D-glucose catabolism

GapMind for catabolism of small carbon sources

D-glucose catabolism

Analysis of pathway glucose in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	ptsG-crr
Acidithiobacillus ferrooxidans ATCC 23270	ptsG-crr
Alicycliphilus denitrificans K601	ptsG-crr
Allochromatium vinosum DSM 180	MFS-glucose, glk
Ammonifex degensii KC4	MFS-glucose, glk
Archaeoglobus veneficus SNP6	ptsG-crr
Arcobacter nitrofigilis DSM 7299	ptsG-crr
Azoarcus sp. BH72	MFS-glucose, glk
Azohydromonas australica DSM 1124	gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571	MFS-glucose, glk
Azospirillum lipoferum B510	mglA, mglB, mglC, glk
Bacillus alkalinitrilicus DSM 22532	ptsG-crr
Beijerinckia indica ATCC 9039	mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969	MFS-glucose, glk
Bradyrhizobium sp. BTAi1	mglA, mglB, mglC, glk
Burkholderia vietnamiensis G4	gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672	ptsG-crr
Caminibacter mediatlanticus TB-2	ptsG-crr
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
Crocosphaera subtropica ATCC 51142	SemiSWEET, glk
Dechloromonas agitata is5	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
Desulfallas geothermicus DSM 3669	MFS-glucose, glk
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
Desulfobulbus mediterraneus DSM 13871	ptsG-crr
Desulfotalea psychrophila LSv54	MFS-glucose, glk
Desulfotomaculum ruminis DSM 2154	ptsG-crr
Desulfovibrio bastinii DSM 16055	ptsG-crr
Desulfovibrio gracilis DSM 16080	ptsG-crr
Desulfovibrio oxyclinae DSM 11498	ptsG-crr
Desulfovibrio zosterae DSM 11974	MFS-glucose, glk
Desulfurobacterium atlanticum DSM 15668	ptsG-crr
Desulfuromonas acetexigens	ptsG-crr
Desulfuromusa kysingii DSM 7343	ptsG-crr
Ferroglobus placidus DSM 10642	ptsG-crr
Frankia alni ACN14A	MFS-glucose, glk
Geobacter lovleyi SZ	ptsG-crr
Geobacter metallireducens GS-15	MFS-glucose, glk
Geobacter uraniireducens Rf4	MFS-glucose, glk
Haloechinothrix alba DSM 45207	MFS-glucose, glk
Haloglycomyces albus DSM 45210	mglA, mglB, mglC, glk
Halomonas desiderata SP1	gtsA, gtsB, gtsC, gtsD, glk
Halorhodospira halophila SL1	ptsG-crr
Heliobacterium modesticaldum Ice1; ATCC 51547	ptsG-crr
Herbaspirillum autotrophicum IAM 14942	MFS-glucose, glk
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 variicola At-22	mglA, mglB, mglC, glk
Kyrpidia tusciae DSM 2912	MFS-glucose, glk
Leptospirillum ferrooxidans C2-3	SemiSWEET, glk
Malonomonas rubra DSM 5091	MFS-glucose, 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 barkeri Fusaro	ptsG-crr
Methanosarcina mazei Go1	ptsG-crr
Methanothermobacter thermautotrophicus Delta H	ptsG-crr
Methylobacterium nodulans ORS 2060	ptsG-crr
Methylobacterium sp. 4-46	ptsG-crr
Methylocapsa acidiphila B2	ptsG-crr
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	SSS-glucose, glk
Methylomonas methanica MC09	MFS-glucose, glk
Methylosarcina fibrata AML-C10	MFS-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
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 phymatum STM815	gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia sp. CCGE1002	gtsA, gtsB, gtsC, gtsD, glk
Pelobacter propionicus DSM 2379	SemiSWEET, glk
Persephonella marina EX-H1	ptsG-crr
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 stutzeri A1501	gtsA, gtsB, gtsC, gtsD, glk
Pyrolobus fumarii 1A	ptsG-crr
Rhizobium etli CFN 42	gtsA, gtsB, gtsC, gtsD, glk
Rhizobium leguminosarum 3841	aglE', aglF', aglG', aglK', glk
Rhizobium leguminosarum WSM1325	aglE', aglF', aglG', aglK', glk
Rhodobacter sphaeroides ATCC 17029	aglE', aglF', aglG', aglK', 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
Saccharomonospora cyanea NA-134	MFS-glucose, glk
Sedimenticola selenatireducens DSM 17993	MFS-glucose, glk
Sinorhizobium fredii NGR234	gtsA, gtsB, gtsC, gtsD, glk
Sinorhizobium medicae WSM419	aglE', aglF', aglG', aglK', glk
Sphingomonas wittichii RW1	ptsG-crr
Stenotrophomonas chelatiphaga DSM 21508	MFS-glucose, glk
Steroidobacter denitrificans DSM 18526	MFS-glucose, 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
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
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
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
Trichodesmium erythraeum IMS101	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 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