GapMind for catabolism of small carbon sources

 

D-fructose catabolism

Analysis of pathway fructose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 fruII-ABC, 1pfk, fba, tpi
Acidithiobacillus ferrooxidans ATCC 23270 fruII-ABC, 1pfk, fba, tpi
Acidovorax sp. GW101-3H11 frcA, frcB, frcC, scrK
Algiphilus aromaticivorans DG1253 fruII-ABC, 1pfk, fba, tpi
Alicycliphilus denitrificans K601 fruII-ABC, 1pfk, fba, tpi
Alkalihalobacterium alkalinitrilicum DSM 22532 fruII-ABC, 1pfk, fba, tpi
Allochromatium vinosum DSM 180 Slc2a5, scrK
Ammonifex degensii KC4 fruII-ABC, 1pfk, fba, tpi
Anaerobutyricum hallii DSM 3353 fruII-ABC, 1pfk, fba, tpi
Aquimarina longa SW024 fruII-ABC, 1pfk, fba, tpi
Archaeoglobus veneficus SNP6 fruII-ABC, 1pfk, fba, tpi
Arcobacter nitrofigilis DSM 7299 fruII-ABC, 1pfk, fba, tpi
Azoarcus olearius BH72 fruII-ABC, 1pfk, fba, tpi
Azohydromonas australica DSM 1124 fruII-ABC, 1pfk, fba, tpi
Azorhizobium caulinodans ORS 571 fruII-ABC, 1pfk, fba, tpi
Azospirillum brasilense Sp245 fruA, fruI, 1pfk, fba, tpi
Azospirillum sp. B510 fruA, fruI, 1pfk, fba, tpi
Bacteroides thetaiotaomicron VPI-5482 BT1758, scrK
Beijerinckia indica ATCC 9039 frcA, frcB, frcC, scrK
Beijerinckia mobilis UQM 1969 fruP, scrK
Billgrantia desiderata SP1 fruA, fruI, 1pfk, fba, tpi
Bradyrhizobium sp. BTAi1 frcA, frcB, frcC, scrK
Brevundimonas sp. GW460-12-10-14-LB2 fruP, scrK
Burkholderia phytofirmans PsJN frcA, frcB, frcC, scrK
Burkholderia vietnamiensis G4 frcA, frcB, frcC, scrK
Calditerrivibrio nitroreducens DSM 19672 fruII-ABC, 1pfk, fba, tpi
Caminibacter mediatlanticus TB-2 fruII-ABC, 1pfk, fba, tpi
Carboxydothermus pertinax Ug1 fruII-ABC, 1pfk, fba, tpi
Caulobacter crescentus NA1000 glcP, scrK
Cereibacter sphaeroides ATCC 17029 fruA, fruI, 1pfk, fba, tpi
Chlorobaculum parvum NCIB 8327 fruII-ABC, 1pfk, fba, tpi
Chlorobaculum tepidum TLS fruII-ABC, 1pfk, fba, tpi
Chlorobium limicola DSM 245 fruII-ABC, 1pfk, fba, tpi
Chlorobium phaeobacteroides BS1 fruII-ABC, 1pfk, fba, tpi
Clostridium acetobutylicum ATCC 824 fruII-ABC, 1pfk, fba, tpi
Clostridium kluyveri DSM 555 fruII-ABC, 1pfk, fba, tpi
Clostridium tyrobutyricum FAM22553 fruII-ABC, 1pfk, fba, tpi
Crocosphaera subtropica ATCC 51142 fruII-ABC, 1pfk, fba, tpi
Cupriavidus basilensis FW507-4G11 frcA, frcB, frcC, scrK
Dechloromonas agitata is5 fruII-ABC, 1pfk, fba, tpi
Dechlorosoma suillum PS fruII-ABC, 1pfk, fba, tpi
Dehalococcoides mccartyi 195 fruII-ABC, 1pfk, fba, tpi
Denitrovibrio acetiphilus DSM 12809 fruII-ABC, 1pfk, fba, tpi
Derxia gummosa DSM 723 frcA, frcB, frcC, scrK
Desulfacinum hydrothermale DSM 13146 fruII-ABC, 1pfk, fba, tpi
Desulfacinum infernum DSM 9756 fruII-ABC, 1pfk, fba, tpi
Desulfarculus baarsii DSM 2075 Slc2a5, scrK
Desulfatibacillum aliphaticivorans DSM 15576 fruII-ABC, 1pfk, fba, tpi
Desulfatiglans anilini DSM 4660 fruII-ABC, 1pfk, fba, tpi
Desulfitobacterium hafniense DCB-2 fruII-ABC, 1pfk, fba, tpi
Desulfobacca acetoxidans DSM 11109 fruII-ABC, 1pfk, fba, tpi
Desulfobacter vibrioformis DSM 8776 Slc2a5, scrK
Desulfogranum mediterraneum DSM 13871 Slc2a5, scrK
Desulforamulus ruminis DSM 2154 fruII-ABC, 1pfk, fba, tpi
Desulfoscipio geothermicus DSM 3669 fruII-ABC, 1pfk, fba, tpi
Desulfotalea psychrophila LSv54 fruII-ABC, 1pfk, fba, tpi
Desulfovibrio oxyclinae DSM 11498 fruII-ABC, 1pfk, fba, tpi
Desulfovibrio vulgaris Hildenborough JW710 fruII-ABC, 1pfk, fba, tpi
Desulfovibrio vulgaris Miyazaki F fruII-ABC, 1pfk, fba, tpi
Desulfurobacterium atlanticum DSM 15668 fruII-ABC, 1pfk, fba, tpi
Desulfuromonas acetexigens fruII-ABC, 1pfk, fba, tpi
Desulfuromusa kysingii DSM 7343 fruII-ABC, 1pfk, fba, tpi
Dinoroseobacter shibae DFL-12 frcA, frcB, frcC, scrK
Dyella japonica UNC79MFTsu3.2 fruP, scrK
Echinicola vietnamensis KMM 6221, DSM 17526 glcP, scrK
Escherichia coli BW25113 fruA, fruB, 1pfk, fba, tpi
Ferroglobus placidus DSM 10642 fruII-ABC, 1pfk, fba, tpi
Frankia alni ACN14a fruII-ABC, 1pfk, fba, tpi
Geobacter metallireducens GS-15 Slc2a5, scrK
Geotalea uraniireducens Rf4 Slc2a5, scrK
Halococcus hamelinensis 100A6 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloechinothrix alba DSM 45207 fruII-ABC, 1pfk, fba, tpi
Haloferax volcanii DS2 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloglycomyces albus DSM 45210 glcP, scrK
Halorhodospira halophila SL1 fruII-ABC, 1pfk, fba, tpi
Heliomicrobium modesticaldum Ice1; ATCC 51547 fruII-ABC, 1pfk, fba, tpi
Herbaspirillum autotrophicum IAM 14942 fruA, fruI, 1pfk, fba, tpi
Herbaspirillum seropedicae SmR1 frcA, frcB, frcC, scrK
Hippea alviniae EP5-r fruII-ABC, 1pfk, fba, tpi
Hydrogenophaga taeniospiralis NBRC 102512 frcA, frcB, frcC, scrK
Hydrogenovibrio halophilus DSM 15072 Slc2a5, scrK
Hydrogenovibrio kuenenii DSM 12350 Slc2a5, scrK
Hydrogenovibrio marinus DSM 11271 Slc2a5, scrK
Hyphomicrobium sulfonivorans WDL6 fruII-ABC, 1pfk, fba, tpi
Klebsiella michiganensis M5al fruA, fruB, 1pfk, fba, tpi
Klebsiella variicola At-22 fruA, fruB, 1pfk, fba, tpi
Kyrpidia tusciae DSM 2912 Slc2a5, scrK
Leptospirillum ferrooxidans C2-3 fruII-ABC, 1pfk, fba, tpi
Magnetospirillum magneticum AMB-1 Slc2a5, scrK
Malonomonas rubra DSM 5091 fruA, fruI, 1pfk, fba, tpi
Maridesulfovibrio bastinii DSM 16055 fruII-ABC, 1pfk, fba, tpi
Maridesulfovibrio zosterae DSM 11974 fruA, fruI, 1pfk, fba, tpi
Marinobacter adhaerens HP15 fruA, fruI, 1pfk, fba, tpi
Mesorhizobium ciceri WSM1271 frcA, frcB, frcC, scrK
Methanobacterium lacus AL-21 fruII-ABC, 1pfk, fba, tpi
Methanococcus aeolicus Nankai-3 fruII-ABC, 1pfk, fba, tpi
Methanococcus maripaludis C5 fruII-ABC, 1pfk, fba, tpi
Methanosarcina acetivorans C2A fruII-ABC, 1pfk, fba, tpi
Methanosarcina mazei Go1 fruII-ABC, 1pfk, fba, tpi
Methanospirillum lacunae Ki8-1 fruII-ABC, 1pfk, fba, tpi
Methanothermobacter thermautotrophicus Delta H fruII-ABC, 1pfk, fba, tpi
Methylobacterium nodulans ORS 2060 Slc2a5, scrK
Methylobacterium sp. 4-46 Apr-46 Slc2a5, scrK
Methylocapsa acidiphila B2 fruII-ABC, 1pfk, fba, tpi
Methylocapsa aurea KYG fruII-ABC, 1pfk, fba, tpi
Methylocella silvestris BL2 Slc2a5, scrK
Methylococcus capsulatus Bath Slc2a5, scrK
Methylocystis bryophila S285 fruII-ABC, 1pfk, fba, tpi
Methyloferula stellata AR4T fruII-ABC, 1pfk, fba, tpi
Methylohalobius crimeensis 10Ki fruII-ABC, 1pfk, fba, tpi
Methylomonas methanica MC09 fruP, scrK
Methylosarcina fibrata AML-C10 fruP, scrK
Methylotuvimicrobium alcaliphilum 20Z fruII-ABC, 1pfk, fba, tpi
Methylovulum miyakonense HT12 Slc2a5, scrK
Mycolicibacterium vanbaalenii PYR-1 fruII-ABC, 1pfk, fba, tpi
Nitratifractor salsuginis DSM 16511 fruII-ABC, 1pfk, fba, tpi
Nitratiruptor tergarcus DSM 16512 fruII-ABC, 1pfk, fba, tpi
Nitriliruptor alkaliphilus DSM 45188 fruII-ABC*, 1pfk, fba, tpi
Nocardioides dokdonensis FR1436 fruII-ABC, 1pfk, fba, tpi
Nocardiopsis lucentensis DSM 44048 frcA, frcB, frcC, scrK
Nostoc punctiforme ATCC 29133; PCC 73102 glcP, scrK
Novosphingobium aromaticivorans DSM 12444 glcP, scrK
Oleispira antarctica fruII-ABC, 1pfk, fba, tpi
Paraburkholderia atlantica CCGE1002 frcA, frcB, frcC, scrK
Paraburkholderia bryophila 376MFSha3.1 frcA, frcB, frcC, scrK
Paraburkholderia phymatum STM815 frcA, frcB, frcC, scrK
Paucidesulfovibrio gracilis DSM 16080 fruII-ABC, 1pfk, fba, tpi
Pedobacter sp. GW460-11-11-14-LB5 glcP, scrK
Pelobacter propionicus DSM 2379 fruII-ABC, 1pfk, fba, tpi
Persephonella marina EX-H1 fruII-ABC, 1pfk, fba, tpi
Phaeacidiphilus oryzae TH49 fruII-ABC, 1pfk, fba, tpi
Phaeobacter inhibens BS107 frcA, frcB, frcC, scrK
Polaromonas naphthalenivorans CJ2 frcA, frcB, frcC, scrK
Prosthecochloris aestuarii DSM 271 Slc2a5, scrK
Pseudarthrobacter sulfonivorans Ar51 frcA, frcB, frcC, scrK
Pseudomonas benzenivorans DSM 8628 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N1B4 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2C3 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2E2 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens FW300-N2E3 fruA, fruI, 1pfk, fba, tpi
Pseudomonas fluorescens GW456-L13 fruA, fruI, 1pfk, fba, tpi
Pseudomonas putida KT2440 fruA, fruI, 1pfk, fba, tpi
Pseudomonas simiae WCS417 fruA, fruI, 1pfk, fba, tpi
Pseudomonas stutzeri RCH2 fruA, fruI, 1pfk, fba, tpi
Pyrolobus fumarii 1A fruII-ABC, 1pfk, fba, tpi
Rhizobium etli CFN 42 frcA, frcB, frcC, scrK
Rhizobium johnstonii 3841 frcA, frcB, frcC, scrK
Rhizobium leguminosarum WSM1325 frcA, frcB, frcC, scrK
Rhizorhabdus wittichii RW1 Slc2a5, scrK
Rhodanobacter denitrificans FW104-10B01 fruP, scrK
Rhodomicrobium vannielii ATCC 17100 Slc2a5, scrK
Rhodopseudomonas palustris CGA009 fruII-ABC, 1pfk, fba, tpi
Rhodospirillum centenum SW; ATCC 51521 Slc2a5, scrK
Rhodospirillum rubrum ATCC 11170 fruA, fruI, 1pfk, fba, tpi
Roseburia faecis M72 fruII-ABC, 1pfk, fba, tpi
Saccharomonospora cyanea NA-134 fruE, fruF, fruG, fruK, scrK
Sedimenticola selenatireducens DSM 17993 Slc2a5, scrK
Shewanella amazonensis SB2B fruP, scrK
Shewanella loihica PV-4 fruP, scrK
Shewanella oneidensis MR-1 fruII-ABC, 1pfk, fba, tpi
Shewanella sp. ANA-3 fruP, scrK
Sinorhizobium fredii NGR234 frcA, frcB, frcC, scrK
Sinorhizobium medicae WSM419 frcA, frcB, frcC, scrK
Sinorhizobium meliloti 1021 frcA, frcB, frcC, scrK
Sphingomonas koreensis DSMZ 15582 glcP, scrK
Stenotrophomonas chelatiphaga DSM 21508 fruP, scrK
Steroidobacter denitrificans DSM 18526 fruII-ABC, 1pfk, fba, tpi
Stutzerimonas stutzeri A1501 fruA, fruI, 1pfk, fba, tpi
Sulfuricurvum kujiense DSM 16994 fruII-ABC, 1pfk, fba, tpi
Sulfurihydrogenibium azorense Az-Fu1 fruII-ABC, 1pfk, fba, tpi
Sulfurihydrogenibium subterraneum DSM 15120 fruII-ABC, 1pfk, fba, tpi
Sulfurimonas denitrificans DSM 1251 fruII-ABC, 1pfk, fba, tpi
Sulfuritalea hydrogenivorans DSM 22779 Slc2a5, scrK
Sulfurivirga caldicuralii DSM 17737 Slc2a5, scrK
Synechococcus elongatus PCC 7942 fruII-ABC, 1pfk, fba, tpi
Teredinibacter turnerae T7901 glcP, scrK
Thauera aminoaromatica S2 Slc2a5, scrK
Thermithiobacillus tepidarius DSM 3134 fruII-ABC, 1pfk, fba, tpi
Thermocrinis albus DSM 14484 fruII-ABC, 1pfk, fba, tpi
Thermodesulforhabdus norvegica DSM 9990 fruII-ABC, 1pfk, fba, tpi
Thermomonospora curvata DSM 43183 fruII-ABC, 1pfk, fba, tpi
Thermovibrio ammonificans HB-1 fruII-ABC, 1pfk, fba, tpi
Thermus aquaticus YT-1 fruII-ABC, 1pfk, fba, tpi
Thioalkalivibrio denitrificans ALJD Slc2a5, scrK
Thioalkalivibrio halophilus HL17 Slc2a5, scrK
Thioalkalivibrio paradoxus ARh 1 Slc2a5, scrK
Thioalkalivibrio thiocyanodenitrificans ARhD 1 Slc2a5, scrK
Thiohalomonas denitrificans HLD2 Slc2a5, scrK
Thiohalospira halophila HL 3 Slc2a5, scrK
Thiomicrorhabdus arctica DSM 13458 Slc2a5, scrK
Thiomicrorhabdus chilensis DSM 12352 Slc2a5, scrK
Thiomicrospira cyclica ALM1 fruII-ABC, 1pfk, fba, tpi
Thiomicrospira microaerophila ASL8-2 fruII-ABC, 1pfk, fba, tpi
Thiomicrospira pelophila DSM 1534 Slc2a5, scrK
Thiothrix lacustris DSM 21227 Slc2a5, scrK
Tistlia consotensis USBA 355 frcA, frcB, frcC, scrK
Trichlorobacter lovleyi SZ fruII-ABC, 1pfk, fba, tpi
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome fruII-ABC, 1pfk, fba, tpi
Trichormus variabilis ATCC 29413 frcA, frcB, frcC, scrK
Xanthobacter autotrophicus Py2 frcA, frcB, frcC, scrK
Xenophilus azovorans DSM 13620 Slc2a5, scrK

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