GapMind for catabolism of small carbon sources

 

propionate catabolism

Analysis of pathway propionate in 150 genomes

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

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.

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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