GapMind for catabolism of small carbon sources

 

lactose catabolism

Analysis of pathway lactose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Azospirillum brasilense Sp245 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Bacteroides thetaiotaomicron VPI-5482 lacP, lacZ, galK, galT, galE, pgmA, glk
Burkholderia phytofirmans PsJN lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Caulobacter crescentus NA1000 lacA', lacC', lacB', klh, MFS-glucose, glk
Cupriavidus basilensis 4G11 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Dechlorosoma suillum PS lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio vulgaris Hildenborough lacP, lacZ, galK, galT, galE, pgmA, glk
Desulfovibrio vulgaris Miyazaki F lacP, lacZ, galK, galT, galE, pgmA, glk
Dinoroseobacter shibae DFL-12 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Dyella japonica UNC79MFTsu3.2 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Echinicola vietnamensis KMM 6221, DSM 17526 lacA', lacC', lacB', klh, MFS-glucose, glk
Escherichia coli BW25113 lacY, lacZ, galK, galT, galE, pgmA, glk
Herbaspirillum seropedicae SmR1 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Klebsiella michiganensis M5al lacIIA, lacIIB, lacIIC, pbgal, lacA, lacB, lacC, gatY, gatZ, tpi, glk
Magnetospirillum magneticum AMB-1 lacP, lacZ, galK, galT, galE, pgmA, glk
Marinobacter adhaerens HP15 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pedobacter sp. GW460-11-11-14-LB5 lacA', lacC', lacB', klh, SSS-glucose, glk
Phaeobacter inhibens BS107 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas fluorescens FW300-N1B4 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas fluorescens FW300-N2C3 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas fluorescens FW300-N2E2 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas fluorescens FW300-N2E3 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens GW456-L13 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas putida KT2440 lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Pseudomonas stutzeri RCH2 lacP, lacZ, galK, galT, galE, pgmA, glk
Shewanella amazonensis SB2B lacP, lacZ, galK, galT, galE, pgmA, glk
Shewanella loihica PV-4 lacP, lacZ, galK, galT, galE, pgmA, glk
Shewanella oneidensis MR-1 lacP, lacZ, galK, galT, galE, pgmA, glk
Shewanella sp. ANA-3 lacP, lacZ, galK, galT, galE, pgmA, glk
Sinorhizobium meliloti 1021 lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk
Sphingomonas koreensis DSMZ 15582 lacA', lacC', lacB', klh, MFS-glucose, glk
Synechococcus elongatus PCC 7942 lacP, lacZ, galK, galT, galE, pgmA, glk

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