ethanol catabolism

GapMind for catabolism of small carbon sources

ethanol catabolism

Analysis of pathway ethanol in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	etoh-dh-nad, adh, acs
Acidithiobacillus ferrooxidans ATCC 23270	etoh-dh-nad, adh, acs
Alicycliphilus denitrificans K601	etoh-dh-nad, adh, acs
Allochromatium vinosum DSM 180	etoh-dh-nad, adh, ackA, pta
Ammonifex degensii KC4	etoh-dh-nad, adh, acs
Archaeoglobus veneficus SNP6	etoh-dh-nad, adh, acs
Arcobacter nitrofigilis DSM 7299	etoh-dh-c, adh, ackA, pta
Azoarcus sp. BH72	etoh-dh-nad, adh, acs
Azohydromonas australica DSM 1124	etoh-dh-nad, adh, ackA, pta
Azorhizobium caulinodans ORS 571	etoh-dh-nad, adh, acs
Azospirillum lipoferum B510	etoh-dh-nad, adh, acs
Bacillus alkalinitrilicus DSM 22532	etoh-dh-nad, adh, ackA, pta
Beijerinckia indica ATCC 9039	etoh-dh-nad, adh, acs
Beijerinckia mobilis UQM 1969	etoh-dh-nad, adh, acs
Bradyrhizobium sp. BTAi1	etoh-dh-nad, adh, acs
Burkholderia vietnamiensis G4	etoh-dh-nad, adh, acs
Calditerrivibrio nitroreducens DSM 19672	etoh-dh-nad, adh, ackA, pta
Caminibacter mediatlanticus TB-2	etoh-dh-nad, adh, acs
Chlorobaculum parvum NCIB 8327	etoh-dh-nad, adh, acs
Chlorobaculum tepidum TLS	etoh-dh-nad, adh, acs
Chlorobium limicola DSM 245	etoh-dh-nad, adh, acs
Chlorobium phaeobacteroides BS1	etoh-dh-nad, adh, acs
Clostridium acetobutylicum ATCC 824	etoh-dh-nad, adh, ackA, pta
Clostridium kluyveri DSM 555	etoh-dh-nad, adh, ackA, pta
Crocosphaera subtropica ATCC 51142	etoh-dh-nad, adh, ackA, pta
Dechloromonas agitata is5	etoh-dh-nad, adh, ackA, pta
Dehalococcoides mccartyi 195	etoh-dh-nad, ald-dh-CoA
Denitrovibrio acetiphilus DSM 12809	etoh-dh-nad, adh, ackA, pta
Derxia gummosa DSM 723	etoh-dh-nad, ald-dh-CoA
Desulfacinum hydrothermale DSM 13146	etoh-dh-nad, ald-dh-CoA
Desulfacinum infernum DSM 9756	etoh-dh-nad, ald-dh-CoA
Desulfallas geothermicus DSM 3669	etoh-dh-nad, ald-dh-CoA
Desulfarculus baarsii DSM 2075	etoh-dh-nad, adh, ackA, pta
Desulfatibacillum aliphaticivorans DSM 15576	etoh-dh-nad, adh, acs
Desulfatiglans anilini DSM 4660	etoh-dh-nad, adh, acs
Desulfitobacterium hafniense DCB-2	etoh-dh-nad, ald-dh-CoA
Desulfobacca acetoxidans DSM 11109	etoh-dh-nad, ald-dh-CoA
Desulfobacter vibrioformis DSM 8776	etoh-dh-nad, adh, ackA, pta
Desulfobulbus mediterraneus DSM 13871	etoh-dh-nad, adh, ackA, pta
Desulfotalea psychrophila LSv54	etoh-dh-nad, adh, ackA, pta
Desulfotomaculum ruminis DSM 2154	etoh-dh-nad, ald-dh-CoA
Desulfovibrio bastinii DSM 16055	etoh-dh-nad, adh, ackA, pta
Desulfovibrio gracilis DSM 16080	etoh-dh-nad, adh, ackA, pta
Desulfovibrio oxyclinae DSM 11498	etoh-dh-nad, adh, ackA, pta
Desulfovibrio zosterae DSM 11974	etoh-dh-nad, ald-dh-CoA *
Desulfurobacterium atlanticum DSM 15668	etoh-dh-nad, adh, acs
Desulfuromonas acetexigens	etoh-dh-nad, adh, ackA, pta
Desulfuromusa kysingii DSM 7343	etoh-dh-nad, adh, ackA, pta
Ferroglobus placidus DSM 10642	etoh-dh-nad, ald-dh-CoA
Frankia alni ACN14A	etoh-dh-nad, adh, acs
Geobacter lovleyi SZ	etoh-dh-nad, adh, ackA, pta
Geobacter metallireducens GS-15	etoh-dh-nad, adh, ackA, pta
Geobacter uraniireducens Rf4	etoh-dh-nad, adh, ackA, pta
Haloechinothrix alba DSM 45207	etoh-dh-nad, adh, acs
Haloglycomyces albus DSM 45210	etoh-dh-nad, adh, ackA, pta
Halomonas desiderata SP1	etoh-dh-nad, adh, ackA, pta
Halorhodospira halophila SL1	etoh-dh-nad, adh, acs
Heliobacterium modesticaldum Ice1; ATCC 51547	etoh-dh-nad, ald-dh-CoA
Herbaspirillum autotrophicum IAM 14942	etoh-dh-nad, adh, acs
Hydrogenophaga taeniospiralis NBRC 102512	etoh-dh-nad, adh, acs
Hydrogenovibrio halophilus DSM 15072	etoh-dh-nad, adh, ackA, pta
Hydrogenovibrio kuenenii DSM 12350	etoh-dh-nad, adh, ackA, pta
Hydrogenovibrio marinus DSM 11271	etoh-dh-nad, adh, ackA, pta
Hyphomicrobium sulfonivorans WDL6	etoh-dh-c, adh, acs
Klebsiella variicola At-22	etoh-dh-nad, adh, ackA, pta
Kyrpidia tusciae DSM 2912	etoh-dh-nad, adh, acs
Leptospirillum ferrooxidans C2-3	etoh-dh-nad, adh, acs
Malonomonas rubra DSM 5091	etoh-dh-nad, adh, ackA, pta
Mesorhizobium ciceri WSM1271	etoh-dh-nad, adh, acs
Methanobacterium lacus AL-21	etoh-dh-nad, adh, acs
Methanococcus aeolicus Nankai-3	etoh-dh-nad, ald-dh-CoA
Methanococcus maripaludis C5	etoh-dh-nad, ald-dh-CoA
Methanosarcina acetivorans C2A	etoh-dh-nad, adh, ackA, pta
Methanosarcina barkeri Fusaro	etoh-dh-nad, adh, ackA, pta
Methanosarcina mazei Go1	etoh-dh-nad, adh, ackA, pta
Methanothermobacter thermautotrophicus Delta H	etoh-dh-nad, ald-dh-CoA
Methylobacterium nodulans ORS 2060	etoh-dh-nad, adh, acs
Methylobacterium sp. 4-46	etoh-dh-nad, adh, acs
Methylocapsa acidiphila B2	etoh-dh-nad, adh, acs
Methylocapsa aurea KYG T	etoh-dh-nad, adh, acs
Methylocella silvestris BL2	etoh-dh-nad, adh, acs
Methylococcus capsulatus Bath	etoh-dh-nad, adh, acs
Methylocystis bryophila S285	etoh-dh-nad, adh, acs
Methyloferula stellata AR4T	etoh-dh-nad, adh, acs
Methylohalobius crimeensis 10Ki	etoh-dh-nad, adh, acs
Methylomicrobium alcaliphilum 20Z	etoh-dh-nad, adh, ackA, pta
Methylomonas methanica MC09	etoh-dh-nad, adh, ackA, pta
Methylosarcina fibrata AML-C10	etoh-dh-nad, adh, acs
Methylovulum miyakonense HT12	etoh-dh-nad, adh, acs
Mycolicibacterium vanbaalenii PYR-1	etoh-dh-nad, adh, ackA, pta
Nitratifractor salsuginis DSM 16511	etoh-dh-nad, adh, ackA, pta
Nitratiruptor tergarcus DSM 16512	etoh-dh-nad, adh, acs
Nitriliruptor alkaliphilus DSM 45188	etoh-dh-nad, adh, acs
Nocardiopsis lucentensis DSM 44048	etoh-dh-nad, adh, acs
Nostoc punctiforme ATCC 29133; PCC 73102	etoh-dh-nad, adh, acs
Novosphingobium aromaticivorans DSM 12444	etoh-dh-nad, adh, acs
Oleispira antarctica	etoh-dh-nad, ald-dh-CoA
Paraburkholderia phymatum STM815	etoh-dh-nad, adh, ackA, pta
Paraburkholderia sp. CCGE1002	etoh-dh-nad, adh, acs
Pelobacter propionicus DSM 2379	etoh-dh-nad, adh, ackA, pta
Persephonella marina EX-H1	etoh-dh-nad, adh, acs
Polaromonas naphthalenivorans CJ2	etoh-dh-nad, adh, ackA, pta
Prosthecochloris aestuarii DSM 271	etoh-dh-nad, adh, acs
Pseudarthrobacter sulfonivorans Ar51	etoh-dh-nad, adh, ackA, pta
Pseudomonas benzenivorans DSM 8628	etoh-dh-nad, adh, ackA, pta
Pseudomonas stutzeri A1501	etoh-dh-nad, adh, ackA, pta
Pyrolobus fumarii 1A	etoh-dh-nad, ald-dh-CoA
Rhizobium etli CFN 42	etoh-dh-nad, adh, acs
Rhizobium leguminosarum 3841	etoh-dh-nad, adh, acs
Rhizobium leguminosarum WSM1325	etoh-dh-nad, adh, acs
Rhodobacter sphaeroides ATCC 17029	etoh-dh-nad, adh, acs
Rhodomicrobium vannielii ATCC 17100	etoh-dh-nad, adh, acs
Rhodopseudomonas palustris CGA009	etoh-dh-nad, adh, acs
Rhodospirillum centenum SW; ATCC 51521	etoh-dh-nad, adh, acs
Rhodospirillum rubrum ATCC 11170	etoh-dh-nad, adh, ackA, pta
Saccharomonospora cyanea NA-134	etoh-dh-nad, adh, acs
Sedimenticola selenatireducens DSM 17993	etoh-dh-nad, adh, ackA, pta
Sinorhizobium fredii NGR234	etoh-dh-nad, adh, acs
Sinorhizobium medicae WSM419	etoh-dh-nad, adh, ackA, pta
Sphingomonas wittichii RW1	etoh-dh-nad, adh, acs
Stenotrophomonas chelatiphaga DSM 21508	etoh-dh-nad, adh, acs
Steroidobacter denitrificans DSM 18526	etoh-dh-nad, adh, ackA, pta
Sulfuricurvum kujiense DSM 16994	etoh-dh-nad, adh, ackA, pta
Sulfurihydrogenibium azorense Az-Fu1	etoh-dh-nad, adh, acs
Sulfurihydrogenibium subterraneum DSM 15120	etoh-dh-nad, adh, acs
Sulfurimonas denitrificans DSM 1251	etoh-dh-nad, adh, ackA, pta
Sulfuritalea hydrogenivorans DSM 22779	etoh-dh-nad, adh, acs
Sulfurivirga caldicuralii DSM 17737	etoh-dh-nad, adh, acs
Teredinibacter turnerae T7901	etoh-dh-nad, adh, ackA, pta
Thauera aminoaromatica S2	etoh-dh-nad, ald-dh-CoA
Thermithiobacillus tepidarius DSM 3134	etoh-dh-nad, adh, acs
Thermocrinis albus DSM 14484	etoh-dh-nad, adh, acs
Thermodesulforhabdus norvegica DSM 9990	etoh-dh-nad, adh, acs
Thermomonospora curvata DSM 43183	etoh-dh-nad, adh, acs
Thermovibrio ammonificans HB-1	etoh-dh-nad, adh, acs
Thioalkalivibrio denitrificans ALJD	etoh-dh-nad, adh, ackA, pta
Thioalkalivibrio halophilus HL17	etoh-dh-nad, adh, acs
Thioalkalivibrio paradoxus ARh 1	etoh-dh-nad, adh, acs
Thioalkalivibrio thiocyanodenitrificans ARhD 1	etoh-dh-nad, adh, ackA, pta
Thiohalomonas denitrificans HLD2	etoh-dh-nad, adh, acs
Thiomicrorhabdus arctica DSM 13458	etoh-dh-nad, ald-dh-CoA
Thiomicrorhabdus chilensis DSM 12352	etoh-dh-nad, adh, acs
Thiomicrospira cyclica ALM1	etoh-dh-nad, adh, acs
Thiomicrospira microaerophila ASL8-2	etoh-dh-nad, adh, acs
Thiomicrospira pelophila DSM 1534	etoh-dh-nad, adh, acs
Thiothrix lacustris DSM 21227	etoh-dh-nad, adh, ackA, pta
Trichodesmium erythraeum IMS101	etoh-dh-nad, adh, acs
Trichormus variabilis ATCC 29413	etoh-dh-nad, adh, acs
Xanthobacter autotrophicus Py2	etoh-dh-nad, adh, acs
Xenophilus azovorans DSM 13620	etoh-dh-nad, adh, 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources