GapMind for catabolism of small carbon sources

 

D-gluconate catabolism

Analysis of pathway gluconate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 gntT, gntK, gnd
Actinokineospora bangkokensis 44EHW gntT, gntK, edd, eda
Actinomyces timonensis 7400942 gntT, gntK, gnd
Algiphilus aromaticivorans DG1253 gntT, gntK, gnd
Algoriphagus aquaeductus T4 gntT, gntK, gnd
Algoriphagus machipongonensis PR1 gntT, gntK, gnd
Alicyclobacillus ferrooxydans TC-34 gntT, gntK, gnd
Alishewanella agri BL06 gntT, gntK, edd, eda
Alistipes indistinctus YIT 12060 gntT, gntK, gnd
Alistipes shahii WAL 8301 gntT, gntK, edd, eda
Alkalitalea saponilacus SC/BZ-SP2 gntT, gntK, gnd
Amantichitinum ursilacus IGB-41 gntT, gntK, edd, eda
Amphibacillus jilinensis Y1 gntT, gntK, gnd
Amphritea japonica JAMM 1866 gntT, gntK, gnd
Amycolatopsis halophila YIM 93223 gntT, gntK, edd, eda
Amycolatopsis xylanica CPCC 202699 gntT, gntK, edd, eda
Aquimarina agarilytica ZC1 gntT, gntK, gnd
Aquimarina longa SW024 gntT, gntK, gnd
Aquimarina macrocephali JAMB N27 gntT, gntK, gnd
Archaeoglobus sulfaticallidus PM70-1 gntT, gntK, gnd
Arcticibacter svalbardensis MN12-7 gntT, gntK, gnd
Ardenticatena maritima 110S gntT, gntK, gnd
Arenimonas metalli CF5-1 gntT, gntK, gnd
Arenitalea lutea P7-3-5 gntT, gntK, gnd
Azospirillum humicireducens SgZ-5 gntA, gntB, gntC, gntK, edd, eda
Azospirillum thiophilum BV-S gntA, gntB, gntC, gntK, edd, eda
Bacillus altitudinis 41KF2b gntT, gntK, gnd
Bacillus coahuilensis m4-4 gntT, gntK, gnd
Bacillus cytotoxicus NVH 391-98 gntT, gntK, gnd
Bacillus horneckiae 1P01SC gntT, gntK, gnd
Bacillus okhensis Kh10-101 gntT, gntK, gnd
Bacillus safensis FO-36b gntT, gntK, gnd
Bacillus velezensis CBMB205 gntT, gntK, gnd
Bacteroides clarus YIT 12056 gntT, gntK, gnd
Bacteroides faecis MAJ27 gntT, gntK, gnd
Bacteroides fluxus YIT 12057 gntT, gntK, gnd
Bacteroides oleiciplenus YIT 12058 gntT, gntK, gnd
Barnesiella intestinihominis YIT 11860 gntT, gntK, gnd
Belnapia rosea CPCC 100156 gntT, gntK, gnd
Bizionia argentinensis JUB59 gntT, gntK, gnd
Bradyrhizobium diazoefficiens USDA110 gntT, gntK, gnd
Brevibacterium jeotgali SJ5-8 gntT, gntK, gnd
Brucella inopinata BO1 gntT, gntK, edd, eda
Brucella microti CCM 4915 gntT, gntK, edd, eda
Bryobacter aggregatus MPL3 gntT, gntK, gnd
Caldicellulosiruptor hydrothermalis 108 gntT, gntK, edd, eda
Caldicellulosiruptor kronotskyensis 2002 gntT, gntK, edd, eda
Carboxydothermus pertinax Ug1 gntT, gntK, gnd
Catellicoccus marimammalium M35/04/3 gntT, gntK, gnd
Chromobacterium vaccinii MWU205 gntT, gntK, edd, eda
Chryseobacterium angstadtii KM gntT, gntK, gnd
Chryseobacterium arthrosphaerae CC-VM-7 gntT, gntK, edd, eda
Chryseobacterium viscerum 687B-08 gntT, gntK, gnd
Cloacibacillus porcorum CL-84 gntT, gntK, gnd
Cobetia crustatorum JO1 gntA, gntB, gntC, gntK, edd, eda
Collimonas arenae Ter10 gntT, gntK, gnd
Collimonas pratensis Ter91 gntT, gntK, edd, eda
Collinsella tanakaei YIT 12063 gntT, gntK, edd, eda
Coprobacter fastidiosus NSB1 gntT, gntK, gnd
Corynebacterium deserti GIMN1.010 gntT, gntK, gnd
Corynebacterium frankenforstense ST18 gntT, gntK, gnd
Corynebacterium lactis RW2-5 gntT, gntK, gnd
Croceitalea dokdonensis DOKDO 023 gntT, gntK, gnd
Cronobacter condimenti 1330 gntT, gntK, edd, eda
Cronobacter muytjensii ATCC 51329 gntT, gntK, edd, eda
Cronobacter universalis NCTC 9529 gntT, gntK, edd, eda
Desulfatitalea tepidiphila S28bF gntT, gntK, gnd
Desulfotomaculum hydrothermale Lam5 gntT, gntK, gnd
Dethiosulfovibrio salsuginis USBA 82 gntT, gntK, gnd
Devosia chinhatensis IPL18 gntA, gntB, gntC, gntK, edd, eda
Devriesea agamarum IMP2 gntT, gntK, gnd
Dialister succinatiphilus YIT 11850 gntT, gntK, gnd
Dietzia timorensis ID05-A0528 gntT, gntK, gnd
Dokdonella koreensis DS-123 gntT, gntK, gnd
Domibacillus robiginosus WS 4628 gntT, gntK, gnd
Duganella sacchari Sac-22 gntT, gntK, edd, eda
Dyadobacter tibetensis Y620-1 gntT, gntK, gnd
Dyella jiangningensis SBZ3-12 gntT, gntK, edd, eda
Endozoicomonas montiporae CL-33 gntT, gntK, gnd
Enterococcus termitis LMG 8895 gntEIIA, gntEIIB, gntEIIC, gntEIID, gnd
Enterorhabdus caecimuris B7 gntT, gntK, gnd
Epibacterium ulvae U95 gntT, gntK, edd, eda
Erythrobacter gangjinensis K7-2 gntT, gntK, edd, eda
Erythrobacter marinus HWDM-33 gntT, gntK, edd, eda
Ethanoligenens harbinense YUAN-3 gntT, gntK, gnd
Fervidicella metallireducens AeB gntT, gntK, gnd
Fibrella aestuarina BUZ 2 gntT, gntK, gnd
Flammeovirga pacifica WPAGA1 gntT, gntK, edd, eda
Flaviramulus ichthyoenteri Th78 gntT, gntK, gnd
Flavobacterium beibuense F44-8 gntT, gntK, edd, eda
Flavobacterium glycines Gm-149 gntT, gntK, edd, eda
Flavobacterium sp. LM5 gntT, gntK, gnd
Flavobacterium ummariense DS-12 gntT, gntK, gnd
Frischella perrara PEB0191 gntT, gntK, gnd
Galbibacter marinus ck-I2-15 gntT, gntK, gnd
Gallaecimonas xiamenensis 3-C-1 gntT, gntK, edd, eda
Geobacter daltonii FRC-32 gntT, gntK, gnd
Gillisia marina CBA3202 gntT, gntK, gnd
Gracilibacillus halophilus YIM-C55.5 gntT, gntK, gnd
Granulicella mallensis MP5ACTX8 gntT, gntK, edd, eda
Granulicella tundricola MP5ACTX9 gntT, gntK, gnd
Hafnia paralvei ATCC 29927 gntT, gntK, edd, eda
Haladaptatus cibarius D43 gntT, gntK, gnd
Halioglobus japonicus S1-36 gntT, gntK, edd, eda
Halobacillus alkaliphilus FP5 gntT, gntK, gnd
Halococcus hamelinensis 100A6 gntT, gntK, gnd
Halomonas salina B6 gntT, gntK, edd, eda
Halomonas smyrnensis AAD6 gntA, gntB, gntC, gntK, edd, eda
Halomonas stevensii S18214 gntA, gntB, gntC, gntK, edd, eda
Halomonas titanicae BH1 gntA, gntB, gntC, gntK, edd, eda
Halomonas xinjiangensis TRM 0175 gntT, gntK, edd, eda
Halopiger salifodinae KCY07-B2 gntT, gntK, gnd
Halostagnicola larsenii XH-48 gntT, gntK, gnd
Haloterrigena daqingensis JX313 gntT, gntK, gnd
Herbaspirillum aquaticum IEH 4430 gntT, gntK, edd, eda
Hippea alviniae EP5-r gntT, gntK, gnd
Hippea jasoniae Mar08-272r gntT, gntK, gnd
Hoeflea phototrophica DFL-43 gntT, gntK, edd, eda
Hyphomicrobium nitrativorans NL23 gntT, gntK, gnd
Imtechella halotolerans K1 gntT, gntK, gnd
Indibacter alkaliphilus LW1 gntT, gntK, gnd
Jannaschia aquimarina GSW-M26 gntT, gntK, edd, eda
Jeotgalibacillus soli P9 gntT, gntK, gnd
Kangiella geojedonensis YCS-5 gntT, gntK, gnd
Knoellia flava TL1 gntT, gntK, gnd
Kocuria flava HO-9041 gntT, gntK, gnd
Kocuria turfanensis HO-9042 gntT, gntK, gnd
Laceyella sediminis RHA1 gntT, gntK, gnd
Lacinutrix algicola AKS293 gntT, gntK, edd, eda
Lacinutrix himadriensis E4-9a gntT, gntK, gnd
Lacinutrix mariniflava AKS432 gntT, gntK, edd, eda
Lactobacillus curieae CCTCC M 2011381 gntT, gntK, gnd
Lactobacillus delbrueckii ZN7a-9 gntT, gntK, gnd
Lactobacillus hokkaidonensis LOOC260 gntT, gntK, gnd
Lactobacillus oryzae SG293 gntT, gntK, gnd
Lactobacillus pobuzihii E100301 gntT, gntK, gnd
Lactobacillus shenzhenensis LY-73 gntT, gntK, gnd
Lactobacillus silagei IWT126 gntT, gntK, gnd
Leeuwenhoekiella blandensis MED217 gntT, gntK, gnd
Lentibacillus jeotgali Grbi gntT, gntK, gnd
Limnohabitans curvus MWH-C5 gntA, gntB, gntC, gntK, edd, eda
Limnohabitans parvus II-B4 gntA, gntB, gntC, gntK, edd, eda
Listeria fleischmannii LU2006-1 gntT, gntK, gnd
Luteimonas huabeiensis HB2 gntT, gntK, edd, eda
Luteipulveratus mongoliensis MN07-A0370 gntT, gntK, gnd
Lutibaculum baratangense AMV1 gntT, gntK, gnd
Lysobacter daejeonensis GH1-9 gntT, gntK, edd, eda
Magnetovibrio blakemorei MV-1 gntT, gntK, gnd
Marinicella litoralis KMM 3900 gntT, gntK, gnd
Mariniradius saccharolyticus AK6 gntT, gntK, gnd
Marinobacter algicola DG893 gntT, gntK, edd, eda
Marinobacter guineae M3B gntT, gntK, edd, eda
Marinobacter psychrophilus 20041 gntT, gntK, edd, eda
Marinomonas arctica 328 gntT, gntK, edd, eda
Marivita geojedonensis DPG-138 gntT, gntK, edd, eda
Martelella endophytica YC6887 gntT, gntK, edd, eda
Megamonas funiformis YIT 11815 gntT, gntK, gnd
Mesorhizobium ciceri WSM1271 gntT, gntK, edd, eda
Methanobacterium arcticum M2 gntT, gntK, gnd
Methanobacterium veterum MK4 gntT, gntK, gnd
Methanocella arvoryzae MRE50 gntT, gntK, gnd
Methanococcus aeolicus Nankai-3 gntT, gntK, gnd
Methanoculleus horonobensis T10 gntT, gntK, gnd
Methanolinea tarda NOBI-1 gntT, gntK, gnd
Methanosarcina soligelidi SMA-21 gntT, gntK, gnd
Methanospirillum lacunae Ki8-1 gntT, gntK, gnd
Methanospirillum stamsii Pt1 gntT, gntK, gnd
Methylibium petroleiphilum PM1 gntT, gntK, gnd
Methylobacterium gossipiicola Gh-105 gntT, gntK, edd, eda
Methylocapsa aurea KYG gntT, gntK, edd, eda
Methylotenera versatilis 301 gntT, gntK, edd, eda
Microbacterium profundi Shh49 gntT, gntK, gnd
Microvirga lotononidis WSM3557 gntA, gntB, gntC, gntK, edd, eda
Moritella dasanensis ArB 0140 gntT, gntK, gnd
Mucilaginibacter gossypii Gh-67 gntT, gntK, gnd
Mucilaginibacter gossypiicola Gh-48 gntT, gntK, gnd
Mucilaginibacter mallensis MP1X4 gntT, gntK, gnd
Nafulsella turpanensis ZLM-10 gntT, gntK, gnd
Natronomonas moolapensis 8.8.11 gntT, gntK, gnd
Nautilia profundicola AmH gntT, gntK, gnd
Neiella marina J221 gntT, gntK, gnd
Neptunomonas antarctica S3-22 gntT, gntK, edd, eda
Nocardioides daejeonensis MJ31 gntT, gntK, gnd
Nocardioides dokdonensis FR1436 gntT, gntK, gnd
Nocardiopsis baichengensis YIM 90130 gntT, gntK, edd, eda
Nocardiopsis gilva YIM 90087 gntT, gntK, edd, eda
Novosphingobium barchaimii LL02 gntT, gntK, edd, eda
Novosphingobium fuchskuhlense FNE08-7 gntT, gntK, edd, eda
Novosphingobium lindaniclasticum LE124 gntT, gntK, edd, eda
Oceanisphaera arctica V1-41 gntT, gntK, edd, eda
Ochrobactrum rhizosphaerae PR17 gntA, gntB, gntC, gntK, edd, eda
Ochrobactrum thiophenivorans DSM 7216 gntT, gntK, edd, eda
Oscillibacter ruminantium GH1 gntA, gntB, gntC, gntK, edd, eda
Paenisporosarcina indica PN2 gntT, gntK, gnd
Palaeococcus pacificus DY20341 gntT, gntK, gnd
Paludibacter propionicigenes WB4 gntT, gntK, gnd
Pandoraea thiooxydans ATSB16 gntT, gntK, edd, eda
Pantoea rwandensis LMG 26275 gntT, gntK, gnd
Pedobacter arcticus A12 gntT, gntK, gnd
Photobacterium gaetbulicola Gung47 gntT, gntK, edd, eda
Photobacterium jeanii R-40508 gntT, gntK, edd, eda
Phyllobacterium brassicacearum STM 196 gntA, gntB, gntC, gntK, edd, eda
Phyllobacterium endophyticum PEPV15 gntT, gntK, edd, eda
Phyllobacterium leguminum ORS 1419 gntA, gntB, gntC, gntK, edd, eda
Planktomarina temperata RCA23 gntT, gntK, edd, eda
Planococcus halocryophilus Or1 gntT, gntK, gnd
Pleomorphomonas diazotrophica R5-392 gntA, gntB, gntC, gntK, edd, eda
Polaribacter dokdonensis DSW-5 gntT, gntK, gnd
Pontibacillus litoralis JSM 072002 gntT, gntK, gnd
Pontibacter lucknowensis DM9 gntT, gntK, gnd
Pontibacter ramchanderi LP43 gntT, gntK, gnd
Pontimonas salivibrio CL-TW6 gntT, gntK, gnd
Porphyrobacter dokdonensis DSW-74 gntT, gntK, edd, eda
Pseudoalteromonas arctica A 37-1-2 gntT, gntK, edd, eda
Pseudomonas baetica a390 gntT, gntK, edd, eda
Pseudomonas litoralis 2SM5 gntT, gntK, edd, eda
Pseudomonas taeanensis MS-3 gntA, gntB, gntC, gntK, edd, eda
Pseudovibrio axinellae Ad2 gntT, gntK, gnd
Psychrobacter arcticus 273-4 gntT, gntK, gnd
Psychrobacter cryohalolentis K5 gntT, gntK, gnd
Psychromonas ingrahamii 37 gntT, gntK, gnd
Psychromonas ossibalaenae JAMM 0738 gntT, gntK, edd, eda
Rhizobium freirei PRF 81 gntT, gntK, edd, eda
Rhizobium grahamii CCGE 502 gntT, gntK, edd, eda
Rhizobium subbaraonis JC85 gntA, gntB, gntC, gntK, edd, eda
Rhodanobacter denitrificans 2APBS1 gntT, gntK, edd, eda
Rhodobacter johrii JA192 gntA, gntB, gntC, gntK, edd, eda
Rhodobacter maris JA276 gntT, gntK, edd, eda
Rhodobacter ovatus JA234 gntA, gntB, gntC, gntK, edd, eda
Rhodobacter viridis JA737 gntT, gntK, edd, eda
Rhodococcus qingshengii djl-6-2 gntT, gntK, gnd
Rhodopseudomonas pseudopalustris DSM 123 gntT, gntK, gnd
Roseateles aquatilis CCUG 48205 gntA, gntB, gntC, gntK, edd, eda
Roseivirga spongicola UST030701-084 gntT, gntK, gnd
Rubrivirga marina SAORIC-28 gntT, gntK, gnd
Ruegeria conchae TW15 gntT, gntK, edd, eda
Saccharomonospora marina XMU15 gntT, gntK, edd, eda
Salinicoccus carnicancri Crm gntT, gntK, gnd
Serinicoccus profundi MCCC 1A05965 gntT, gntK, gnd
Shewanella halifaxensis HAW-EB4 gntT, gntK, edd, eda
Skermanella stibiiresistens SB22 gntT, gntK, edd, eda
Snodgrassella alvi wkB2 gntT, gntK, gnd
Sphaerochaeta globosa Buddy gntT, gntK, gnd
Sphaerochaeta pleomorpha Grapes gntT, gntK, gnd
Sphingobium baderi LL03 gntT, gntK, edd, eda
Sphingobium czechense LL01 gntT, gntK, edd, eda
Sphingobium quisquiliarum P25 gntT, gntK, edd, eda
Sphingomonas histidinilytica UM2 gntT, gntK, edd, eda
Sphingomonas indica Dd16 gntT, gntK, gnd
Sphingomonas laterariae LNB2 gntT, gntK, edd, eda
Sphingopyxis indica DS15 gntT, gntK, edd, eda
Sphingopyxis terrae UI2 gntT, gntK, edd, eda
Sporolactobacillus vineae SL153 gntT, gntK, gnd
Streptacidiphilus oryzae TH49 gntT, gntK, gnd
Streptococcus anginosus CCUG 39159 gntT, gntK, gnd
Streptococcus massiliensis 4401825 gntT, gntK, gnd
Streptococcus oralis 7747 gntT, gntK, gnd
Streptococcus oralis AZ_3a gntT, gntK, gnd
Streptomyces kebangsaanensis SUK12 gntT, gntK, gnd
Succinatimonas hippei YIT 12066 gntT, gntK, edd, eda
Sulfurimonas gotlandica GD1 gntT, gntK, gnd
Tatumella morbirosei LMG 23360 gntT, gntK, gnd
Thauera humireducens SgZ-1 gntA, gntB, gntC, gntK, gnd
Thermoactinomyces daqus H-18 gntT, gntK, gnd
Thermobifida halotolerans YIM 90462 gntT, gntK, gnd
Thermodesulfovibrio aggregans TGE-P1 gntT, gntK, gnd
Thermophagus xiamenensis HS1 gntT, gntK, gnd
Thermovenabulum gondwanense R270 gntT, gntK, edd, eda
Thioclava dalianensis DLFJ1-1 gntA, gntB, gntC, gntK, edd, eda
Thiohalospira halophila HL 3 gntT, gntK, gnd
Tistlia consotensis USBA 355 gntA, gntB, gntC, gntK, edd, eda
Vagococcus penaei CD276 gntT, gntK, gnd
Verminephrobacter eiseniae EF01-2 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Weissella oryzae SG25 gntT, gntK, gnd
Williamsia sterculiae CPCC 203464 gntT, gntK, gnd
Yersinia intermedia Y228 gntT, gntK, edd, eda

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