GapMind for catabolism of small carbon sources

 

D-fructose catabolism

Analysis of pathway fructose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 fruII-ABC, 1pfk, fba, tpi
Actinokineospora bangkokensis 44EHW fruII-ABC, 1pfk, fba, tpi
Actinomyces timonensis 7400942 fruII-ABC, 1pfk, fba, tpi
Algiphilus aromaticivorans DG1253 fruII-ABC, 1pfk, fba, tpi
Algoriphagus aquaeductus T4 glcP, scrK
Algoriphagus machipongonensis PR1 glcP, scrK
Alicyclobacillus ferrooxydans TC-34 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Alishewanella agri BL06 fruP, scrK
Alistipes indistinctus YIT 12060 BT1758, scrK
Alistipes shahii WAL 8301 BT1758, scrK
Alkalitalea saponilacus SC/BZ-SP2 fruII-ABC, 1pfk, fba, tpi
Amantichitinum ursilacus IGB-41 frcA, frcB, frcC, scrK
Amphibacillus jilinensis Y1 fruII-ABC, 1pfk, fba, tpi
Amphritea japonica JAMM 1866 fruII-ABC, 1pfk, fba, tpi
Amycolatopsis halophila YIM 93223 fruII-ABC*, 1pfk, fba, tpi
Amycolatopsis xylanica CPCC 202699 frcA, frcB, frcC, scrK
Aquimarina agarilytica ZC1 fruII-ABC, 1pfk, fba, tpi
Aquimarina longa SW024 fruII-ABC, 1pfk, fba, tpi
Aquimarina macrocephali JAMB N27 fruII-ABC, 1pfk, fba, tpi
Archaeoglobus sulfaticallidus PM70-1 fruII-ABC, 1pfk, fba, tpi
Arcticibacter svalbardensis MN12-7 fruII-ABC, 1pfk, fba, tpi
Ardenticatena maritima 110S Slc2a5, scrK
Arenimonas metalli CF5-1 fruII-ABC, 1pfk, fba, tpi
Arenitalea lutea P7-3-5 glcP, scrK
Azospirillum humicireducens SgZ-5 fruA, fruI, 1pfk, fba, tpi
Azospirillum thiophilum BV-S fruA, fruI, 1pfk, fba, tpi
Bacillus altitudinis 41KF2b fruII-ABC, 1pfk, fba, tpi
Bacillus coahuilensis m4-4 Slc2a5, scrK
Bacillus cytotoxicus NVH 391-98 fruII-ABC, 1pfk, fba, tpi
Bacillus horneckiae 1P01SC fruII-ABC, 1pfk, fba, tpi
Bacillus okhensis Kh10-101 fruII-ABC, 1pfk, fba, tpi
Bacillus safensis FO-36b fruII-ABC, 1pfk, fba, tpi
Bacillus velezensis CBMB205 fruII-ABC, 1pfk, fba, tpi
Bacteroides clarus YIT 12056 BT1758, scrK
Bacteroides faecis MAJ27 BT1758, scrK
Bacteroides fluxus YIT 12057 BT1758, scrK
Bacteroides oleiciplenus YIT 12058 BT1758, scrK
Barnesiella intestinihominis YIT 11860 fruII-ABC, 1pfk, fba, tpi
Belnapia rosea CPCC 100156 fruA, fruI, 1pfk, fba, tpi
Bizionia argentinensis JUB59 fruII-ABC, 1pfk, fba, tpi
Bradyrhizobium diazoefficiens USDA110 frcA, frcB, frcC, scrK
Brevibacterium jeotgali SJ5-8 fruII-ABC, 1pfk, fba, tpi
Brucella inopinata BO1 fruP, scrK
Brucella microti CCM 4915 fruP, scrK
Bryobacter aggregatus MPL3 Slc2a5, scrK
Caldicellulosiruptor hydrothermalis 108 fruII-ABC, 1pfk, fba, tpi
Caldicellulosiruptor kronotskyensis 2002 fruII-ABC, 1pfk, fba, tpi
Carboxydothermus pertinax Ug1 fruII-ABC, 1pfk, fba, tpi
Catellicoccus marimammalium M35/04/3 fruII-ABC, 1pfk, fba, tpi
Chromobacterium vaccinii MWU205 frcA, frcB, frcC, scrK
Chryseobacterium angstadtii KM fruP, scrK
Chryseobacterium arthrosphaerae CC-VM-7 fruII-ABC, 1pfk, fba, tpi
Chryseobacterium viscerum 687B-08 glcP, scrK
Cloacibacillus porcorum CL-84 Slc2a5, scrK
Cobetia crustatorum JO1 fruA, fruI, 1pfk, fba, tpi
Collimonas arenae Ter10 frcA, frcB, frcC, scrK
Collimonas pratensis Ter91 frcA, frcB, frcC, scrK
Collinsella tanakaei YIT 12063 fruII-ABC, 1pfk, fba, tpi
Coprobacter fastidiosus NSB1 BT1758, scrK
Corynebacterium deserti GIMN1.010 fruII-ABC, 1pfk, fba, tpi
Corynebacterium frankenforstense ST18 fruII-ABC, 1pfk, fba, tpi
Corynebacterium lactis RW2-5 fruII-ABC, 1pfk, fba, tpi
Croceitalea dokdonensis DOKDO 023 glcP, scrK
Cronobacter condimenti 1330 fruA, fruB, 1pfk, fba, tpi
Cronobacter muytjensii ATCC 51329 fruA, fruB, 1pfk, fba, tpi
Cronobacter universalis NCTC 9529 fruA, fruB, 1pfk, fba, tpi
Desulfatitalea tepidiphila S28bF fruII-ABC, 1pfk, fba, tpi
Desulfotomaculum hydrothermale Lam5 fruII-ABC, 1pfk, fba, tpi
Dethiosulfovibrio salsuginis USBA 82 Slc2a5, scrK
Devosia chinhatensis IPL18 frcA, frcB, frcC, scrK
Devriesea agamarum IMP2 fruII-ABC, 1pfk, fba, tpi
Dialister succinatiphilus YIT 11850 Slc2a5, scrK
Dietzia timorensis ID05-A0528 fruII-ABC, 1pfk, fba, tpi
Dokdonella koreensis DS-123 fruII-ABC, 1pfk, fba, tpi
Domibacillus robiginosus WS 4628 fruII-ABC, 1pfk, fba, tpi
Duganella sacchari Sac-22 fruP, scrK
Dyadobacter tibetensis Y620-1 glcP, scrK
Dyella jiangningensis SBZ3-12 glcP, scrK
Endozoicomonas montiporae CL-33 fruII-ABC, 1pfk, fba, tpi
Enterococcus termitis LMG 8895 fruII-ABC, 1pfk, fba, tpi
Enterorhabdus caecimuris B7 fruII-ABC, 1pfk, fba, tpi
Epibacterium ulvae U95 Slc2a5, scrK
Erythrobacter gangjinensis K7-2 fruII-ABC, 1pfk, fba, tpi
Erythrobacter marinus HWDM-33 glcP, scrK
Ethanoligenens harbinense YUAN-3 fruII-ABC, 1pfk, fba, tpi
Fervidicella metallireducens AeB fruII-ABC, 1pfk, fba, tpi
Fibrella aestuarina BUZ 2 glcP, scrK
Flammeovirga pacifica WPAGA1 BT1758, scrK
Flaviramulus ichthyoenteri Th78 fruII-ABC, 1pfk, fba, tpi
Flavobacterium beibuense F44-8 fruII-ABC, 1pfk, fba, tpi
Flavobacterium glycines Gm-149 glcP, scrK
Flavobacterium sp. LM5 fruII-ABC, 1pfk, fba, tpi
Flavobacterium ummariense DS-12 fruII-ABC, 1pfk, fba, tpi
Frischella perrara PEB0191 fruA, fruB, 1pfk, fba, tpi
Galbibacter marinus ck-I2-15 glcP, scrK
Gallaecimonas xiamenensis 3-C-1 fruP, scrK
Geobacter daltonii FRC-32 Slc2a5, scrK
Gillisia marina CBA3202 glcP, scrK
Gracilibacillus halophilus YIM-C55.5 fruII-ABC, 1pfk, fba, tpi
Granulicella mallensis MP5ACTX8 glcP, scrK
Granulicella tundricola MP5ACTX9 glcP, scrK
Hafnia paralvei ATCC 29927 fruA, fruB, 1pfk, fba, tpi
Haladaptatus cibarius D43 fruII-ABC, 1pfk, fba, tpi
Halioglobus japonicus S1-36 fruII-ABC, 1pfk, fba, tpi
Halobacillus alkaliphilus FP5 fruII-ABC, 1pfk, fba, tpi
Halococcus hamelinensis 100A6 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Halomonas salina B6 fruA, fruI, 1pfk, fba, tpi
Halomonas smyrnensis AAD6 fruA, fruI, 1pfk, fba, tpi
Halomonas stevensii S18214 fruA, fruI, 1pfk, fba, tpi
Halomonas titanicae BH1 fruA, fruI, 1pfk, fba, tpi
Halomonas xinjiangensis TRM 0175 fruA, fruI, 1pfk, fba, tpi
Halopiger salifodinae KCY07-B2 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Halostagnicola larsenii XH-48 fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloterrigena daqingensis JX313 fruII-ABC, 1pfk, fba, tpi
Herbaspirillum aquaticum IEH 4430 frcA, frcB, frcC, scrK
Hippea alviniae EP5-r fruII-ABC, 1pfk, fba, tpi
Hippea jasoniae Mar08-272r Slc2a5, scrK
Hoeflea phototrophica DFL-43 frcA, frcB, frcC, scrK
Hyphomicrobium nitrativorans NL23 fruII-ABC, 1pfk, fba, tpi
Imtechella halotolerans K1 fruII-ABC, 1pfk, fba, tpi
Indibacter alkaliphilus LW1 glcP, scrK
Jannaschia aquimarina GSW-M26 frcA, frcB, frcC, scrK
Jeotgalibacillus soli P9 fruII-ABC, 1pfk, fba, tpi
Kangiella geojedonensis YCS-5 fruII-ABC, 1pfk, fba, tpi
Knoellia flava TL1 frcA, frcB, frcC, scrK
Kocuria flava HO-9041 fruII-ABC, 1pfk, fba, tpi
Kocuria turfanensis HO-9042 fruII-ABC, 1pfk, fba, tpi
Laceyella sediminis RHA1 fruII-ABC, 1pfk, fba, tpi
Lacinutrix algicola AKS293 fruII-ABC, 1pfk, fba, tpi
Lacinutrix himadriensis E4-9a Slc2a5, scrK
Lacinutrix mariniflava AKS432 glcP, scrK
Lactobacillus curieae CCTCC M 2011381 Slc2a5, scrK
Lactobacillus delbrueckii ZN7a-9 fruII-ABC, 1pfk, fba, tpi
Lactobacillus hokkaidonensis LOOC260 Slc2a5, scrK
Lactobacillus oryzae SG293 Slc2a5, scrK
Lactobacillus pobuzihii E100301 fruII-ABC, 1pfk, fba, tpi
Lactobacillus shenzhenensis LY-73 fruII-ABC, 1pfk, fba, tpi
Lactobacillus silagei IWT126 Slc2a5, scrK
Leeuwenhoekiella blandensis MED217 glcP, scrK
Lentibacillus jeotgali Grbi fruII-ABC, 1pfk, fba, tpi
Limnohabitans curvus MWH-C5 frcA, frcB, frcC, scrK
Limnohabitans parvus II-B4 frcA, frcB, frcC, scrK
Listeria fleischmannii LU2006-1 fruII-ABC, 1pfk, fba, tpi
Luteimonas huabeiensis HB2 glcP, scrK
Luteipulveratus mongoliensis MN07-A0370 fruII-ABC, 1pfk, fba, tpi
Lutibaculum baratangense AMV1 Slc2a5, scrK
Lysobacter daejeonensis GH1-9 fruII-ABC, 1pfk, fba, tpi
Magnetovibrio blakemorei MV-1 Slc2a5, scrK
Marinicella litoralis KMM 3900 fruII-ABC, 1pfk, fba, tpi
Mariniradius saccharolyticus AK6 glcP, scrK
Marinobacter algicola DG893 fruA, fruI, 1pfk, fba, tpi
Marinobacter guineae M3B fruA, fruI, 1pfk, fba, tpi
Marinobacter psychrophilus 20041 Slc2a5, scrK
Marinomonas arctica 328 frcA, frcB, frcC, scrK
Marivita geojedonensis DPG-138 frcA, frcB, frcC, scrK
Martelella endophytica YC6887 Slc2a5, scrK
Megamonas funiformis YIT 11815 fruII-ABC, 1pfk, fba, tpi
Mesorhizobium ciceri WSM1271 frcA, frcB, frcC, scrK
Methanobacterium arcticum M2 fruII-ABC, 1pfk, fba, tpi
Methanobacterium veterum MK4 fruII-ABC, 1pfk, fba, tpi
Methanocella arvoryzae MRE50 fruII-ABC, 1pfk, fba, tpi
Methanococcus aeolicus Nankai-3 fruII-ABC, 1pfk, fba, tpi
Methanoculleus horonobensis T10 fruII-ABC, 1pfk, fba, tpi
Methanolinea tarda NOBI-1 fruII-ABC, 1pfk, fba, tpi
Methanosarcina soligelidi SMA-21 fruII-ABC, 1pfk, fba, tpi
Methanospirillum lacunae Ki8-1 fruII-ABC, 1pfk, fba, tpi
Methanospirillum stamsii Pt1 fruII-ABC, 1pfk, fba, tpi
Methylibium petroleiphilum PM1 fruII-ABC, 1pfk, fba, tpi
Methylobacterium gossipiicola Gh-105 fruA, fruI, 1pfk, fba, tpi
Methylocapsa aurea KYG fruII-ABC, 1pfk, fba, tpi
Methylotenera versatilis 301 fruA, fruI, 1pfk, fba, tpi
Microbacterium profundi Shh49 fruII-ABC, 1pfk, fba, tpi
Microvirga lotononidis WSM3557 frcA, frcB, frcC, scrK
Moritella dasanensis ArB 0140 fruA, fruB, 1pfk, fba, tpi
Mucilaginibacter gossypii Gh-67 glcP, scrK
Mucilaginibacter gossypiicola Gh-48 glcP, scrK
Mucilaginibacter mallensis MP1X4 glcP, scrK
Nafulsella turpanensis ZLM-10 glcP, scrK
Natronomonas moolapensis 8.8.11 fruII-ABC, 1pfk, fba, tpi
Nautilia profundicola AmH fruII-ABC, 1pfk, fba, tpi
Neiella marina J221 glcP, scrK
Neptunomonas antarctica S3-22 Slc2a5, scrK
Nocardioides daejeonensis MJ31 fruII-ABC, 1pfk, fba, tpi
Nocardioides dokdonensis FR1436 fruII-ABC, 1pfk, fba, tpi
Nocardiopsis baichengensis YIM 90130 fruII-ABC, 1pfk, fba, tpi
Nocardiopsis gilva YIM 90087 frcA, frcB, frcC, scrK
Novosphingobium barchaimii LL02 glcP, scrK
Novosphingobium fuchskuhlense FNE08-7 fruP, scrK
Novosphingobium lindaniclasticum LE124 glcP, scrK
Oceanisphaera arctica V1-41 fruA, fruI, 1pfk, fba, tpi
Ochrobactrum rhizosphaerae PR17 frcA, frcB, frcC, scrK
Ochrobactrum thiophenivorans DSM 7216 frcA, frcB, frcC, scrK
Oscillibacter ruminantium GH1 Slc2a5, scrK
Paenisporosarcina indica PN2 fruII-ABC, 1pfk, fba, tpi
Palaeococcus pacificus DY20341 fruII-ABC, 1pfk, fba, tpi
Paludibacter propionicigenes WB4 fruII-ABC, 1pfk, fba, tpi
Pandoraea thiooxydans ATSB16 fruII-ABC, 1pfk, fba, tpi
Pantoea rwandensis LMG 26275 frcA, frcB, frcC, scrK
Pedobacter arcticus A12 fruII-ABC, 1pfk, fba, tpi
Photobacterium gaetbulicola Gung47 fruA, fruB, 1pfk, fba, tpi
Photobacterium jeanii R-40508 fruA, fruB, 1pfk, fba, tpi
Phyllobacterium brassicacearum STM 196 frcA, frcB, frcC, scrK
Phyllobacterium endophyticum PEPV15 frcA, frcB, frcC, scrK
Phyllobacterium leguminum ORS 1419 frcA, frcB, frcC, scrK
Planktomarina temperata RCA23 frcA, frcB, frcC, scrK
Planococcus halocryophilus Or1 fruII-ABC, 1pfk, fba, tpi
Pleomorphomonas diazotrophica R5-392 frcA, frcB, frcC, scrK
Polaribacter dokdonensis DSW-5 glcP, scrK
Pontibacillus litoralis JSM 072002 fruII-ABC, 1pfk, fba, tpi
Pontibacter lucknowensis DM9 fruII-ABC, 1pfk, fba, tpi
Pontibacter ramchanderi LP43 fruII-ABC, 1pfk, fba, tpi
Pontimonas salivibrio CL-TW6 fruII-ABC, 1pfk, fba, tpi
Porphyrobacter dokdonensis DSW-74 fruP, scrK
Pseudoalteromonas arctica A 37-1-2 glcP, scrK
Pseudomonas baetica a390 fruA, fruI, 1pfk, fba, tpi
Pseudomonas litoralis 2SM5 fruII-ABC, 1pfk, fba, tpi
Pseudomonas taeanensis MS-3 fruA, fruI, 1pfk, fba, tpi
Pseudovibrio axinellae Ad2 glcP, scrK
Psychrobacter arcticus 273-4 fruII-ABC, 1pfk, fba, tpi
Psychrobacter cryohalolentis K5 fruII-ABC, 1pfk, fba, tpi
Psychromonas ingrahamii 37 fruA, fruB, 1pfk, fba, tpi
Psychromonas ossibalaenae JAMM 0738 fruA, fruB, 1pfk, fba, tpi
Rhizobium freirei PRF 81 frcA, frcB, frcC, scrK
Rhizobium grahamii CCGE 502 frcA, frcB, frcC, scrK
Rhizobium subbaraonis JC85 frcA, frcB, frcC, scrK
Rhodanobacter denitrificans 2APBS1 fruP, scrK
Rhodobacter johrii JA192 fruA, fruI, 1pfk, fba, tpi
Rhodobacter maris JA276 fruA, fruI, 1pfk, fba, tpi
Rhodobacter ovatus JA234 frcA, frcB, frcC, scrK
Rhodobacter viridis JA737 fruA, fruI, 1pfk, fba, tpi
Rhodococcus qingshengii djl-6-2 fruII-ABC, 1pfk, fba, tpi
Rhodopseudomonas pseudopalustris DSM 123 fruII-ABC, 1pfk, fba, tpi
Roseateles aquatilis CCUG 48205 Slc2a5, scrK
Roseivirga spongicola UST030701-084 glcP, scrK
Rubrivirga marina SAORIC-28 glcP, scrK
Ruegeria conchae TW15 frcA, frcB, frcC, scrK
Saccharomonospora marina XMU15 fruII-ABC, 1pfk, fba, tpi
Salinicoccus carnicancri Crm fruII-ABC, 1pfk, fba, tpi
Serinicoccus profundi MCCC 1A05965 frcA, frcB, frcC, scrK
Shewanella halifaxensis HAW-EB4 fruII-ABC, 1pfk, fba, tpi
Skermanella stibiiresistens SB22 fruA, fruI, 1pfk, fba, tpi
Snodgrassella alvi wkB2 fruII-ABC, 1pfk, fba, tpi
Sphaerochaeta globosa Buddy fruE, fruF, fruG, fruK, scrK
Sphaerochaeta pleomorpha Grapes fruII-ABC, 1pfk, fba, tpi
Sphingobium baderi LL03 fruP, scrK
Sphingobium czechense LL01 glcP, scrK
Sphingobium quisquiliarum P25 glcP, scrK
Sphingomonas histidinilytica UM2 Slc2a5, scrK
Sphingomonas indica Dd16 fruII-ABC, 1pfk, fba, tpi
Sphingomonas laterariae LNB2 fruP, scrK
Sphingopyxis indica DS15 glcP, scrK
Sphingopyxis terrae UI2 fruP, scrK
Sporolactobacillus vineae SL153 levDE, levF, levG
Streptacidiphilus oryzae TH49 fruII-ABC, 1pfk, fba, tpi
Streptococcus anginosus CCUG 39159 fruII-ABC, 1pfk, fba, tpi
Streptococcus massiliensis 4401825 fruII-ABC, 1pfk, fba, tpi
Streptococcus oralis 7747 fruII-ABC, 1pfk, fba, tpi
Streptococcus oralis AZ_3a fruII-ABC, 1pfk, fba, tpi
Streptomyces kebangsaanensis SUK12 fruII-ABC, 1pfk, fba, tpi
Succinatimonas hippei YIT 12066 frcA, frcB, frcC, scrK
Sulfurimonas gotlandica GD1 fruII-ABC, 1pfk, fba, tpi
Tatumella morbirosei LMG 23360 fruA, fruB, 1pfk, fba, tpi
Thauera humireducens SgZ-1 Slc2a5, scrK
Thermoactinomyces daqus H-18 fruII-ABC, 1pfk, fba, tpi
Thermobifida halotolerans YIM 90462 glcP, scrK
Thermodesulfovibrio aggregans TGE-P1 Slc2a5, scrK
Thermophagus xiamenensis HS1 BT1758, scrK
Thermovenabulum gondwanense R270 fruII-ABC, 1pfk, fba, tpi
Thioclava dalianensis DLFJ1-1 frcA, frcB, frcC, scrK
Thiohalospira halophila HL 3 Slc2a5, scrK
Tistlia consotensis USBA 355 frcA, frcB, frcC, scrK
Vagococcus penaei CD276 fruII-ABC, 1pfk, fba, tpi
Verminephrobacter eiseniae EF01-2 frcA, frcB, frcC, scrK
Weissella oryzae SG25 levDE, levF, levG
Williamsia sterculiae CPCC 203464 fruII-ABC, 1pfk, fba, tpi
Yersinia intermedia Y228 fruA, fruB, 1pfk, fba, tpi

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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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