GapMind for catabolism of small carbon sources

 

2-oxoglutarate (alpha-ketoglutarate) catabolism

Analysis of pathway 2-oxoglutarate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 dctP, dctQ, dctM
Actinokineospora bangkokensis 44EHW kgtP
Actinomyces timonensis 7400942 kgtP
Algiphilus aromaticivorans DG1253 kgtP
Algoriphagus aquaeductus T4 kgtP
Algoriphagus machipongonensis PR1 kgtP
Alicyclobacillus ferrooxydans TC-34 kgtP
Alishewanella agri BL06 kgtP
Alistipes indistinctus YIT 12060 kgtP
Alistipes shahii WAL 8301 kgtP
Alkalitalea saponilacus SC/BZ-SP2 kgtP
Amantichitinum ursilacus IGB-41 kgtP
Amphibacillus jilinensis Y1 kgtP
Amphritea japonica JAMM 1866 dctP, dctQ, dctM
Amycolatopsis halophila YIM 93223 kgtP
Amycolatopsis xylanica CPCC 202699 kgtP
Aquimarina agarilytica ZC1 kgtP
Aquimarina longa SW024 kgtP
Aquimarina macrocephali JAMB N27 kgtP
Archaeoglobus sulfaticallidus PM70-1 Psest_0084, Psest_0085
Arcticibacter svalbardensis MN12-7 kgtP
Ardenticatena maritima 110S kgtP
Arenimonas metalli CF5-1 kgtP
Arenitalea lutea P7-3-5 kgtP
Azospirillum humicireducens SgZ-5 Psest_0084, Psest_0085
Azospirillum thiophilum BV-S Psest_0084, Psest_0085
Bacillus altitudinis 41KF2b kgtP
Bacillus coahuilensis m4-4 Psest_0084, Psest_0085
Bacillus cytotoxicus NVH 391-98 kgtP
Bacillus horneckiae 1P01SC Psest_0084, Psest_0085
Bacillus okhensis Kh10-101 Psest_0084, Psest_0085
Bacillus safensis FO-36b kgtP
Bacillus velezensis CBMB205 csbX
Bacteroides clarus YIT 12056 kgtP
Bacteroides faecis MAJ27 kgtP
Bacteroides fluxus YIT 12057 kgtP
Bacteroides oleiciplenus YIT 12058 kgtP
Barnesiella intestinihominis YIT 11860 kgtP
Belnapia rosea CPCC 100156 Psest_0084, Psest_0085
Bizionia argentinensis JUB59 kgtP
Bradyrhizobium diazoefficiens USDA110 Psest_0084, Psest_0085
Brevibacterium jeotgali SJ5-8 kgtP
Brucella inopinata BO1 kgtP
Brucella microti CCM 4915 kgtP
Bryobacter aggregatus MPL3 kgtP
Caldicellulosiruptor hydrothermalis 108 kgtP
Caldicellulosiruptor kronotskyensis 2002 kgtP
Carboxydothermus pertinax Ug1 kgtP
Catellicoccus marimammalium M35/04/3 kgtP
Chromobacterium vaccinii MWU205 dctP, dctQ, dctM
Chryseobacterium angstadtii KM kgtP
Chryseobacterium arthrosphaerae CC-VM-7 kgtP
Chryseobacterium viscerum 687B-08 kgtP
Cloacibacillus porcorum CL-84 Psest_0084, Psest_0085
Cobetia crustatorum JO1 dctP, dctQ, dctM
Collimonas arenae Ter10 kgtP
Collimonas pratensis Ter91 kgtP
Collinsella tanakaei YIT 12063 kgtP
Coprobacter fastidiosus NSB1 kgtP
Corynebacterium deserti GIMN1.010 csbX
Corynebacterium frankenforstense ST18 csbX
Corynebacterium lactis RW2-5 kgtP
Croceitalea dokdonensis DOKDO 023 kgtP
Cronobacter condimenti 1330 kgtP
Cronobacter muytjensii ATCC 51329 kgtP
Cronobacter universalis NCTC 9529 kgtP
Desulfatitalea tepidiphila S28bF Psest_0084, Psest_0085
Desulfotomaculum hydrothermale Lam5 Psest_0084, Psest_0085
Dethiosulfovibrio salsuginis USBA 82 Psest_0084, Psest_0085
Devosia chinhatensis IPL18 Psest_0084, Psest_0085
Devriesea agamarum IMP2 kgtP
Dialister succinatiphilus YIT 11850 Psest_0084, Psest_0085
Dietzia timorensis ID05-A0528 kgtP
Dokdonella koreensis DS-123 kgtP
Domibacillus robiginosus WS 4628 csbX
Duganella sacchari Sac-22 kgtP
Dyadobacter tibetensis Y620-1 kgtP
Dyella jiangningensis SBZ3-12 kgtP
Endozoicomonas montiporae CL-33 Psest_0084, Psest_0085
Enterococcus termitis LMG 8895 csbX
Enterorhabdus caecimuris B7 kgtP
Epibacterium ulvae U95 dctP, dctQ, dctM
Erythrobacter gangjinensis K7-2 kgtP
Erythrobacter marinus HWDM-33 kgtP
Ethanoligenens harbinense YUAN-3 kgtP
Fervidicella metallireducens AeB kgtP
Fibrella aestuarina BUZ 2 kgtP
Flammeovirga pacifica WPAGA1 kgtP
Flaviramulus ichthyoenteri Th78 kgtP
Flavobacterium beibuense F44-8 kgtP
Flavobacterium glycines Gm-149 kgtP
Flavobacterium sp. LM5 kgtP
Flavobacterium ummariense DS-12 kgtP
Frischella perrara PEB0191 kgtP
Galbibacter marinus ck-I2-15 kgtP
Gallaecimonas xiamenensis 3-C-1 Psest_0084, Psest_0085
Geobacter daltonii FRC-32 kgtP
Gillisia marina CBA3202 kgtP
Gracilibacillus halophilus YIM-C55.5 kgtP
Granulicella mallensis MP5ACTX8 kgtP
Granulicella tundricola MP5ACTX9 kgtP
Hafnia paralvei ATCC 29927 kgtP
Haladaptatus cibarius D43 kgtP
Halioglobus japonicus S1-36 kgtP
Halobacillus alkaliphilus FP5 Psest_0084, Psest_0085
Halococcus hamelinensis 100A6 kgtP
Halomonas salina B6 Psest_0084, Psest_0085
Halomonas smyrnensis AAD6 Psest_0084, Psest_0085
Halomonas stevensii S18214 Psest_0084, Psest_0085
Halomonas titanicae BH1 Psest_0084, Psest_0085
Halomonas xinjiangensis TRM 0175 Psest_0084, Psest_0085
Halopiger salifodinae KCY07-B2 Psest_0084, Psest_0085
Halostagnicola larsenii XH-48 kgtP
Haloterrigena daqingensis JX313 Psest_0084, Psest_0085
Herbaspirillum aquaticum IEH 4430 kgtP
Hippea alviniae EP5-r Psest_0084, Psest_0085
Hippea jasoniae Mar08-272r Psest_0084, Psest_0085
Hoeflea phototrophica DFL-43 Psest_0084, Psest_0085
Hyphomicrobium nitrativorans NL23 dctP, dctQ, dctM
Imtechella halotolerans K1 kgtP
Indibacter alkaliphilus LW1 csbX
Jannaschia aquimarina GSW-M26 dctP, dctQ, dctM
Jeotgalibacillus soli P9 Psest_0084, Psest_0085
Kangiella geojedonensis YCS-5 kgtP
Knoellia flava TL1 kgtP
Kocuria flava HO-9041 kgtP
Kocuria turfanensis HO-9042 kgtP
Laceyella sediminis RHA1 kgtP
Lacinutrix algicola AKS293 kgtP
Lacinutrix himadriensis E4-9a kgtP
Lacinutrix mariniflava AKS432 kgtP
Lactobacillus curieae CCTCC M 2011381 kgtP
Lactobacillus delbrueckii ZN7a-9 kgtP
Lactobacillus hokkaidonensis LOOC260 csbX
Lactobacillus oryzae SG293 kgtP
Lactobacillus pobuzihii E100301 kgtP
Lactobacillus shenzhenensis LY-73 kgtP
Lactobacillus silagei IWT126 kgtP
Leeuwenhoekiella blandensis MED217 kgtP
Lentibacillus jeotgali Grbi csbX
Limnohabitans curvus MWH-C5 kgtP
Limnohabitans parvus II-B4 Psest_0084, Psest_0085
Listeria fleischmannii LU2006-1 kgtP
Luteimonas huabeiensis HB2 kgtP
Luteipulveratus mongoliensis MN07-A0370 kgtP
Lutibaculum baratangense AMV1 Psest_0084, Psest_0085
Lysobacter daejeonensis GH1-9 kgtP
Magnetovibrio blakemorei MV-1 dctP, dctQ, dctM
Marinicella litoralis KMM 3900 kgtP
Mariniradius saccharolyticus AK6 kgtP
Marinobacter algicola DG893 Psest_0084, Psest_0085
Marinobacter guineae M3B Psest_0084, Psest_0085
Marinobacter psychrophilus 20041 Psest_0084, Psest_0085
Marinomonas arctica 328 Psest_0084, Psest_0085
Marivita geojedonensis DPG-138 Psest_0084, Psest_0085
Martelella endophytica YC6887 kgtP
Megamonas funiformis YIT 11815 kgtP
Mesorhizobium ciceri WSM1271 Psest_0084, Psest_0085
Methanobacterium arcticum M2 kgtP
Methanobacterium veterum MK4 kgtP
Methanocella arvoryzae MRE50 Psest_0084, Psest_0085
Methanococcus aeolicus Nankai-3 kgtP
Methanoculleus horonobensis T10 kgtP
Methanolinea tarda NOBI-1 kgtP
Methanosarcina soligelidi SMA-21 kgtP
Methanospirillum lacunae Ki8-1 kgtP
Methanospirillum stamsii Pt1 kgtP
Methylibium petroleiphilum PM1 kgtP
Methylobacterium gossipiicola Gh-105 kgtP
Methylocapsa aurea KYG kgtP
Methylotenera versatilis 301 kgtP
Microbacterium profundi Shh49 kgtP
Microvirga lotononidis WSM3557 Psest_0084, Psest_0085
Moritella dasanensis ArB 0140 dctP, dctQ, dctM
Mucilaginibacter gossypii Gh-67 kgtP
Mucilaginibacter gossypiicola Gh-48 kgtP
Mucilaginibacter mallensis MP1X4 kgtP
Nafulsella turpanensis ZLM-10 kgtP
Natronomonas moolapensis 8.8.11 kgtP
Nautilia profundicola AmH dctP, dctQ, dctM
Neiella marina J221 kgtP
Neptunomonas antarctica S3-22 dctP, dctQ, dctM
Nocardioides daejeonensis MJ31 kgtP
Nocardioides dokdonensis FR1436 kgtP
Nocardiopsis baichengensis YIM 90130 csbX
Nocardiopsis gilva YIM 90087 csbX
Novosphingobium barchaimii LL02 kgtP
Novosphingobium fuchskuhlense FNE08-7 kgtP
Novosphingobium lindaniclasticum LE124 kgtP
Oceanisphaera arctica V1-41 Psest_0084, Psest_0085
Ochrobactrum rhizosphaerae PR17 Psest_0084, Psest_0085
Ochrobactrum thiophenivorans DSM 7216 kgtP
Oscillibacter ruminantium GH1 Psest_0084, Psest_0085
Paenisporosarcina indica PN2 kgtP
Palaeococcus pacificus DY20341 Psest_0084, Psest_0085
Paludibacter propionicigenes WB4 kgtP
Pandoraea thiooxydans ATSB16 kgtP
Pantoea rwandensis LMG 26275 kgtP
Pedobacter arcticus A12 kgtP
Photobacterium gaetbulicola Gung47 Psest_0084, Psest_0085
Photobacterium jeanii R-40508 kgtP
Phyllobacterium brassicacearum STM 196 kgtP
Phyllobacterium endophyticum PEPV15 Psest_0084, Psest_0085
Phyllobacterium leguminum ORS 1419 kgtP
Planktomarina temperata RCA23 dctP, dctQ, dctM
Planococcus halocryophilus Or1 Psest_0084, Psest_0085
Pleomorphomonas diazotrophica R5-392 kgtP
Polaribacter dokdonensis DSW-5 kgtP
Pontibacillus litoralis JSM 072002 Psest_0084, Psest_0085
Pontibacter lucknowensis DM9 kgtP
Pontibacter ramchanderi LP43 kgtP
Pontimonas salivibrio CL-TW6 kgtP
Porphyrobacter dokdonensis DSW-74 kgtP
Pseudoalteromonas arctica A 37-1-2 kgtP
Pseudomonas baetica a390 kgtP
Pseudomonas litoralis 2SM5 Psest_0084, Psest_0085
Pseudomonas taeanensis MS-3 Psest_0084, Psest_0085
Pseudovibrio axinellae Ad2 dctP, dctQ, dctM
Psychrobacter arcticus 273-4 Psest_0084, Psest_0085
Psychrobacter cryohalolentis K5 Psest_0084, Psest_0085
Psychromonas ingrahamii 37 dctP, dctQ, dctM
Psychromonas ossibalaenae JAMM 0738 dctP, dctQ, dctM
Rhizobium freirei PRF 81 kgtP
Rhizobium grahamii CCGE 502 kgtP
Rhizobium subbaraonis JC85 kgtP
Rhodanobacter denitrificans 2APBS1 kgtP
Rhodobacter johrii JA192 Psest_0084, Psest_0085
Rhodobacter maris JA276 Psest_0084, Psest_0085
Rhodobacter ovatus JA234 kgtP
Rhodobacter viridis JA737 dctP, dctQ, dctM
Rhodococcus qingshengii djl-6-2 kgtP
Rhodopseudomonas pseudopalustris DSM 123 Psest_0084, Psest_0085
Roseateles aquatilis CCUG 48205 kgtP
Roseivirga spongicola UST030701-084 kgtP
Rubrivirga marina SAORIC-28 kgtP
Ruegeria conchae TW15 dctP, dctQ, dctM
Saccharomonospora marina XMU15 kgtP
Salinicoccus carnicancri Crm Psest_0084, Psest_0085
Serinicoccus profundi MCCC 1A05965 kgtP
Shewanella halifaxensis HAW-EB4 kgtP
Skermanella stibiiresistens SB22 Psest_0084, Psest_0085
Snodgrassella alvi wkB2 kgtP
Sphaerochaeta globosa Buddy Psest_0084, Psest_0085
Sphaerochaeta pleomorpha Grapes Psest_0084, Psest_0085
Sphingobium baderi LL03 kgtP
Sphingobium czechense LL01 kgtP
Sphingobium quisquiliarum P25 kgtP
Sphingomonas histidinilytica UM2 kgtP
Sphingomonas indica Dd16 kgtP
Sphingomonas laterariae LNB2 kgtP
Sphingopyxis indica DS15 kgtP
Sphingopyxis terrae UI2 kgtP
Sporolactobacillus vineae SL153 kgtP
Streptacidiphilus oryzae TH49 kgtP
Streptococcus anginosus CCUG 39159 kgtP
Streptococcus massiliensis 4401825 kgtP
Streptococcus oralis 7747 kgtP
Streptococcus oralis AZ_3a kgtP
Streptomyces kebangsaanensis SUK12 kgtP
Succinatimonas hippei YIT 12066 kgtP
Sulfurimonas gotlandica GD1 kgtP
Tatumella morbirosei LMG 23360 kgtP
Thauera humireducens SgZ-1 dctP, dctQ, dctM
Thermoactinomyces daqus H-18 kgtP
Thermobifida halotolerans YIM 90462 kgtP
Thermodesulfovibrio aggregans TGE-P1 kgtP
Thermophagus xiamenensis HS1 kgtP
Thermovenabulum gondwanense R270 Psest_0084*, Psest_0085
Thioclava dalianensis DLFJ1-1 dctP, dctQ, dctM
Thiohalospira halophila HL 3 kgtP
Tistlia consotensis USBA 355 Psest_0084, Psest_0085
Vagococcus penaei CD276 kgtP
Verminephrobacter eiseniae EF01-2 kgtP
Weissella oryzae SG25 kgtP
Williamsia sterculiae CPCC 203464 kgtP
Yersinia intermedia Y228 kgtP

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