GapMind for catabolism of small carbon sources

 

D-lactate catabolism

Analysis of pathway D-lactate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 lctP, D-LDH
Acidithiobacillus ferrooxidans ATCC 23270 lctP, glcD, glcE, glcF
Acidovorax sp. GW101-3H11 lctP, glcD, glcE, glcF
Algiphilus aromaticivorans DG1253 lctP, D-LDH
Alicycliphilus denitrificans K601 lctP, glcD, glcE, glcF
Alkalihalobacterium alkalinitrilicum DSM 22532 lctP, D-LDH
Allochromatium vinosum DSM 180 lctP, glcD, glcE, glcF
Ammonifex degensii KC4 lctP, D-LDH
Anaerobutyricum hallii DSM 3353 larD, lctB, lctC, lctD
Aquimarina longa SW024 lctP, D-LDH
Archaeoglobus veneficus SNP6 lctP, D-LDH
Arcobacter nitrofigilis DSM 7299 lctP, D-LDH
Azoarcus olearius BH72 lctP, glcD, glcE, glcF
Azohydromonas australica DSM 1124 lctP, glcD, glcE, glcF
Azorhizobium caulinodans ORS 571 lctP, glcD, glcE, glcF
Azospirillum brasilense Sp245 lctP, glcD, glcE, glcF
Azospirillum sp. B510 lctP, glcD, glcE, glcF
Bacteroides thetaiotaomicron VPI-5482 lctP, D-LDH
Beijerinckia indica ATCC 9039 lctP, glcD, glcE, glcF
Beijerinckia mobilis UQM 1969 lctP, glcD, glcE, glcF
Billgrantia desiderata SP1 lctP, glcD, glcE, glcF
Bradyrhizobium sp. BTAi1 lctP, glcD, glcE, glcF
Brevundimonas sp. GW460-12-10-14-LB2 lctP, D-LDH
Burkholderia phytofirmans PsJN mctP, glcD, glcE, glcF
Burkholderia vietnamiensis G4 lctP, glcD, glcE, glcF
Calditerrivibrio nitroreducens DSM 19672 lctP, D-LDH
Caminibacter mediatlanticus TB-2 lctP, D-LDH
Carboxydothermus pertinax Ug1 lctP, D-LDH
Caulobacter crescentus NA1000 lctP, D-LDH
Cereibacter sphaeroides ATCC 17029 lctP, glcD, glcE, glcF
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
Clostridium tyrobutyricum FAM22553 lctP, lctB, lctC, lctD
Crocosphaera subtropica ATCC 51142 lctP, D-LDH
Cupriavidus basilensis FW507-4G11 lctP, glcD, glcE, glcF
Dechloromonas agitata is5 lctP, D-LDH
Dechlorosoma suillum PS lctP, glcD, glcE, glcF
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
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
Desulfogranum mediterraneum DSM 13871 lctP, D-LDH
Desulforamulus ruminis DSM 2154 lctP, D-LDH
Desulfoscipio geothermicus DSM 3669 lctP, glcD, glcE, glcF
Desulfotalea psychrophila LSv54 lctP, D-LDH
Desulfovibrio oxyclinae DSM 11498 lctP, D-LDH
Desulfovibrio vulgaris Hildenborough JW710 lctP, D-LDH
Desulfovibrio vulgaris Miyazaki F lctP, D-LDH
Desulfurobacterium atlanticum DSM 15668 lctP, D-LDH
Desulfuromonas acetexigens lctP, D-LDH
Desulfuromusa kysingii DSM 7343 lctP, D-LDH
Dinoroseobacter shibae DFL-12 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Dyella japonica UNC79MFTsu3.2 lctP, D-LDH
Echinicola vietnamensis KMM 6221, DSM 17526 larD, D-LDH
Escherichia coli BW25113 lctP, glcD, glcE, glcF
Ferroglobus placidus DSM 10642 lctP, D-LDH
Frankia alni ACN14a mctP, D-LDH
Geobacter metallireducens GS-15 lctP, D-LDH
Geotalea uraniireducens Rf4 lctP, D-LDH
Halococcus hamelinensis 100A6 lctP, D-LDH
Haloechinothrix alba DSM 45207 lctP, D-LDH
Haloferax volcanii DS2 lctP, D-LDH
Haloglycomyces albus DSM 45210 lctP, D-LDH
Halorhodospira halophila SL1 lctP, glcD, glcE, glcF
Heliomicrobium modesticaldum Ice1; ATCC 51547 lctP, D-LDH
Herbaspirillum autotrophicum IAM 14942 lctP, glcD, glcE, glcF
Herbaspirillum seropedicae SmR1 lctP, glcD, glcE, glcF
Hippea alviniae EP5-r lctP, D-LDH
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 michiganensis M5al lctP, D-LDH
Klebsiella variicola At-22 lctP, D-LDH
Kyrpidia tusciae DSM 2912 lctP, D-LDH
Leptospirillum ferrooxidans C2-3 lctP, D-LDH
Magnetospirillum magneticum AMB-1 lctP, D-LDH
Malonomonas rubra DSM 5091 lctP, D-LDH
Maridesulfovibrio bastinii DSM 16055 lctP, D-LDH
Maridesulfovibrio zosterae DSM 11974 lctP, D-LDH
Marinobacter adhaerens HP15 lctP, glcD, glcE, glcF
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 mazei Go1 lctP, D-LDH
Methanospirillum lacunae Ki8-1 lctP, D-LDH
Methanothermobacter thermautotrophicus Delta H lctP, D-LDH
Methylobacterium nodulans ORS 2060 lctP, glcD, glcE, glcF
Methylobacterium sp. 4-46 Apr-46 lctP, glcD, glcE, glcF
Methylocapsa acidiphila B2 mctP, glcD, glcE, glcF
Methylocapsa aurea KYG 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
Methylomonas methanica MC09 lctP, D-LDH
Methylosarcina fibrata AML-C10 lctP, glcD, glcE, glcF
Methylotuvimicrobium alcaliphilum 20Z 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
Nocardioides dokdonensis FR1436 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 atlantica CCGE1002 mctP, glcD, glcE, glcF
Paraburkholderia bryophila 376MFSha3.1 mctP, glcD, glcE, glcF
Paraburkholderia phymatum STM815 lctP, glcD, glcE, glcF
Paucidesulfovibrio gracilis DSM 16080 lctP, D-LDH
Pedobacter sp. GW460-11-11-14-LB5 lctP, D-LDH
Pelobacter propionicus DSM 2379 lctP, D-LDH
Persephonella marina EX-H1 lctP, D-LDH
Phaeacidiphilus oryzae TH49 mctP, D-LDH
Phaeobacter inhibens BS107 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
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 fluorescens FW300-N1B4 lctP, glcD, glcE, glcF
Pseudomonas fluorescens FW300-N2C3 lctP, glcD, glcE, glcF
Pseudomonas fluorescens FW300-N2E2 lctP, glcD, glcE, glcF
Pseudomonas fluorescens FW300-N2E3 lctP, glcD, glcE, glcF
Pseudomonas fluorescens GW456-L13 lctP, D-LDH
Pseudomonas putida KT2440 lctP, glcD, glcE, glcF
Pseudomonas simiae WCS417 lctP, D-LDH
Pseudomonas stutzeri RCH2 lctP, glcD, glcE, glcF
Pyrolobus fumarii 1A lctP, D-LDH
Rhizobium etli CFN 42 mctP, glcD, glcE, glcF
Rhizobium johnstonii 3841 mctP, glcD, glcE, glcF
Rhizobium leguminosarum WSM1325 mctP, glcD, glcE, glcF
Rhizorhabdus wittichii RW1 lctP, glcD, glcE, glcF
Rhodanobacter denitrificans FW104-10B01 lctP, D-LDH
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
Roseburia faecis M72 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
Shewanella amazonensis SB2B lctP, D-LDH
Shewanella loihica PV-4 lctP, D-LDH
Shewanella oneidensis MR-1 lctP, D-LDH
Shewanella sp. ANA-3 lctP, D-LDH
Sinorhizobium fredii NGR234 mctP, glcD, glcE, glcF
Sinorhizobium medicae WSM419 lctP, glcD, glcE, glcF
Sinorhizobium meliloti 1021 lctP, glcD, glcE, glcF
Sphingomonas koreensis DSMZ 15582 lctP, glcD, glcE, glcF
Stenotrophomonas chelatiphaga DSM 21508 lctP, D-LDH
Steroidobacter denitrificans DSM 18526 lctP, D-LDH
Stutzerimonas stutzeri A1501 lctP, glcD, glcE, glcF
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
Synechococcus elongatus PCC 7942 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
Thermus aquaticus YT-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
Thiohalospira halophila HL 3 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
Tistlia consotensis USBA 355 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Trichlorobacter lovleyi SZ lctP, D-LDH
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome 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 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