GapMind for catabolism of small carbon sources

 

D-lactate catabolism

Analysis of pathway D-lactate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 lctP, glcD, glcE, glcF
Actinokineospora bangkokensis 44EHW mctP, D-LDH
Actinomyces timonensis 7400942 lctP, D-LDH
Algiphilus aromaticivorans DG1253 lctP, D-LDH
Algoriphagus aquaeductus T4 lctP, D-LDH
Algoriphagus machipongonensis PR1 larD, D-LDH
Alicyclobacillus ferrooxydans TC-34 lctP, D-LDH
Alishewanella agri BL06 lctP, D-LDH
Alistipes indistinctus YIT 12060 lctP, D-LDH
Alistipes shahii WAL 8301 lctP, D-LDH
Alkalitalea saponilacus SC/BZ-SP2 lctP, D-LDH
Amantichitinum ursilacus IGB-41 lctP, D-LDH
Amphibacillus jilinensis Y1 lctP, D-LDH
Amphritea japonica JAMM 1866 lctP, glcD, glcE, glcF
Amycolatopsis halophila YIM 93223 lctP, D-LDH
Amycolatopsis xylanica CPCC 202699 lctP, D-LDH
Aquimarina agarilytica ZC1 lctP, D-LDH
Aquimarina longa SW024 lctP, D-LDH
Aquimarina macrocephali JAMB N27 lctP, D-LDH
Archaeoglobus sulfaticallidus PM70-1 lctP*, D-LDH
Arcticibacter svalbardensis MN12-7 lctP, D-LDH
Ardenticatena maritima 110S larD, D-LDH
Arenimonas metalli CF5-1 lctP, D-LDH
Arenitalea lutea P7-3-5 larD, D-LDH
Azospirillum humicireducens SgZ-5 lctP, D-LDH
Azospirillum thiophilum BV-S lctP, D-LDH
Bacillus altitudinis 41KF2b lctP, D-LDH
Bacillus coahuilensis m4-4 lctP, D-LDH
Bacillus cytotoxicus NVH 391-98 lctP, D-LDH
Bacillus horneckiae 1P01SC lctP, D-LDH
Bacillus okhensis Kh10-101 larD, D-LDH
Bacillus safensis FO-36b lctP, D-LDH
Bacillus velezensis CBMB205 lctP, D-LDH
Bacteroides clarus YIT 12056 lctP, D-LDH
Bacteroides faecis MAJ27 lctP, D-LDH
Bacteroides fluxus YIT 12057 lctP, D-LDH
Bacteroides oleiciplenus YIT 12058 lctP, D-LDH
Barnesiella intestinihominis YIT 11860 lctP, D-LDH
Belnapia rosea CPCC 100156 lctP, glcD, glcE, glcF
Bizionia argentinensis JUB59 lctP, D-LDH
Bradyrhizobium diazoefficiens USDA110 lctP, glcD, glcE, glcF
Brevibacterium jeotgali SJ5-8 lctP, D-LDH
Brucella inopinata BO1 lctP, glcD, glcE, glcF
Brucella microti CCM 4915 lctP, glcD, glcE, glcF
Bryobacter aggregatus MPL3 lctP, D-LDH
Caldicellulosiruptor hydrothermalis 108 lctP, D-LDH
Caldicellulosiruptor kronotskyensis 2002 lctP, D-LDH
Carboxydothermus pertinax Ug1 lctP, D-LDH
Catellicoccus marimammalium M35/04/3 lctP, D-LDH
Chromobacterium vaccinii MWU205 lctP, D-LDH
Chryseobacterium angstadtii KM lctP, D-LDH
Chryseobacterium arthrosphaerae CC-VM-7 larD, D-LDH
Chryseobacterium viscerum 687B-08 lctP, D-LDH
Cloacibacillus porcorum CL-84 lctP, D-LDH
Cobetia crustatorum JO1 lctP, D-LDH
Collimonas arenae Ter10 lctP, D-LDH
Collimonas pratensis Ter91 lctP, glcD, glcE, glcF
Collinsella tanakaei YIT 12063 larD, D-LDH
Coprobacter fastidiosus NSB1 lctP, D-LDH
Corynebacterium deserti GIMN1.010 lctP, D-LDH
Corynebacterium frankenforstense ST18 lctP, D-LDH
Corynebacterium lactis RW2-5 lctP, D-LDH
Croceitalea dokdonensis DOKDO 023 lctP, D-LDH
Cronobacter condimenti 1330 lctP, D-LDH
Cronobacter muytjensii ATCC 51329 lctP, D-LDH
Cronobacter universalis NCTC 9529 lctP, D-LDH
Desulfatitalea tepidiphila S28bF lctP, D-LDH
Desulfotomaculum hydrothermale Lam5 lctP, D-LDH
Dethiosulfovibrio salsuginis USBA 82 lctP, D-LDH
Devosia chinhatensis IPL18 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, D-LDH
Devriesea agamarum IMP2 lctP, D-LDH
Dialister succinatiphilus YIT 11850 lctP, D-LDH
Dietzia timorensis ID05-A0528 lctP, D-LDH
Dokdonella koreensis DS-123 lctP, D-LDH
Domibacillus robiginosus WS 4628 lctP, D-LDH
Duganella sacchari Sac-22 lctP, glcD, glcE, glcF
Dyadobacter tibetensis Y620-1 larD, D-LDH
Dyella jiangningensis SBZ3-12 lctP, D-LDH
Endozoicomonas montiporae CL-33 lctP, D-LDH
Enterococcus termitis LMG 8895 larD, D-LDH
Enterorhabdus caecimuris B7 lctP, D-LDH
Epibacterium ulvae U95 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Erythrobacter gangjinensis K7-2 lctP, D-LDH
Erythrobacter marinus HWDM-33 lctP, D-LDH
Ethanoligenens harbinense YUAN-3 lctP, D-LDH
Fervidicella metallireducens AeB lctP, D-LDH
Fibrella aestuarina BUZ 2 larD, D-LDH
Flammeovirga pacifica WPAGA1 lctP, D-LDH
Flaviramulus ichthyoenteri Th78 lctP, D-LDH
Flavobacterium beibuense F44-8 lctP, D-LDH
Flavobacterium glycines Gm-149 lctP, D-LDH
Flavobacterium sp. LM5 lctP, D-LDH*
Flavobacterium ummariense DS-12 lctP, D-LDH
Frischella perrara PEB0191 lctP, D-LDH
Galbibacter marinus ck-I2-15 lctP, D-LDH
Gallaecimonas xiamenensis 3-C-1 lctP, D-LDH
Geobacter daltonii FRC-32 lctP, D-LDH
Gillisia marina CBA3202 lctP, D-LDH
Gracilibacillus halophilus YIM-C55.5 lctP, D-LDH
Granulicella mallensis MP5ACTX8 mctP, D-LDH
Granulicella tundricola MP5ACTX9 larD, D-LDH
Hafnia paralvei ATCC 29927 lctP, D-LDH
Haladaptatus cibarius D43 lctP, D-LDH
Halioglobus japonicus S1-36 lctP, glcD, glcE, glcF
Halobacillus alkaliphilus FP5 lctP, D-LDH
Halococcus hamelinensis 100A6 lctP, D-LDH
Halomonas salina B6 lctP, glcD, glcE, glcF
Halomonas smyrnensis AAD6 lctP, glcD, glcE, glcF
Halomonas stevensii S18214 lctP, glcD, glcE, glcF
Halomonas titanicae BH1 lctP, glcD, glcE, glcF
Halomonas xinjiangensis TRM 0175 lctP, glcD, glcE, glcF
Halopiger salifodinae KCY07-B2 lctP, D-LDH
Halostagnicola larsenii XH-48 lctP, D-LDH
Haloterrigena daqingensis JX313 lctP, D-LDH
Herbaspirillum aquaticum IEH 4430 mctP, glcD, glcE, glcF
Hippea alviniae EP5-r lctP, D-LDH
Hippea jasoniae Mar08-272r lctP, D-LDH
Hoeflea phototrophica DFL-43 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Hyphomicrobium nitrativorans NL23 lctP, glcD, glcE, glcF
Imtechella halotolerans K1 lctP, D-LDH
Indibacter alkaliphilus LW1 larD, D-LDH
Jannaschia aquimarina GSW-M26 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Jeotgalibacillus soli P9 larD, D-LDH
Kangiella geojedonensis YCS-5 lctP, D-LDH
Knoellia flava TL1 mctP, D-LDH
Kocuria flava HO-9041 lctP, D-LDH
Kocuria turfanensis HO-9042 lctP, D-LDH
Laceyella sediminis RHA1 lctP, D-LDH
Lacinutrix algicola AKS293 lctP, D-LDH
Lacinutrix himadriensis E4-9a lctP, D-LDH
Lacinutrix mariniflava AKS432 larD, D-LDH
Lactobacillus curieae CCTCC M 2011381 lctP, D-LDH
Lactobacillus delbrueckii ZN7a-9 larD, D-LDH
Lactobacillus hokkaidonensis LOOC260 lctP, D-LDH
Lactobacillus oryzae SG293 lctP, D-LDH
Lactobacillus pobuzihii E100301 larD, D-LDH
Lactobacillus shenzhenensis LY-73 larD, D-LDH
Lactobacillus silagei IWT126 larD, D-LDH
Leeuwenhoekiella blandensis MED217 lctP, D-LDH
Lentibacillus jeotgali Grbi lctP, D-LDH
Limnohabitans curvus MWH-C5 lctP, glcD, glcE, glcF
Limnohabitans parvus II-B4 lctP, glcD, glcE, glcF
Listeria fleischmannii LU2006-1 lctP, D-LDH
Luteimonas huabeiensis HB2 lctP, D-LDH
Luteipulveratus mongoliensis MN07-A0370 mctP, glcD, glcE, glcF
Lutibaculum baratangense AMV1 lctP, glcD, glcE, glcF
Lysobacter daejeonensis GH1-9 lctP, D-LDH
Magnetovibrio blakemorei MV-1 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Marinicella litoralis KMM 3900 lctP, D-LDH
Mariniradius saccharolyticus AK6 larD, D-LDH
Marinobacter algicola DG893 lctP, glcD, glcE, glcF
Marinobacter guineae M3B PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Marinobacter psychrophilus 20041 lctP, glcD, glcE, glcF
Marinomonas arctica 328 lctP, D-LDH
Marivita geojedonensis DPG-138 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Martelella endophytica YC6887 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Megamonas funiformis YIT 11815 lctP, lctB, lctC, lctD
Mesorhizobium ciceri WSM1271 lctP, glcD, glcE, glcF
Methanobacterium arcticum M2 lctP, D-LDH
Methanobacterium veterum MK4 lctP, D-LDH
Methanocella arvoryzae MRE50 lctP, D-LDH
Methanococcus aeolicus Nankai-3 lctP, D-LDH
Methanoculleus horonobensis T10 lctP, D-LDH
Methanolinea tarda NOBI-1 lctP, D-LDH
Methanosarcina soligelidi SMA-21 lctP, D-LDH
Methanospirillum lacunae Ki8-1 lctP, D-LDH
Methanospirillum stamsii Pt1 lctP, D-LDH
Methylibium petroleiphilum PM1 lctP, glcD, glcE, glcF
Methylobacterium gossipiicola Gh-105 lctP, glcD, glcE, glcF
Methylocapsa aurea KYG mctP, glcD, glcE, glcF
Methylotenera versatilis 301 lctP, D-LDH
Microbacterium profundi Shh49 lctP, D-LDH
Microvirga lotononidis WSM3557 lctP, glcD, glcE, glcF
Moritella dasanensis ArB 0140 lctP, D-LDH
Mucilaginibacter gossypii Gh-67 larD, D-LDH
Mucilaginibacter gossypiicola Gh-48 larD, D-LDH
Mucilaginibacter mallensis MP1X4 larD, D-LDH
Nafulsella turpanensis ZLM-10 lctP, D-LDH
Natronomonas moolapensis 8.8.11 lctP, D-LDH
Nautilia profundicola AmH lctP, D-LDH
Neiella marina J221 lctP, D-LDH
Neptunomonas antarctica S3-22 lctP, glcD, glcE, glcF
Nocardioides daejeonensis MJ31 lctP, D-LDH
Nocardioides dokdonensis FR1436 lctP, D-LDH
Nocardiopsis baichengensis YIM 90130 lctP, glcD, glcE, glcF
Nocardiopsis gilva YIM 90087 lctP, glcD, glcE, glcF
Novosphingobium barchaimii LL02 lctP, D-LDH
Novosphingobium fuchskuhlense FNE08-7 lctP, glcD, glcE, glcF
Novosphingobium lindaniclasticum LE124 lctP, D-LDH
Oceanisphaera arctica V1-41 lctP, D-LDH
Ochrobactrum rhizosphaerae PR17 lctP, glcD, glcE, glcF
Ochrobactrum thiophenivorans DSM 7216 larD, glcD, glcE, glcF
Oscillibacter ruminantium GH1 lctP, D-LDH
Paenisporosarcina indica PN2 lctP, D-LDH
Palaeococcus pacificus DY20341 lctP, D-LDH
Paludibacter propionicigenes WB4 lctP, D-LDH
Pandoraea thiooxydans ATSB16 mctP, glcD, glcE, glcF
Pantoea rwandensis LMG 26275 lctP, D-LDH
Pedobacter arcticus A12 lctP, D-LDH
Photobacterium gaetbulicola Gung47 lctP, D-LDH
Photobacterium jeanii R-40508 lctP, D-LDH
Phyllobacterium brassicacearum STM 196 mctP, glcD, glcE, glcF
Phyllobacterium endophyticum PEPV15 lctP, glcD, glcE, glcF
Phyllobacterium leguminum ORS 1419 lctP, glcD, glcE, glcF
Planktomarina temperata RCA23 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Planococcus halocryophilus Or1 larD, D-LDH
Pleomorphomonas diazotrophica R5-392 lctP, D-LDH
Polaribacter dokdonensis DSW-5 lctP, D-LDH
Pontibacillus litoralis JSM 072002 lctP, D-LDH
Pontibacter lucknowensis DM9 lctP, D-LDH
Pontibacter ramchanderi LP43 lctP, D-LDH
Pontimonas salivibrio CL-TW6 lctP, D-LDH
Porphyrobacter dokdonensis DSW-74 lctP, D-LDH
Pseudoalteromonas arctica A 37-1-2 lctP, D-LDH
Pseudomonas baetica a390 lctP, glcD, glcE, glcF
Pseudomonas litoralis 2SM5 lctP, D-LDH
Pseudomonas taeanensis MS-3 lctP, glcD, glcE, glcF
Pseudovibrio axinellae Ad2 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Psychrobacter arcticus 273-4 lctP, glcD, glcE, glcF
Psychrobacter cryohalolentis K5 lctP, glcD, glcE, glcF
Psychromonas ingrahamii 37 lctP, D-LDH
Psychromonas ossibalaenae JAMM 0738 lctP, D-LDH
Rhizobium freirei PRF 81 mctP, glcD, glcE, glcF
Rhizobium grahamii CCGE 502 mctP, glcD, glcE, glcF
Rhizobium subbaraonis JC85 lctP, glcD, glcE, glcF
Rhodanobacter denitrificans 2APBS1 lctP, D-LDH
Rhodobacter johrii JA192 lctP, glcD, glcE, glcF
Rhodobacter maris JA276 lctP, glcD, glcE, glcF
Rhodobacter ovatus JA234 lctP, glcD, glcE, glcF
Rhodobacter viridis JA737 lctP, glcD, glcE, glcF
Rhodococcus qingshengii djl-6-2 lctP, D-LDH
Rhodopseudomonas pseudopalustris DSM 123 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Roseateles aquatilis CCUG 48205 lctP, D-LDH
Roseivirga spongicola UST030701-084 lctP, D-LDH
Rubrivirga marina SAORIC-28 lctP, D-LDH
Ruegeria conchae TW15 lctP, glcD, glcE, glcF
Saccharomonospora marina XMU15 mctP, glcD, glcE, glcF
Salinicoccus carnicancri Crm lctP, D-LDH
Serinicoccus profundi MCCC 1A05965 lctP, glcD, glcE, glcF
Shewanella halifaxensis HAW-EB4 lctP, D-LDH
Skermanella stibiiresistens SB22 lctP, glcD, glcE, glcF
Snodgrassella alvi wkB2 lctP, D-LDH
Sphaerochaeta globosa Buddy lctP, D-LDH
Sphaerochaeta pleomorpha Grapes lctP, D-LDH
Sphingobium baderi LL03 lctP, D-LDH
Sphingobium czechense LL01 lctP, D-LDH
Sphingobium quisquiliarum P25 lctP, D-LDH
Sphingomonas histidinilytica UM2 lctP, glcD, glcE, glcF
Sphingomonas indica Dd16 lctP, D-LDH
Sphingomonas laterariae LNB2 lctP, D-LDH
Sphingopyxis indica DS15 lctP, D-LDH
Sphingopyxis terrae UI2 lctP, D-LDH
Sporolactobacillus vineae SL153 larD, D-LDH
Streptacidiphilus oryzae TH49 mctP, D-LDH
Streptococcus anginosus CCUG 39159 lctP, D-LDH
Streptococcus massiliensis 4401825 lctP, D-LDH
Streptococcus oralis 7747 lctP, D-LDH
Streptococcus oralis AZ_3a lctP, D-LDH
Streptomyces kebangsaanensis SUK12 mctP, D-LDH
Succinatimonas hippei YIT 12066 lctP, D-LDH
Sulfurimonas gotlandica GD1 lctP, D-LDH
Tatumella morbirosei LMG 23360 lctP, D-LDH
Thauera humireducens SgZ-1 lctP, glcD, glcE, glcF
Thermoactinomyces daqus H-18 lctP, glcD, glcE, glcF
Thermobifida halotolerans YIM 90462 lctP, D-LDH
Thermodesulfovibrio aggregans TGE-P1 lctP, D-LDH
Thermophagus xiamenensis HS1 lctP, D-LDH
Thermovenabulum gondwanense R270 lctP, D-LDH
Thioclava dalianensis DLFJ1-1 lctP, glcD, glcE, glcF
Thiohalospira halophila HL 3 lctP, glcD, glcE, glcF
Tistlia consotensis USBA 355 PGA1_c12640, PGA1_c12650, PGA1_c12660, PGA1_c12670, glcD, glcE, glcF
Vagococcus penaei CD276 larD, D-LDH
Verminephrobacter eiseniae EF01-2 lctP, glcD, glcE, glcF
Weissella oryzae SG25 larD, D-LDH
Williamsia sterculiae CPCC 203464 lctP, D-LDH
Yersinia intermedia Y228 lctP, D-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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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