xylitol catabolism

GapMind for catabolism of small carbon sources

xylitol catabolism

Analysis of pathway xylitol in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	fruI, x5p-reductase
Acidithiobacillus ferrooxidans ATCC 23270	fruI, x5p-reductase
Alicycliphilus denitrificans K601	fruI, x5p-reductase
Allochromatium vinosum DSM 180	fruI, x5p-reductase
Ammonifex degensii KC4	fruI, x5p-reductase
Archaeoglobus veneficus SNP6	fruI, x5p-reductase
Arcobacter nitrofigilis DSM 7299	fruI, x5p-reductase
Azoarcus sp. BH72	fruI, x5p-reductase
Azohydromonas australica DSM 1124	fruI, x5p-reductase
Azorhizobium caulinodans ORS 571	fruI, x5p-reductase
Azospirillum lipoferum B510	PLT5, xdhA, xylB
Bacillus alkalinitrilicus DSM 22532	fruI, x5p-reductase
Beijerinckia indica ATCC 9039	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Beijerinckia mobilis UQM 1969	fruI, x5p-reductase
Bradyrhizobium sp. BTAi1	PLT5, xdhA, xylB
Burkholderia vietnamiensis G4	PLT5, xdhA, xylB
Calditerrivibrio nitroreducens DSM 19672	fruI, x5p-reductase
Caminibacter mediatlanticus TB-2	fruI, x5p-reductase
Chlorobaculum parvum NCIB 8327	fruI, x5p-reductase
Chlorobaculum tepidum TLS	fruI, x5p-reductase
Chlorobium limicola DSM 245	fruI, x5p-reductase
Chlorobium phaeobacteroides BS1	fruI, x5p-reductase
Clostridium acetobutylicum ATCC 824	fruI, x5p-reductase
Clostridium kluyveri DSM 555	fruI, x5p-reductase
Crocosphaera subtropica ATCC 51142	fruI, x5p-reductase
Dechloromonas agitata is5	fruI, x5p-reductase
Dehalococcoides mccartyi 195	fruI, x5p-reductase
Denitrovibrio acetiphilus DSM 12809	fruI, x5p-reductase
Derxia gummosa DSM 723	PLT5, xdhA, xylB
Desulfacinum hydrothermale DSM 13146	fruI, x5p-reductase
Desulfacinum infernum DSM 9756	fruI, x5p-reductase
Desulfallas geothermicus DSM 3669	fruI, x5p-reductase
Desulfarculus baarsii DSM 2075	fruI, x5p-reductase
Desulfatibacillum aliphaticivorans DSM 15576	fruI, x5p-reductase
Desulfatiglans anilini DSM 4660	fruI, x5p-reductase
Desulfitobacterium hafniense DCB-2	fruI, x5p-reductase
Desulfobacca acetoxidans DSM 11109	fruI, x5p-reductase
Desulfobacter vibrioformis DSM 8776	fruI, x5p-reductase
Desulfobulbus mediterraneus DSM 13871	fruI, x5p-reductase
Desulfotalea psychrophila LSv54	fruI, x5p-reductase
Desulfotomaculum ruminis DSM 2154	PLT5, xdhA, xylB
Desulfovibrio bastinii DSM 16055	fruI, x5p-reductase
Desulfovibrio gracilis DSM 16080	fruI, x5p-reductase
Desulfovibrio oxyclinae DSM 11498	fruI, x5p-reductase
Desulfovibrio zosterae DSM 11974	fruI, x5p-reductase
Desulfurobacterium atlanticum DSM 15668	fruI, x5p-reductase
Desulfuromonas acetexigens	fruI, x5p-reductase
Desulfuromusa kysingii DSM 7343	fruI, x5p-reductase
Ferroglobus placidus DSM 10642	fruI, x5p-reductase
Frankia alni ACN14A	fruI, x5p-reductase
Geobacter lovleyi SZ	fruI, x5p-reductase
Geobacter metallireducens GS-15	fruI, x5p-reductase
Geobacter uraniireducens Rf4	fruI, x5p-reductase
Haloechinothrix alba DSM 45207	PLT5, xdhA, xylB
Haloglycomyces albus DSM 45210	fruI, x5p-reductase
Halomonas desiderata SP1	fruI, x5p-reductase
Halorhodospira halophila SL1	fruI, x5p-reductase
Heliobacterium modesticaldum Ice1; ATCC 51547	fruI, x5p-reductase
Herbaspirillum autotrophicum IAM 14942	fruI, x5p-reductase
Hydrogenophaga taeniospiralis NBRC 102512	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Hydrogenovibrio halophilus DSM 15072	fruI, x5p-reductase
Hydrogenovibrio kuenenii DSM 12350	fruI, x5p-reductase
Hydrogenovibrio marinus DSM 11271	fruI, x5p-reductase
Hyphomicrobium sulfonivorans WDL6	fruI, x5p-reductase
Klebsiella variicola At-22	fruI, x5p-reductase
Kyrpidia tusciae DSM 2912	fruI, x5p-reductase
Leptospirillum ferrooxidans C2-3	fruI, x5p-reductase
Malonomonas rubra DSM 5091	fruI, x5p-reductase
Mesorhizobium ciceri WSM1271	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Methanobacterium lacus AL-21	fruI, x5p-reductase
Methanococcus aeolicus Nankai-3	fruI, x5p-reductase
Methanococcus maripaludis C5	fruI, x5p-reductase
Methanosarcina acetivorans C2A	fruI, x5p-reductase
Methanosarcina barkeri Fusaro	fruI, x5p-reductase
Methanosarcina mazei Go1	fruI, x5p-reductase
Methanothermobacter thermautotrophicus Delta H	fruI, x5p-reductase
Methylobacterium nodulans ORS 2060	fruI, x5p-reductase
Methylobacterium sp. 4-46	fruI, x5p-reductase
Methylocapsa acidiphila B2	fruI, x5p-reductase
Methylocapsa aurea KYG T	fruI, x5p-reductase
Methylocella silvestris BL2	fruI, x5p-reductase
Methylococcus capsulatus Bath	fruI, x5p-reductase
Methylocystis bryophila S285	fruI, x5p-reductase
Methyloferula stellata AR4T	fruI, x5p-reductase
Methylohalobius crimeensis 10Ki	fruI, x5p-reductase
Methylomicrobium alcaliphilum 20Z	fruI, x5p-reductase
Methylomonas methanica MC09	fruI, x5p-reductase
Methylosarcina fibrata AML-C10	fruI, x5p-reductase
Methylovulum miyakonense HT12	fruI, x5p-reductase
Mycolicibacterium vanbaalenii PYR-1	PLT5, xdhA, xylB
Nitratifractor salsuginis DSM 16511	fruI, x5p-reductase
Nitratiruptor tergarcus DSM 16512	fruI, x5p-reductase
Nitriliruptor alkaliphilus DSM 45188	PLT5, xdhA, xylB
Nocardiopsis lucentensis DSM 44048	PLT5, xdhA, xylB
Nostoc punctiforme ATCC 29133; PCC 73102	fruI, x5p-reductase
Novosphingobium aromaticivorans DSM 12444	PLT5, xdhA, xylB
Oleispira antarctica	fruI, x5p-reductase
Paraburkholderia phymatum STM815	HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Paraburkholderia sp. CCGE1002	HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Pelobacter propionicus DSM 2379	fruI, x5p-reductase
Persephonella marina EX-H1	fruI, x5p-reductase
Polaromonas naphthalenivorans CJ2	fruI, x5p-reductase
Prosthecochloris aestuarii DSM 271	fruI, x5p-reductase
Pseudarthrobacter sulfonivorans Ar51	PLT5, xdhA, xylB
Pseudomonas benzenivorans DSM 8628	fruI, x5p-reductase
Pseudomonas stutzeri A1501	PLT5, xdhA, xylB
Pyrolobus fumarii 1A	fruI, x5p-reductase
Rhizobium etli CFN 42	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizobium leguminosarum 3841	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizobium leguminosarum WSM1325	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhodobacter sphaeroides ATCC 17029	PLT5, xdhA, xylB
Rhodomicrobium vannielii ATCC 17100	fruI, x5p-reductase
Rhodopseudomonas palustris CGA009	fruI, x5p-reductase
Rhodospirillum centenum SW; ATCC 51521	fruI, x5p-reductase
Rhodospirillum rubrum ATCC 11170	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Saccharomonospora cyanea NA-134	PLT5, xdhA, xylB
Sedimenticola selenatireducens DSM 17993	fruI, x5p-reductase
Sinorhizobium fredii NGR234	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sinorhizobium medicae WSM419	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sphingomonas wittichii RW1	fruI, x5p-reductase
Stenotrophomonas chelatiphaga DSM 21508	PLT5, xdhA, xylB
Steroidobacter denitrificans DSM 18526	fruI, x5p-reductase
Sulfuricurvum kujiense DSM 16994	fruI, x5p-reductase
Sulfurihydrogenibium azorense Az-Fu1	fruI, x5p-reductase
Sulfurihydrogenibium subterraneum DSM 15120	fruI, x5p-reductase
Sulfurimonas denitrificans DSM 1251	fruI, x5p-reductase
Sulfuritalea hydrogenivorans DSM 22779	fruI, x5p-reductase
Sulfurivirga caldicuralii DSM 17737	fruI, x5p-reductase
Teredinibacter turnerae T7901	PLT5, xdhA, xylB
Thauera aminoaromatica S2	fruI, x5p-reductase
Thermithiobacillus tepidarius DSM 3134	fruI, x5p-reductase
Thermocrinis albus DSM 14484	fruI, x5p-reductase
Thermodesulforhabdus norvegica DSM 9990	fruI, x5p-reductase
Thermomonospora curvata DSM 43183	fruI, x5p-reductase
Thermovibrio ammonificans HB-1	fruI, x5p-reductase
Thioalkalivibrio denitrificans ALJD	fruI, x5p-reductase
Thioalkalivibrio halophilus HL17	fruI, x5p-reductase
Thioalkalivibrio paradoxus ARh 1	fruI, x5p-reductase
Thioalkalivibrio thiocyanodenitrificans ARhD 1	fruI, x5p-reductase
Thiohalomonas denitrificans HLD2	fruI, x5p-reductase
Thiomicrorhabdus arctica DSM 13458	fruI, x5p-reductase
Thiomicrorhabdus chilensis DSM 12352	fruI, x5p-reductase
Thiomicrospira cyclica ALM1	fruI, x5p-reductase
Thiomicrospira microaerophila ASL8-2	fruI, x5p-reductase
Thiomicrospira pelophila DSM 1534	fruI, x5p-reductase
Thiothrix lacustris DSM 21227	PLT5, xdhA, xylB
Trichodesmium erythraeum IMS101	fruI, x5p-reductase
Trichormus variabilis ATCC 29413	fruI, x5p-reductase
Xanthobacter autotrophicus Py2	fruI, x5p-reductase
Xenophilus azovorans DSM 13620	PLT5, xdhA, xylB

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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources