step manZ for D-cellobiose catabolism in Klebsiella michiganensis M5al

3 candidates for manZ: glucose PTS, enzyme EIID

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BWI76_RS17900 PTS mannose transporter subunit IID PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized) 93% 100% 525.8 Lmo0781 protein, component of Constitutively synthesized sensor, MpoABCD, controlling man operon (see TC# 4.A.6.1.15) expression by interacting with and phosphorylating ManR, the transcriptional regulator of the man operon 74% 432.6
med BWI76_RS01725 PTS mannose/fructose/sorbose family transporter subunit IID PTS system mannose-specific EIID component; EII-M-Man; EIID-Man; Mannose permease IID component (characterized) 62% 96% 344.7 PTS system sorbose-specific EIID component; EIID-Sor; Sorbose permease IID component 97% 528.9
lo BWI76_RS03970 PTS mannose/fructose/sorbose family transporter subunit IID PTND aka MANZ aka PTSM aka GPTB aka B1819, component of The mannose (glucose, 2-deoxyglucose, glucosamine, N-acetylglucosamine, N-acetylmannosamine, mannosamine and fructose) PTS porter/group translocator, ManXYZ (Rephaeli and Saier 1980; Plumbridge 2015). Catalyzes xylose facilitated diffusion in lactobacilli. The order of D-sugar substrate affinities is: glucose > mannose > 2-deoxyglucose > N-acetylglucosamine > glucosamine > N-acetylmannosamine > mannosamine > fructose (characterized) 38% 99% 211.5 PTS mannose transporter subunit IID, component of PTS uptake system for glucoselysine and fructoselysine, GfrABCD 86% 488.0

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 manZ

Or cluster all characterized manZ 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