GapMind for catabolism of small carbon sources

 

L-lactate catabolism

Analysis of pathway L-lactate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 lctP, L-LDH
Acidithiobacillus ferrooxidans ATCC 23270 lctP, lctO, acs
Acidovorax sp. GW101-3H11 lctP, lctO, acs
Algiphilus aromaticivorans DG1253 Shew_2731, Shew_2732, lctO, acs
Alicycliphilus denitrificans K601 lctP, L-LDH
Alkalihalobacterium alkalinitrilicum DSM 22532 lctP, lutA, lutB, lutC
Allochromatium vinosum DSM 180 Shew_2731, Shew_2732, lctO, ackA, pta
Ammonifex degensii KC4 lctP, L-LDH
Anaerobutyricum hallii DSM 3353 larD, L-LDH
Aquimarina longa SW024 Shew_2731, Shew_2732, lctO, ackA, pta
Archaeoglobus veneficus SNP6 lctP, lctO, acs
Arcobacter nitrofigilis DSM 7299 lctP, L-LDH
Azoarcus olearius BH72 lctP, lutA, lutB, lutC
Azohydromonas australica DSM 1124 lctP, lctO, ackA, pta
Azorhizobium caulinodans ORS 571 lctP, L-LDH
Azospirillum brasilense Sp245 lctP, lutA, lutB, lutC
Azospirillum sp. B510 lctP, lutA, lutB, lutC
Bacteroides thetaiotaomicron VPI-5482 lctP, lldE, lldF, lldG
Beijerinckia indica ATCC 9039 lctP, L-LDH
Beijerinckia mobilis UQM 1969 lctP, L-LDH
Billgrantia desiderata SP1 lctP, lutA, lutB, lutC
Bradyrhizobium sp. BTAi1 lctP, L-LDH
Brevundimonas sp. GW460-12-10-14-LB2 lctP, L-LDH
Burkholderia phytofirmans PsJN mctP, lldE, lldF, lldG
Burkholderia vietnamiensis G4 lctP, lldE, lldF, lldG
Calditerrivibrio nitroreducens DSM 19672 SfMCT, L-LDH
Caminibacter mediatlanticus TB-2 lctP, L-LDH
Carboxydothermus pertinax Ug1 lctP, lutA, lutB, lutC
Caulobacter crescentus NA1000 lctP, L-LDH
Cereibacter sphaeroides ATCC 17029 Shew_2731, Shew_2732, L-LDH
Chlorobaculum parvum NCIB 8327 Shew_2731, Shew_2732, L-LDH
Chlorobaculum tepidum TLS Shew_2731, Shew_2732, L-LDH
Chlorobium limicola DSM 245 Shew_2731, Shew_2732, L-LDH
Chlorobium phaeobacteroides BS1 Shew_2731, Shew_2732, L-LDH
Clostridium acetobutylicum ATCC 824 larD, L-LDH
Clostridium kluyveri DSM 555 lctP, L-LDH
Clostridium tyrobutyricum FAM22553 lctP, L-LDH
Crocosphaera subtropica ATCC 51142 lctP, lctO, ackA, pta
Cupriavidus basilensis FW507-4G11 lctP, lutA, lutB, lutC
Dechloromonas agitata is5 Shew_2731, Shew_2732, lutA, lutB, lutC
Dechlorosoma suillum PS lctP, lctO, acs
Dehalococcoides mccartyi 195 lctP, L-LDH
Denitrovibrio acetiphilus DSM 12809 lctP, L-LDH
Derxia gummosa DSM 723 lctP, lutA, lutB, lutC
Desulfacinum hydrothermale DSM 13146 SfMCT, DVU3033*, DVU3032
Desulfacinum infernum DSM 9756 SfMCT, L-LDH
Desulfarculus baarsii DSM 2075 SfMCT, L-LDH
Desulfatibacillum aliphaticivorans DSM 15576 lctP, lutA, lutB, lutC
Desulfatiglans anilini DSM 4660 Shew_2731, Shew_2732, L-LDH
Desulfitobacterium hafniense DCB-2 lctP, L-LDH
Desulfobacca acetoxidans DSM 11109 SfMCT, L-LDH
Desulfobacter vibrioformis DSM 8776 lctP, L-LDH
Desulfogranum mediterraneum DSM 13871 lctP, DVU3033, DVU3032
Desulforamulus ruminis DSM 2154 lctP, lctO, ackA, pta
Desulfoscipio geothermicus DSM 3669 lctP, lctO, acs
Desulfotalea psychrophila LSv54 lctP, DVU3033, DVU3032
Desulfovibrio oxyclinae DSM 11498 lctP, DVU3033, DVU3032
Desulfovibrio vulgaris Hildenborough JW710 lctP, lutA, lutB, lutC
Desulfovibrio vulgaris Miyazaki F lctP, lutA, lutB, lutC
Desulfurobacterium atlanticum DSM 15668 lctP, L-LDH
Desulfuromonas acetexigens Shew_2731, Shew_2732, L-LDH
Desulfuromusa kysingii DSM 7343 Shew_2731, Shew_2732, L-LDH
Dinoroseobacter shibae DFL-12 Shew_2731, Shew_2732, L-LDH
Dyella japonica UNC79MFTsu3.2 lctP, L-LDH
Echinicola vietnamensis KMM 6221, DSM 17526 Shew_2731, Shew_2732, lldE, lldF, lldG
Escherichia coli BW25113 lctP, L-LDH
Ferroglobus placidus DSM 10642 SfMCT, L-LDH
Frankia alni ACN14a mctP, lctO, acs
Geobacter metallireducens GS-15 SfMCT, L-LDH
Geotalea uraniireducens Rf4 lctP, L-LDH
Halococcus hamelinensis 100A6 lctP, lctO, acs
Haloechinothrix alba DSM 45207 Shew_2731, Shew_2732, lutA, lutB, lutC
Haloferax volcanii DS2 lctP, L-LDH
Haloglycomyces albus DSM 45210 lctP, lctO, ackA, pta
Halorhodospira halophila SL1 lctP, lctO, acs
Heliomicrobium modesticaldum Ice1; ATCC 51547 lctP, L-LDH
Herbaspirillum autotrophicum IAM 14942 lctP, lctO, acs
Herbaspirillum seropedicae SmR1 lctP, L-LDH
Hippea alviniae EP5-r lctP, L-LDH
Hydrogenophaga taeniospiralis NBRC 102512 Shew_2731, Shew_2732, lctO, acs
Hydrogenovibrio halophilus DSM 15072 lctP, lctO, ackA, pta
Hydrogenovibrio kuenenii DSM 12350 lctP, lctO, ackA, pta
Hydrogenovibrio marinus DSM 11271 lctP, lctO, ackA, pta
Hyphomicrobium sulfonivorans WDL6 lctP, lctO, acs
Klebsiella michiganensis M5al lctP, L-LDH
Klebsiella variicola At-22 lctP, L-LDH
Kyrpidia tusciae DSM 2912 lctP, lutA, lutB, lutC
Leptospirillum ferrooxidans C2-3 lctP, L-LDH
Magnetospirillum magneticum AMB-1 lctP, lutA, lutB, lutC
Malonomonas rubra DSM 5091 Shew_2731, Shew_2732, DVU3033, DVU3032
Maridesulfovibrio bastinii DSM 16055 lctP, DVU3033, DVU3032
Maridesulfovibrio zosterae DSM 11974 lctP, DVU3033, DVU3032
Marinobacter adhaerens HP15 Shew_2731, Shew_2732, lutA, lutB, lutC
Mesorhizobium ciceri WSM1271 lctP, L-LDH
Methanobacterium lacus AL-21 lctP, lctO, acs
Methanococcus aeolicus Nankai-3 lctP, L-LDH
Methanococcus maripaludis C5 lctP, L-LDH
Methanosarcina acetivorans C2A lctP, L-LDH
Methanosarcina mazei Go1 lctP, L-LDH
Methanospirillum lacunae Ki8-1 lctP, lctO, acs
Methanothermobacter thermautotrophicus Delta H lctP, L-LDH
Methylobacterium nodulans ORS 2060 lctP, L-LDH
Methylobacterium sp. 4-46 Apr-46 lctP, L-LDH
Methylocapsa acidiphila B2 mctP, L-LDH
Methylocapsa aurea KYG mctP, L-LDH
Methylocella silvestris BL2 lctP, L-LDH
Methylococcus capsulatus Bath lctP, lctO, acs
Methylocystis bryophila S285 lctP, L-LDH
Methyloferula stellata AR4T lctP, lutA, lutB, lutC
Methylohalobius crimeensis 10Ki lctP, lctO, acs
Methylomonas methanica MC09 lctP, lctO, ackA, pta
Methylosarcina fibrata AML-C10 lctP, L-LDH
Methylotuvimicrobium alcaliphilum 20Z lctP, L-LDH
Methylovulum miyakonense HT12 lctP, lctO, acs
Mycolicibacterium vanbaalenii PYR-1 lctP, lctO, ackA, pta
Nitratifractor salsuginis DSM 16511 lctP, lldE, lldF, lldG
Nitratiruptor tergarcus DSM 16512 lctP, L-LDH
Nitriliruptor alkaliphilus DSM 45188 Shew_2731, Shew_2732, lctO, acs
Nocardioides dokdonensis FR1436 Shew_2731, Shew_2732, lctO, acs
Nocardiopsis lucentensis DSM 44048 larD, lutA, lutB, lutC
Nostoc punctiforme ATCC 29133; PCC 73102 lctP, lctO, acs
Novosphingobium aromaticivorans DSM 12444 lctP, L-LDH
Oleispira antarctica Shew_2731, Shew_2732, lctO, ackA, pta
Paraburkholderia atlantica CCGE1002 mctP, lldE, lldF, lldG
Paraburkholderia bryophila 376MFSha3.1 mctP, lldE, lldF, lldG
Paraburkholderia phymatum STM815 lctP, lutA, lutB, lutC
Paucidesulfovibrio gracilis DSM 16080 lctP, DVU3033, DVU3032
Pedobacter sp. GW460-11-11-14-LB5 lctP, L-LDH
Pelobacter propionicus DSM 2379 lctP, L-LDH
Persephonella marina EX-H1 lctP, lctO, acs
Phaeacidiphilus oryzae TH49 mctP, lctO, acs
Phaeobacter inhibens BS107 lctP, L-LDH
Polaromonas naphthalenivorans CJ2 lctP, lctO, ackA, pta
Prosthecochloris aestuarii DSM 271 Shew_2731, Shew_2732, L-LDH
Pseudarthrobacter sulfonivorans Ar51 larD, L-LDH
Pseudomonas benzenivorans DSM 8628 Shew_2731, Shew_2732, lutA, lutB, lutC
Pseudomonas fluorescens FW300-N1B4 lctP, lutA, lutB, lutC
Pseudomonas fluorescens FW300-N2C3 lctP, lutA, lutB, lutC
Pseudomonas fluorescens FW300-N2E2 lctP, lutA, lutB*, lutC
Pseudomonas fluorescens FW300-N2E3 lctP, lutA, lutB, lutC
Pseudomonas fluorescens GW456-L13 lctP, lutA, lutB, lutC
Pseudomonas putida KT2440 lctP, L-LDH
Pseudomonas simiae WCS417 lctP, L-LDH
Pseudomonas stutzeri RCH2 lctP, lutA, lutB, lutC
Pyrolobus fumarii 1A lctP, L-LDH
Rhizobium etli CFN 42 mctP, L-LDH
Rhizobium johnstonii 3841 mctP, L-LDH
Rhizobium leguminosarum WSM1325 mctP, L-LDH
Rhizorhabdus wittichii RW1 lctP, L-LDH
Rhodanobacter denitrificans FW104-10B01 lctP, lctO, acs
Rhodomicrobium vannielii ATCC 17100 lctP, L-LDH
Rhodopseudomonas palustris CGA009 lctP, L-LDH
Rhodospirillum centenum SW; ATCC 51521 Shew_2731, Shew_2732, L-LDH
Rhodospirillum rubrum ATCC 11170 lctP, lutA, lutB, lutC
Roseburia faecis M72 lctP, L-LDH
Saccharomonospora cyanea NA-134 lctP, lctO, acs
Sedimenticola selenatireducens DSM 17993 lctP, lutA, lutB, lutC
Shewanella amazonensis SB2B Shew_2731, Shew_2732, lldE, lldF, lldG
Shewanella loihica PV-4 Shew_2731, Shew_2732, lldE, lldF, lldG
Shewanella oneidensis MR-1 Shew_2731, Shew_2732, lldE, lldF, lldG
Shewanella sp. ANA-3 Shew_2731, Shew_2732, lldE, lldF, lldG
Sinorhizobium fredii NGR234 mctP, L-LDH
Sinorhizobium medicae WSM419 lctP, lctO, ackA, pta
Sinorhizobium meliloti 1021 lctP, L-LDH
Sphingomonas koreensis DSMZ 15582 lctP, L-LDH
Stenotrophomonas chelatiphaga DSM 21508 lctP, L-LDH
Steroidobacter denitrificans DSM 18526 lctP, lctO, ackA, pta
Stutzerimonas stutzeri A1501 lctP, lutA, lutB, lutC
Sulfuricurvum kujiense DSM 16994 lctP, L-LDH
Sulfurihydrogenibium azorense Az-Fu1 lctP, L-LDH
Sulfurihydrogenibium subterraneum DSM 15120 lctP, L-LDH
Sulfurimonas denitrificans DSM 1251 lctP, L-LDH
Sulfuritalea hydrogenivorans DSM 22779 lctP, L-LDH
Sulfurivirga caldicuralii DSM 17737 Shew_2731, Shew_2732, lctO, acs
Synechococcus elongatus PCC 7942 lctP, lctO, acs
Teredinibacter turnerae T7901 lctP, lctO, ackA, pta
Thauera aminoaromatica S2 lctP, lutA, lutB, lutC
Thermithiobacillus tepidarius DSM 3134 lctP, lctO, acs
Thermocrinis albus DSM 14484 lctP, L-LDH
Thermodesulforhabdus norvegica DSM 9990 SfMCT, L-LDH
Thermomonospora curvata DSM 43183 lctP, lctO, acs
Thermovibrio ammonificans HB-1 lctP, L-LDH
Thermus aquaticus YT-1 Shew_2731, Shew_2732, L-LDH
Thioalkalivibrio denitrificans ALJD lctP, L-LDH
Thioalkalivibrio halophilus HL17 lctP, lctO, acs
Thioalkalivibrio paradoxus ARh 1 lctP, L-LDH
Thioalkalivibrio thiocyanodenitrificans ARhD 1 lctP, L-LDH
Thiohalomonas denitrificans HLD2 Shew_2731, Shew_2732, lctO, acs
Thiohalospira halophila HL 3 lctP, L-LDH
Thiomicrorhabdus arctica DSM 13458 lctP, L-LDH
Thiomicrorhabdus chilensis DSM 12352 lctP, lctO, acs
Thiomicrospira cyclica ALM1 lctP, lctO, acs
Thiomicrospira microaerophila ASL8-2 lctP, lctO, acs
Thiomicrospira pelophila DSM 1534 lctP, lctO, acs
Thiothrix lacustris DSM 21227 lctP, lutA, lutB, lutC
Tistlia consotensis USBA 355 lctP, L-LDH
Trichlorobacter lovleyi SZ SfMCT, L-LDH
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome Shew_2731, Shew_2732, lctO, acs
Trichormus variabilis ATCC 29413 Shew_2731, Shew_2732, lctO, acs
Xanthobacter autotrophicus Py2 lctP, L-LDH
Xenophilus azovorans DSM 13620 lctP, L-LDH

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