GapMind for catabolism of small carbon sources


2-oxoglutarate (alpha-ketoglutarate) catabolism

Analysis of pathway 2-oxoglutarate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 kgtP
Acidithiobacillus ferrooxidans ATCC 23270 kgtP
Acidovorax sp. GW101-3H11 kgtP
Algiphilus aromaticivorans DG1253 kgtP
Alicycliphilus denitrificans K601 kgtP
Alkalihalobacterium alkalinitrilicum DSM 22532 Psest_0084, Psest_0085
Allochromatium vinosum DSM 180 dctP, dctQ, dctM
Ammonifex degensii KC4 kgtP
Anaerobutyricum hallii DSM 3353 kgtP
Aquimarina longa SW024 kgtP
Archaeoglobus veneficus SNP6 Psest_0084, Psest_0085
Arcobacter nitrofigilis DSM 7299 Psest_0084, Psest_0085
Azoarcus olearius BH72 Psest_0084, Psest_0085
Azohydromonas australica DSM 1124 kgtP
Azorhizobium caulinodans ORS 571 Psest_0084, Psest_0085
Azospirillum brasilense Sp245 Psest_0084, Psest_0085
Azospirillum sp. B510 Psest_0084, Psest_0085
Bacteroides thetaiotaomicron VPI-5482 kgtP
Beijerinckia indica ATCC 9039 kgtP
Beijerinckia mobilis UQM 1969 kgtP
Billgrantia desiderata SP1 Psest_0084, Psest_0085
Bradyrhizobium sp. BTAi1 Psest_0084, Psest_0085
Brevundimonas sp. GW460-12-10-14-LB2 kgtP
Burkholderia phytofirmans PsJN kgtP
Burkholderia vietnamiensis G4 kgtP
Calditerrivibrio nitroreducens DSM 19672 Psest_0084, Psest_0085
Caminibacter mediatlanticus TB-2 dctP, dctQ, dctM
Carboxydothermus pertinax Ug1 kgtP
Caulobacter crescentus NA1000 kgtP
Cereibacter sphaeroides ATCC 17029 Psest_0084, Psest_0085
Chlorobaculum parvum NCIB 8327 kgtP
Chlorobaculum tepidum TLS kgtP
Chlorobium limicola DSM 245 kgtP
Chlorobium phaeobacteroides BS1 kgtP
Clostridium acetobutylicum ATCC 824 kgtP
Clostridium kluyveri DSM 555 kgtP
Clostridium tyrobutyricum FAM22553 kgtP
Crocosphaera subtropica ATCC 51142 kgtP
Cupriavidus basilensis FW507-4G11 kgtP
Dechloromonas agitata is5 dctP, dctQ, dctM
Dechlorosoma suillum PS dctP, dctQ, dctM
Dehalococcoides mccartyi 195 kgtP
Denitrovibrio acetiphilus DSM 12809 Psest_0084, Psest_0085
Derxia gummosa DSM 723 dctP, dctQ, dctM
Desulfacinum hydrothermale DSM 13146 Psest_0084, Psest_0085
Desulfacinum infernum DSM 9756 Psest_0084, Psest_0085
Desulfarculus baarsii DSM 2075 kgtP
Desulfatibacillum aliphaticivorans DSM 15576 Psest_0084, Psest_0085
Desulfatiglans anilini DSM 4660 kgtP
Desulfitobacterium hafniense DCB-2 dctP, dctQ, dctM
Desulfobacca acetoxidans DSM 11109 kgtP
Desulfobacter vibrioformis DSM 8776 kgtP
Desulfogranum mediterraneum DSM 13871 dctP, dctQ, dctM
Desulforamulus ruminis DSM 2154 kgtP
Desulfoscipio geothermicus DSM 3669 Psest_0084, Psest_0085
Desulfotalea psychrophila LSv54 kgtP
Desulfovibrio oxyclinae DSM 11498 kgtP
Desulfovibrio vulgaris Hildenborough JW710 kgtP
Desulfovibrio vulgaris Miyazaki F kgtP
Desulfurobacterium atlanticum DSM 15668 kgtP
Desulfuromonas acetexigens kgtP
Desulfuromusa kysingii DSM 7343 dctP, dctQ, dctM
Dinoroseobacter shibae DFL-12 Psest_0084, Psest_0085
Dyella japonica UNC79MFTsu3.2 kgtP
Echinicola vietnamensis KMM 6221, DSM 17526 kgtP
Escherichia coli BW25113 kgtP
Ferroglobus placidus DSM 10642 Psest_0084, Psest_0085
Frankia alni ACN14a kgtP
Geobacter metallireducens GS-15 kgtP
Geotalea uraniireducens Rf4 kgtP
Halococcus hamelinensis 100A6 kgtP
Haloechinothrix alba DSM 45207 kgtP
Haloferax volcanii DS2 kgtP
Haloglycomyces albus DSM 45210 kgtP
Halorhodospira halophila SL1 Psest_0084, Psest_0085
Heliomicrobium modesticaldum Ice1; ATCC 51547 kgtP
Herbaspirillum autotrophicum IAM 14942 kgtP
Herbaspirillum seropedicae SmR1 kgtP
Hippea alviniae EP5-r Psest_0084, Psest_0085
Hydrogenophaga taeniospiralis NBRC 102512 Psest_0084, Psest_0085*
Hydrogenovibrio halophilus DSM 15072 kgtP
Hydrogenovibrio kuenenii DSM 12350 kgtP
Hydrogenovibrio marinus DSM 11271 kgtP
Hyphomicrobium sulfonivorans WDL6 kgtP
Klebsiella michiganensis M5al kgtP
Klebsiella variicola At-22 kgtP
Kyrpidia tusciae DSM 2912 kgtP
Leptospirillum ferrooxidans C2-3 kgtP
Magnetospirillum magneticum AMB-1 Psest_0084, Psest_0085
Malonomonas rubra DSM 5091 Psest_0084, Psest_0085
Maridesulfovibrio bastinii DSM 16055 kgtP
Maridesulfovibrio zosterae DSM 11974 kgtP
Marinobacter adhaerens HP15 Psest_0084, Psest_0085
Mesorhizobium ciceri WSM1271 Psest_0084, Psest_0085
Methanobacterium lacus AL-21 kgtP
Methanococcus aeolicus Nankai-3 kgtP
Methanococcus maripaludis C5 kgtP
Methanosarcina acetivorans C2A kgtP
Methanosarcina mazei Go1 kgtP
Methanospirillum lacunae Ki8-1 kgtP
Methanothermobacter thermautotrophicus Delta H kgtP
Methylobacterium nodulans ORS 2060 kgtP
Methylobacterium sp. 4-46 Apr-46 kgtP
Methylocapsa acidiphila B2 kgtP
Methylocapsa aurea KYG kgtP
Methylocella silvestris BL2 kgtP
Methylococcus capsulatus Bath kgtP
Methylocystis bryophila S285 kgtP
Methyloferula stellata AR4T kgtP
Methylohalobius crimeensis 10Ki kgtP
Methylomonas methanica MC09 kgtP
Methylosarcina fibrata AML-C10 kgtP
Methylotuvimicrobium alcaliphilum 20Z kgtP
Methylovulum miyakonense HT12 kgtP
Mycolicibacterium vanbaalenii PYR-1 Psest_0084, Psest_0085
Nitratifractor salsuginis DSM 16511 kgtP
Nitratiruptor tergarcus DSM 16512 kgtP
Nitriliruptor alkaliphilus DSM 45188 kgtP
Nocardioides dokdonensis FR1436 kgtP
Nocardiopsis lucentensis DSM 44048 kgtP
Nostoc punctiforme ATCC 29133; PCC 73102 kgtP
Novosphingobium aromaticivorans DSM 12444 kgtP
Oleispira antarctica kgtP
Paraburkholderia atlantica CCGE1002 kgtP
Paraburkholderia bryophila 376MFSha3.1 kgtP
Paraburkholderia phymatum STM815 kgtP
Paucidesulfovibrio gracilis DSM 16080 kgtP
Pedobacter sp. GW460-11-11-14-LB5 kgtP
Pelobacter propionicus DSM 2379 kgtP
Persephonella marina EX-H1 kgtP
Phaeacidiphilus oryzae TH49 kgtP
Phaeobacter inhibens BS107 dctP, dctQ, dctM
Polaromonas naphthalenivorans CJ2 kgtP
Prosthecochloris aestuarii DSM 271 kgtP
Pseudarthrobacter sulfonivorans Ar51 kgtP
Pseudomonas benzenivorans DSM 8628 Psest_0084, Psest_0085
Pseudomonas fluorescens FW300-N1B4 kgtP
Pseudomonas fluorescens FW300-N2C3 kgtP
Pseudomonas fluorescens FW300-N2E2 Psest_0084, Psest_0085
Pseudomonas fluorescens FW300-N2E3 kgtP
Pseudomonas fluorescens GW456-L13 kgtP
Pseudomonas putida KT2440 Psest_0084, Psest_0085
Pseudomonas simiae WCS417 kgtP
Pseudomonas stutzeri RCH2 Psest_0084, Psest_0085
Pyrolobus fumarii 1A kgtP
Rhizobium etli CFN 42 kgtP
Rhizobium johnstonii 3841 kgtP
Rhizobium leguminosarum WSM1325 kgtP
Rhizorhabdus wittichii RW1 kgtP
Rhodanobacter denitrificans FW104-10B01 kgtP
Rhodomicrobium vannielii ATCC 17100 kgtP
Rhodopseudomonas palustris CGA009 Psest_0084, Psest_0085
Rhodospirillum centenum SW; ATCC 51521 kgtP
Rhodospirillum rubrum ATCC 11170 dctP, dctQ, dctM
Roseburia faecis M72 kgtP
Saccharomonospora cyanea NA-134 kgtP
Sedimenticola selenatireducens DSM 17993 dctP, dctQ, dctM
Shewanella amazonensis SB2B dctP, dctQ, dctM
Shewanella loihica PV-4 dctP, dctQ, dctM
Shewanella oneidensis MR-1 dctP, dctQ, dctM
Shewanella sp. ANA-3 dctP, dctQ, dctM
Sinorhizobium fredii NGR234 kgtP
Sinorhizobium medicae WSM419 kgtP
Sinorhizobium meliloti 1021 kgtP
Sphingomonas koreensis DSMZ 15582 kgtP
Stenotrophomonas chelatiphaga DSM 21508 kgtP
Steroidobacter denitrificans DSM 18526 kgtP
Stutzerimonas stutzeri A1501 Psest_0084, Psest_0085
Sulfuricurvum kujiense DSM 16994 kgtP
Sulfurihydrogenibium azorense Az-Fu1 kgtP
Sulfurihydrogenibium subterraneum DSM 15120 kgtP
Sulfurimonas denitrificans DSM 1251 kgtP
Sulfuritalea hydrogenivorans DSM 22779 Psest_0084, Psest_0085
Sulfurivirga caldicuralii DSM 17737 kgtP
Synechococcus elongatus PCC 7942 kgtP
Teredinibacter turnerae T7901 kgtP
Thauera aminoaromatica S2 Psest_0084*, Psest_0085
Thermithiobacillus tepidarius DSM 3134 kgtP
Thermocrinis albus DSM 14484 kgtP
Thermodesulforhabdus norvegica DSM 9990 Psest_0084, Psest_0085
Thermomonospora curvata DSM 43183 kgtP
Thermovibrio ammonificans HB-1 kgtP
Thermus aquaticus YT-1 Psest_0084, Psest_0085
Thioalkalivibrio denitrificans ALJD kgtP
Thioalkalivibrio halophilus HL17 kgtP
Thioalkalivibrio paradoxus ARh 1 Psest_0084, Psest_0085
Thioalkalivibrio thiocyanodenitrificans ARhD 1 kgtP
Thiohalomonas denitrificans HLD2 kgtP
Thiohalospira halophila HL 3 kgtP
Thiomicrorhabdus arctica DSM 13458 kgtP
Thiomicrorhabdus chilensis DSM 12352 kgtP
Thiomicrospira cyclica ALM1 kgtP
Thiomicrospira microaerophila ASL8-2 kgtP
Thiomicrospira pelophila DSM 1534 kgtP
Thiothrix lacustris DSM 21227 dctP, dctQ, dctM
Tistlia consotensis USBA 355 Psest_0084, Psest_0085
Trichlorobacter lovleyi SZ kgtP
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome kgtP
Trichormus variabilis ATCC 29413 kgtP
Xanthobacter autotrophicus Py2 kgtP
Xenophilus azovorans DSM 13620 Psest_0084, Psest_0085

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