GapMind for catabolism of small carbon sources

 

D-gluconate catabolism

Analysis of pathway gluconate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 gntT, gntK, gnd
Acidithiobacillus ferrooxidans ATCC 23270 gntT, gntK, gnd
Acidovorax sp. GW101-3H11 gntA, gntB, gntC, gntK, edd, eda
Algiphilus aromaticivorans DG1253 gntT, gntK, gnd
Alicycliphilus denitrificans K601 gntA, gntB, gntC, gntK, edd, eda
Alkalihalobacterium alkalinitrilicum DSM 22532 gntT, gntK, gnd
Allochromatium vinosum DSM 180 gntT, gntK, gnd
Ammonifex degensii KC4 gntT, gntK, gnd
Anaerobutyricum hallii DSM 3353 gntT, gntK, gnd
Aquimarina longa SW024 gntT, gntK, gnd
Archaeoglobus veneficus SNP6 gntT, gntK, gnd
Arcobacter nitrofigilis DSM 7299 gntT, gntK, edd, eda
Azoarcus olearius BH72 gntT, gntK, gnd
Azohydromonas australica DSM 1124 gntA, gntB, gntC, gntK, edd, eda
Azorhizobium caulinodans ORS 571 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Azospirillum brasilense Sp245 gntA, gntB, gntC, gntK, gnd
Azospirillum sp. B510 gntA, gntB, gntC, gntK, edd, eda
Bacteroides thetaiotaomicron VPI-5482 gntT, gntK, gnd
Beijerinckia indica ATCC 9039 gntT, gntK, edd, eda
Beijerinckia mobilis UQM 1969 gntT, gntK, edd, eda
Billgrantia desiderata SP1 gntA, gntB, gntC, gntK, edd, eda
Bradyrhizobium sp. BTAi1 gntT, gntK, gnd
Brevundimonas sp. GW460-12-10-14-LB2 gntT, gntK, edd, eda
Burkholderia phytofirmans PsJN gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Burkholderia vietnamiensis G4 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Calditerrivibrio nitroreducens DSM 19672 gntT, gntK, gnd
Caminibacter mediatlanticus TB-2 gntT, gntK, gnd
Carboxydothermus pertinax Ug1 gntT, gntK, gnd
Caulobacter crescentus NA1000 gntT, gntK, edd, eda
Cereibacter sphaeroides ATCC 17029 gntA, gntB, gntC, gntK, edd, eda
Chlorobaculum parvum NCIB 8327 gntT, gntK, gnd
Chlorobaculum tepidum TLS gntT, gntK, gnd
Chlorobium limicola DSM 245 gntT, gntK, gnd
Chlorobium phaeobacteroides BS1 gntT, gntK, gnd
Clostridium acetobutylicum ATCC 824 gntT, gntK, edd, eda
Clostridium kluyveri DSM 555 gntT, gntK, gnd
Clostridium tyrobutyricum FAM22553 gntT, gntK, gnd
Crocosphaera subtropica ATCC 51142 gntT, gntK, gnd
Cupriavidus basilensis FW507-4G11 gntT, gntK, edd, eda
Dechloromonas agitata is5 gntT, gntK, gnd
Dechlorosoma suillum PS gntT, gntK, gnd
Dehalococcoides mccartyi 195 gntT, gntK, gnd
Denitrovibrio acetiphilus DSM 12809 gntT, gntK, gnd
Derxia gummosa DSM 723 gntT, gntK, edd, eda
Desulfacinum hydrothermale DSM 13146 gntT, gntK, gnd
Desulfacinum infernum DSM 9756 gntT, gntK, edd, eda
Desulfarculus baarsii DSM 2075 gntT, gntK, gnd
Desulfatibacillum aliphaticivorans DSM 15576 gntT, gntK, gnd
Desulfatiglans anilini DSM 4660 gntT, gntK, gnd
Desulfitobacterium hafniense DCB-2 gntT, gntK, gnd
Desulfobacca acetoxidans DSM 11109 gntT, gntK, gnd
Desulfobacter vibrioformis DSM 8776 gntT, gntK, gnd
Desulfogranum mediterraneum DSM 13871 gntT, gntK, gnd
Desulforamulus ruminis DSM 2154 gntT, gntK, edd, eda
Desulfoscipio geothermicus DSM 3669 gntA, gntB, gntC, gntK, gnd
Desulfotalea psychrophila LSv54 gntT, gntK, gnd
Desulfovibrio oxyclinae DSM 11498 gntT, gntK, gnd
Desulfovibrio vulgaris Hildenborough JW710 gntA, gntB, gntC, gntK, gnd
Desulfovibrio vulgaris Miyazaki F gntT, gntK, gnd
Desulfurobacterium atlanticum DSM 15668 gntT, gntK, gnd
Desulfuromonas acetexigens gntT, gntK, gnd
Desulfuromusa kysingii DSM 7343 gntT, gntK, gnd
Dinoroseobacter shibae DFL-12 gntT, gntK, edd, eda
Dyella japonica UNC79MFTsu3.2 gntT, gntK, edd, eda
Echinicola vietnamensis KMM 6221, DSM 17526 gntT, gntK, gnd
Escherichia coli BW25113 gntT, gntK, edd, eda
Ferroglobus placidus DSM 10642 gntT, gntK, gnd
Frankia alni ACN14a gntT, gntK, gnd
Geobacter metallireducens GS-15 gntT, gntK, gnd
Geotalea uraniireducens Rf4 gntT, gntK, gnd
Halococcus hamelinensis 100A6 gntT, gntK, gnd
Haloechinothrix alba DSM 45207 gntT, gntK, edd, eda
Haloferax volcanii DS2 gntT, gntK, gnd
Haloglycomyces albus DSM 45210 gntT, gntK, gnd
Halorhodospira halophila SL1 gntT, gntK, gnd
Heliomicrobium modesticaldum Ice1; ATCC 51547 gntT, gntK, gnd
Herbaspirillum autotrophicum IAM 14942 gntT, gntK, edd, eda
Herbaspirillum seropedicae SmR1 gntT, gntK, edd, eda
Hippea alviniae EP5-r gntT, gntK, gnd
Hydrogenophaga taeniospiralis NBRC 102512 gntA, gntB, gntC, gntK, edd, eda
Hydrogenovibrio halophilus DSM 15072 gntT, gntK, gnd
Hydrogenovibrio kuenenii DSM 12350 gntT, gntK, gnd
Hydrogenovibrio marinus DSM 11271 gntT, gntK, gnd
Hyphomicrobium sulfonivorans WDL6 gntT, gntK, gnd
Klebsiella michiganensis M5al gntT, gntK, edd, eda
Klebsiella variicola At-22 gntT, gntK, edd, eda
Kyrpidia tusciae DSM 2912 gntT, gntK, gnd
Leptospirillum ferrooxidans C2-3 gntT, gntK, gnd
Magnetospirillum magneticum AMB-1 gntT, gntK, gnd
Malonomonas rubra DSM 5091 gntT, gntK, gnd
Maridesulfovibrio bastinii DSM 16055 gntT, gntK, gnd
Maridesulfovibrio zosterae DSM 11974 gntA, gntB, gntC, gntK, gnd
Marinobacter adhaerens HP15 gntT, gntK, edd, eda
Mesorhizobium ciceri WSM1271 gntT, gntK, edd, eda
Methanobacterium lacus AL-21 gntT, gntK, gnd
Methanococcus aeolicus Nankai-3 gntT, gntK, gnd
Methanococcus maripaludis C5 gntT, gntK, gnd
Methanosarcina acetivorans C2A gntT, gntK, gnd
Methanosarcina mazei Go1 gntT, gntK, gnd
Methanospirillum lacunae Ki8-1 gntT, gntK, gnd
Methanothermobacter thermautotrophicus Delta H gntT, gntK, gnd
Methylobacterium nodulans ORS 2060 gntT, gntK, gnd
Methylobacterium sp. 4-46 Apr-46 gntT, gntK, edd, eda
Methylocapsa acidiphila B2 gntT, gntK, gnd
Methylocapsa aurea KYG gntT, gntK, edd, eda
Methylocella silvestris BL2 gntT, gntK, edd, eda
Methylococcus capsulatus Bath gntT, gntK, edd, eda
Methylocystis bryophila S285 gntT, gntK, gnd
Methyloferula stellata AR4T gntT, gntK, gnd
Methylohalobius crimeensis 10Ki gntT, gntK, gnd
Methylomonas methanica MC09 gntT, gntK, edd, eda
Methylosarcina fibrata AML-C10 gntT, gntK, edd, eda
Methylotuvimicrobium alcaliphilum 20Z gntT, gntK, edd, eda
Methylovulum miyakonense HT12 gntT, gntK, edd, eda
Mycolicibacterium vanbaalenii PYR-1 gntT, gntK, gnd
Nitratifractor salsuginis DSM 16511 gntT, gntK, gnd
Nitratiruptor tergarcus DSM 16512 gntT, gntK, gnd
Nitriliruptor alkaliphilus DSM 45188 gntT, gntK, edd, eda
Nocardioides dokdonensis FR1436 gntT, gntK, gnd
Nocardiopsis lucentensis DSM 44048 gntT, gntK, edd, eda
Nostoc punctiforme ATCC 29133; PCC 73102 gntT, gntK, gnd
Novosphingobium aromaticivorans DSM 12444 gntT, gntK, edd, eda
Oleispira antarctica gntT, gntK, edd, eda
Paraburkholderia atlantica CCGE1002 gntT, gntK, edd, eda
Paraburkholderia bryophila 376MFSha3.1 gntT, gntK, edd, eda
Paraburkholderia phymatum STM815 gntT, gntK, edd, eda
Paucidesulfovibrio gracilis DSM 16080 gntT, gntK, gnd
Pedobacter sp. GW460-11-11-14-LB5 gntT, gntK, gnd
Pelobacter propionicus DSM 2379 gntT, gntK, gnd
Persephonella marina EX-H1 gntT, gntK, gnd
Phaeacidiphilus oryzae TH49 gntT, gntK, gnd
Phaeobacter inhibens BS107 gntT, gntK, edd, eda
Polaromonas naphthalenivorans CJ2 gntA, gntB, gntC, gntK, edd, eda
Prosthecochloris aestuarii DSM 271 gntT, gntK, gnd
Pseudarthrobacter sulfonivorans Ar51 gntT, gntK, gnd
Pseudomonas benzenivorans DSM 8628 gntA, gntB, gntC, gntK, edd, eda
Pseudomonas fluorescens FW300-N1B4 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2C3 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2E2 gntT, gntK, edd, eda
Pseudomonas fluorescens FW300-N2E3 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas fluorescens GW456-L13 gntT, gntK, edd, eda
Pseudomonas putida KT2440 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas simiae WCS417 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Pseudomonas stutzeri RCH2 gntA, gntB, gntC, gntK, edd, eda
Pyrolobus fumarii 1A gntT, gntK, gnd
Rhizobium etli CFN 42 gntA, gntB, gntC, gntK, edd, eda
Rhizobium johnstonii 3841 gntT, gntK, edd, eda
Rhizobium leguminosarum WSM1325 gntT, gntK, edd, eda
Rhizorhabdus wittichii RW1 gntT, gntK, edd, eda
Rhodanobacter denitrificans FW104-10B01 gntT, gntK, edd, eda
Rhodomicrobium vannielii ATCC 17100 gntT, gntK, edd, eda
Rhodopseudomonas palustris CGA009 gntT, gntK, gnd
Rhodospirillum centenum SW; ATCC 51521 gntT, gntK, gnd
Rhodospirillum rubrum ATCC 11170 gntT, gntK, gnd
Roseburia faecis M72 gntT, gntK, gnd
Saccharomonospora cyanea NA-134 gntT, gntK, edd, eda
Sedimenticola selenatireducens DSM 17993 gntT, gntK, gnd
Shewanella amazonensis SB2B gntT, gntK, edd, eda
Shewanella loihica PV-4 gntT, gntK, edd, eda
Shewanella oneidensis MR-1 gntT, gntK, edd, eda
Shewanella sp. ANA-3 gntT, gntK, edd, eda
Sinorhizobium fredii NGR234 gntA, gntB, gntC, gntK, edd, eda
Sinorhizobium medicae WSM419 gntA, gntB, gntC, gntK, edd, eda
Sinorhizobium meliloti 1021 gntA, gntB, gntC, gntK, edd, eda
Sphingomonas koreensis DSMZ 15582 gntT, gntK, edd, eda
Stenotrophomonas chelatiphaga DSM 21508 gadh1, gadh2, gadh3, kguT, kguK, kguD, edd, eda
Steroidobacter denitrificans DSM 18526 gntT, gntK, gnd
Stutzerimonas stutzeri A1501 gntA, gntB, gntC, gntK, edd, eda
Sulfuricurvum kujiense DSM 16994 gntT, gntK, gnd
Sulfurihydrogenibium azorense Az-Fu1 gntT, gntK, gnd
Sulfurihydrogenibium subterraneum DSM 15120 gntT, gntK, gnd
Sulfurimonas denitrificans DSM 1251 gntT, gntK, gnd
Sulfuritalea hydrogenivorans DSM 22779 gntT, gntK, gnd
Sulfurivirga caldicuralii DSM 17737 gntT, gntK, gnd
Synechococcus elongatus PCC 7942 gntT, gntK, gnd
Teredinibacter turnerae T7901 gntT, gntK, gnd
Thauera aminoaromatica S2 gntT, gntK, gnd
Thermithiobacillus tepidarius DSM 3134 gntT, gntK, gnd
Thermocrinis albus DSM 14484 gntT, gntK, gnd
Thermodesulforhabdus norvegica DSM 9990 gntA, gntB, gntC, gntK, gnd
Thermomonospora curvata DSM 43183 gntT, gntK, edd, eda
Thermovibrio ammonificans HB-1 gntT, gntK, gnd
Thermus aquaticus YT-1 gntT, gntK, gnd
Thioalkalivibrio denitrificans ALJD gntT, gntK, gnd
Thioalkalivibrio halophilus HL17 gntT, gntK, gnd
Thioalkalivibrio paradoxus ARh 1 gntT, gntK, gnd
Thioalkalivibrio thiocyanodenitrificans ARhD 1 gntT, gntK, gnd
Thiohalomonas denitrificans HLD2 gntT, gntK, gnd
Thiohalospira halophila HL 3 gntT, gntK, gnd
Thiomicrorhabdus arctica DSM 13458 gntT, gntK, gnd
Thiomicrorhabdus chilensis DSM 12352 gntT, gntK, gnd
Thiomicrospira cyclica ALM1 gntT, gntK, gnd
Thiomicrospira microaerophila ASL8-2 gntT, gntK, gnd
Thiomicrospira pelophila DSM 1534 gntT, gntK, gnd
Thiothrix lacustris DSM 21227 gntT, gntK, edd, eda
Tistlia consotensis USBA 355 gntA, gntB, gntC, gntK, edd, eda
Trichlorobacter lovleyi SZ gntT, gntK, gnd
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome gntT, gntK, gnd
Trichormus variabilis ATCC 29413 gntT, gntK, gnd
Xanthobacter autotrophicus Py2 gntT, gntK, edd, eda
Xenophilus azovorans DSM 13620 gntA, gntB, gntC, 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 Apr 09 2024. 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