GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism

Analysis of pathway deoxyribose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 deoP, deoK, deoC, adh, acs
Azospirillum brasilense Sp245 deoP, deoK, deoC, adh, acs
Bacteroides thetaiotaomicron VPI-5482 deoP, deoK, deoC, adh, ackA, pta
Burkholderia phytofirmans PsJN drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Caulobacter crescentus NA1000 deoP, deoK, deoC, adh, acs
Cupriavidus basilensis 4G11 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Dechlorosoma suillum PS deoP, deoK, deoC, adh, acs
Desulfovibrio vulgaris Hildenborough deoP, deoK, deoC, adh, ackA, pta
Desulfovibrio vulgaris Miyazaki F deoP, deoK, deoC, ald-dh-CoA
Dinoroseobacter shibae DFL-12 deoP, deoK, deoC, adh, ackA, pta
Dyella japonica UNC79MFTsu3.2 deoP, deoK, deoC, adh, acs
Echinicola vietnamensis KMM 6221, DSM 17526 deoP, deoK, deoC, adh, acs
Escherichia coli BW25113 deoP, deoK, deoC, adh, ackA, pta
Herbaspirillum seropedicae SmR1 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Klebsiella michiganensis M5al deoP, deoK, deoC, adh, ackA, pta
Magnetospirillum magneticum AMB-1 deoP, deoK, deoC, adh, acs
Marinobacter adhaerens HP15 deoP, deoK, deoC, adh, ackA, pta
Paraburkholderia bryophila 376MFSha3.1 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pedobacter sp. GW460-11-11-14-LB5 deoP, deoK, deoC, adh, ackA, pta
Phaeobacter inhibens BS107 deoP, deoK, deoC, adh, acs
Pseudomonas fluorescens FW300-N1B4 deoP, deoK, deoC, adh, ackA, pta
Pseudomonas fluorescens FW300-N2C3 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E2 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pseudomonas fluorescens FW300-N2E3 deoP, deoK, deoC, adh, ackA, pta
Pseudomonas fluorescens GW456-L13 deoP, deoK, deoC, adh, ackA, pta
Pseudomonas putida KT2440 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pseudomonas simiae WCS417 drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB
Pseudomonas stutzeri RCH2 deoP, deoK, deoC, adh, ackA, pta
Shewanella amazonensis SB2B deoP, deoK, deoC, adh, ackA, pta
Shewanella loihica PV-4 deoP, deoK, deoC, adh, ackA, pta
Shewanella oneidensis MR-1 deoP, deoK, deoC, adh, ackA, pta
Shewanella sp. ANA-3 deoP, deoK, deoC, adh, ackA, pta
Sinorhizobium meliloti 1021 deoP, deoK, deoC, adh, ackA, pta
Sphingomonas koreensis DSMZ 15582 deoP, deoK, deoC, adh, acs
Synechococcus elongatus PCC 7942 deoP, deoK, deoC, adh, acs

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