xylitol catabolism

GapMind for catabolism of small carbon sources

xylitol catabolism

Analysis of pathway xylitol in 276 genomes

Genome	Best path
Acidovorax caeni R-24608	fruI, x5p-reductase
Actinokineospora bangkokensis 44EHW	PLT5, xdhA, xylB
Actinomyces timonensis 7400942	fruI, x5p-reductase
Algiphilus aromaticivorans DG1253	fruI, x5p-reductase
Algoriphagus aquaeductus T4	PLT5, xdhA, xylB
Algoriphagus machipongonensis PR1	PLT5, xdhA, xylB
Alicyclobacillus ferrooxydans TC-34	fruI, x5p-reductase
Alishewanella agri BL06	fruI, x5p-reductase
Alistipes indistinctus YIT 12060	PLT5, xdhA, xylB
Alistipes shahii WAL 8301	fruI, x5p-reductase
Alkalitalea saponilacus SC/BZ-SP2	fruI, x5p-reductase
Amantichitinum ursilacus IGB-41	PLT5, xdhA, xylB
Amphibacillus jilinensis Y1	fruI, x5p-reductase
Amphritea japonica JAMM 1866	fruI, x5p-reductase
Amycolatopsis halophila YIM 93223	fruI, x5p-reductase
Amycolatopsis xylanica CPCC 202699	PLT5, xdhA, xylB
Aquimarina agarilytica ZC1	PLT5, xdhA, xylB
Aquimarina longa SW024	fruI, x5p-reductase
Aquimarina macrocephali JAMB N27	fruI, x5p-reductase
Archaeoglobus sulfaticallidus PM70-1	fruI, x5p-reductase
Arcticibacter svalbardensis MN12-7	PLT5, xdhA, xylB
Ardenticatena maritima 110S	PLT5, xdhA, xylB
Arenimonas metalli CF5-1	fruI, x5p-reductase
Arenitalea lutea P7-3-5	PLT5, xdhA, xylB
Azospirillum humicireducens SgZ-5	PLT5, xdhA, xylB
Azospirillum thiophilum BV-S	PLT5, xdhA, xylB
Bacillus altitudinis 41KF2b	EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
Bacillus coahuilensis m4-4	fruI, x5p-reductase
Bacillus cytotoxicus NVH 391-98	fruI, x5p-reductase
Bacillus horneckiae 1P01SC	fruI, x5p-reductase
Bacillus okhensis Kh10-101	fruI, x5p-reductase
Bacillus safensis FO-36b	EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
Bacillus velezensis CBMB205	PLT5, xdhA, xylB
Bacteroides clarus YIT 12056	PLT5, xdhA, xylB
Bacteroides faecis MAJ27	PLT5, xdhA, xylB
Bacteroides fluxus YIT 12057	PLT5, xdhA, xylB
Bacteroides oleiciplenus YIT 12058	PLT5, xdhA, xylB
Barnesiella intestinihominis YIT 11860	fruI, x5p-reductase
Belnapia rosea CPCC 100156	fruI, x5p-reductase
Bizionia argentinensis JUB59	fruI, x5p-reductase
Bradyrhizobium diazoefficiens USDA110	PLT5, xdhA, xylB
Brevibacterium jeotgali SJ5-8	fruI, x5p-reductase
Brucella inopinata BO1	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Brucella microti CCM 4915	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Bryobacter aggregatus MPL3	PLT5, xdhA, xylB
Caldicellulosiruptor hydrothermalis 108	fruI, x5p-reductase
Caldicellulosiruptor kronotskyensis 2002	PLT5, xdhA, xylB
Carboxydothermus pertinax Ug1	fruI, x5p-reductase
Catellicoccus marimammalium M35/04/3	fruI, x5p-reductase
Chromobacterium vaccinii MWU205	fruI, x5p-reductase
Chryseobacterium angstadtii KM	fruI, x5p-reductase
Chryseobacterium arthrosphaerae CC-VM-7	PLT5, xdhA, xylB
Chryseobacterium viscerum 687B-08	fruI, x5p-reductase
Cloacibacillus porcorum CL-84	PLT5, xdhA, xylB
Cobetia crustatorum JO1	fruI, x5p-reductase
Collimonas arenae Ter10	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Collimonas pratensis Ter91	HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Collinsella tanakaei YIT 12063	fruI, x5p-reductase
Coprobacter fastidiosus NSB1	PLT5, xdhA, xylB
Corynebacterium deserti GIMN1.010	PLT5, xdhA, xylB
Corynebacterium frankenforstense ST18	PLT5, xdhA, xylB
Corynebacterium lactis RW2-5	fruI, x5p-reductase
Croceitalea dokdonensis DOKDO 023	PLT5, xdhA, xylB
Cronobacter condimenti 1330	PLT5, xdhA, xylB
Cronobacter muytjensii ATCC 51329	PLT5, xdhA, xylB
Cronobacter universalis NCTC 9529	PLT5, xdhA, xylB
Desulfatitalea tepidiphila S28bF	fruI, x5p-reductase
Desulfotomaculum hydrothermale Lam5	PLT5, xdhA, xylB
Dethiosulfovibrio salsuginis USBA 82	fruI, x5p-reductase
Devosia chinhatensis IPL18	PLT5, xdhA, xylB
Devriesea agamarum IMP2	fruI, x5p-reductase
Dialister succinatiphilus YIT 11850	fruI, x5p-reductase
Dietzia timorensis ID05-A0528	fruI, x5p-reductase
Dokdonella koreensis DS-123	fruI, x5p-reductase
Domibacillus robiginosus WS 4628	fruI, x5p-reductase
Duganella sacchari Sac-22	fruI, x5p-reductase
Dyadobacter tibetensis Y620-1	PLT5, xdhA, xylB
Dyella jiangningensis SBZ3-12	PLT5, xdhA, xylB
Endozoicomonas montiporae CL-33	fruI, x5p-reductase
Enterococcus termitis LMG 8895	fruI, x5p-reductase
Enterorhabdus caecimuris B7	fruI, x5p-reductase
Epibacterium ulvae U95	fruI, x5p-reductase
Erythrobacter gangjinensis K7-2	fruI, x5p-reductase
Erythrobacter marinus HWDM-33	fruI, x5p-reductase
Ethanoligenens harbinense YUAN-3	fruI, x5p-reductase
Fervidicella metallireducens AeB	fruI, x5p-reductase
Fibrella aestuarina BUZ 2	PLT5, xdhA, xylB
Flammeovirga pacifica WPAGA1	PLT5, xdhA, xylB
Flaviramulus ichthyoenteri Th78	PLT5, xdhA, xylB
Flavobacterium beibuense F44-8	PLT5, xdhA, xylB
Flavobacterium glycines Gm-149	PLT5, xdhA, xylB
Flavobacterium sp. LM5	fruI, x5p-reductase
Flavobacterium ummariense DS-12	fruI, x5p-reductase
Frischella perrara PEB0191	fruI, x5p-reductase
Galbibacter marinus ck-I2-15	PLT5, xdhA, xylB
Gallaecimonas xiamenensis 3-C-1	fruI, x5p-reductase
Geobacter daltonii FRC-32	fruI, x5p-reductase
Gillisia marina CBA3202	fruI, x5p-reductase
Gracilibacillus halophilus YIM-C55.5	PLT5, xdhA, xylB
Granulicella mallensis MP5ACTX8	PLT5, xdhA, xylB
Granulicella tundricola MP5ACTX9	PLT5, xdhA, xylB
Hafnia paralvei ATCC 29927	fruI, x5p-reductase
Haladaptatus cibarius D43	PLT5, xdhA, xylB
Halioglobus japonicus S1-36	fruI, x5p-reductase
Halobacillus alkaliphilus FP5	fruI, x5p-reductase
Halococcus hamelinensis 100A6	PLT5, xdhA, xylB
Halomonas salina B6	PLT5, xdhA, xylB
Halomonas smyrnensis AAD6	fruI, x5p-reductase
Halomonas stevensii S18214	fruI, x5p-reductase
Halomonas titanicae BH1	PLT5, xdhA, xylB
Halomonas xinjiangensis TRM 0175	fruI, x5p-reductase
Halopiger salifodinae KCY07-B2	fruI, x5p-reductase
Halostagnicola larsenii XH-48	fruI, x5p-reductase
Haloterrigena daqingensis JX313	fruI, x5p-reductase
Herbaspirillum aquaticum IEH 4430	HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Hippea alviniae EP5-r	fruI, x5p-reductase
Hippea jasoniae Mar08-272r	fruI, x5p-reductase
Hoeflea phototrophica DFL-43	Dshi_0546, Dshi_0547, Dshi_0548, Dshi_0549, xdhA, xylB
Hyphomicrobium nitrativorans NL23	fruI, x5p-reductase
Imtechella halotolerans K1	fruI, x5p-reductase
Indibacter alkaliphilus LW1	PLT5, xdhA, xylB
Jannaschia aquimarina GSW-M26	PLT5, xdhA, xylB
Jeotgalibacillus soli P9	fruI, x5p-reductase
Kangiella geojedonensis YCS-5	fruI, x5p-reductase
Knoellia flava TL1	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Kocuria flava HO-9041	fruI, x5p-reductase
Kocuria turfanensis HO-9042	PLT5, xdhA, xylB
Laceyella sediminis RHA1	fruI, x5p-reductase
Lacinutrix algicola AKS293	fruI, x5p-reductase
Lacinutrix himadriensis E4-9a	fruI, x5p-reductase
Lacinutrix mariniflava AKS432	fruI, x5p-reductase
Lactobacillus curieae CCTCC M 2011381	PLT5, xdhA, xylB
Lactobacillus delbrueckii ZN7a-9	fruI, x5p-reductase
Lactobacillus hokkaidonensis LOOC260	PLT5, xdhA, xylB
Lactobacillus oryzae SG293	PLT5, xdhA, xylB
Lactobacillus pobuzihii E100301	fruI, x5p-reductase
Lactobacillus shenzhenensis LY-73	fruI, x5p-reductase
Lactobacillus silagei IWT126	PLT5, xdhA, xylB
Leeuwenhoekiella blandensis MED217	PLT5, xdhA, xylB
Lentibacillus jeotgali Grbi	PLT5, xdhA, xylB
Limnohabitans curvus MWH-C5	fruI, x5p-reductase
Limnohabitans parvus II-B4	fruI, x5p-reductase
Listeria fleischmannii LU2006-1	fruI, x5p-reductase
Luteimonas huabeiensis HB2	PLT5, xdhA, xylB
Luteipulveratus mongoliensis MN07-A0370	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Lutibaculum baratangense AMV1	PLT5, xdhA, xylB
Lysobacter daejeonensis GH1-9	fruI, x5p-reductase
Magnetovibrio blakemorei MV-1	fruI, x5p-reductase
Marinicella litoralis KMM 3900	fruI, x5p-reductase
Mariniradius saccharolyticus AK6	PLT5, xdhA, xylB
Marinobacter algicola DG893	fruI, x5p-reductase
Marinobacter guineae M3B	fruI, x5p-reductase
Marinobacter psychrophilus 20041	fruI, x5p-reductase
Marinomonas arctica 328	PLT5, xdhA, xylB
Marivita geojedonensis DPG-138	PLT5, xdhA, xylB
Martelella endophytica YC6887	PLT5, xdhA, xylB
Megamonas funiformis YIT 11815	EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
Mesorhizobium ciceri WSM1271	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Methanobacterium arcticum M2	fruI, x5p-reductase
Methanobacterium veterum MK4	fruI, x5p-reductase
Methanocella arvoryzae MRE50	fruI, x5p-reductase
Methanococcus aeolicus Nankai-3	fruI, x5p-reductase
Methanoculleus horonobensis T10	fruI, x5p-reductase
Methanolinea tarda NOBI-1	fruI, x5p-reductase
Methanosarcina soligelidi SMA-21	fruI, x5p-reductase
Methanospirillum lacunae Ki8-1	fruI, x5p-reductase
Methanospirillum stamsii Pt1	fruI, x5p-reductase
Methylibium petroleiphilum PM1	fruI, x5p-reductase
Methylobacterium gossipiicola Gh-105	fruI, x5p-reductase
Methylocapsa aurea KYG	fruI, x5p-reductase
Methylotenera versatilis 301	fruI, x5p-reductase
Microbacterium profundi Shh49	PLT5, xdhA, xylB
Microvirga lotononidis WSM3557	PLT5, xdhA, xylB
Moritella dasanensis ArB 0140	fruI, x5p-reductase
Mucilaginibacter gossypii Gh-67	PLT5, xdhA, xylB
Mucilaginibacter gossypiicola Gh-48	PLT5, xdhA, xylB
Mucilaginibacter mallensis MP1X4	PLT5, xdhA, xylB
Nafulsella turpanensis ZLM-10	PLT5, xdhA, xylB
Natronomonas moolapensis 8.8.11	fruI, x5p-reductase
Nautilia profundicola AmH	fruI, x5p-reductase
Neiella marina J221	PLT5, xdhA, xylB
Neptunomonas antarctica S3-22	PLT5, xdhA, xylB
Nocardioides daejeonensis MJ31	fruI, x5p-reductase
Nocardioides dokdonensis FR1436	fruI, x5p-reductase
Nocardiopsis baichengensis YIM 90130	fruI, x5p-reductase
Nocardiopsis gilva YIM 90087	PLT5, xdhA, xylB
Novosphingobium barchaimii LL02	fruI, x5p-reductase
Novosphingobium fuchskuhlense FNE08-7	fruI, x5p-reductase
Novosphingobium lindaniclasticum LE124	fruI, x5p-reductase
Oceanisphaera arctica V1-41	fruI, x5p-reductase
Ochrobactrum rhizosphaerae PR17	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Ochrobactrum thiophenivorans DSM 7216	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Oscillibacter ruminantium GH1	PLT5, xdhA, xylB
Paenisporosarcina indica PN2	PLT5, xdhA, xylB
Palaeococcus pacificus DY20341	fruI, x5p-reductase
Paludibacter propionicigenes WB4	PLT5, xdhA, xylB
Pandoraea thiooxydans ATSB16	fruI, x5p-reductase
Pantoea rwandensis LMG 26275	PLT5, xdhA, xylB
Pedobacter arcticus A12	PLT5, xdhA, xylB
Photobacterium gaetbulicola Gung47	fruI, x5p-reductase
Photobacterium jeanii R-40508	fruI, x5p-reductase
Phyllobacterium brassicacearum STM 196	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Phyllobacterium endophyticum PEPV15	Dshi_0546, Dshi_0547, Dshi_0548, Dshi_0549, xdhA, xylB
Phyllobacterium leguminum ORS 1419	PLT5, xdhA, xylB
Planktomarina temperata RCA23	PLT5, xdhA, xylB
Planococcus halocryophilus Or1	fruI, x5p-reductase
Pleomorphomonas diazotrophica R5-392	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Polaribacter dokdonensis DSW-5	fruI, x5p-reductase
Pontibacillus litoralis JSM 072002	fruI, x5p-reductase
Pontibacter lucknowensis DM9	PLT5, xdhA, xylB
Pontibacter ramchanderi LP43	fruI, x5p-reductase
Pontimonas salivibrio CL-TW6	PLT5, xdhA, xylB
Porphyrobacter dokdonensis DSW-74	fruI, x5p-reductase
Pseudoalteromonas arctica A 37-1-2	fruI, x5p-reductase
Pseudomonas baetica a390	PLT5, xdhA, xylB
Pseudomonas litoralis 2SM5	fruI, x5p-reductase
Pseudomonas taeanensis MS-3	fruI, x5p-reductase
Pseudovibrio axinellae Ad2	fruI, x5p-reductase
Psychrobacter arcticus 273-4	fruI, x5p-reductase
Psychrobacter cryohalolentis K5	fruI, x5p-reductase
Psychromonas ingrahamii 37	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Psychromonas ossibalaenae JAMM 0738	PLT5, xdhA, xylB
Rhizobium freirei PRF 81	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizobium grahamii CCGE 502	PLT5, xdhA, xylB
Rhizobium subbaraonis JC85	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhodanobacter denitrificans 2APBS1	fruI, x5p-reductase
Rhodobacter johrii JA192	PLT5, xdhA, xylB
Rhodobacter maris JA276	PLT5, xdhA, xylB
Rhodobacter ovatus JA234	PLT5, xdhA, xylB
Rhodobacter viridis JA737	fruI, x5p-reductase
Rhodococcus qingshengii djl-6-2	PLT5, xdhA, xylB
Rhodopseudomonas pseudopalustris DSM 123	fruI, x5p-reductase
Roseateles aquatilis CCUG 48205	fruI, x5p-reductase
Roseivirga spongicola UST030701-084	PLT5, xdhA, xylB
Rubrivirga marina SAORIC-28	PLT5, xdhA, xylB
Ruegeria conchae TW15	PLT5, xdhA, xylB
Saccharomonospora marina XMU15	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Salinicoccus carnicancri Crm	fruI, x5p-reductase
Serinicoccus profundi MCCC 1A05965	fruI, x5p-reductase
Shewanella halifaxensis HAW-EB4	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Skermanella stibiiresistens SB22	Dshi_0546, Dshi_0547, Dshi_0548, Dshi_0549, xdhA, xylB
Snodgrassella alvi wkB2	fruI, x5p-reductase
Sphaerochaeta globosa Buddy	PLT5, xdhA, xylB
Sphaerochaeta pleomorpha Grapes	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sphingobium baderi LL03	fruI, x5p-reductase
Sphingobium czechense LL01	fruI, x5p-reductase
Sphingobium quisquiliarum P25	fruI, x5p-reductase
Sphingomonas histidinilytica UM2	fruI, x5p-reductase
Sphingomonas indica Dd16	fruI, x5p-reductase
Sphingomonas laterariae LNB2	fruI, x5p-reductase
Sphingopyxis indica DS15	PLT5, xdhA, xylB
Sphingopyxis terrae UI2	fruI, x5p-reductase
Sporolactobacillus vineae SL153	fruI, x5p-reductase
Streptacidiphilus oryzae TH49	PLT5, xdhA, xylB
Streptococcus anginosus CCUG 39159	fruI, x5p-reductase
Streptococcus massiliensis 4401825	fruI, x5p-reductase
Streptococcus oralis 7747	fruI, x5p-reductase
Streptococcus oralis AZ_3a	fruI, x5p-reductase
Streptomyces kebangsaanensis SUK12	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Succinatimonas hippei YIT 12066	PLT5, xdhA, xylB
Sulfurimonas gotlandica GD1	fruI, x5p-reductase
Tatumella morbirosei LMG 23360	fruI, x5p-reductase
Thauera humireducens SgZ-1	fruI, x5p-reductase
Thermoactinomyces daqus H-18	fruI, x5p-reductase
Thermobifida halotolerans YIM 90462	fruI, x5p-reductase
Thermodesulfovibrio aggregans TGE-P1	fruI, x5p-reductase
Thermophagus xiamenensis HS1	PLT5, xdhA, xylB
Thermovenabulum gondwanense R270	EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
Thioclava dalianensis DLFJ1-1	PLT5, xdhA, xylB
Thiohalospira halophila HL 3	fruI, x5p-reductase
Tistlia consotensis USBA 355	fruI, x5p-reductase
Vagococcus penaei CD276	fruI, x5p-reductase
Verminephrobacter eiseniae EF01-2	PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Weissella oryzae SG25	PLT5, xdhA, xylB
Williamsia sterculiae CPCC 203464	PLT5, xdhA, xylB
Yersinia intermedia Y228	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