GapMind for catabolism of small carbon sources

 

D-maltose catabolism

Analysis of pathway maltose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 susB, gtsA, gtsB, gtsC, gtsD, glk
Azospirillum brasilense Sp245 susB, mglA, mglB, mglC, glk
Bacteroides thetaiotaomicron VPI-5482 susB, SSS-glucose, glk
Burkholderia phytofirmans PsJN susB, gtsA, gtsB, gtsC, gtsD, glk
Caulobacter crescentus NA1000 malI, susB, glk
Cupriavidus basilensis 4G11 susB, mglA, mglB, mglC, glk
Dechlorosoma suillum PS susB, ptsG-crr
Desulfovibrio vulgaris Hildenborough susB, ptsG-crr
Desulfovibrio vulgaris Miyazaki F susB, ptsG-crr
Dinoroseobacter shibae DFL-12 aglE, aglF, aglG, aglK, susB, glk
Dyella japonica UNC79MFTsu3.2 malI, susB, glk
Echinicola vietnamensis KMM 6221, DSM 17526 malI, susB, glk
Escherichia coli BW25113 malE, malF, malG, malK, susB, glk
Herbaspirillum seropedicae SmR1 susB, mglA, mglB, mglC, glk
Klebsiella michiganensis M5al malE, malF, malG, malK, susB, glk
Magnetospirillum magneticum AMB-1 susB, SemiSWEET, glk
Marinobacter adhaerens HP15 susB, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 susB, gtsA, gtsB, gtsC, gtsD, glk
Pedobacter sp. GW460-11-11-14-LB5 malI, malP, pgmB, glk
Phaeobacter inhibens BS107 aglE, aglF, aglG, aglK, susB, glk
Pseudomonas fluorescens FW300-N1B4 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2C3 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E2 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E3 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens GW456-L13 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas putida KT2440 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 susB, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas stutzeri RCH2 malE, malF, malG, malK, susB, glk
Shewanella amazonensis SB2B malI, susB, glk
Shewanella loihica PV-4 malI, susB, glk
Shewanella oneidensis MR-1 malI, susB, glk
Shewanella sp. ANA-3 malI, susB, glk
Sinorhizobium meliloti 1021 thuE, thuF, thuG, thuK, susB, glk
Sphingomonas koreensis DSMZ 15582 malI, susB, glk
Synechococcus elongatus PCC 7942 thuE, thuF, thuG, thuK, susB, 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.

Links

Downloads

Related tools

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