D-glucose catabolism

GapMind for catabolism of small carbon sources

D-glucose catabolism

Analysis of pathway glucose in 201 genomes

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

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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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