GapMind for catabolism of small carbon sources

 

L-malate catabolism

Analysis of pathway L-malate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 dctM, dctP, dctQ
Actinokineospora bangkokensis 44EHW dctA
Actinomyces timonensis 7400942 sdlC
Algiphilus aromaticivorans DG1253 sdlC
Algoriphagus aquaeductus T4 sdlC
Algoriphagus machipongonensis PR1 sdlC
Alicyclobacillus ferrooxydans TC-34 dctA
Alishewanella agri BL06 sdlC
Alistipes indistinctus YIT 12060 sdlC
Alistipes shahii WAL 8301 sdlC
Alkalitalea saponilacus SC/BZ-SP2 sdlC
Amantichitinum ursilacus IGB-41 dctA
Amphibacillus jilinensis Y1 sdlC
Amphritea japonica JAMM 1866 dctM, dctP, dctQ
Amycolatopsis halophila YIM 93223 sdlC
Amycolatopsis xylanica CPCC 202699 dctA
Aquimarina agarilytica ZC1 sdlC
Aquimarina longa SW024 sdlC
Aquimarina macrocephali JAMB N27 sdlC
Archaeoglobus sulfaticallidus PM70-1 sdlC
Arcticibacter svalbardensis MN12-7 dctA
Ardenticatena maritima 110S sdlC
Arenimonas metalli CF5-1 sdlC
Arenitalea lutea P7-3-5 sdlC
Azospirillum humicireducens SgZ-5 dctA
Azospirillum thiophilum BV-S dctA
Bacillus altitudinis 41KF2b sdlC
Bacillus coahuilensis m4-4 Dshi_1194, Dshi_1195
Bacillus cytotoxicus NVH 391-98 dctA
Bacillus horneckiae 1P01SC sdlC
Bacillus okhensis Kh10-101 sdlC
Bacillus safensis FO-36b dctA
Bacillus velezensis CBMB205 dctA
Bacteroides clarus YIT 12056 sdlC
Bacteroides faecis MAJ27 sdlC
Bacteroides fluxus YIT 12057 sdlC
Bacteroides oleiciplenus YIT 12058 sdlC
Barnesiella intestinihominis YIT 11860 sdlC
Belnapia rosea CPCC 100156 dctA
Bizionia argentinensis JUB59 sdlC
Bradyrhizobium diazoefficiens USDA110 dctM, dctP, dctQ
Brevibacterium jeotgali SJ5-8 sdlC
Brucella inopinata BO1 sdlC
Brucella microti CCM 4915 sdlC
Bryobacter aggregatus MPL3 dctA
Caldicellulosiruptor hydrothermalis 108 mleP
Caldicellulosiruptor kronotskyensis 2002 mleP
Carboxydothermus pertinax Ug1 dctA
Catellicoccus marimammalium M35/04/3 sdlC
Chromobacterium vaccinii MWU205 dctM, dctP, dctQ
Chryseobacterium angstadtii KM dctA
Chryseobacterium arthrosphaerae CC-VM-7 dctA
Chryseobacterium viscerum 687B-08 dctA
Cloacibacillus porcorum CL-84 sdlC
Cobetia crustatorum JO1 sdlC
Collimonas arenae Ter10 dctA
Collimonas pratensis Ter91 dctA
Collinsella tanakaei YIT 12063 sdlC
Coprobacter fastidiosus NSB1 sdlC
Corynebacterium deserti GIMN1.010 sdlC
Corynebacterium frankenforstense ST18 sdlC
Corynebacterium lactis RW2-5 sdlC
Croceitalea dokdonensis DOKDO 023 sdlC
Cronobacter condimenti 1330 dctA
Cronobacter muytjensii ATCC 51329 dctA
Cronobacter universalis NCTC 9529 dctA
Desulfatitalea tepidiphila S28bF sdlC
Desulfotomaculum hydrothermale Lam5 dctA
Dethiosulfovibrio salsuginis USBA 82 maeN
Devosia chinhatensis IPL18 sdlC
Devriesea agamarum IMP2 sdlC
Dialister succinatiphilus YIT 11850 mleP
Dietzia timorensis ID05-A0528 sdlC
Dokdonella koreensis DS-123 sdlC
Domibacillus robiginosus WS 4628 dctA
Duganella sacchari Sac-22 dctM, dctP, dctQ
Dyadobacter tibetensis Y620-1 dctA
Dyella jiangningensis SBZ3-12 sdlC
Endozoicomonas montiporae CL-33 sdlC
Enterococcus termitis LMG 8895 sdlC
Enterorhabdus caecimuris B7 sdlC
Epibacterium ulvae U95 dctM, dctP, dctQ
Erythrobacter gangjinensis K7-2 sdlC
Erythrobacter marinus HWDM-33 sdlC
Ethanoligenens harbinense YUAN-3 sdlC
Fervidicella metallireducens AeB mleP
Fibrella aestuarina BUZ 2 dctA
Flammeovirga pacifica WPAGA1 sdlC
Flaviramulus ichthyoenteri Th78 sdlC
Flavobacterium beibuense F44-8 sdlC
Flavobacterium glycines Gm-149 sdlC
Flavobacterium sp. LM5 dctA
Flavobacterium ummariense DS-12 dctA
Frischella perrara PEB0191 dctA
Galbibacter marinus ck-I2-15 sdlC
Gallaecimonas xiamenensis 3-C-1 sdlC
Geobacter daltonii FRC-32 sdlC
Gillisia marina CBA3202 sdlC
Gracilibacillus halophilus YIM-C55.5 sdlC
Granulicella mallensis MP5ACTX8 maeN
Granulicella tundricola MP5ACTX9 dctA
Hafnia paralvei ATCC 29927 dctA
Haladaptatus cibarius D43 sdlC
Halioglobus japonicus S1-36 sdlC
Halobacillus alkaliphilus FP5 sdlC
Halococcus hamelinensis 100A6 sdlC
Halomonas salina B6 Dshi_1194, Dshi_1195
Halomonas smyrnensis AAD6 Dshi_1194, Dshi_1195
Halomonas stevensii S18214 Dshi_1194, Dshi_1195
Halomonas titanicae BH1 Dshi_1194, Dshi_1195
Halomonas xinjiangensis TRM 0175 Dshi_1194, Dshi_1195
Halopiger salifodinae KCY07-B2 sdlC
Halostagnicola larsenii XH-48 sdlC
Haloterrigena daqingensis JX313 sdlC
Herbaspirillum aquaticum IEH 4430 dctM, dctP, dctQ
Hippea alviniae EP5-r dctM, dctP, dctQ
Hippea jasoniae Mar08-272r dctM, dctP, dctQ
Hoeflea phototrophica DFL-43 Dshi_1194, Dshi_1195
Hyphomicrobium nitrativorans NL23 dctM, dctP, dctQ
Imtechella halotolerans K1 sdlC
Indibacter alkaliphilus LW1 sdlC
Jannaschia aquimarina GSW-M26 dctM, dctP, dctQ
Jeotgalibacillus soli P9 sdlC
Kangiella geojedonensis YCS-5 sdlC
Knoellia flava TL1 dctA
Kocuria flava HO-9041 sdlC
Kocuria turfanensis HO-9042 sdlC
Laceyella sediminis RHA1 dctA
Lacinutrix algicola AKS293 sdlC
Lacinutrix himadriensis E4-9a sdlC
Lacinutrix mariniflava AKS432 sdlC
Lactobacillus curieae CCTCC M 2011381 dctA
Lactobacillus delbrueckii ZN7a-9 sdlC
Lactobacillus hokkaidonensis LOOC260 mleP
Lactobacillus oryzae SG293 dctA
Lactobacillus pobuzihii E100301 mleP
Lactobacillus shenzhenensis LY-73 mleP
Lactobacillus silagei IWT126 dctA
Leeuwenhoekiella blandensis MED217 sdlC
Lentibacillus jeotgali Grbi sdlC
Limnohabitans curvus MWH-C5 dctA
Limnohabitans parvus II-B4 sdlC
Listeria fleischmannii LU2006-1 sdlC
Luteimonas huabeiensis HB2 dctA
Luteipulveratus mongoliensis MN07-A0370 dctA
Lutibaculum baratangense AMV1 Dshi_1194, Dshi_1195
Lysobacter daejeonensis GH1-9 sdlC
Magnetovibrio blakemorei MV-1 dctM, dctP, dctQ
Marinicella litoralis KMM 3900 sdlC
Mariniradius saccharolyticus AK6 sdlC
Marinobacter algicola DG893 Dshi_1194, Dshi_1195
Marinobacter guineae M3B Dshi_1194, Dshi_1195
Marinobacter psychrophilus 20041 Dshi_1194, Dshi_1195
Marinomonas arctica 328 dctM, dctP, dctQ
Marivita geojedonensis DPG-138 Dshi_1194, Dshi_1195
Martelella endophytica YC6887 sdlC
Megamonas funiformis YIT 11815 sdlC
Mesorhizobium ciceri WSM1271 dctA
Methanobacterium arcticum M2 sdlC
Methanobacterium veterum MK4 sdlC
Methanocella arvoryzae MRE50 sdlC
Methanococcus aeolicus Nankai-3 sdlC
Methanoculleus horonobensis T10 sdlC
Methanolinea tarda NOBI-1 sdlC
Methanosarcina soligelidi SMA-21 sdlC
Methanospirillum lacunae Ki8-1 sdlC
Methanospirillum stamsii Pt1 sdlC
Methylibium petroleiphilum PM1 dctA
Methylobacterium gossipiicola Gh-105 dctA
Methylocapsa aurea KYG dctA
Methylotenera versatilis 301 sdlC
Microbacterium profundi Shh49 dctA
Microvirga lotononidis WSM3557 dctA
Moritella dasanensis ArB 0140 dctM, dctP, dctQ
Mucilaginibacter gossypii Gh-67 dctA
Mucilaginibacter gossypiicola Gh-48 dctA
Mucilaginibacter mallensis MP1X4 dctA
Nafulsella turpanensis ZLM-10 sdlC
Natronomonas moolapensis 8.8.11 sdlC
Nautilia profundicola AmH dctM, dctP, dctQ
Neiella marina J221 sdlC
Neptunomonas antarctica S3-22 dctM, dctP, dctQ
Nocardioides daejeonensis MJ31 sdlC
Nocardioides dokdonensis FR1436 sdlC
Nocardiopsis baichengensis YIM 90130 sdlC
Nocardiopsis gilva YIM 90087 sdlC
Novosphingobium barchaimii LL02 dctA
Novosphingobium fuchskuhlense FNE08-7 sdlC
Novosphingobium lindaniclasticum LE124 dctA
Oceanisphaera arctica V1-41 sdlC
Ochrobactrum rhizosphaerae PR17 dctA
Ochrobactrum thiophenivorans DSM 7216 dctA
Oscillibacter ruminantium GH1 Dshi_1194, Dshi_1195
Paenisporosarcina indica PN2 dctA
Palaeococcus pacificus DY20341 sdlC
Paludibacter propionicigenes WB4 sdlC
Pandoraea thiooxydans ATSB16 dctA
Pantoea rwandensis LMG 26275 dctA
Pedobacter arcticus A12 sdlC
Photobacterium gaetbulicola Gung47 sdlC
Photobacterium jeanii R-40508 sdlC
Phyllobacterium brassicacearum STM 196 dctA
Phyllobacterium endophyticum PEPV15 dctA
Phyllobacterium leguminum ORS 1419 sdlC
Planktomarina temperata RCA23 dctM, dctP, dctQ
Planococcus halocryophilus Or1 maeN
Pleomorphomonas diazotrophica R5-392 maeN
Polaribacter dokdonensis DSW-5 sdlC
Pontibacillus litoralis JSM 072002 sdlC
Pontibacter lucknowensis DM9 dctA
Pontibacter ramchanderi LP43 dctA
Pontimonas salivibrio CL-TW6 sdlC
Porphyrobacter dokdonensis DSW-74 dctA
Pseudoalteromonas arctica A 37-1-2 sdlC
Pseudomonas baetica a390 dctA
Pseudomonas litoralis 2SM5 sdlC
Pseudomonas taeanensis MS-3 dctM, dctP, dctQ
Pseudovibrio axinellae Ad2 dctM, dctP, dctQ
Psychrobacter arcticus 273-4 sdlC
Psychrobacter cryohalolentis K5 sdlC
Psychromonas ingrahamii 37 dctM, dctP, dctQ
Psychromonas ossibalaenae JAMM 0738 dctM, dctP, dctQ
Rhizobium freirei PRF 81 dctA
Rhizobium grahamii CCGE 502 dctA
Rhizobium subbaraonis JC85 dctA
Rhodanobacter denitrificans 2APBS1 sdlC
Rhodobacter johrii JA192 dctM, dctP, dctQ
Rhodobacter maris JA276 dctM, dctP, dctQ
Rhodobacter ovatus JA234 sdlC
Rhodobacter viridis JA737 dctM, dctP, dctQ
Rhodococcus qingshengii djl-6-2 dctA
Rhodopseudomonas pseudopalustris DSM 123 dctM, dctP, dctQ
Roseateles aquatilis CCUG 48205 dctM, dctP, dctQ
Roseivirga spongicola UST030701-084 sdlC
Rubrivirga marina SAORIC-28 sdlC
Ruegeria conchae TW15 dctM, dctP, dctQ
Saccharomonospora marina XMU15 sdlC
Salinicoccus carnicancri Crm sdlC
Serinicoccus profundi MCCC 1A05965 sdlC
Shewanella halifaxensis HAW-EB4 sdlC
Skermanella stibiiresistens SB22 sdlC
Snodgrassella alvi wkB2 dctA
Sphaerochaeta globosa Buddy sdlC
Sphaerochaeta pleomorpha Grapes mleP
Sphingobium baderi LL03 dctA
Sphingobium czechense LL01 dctA
Sphingobium quisquiliarum P25 dctA
Sphingomonas histidinilytica UM2 dctA
Sphingomonas indica Dd16 dctA
Sphingomonas laterariae LNB2 dctA
Sphingopyxis indica DS15 dctA
Sphingopyxis terrae UI2 dctA
Sporolactobacillus vineae SL153 dctA
Streptacidiphilus oryzae TH49 dctA
Streptococcus anginosus CCUG 39159 sdlC
Streptococcus massiliensis 4401825 maeN
Streptococcus oralis 7747 sdlC
Streptococcus oralis AZ_3a sdlC
Streptomyces kebangsaanensis SUK12 dctA
Succinatimonas hippei YIT 12066 sdlC
Sulfurimonas gotlandica GD1 sdlC
Tatumella morbirosei LMG 23360 dctA
Thauera humireducens SgZ-1 dctM, dctP, dctQ
Thermoactinomyces daqus H-18 dctA
Thermobifida halotolerans YIM 90462 sdlC
Thermodesulfovibrio aggregans TGE-P1 sdlC
Thermophagus xiamenensis HS1 sdlC
Thermovenabulum gondwanense R270 dctM, dctP, dctQ
Thioclava dalianensis DLFJ1-1 dctM, dctP, dctQ
Thiohalospira halophila HL 3 sdlC
Tistlia consotensis USBA 355 dctM, dctP, dctQ
Vagococcus penaei CD276 maeN
Verminephrobacter eiseniae EF01-2 dctA
Weissella oryzae SG25 mleP
Williamsia sterculiae CPCC 203464 dctA
Yersinia intermedia Y228 dctA

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