GapMind for catabolism of small carbon sources

 

Finding step garD for D-galacturonate catabolism in Burkholderia phytofirmans PsJN

5 candidates for garD: meso-galactarate dehydratase (L-threo-forming) GarD

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi BPHYT_RS24160 D-galactarate dehydratase Galactarate dehydratase (EC 4.2.1.42) (characterized) 73% 98% 786.9 D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism 32% 267.7
hi BPHYT_RS24160 D-galactarate dehydratase garD: galactarate dehydratase (EC 4.2.1.42) (TIGR03248) 100% 924.8 D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism 32% 267.7
lo BPHYT_RS28730 galactarate dehydratase Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized) 40% 94% 329.3 D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism 54% 516.9
lo BPHYT_RS27220 galactarate dehydratase Galactarate dehydratase (L-threo-forming); GalcD; EC 4.2.1.42 (characterized) 38% 95% 321.2 D-arabinoate dehydratase (EC 4.2.1.5); also involved in L-fucose catabolism 54% 521.9
lo BPHYT_RS31620 mandelate racemase L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized) 31% 89% 145.6 dehydratase involved in L-fucose catabolism 32% 164.9
lo BPHYT_RS20755 fuconate dehydratase L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized) 32% 64% 110.5 Mitochondrial enolase superfamily member 1; Antisense RNA to thymidylate synthase; rTS; L-fuconate dehydratase; EC 4.2.1.68 62% 563.5

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 garD

Or cluster all characterized garD 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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