GapMind for catabolism of small carbon sources

 

D-galactose catabolism

Analysis of pathway galactose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
Azospirillum brasilense Sp245 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Bacteroides thetaiotaomicron VPI-5482 galP, galK, galT, galE, pgmA
Burkholderia phytofirmans PsJN ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Caulobacter crescentus NA1000 HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
Cupriavidus basilensis 4G11 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Dechlorosoma suillum PS galP, galK, galT, galE, pgmA
Desulfovibrio vulgaris Hildenborough galP, galK, galT, galE, pgmA
Desulfovibrio vulgaris Miyazaki F galP, galK, galT, galE, pgmA
Dinoroseobacter shibae DFL-12 SGLT1, galdh, galactonolactonase, dgoD, dgoK, dgoA
Dyella japonica UNC79MFTsu3.2 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Echinicola vietnamensis KMM 6221, DSM 17526 HP1174, galK, galT, galE, pgmA
Escherichia coli BW25113 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Herbaspirillum seropedicae SmR1 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Klebsiella michiganensis M5al ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Magnetospirillum magneticum AMB-1 galP, galK, galT, galE, pgmA
Marinobacter adhaerens HP15 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Paraburkholderia bryophila 376MFSha3.1 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pedobacter sp. GW460-11-11-14-LB5 galP, galK, galT, galE, pgmA
Phaeobacter inhibens BS107 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N1B4 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2C3 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2E2 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2E3 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens GW456-L13 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas putida KT2440 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Pseudomonas simiae WCS417 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas stutzeri RCH2 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Shewanella amazonensis SB2B HP1174, galK, galT, galE, pgmA
Shewanella loihica PV-4 HP1174, galK, galT, galE, pgmA
Shewanella oneidensis MR-1 galP, galK, galT, galE, pgmA
Shewanella sp. ANA-3 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Sinorhizobium meliloti 1021 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Sphingomonas koreensis DSMZ 15582 HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
Synechococcus elongatus PCC 7942 galP, galK, galT, galE, pgmA

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

This GapMind analysis is from May 21 2021. The underlying query database was built on May 21 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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