GapMind for catabolism of small carbon sources

 

L-lactate catabolism

Analysis of pathway L-lactate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 lctP, L-LDH
Actinokineospora bangkokensis 44EHW mctP, lctO, acs
Actinomyces timonensis 7400942 lctP, L-LDH
Algiphilus aromaticivorans DG1253 Shew_2731, Shew_2732, lctO, acs
Algoriphagus aquaeductus T4 Shew_2731, Shew_2732, lldE, lldF, lldG
Algoriphagus machipongonensis PR1 Shew_2731, Shew_2732, lldE, lldF, lldG
Alicyclobacillus ferrooxydans TC-34 lctP, lctO, acs
Alishewanella agri BL06 lctP, lctO, acs
Alistipes indistinctus YIT 12060 lctP, lctO, ackA, pta
Alistipes shahii WAL 8301 lctP, L-LDH
Alkalitalea saponilacus SC/BZ-SP2 SfMCT, L-LDH
Amantichitinum ursilacus IGB-41 lctP, lldE, lldF, lldG
Amphibacillus jilinensis Y1 SfMCT, lctO, ackA, pta
Amphritea japonica JAMM 1866 Shew_2731, Shew_2732, lutA, lutB, lutC
Amycolatopsis halophila YIM 93223 Shew_2731, Shew_2732, lctO, acs
Amycolatopsis xylanica CPCC 202699 lctP, lctO, acs
Aquimarina agarilytica ZC1 lctP, lctO, ackA, pta
Aquimarina longa SW024 Shew_2731, Shew_2732, lctO, ackA, pta
Aquimarina macrocephali JAMB N27 Shew_2731, Shew_2732, lctO, ackA, pta
Archaeoglobus sulfaticallidus PM70-1 lctP*, lctO, acs
Arcticibacter svalbardensis MN12-7 lctP, L-LDH
Ardenticatena maritima 110S Shew_2731, Shew_2732, L-LDH
Arenimonas metalli CF5-1 lctP, lctO, acs
Arenitalea lutea P7-3-5 Shew_2731, Shew_2732, lldE, lldF, lldG
Azospirillum humicireducens SgZ-5 lctP, lutA, lutB, lutC
Azospirillum thiophilum BV-S lctP, lctO, acs
Bacillus altitudinis 41KF2b lctP, lutA, lutB, lutC
Bacillus coahuilensis m4-4 lctP, L-LDH
Bacillus cytotoxicus NVH 391-98 lctP, lutA, lutB, lutC
Bacillus horneckiae 1P01SC lctP, lutA, lutB, lutC
Bacillus okhensis Kh10-101 SfMCT, lutA, lutB, lutC
Bacillus safensis FO-36b lctP, lutA, lutB, lutC
Bacillus velezensis CBMB205 lctP, lutA, lutB, lutC
Bacteroides clarus YIT 12056 lctP, lctO, ackA, pta
Bacteroides faecis MAJ27 lctP, lldE, lldF, lldG
Bacteroides fluxus YIT 12057 lctP, lctO, ackA, pta
Bacteroides oleiciplenus YIT 12058 lctP, lctO, ackA, pta
Barnesiella intestinihominis YIT 11860 lctP, L-LDH
Belnapia rosea CPCC 100156 lctP, lutA, lutB, lutC
Bizionia argentinensis JUB59 lctP, lctO, acs
Bradyrhizobium diazoefficiens USDA110 lctP, L-LDH
Brevibacterium jeotgali SJ5-8 lctP, lutA, lutB, lutC
Brucella inopinata BO1 lctP, L-LDH
Brucella microti CCM 4915 lctP, L-LDH
Bryobacter aggregatus MPL3 lctP, lctO, acs
Caldicellulosiruptor hydrothermalis 108 lctP, L-LDH
Caldicellulosiruptor kronotskyensis 2002 SfMCT, L-LDH
Carboxydothermus pertinax Ug1 lctP, lutA, lutB, lutC
Catellicoccus marimammalium M35/04/3 lctP, L-LDH
Chromobacterium vaccinii MWU205 lctP, lutA, lutB, lutC
Chryseobacterium angstadtii KM lctP, lctO, acs
Chryseobacterium arthrosphaerae CC-VM-7 larD, lctO, acs
Chryseobacterium viscerum 687B-08 lctP, lctO, acs
Cloacibacillus porcorum CL-84 lctP, lctO, ackA, pta
Cobetia crustatorum JO1 lctP, L-LDH
Collimonas arenae Ter10 lctP, L-LDH
Collimonas pratensis Ter91 lctP, L-LDH
Collinsella tanakaei YIT 12063 larD, L-LDH
Coprobacter fastidiosus NSB1 lctP, lldE, lldF, lldG
Corynebacterium deserti GIMN1.010 lctP, L-LDH
Corynebacterium frankenforstense ST18 lctP, L-LDH
Corynebacterium lactis RW2-5 lctP, L-LDH
Croceitalea dokdonensis DOKDO 023 Shew_2731, Shew_2732, L-LDH
Cronobacter condimenti 1330 lctP, L-LDH
Cronobacter muytjensii ATCC 51329 lctP, L-LDH
Cronobacter universalis NCTC 9529 lctP, L-LDH
Desulfatitalea tepidiphila S28bF SfMCT, DVU3033, DVU3032
Desulfotomaculum hydrothermale Lam5 lctP, L-LDH
Dethiosulfovibrio salsuginis USBA 82 lctP, lctO, ackA, pta
Devosia chinhatensis IPL18 lctP, L-LDH
Devriesea agamarum IMP2 lctP, L-LDH
Dialister succinatiphilus YIT 11850 lctP, L-LDH
Dietzia timorensis ID05-A0528 lctP, L-LDH
Dokdonella koreensis DS-123 lctP, lutA, lutB, lutC
Domibacillus robiginosus WS 4628 lctP, lutA, lutB, lutC
Duganella sacchari Sac-22 lctP, L-LDH
Dyadobacter tibetensis Y620-1 larD, lldE, lldF, lldG
Dyella jiangningensis SBZ3-12 lctP, L-LDH
Endozoicomonas montiporae CL-33 SfMCT, L-LDH
Enterococcus termitis LMG 8895 SfMCT, L-LDH
Enterorhabdus caecimuris B7 lctP, lctO, ackA, pta
Epibacterium ulvae U95 lctP, L-LDH
Erythrobacter gangjinensis K7-2 Shew_2731, Shew_2732, L-LDH
Erythrobacter marinus HWDM-33 lctP, L-LDH
Ethanoligenens harbinense YUAN-3 lctP, L-LDH
Fervidicella metallireducens AeB lctP, lctO, ackA, pta
Fibrella aestuarina BUZ 2 larD, lldE, lldF, lldG
Flammeovirga pacifica WPAGA1 lctP, lldE, lldF, lldG
Flaviramulus ichthyoenteri Th78 Shew_2731, Shew_2732, L-LDH
Flavobacterium beibuense F44-8 lctP, lctO, acs
Flavobacterium glycines Gm-149 lctP, lldE, lldF, lldG
Flavobacterium sp. LM5 lctP, L-LDH
Flavobacterium ummariense DS-12 lctP, lctO, acs
Frischella perrara PEB0191 lctP, L-LDH
Galbibacter marinus ck-I2-15 Shew_2731, Shew_2732, L-LDH
Gallaecimonas xiamenensis 3-C-1 lctP, L-LDH
Geobacter daltonii FRC-32 SfMCT, L-LDH
Gillisia marina CBA3202 lctP, L-LDH
Gracilibacillus halophilus YIM-C55.5 Shew_2731, Shew_2732, lutA, lutB, lutC
Granulicella mallensis MP5ACTX8 mctP, lutA, lutB, lutC
Granulicella tundricola MP5ACTX9 SfMCT, L-LDH
Hafnia paralvei ATCC 29927 lctP, L-LDH
Haladaptatus cibarius D43 lctP, lctO, acs
Halioglobus japonicus S1-36 Shew_2731, Shew_2732, lutA, lutB, lutC
Halobacillus alkaliphilus FP5 lctP, L-LDH
Halococcus hamelinensis 100A6 lctP, lctO, acs
Halomonas salina B6 lctP, lutA, lutB, lutC
Halomonas smyrnensis AAD6 lctP, lctO, acs
Halomonas stevensii S18214 lctP, L-LDH
Halomonas titanicae BH1 lctP, L-LDH
Halomonas xinjiangensis TRM 0175 lctP, lutA, lutB, lutC
Halopiger salifodinae KCY07-B2 lctP, lctO, acs
Halostagnicola larsenii XH-48 lctP, lctO, acs
Haloterrigena daqingensis JX313 lctP, lctO, acs
Herbaspirillum aquaticum IEH 4430 mctP, L-LDH
Hippea alviniae EP5-r lctP, L-LDH
Hippea jasoniae Mar08-272r lctP, L-LDH
Hoeflea phototrophica DFL-43 lctP, L-LDH
Hyphomicrobium nitrativorans NL23 lctP, lctO, acs
Imtechella halotolerans K1 lctP, lctO, ackA, pta
Indibacter alkaliphilus LW1 Shew_2731, Shew_2732, lldE, lldF, lldG
Jannaschia aquimarina GSW-M26 lctP, L-LDH
Jeotgalibacillus soli P9 SfMCT, lutA, lutB, lutC
Kangiella geojedonensis YCS-5 lctP, lctO, acs
Knoellia flava TL1 mctP, lutA, lutB, lutC
Kocuria flava HO-9041 lctP, L-LDH
Kocuria turfanensis HO-9042 lctP, L-LDH
Laceyella sediminis RHA1 lctP, L-LDH
Lacinutrix algicola AKS293 Shew_2731, Shew_2732, lctO, acs
Lacinutrix himadriensis E4-9a lctP, L-LDH
Lacinutrix mariniflava AKS432 Shew_2731, Shew_2732, lctO, acs
Lactobacillus curieae CCTCC M 2011381 lctP, lctO, ackA, pta
Lactobacillus delbrueckii ZN7a-9 larD, lctO, ackA, pta
Lactobacillus hokkaidonensis LOOC260 lctP, lctO, ackA, pta
Lactobacillus oryzae SG293 lctP, L-LDH
Lactobacillus pobuzihii E100301 larD, lctO, ackA, pta
Lactobacillus shenzhenensis LY-73 larD, lctO, ackA, pta
Lactobacillus silagei IWT126 larD, lctO, ackA, pta
Leeuwenhoekiella blandensis MED217 Shew_2731, Shew_2732, L-LDH
Lentibacillus jeotgali Grbi lctP, lutA, lutB, lutC
Limnohabitans curvus MWH-C5 lctP, L-LDH
Limnohabitans parvus II-B4 lctP, lctO, acs
Listeria fleischmannii LU2006-1 lctP, L-LDH
Luteimonas huabeiensis HB2 lctP, L-LDH
Luteipulveratus mongoliensis MN07-A0370 mctP, lctO, ackA, pta
Lutibaculum baratangense AMV1 lctP, lutA, lutB, lutC
Lysobacter daejeonensis GH1-9 lctP, lctO, acs
Magnetovibrio blakemorei MV-1 lctP, L-LDH
Marinicella litoralis KMM 3900 Shew_2731, Shew_2732, lctO, acs
Mariniradius saccharolyticus AK6 Shew_2731, Shew_2732, lldE, lldF, lldG
Marinobacter algicola DG893 Shew_2731, Shew_2732, lutA, lutB, lutC
Marinobacter guineae M3B Shew_2731, Shew_2732, lutA, lutB, lutC
Marinobacter psychrophilus 20041 lctP, L-LDH
Marinomonas arctica 328 Shew_2731, Shew_2732, L-LDH
Marivita geojedonensis DPG-138 Shew_2731, Shew_2732, L-LDH
Martelella endophytica YC6887 lctP, L-LDH
Megamonas funiformis YIT 11815 lctP, L-LDH
Mesorhizobium ciceri WSM1271 lctP, L-LDH
Methanobacterium arcticum M2 lctP, lctO, acs
Methanobacterium veterum MK4 lctP, lctO, acs
Methanocella arvoryzae MRE50 lctP, lctO, acs
Methanococcus aeolicus Nankai-3 lctP, L-LDH
Methanoculleus horonobensis T10 SfMCT, L-LDH
Methanolinea tarda NOBI-1 SfMCT, lctO, acs
Methanosarcina soligelidi SMA-21 lctP, L-LDH
Methanospirillum lacunae Ki8-1 lctP, lctO, acs
Methanospirillum stamsii Pt1 SfMCT, lctO, acs
Methylibium petroleiphilum PM1 lctP, L-LDH
Methylobacterium gossipiicola Gh-105 lctP, lctO, acs
Methylocapsa aurea KYG mctP, L-LDH
Methylotenera versatilis 301 lctP, lctO, acs
Microbacterium profundi Shh49 lctP, lctO, ackA, pta
Microvirga lotononidis WSM3557 lctP, lctO, acs
Moritella dasanensis ArB 0140 Shew_2731, Shew_2732, lutA, lutB, lutC
Mucilaginibacter gossypii Gh-67 larD, lldE, lldF, lldG
Mucilaginibacter gossypiicola Gh-48 larD, lldE, lldF, lldG
Mucilaginibacter mallensis MP1X4 larD, lctO, acs
Nafulsella turpanensis ZLM-10 lctP, L-LDH
Natronomonas moolapensis 8.8.11 lctP, lctO, acs
Nautilia profundicola AmH lctP, L-LDH
Neiella marina J221 Shew_2731, Shew_2732, lctO, ackA, pta
Neptunomonas antarctica S3-22 Shew_2731, Shew_2732, lctO, acs
Nocardioides daejeonensis MJ31 lctP, L-LDH
Nocardioides dokdonensis FR1436 Shew_2731, Shew_2732, lctO, acs
Nocardiopsis baichengensis YIM 90130 lctP, lutA, lutB, lutC
Nocardiopsis gilva YIM 90087 lctP, lctO, ackA, pta
Novosphingobium barchaimii LL02 lctP, lctO, acs
Novosphingobium fuchskuhlense FNE08-7 lctP, L-LDH
Novosphingobium lindaniclasticum LE124 lctP, L-LDH
Oceanisphaera arctica V1-41 lctP, lutA, lutB, lutC
Ochrobactrum rhizosphaerae PR17 lctP, L-LDH
Ochrobactrum thiophenivorans DSM 7216 larD, L-LDH
Oscillibacter ruminantium GH1 lctP, L-LDH
Paenisporosarcina indica PN2 lctP, lutA, lutB, lutC
Palaeococcus pacificus DY20341 lctP, L-LDH
Paludibacter propionicigenes WB4 lctP, lctO, ackA, pta
Pandoraea thiooxydans ATSB16 lctP, lutA, lutB, lutC
Pantoea rwandensis LMG 26275 lctP, L-LDH
Pedobacter arcticus A12 lctP, lldE, lldF, lldG
Photobacterium gaetbulicola Gung47 Shew_2731, Shew_2732, lutA, lutB, lutC
Photobacterium jeanii R-40508 Shew_2731, Shew_2732, lutA, lutB, lutC
Phyllobacterium brassicacearum STM 196 mctP, L-LDH
Phyllobacterium endophyticum PEPV15 lctP, L-LDH
Phyllobacterium leguminum ORS 1419 lctP, L-LDH
Planktomarina temperata RCA23 lctP, L-LDH
Planococcus halocryophilus Or1 SfMCT, L-LDH
Pleomorphomonas diazotrophica R5-392 lctP, lutA, lutB, lutC
Polaribacter dokdonensis DSW-5 lctP, lctO, ackA, pta
Pontibacillus litoralis JSM 072002 lctP, lutA, lutB, lutC
Pontibacter lucknowensis DM9 Shew_2731, Shew_2732, L-LDH
Pontibacter ramchanderi LP43 Shew_2731, Shew_2732, L-LDH
Pontimonas salivibrio CL-TW6 lctP, L-LDH
Porphyrobacter dokdonensis DSW-74 Shew_2731, Shew_2732, lctO, acs
Pseudoalteromonas arctica A 37-1-2 Shew_2731, Shew_2732, lctO, ackA, pta
Pseudomonas baetica a390 lctP, lutA, lutB, lutC
Pseudomonas litoralis 2SM5 Shew_2731, Shew_2732, L-LDH
Pseudomonas taeanensis MS-3 Shew_2731, Shew_2732, L-LDH
Pseudovibrio axinellae Ad2 lctP, L-LDH
Psychrobacter arcticus 273-4 lctP, L-LDH
Psychrobacter cryohalolentis K5 lctP, L-LDH
Psychromonas ingrahamii 37 Shew_2731, Shew_2732, lutA, lutB, lutC
Psychromonas ossibalaenae JAMM 0738 Shew_2731, Shew_2732, lctO, ackA, pta
Rhizobium freirei PRF 81 mctP, lctO, acs
Rhizobium grahamii CCGE 502 mctP, L-LDH
Rhizobium subbaraonis JC85 lctP, L-LDH
Rhodanobacter denitrificans 2APBS1 lctP, lctO, acs
Rhodobacter johrii JA192 Shew_2731, Shew_2732, L-LDH
Rhodobacter maris JA276 Shew_2731, Shew_2732, L-LDH
Rhodobacter ovatus JA234 Shew_2731, Shew_2732, L-LDH
Rhodobacter viridis JA737 lctP, L-LDH
Rhodococcus qingshengii djl-6-2 lctP, L-LDH
Rhodopseudomonas pseudopalustris DSM 123 lctP, L-LDH
Roseateles aquatilis CCUG 48205 lctP, L-LDH
Roseivirga spongicola UST030701-084 lctP, lctO, acs
Rubrivirga marina SAORIC-28 Shew_2731, Shew_2732, L-LDH
Ruegeria conchae TW15 Shew_2731, Shew_2732, L-LDH
Saccharomonospora marina XMU15 Shew_2731, Shew_2732, lctO, acs
Salinicoccus carnicancri Crm lctP, L-LDH
Serinicoccus profundi MCCC 1A05965 lctP, lutA, lutB, lutC
Shewanella halifaxensis HAW-EB4 Shew_2731, Shew_2732, lldE, lldF, lldG
Skermanella stibiiresistens SB22 lctP, lutA, lutB, lutC
Snodgrassella alvi wkB2 lctP, L-LDH
Sphaerochaeta globosa Buddy lctP, lctO, ackA, pta
Sphaerochaeta pleomorpha Grapes lctP, lctO, ackA, pta
Sphingobium baderi LL03 lctP, lctO, acs
Sphingobium czechense LL01 lctP, L-LDH
Sphingobium quisquiliarum P25 lctP, L-LDH
Sphingomonas histidinilytica UM2 lctP, L-LDH
Sphingomonas indica Dd16 lctP, L-LDH
Sphingomonas laterariae LNB2 lctP, L-LDH
Sphingopyxis indica DS15 lctP, lctO, acs
Sphingopyxis terrae UI2 lctP, lctO, acs
Sporolactobacillus vineae SL153 lctP, lutA, lutB, lutC
Streptacidiphilus oryzae TH49 mctP, lctO, acs
Streptococcus anginosus CCUG 39159 lctP, lctO, ackA, pta
Streptococcus massiliensis 4401825 lctP, L-LDH
Streptococcus oralis 7747 lctP, lctO, ackA, pta
Streptococcus oralis AZ_3a lctP, L-LDH
Streptomyces kebangsaanensis SUK12 mctP, lctO, acs
Succinatimonas hippei YIT 12066 lctP, lctO, ackA, pta
Sulfurimonas gotlandica GD1 lctP, L-LDH
Tatumella morbirosei LMG 23360 lctP, L-LDH
Thauera humireducens SgZ-1 lctP, lutA, lutB, lutC
Thermoactinomyces daqus H-18 lctP, lutA, lutB, lutC
Thermobifida halotolerans YIM 90462 lctP, L-LDH
Thermodesulfovibrio aggregans TGE-P1 lctP, DVU3033, DVU3032
Thermophagus xiamenensis HS1 lctP, L-LDH
Thermovenabulum gondwanense R270 lctP, lctO, ackA, pta
Thioclava dalianensis DLFJ1-1 Shew_2731, Shew_2732, L-LDH
Thiohalospira halophila HL 3 lctP, L-LDH
Tistlia consotensis USBA 355 lctP, L-LDH
Vagococcus penaei CD276 larD, L-LDH
Verminephrobacter eiseniae EF01-2 lctP, lctO, acs
Weissella oryzae SG25 larD, lctO, ackA, pta
Williamsia sterculiae CPCC 203464 lctP, lctO, ackA, pta
Yersinia intermedia Y228 lctP, lctO, ackA, pta

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