GapMind for catabolism of small carbon sources

 

succinate catabolism

Analysis of pathway succinate in 276 genomes

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