GapMind for catabolism of small carbon sources


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:

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