D-lactate catabolism

GapMind for catabolism of small carbon sources

D-lactate catabolism

Analysis of pathway D-lactate in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	lctP, D-LDH
Acidithiobacillus ferrooxidans ATCC 23270	lctP, glcD, glcE, glcF
Alicycliphilus denitrificans K601	lctP, glcD, glcE, glcF
Allochromatium vinosum DSM 180	lctP, glcD, glcE, glcF
Ammonifex degensii KC4	lctP, D-LDH
Archaeoglobus veneficus SNP6	lctP, D-LDH
Arcobacter nitrofigilis DSM 7299	lctP, D-LDH
Azoarcus sp. BH72	lctP, glcD, glcE, glcF
Azohydromonas australica DSM 1124	lctP, glcD, glcE, glcF
Azorhizobium caulinodans ORS 571	lctP, glcD, glcE, glcF
Azospirillum lipoferum B510	lctP, glcD, glcE, glcF
Bacillus alkalinitrilicus DSM 22532	lctP, D-LDH
Beijerinckia indica ATCC 9039	lctP, glcD, glcE, glcF
Beijerinckia mobilis UQM 1969	lctP, glcD, glcE, glcF
Bradyrhizobium sp. BTAi1	lctP, glcD, glcE, glcF
Burkholderia vietnamiensis G4	lctP, glcD, glcE, glcF
Calditerrivibrio nitroreducens DSM 19672	lctP, D-LDH
Caminibacter mediatlanticus TB-2	lctP, D-LDH
Chlorobaculum parvum NCIB 8327	lctP, D-LDH
Chlorobaculum tepidum TLS	lctP, D-LDH
Chlorobium limicola DSM 245	lctP, D-LDH
Chlorobium phaeobacteroides BS1	lctP, D-LDH
Clostridium acetobutylicum ATCC 824	larD, lctB, lctC, lctD
Clostridium kluyveri DSM 555	lctP, D-LDH
Crocosphaera subtropica ATCC 51142	lctP, D-LDH
Dechloromonas agitata is5	lctP, D-LDH
Dehalococcoides mccartyi 195	lctP, D-LDH
Denitrovibrio acetiphilus DSM 12809	lctP, D-LDH
Derxia gummosa DSM 723	lctP, glcD, glcE, glcF
Desulfacinum hydrothermale DSM 13146	lctP, D-LDH
Desulfacinum infernum DSM 9756	lctP, D-LDH
Desulfallas geothermicus DSM 3669	lctP, glcD, glcE, glcF
Desulfarculus baarsii DSM 2075	lctP, D-LDH
Desulfatibacillum aliphaticivorans DSM 15576	lctP, D-LDH
Desulfatiglans anilini DSM 4660	lctP, D-LDH
Desulfitobacterium hafniense DCB-2	lctP, D-LDH
Desulfobacca acetoxidans DSM 11109	lctP, lctB, lctC, lctD
Desulfobacter vibrioformis DSM 8776	lctP, D-LDH
Desulfobulbus mediterraneus DSM 13871	lctP, D-LDH
Desulfotalea psychrophila LSv54	lctP, D-LDH
Desulfotomaculum ruminis DSM 2154	lctP, D-LDH
Desulfovibrio bastinii DSM 16055	lctP, D-LDH
Desulfovibrio gracilis DSM 16080	lctP, D-LDH
Desulfovibrio oxyclinae DSM 11498	lctP, D-LDH
Desulfovibrio zosterae DSM 11974	lctP, D-LDH
Desulfurobacterium atlanticum DSM 15668	lctP, D-LDH
Desulfuromonas acetexigens	lctP, D-LDH
Desulfuromusa kysingii DSM 7343	lctP, D-LDH
Ferroglobus placidus DSM 10642	lctP, D-LDH
Frankia alni ACN14A	mctP, D-LDH
Geobacter lovleyi SZ	lctP, D-LDH
Geobacter metallireducens GS-15	lctP, D-LDH
Geobacter uraniireducens Rf4	lctP, D-LDH
Haloechinothrix alba DSM 45207	lctP, D-LDH
Haloglycomyces albus DSM 45210	lctP, D-LDH
Halomonas desiderata SP1	lctP, glcD, glcE, glcF
Halorhodospira halophila SL1	lctP, glcD, glcE, glcF
Heliobacterium modesticaldum Ice1; ATCC 51547	lctP, D-LDH
Herbaspirillum autotrophicum IAM 14942	lctP, glcD, glcE, glcF
Hydrogenophaga taeniospiralis NBRC 102512	lctP, glcD, glcE, glcF
Hydrogenovibrio halophilus DSM 15072	lctP, D-LDH
Hydrogenovibrio kuenenii DSM 12350	lctP, D-LDH
Hydrogenovibrio marinus DSM 11271	lctP, D-LDH
Hyphomicrobium sulfonivorans WDL6	lctP, glcD, glcE, glcF
Klebsiella variicola At-22	lctP, D-LDH
Kyrpidia tusciae DSM 2912	lctP, D-LDH
Leptospirillum ferrooxidans C2-3	lctP, D-LDH
Malonomonas rubra DSM 5091	lctP, D-LDH
Mesorhizobium ciceri WSM1271	lctP, glcD, glcE, glcF
Methanobacterium lacus AL-21	lctP, D-LDH
Methanococcus aeolicus Nankai-3	lctP, D-LDH
Methanococcus maripaludis C5	lctP, D-LDH
Methanosarcina acetivorans C2A	lctP, D-LDH
Methanosarcina barkeri Fusaro	lctP, D-LDH
Methanosarcina mazei Go1	lctP, D-LDH
Methanothermobacter thermautotrophicus Delta H	lctP, D-LDH
Methylobacterium nodulans ORS 2060	lctP, glcD, glcE, glcF
Methylobacterium sp. 4-46	lctP, glcD, glcE, glcF
Methylocapsa acidiphila B2	mctP, glcD, glcE, glcF
Methylocapsa aurea KYG T	mctP, glcD, glcE, glcF
Methylocella silvestris BL2	lctP, glcD, glcE, glcF
Methylococcus capsulatus Bath	lctP, glcD, glcE, glcF
Methylocystis bryophila S285	lctP, glcD, glcE, glcF
Methyloferula stellata AR4T	lctP, glcD, glcE, glcF
Methylohalobius crimeensis 10Ki	lctP, glcD, glcE, glcF
Methylomicrobium alcaliphilum 20Z	lctP, glcD, glcE, glcF
Methylomonas methanica MC09	lctP, D-LDH
Methylosarcina fibrata AML-C10	lctP, glcD, glcE, glcF
Methylovulum miyakonense HT12	lctP, D-LDH
Mycolicibacterium vanbaalenii PYR-1	lctP, D-LDH
Nitratifractor salsuginis DSM 16511	lctP, D-LDH
Nitratiruptor tergarcus DSM 16512	lctP, D-LDH
Nitriliruptor alkaliphilus DSM 45188	lctP, D-LDH
Nocardiopsis lucentensis DSM 44048	larD, glcD, glcE, glcF
Nostoc punctiforme ATCC 29133; PCC 73102	lctP, D-LDH
Novosphingobium aromaticivorans DSM 12444	lctP, D-LDH
Oleispira antarctica	lctP, D-LDH
Paraburkholderia phymatum STM815	lctP, glcD, glcE, glcF
Paraburkholderia sp. CCGE1002	mctP, glcD, glcE, glcF
Pelobacter propionicus DSM 2379	lctP, D-LDH
Persephonella marina EX-H1	lctP, D-LDH
Polaromonas naphthalenivorans CJ2	lctP, glcD, glcE, glcF
Prosthecochloris aestuarii DSM 271	lctP, D-LDH
Pseudarthrobacter sulfonivorans Ar51	larD, D-LDH
Pseudomonas benzenivorans DSM 8628	lctP, glcD, glcE, glcF
Pseudomonas stutzeri A1501	lctP, glcD, glcE, glcF
Pyrolobus fumarii 1A	lctP, D-LDH
Rhizobium etli CFN 42	mctP, glcD, glcE, glcF
Rhizobium leguminosarum 3841	mctP, glcD, glcE, glcF
Rhizobium leguminosarum WSM1325	mctP, glcD, glcE, glcF
Rhodobacter sphaeroides ATCC 17029	lctP, glcD, glcE, glcF
Rhodomicrobium vannielii ATCC 17100	lctP, glcD, glcE, glcF
Rhodopseudomonas palustris CGA009	PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Rhodospirillum centenum SW; ATCC 51521	lctP, glcD, glcE, glcF
Rhodospirillum rubrum ATCC 11170	lctP, D-LDH
Saccharomonospora cyanea NA-134	lctP, glcD, glcE, glcF
Sedimenticola selenatireducens DSM 17993	PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Sinorhizobium fredii NGR234	mctP, glcD, glcE, glcF
Sinorhizobium medicae WSM419	lctP, glcD, glcE, glcF
Sphingomonas wittichii RW1	lctP, glcD, glcE, glcF
Stenotrophomonas chelatiphaga DSM 21508	lctP, D-LDH
Steroidobacter denitrificans DSM 18526	lctP, D-LDH
Sulfuricurvum kujiense DSM 16994	lctP, D-LDH
Sulfurihydrogenibium azorense Az-Fu1	lctP, D-LDH
Sulfurihydrogenibium subterraneum DSM 15120	lctP, D-LDH
Sulfurimonas denitrificans DSM 1251	lctP, D-LDH
Sulfuritalea hydrogenivorans DSM 22779	lctP, glcD, glcE, glcF
Sulfurivirga caldicuralii DSM 17737	lctP, D-LDH
Teredinibacter turnerae T7901	lctP, D-LDH
Thauera aminoaromatica S2	lctP, glcD, glcE, glcF
Thermithiobacillus tepidarius DSM 3134	lctP, glcD, glcE, glcF
Thermocrinis albus DSM 14484	lctP, D-LDH
Thermodesulforhabdus norvegica DSM 9990	lctP, lctB, lctC, lctD
Thermomonospora curvata DSM 43183	lctP, glcD, glcE, glcF
Thermovibrio ammonificans HB-1	lctP, D-LDH
Thioalkalivibrio denitrificans ALJD	lctP, glcD, glcE, glcF
Thioalkalivibrio halophilus HL17	lctP, glcD, glcE, glcF
Thioalkalivibrio paradoxus ARh 1	lctP, glcD, glcE, glcF
Thioalkalivibrio thiocyanodenitrificans ARhD 1	lctP, glcD, glcE, glcF
Thiohalomonas denitrificans HLD2	lctP, glcD, glcE, glcF
Thiomicrorhabdus arctica DSM 13458	lctP, D-LDH
Thiomicrorhabdus chilensis DSM 12352	lctP, D-LDH
Thiomicrospira cyclica ALM1	lctP, D-LDH
Thiomicrospira microaerophila ASL8-2	lctP, D-LDH
Thiomicrospira pelophila DSM 1534	lctP, D-LDH
Thiothrix lacustris DSM 21227	lctP, glcD, glcE, glcF
Trichodesmium erythraeum IMS101	lctP, glcD, glcE, glcF
Trichormus variabilis ATCC 29413	lctP, D-LDH
Xanthobacter autotrophicus Py2	lctP, glcD, glcE, glcF
Xenophilus azovorans DSM 13620	lctP, glcD, glcE, glcF

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