GapMind for catabolism of small carbon sources

 

citrate catabolism

Analysis of pathway citrate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 SLC13A5, acn, icd
Acidithiobacillus ferrooxidans ATCC 23270 SLC13A5, acn, icd
Acidovorax sp. GW101-3H11 tctA, tctB, tctC, acn, icd
Algiphilus aromaticivorans DG1253 SLC13A5, acn, icd
Alicycliphilus denitrificans K601 citA, acn, icd
Alkalihalobacterium alkalinitrilicum DSM 22532 citM, acn, icd
Allochromatium vinosum DSM 180 SLC13A5, acn, icd
Ammonifex degensii KC4 SLC13A5, acn, icd
Anaerobutyricum hallii DSM 3353 SLC13A5, acn, icd
Aquimarina longa SW024 SLC13A5, acn, icd
Archaeoglobus veneficus SNP6 SLC13A5, acn, icd
Arcobacter nitrofigilis DSM 7299 citT, acn, icd
Azoarcus olearius BH72 SLC13A5, acn, icd
Azohydromonas australica DSM 1124 tctA, tctB, tctC, acn, icd
Azorhizobium caulinodans ORS 571 citA, acn, icd
Azospirillum brasilense Sp245 tctA, tctB, tctC, acn, icd
Azospirillum sp. B510 citW, citD, citE, citF
Bacteroides thetaiotaomicron VPI-5482 SLC13A5, acn, icd
Beijerinckia indica ATCC 9039 SLC13A5, acn, icd
Beijerinckia mobilis UQM 1969 SLC13A5, acn, icd
Billgrantia desiderata SP1 tctA, tctB, tctC, acn, icd
Bradyrhizobium sp. BTAi1 citA, acn, icd
Brevundimonas sp. GW460-12-10-14-LB2 SLC13A5, acn, icd
Burkholderia phytofirmans PsJN citA, acn, icd
Burkholderia vietnamiensis G4 citA, acn, icd
Calditerrivibrio nitroreducens DSM 19672 SLC13A5, acn, icd
Caminibacter mediatlanticus TB-2 SLC13A5, acn, icd
Carboxydothermus pertinax Ug1 cit1, acn, icd
Caulobacter crescentus NA1000 SLC13A5, acn, icd
Cereibacter sphaeroides ATCC 17029 tctA, tctB, tctC, acn, icd
Chlorobaculum parvum NCIB 8327 SLC13A5, acn, icd
Chlorobaculum tepidum TLS SLC13A5, acn, icd
Chlorobium limicola DSM 245 SLC13A5, acn, icd
Chlorobium phaeobacteroides BS1 SLC13A5, acn, icd
Clostridium acetobutylicum ATCC 824 cit1, acn, icd
Clostridium kluyveri DSM 555 SLC13A5, acn, icd
Clostridium tyrobutyricum FAM22553 SLC13A5, acn, icd
Crocosphaera subtropica ATCC 51142 SLC13A5, acn, icd
Cupriavidus basilensis FW507-4G11 citA, acn, icd
Dechloromonas agitata is5 SLC13A5, acn, icd
Dechlorosoma suillum PS SLC13A5, acn, icd
Dehalococcoides mccartyi 195 SLC13A5, acn, icd
Denitrovibrio acetiphilus DSM 12809 SLC13A5, acn, icd
Derxia gummosa DSM 723 citA, acn, icd
Desulfacinum hydrothermale DSM 13146 SLC13A5, acn, icd
Desulfacinum infernum DSM 9756 SLC13A5, acn, icd
Desulfarculus baarsii DSM 2075 SLC13A5, acn, icd
Desulfatibacillum aliphaticivorans DSM 15576 SLC13A5, acn, icd
Desulfatiglans anilini DSM 4660 SLC13A5, acn, icd
Desulfitobacterium hafniense DCB-2 tctA, tctB, tctC, citD, citE, citF
Desulfobacca acetoxidans DSM 11109 SLC13A5, acn, icd
Desulfobacter vibrioformis DSM 8776 SLC13A5, acn, icd
Desulfogranum mediterraneum DSM 13871 SLC13A5, acn, icd
Desulforamulus ruminis DSM 2154 SLC13A5, acn, icd
Desulfoscipio geothermicus DSM 3669 SLC13A5, acn, icd
Desulfotalea psychrophila LSv54 SLC13A5, acn, icd
Desulfovibrio oxyclinae DSM 11498 SLC13A5, acn, icd
Desulfovibrio vulgaris Hildenborough JW710 SLC13A5, acn, icd
Desulfovibrio vulgaris Miyazaki F SLC13A5, acn, icd
Desulfurobacterium atlanticum DSM 15668 SLC13A5, acn, icd
Desulfuromonas acetexigens SLC13A5, acn, icd
Desulfuromusa kysingii DSM 7343 tctA, tctB, tctC, acn, icd
Dinoroseobacter shibae DFL-12 tctA, tctB, tctC, acn, icd
Dyella japonica UNC79MFTsu3.2 SLC13A5, acn, icd
Echinicola vietnamensis KMM 6221, DSM 17526 SLC13A5, acn, icd
Escherichia coli BW25113 fecB, fecC, fecD, fecE, citD, citE, citF
Ferroglobus placidus DSM 10642 SLC13A5, acn, icd
Frankia alni ACN14a SLC13A5, acn, icd
Geobacter metallireducens GS-15 SLC13A5, acn, icd
Geotalea uraniireducens Rf4 SLC13A5, acn, icd
Halococcus hamelinensis 100A6 SLC13A5, acn, icd
Haloechinothrix alba DSM 45207 tctA, tctB, tctC, acn, icd
Haloferax volcanii DS2 SLC13A5, acn, icd
Haloglycomyces albus DSM 45210 SLC13A5, acn, icd
Halorhodospira halophila SL1 SLC13A5, acn, icd
Heliomicrobium modesticaldum Ice1; ATCC 51547 SLC13A5, acn, icd
Herbaspirillum autotrophicum IAM 14942 citA, acn, icd
Herbaspirillum seropedicae SmR1 citA, acn, icd
Hippea alviniae EP5-r SLC13A5, acn, icd
Hydrogenophaga taeniospiralis NBRC 102512 tctA, tctB, tctC, acn, icd
Hydrogenovibrio halophilus DSM 15072 SLC13A5, acn, icd
Hydrogenovibrio kuenenii DSM 12350 SLC13A5, acn, icd
Hydrogenovibrio marinus DSM 11271 SLC13A5, acn, icd
Hyphomicrobium sulfonivorans WDL6 SLC13A5, acn, icd
Klebsiella michiganensis M5al fecB, fecC, fecD, fecE, citD, citE, citF
Klebsiella variicola At-22 citA, citD, citE, citF
Kyrpidia tusciae DSM 2912 SLC13A5, acn, icd
Leptospirillum ferrooxidans C2-3 SLC13A5, acn, icd
Magnetospirillum magneticum AMB-1 SLC13A5, acn, icd
Malonomonas rubra DSM 5091 SLC13A5, citD, citE, citF
Maridesulfovibrio bastinii DSM 16055 citT, acn, icd
Maridesulfovibrio zosterae DSM 11974 cit1, acn, icd
Marinobacter adhaerens HP15 tctA, tctB, tctC, acn, icd
Mesorhizobium ciceri WSM1271 tctA, tctB, tctC, acn, icd
Methanobacterium lacus AL-21 SLC13A5, acn, icd
Methanococcus aeolicus Nankai-3 SLC13A5, acn, icd
Methanococcus maripaludis C5 SLC13A5, acn, icd
Methanosarcina acetivorans C2A SLC13A5, acn, icd
Methanosarcina mazei Go1 SLC13A5, acn, icd
Methanospirillum lacunae Ki8-1 SLC13A5, acn, icd
Methanothermobacter thermautotrophicus Delta H SLC13A5, acn, icd
Methylobacterium nodulans ORS 2060 citA, acn, icd
Methylobacterium sp. 4-46 Apr-46 citA, acn, icd
Methylocapsa acidiphila B2 SLC13A5, acn, icd
Methylocapsa aurea KYG SLC13A5, acn, icd
Methylocella silvestris BL2 citT, acn, icd
Methylococcus capsulatus Bath SLC13A5, acn, icd
Methylocystis bryophila S285 SLC13A5, acn, icd
Methyloferula stellata AR4T SLC13A5, acn, icd
Methylohalobius crimeensis 10Ki SLC13A5, acn, icd
Methylomonas methanica MC09 SLC13A5, acn, icd
Methylosarcina fibrata AML-C10 SLC13A5, acn, icd
Methylotuvimicrobium alcaliphilum 20Z SLC13A5, acn, icd
Methylovulum miyakonense HT12 SLC13A5, acn, icd
Mycolicibacterium vanbaalenii PYR-1 tctA, tctB, tctC, acn, icd
Nitratifractor salsuginis DSM 16511 SLC13A5, acn, icd
Nitratiruptor tergarcus DSM 16512 SLC13A5, acn, icd
Nitriliruptor alkaliphilus DSM 45188 tctA, tctB, tctC, acn, icd
Nocardioides dokdonensis FR1436 SLC13A5, acn, icd
Nocardiopsis lucentensis DSM 44048 tctA, tctB, tctC, acn, icd
Nostoc punctiforme ATCC 29133; PCC 73102 SLC13A5, acn, icd
Novosphingobium aromaticivorans DSM 12444 citA, acn, icd
Oleispira antarctica SLC13A5, acn, icd
Paraburkholderia atlantica CCGE1002 citA, acn, icd
Paraburkholderia bryophila 376MFSha3.1 citA, acn, icd
Paraburkholderia phymatum STM815 citA, acn, icd
Paucidesulfovibrio gracilis DSM 16080 SLC13A5, acn, icd
Pedobacter sp. GW460-11-11-14-LB5 SLC13A5, acn, icd
Pelobacter propionicus DSM 2379 SLC13A5, citD, citE, citF
Persephonella marina EX-H1 SLC13A5, acn, icd
Phaeacidiphilus oryzae TH49 SLC13A5, acn, icd
Phaeobacter inhibens BS107 tctA, tctB, tctC, acn, icd
Polaromonas naphthalenivorans CJ2 tctA, tctB, tctC, acn, icd
Prosthecochloris aestuarii DSM 271 SLC13A5, acn, icd
Pseudarthrobacter sulfonivorans Ar51 citM, acn, icd
Pseudomonas benzenivorans DSM 8628 tctA, tctB, tctC, acn, icd
Pseudomonas fluorescens FW300-N1B4 citM, acn, icd
Pseudomonas fluorescens FW300-N2C3 tctA, tctB, tctC, acn, icd
Pseudomonas fluorescens FW300-N2E2 tctA, tctB, tctC, acn, icd
Pseudomonas fluorescens FW300-N2E3 citA, acn, icd
Pseudomonas fluorescens GW456-L13 citM, acn, icd
Pseudomonas putida KT2440 citM, acn, icd
Pseudomonas simiae WCS417 citA, acn, icd
Pseudomonas stutzeri RCH2 tctA, tctB, tctC, acn, icd
Pyrolobus fumarii 1A SLC13A5, acn, icd
Rhizobium etli CFN 42 tctA, tctB, tctC, acn, icd
Rhizobium johnstonii 3841 tctA, tctB, tctC, acn, icd
Rhizobium leguminosarum WSM1325 tctA, tctB, tctC, acn, icd
Rhizorhabdus wittichii RW1 SLC13A5, acn, icd
Rhodanobacter denitrificans FW104-10B01 SLC13A5, acn, icd
Rhodomicrobium vannielii ATCC 17100 SLC13A5, acn, icd
Rhodopseudomonas palustris CGA009 SLC13A5, acn, icd
Rhodospirillum centenum SW; ATCC 51521 SLC13A5, acn, icd
Rhodospirillum rubrum ATCC 11170 citM, acn, icd
Roseburia faecis M72 SLC13A5, acn, icd
Saccharomonospora cyanea NA-134 citM, acn, icd
Sedimenticola selenatireducens DSM 17993 SLC13A5, acn, icd
Shewanella amazonensis SB2B SLC13A5, acn, icd
Shewanella loihica PV-4 SLC13A5, acn, icd
Shewanella oneidensis MR-1 SLC13A5, acn, icd
Shewanella sp. ANA-3 SLC13A5, acn, icd
Sinorhizobium fredii NGR234 tctA, tctB, tctC, acn, icd
Sinorhizobium medicae WSM419 tctA, tctB, tctC, acn, icd
Sinorhizobium meliloti 1021 tctA, tctB, tctC, acn, icd
Sphingomonas koreensis DSMZ 15582 SLC13A5, acn, icd
Stenotrophomonas chelatiphaga DSM 21508 citM, acn, icd
Steroidobacter denitrificans DSM 18526 SLC13A5, acn, icd
Stutzerimonas stutzeri A1501 tctA, tctB, tctC, acn, icd
Sulfuricurvum kujiense DSM 16994 SLC13A5, acn, icd
Sulfurihydrogenibium azorense Az-Fu1 SLC13A5, acn, icd
Sulfurihydrogenibium subterraneum DSM 15120 SLC13A5, acn, icd
Sulfurimonas denitrificans DSM 1251 SLC13A5, acn, icd
Sulfuritalea hydrogenivorans DSM 22779 SLC13A5, acn, icd
Sulfurivirga caldicuralii DSM 17737 SLC13A5, acn, icd
Synechococcus elongatus PCC 7942 SLC13A5, acn, icd
Teredinibacter turnerae T7901 SLC13A5, acn, icd
Thauera aminoaromatica S2 tctA, tctB, tctC, acn, icd
Thermithiobacillus tepidarius DSM 3134 SLC13A5, acn, icd
Thermocrinis albus DSM 14484 SLC13A5, acn, icd
Thermodesulforhabdus norvegica DSM 9990 SLC13A5, acn, icd
Thermomonospora curvata DSM 43183 SLC13A5, acn, icd
Thermovibrio ammonificans HB-1 SLC13A5, acn, icd
Thermus aquaticus YT-1 SLC13A5, acn, icd
Thioalkalivibrio denitrificans ALJD SLC13A5, acn, icd
Thioalkalivibrio halophilus HL17 SLC13A5, acn, icd
Thioalkalivibrio paradoxus ARh 1 SLC13A5, acn, icd
Thioalkalivibrio thiocyanodenitrificans ARhD 1 SLC13A5, acn, icd
Thiohalomonas denitrificans HLD2 SLC13A5, acn, icd
Thiohalospira halophila HL 3 SLC13A5, acn, icd
Thiomicrorhabdus arctica DSM 13458 SLC13A5, acn, icd
Thiomicrorhabdus chilensis DSM 12352 SLC13A5, acn, icd
Thiomicrospira cyclica ALM1 SLC13A5, acn, icd
Thiomicrospira microaerophila ASL8-2 SLC13A5, acn, icd
Thiomicrospira pelophila DSM 1534 SLC13A5, acn, icd
Thiothrix lacustris DSM 21227 SLC13A5, acn, icd
Tistlia consotensis USBA 355 tctA, tctB, tctC, acn, icd
Trichlorobacter lovleyi SZ SLC13A5, acn, icd
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome SLC13A5, acn, icd
Trichormus variabilis ATCC 29413 SLC13A5, acn, icd
Xanthobacter autotrophicus Py2 citA, acn, icd
Xenophilus azovorans DSM 13620 tctA, tctB, tctC, acn, icd

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