L-malate catabolism
Analysis of pathway L-malate in 201 genomes
| Genome | Best path |
|---|
| Acidimicrobium ferrooxidans DSM 10331 | sdlC |
| Acidithiobacillus ferrooxidans ATCC 23270 | sdlC |
| Acidovorax sp. GW101-3H11 | dctA |
| Algiphilus aromaticivorans DG1253 | sdlC |
| Alicycliphilus denitrificans K601 | dctA |
| Alkalihalobacterium alkalinitrilicum DSM 22532 | sdlC |
| Allochromatium vinosum DSM 180 | dctM, dctP, dctQ |
| Ammonifex degensii KC4 | sdlC |
| Anaerobutyricum hallii DSM 3353 | sdlC |
| Aquimarina longa SW024 | sdlC |
| Archaeoglobus veneficus SNP6 | sdlC |
| Arcobacter nitrofigilis DSM 7299 | sdlC |
| Azoarcus olearius BH72 | dctM, dctP, dctQ |
| Azohydromonas australica DSM 1124 | dctA |
| Azorhizobium caulinodans ORS 571 | dctA |
| Azospirillum brasilense Sp245 | dctA |
| Azospirillum sp. B510 | dctA |
| Bacteroides thetaiotaomicron VPI-5482 | sdlC |
| Beijerinckia indica ATCC 9039 | dctA |
| Beijerinckia mobilis UQM 1969 | dctA |
| Billgrantia desiderata SP1 | Dshi_1194, Dshi_1195 |
| Bradyrhizobium sp. BTAi1 | dctM, dctP, dctQ |
| Brevundimonas sp. GW460-12-10-14-LB2 | dctA |
| Burkholderia phytofirmans PsJN | dctA |
| Burkholderia vietnamiensis G4 | dctA |
| Calditerrivibrio nitroreducens DSM 19672 | dctM, dctP, dctQ |
| Caminibacter mediatlanticus TB-2 | dctM, dctP, dctQ |
| Carboxydothermus pertinax Ug1 | dctA |
| Caulobacter crescentus NA1000 | dctA |
| Cereibacter sphaeroides ATCC 17029 | dctM, dctP, dctQ |
| Chlorobaculum parvum NCIB 8327 | sdlC |
| Chlorobaculum tepidum TLS | sdlC |
| Chlorobium limicola DSM 245 | sdlC |
| Chlorobium phaeobacteroides BS1 | sdlC |
| Clostridium acetobutylicum ATCC 824 | dctA |
| Clostridium kluyveri DSM 555 | mleP |
| Clostridium tyrobutyricum FAM22553 | dctA |
| Crocosphaera subtropica ATCC 51142 | sdlC |
| Cupriavidus basilensis FW507-4G11 | dctA |
| Dechloromonas agitata is5 | dctM, dctP, dctQ |
| Dechlorosoma suillum PS | dctM, dctP, dctQ |
| Dehalococcoides mccartyi 195 | sdlC |
| Denitrovibrio acetiphilus DSM 12809 | sdlC |
| Derxia gummosa DSM 723 | dctM, dctP, dctQ |
| Desulfacinum hydrothermale DSM 13146 | sdlC |
| Desulfacinum infernum DSM 9756 | sdlC |
| Desulfarculus baarsii DSM 2075 | sdlC |
| Desulfatibacillum aliphaticivorans DSM 15576 | sdlC |
| Desulfatiglans anilini DSM 4660 | sdlC |
| Desulfitobacterium hafniense DCB-2 | sdlC |
| Desulfobacca acetoxidans DSM 11109 | sdlC |
| Desulfobacter vibrioformis DSM 8776 | sdlC |
| Desulfogranum mediterraneum DSM 13871 | dctM, dctP, dctQ |
| Desulforamulus ruminis DSM 2154 | dctA |
| Desulfoscipio geothermicus DSM 3669 | Dshi_1194, Dshi_1195 |
| Desulfotalea psychrophila LSv54 | sdlC |
| Desulfovibrio oxyclinae DSM 11498 | sdlC |
| Desulfovibrio vulgaris Hildenborough JW710 | sdlC |
| Desulfovibrio vulgaris Miyazaki F | sdlC |
| Desulfurobacterium atlanticum DSM 15668 | sdlC |
| Desulfuromonas acetexigens | sdlC |
| Desulfuromusa kysingii DSM 7343 | dctM, dctP, dctQ |
| Dinoroseobacter shibae DFL-12 | Dshi_1194, Dshi_1195 |
| Dyella japonica UNC79MFTsu3.2 | dctA |
| Echinicola vietnamensis KMM 6221, DSM 17526 | sdlC |
| Escherichia coli BW25113 | dctA |
| Ferroglobus placidus DSM 10642 | sdlC |
| Frankia alni ACN14a | dctA |
| Geobacter metallireducens GS-15 | sdlC |
| Geotalea uraniireducens Rf4 | dctM, dctP, dctQ |
| Halococcus hamelinensis 100A6 | sdlC |
| Haloechinothrix alba DSM 45207 | sdlC |
| Haloferax volcanii DS2 | sdlC |
| Haloglycomyces albus DSM 45210 | sdlC |
| Halorhodospira halophila SL1 | Dshi_1194, Dshi_1195 |
| Heliomicrobium modesticaldum Ice1; ATCC 51547 | sdlC |
| Herbaspirillum autotrophicum IAM 14942 | dctM, dctP, dctQ |
| Herbaspirillum seropedicae SmR1 | dctM, dctP, dctQ |
| Hippea alviniae EP5-r | dctM, dctP, dctQ |
| Hydrogenophaga taeniospiralis NBRC 102512 | sdlC |
| Hydrogenovibrio halophilus DSM 15072 | sdlC |
| Hydrogenovibrio kuenenii DSM 12350 | sdlC |
| Hydrogenovibrio marinus DSM 11271 | sdlC |
| Hyphomicrobium sulfonivorans WDL6 | dctA |
| Klebsiella michiganensis M5al | sdlC |
| Klebsiella variicola At-22 | dctA |
| Kyrpidia tusciae DSM 2912 | sdlC |
| Leptospirillum ferrooxidans C2-3 | sdlC |
| Magnetospirillum magneticum AMB-1 | dctM, dctP, dctQ |
| Malonomonas rubra DSM 5091 | sdlC |
| Maridesulfovibrio bastinii DSM 16055 | sdlC |
| Maridesulfovibrio zosterae DSM 11974 | sdlC |
| Marinobacter adhaerens HP15 | Dshi_1194, Dshi_1195 |
| Mesorhizobium ciceri WSM1271 | dctA |
| Methanobacterium lacus AL-21 | sdlC |
| Methanococcus aeolicus Nankai-3 | sdlC |
| Methanococcus maripaludis C5 | sdlC |
| Methanosarcina acetivorans C2A | sdlC |
| Methanosarcina mazei Go1 | sdlC |
| Methanospirillum lacunae Ki8-1 | sdlC |
| Methanothermobacter thermautotrophicus Delta H | sdlC |
| Methylobacterium nodulans ORS 2060 | dctM, dctP, dctQ |
| Methylobacterium sp. 4-46 Apr-46 | dctM, dctP, dctQ |
| Methylocapsa acidiphila B2 | dctA |
| Methylocapsa aurea KYG | dctA |
| Methylocella silvestris BL2 | dctA |
| Methylococcus capsulatus Bath | dctA |
| Methylocystis bryophila S285 | dctA |
| Methyloferula stellata AR4T | dctA |
| Methylohalobius crimeensis 10Ki | sdlC |
| Methylomonas methanica MC09 | dctA |
| Methylosarcina fibrata AML-C10 | sdlC |
| Methylotuvimicrobium alcaliphilum 20Z | sdlC |
| Methylovulum miyakonense HT12 | dctA |
| Mycolicibacterium vanbaalenii PYR-1 | dctA |
| Nitratifractor salsuginis DSM 16511 | dctM, dctP, dctQ |
| Nitratiruptor tergarcus DSM 16512 | sdlC |
| Nitriliruptor alkaliphilus DSM 45188 | sdlC |
| Nocardioides dokdonensis FR1436 | sdlC |
| Nocardiopsis lucentensis DSM 44048 | sdlC |
| Nostoc punctiforme ATCC 29133; PCC 73102 | sdlC |
| Novosphingobium aromaticivorans DSM 12444 | sdlC |
| Oleispira antarctica | sdlC |
| Paraburkholderia atlantica CCGE1002 | dctA |
| Paraburkholderia bryophila 376MFSha3.1 | dctA |
| Paraburkholderia phymatum STM815 | dctA |
| Paucidesulfovibrio gracilis DSM 16080 | sdlC |
| Pedobacter sp. GW460-11-11-14-LB5 | dctA |
| Pelobacter propionicus DSM 2379 | sdlC |
| Persephonella marina EX-H1 | sdlC |
| Phaeacidiphilus oryzae TH49 | dctA |
| Phaeobacter inhibens BS107 | dctM, dctP, dctQ |
| Polaromonas naphthalenivorans CJ2 | dctA |
| Prosthecochloris aestuarii DSM 271 | sdlC |
| Pseudarthrobacter sulfonivorans Ar51 | dctA |
| Pseudomonas benzenivorans DSM 8628 | dctA |
| Pseudomonas fluorescens FW300-N1B4 | dctA |
| Pseudomonas fluorescens FW300-N2C3 | dctA |
| Pseudomonas fluorescens FW300-N2E2 | dctA |
| Pseudomonas fluorescens FW300-N2E3 | dctA |
| Pseudomonas fluorescens GW456-L13 | dctA |
| Pseudomonas putida KT2440 | dctA |
| Pseudomonas simiae WCS417 | dctA |
| Pseudomonas stutzeri RCH2 | sdlC |
| Pyrolobus fumarii 1A | sdlC |
| Rhizobium etli CFN 42 | dctA |
| Rhizobium johnstonii 3841 | dctA |
| Rhizobium leguminosarum WSM1325 | dctA |
| Rhizorhabdus wittichii RW1 | dctA |
| Rhodanobacter denitrificans FW104-10B01 | sdlC |
| Rhodomicrobium vannielii ATCC 17100 | dctA |
| Rhodopseudomonas palustris CGA009 | dctM, dctP, dctQ |
| Rhodospirillum centenum SW; ATCC 51521 | sdlC |
| Rhodospirillum rubrum ATCC 11170 | dctM, dctP, dctQ |
| Roseburia faecis M72 | sdlC |
| Saccharomonospora cyanea NA-134 | sdlC |
| Sedimenticola selenatireducens DSM 17993 | dctM, dctP, dctQ |
| Shewanella amazonensis SB2B | dctM, dctP, dctQ |
| Shewanella loihica PV-4 | dctM, dctP, dctQ |
| Shewanella oneidensis MR-1 | dctM, dctP, dctQ |
| Shewanella sp. ANA-3 | dctM, dctP, dctQ |
| Sinorhizobium fredii NGR234 | dctA |
| Sinorhizobium medicae WSM419 | dctA |
| Sinorhizobium meliloti 1021 | dctA |
| Sphingomonas koreensis DSMZ 15582 | dctA |
| Stenotrophomonas chelatiphaga DSM 21508 | dctA |
| Steroidobacter denitrificans DSM 18526 | sdlC |
| Stutzerimonas stutzeri A1501 | sdlC |
| Sulfuricurvum kujiense DSM 16994 | sdlC |
| Sulfurihydrogenibium azorense Az-Fu1 | sdlC |
| Sulfurihydrogenibium subterraneum DSM 15120 | sdlC |
| Sulfurimonas denitrificans DSM 1251 | sdlC |
| Sulfuritalea hydrogenivorans DSM 22779 | dctM, dctP, dctQ |
| Sulfurivirga caldicuralii DSM 17737 | sdlC |
| Synechococcus elongatus PCC 7942 | sdlC |
| Teredinibacter turnerae T7901 | sdlC |
| Thauera aminoaromatica S2 | dctM, dctP, dctQ |
| Thermithiobacillus tepidarius DSM 3134 | sdlC |
| Thermocrinis albus DSM 14484 | sdlC |
| Thermodesulforhabdus norvegica DSM 9990 | sdlC |
| Thermomonospora curvata DSM 43183 | sdlC |
| Thermovibrio ammonificans HB-1 | sdlC |
| Thermus aquaticus YT-1 | sdlC |
| Thioalkalivibrio denitrificans ALJD | sdlC |
| Thioalkalivibrio halophilus HL17 | sdlC |
| Thioalkalivibrio paradoxus ARh 1 | Dshi_1194, Dshi_1195 |
| Thioalkalivibrio thiocyanodenitrificans ARhD 1 | sdlC |
| Thiohalomonas denitrificans HLD2 | sdlC |
| Thiohalospira halophila HL 3 | sdlC |
| Thiomicrorhabdus arctica DSM 13458 | sdlC |
| Thiomicrorhabdus chilensis DSM 12352 | sdlC |
| Thiomicrospira cyclica ALM1 | sdlC |
| Thiomicrospira microaerophila ASL8-2 | sdlC |
| Thiomicrospira pelophila DSM 1534 | sdlC |
| Thiothrix lacustris DSM 21227 | dctM, dctP, dctQ |
| Tistlia consotensis USBA 355 | dctM, dctP, dctQ |
| Trichlorobacter lovleyi SZ | dctM, dctP, dctQ |
| Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome | sdlC |
| Trichormus variabilis ATCC 29413 | sdlC |
| Xanthobacter autotrophicus Py2 | dctA |
| Xenophilus azovorans DSM 13620 | dctA |
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:
- 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:
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