D-fructose catabolism

GapMind for catabolism of small carbon sources

D-fructose catabolism

Analysis of pathway fructose in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	fruII-ABC, 1pfk, fba, tpi
Acidithiobacillus ferrooxidans ATCC 23270	fruII-ABC, 1pfk, fba, tpi
Alicycliphilus denitrificans K601	fruII-ABC, 1pfk, fba, tpi
Allochromatium vinosum DSM 180	Slc2a5, scrK
Ammonifex degensii KC4	fruII-ABC, 1pfk, fba, tpi
Archaeoglobus veneficus SNP6	fruII-ABC, 1pfk, fba, tpi
Arcobacter nitrofigilis DSM 7299	fruII-ABC, 1pfk, fba, tpi
Azoarcus sp. 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 lipoferum B510	fruA, fruI, 1pfk, fba, tpi
Bacillus alkalinitrilicus DSM 22532	fruII-ABC, 1pfk, fba, tpi
Beijerinckia indica ATCC 9039	frcA, frcB, frcC, scrK
Beijerinckia mobilis UQM 1969	fruP, scrK
Bradyrhizobium sp. BTAi1	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
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
Crocosphaera subtropica ATCC 51142	fruII-ABC, 1pfk, fba, tpi
Dechloromonas agitata is5	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
Desulfallas geothermicus DSM 3669	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
Desulfobulbus mediterraneus DSM 13871	Slc2a5, scrK
Desulfotalea psychrophila LSv54	fruII-ABC, 1pfk, fba, tpi
Desulfotomaculum ruminis DSM 2154	fruII-ABC, 1pfk, fba, tpi
Desulfovibrio bastinii DSM 16055	fruII-ABC, 1pfk, fba, tpi
Desulfovibrio gracilis DSM 16080	fruII-ABC, 1pfk, fba, tpi
Desulfovibrio oxyclinae DSM 11498	fruII-ABC, 1pfk, fba, tpi
Desulfovibrio zosterae DSM 11974	fruA, fruI, 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
Ferroglobus placidus DSM 10642	fruII-ABC, 1pfk, fba, tpi
Frankia alni ACN14A	fruII-ABC, 1pfk, fba, tpi
Geobacter lovleyi SZ	fruII-ABC, 1pfk, fba, tpi
Geobacter metallireducens GS-15	Slc2a5, scrK
Geobacter uraniireducens Rf4	Slc2a5, scrK
Haloechinothrix alba DSM 45207	fruII-ABC, 1pfk, fba, tpi
Haloglycomyces albus DSM 45210	glcP, scrK
Halomonas desiderata SP1	fruA, fruI, 1pfk, fba, tpi
Halorhodospira halophila SL1	fruII-ABC, 1pfk, fba, tpi
Heliobacterium modesticaldum Ice1; ATCC 51547	fruII-ABC, 1pfk, fba, tpi
Herbaspirillum autotrophicum IAM 14942	fruA, fruI, 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 variicola At-22	fruA, fruB, 1pfk, fba, tpi
Kyrpidia tusciae DSM 2912	Slc2a5, scrK
Leptospirillum ferrooxidans C2-3	fruII-ABC, 1pfk, fba, tpi
Malonomonas rubra DSM 5091	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 barkeri Fusaro	fruII-ABC, 1pfk, fba, tpi
Methanosarcina mazei Go1	fruII-ABC, 1pfk, fba, tpi
Methanothermobacter thermautotrophicus Delta H	fruII-ABC, 1pfk, fba, tpi
Methylobacterium nodulans ORS 2060	Slc2a5, scrK
Methylobacterium sp. 4-46	Slc2a5, scrK
Methylocapsa acidiphila B2	fruII-ABC, 1pfk, fba, tpi
Methylocapsa aurea KYG T	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	Slc2a5, scrK
Methylomicrobium alcaliphilum 20Z	fruII-ABC, 1pfk, fba, tpi
Methylomonas methanica MC09	fruP, scrK
Methylosarcina fibrata AML-C10	fruP, scrK
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
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 phymatum STM815	frcA, frcB, frcC, scrK
Paraburkholderia sp. CCGE1002	frcA, frcB, frcC, scrK
Pelobacter propionicus DSM 2379	fruII-ABC, 1pfk, fba, tpi
Persephonella marina EX-H1	fruII-ABC, 1pfk, fba, tpi
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 stutzeri A1501	fruA, fruI, 1pfk, fba, tpi
Pyrolobus fumarii 1A	fruII-ABC, 1pfk, fba, tpi
Rhizobium etli CFN 42	frcA, frcB, frcC, scrK
Rhizobium leguminosarum 3841	frcA, frcB, frcC, scrK
Rhizobium leguminosarum WSM1325	frcA, frcB, frcC, scrK
Rhodobacter sphaeroides ATCC 17029	fruA, fruI, 1pfk, fba, tpi
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
Saccharomonospora cyanea NA-134	fruE, fruF, fruG, fruK, scrK
Sedimenticola selenatireducens DSM 17993	Slc2a5, scrK
Sinorhizobium fredii NGR234	frcA, frcB, frcC, scrK
Sinorhizobium medicae WSM419	frcA, frcB, frcC, scrK
Sphingomonas wittichii RW1	Slc2a5, scrK
Stenotrophomonas chelatiphaga DSM 21508	fruP, scrK
Steroidobacter denitrificans DSM 18526	fruII-ABC, 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
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
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
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
Trichodesmium erythraeum IMS101	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 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

Related tools

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