GapMind for catabolism of small carbon sources

 

pyruvate catabolism

Analysis of pathway pyruvate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 dctM, dctP, dctQ
Actinokineospora bangkokensis 44EHW mctC
Actinomyces timonensis 7400942 btsT
Algiphilus aromaticivorans DG1253 dctM, dctP, dctQ
Algoriphagus aquaeductus T4 yjcH, actP
Algoriphagus machipongonensis PR1 yjcH, actP
Alicyclobacillus ferrooxydans TC-34 mctP
Alishewanella agri BL06 yjcH, actP
Alistipes indistinctus YIT 12060 SLC5A8
Alistipes shahii WAL 8301 SLC5A8
Alkalitalea saponilacus SC/BZ-SP2 SLC5A8
Amantichitinum ursilacus IGB-41 yjcH, actP
Amphibacillus jilinensis Y1 SLC5A8
Amphritea japonica JAMM 1866 dctM, dctP, dctQ
Amycolatopsis halophila YIM 93223 yjcH, actP
Amycolatopsis xylanica CPCC 202699 mctC
Aquimarina agarilytica ZC1 SLC5A8
Aquimarina longa SW024 dctM, dctP, dctQ
Aquimarina macrocephali JAMB N27 dctM, dctP, dctQ
Archaeoglobus sulfaticallidus PM70-1 SLC5A8
Arcticibacter svalbardensis MN12-7 SLC5A8
Ardenticatena maritima 110S dctM, dctP, dctQ
Arenimonas metalli CF5-1 dctM, dctP, dctQ
Arenitalea lutea P7-3-5 yjcH, actP
Azospirillum humicireducens SgZ-5 yjcH, actP
Azospirillum thiophilum BV-S dctM, dctP, dctQ
Bacillus altitudinis 41KF2b mctC
Bacillus coahuilensis m4-4 SLC5A8
Bacillus cytotoxicus NVH 391-98 cstA, ybdD
Bacillus horneckiae 1P01SC mctC
Bacillus okhensis Kh10-101 yjcH, actP
Bacillus safensis FO-36b mctC
Bacillus velezensis CBMB205 mctP
Bacteroides clarus YIT 12056 SLC5A8
Bacteroides faecis MAJ27 SLC5A8
Bacteroides fluxus YIT 12057 SLC5A8
Bacteroides oleiciplenus YIT 12058 SLC5A8
Barnesiella intestinihominis YIT 11860 SLC5A8
Belnapia rosea CPCC 100156 dctM, dctP, dctQ
Bizionia argentinensis JUB59 SLC5A8
Bradyrhizobium diazoefficiens USDA110 dctM, dctP, dctQ
Brevibacterium jeotgali SJ5-8 SLC5A8
Brucella inopinata BO1 dctM, dctP, dctQ
Brucella microti CCM 4915 dctM, dctP, dctQ
Bryobacter aggregatus MPL3 btsT
Caldicellulosiruptor hydrothermalis 108 SLC5A8
Caldicellulosiruptor kronotskyensis 2002 cstA, ybdD
Carboxydothermus pertinax Ug1 mctC
Catellicoccus marimammalium M35/04/3 SLC5A8
Chromobacterium vaccinii MWU205 yjcH, actP
Chryseobacterium angstadtii KM cstA, ybdD
Chryseobacterium arthrosphaerae CC-VM-7 cstA, ybdD
Chryseobacterium viscerum 687B-08 cstA, ybdD
Cloacibacillus porcorum CL-84 SLC5A8
Cobetia crustatorum JO1 dctM, dctP, dctQ
Collimonas arenae Ter10 cstA, ybdD
Collimonas pratensis Ter91 cstA, ybdD
Collinsella tanakaei YIT 12063 SLC5A8
Coprobacter fastidiosus NSB1 SLC5A8
Corynebacterium deserti GIMN1.010 mctC
Corynebacterium frankenforstense ST18 mctC
Corynebacterium lactis RW2-5 mctC
Croceitalea dokdonensis DOKDO 023 yjcH, actP
Cronobacter condimenti 1330 yjcH, actP
Cronobacter muytjensii ATCC 51329 yjcH, actP
Cronobacter universalis NCTC 9529 yjcH, actP
Desulfatitalea tepidiphila S28bF dctM, dctP, dctQ
Desulfotomaculum hydrothermale Lam5 SLC5A8
Dethiosulfovibrio salsuginis USBA 82 SLC5A8
Devosia chinhatensis IPL18 dctM, dctP, dctQ
Devriesea agamarum IMP2 btsT
Dialister succinatiphilus YIT 11850 SLC5A8
Dietzia timorensis ID05-A0528 mctC
Dokdonella koreensis DS-123 cstA, ybdD
Domibacillus robiginosus WS 4628 mctC
Duganella sacchari Sac-22 cstA, ybdD
Dyadobacter tibetensis Y620-1 SLC5A8
Dyella jiangningensis SBZ3-12 cstA, ybdD
Endozoicomonas montiporae CL-33 yjcH, actP
Enterococcus termitis LMG 8895 SLC5A8
Enterorhabdus caecimuris B7 SLC5A8
Epibacterium ulvae U95 dctM, dctP, dctQ
Erythrobacter gangjinensis K7-2 yjcH, actP
Erythrobacter marinus HWDM-33 SLC5A8
Ethanoligenens harbinense YUAN-3 SLC5A8
Fervidicella metallireducens AeB SLC5A8
Fibrella aestuarina BUZ 2 SLC5A8
Flammeovirga pacifica WPAGA1 dctM, dctP, dctQ
Flaviramulus ichthyoenteri Th78 yjcH, actP
Flavobacterium beibuense F44-8 SLC5A8
Flavobacterium glycines Gm-149 SLC5A8
Flavobacterium sp. LM5 SLC5A8
Flavobacterium ummariense DS-12 SLC5A8
Frischella perrara PEB0191 cstA, ybdD
Galbibacter marinus ck-I2-15 yjcH, actP
Gallaecimonas xiamenensis 3-C-1 yjcH, actP
Geobacter daltonii FRC-32 mctC
Gillisia marina CBA3202 SLC5A8
Gracilibacillus halophilus YIM-C55.5 yjcH, actP
Granulicella mallensis MP5ACTX8 mctP
Granulicella tundricola MP5ACTX9 SLC5A8
Hafnia paralvei ATCC 29927 yjcH, actP
Haladaptatus cibarius D43 mctC
Halioglobus japonicus S1-36 yjcH, actP
Halobacillus alkaliphilus FP5 yjcH, actP
Halococcus hamelinensis 100A6 yjcH, actP
Halomonas salina B6 yjcH, actP
Halomonas smyrnensis AAD6 yjcH, actP
Halomonas stevensii S18214 yjcH, actP
Halomonas titanicae BH1 yjcH, actP
Halomonas xinjiangensis TRM 0175 yjcH, actP
Halopiger salifodinae KCY07-B2 MCT4
Halostagnicola larsenii XH-48 SLC5A8
Haloterrigena daqingensis JX313 SLC5A8
Herbaspirillum aquaticum IEH 4430 cstA, ybdD
Hippea alviniae EP5-r SLC5A8
Hippea jasoniae Mar08-272r SLC5A8
Hoeflea phototrophica DFL-43 dctM, dctP, dctQ
Hyphomicrobium nitrativorans NL23 dctM, dctP, dctQ
Imtechella halotolerans K1 SLC5A8
Indibacter alkaliphilus LW1 yjcH, actP
Jannaschia aquimarina GSW-M26 yjcH, actP
Jeotgalibacillus soli P9 mctC
Kangiella geojedonensis YCS-5 dctM, dctP, dctQ
Knoellia flava TL1 mctC
Kocuria flava HO-9041 mctC
Kocuria turfanensis HO-9042 mctC
Laceyella sediminis RHA1 cstA, ybdD
Lacinutrix algicola AKS293 yjcH, actP
Lacinutrix himadriensis E4-9a yjcH, actP
Lacinutrix mariniflava AKS432 yjcH, actP
Lactobacillus curieae CCTCC M 2011381 SLC5A8
Lactobacillus delbrueckii ZN7a-9 SLC5A8
Lactobacillus hokkaidonensis LOOC260 SLC5A8
Lactobacillus oryzae SG293 SLC5A8
Lactobacillus pobuzihii E100301 SLC5A8
Lactobacillus shenzhenensis LY-73 SLC5A8
Lactobacillus silagei IWT126 SLC5A8
Leeuwenhoekiella blandensis MED217 yjcH, actP
Lentibacillus jeotgali Grbi mctC
Limnohabitans curvus MWH-C5 dctM, dctP, dctQ
Limnohabitans parvus II-B4 dctM, dctP, dctQ
Listeria fleischmannii LU2006-1 SLC5A8
Luteimonas huabeiensis HB2 cstA, ybdD
Luteipulveratus mongoliensis MN07-A0370 mctC
Lutibaculum baratangense AMV1 dctM, dctP, dctQ
Lysobacter daejeonensis GH1-9 cstA, ybdD
Magnetovibrio blakemorei MV-1 dctM, dctP, dctQ
Marinicella litoralis KMM 3900 yjcH, actP
Mariniradius saccharolyticus AK6 yjcH, actP
Marinobacter algicola DG893 yjcH, actP
Marinobacter guineae M3B yjcH, actP
Marinobacter psychrophilus 20041 yjcH, actP
Marinomonas arctica 328 yjcH, actP
Marivita geojedonensis DPG-138 yjcH, actP
Martelella endophytica YC6887 dctM, dctP, dctQ
Megamonas funiformis YIT 11815 SLC5A8
Mesorhizobium ciceri WSM1271 dctM, dctP, dctQ
Methanobacterium arcticum M2 SLC5A8
Methanobacterium veterum MK4 SLC5A8
Methanocella arvoryzae MRE50 mctC
Methanococcus aeolicus Nankai-3 SLC5A8
Methanoculleus horonobensis T10 SLC5A8
Methanolinea tarda NOBI-1 SLC5A8
Methanosarcina soligelidi SMA-21 SLC5A8
Methanospirillum lacunae Ki8-1 mctC
Methanospirillum stamsii Pt1 cstA, ybdD
Methylibium petroleiphilum PM1 dctM, dctP, dctQ
Methylobacterium gossipiicola Gh-105 yjcH, actP
Methylocapsa aurea KYG mctP
Methylotenera versatilis 301 btsT
Microbacterium profundi Shh49 mctC
Microvirga lotononidis WSM3557 dctM, dctP, dctQ
Moritella dasanensis ArB 0140 yjcH, actP
Mucilaginibacter gossypii Gh-67 SLC5A8
Mucilaginibacter gossypiicola Gh-48 SLC5A8
Mucilaginibacter mallensis MP1X4 SLC5A8
Nafulsella turpanensis ZLM-10 SLC5A8
Natronomonas moolapensis 8.8.11 SLC5A8
Nautilia profundicola AmH yjcH, actP
Neiella marina J221 dctM, dctP, dctQ
Neptunomonas antarctica S3-22 dctM, dctP, dctQ
Nocardioides daejeonensis MJ31 mctC
Nocardioides dokdonensis FR1436 mctC
Nocardiopsis baichengensis YIM 90130 mctC
Nocardiopsis gilva YIM 90087 mctC
Novosphingobium barchaimii LL02 cstA, ybdD
Novosphingobium fuchskuhlense FNE08-7 SLC5A8
Novosphingobium lindaniclasticum LE124 cstA, ybdD
Oceanisphaera arctica V1-41 SLC5A8
Ochrobactrum rhizosphaerae PR17 SLC5A8
Ochrobactrum thiophenivorans DSM 7216 SLC5A8
Oscillibacter ruminantium GH1 SLC5A8
Paenisporosarcina indica PN2 mctC
Palaeococcus pacificus DY20341 SLC5A8
Paludibacter propionicigenes WB4 SLC5A8
Pandoraea thiooxydans ATSB16 mctP
Pantoea rwandensis LMG 26275 yjcH, actP
Pedobacter arcticus A12 SLC5A8
Photobacterium gaetbulicola Gung47 yjcH, actP
Photobacterium jeanii R-40508 yjcH, actP
Phyllobacterium brassicacearum STM 196 dctM, dctP, dctQ
Phyllobacterium endophyticum PEPV15 dctM, dctP, dctQ
Phyllobacterium leguminum ORS 1419 dctM, dctP, dctQ
Planktomarina temperata RCA23 dctM, dctP, dctQ
Planococcus halocryophilus Or1 mctC
Pleomorphomonas diazotrophica R5-392 dctM, dctP, dctQ
Polaribacter dokdonensis DSW-5 SLC5A8
Pontibacillus litoralis JSM 072002 SLC5A8
Pontibacter lucknowensis DM9 yjcH, actP
Pontibacter ramchanderi LP43 yjcH, actP
Pontimonas salivibrio CL-TW6 SLC5A8
Porphyrobacter dokdonensis DSW-74 yjcH, actP
Pseudoalteromonas arctica A 37-1-2 yjcH, actP
Pseudomonas baetica a390 yjcH, actP
Pseudomonas litoralis 2SM5 yjcH, actP
Pseudomonas taeanensis MS-3 yjcH, actP
Pseudovibrio axinellae Ad2 dctM, dctP, dctQ
Psychrobacter arcticus 273-4 yjcH, actP
Psychrobacter cryohalolentis K5 yjcH, actP
Psychromonas ingrahamii 37 dctM, dctP, dctQ
Psychromonas ossibalaenae JAMM 0738 yjcH, actP
Rhizobium freirei PRF 81 mctP
Rhizobium grahamii CCGE 502 mctP
Rhizobium subbaraonis JC85 dctM, dctP, dctQ
Rhodanobacter denitrificans 2APBS1 cstA, ybdD
Rhodobacter johrii JA192 dctM, dctP, dctQ
Rhodobacter maris JA276 dctM, dctP, dctQ
Rhodobacter ovatus JA234 yjcH, actP
Rhodobacter viridis JA737 dctM, dctP, dctQ
Rhodococcus qingshengii djl-6-2 mctC
Rhodopseudomonas pseudopalustris DSM 123 cstA, ybdD
Roseateles aquatilis CCUG 48205 cstA, ybdD
Roseivirga spongicola UST030701-084 SLC5A8
Rubrivirga marina SAORIC-28 yjcH, actP
Ruegeria conchae TW15 yjcH, actP
Saccharomonospora marina XMU15 mctC
Salinicoccus carnicancri Crm mctC
Serinicoccus profundi MCCC 1A05965 yjcH, actP
Shewanella halifaxensis HAW-EB4 yjcH, actP
Skermanella stibiiresistens SB22 yjcH, actP
Snodgrassella alvi wkB2 SLC5A8
Sphaerochaeta globosa Buddy SLC5A8
Sphaerochaeta pleomorpha Grapes SLC5A8
Sphingobium baderi LL03 cstA, ybdD
Sphingobium czechense LL01 cstA, ybdD
Sphingobium quisquiliarum P25 cstA, ybdD
Sphingomonas histidinilytica UM2 cstA, ybdD
Sphingomonas indica Dd16 SLC5A8
Sphingomonas laterariae LNB2 SLC5A8
Sphingopyxis indica DS15 SLC5A8
Sphingopyxis terrae UI2 SLC5A8
Sporolactobacillus vineae SL153 mctC
Streptacidiphilus oryzae TH49 mctC
Streptococcus anginosus CCUG 39159 SLC5A8
Streptococcus massiliensis 4401825 SLC5A8
Streptococcus oralis 7747 SLC5A8
Streptococcus oralis AZ_3a SLC5A8
Streptomyces kebangsaanensis SUK12 mctC
Succinatimonas hippei YIT 12066 SLC5A8
Sulfurimonas gotlandica GD1 yjcH, actP
Tatumella morbirosei LMG 23360 yjcH, actP
Thauera humireducens SgZ-1 dctM, dctP, dctQ
Thermoactinomyces daqus H-18 cstA, ybdD
Thermobifida halotolerans YIM 90462 mctC
Thermodesulfovibrio aggregans TGE-P1 yjcH, actP
Thermophagus xiamenensis HS1 SLC5A8
Thermovenabulum gondwanense R270 SLC5A8
Thioclava dalianensis DLFJ1-1 dctM, dctP, dctQ
Thiohalospira halophila HL 3 yjcH, actP
Tistlia consotensis USBA 355 dctM, dctP, dctQ
Vagococcus penaei CD276 SLC5A8
Verminephrobacter eiseniae EF01-2 dctM, dctP, dctQ
Weissella oryzae SG25 SLC5A8
Williamsia sterculiae CPCC 203464 cstA, ybdD
Yersinia intermedia Y228 yjcH, actP

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