GapMind for catabolism of small carbon sources

 

fumarate catabolism

Analysis of pathway fumarate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 dctM, dctP, dctQ
Actinokineospora bangkokensis 44EHW dctA
Actinomyces timonensis 7400942 dctA
Algiphilus aromaticivorans DG1253 sdcL
Algoriphagus aquaeductus T4 sdcL
Algoriphagus machipongonensis PR1 sdcL
Alicyclobacillus ferrooxydans TC-34 SLC26dg
Alishewanella agri BL06 sdcL
Alistipes indistinctus YIT 12060 dctA
Alistipes shahii WAL 8301 dctA
Alkalitalea saponilacus SC/BZ-SP2 sdcL
Amantichitinum ursilacus IGB-41 dctA
Amphibacillus jilinensis Y1 SLC26dg
Amphritea japonica JAMM 1866 dctM, dctP, dctQ
Amycolatopsis halophila YIM 93223 sdcL
Amycolatopsis xylanica CPCC 202699 dctA
Aquimarina agarilytica ZC1 SLC26dg
Aquimarina longa SW024 sdcL
Aquimarina macrocephali JAMB N27 sdcL
Archaeoglobus sulfaticallidus PM70-1 sdcL
Arcticibacter svalbardensis MN12-7 SLC26dg
Ardenticatena maritima 110S dctA
Arenimonas metalli CF5-1 SLC26dg
Arenitalea lutea P7-3-5 sdcL
Azospirillum humicireducens SgZ-5 dctA
Azospirillum thiophilum BV-S dctA
Bacillus altitudinis 41KF2b dctA
Bacillus coahuilensis m4-4 Dshi_1194, Dshi_1195
Bacillus cytotoxicus NVH 391-98 dctA
Bacillus horneckiae 1P01SC dctA
Bacillus okhensis Kh10-101 sdcL
Bacillus safensis FO-36b dctA
Bacillus velezensis CBMB205 dctA
Bacteroides clarus YIT 12056 dauA
Bacteroides faecis MAJ27 dauA
Bacteroides fluxus YIT 12057 sdcL
Bacteroides oleiciplenus YIT 12058 dauA
Barnesiella intestinihominis YIT 11860 dauA
Belnapia rosea CPCC 100156 dctA
Bizionia argentinensis JUB59 SLC26dg
Bradyrhizobium diazoefficiens USDA110 dctM, dctP, dctQ
Brevibacterium jeotgali SJ5-8 SLC26dg
Brucella inopinata BO1 dctA
Brucella microti CCM 4915 dctA
Bryobacter aggregatus MPL3 dctA
Caldicellulosiruptor hydrothermalis 108 dctA
Caldicellulosiruptor kronotskyensis 2002 dctA
Carboxydothermus pertinax Ug1 dctA
Catellicoccus marimammalium M35/04/3 dctA
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 dauA
Cobetia crustatorum JO1 sdcL
Collimonas arenae Ter10 dctA
Collimonas pratensis Ter91 dctA
Collinsella tanakaei YIT 12063 dauA
Coprobacter fastidiosus NSB1 dauA
Corynebacterium deserti GIMN1.010 dctA
Corynebacterium frankenforstense ST18 sdcL
Corynebacterium lactis RW2-5 dctA
Croceitalea dokdonensis DOKDO 023 sdcL
Cronobacter condimenti 1330 dctA
Cronobacter muytjensii ATCC 51329 dctA
Cronobacter universalis NCTC 9529 dctA
Desulfatitalea tepidiphila S28bF dctA
Desulfotomaculum hydrothermale Lam5 dctA
Dethiosulfovibrio salsuginis USBA 82 dctA
Devosia chinhatensis IPL18 SLC26dg
Devriesea agamarum IMP2 dctA
Dialister succinatiphilus YIT 11850 dctA
Dietzia timorensis ID05-A0528 dctA
Dokdonella koreensis DS-123 dauA
Domibacillus robiginosus WS 4628 dctA
Duganella sacchari Sac-22 dctM, dctP, dctQ
Dyadobacter tibetensis Y620-1 dctA
Dyella jiangningensis SBZ3-12 dctA
Endozoicomonas montiporae CL-33 sdcL
Enterococcus termitis LMG 8895 dctA
Enterorhabdus caecimuris B7 dauA
Epibacterium ulvae U95 dctM, dctP, dctQ
Erythrobacter gangjinensis K7-2 SLC26dg
Erythrobacter marinus HWDM-33 sdcL
Ethanoligenens harbinense YUAN-3 dctA
Fervidicella metallireducens AeB dctA
Fibrella aestuarina BUZ 2 dctA
Flammeovirga pacifica WPAGA1 SLC26dg
Flaviramulus ichthyoenteri Th78 SLC26dg
Flavobacterium beibuense F44-8 sdcL
Flavobacterium glycines Gm-149 SLC26dg
Flavobacterium sp. LM5 dctA
Flavobacterium ummariense DS-12 SLC26dg
Frischella perrara PEB0191 dauA
Galbibacter marinus ck-I2-15 sdcL
Gallaecimonas xiamenensis 3-C-1 sdcL
Geobacter daltonii FRC-32 sdcL
Gillisia marina CBA3202 sdcL
Gracilibacillus halophilus YIM-C55.5 dctA
Granulicella mallensis MP5ACTX8 SLC26dg
Granulicella tundricola MP5ACTX9 dctA
Hafnia paralvei ATCC 29927 dctA
Haladaptatus cibarius D43 dctA
Halioglobus japonicus S1-36 SLC26dg
Halobacillus alkaliphilus FP5 sdcL
Halococcus hamelinensis 100A6 sdcL
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 sdcL
Halostagnicola larsenii XH-48 dctA
Haloterrigena daqingensis JX313 sdcL
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 sdcL
Indibacter alkaliphilus LW1 sdcL
Jannaschia aquimarina GSW-M26 dctM, dctP, dctQ
Jeotgalibacillus soli P9 sdcL
Kangiella geojedonensis YCS-5 dctA
Knoellia flava TL1 dctA
Kocuria flava HO-9041 dctA
Kocuria turfanensis HO-9042 dctA
Laceyella sediminis RHA1 dctA
Lacinutrix algicola AKS293 SLC26dg
Lacinutrix himadriensis E4-9a SLC26dg
Lacinutrix mariniflava AKS432 SLC26dg
Lactobacillus curieae CCTCC M 2011381 dctA
Lactobacillus delbrueckii ZN7a-9 dctA
Lactobacillus hokkaidonensis LOOC260 dctA
Lactobacillus oryzae SG293 dctA
Lactobacillus pobuzihii E100301 dctA
Lactobacillus shenzhenensis LY-73 dctA
Lactobacillus silagei IWT126 dctA
Leeuwenhoekiella blandensis MED217 sdcL
Lentibacillus jeotgali Grbi sdcL
Limnohabitans curvus MWH-C5 dctA
Limnohabitans parvus II-B4 dauA
Listeria fleischmannii LU2006-1 dctA
Luteimonas huabeiensis HB2 dctA
Luteipulveratus mongoliensis MN07-A0370 dctA
Lutibaculum baratangense AMV1 Dshi_1194, Dshi_1195
Lysobacter daejeonensis GH1-9 SLC26dg
Magnetovibrio blakemorei MV-1 dauA
Marinicella litoralis KMM 3900 SLC26dg
Mariniradius saccharolyticus AK6 sdcL
Marinobacter algicola DG893 Dshi_1194, Dshi_1195
Marinobacter guineae M3B Dshi_1194, Dshi_1195
Marinobacter psychrophilus 20041 Dshi_1194, Dshi_1195
Marinomonas arctica 328 SLC26dg
Marivita geojedonensis DPG-138 Dshi_1194, Dshi_1195
Martelella endophytica YC6887 SLC26dg
Megamonas funiformis YIT 11815 dctA
Mesorhizobium ciceri WSM1271 dctA
Methanobacterium arcticum M2 sdcL
Methanobacterium veterum MK4 sdcL
Methanocella arvoryzae MRE50 dctA
Methanococcus aeolicus Nankai-3 SLC26dg
Methanoculleus horonobensis T10 sdcL
Methanolinea tarda NOBI-1 dctA
Methanosarcina soligelidi SMA-21 dctA
Methanospirillum lacunae Ki8-1 dctA
Methanospirillum stamsii Pt1 sdcL
Methylibium petroleiphilum PM1 dctA
Methylobacterium gossipiicola Gh-105 dctA
Methylocapsa aurea KYG dctA
Methylotenera versatilis 301 dauA
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 sdcL
Natronomonas moolapensis 8.8.11 dctA
Nautilia profundicola AmH SLC26dg
Neiella marina J221 sdcL
Neptunomonas antarctica S3-22 dctM, dctP, dctQ
Nocardioides daejeonensis MJ31 SLC26dg
Nocardioides dokdonensis FR1436 sdcL
Nocardiopsis baichengensis YIM 90130 sdcL
Nocardiopsis gilva YIM 90087 sdcL
Novosphingobium barchaimii LL02 dctA
Novosphingobium fuchskuhlense FNE08-7 sdcL
Novosphingobium lindaniclasticum LE124 dctA
Oceanisphaera arctica V1-41 sdcL
Ochrobactrum rhizosphaerae PR17 dctA
Ochrobactrum thiophenivorans DSM 7216 dctA
Oscillibacter ruminantium GH1 dauA
Paenisporosarcina indica PN2 dctA
Palaeococcus pacificus DY20341 dctA
Paludibacter propionicigenes WB4 dauA
Pandoraea thiooxydans ATSB16 dctA
Pantoea rwandensis LMG 26275 dctA
Pedobacter arcticus A12 sdcL
Photobacterium gaetbulicola Gung47 sdcL
Photobacterium jeanii R-40508 sdcL
Phyllobacterium brassicacearum STM 196 dctA
Phyllobacterium endophyticum PEPV15 dctA
Phyllobacterium leguminum ORS 1419 SLC26dg
Planktomarina temperata RCA23 dctM, dctP, dctQ
Planococcus halocryophilus Or1 SLC26dg
Pleomorphomonas diazotrophica R5-392 dctA
Polaribacter dokdonensis DSW-5 sdcL
Pontibacillus litoralis JSM 072002 sdcL
Pontibacter lucknowensis DM9 dctA
Pontibacter ramchanderi LP43 dctA
Pontimonas salivibrio CL-TW6 SLC26dg
Porphyrobacter dokdonensis DSW-74 dctA
Pseudoalteromonas arctica A 37-1-2 sdcL
Pseudomonas baetica a390 dctA
Pseudomonas litoralis 2SM5 sdcL
Pseudomonas taeanensis MS-3 SLC26dg
Pseudovibrio axinellae Ad2 SLC26dg
Psychrobacter arcticus 273-4 sdcL
Psychrobacter cryohalolentis K5 sdcL
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 dctA
Rhodobacter johrii JA192 dctM, dctP, dctQ
Rhodobacter maris JA276 dctM, dctP, dctQ
Rhodobacter ovatus JA234 dctA
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 sdcL
Rubrivirga marina SAORIC-28 sdcL
Ruegeria conchae TW15 dctM, dctP, dctQ
Saccharomonospora marina XMU15 sdcL
Salinicoccus carnicancri Crm sdcL
Serinicoccus profundi MCCC 1A05965 sdcL
Shewanella halifaxensis HAW-EB4 sdcL
Skermanella stibiiresistens SB22 dctA
Snodgrassella alvi wkB2 dctA
Sphaerochaeta globosa Buddy dauA
Sphaerochaeta pleomorpha Grapes dauA
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 dctA
Streptococcus massiliensis 4401825 dctA
Streptococcus oralis 7747 dctA
Streptococcus oralis AZ_3a dctA
Streptomyces kebangsaanensis SUK12 dctA
Succinatimonas hippei YIT 12066 dauA
Sulfurimonas gotlandica GD1 SLC26dg
Tatumella morbirosei LMG 23360 dctA
Thauera humireducens SgZ-1 dctM, dctP, dctQ
Thermoactinomyces daqus H-18 dctA
Thermobifida halotolerans YIM 90462 SLC26dg
Thermodesulfovibrio aggregans TGE-P1 dctA
Thermophagus xiamenensis HS1 dctA
Thermovenabulum gondwanense R270 dctM, dctP, dctQ
Thioclava dalianensis DLFJ1-1 dctM, dctP, dctQ
Thiohalospira halophila HL 3 dauA
Tistlia consotensis USBA 355 SLC26dg
Vagococcus penaei CD276 SLC26dg
Verminephrobacter eiseniae EF01-2 dctA
Weissella oryzae SG25 dctA
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