GapMind for catabolism of small carbon sources

 

xylitol catabolism

Analysis of pathway xylitol in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 fruI, x5p-reductase
Acidithiobacillus ferrooxidans ATCC 23270 fruI, x5p-reductase
Acidovorax sp. GW101-3H11 PLT5, xdhA, xylB
Algiphilus aromaticivorans DG1253 fruI, x5p-reductase
Alicycliphilus denitrificans K601 fruI, x5p-reductase
Alkalihalobacterium alkalinitrilicum DSM 22532 fruI, x5p-reductase
Allochromatium vinosum DSM 180 fruI, x5p-reductase
Ammonifex degensii KC4 fruI, x5p-reductase
Anaerobutyricum hallii DSM 3353 fruI, x5p-reductase
Aquimarina longa SW024 fruI, x5p-reductase
Archaeoglobus veneficus SNP6 fruI, x5p-reductase
Arcobacter nitrofigilis DSM 7299 fruI, x5p-reductase
Azoarcus olearius BH72 fruI, x5p-reductase
Azohydromonas australica DSM 1124 fruI, x5p-reductase
Azorhizobium caulinodans ORS 571 fruI, x5p-reductase
Azospirillum brasilense Sp245 fruI, x5p-reductase
Azospirillum sp. B510 PLT5, xdhA, xylB
Bacteroides thetaiotaomicron VPI-5482 PLT5, xdhA, xylB
Beijerinckia indica ATCC 9039 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Beijerinckia mobilis UQM 1969 fruI, x5p-reductase
Billgrantia desiderata SP1 fruI, x5p-reductase
Bradyrhizobium sp. BTAi1 PLT5, xdhA, xylB
Brevundimonas sp. GW460-12-10-14-LB2 fruI, x5p-reductase
Burkholderia phytofirmans PsJN PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Burkholderia vietnamiensis G4 PLT5, xdhA, xylB
Calditerrivibrio nitroreducens DSM 19672 fruI, x5p-reductase
Caminibacter mediatlanticus TB-2 fruI, x5p-reductase
Carboxydothermus pertinax Ug1 fruI, x5p-reductase
Caulobacter crescentus NA1000 fruI, x5p-reductase
Cereibacter sphaeroides ATCC 17029 PLT5, xdhA, xylB
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
Clostridium tyrobutyricum FAM22553 EIIA-Axl, EIIB-Axl, EIIC-Axl, x5p-reductase
Crocosphaera subtropica ATCC 51142 fruI, x5p-reductase
Cupriavidus basilensis FW507-4G11 fruI, x5p-reductase
Dechloromonas agitata is5 fruI, x5p-reductase
Dechlorosoma suillum PS 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
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
Desulfogranum mediterraneum DSM 13871 fruI, x5p-reductase
Desulforamulus ruminis DSM 2154 PLT5, xdhA, xylB
Desulfoscipio geothermicus DSM 3669 fruI, x5p-reductase
Desulfotalea psychrophila LSv54 fruI, x5p-reductase
Desulfovibrio oxyclinae DSM 11498 fruI, x5p-reductase
Desulfovibrio vulgaris Hildenborough JW710 fruI, x5p-reductase
Desulfovibrio vulgaris Miyazaki F fruI, x5p-reductase
Desulfurobacterium atlanticum DSM 15668 fruI, x5p-reductase
Desulfuromonas acetexigens fruI, x5p-reductase
Desulfuromusa kysingii DSM 7343 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
Ferroglobus placidus DSM 10642 fruI, x5p-reductase
Frankia alni ACN14a fruI, x5p-reductase
Geobacter metallireducens GS-15 fruI, x5p-reductase
Geotalea uraniireducens Rf4 fruI, x5p-reductase
Halococcus hamelinensis 100A6 PLT5, xdhA, xylB
Haloechinothrix alba DSM 45207 PLT5, xdhA, xylB
Haloferax volcanii DS2 fruI, x5p-reductase
Haloglycomyces albus DSM 45210 fruI, x5p-reductase
Halorhodospira halophila SL1 fruI, x5p-reductase
Heliomicrobium modesticaldum Ice1; ATCC 51547 fruI, x5p-reductase
Herbaspirillum autotrophicum IAM 14942 fruI, x5p-reductase
Herbaspirillum seropedicae SmR1 HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Hippea alviniae EP5-r 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 michiganensis M5al PLT5, xdhA, xylB
Klebsiella variicola At-22 fruI, x5p-reductase
Kyrpidia tusciae DSM 2912 fruI, x5p-reductase
Leptospirillum ferrooxidans C2-3 fruI, x5p-reductase
Magnetospirillum magneticum AMB-1 fruI, x5p-reductase
Malonomonas rubra DSM 5091 fruI, x5p-reductase
Maridesulfovibrio bastinii DSM 16055 fruI, x5p-reductase
Maridesulfovibrio zosterae DSM 11974 fruI, x5p-reductase
Marinobacter adhaerens HP15 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 mazei Go1 fruI, x5p-reductase
Methanospirillum lacunae Ki8-1 fruI, x5p-reductase
Methanothermobacter thermautotrophicus Delta H fruI, x5p-reductase
Methylobacterium nodulans ORS 2060 fruI, x5p-reductase
Methylobacterium sp. 4-46 Apr-46 fruI, x5p-reductase
Methylocapsa acidiphila B2 fruI, x5p-reductase
Methylocapsa aurea KYG 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
Methylomonas methanica MC09 fruI, x5p-reductase
Methylosarcina fibrata AML-C10 fruI, x5p-reductase
Methylotuvimicrobium alcaliphilum 20Z 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
Nocardioides dokdonensis FR1436 fruI, x5p-reductase
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 atlantica CCGE1002 HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Paraburkholderia bryophila 376MFSha3.1 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Paraburkholderia phymatum STM815 HSERO_RS17000, HSERO_RS17005, HSERO_RS17010, HSERO_RS17020, xdhA, xylB
Paucidesulfovibrio gracilis DSM 16080 fruI, x5p-reductase
Pedobacter sp. GW460-11-11-14-LB5 PLT5, xdhA, xylB
Pelobacter propionicus DSM 2379 fruI, x5p-reductase
Persephonella marina EX-H1 fruI, x5p-reductase
Phaeacidiphilus oryzae TH49 PLT5, xdhA, xylB
Phaeobacter inhibens BS107 PLT5, xdhA, xylB
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 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
Pyrolobus fumarii 1A fruI, x5p-reductase
Rhizobium etli CFN 42 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizobium johnstonii 3841 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizobium leguminosarum WSM1325 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Rhizorhabdus wittichii RW1 fruI, x5p-reductase
Rhodanobacter denitrificans FW104-10B01 fruI, x5p-reductase
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
Roseburia faecis M72 fruI, x5p-reductase
Saccharomonospora cyanea NA-134 PLT5, xdhA, xylB
Sedimenticola selenatireducens DSM 17993 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 fredii NGR234 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sinorhizobium medicae WSM419 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sinorhizobium meliloti 1021 PS417_12065, PS417_12060, PS417_12055, xdhA, xylB
Sphingomonas koreensis DSMZ 15582 fruI, x5p-reductase
Stenotrophomonas chelatiphaga DSM 21508 PLT5, xdhA, xylB
Steroidobacter denitrificans DSM 18526 fruI, x5p-reductase
Stutzerimonas stutzeri A1501 PLT5, xdhA, xylB
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
Synechococcus elongatus PCC 7942 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
Thermus aquaticus YT-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
Thiohalospira halophila HL 3 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
Tistlia consotensis USBA 355 fruI, x5p-reductase
Trichlorobacter lovleyi SZ fruI, x5p-reductase
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome 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 Apr 09 2024. 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