GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism

Analysis of pathway cellobiose in 35 genomes

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