GapMind for catabolism of small carbon sources


succinate catabolism

Analysis of pathway succinate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 sdc
Acidithiobacillus ferrooxidans ATCC 23270 sdc
Acidovorax sp. GW101-3H11 dctA
Algiphilus aromaticivorans DG1253 sdc
Alicycliphilus denitrificans K601 dctA
Alkalihalobacterium alkalinitrilicum DSM 22532 sdc
Allochromatium vinosum DSM 180 dctQ, dctM, dctP
Ammonifex degensii KC4 sdc
Anaerobutyricum hallii DSM 3353 sdc
Aquimarina longa SW024 sdc
Archaeoglobus veneficus SNP6 sdc
Arcobacter nitrofigilis DSM 7299 sdc
Azoarcus olearius BH72 dctQ, dctM, dctP
Azohydromonas australica DSM 1124 dctA
Azorhizobium caulinodans ORS 571 dctA
Azospirillum brasilense Sp245 dctA
Azospirillum sp. B510 dctA
Bacteroides thetaiotaomicron VPI-5482 sdc
Beijerinckia indica ATCC 9039 dctA
Beijerinckia mobilis UQM 1969 dctA
Billgrantia desiderata SP1 Dshi_1194, Dshi_1195
Bradyrhizobium sp. BTAi1 dctQ, dctM, dctP
Brevundimonas sp. GW460-12-10-14-LB2 dctA
Burkholderia phytofirmans PsJN dctA
Burkholderia vietnamiensis G4 dctA
Calditerrivibrio nitroreducens DSM 19672 satP
Caminibacter mediatlanticus TB-2 dctQ, dctM, dctP
Carboxydothermus pertinax Ug1 dctA
Caulobacter crescentus NA1000 dctA
Cereibacter sphaeroides ATCC 17029 dctQ, dctM, dctP
Chlorobaculum parvum NCIB 8327 dauA
Chlorobaculum tepidum TLS dauA
Chlorobium limicola DSM 245 dauA
Chlorobium phaeobacteroides BS1 sdc
Clostridium acetobutylicum ATCC 824 dctA
Clostridium kluyveri DSM 555 sdc
Clostridium tyrobutyricum FAM22553 dctA
Crocosphaera subtropica ATCC 51142 sdc
Cupriavidus basilensis FW507-4G11 dctA
Dechloromonas agitata is5 dctQ, dctM, dctP
Dechlorosoma suillum PS dctQ, dctM, dctP
Dehalococcoides mccartyi 195 sdc
Denitrovibrio acetiphilus DSM 12809 satP
Derxia gummosa DSM 723 dctQ, dctM, dctP
Desulfacinum hydrothermale DSM 13146 satP
Desulfacinum infernum DSM 9756 sdc
Desulfarculus baarsii DSM 2075 sdc
Desulfatibacillum aliphaticivorans DSM 15576 satP
Desulfatiglans anilini DSM 4660 satP
Desulfitobacterium hafniense DCB-2 sdc
Desulfobacca acetoxidans DSM 11109 sdc
Desulfobacter vibrioformis DSM 8776 satP
Desulfogranum mediterraneum DSM 13871 dctQ, dctM, dctP
Desulforamulus ruminis DSM 2154 dctA
Desulfoscipio geothermicus DSM 3669 Dshi_1194, Dshi_1195
Desulfotalea psychrophila LSv54 sdc
Desulfovibrio oxyclinae DSM 11498 sdc
Desulfovibrio vulgaris Hildenborough JW710 dauA
Desulfovibrio vulgaris Miyazaki F dauA
Desulfurobacterium atlanticum DSM 15668 sdc
Desulfuromonas acetexigens satP
Desulfuromusa kysingii DSM 7343 dctQ, dctM, dctP
Dinoroseobacter shibae DFL-12 Dshi_1194, Dshi_1195
Dyella japonica UNC79MFTsu3.2 dctA
Echinicola vietnamensis KMM 6221, DSM 17526 sdc
Escherichia coli BW25113 dctA
Ferroglobus placidus DSM 10642 sdc
Frankia alni ACN14a dctA
Geobacter metallireducens GS-15 satP
Geotalea uraniireducens Rf4 dctQ, dctM, dctP
Halococcus hamelinensis 100A6 satP
Haloechinothrix alba DSM 45207 sdc
Haloferax volcanii DS2 sdc
Haloglycomyces albus DSM 45210 dauA
Halorhodospira halophila SL1 Dshi_1194, Dshi_1195
Heliomicrobium modesticaldum Ice1; ATCC 51547 satP
Herbaspirillum autotrophicum IAM 14942 dctQ, dctM, dctP
Herbaspirillum seropedicae SmR1 dctQ, dctM, dctP
Hippea alviniae EP5-r satP
Hydrogenophaga taeniospiralis NBRC 102512 sdc
Hydrogenovibrio halophilus DSM 15072 sdc
Hydrogenovibrio kuenenii DSM 12350 dauA
Hydrogenovibrio marinus DSM 11271 dauA
Hyphomicrobium sulfonivorans WDL6 dctA
Klebsiella michiganensis M5al sdc
Klebsiella variicola At-22 dctA
Kyrpidia tusciae DSM 2912 sdc
Leptospirillum ferrooxidans C2-3 sdc
Magnetospirillum magneticum AMB-1 dctQ, dctM, dctP
Malonomonas rubra DSM 5091 sdc
Maridesulfovibrio bastinii DSM 16055 sdc
Maridesulfovibrio zosterae DSM 11974 sdc
Marinobacter adhaerens HP15 Dshi_1194, Dshi_1195
Mesorhizobium ciceri WSM1271 dctA
Methanobacterium lacus AL-21 satP
Methanococcus aeolicus Nankai-3 sdc
Methanococcus maripaludis C5 satP
Methanosarcina acetivorans C2A satP
Methanosarcina mazei Go1 satP
Methanospirillum lacunae Ki8-1 satP
Methanothermobacter thermautotrophicus Delta H satP
Methylobacterium nodulans ORS 2060 dctQ, dctM, dctP
Methylobacterium sp. 4-46 Apr-46 dctQ, dctM, dctP
Methylocapsa acidiphila B2 dctA
Methylocapsa aurea KYG dctA
Methylocella silvestris BL2 dctA
Methylococcus capsulatus Bath dctA
Methylocystis bryophila S285 dctA
Methyloferula stellata AR4T dctA
Methylohalobius crimeensis 10Ki sdc
Methylomonas methanica MC09 dctA
Methylosarcina fibrata AML-C10 sdc
Methylotuvimicrobium alcaliphilum 20Z sdc
Methylovulum miyakonense HT12 dctA
Mycolicibacterium vanbaalenii PYR-1 dctA
Nitratifractor salsuginis DSM 16511 satP
Nitratiruptor tergarcus DSM 16512 sdc
Nitriliruptor alkaliphilus DSM 45188 sdc
Nocardioides dokdonensis FR1436 sdc
Nocardiopsis lucentensis DSM 44048 sdc
Nostoc punctiforme ATCC 29133; PCC 73102 dauA
Novosphingobium aromaticivorans DSM 12444 sdc
Oleispira antarctica sdc
Paraburkholderia atlantica CCGE1002 dctA
Paraburkholderia bryophila 376MFSha3.1 dctA
Paraburkholderia phymatum STM815 dctA
Paucidesulfovibrio gracilis DSM 16080 sdc
Pedobacter sp. GW460-11-11-14-LB5 dctA
Pelobacter propionicus DSM 2379 satP
Persephonella marina EX-H1 sdc
Phaeacidiphilus oryzae TH49 dctA
Phaeobacter inhibens BS107 dctQ, dctM, dctP
Polaromonas naphthalenivorans CJ2 dctA
Prosthecochloris aestuarii DSM 271 dauA
Pseudarthrobacter sulfonivorans Ar51 dctA
Pseudomonas benzenivorans DSM 8628 dctQ, dctM, dctP
Pseudomonas fluorescens FW300-N1B4 dctA
Pseudomonas fluorescens FW300-N2C3 dctA
Pseudomonas fluorescens FW300-N2E2 dctA
Pseudomonas fluorescens FW300-N2E3 dctA
Pseudomonas fluorescens GW456-L13 dctA
Pseudomonas putida KT2440 dctA
Pseudomonas simiae WCS417 dctQ, dctM, dctP
Pseudomonas stutzeri RCH2 dctQ, dctM, dctP
Pyrolobus fumarii 1A sdc
Rhizobium etli CFN 42 dctA
Rhizobium johnstonii 3841 dctA
Rhizobium leguminosarum WSM1325 dctA
Rhizorhabdus wittichii RW1 dctA
Rhodanobacter denitrificans FW104-10B01 sdc
Rhodomicrobium vannielii ATCC 17100 dctA
Rhodopseudomonas palustris CGA009 dctQ, dctM, dctP
Rhodospirillum centenum SW; ATCC 51521 sdc
Rhodospirillum rubrum ATCC 11170 dctQ, dctM, dctP
Roseburia faecis M72 sdc
Saccharomonospora cyanea NA-134 sdc
Sedimenticola selenatireducens DSM 17993 dctQ, dctM, dctP
Shewanella amazonensis SB2B dctQ, dctM, dctP
Shewanella loihica PV-4 dctQ, dctM, dctP
Shewanella oneidensis MR-1 dctQ, dctM, dctP
Shewanella sp. ANA-3 dctQ, dctM, dctP
Sinorhizobium fredii NGR234 dctA
Sinorhizobium medicae WSM419 dctA
Sinorhizobium meliloti 1021 dctA
Sphingomonas koreensis DSMZ 15582 dctA
Stenotrophomonas chelatiphaga DSM 21508 dctA
Steroidobacter denitrificans DSM 18526 dauA
Stutzerimonas stutzeri A1501 dctQ, dctM, dctP
Sulfuricurvum kujiense DSM 16994 dauA
Sulfurihydrogenibium azorense Az-Fu1 sdc
Sulfurihydrogenibium subterraneum DSM 15120 sdc
Sulfurimonas denitrificans DSM 1251 sdc
Sulfuritalea hydrogenivorans DSM 22779 dctQ, dctM, dctP
Sulfurivirga caldicuralii DSM 17737 sdc
Synechococcus elongatus PCC 7942 sdc
Teredinibacter turnerae T7901 sdc
Thauera aminoaromatica S2 dctQ, dctM, dctP
Thermithiobacillus tepidarius DSM 3134 dauA
Thermocrinis albus DSM 14484 sdc
Thermodesulforhabdus norvegica DSM 9990 sdc
Thermomonospora curvata DSM 43183 sdc
Thermovibrio ammonificans HB-1 sdc
Thermus aquaticus YT-1 sdc
Thioalkalivibrio denitrificans ALJD sdc
Thioalkalivibrio halophilus HL17 sdc
Thioalkalivibrio paradoxus ARh 1 Dshi_1194, Dshi_1195
Thioalkalivibrio thiocyanodenitrificans ARhD 1 sdc
Thiohalomonas denitrificans HLD2 satP
Thiohalospira halophila HL 3 dauA
Thiomicrorhabdus arctica DSM 13458 sdc
Thiomicrorhabdus chilensis DSM 12352 sdc
Thiomicrospira cyclica ALM1 dauA
Thiomicrospira microaerophila ASL8-2 dauA
Thiomicrospira pelophila DSM 1534 sdc
Thiothrix lacustris DSM 21227 dctQ, dctM, dctP
Tistlia consotensis USBA 355 dctQ, dctM, dctP
Trichlorobacter lovleyi SZ dctQ, dctM, dctP
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome sdc
Trichormus variabilis ATCC 29413 sdc
Xanthobacter autotrophicus Py2 dctA
Xenophilus azovorans DSM 13620 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 Apr 09 2024. 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