GapMind for catabolism of small carbon sources

 

pyruvate catabolism

Analysis of pathway pyruvate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 SLC5A8
Acidithiobacillus ferrooxidans ATCC 23270 SLC5A8
Acidovorax sp. GW101-3H11 dctM, dctP, dctQ
Algiphilus aromaticivorans DG1253 dctM, dctP, dctQ
Alicycliphilus denitrificans K601 dctM, dctP, dctQ
Alkalihalobacterium alkalinitrilicum DSM 22532 yjcH, actP
Allochromatium vinosum DSM 180 yjcH, actP
Ammonifex degensii KC4 btsT
Anaerobutyricum hallii DSM 3353 SLC5A8
Aquimarina longa SW024 dctM, dctP, dctQ
Archaeoglobus veneficus SNP6 SLC5A8
Arcobacter nitrofigilis DSM 7299 dctM, dctP, dctQ
Azoarcus olearius BH72 dctM, dctP, dctQ
Azohydromonas australica DSM 1124 yjcH, actP
Azorhizobium caulinodans ORS 571 dctM, dctP, dctQ
Azospirillum brasilense Sp245 dctM, dctP, dctQ
Azospirillum sp. B510 yjcH, actP
Bacteroides thetaiotaomicron VPI-5482 SLC5A8
Beijerinckia indica ATCC 9039 mctP
Beijerinckia mobilis UQM 1969 mctP
Billgrantia desiderata SP1 yjcH, actP
Bradyrhizobium sp. BTAi1 dctM, dctP, dctQ
Brevundimonas sp. GW460-12-10-14-LB2 btsT
Burkholderia phytofirmans PsJN mctC
Burkholderia vietnamiensis G4 yjcH, actP
Calditerrivibrio nitroreducens DSM 19672 dctM, dctP, dctQ
Caminibacter mediatlanticus TB-2 yjcH, actP
Carboxydothermus pertinax Ug1 mctC
Caulobacter crescentus NA1000 SLC5A8
Cereibacter sphaeroides ATCC 17029 dctM, dctP, dctQ
Chlorobaculum parvum NCIB 8327 SLC5A8
Chlorobaculum tepidum TLS yjcH, actP
Chlorobium limicola DSM 245 yjcH, actP
Chlorobium phaeobacteroides BS1 dctM, dctP, dctQ
Clostridium acetobutylicum ATCC 824 cstA, ybdD
Clostridium kluyveri DSM 555 SLC5A8
Clostridium tyrobutyricum FAM22553 cstA, ybdD
Crocosphaera subtropica ATCC 51142 dctM, dctP, dctQ
Cupriavidus basilensis FW507-4G11 dctM, dctP, dctQ
Dechloromonas agitata is5 dctM, dctP, dctQ
Dechlorosoma suillum PS dctM, dctP, dctQ
Dehalococcoides mccartyi 195 SLC5A8
Denitrovibrio acetiphilus DSM 12809 yjcH, actP
Derxia gummosa DSM 723 dctM, dctP, dctQ
Desulfacinum hydrothermale DSM 13146 dctM, dctP, dctQ
Desulfacinum infernum DSM 9756 dctM, dctP, dctQ
Desulfarculus baarsii DSM 2075 SLC5A8
Desulfatibacillum aliphaticivorans DSM 15576 SLC5A8
Desulfatiglans anilini DSM 4660 yjcH, actP
Desulfitobacterium hafniense DCB-2 SLC5A8
Desulfobacca acetoxidans DSM 11109 SLC5A8
Desulfobacter vibrioformis DSM 8776 dctM, dctP, dctQ
Desulfogranum mediterraneum DSM 13871 dctM, dctP, dctQ
Desulforamulus ruminis DSM 2154 SLC5A8
Desulfoscipio geothermicus DSM 3669 SLC5A8
Desulfotalea psychrophila LSv54 SLC5A8
Desulfovibrio oxyclinae DSM 11498 SLC5A8
Desulfovibrio vulgaris Hildenborough JW710 yjcH, actP
Desulfovibrio vulgaris Miyazaki F yjcH, actP
Desulfurobacterium atlanticum DSM 15668 mctC
Desulfuromonas acetexigens yjcH, actP
Desulfuromusa kysingii DSM 7343 dctM, dctP, dctQ
Dinoroseobacter shibae DFL-12 yjcH, actP
Dyella japonica UNC79MFTsu3.2 cstA, ybdD
Echinicola vietnamensis KMM 6221, DSM 17526 yjcH, actP
Escherichia coli BW25113 yjcH, actP
Ferroglobus placidus DSM 10642 SLC5A8
Frankia alni ACN14a mctP
Geobacter metallireducens GS-15 mctC
Geotalea uraniireducens Rf4 mctC
Halococcus hamelinensis 100A6 yjcH, actP
Haloechinothrix alba DSM 45207 yjcH, actP
Haloferax volcanii DS2 mctC
Haloglycomyces albus DSM 45210 mctC
Halorhodospira halophila SL1 SLC5A8
Heliomicrobium modesticaldum Ice1; ATCC 51547 cstA, ybdD
Herbaspirillum autotrophicum IAM 14942 cstA, ybdD
Herbaspirillum seropedicae SmR1 cstA, ybdD
Hippea alviniae EP5-r SLC5A8
Hydrogenophaga taeniospiralis NBRC 102512 dctM, dctP, dctQ
Hydrogenovibrio halophilus DSM 15072 dctM, dctP, dctQ
Hydrogenovibrio kuenenii DSM 12350 yjcH, actP
Hydrogenovibrio marinus DSM 11271 yjcH, actP
Hyphomicrobium sulfonivorans WDL6 dctM, dctP, dctQ
Klebsiella michiganensis M5al yjcH, actP
Klebsiella variicola At-22 yjcH, actP
Kyrpidia tusciae DSM 2912 mctC
Leptospirillum ferrooxidans C2-3 SLC5A8
Magnetospirillum magneticum AMB-1 dctM, dctP, dctQ
Malonomonas rubra DSM 5091 dctM, dctP, dctQ
Maridesulfovibrio bastinii DSM 16055 SLC5A8
Maridesulfovibrio zosterae DSM 11974 SLC5A8
Marinobacter adhaerens HP15 yjcH, actP
Mesorhizobium ciceri WSM1271 dctM, dctP, dctQ
Methanobacterium lacus AL-21 SLC5A8
Methanococcus aeolicus Nankai-3 SLC5A8
Methanococcus maripaludis C5 SLC5A8
Methanosarcina acetivorans C2A SLC5A8
Methanosarcina mazei Go1 SLC5A8
Methanospirillum lacunae Ki8-1 mctC
Methanothermobacter thermautotrophicus Delta H SLC5A8
Methylobacterium nodulans ORS 2060 yjcH, actP
Methylobacterium sp. 4-46 Apr-46 yjcH, actP
Methylocapsa acidiphila B2 mctP
Methylocapsa aurea KYG mctP
Methylocella silvestris BL2 yjcH, actP
Methylococcus capsulatus Bath btsT
Methylocystis bryophila S285 btsT
Methyloferula stellata AR4T mctP
Methylohalobius crimeensis 10Ki dctM, dctP, dctQ
Methylomonas methanica MC09 btsT
Methylosarcina fibrata AML-C10 btsT
Methylotuvimicrobium alcaliphilum 20Z dctM, dctP, dctQ
Methylovulum miyakonense HT12 btsT
Mycolicibacterium vanbaalenii PYR-1 mctC
Nitratifractor salsuginis DSM 16511 dctM, dctP, dctQ
Nitratiruptor tergarcus DSM 16512 yjcH, actP
Nitriliruptor alkaliphilus DSM 45188 yjcH, actP
Nocardioides dokdonensis FR1436 mctC
Nocardiopsis lucentensis DSM 44048 mctC
Nostoc punctiforme ATCC 29133; PCC 73102 yjcH, actP
Novosphingobium aromaticivorans DSM 12444 SLC5A8
Oleispira antarctica yjcH, actP
Paraburkholderia atlantica CCGE1002 yjcH, actP
Paraburkholderia bryophila 376MFSha3.1 mctP
Paraburkholderia phymatum STM815 yjcH, actP
Paucidesulfovibrio gracilis DSM 16080 yjcH, actP
Pedobacter sp. GW460-11-11-14-LB5 SLC5A8
Pelobacter propionicus DSM 2379 cstA, ybdD
Persephonella marina EX-H1 yjcH, actP
Phaeacidiphilus oryzae TH49 mctC
Phaeobacter inhibens BS107 SLC5A8
Polaromonas naphthalenivorans CJ2 dctM, dctP, dctQ
Prosthecochloris aestuarii DSM 271 dctM, dctP, dctQ
Pseudarthrobacter sulfonivorans Ar51 btsT
Pseudomonas benzenivorans DSM 8628 yjcH, actP
Pseudomonas fluorescens FW300-N1B4 yjcH, actP
Pseudomonas fluorescens FW300-N2C3 yjcH, actP
Pseudomonas fluorescens FW300-N2E2 yjcH, actP
Pseudomonas fluorescens FW300-N2E3 yjcH, actP
Pseudomonas fluorescens GW456-L13 yjcH, actP
Pseudomonas putida KT2440 yjcH, actP
Pseudomonas simiae WCS417 yjcH, actP
Pseudomonas stutzeri RCH2 yjcH, actP
Pyrolobus fumarii 1A SLC5A8
Rhizobium etli CFN 42 mctP
Rhizobium johnstonii 3841 mctP
Rhizobium leguminosarum WSM1325 mctP
Rhizorhabdus wittichii RW1 cstA, ybdD
Rhodanobacter denitrificans FW104-10B01 cstA, ybdD
Rhodomicrobium vannielii ATCC 17100 cstA, ybdD
Rhodopseudomonas palustris CGA009 dctM, dctP, dctQ
Rhodospirillum centenum SW; ATCC 51521 yjcH, actP
Rhodospirillum rubrum ATCC 11170 yjcH, actP
Roseburia faecis M72 SLC5A8
Saccharomonospora cyanea NA-134 mctC
Sedimenticola selenatireducens DSM 17993 dctM, dctP, dctQ
Shewanella amazonensis SB2B yjcH, actP
Shewanella loihica PV-4 yjcH, actP
Shewanella oneidensis MR-1 yjcH, actP
Shewanella sp. ANA-3 yjcH, actP
Sinorhizobium fredii NGR234 dctM, dctP, dctQ
Sinorhizobium medicae WSM419 dctM, dctP, dctQ
Sinorhizobium meliloti 1021 dctM, dctP, dctQ
Sphingomonas koreensis DSMZ 15582 SLC5A8
Stenotrophomonas chelatiphaga DSM 21508 cstA, ybdD
Steroidobacter denitrificans DSM 18526 btsT
Stutzerimonas stutzeri A1501 yjcH, actP
Sulfuricurvum kujiense DSM 16994 yjcH, actP
Sulfurihydrogenibium azorense Az-Fu1 yjcH, actP
Sulfurihydrogenibium subterraneum DSM 15120 yjcH, actP
Sulfurimonas denitrificans DSM 1251 yjcH, actP
Sulfuritalea hydrogenivorans DSM 22779 dctM, dctP, dctQ
Sulfurivirga caldicuralii DSM 17737 yjcH, actP
Synechococcus elongatus PCC 7942 SLC5A8
Teredinibacter turnerae T7901 yjcH, actP
Thauera aminoaromatica S2 dctM, dctP, dctQ
Thermithiobacillus tepidarius DSM 3134 btsT
Thermocrinis albus DSM 14484 yjcH, actP
Thermodesulforhabdus norvegica DSM 9990 dctM, dctP, dctQ
Thermomonospora curvata DSM 43183 btsT
Thermovibrio ammonificans HB-1 SLC5A8
Thermus aquaticus YT-1 dctM, dctP, dctQ
Thioalkalivibrio denitrificans ALJD SLC5A8
Thioalkalivibrio halophilus HL17 yjcH, actP
Thioalkalivibrio paradoxus ARh 1 yjcH, actP
Thioalkalivibrio thiocyanodenitrificans ARhD 1 dctM, dctP, dctQ
Thiohalomonas denitrificans HLD2 yjcH, actP
Thiohalospira halophila HL 3 yjcH, actP
Thiomicrorhabdus arctica DSM 13458 yjcH, actP
Thiomicrorhabdus chilensis DSM 12352 dctM, dctP, dctQ
Thiomicrospira cyclica ALM1 dctM, dctP, dctQ
Thiomicrospira microaerophila ASL8-2 dctM, dctP, dctQ
Thiomicrospira pelophila DSM 1534 dctM, dctP, dctQ
Thiothrix lacustris DSM 21227 dctM, dctP, dctQ
Tistlia consotensis USBA 355 dctM, dctP, dctQ
Trichlorobacter lovleyi SZ mctC
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome dctM, dctP, dctQ
Trichormus variabilis ATCC 29413 dctM, dctP, dctQ
Xanthobacter autotrophicus Py2 dctM, dctP, dctQ
Xenophilus azovorans DSM 13620 dctM, dctP, dctQ

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