GapMind for catabolism of small carbon sources


acetate catabolism

Analysis of pathway acetate in 201 genomes

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

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