succinate catabolism
Analysis of pathway succinate in 150 genomes
| Genome | Best path |
|---|
| Acidimicrobium ferrooxidans DSM 10331 | sdc |
| Acidithiobacillus ferrooxidans ATCC 23270 | sdc |
| Alicycliphilus denitrificans K601 | dctA |
| Allochromatium vinosum DSM 180 | dctQ, dctM, dctP |
| Ammonifex degensii KC4 | sdc |
| Archaeoglobus veneficus SNP6 | sdc |
| Arcobacter nitrofigilis DSM 7299 | sdc |
| Azoarcus sp. BH72 | dctQ, dctM, dctP |
| Azohydromonas australica DSM 1124 | dctA |
| Azorhizobium caulinodans ORS 571 | dctA |
| Azospirillum lipoferum B510 | dctA |
| Bacillus alkalinitrilicus DSM 22532 | sdc |
| Beijerinckia indica ATCC 9039 | dctA |
| Beijerinckia mobilis UQM 1969 | dctA |
| Bradyrhizobium sp. BTAi1 | dctQ, dctM, dctP |
| Burkholderia vietnamiensis G4 | dctA |
| Calditerrivibrio nitroreducens DSM 19672 | satP |
| Caminibacter mediatlanticus TB-2 | 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 |
| Crocosphaera subtropica ATCC 51142 | sdc |
| Dechloromonas agitata is5 | 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 |
| Desulfallas geothermicus DSM 3669 | Dshi_1194, Dshi_1195 |
| 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 |
| Desulfobulbus mediterraneus DSM 13871 | dctQ, dctM, dctP |
| Desulfotalea psychrophila LSv54 | sdc |
| Desulfotomaculum ruminis DSM 2154 | dctA |
| Desulfovibrio bastinii DSM 16055 | sdc |
| Desulfovibrio gracilis DSM 16080 | sdc |
| Desulfovibrio oxyclinae DSM 11498 | sdc |
| Desulfovibrio zosterae DSM 11974 | sdc |
| Desulfurobacterium atlanticum DSM 15668 | sdc |
| Desulfuromonas acetexigens | satP |
| Desulfuromusa kysingii DSM 7343 | dctQ, dctM, dctP |
| Ferroglobus placidus DSM 10642 | sdc |
| Frankia alni ACN14A | dctA |
| Geobacter lovleyi SZ | dctQ, dctM, dctP |
| Geobacter metallireducens GS-15 | satP |
| Geobacter uraniireducens Rf4 | dctQ, dctM, dctP |
| Haloechinothrix alba DSM 45207 | sdc |
| Haloglycomyces albus DSM 45210 | dauA |
| Halomonas desiderata SP1 | Dshi_1194, Dshi_1195 |
| Halorhodospira halophila SL1 | Dshi_1194, Dshi_1195 |
| Heliobacterium modesticaldum Ice1; ATCC 51547 | satP |
| Herbaspirillum autotrophicum IAM 14942 | dctQ, dctM, dctP |
| 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 variicola At-22 | dctA |
| Kyrpidia tusciae DSM 2912 | sdc |
| Leptospirillum ferrooxidans C2-3 | sdc |
| Malonomonas rubra DSM 5091 | sdc |
| Mesorhizobium ciceri WSM1271 | dctA |
| Methanobacterium lacus AL-21 | satP |
| Methanococcus aeolicus Nankai-3 | sdc |
| Methanococcus maripaludis C5 | satP |
| Methanosarcina acetivorans C2A | satP |
| Methanosarcina barkeri Fusaro | satP |
| Methanosarcina mazei Go1 | satP |
| Methanothermobacter thermautotrophicus Delta H | satP |
| Methylobacterium nodulans ORS 2060 | dctQ, dctM, dctP |
| Methylobacterium sp. 4-46 | dctQ, dctM, dctP |
| Methylocapsa acidiphila B2 | dctA |
| Methylocapsa aurea KYG T | dctA |
| Methylocella silvestris BL2 | dctA |
| Methylococcus capsulatus Bath | dctA |
| Methylocystis bryophila S285 | dctA |
| Methyloferula stellata AR4T | dctA |
| Methylohalobius crimeensis 10Ki | sdc |
| Methylomicrobium alcaliphilum 20Z | sdc |
| Methylomonas methanica MC09 | dctA |
| Methylosarcina fibrata AML-C10 | 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 |
| Nocardiopsis lucentensis DSM 44048 | sdc |
| Nostoc punctiforme ATCC 29133; PCC 73102 | dauA |
| Novosphingobium aromaticivorans DSM 12444 | sdc |
| Oleispira antarctica | sdc |
| Paraburkholderia phymatum STM815 | dctA |
| Paraburkholderia sp. CCGE1002 | dctA |
| Pelobacter propionicus DSM 2379 | satP |
| Persephonella marina EX-H1 | sdc |
| Polaromonas naphthalenivorans CJ2 | dctA |
| Prosthecochloris aestuarii DSM 271 | dauA |
| Pseudarthrobacter sulfonivorans Ar51 | dctA |
| Pseudomonas benzenivorans DSM 8628 | dctQ, dctM, dctP |
| Pseudomonas stutzeri A1501 | dctQ, dctM, dctP |
| Pyrolobus fumarii 1A | sdc |
| Rhizobium etli CFN 42 | dctA |
| Rhizobium leguminosarum 3841 | dctA |
| Rhizobium leguminosarum WSM1325 | dctA |
| Rhodobacter sphaeroides ATCC 17029 | dctQ, dctM, dctP |
| Rhodomicrobium vannielii ATCC 17100 | dctA |
| Rhodopseudomonas palustris CGA009 | dctQ, dctM, dctP |
| Rhodospirillum centenum SW; ATCC 51521 | sdc |
| Rhodospirillum rubrum ATCC 11170 | dctQ, dctM, dctP |
| Saccharomonospora cyanea NA-134 | sdc |
| Sedimenticola selenatireducens DSM 17993 | dctQ, dctM, dctP |
| Sinorhizobium fredii NGR234 | dctA |
| Sinorhizobium medicae WSM419 | dctA |
| Sphingomonas wittichii RW1 | dctA |
| Stenotrophomonas chelatiphaga DSM 21508 | dctA |
| Steroidobacter denitrificans DSM 18526 | dauA |
| 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 |
| 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 |
| 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 |
| 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 |
| Trichodesmium erythraeum IMS101 | 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 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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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