GapMind for catabolism of small carbon sources


xylitol catabolism

Analysis of pathway xylitol in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 PLT5, xdhA, xylB
Azospirillum brasilense Sp245 fruI, x5p-reductase
Bacteroides thetaiotaomicron VPI-5482 PLT5, xdhA, xylB
Burkholderia phytofirmans PsJN PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Caulobacter crescentus NA1000 fruI, x5p-reductase
Cupriavidus basilensis 4G11 fruI, x5p-reductase
Dechlorosoma suillum PS fruI, x5p-reductase
Desulfovibrio vulgaris Hildenborough fruI, x5p-reductase
Desulfovibrio vulgaris Miyazaki F fruI, x5p-reductase
Dinoroseobacter shibae DFL-12 Dshi_0546, Dshi_0547, Dshi_0548, Dshi_0549, xdhA, xylB
Dyella japonica UNC79MFTsu3.2 PLT5, xdhA, xylB
Echinicola vietnamensis KMM 6221, DSM 17526 PLT5, xdhA, xylB
Escherichia coli BW25113 PLT5, xdhA, xylB
Herbaspirillum seropedicae SmR1 HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Klebsiella michiganensis M5al fruI, x5p-reductase
Magnetospirillum magneticum AMB-1 fruI, x5p-reductase
Marinobacter adhaerens HP15 fruI, x5p-reductase
Paraburkholderia bryophila 376MFSha3.1 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Pedobacter sp. GW460-11-11-14-LB5 PLT5, xdhA, xylB
Phaeobacter inhibens BS107 PLT5, xdhA, xylB
Pseudomonas fluorescens FW300-N1B4 PLT5, xdhA, xylB
Pseudomonas fluorescens FW300-N2C3 PLT5, xdhA, xylB
Pseudomonas fluorescens FW300-N2E2 PLT5, xdhA, xylB
Pseudomonas fluorescens FW300-N2E3 PLT5, xdhA, xylB
Pseudomonas fluorescens GW456-L13 PLT5, xdhA, xylB
Pseudomonas putida KT2440 fruI, x5p-reductase
Pseudomonas simiae WCS417 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Pseudomonas stutzeri RCH2 fruI, x5p-reductase
Shewanella amazonensis SB2B fruI, x5p-reductase
Shewanella loihica PV-4 fruI, x5p-reductase
Shewanella oneidensis MR-1 fruI, x5p-reductase
Shewanella sp. ANA-3 fruI, x5p-reductase
Sinorhizobium meliloti 1021 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sphingomonas koreensis DSMZ 15582 fruI, x5p-reductase
Synechococcus elongatus PCC 7942 fruI, x5p-reductase

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 Sep 17 2021. The underlying query database was built on Sep 17 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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