L-lactate catabolism

GapMind for catabolism of small carbon sources

L-lactate catabolism

Analysis of pathway L-lactate in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	lctP, L-LDH
Acidithiobacillus ferrooxidans ATCC 23270	lctP, lctO, acs
Alicycliphilus denitrificans K601	lctP, L-LDH
Allochromatium vinosum DSM 180	Shew_2731, Shew_2732, lctO, ackA, pta
Ammonifex degensii KC4	lctP, L-LDH
Archaeoglobus veneficus SNP6	lctP, lctO, acs
Arcobacter nitrofigilis DSM 7299	lctP, L-LDH
Azoarcus sp. BH72	lctP, lutA, lutB, lutC
Azohydromonas australica DSM 1124	lctP, lctO, ackA, pta
Azorhizobium caulinodans ORS 571	lctP, L-LDH
Azospirillum lipoferum B510	lctP, lutA, lutB, lutC
Bacillus alkalinitrilicus DSM 22532	lctP, lutA, lutB, lutC
Beijerinckia indica ATCC 9039	lctP, L-LDH
Beijerinckia mobilis UQM 1969	lctP, L-LDH
Bradyrhizobium sp. BTAi1	lctP, L-LDH
Burkholderia vietnamiensis G4	lctP, lldE, lldF, lldG
Calditerrivibrio nitroreducens DSM 19672	SfMCT, L-LDH
Caminibacter mediatlanticus TB-2	lctP, 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
Crocosphaera subtropica ATCC 51142	lctP, lctO, ackA, pta
Dechloromonas agitata is5	Shew_2731, Shew_2732, lutA, lutB, lutC
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, L-LDH
Desulfacinum infernum DSM 9756	SfMCT, L-LDH
Desulfallas geothermicus DSM 3669	lctP, lctO, acs
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
Desulfobulbus mediterraneus DSM 13871	lctP, DVU3033, DVU3032
Desulfotalea psychrophila LSv54	lctP, DVU3033, DVU3032
Desulfotomaculum ruminis DSM 2154	lctP, lctO, ackA, pta
Desulfovibrio bastinii DSM 16055	lctP, DVU3033, DVU3032
Desulfovibrio gracilis DSM 16080	lctP, DVU3033, DVU3032
Desulfovibrio oxyclinae DSM 11498	lctP, DVU3033, DVU3032
Desulfovibrio zosterae DSM 11974	lctP, DVU3033, DVU3032
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
Ferroglobus placidus DSM 10642	SfMCT, L-LDH
Frankia alni ACN14A	mctP, lctO, acs
Geobacter lovleyi SZ	SfMCT, L-LDH
Geobacter metallireducens GS-15	SfMCT, L-LDH
Geobacter uraniireducens Rf4	lctP, L-LDH
Haloechinothrix alba DSM 45207	Shew_2731, Shew_2732, lutA, lutB, lutC
Haloglycomyces albus DSM 45210	lctP, lctO, ackA, pta
Halomonas desiderata SP1	lctP, lutA, lutB, lutC
Halorhodospira halophila SL1	lctP, lctO, acs
Heliobacterium modesticaldum Ice1; ATCC 51547	lctP, L-LDH
Herbaspirillum autotrophicum IAM 14942	lctP, lctO, acs
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 variicola At-22	lctP, L-LDH
Kyrpidia tusciae DSM 2912	lctP, lutA, lutB, lutC
Leptospirillum ferrooxidans C2-3	lctP, L-LDH
Malonomonas rubra DSM 5091	Shew_2731, Shew_2732, DVU3033, DVU3032
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 barkeri Fusaro	lctP, L-LDH
Methanosarcina mazei Go1	lctP, L-LDH
Methanothermobacter thermautotrophicus Delta H	lctP, L-LDH
Methylobacterium nodulans ORS 2060	lctP, L-LDH
Methylobacterium sp. 4-46	lctP, L-LDH
Methylocapsa acidiphila B2	mctP, L-LDH
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	lctP, L-LDH
Methylomonas methanica MC09	lctP, lctO, ackA, pta
Methylosarcina fibrata AML-C10	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
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 phymatum STM815	lctP, lutA, lutB, lutC
Paraburkholderia sp. CCGE1002	mctP, lldE, lldF, lldG
Pelobacter propionicus DSM 2379	lctP, L-LDH
Persephonella marina EX-H1	lctP, lctO, acs
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 stutzeri A1501	lctP, lutA, lutB, lutC
Pyrolobus fumarii 1A	lctP, L-LDH
Rhizobium etli CFN 42	mctP, L-LDH
Rhizobium leguminosarum 3841	mctP, L-LDH
Rhizobium leguminosarum WSM1325	mctP, L-LDH
Rhodobacter sphaeroides ATCC 17029	Shew_2731, Shew_2732, L-LDH
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
Saccharomonospora cyanea NA-134	lctP, lctO, acs
Sedimenticola selenatireducens DSM 17993	lctP, lutA, lutB, lutC
Sinorhizobium fredii NGR234	mctP, L-LDH
Sinorhizobium medicae WSM419	lctP, lctO, ackA, pta
Sphingomonas wittichii RW1	lctP, L-LDH
Stenotrophomonas chelatiphaga DSM 21508	lctP, L-LDH
Steroidobacter denitrificans DSM 18526	lctP, lctO, ackA, pta
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
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
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
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
Trichodesmium erythraeum IMS101	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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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

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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:

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