GapMind for catabolism of small carbon sources

 

D-glucose catabolism

Analysis of pathway glucose in 276 genomes

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

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.

Links

Downloads

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:

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