citrate catabolism

GapMind for catabolism of small carbon sources

citrate catabolism

Analysis of pathway citrate in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	SLC13A5, acn, icd
Acidithiobacillus ferrooxidans ATCC 23270	SLC13A5, acn, icd
Alicycliphilus denitrificans K601	citA, acn, icd
Allochromatium vinosum DSM 180	SLC13A5, acn, icd
Ammonifex degensii KC4	SLC13A5, acn, icd
Archaeoglobus veneficus SNP6	SLC13A5, acn, icd
Arcobacter nitrofigilis DSM 7299	citT, acn, icd
Azoarcus sp. BH72	SLC13A5, acn, icd
Azohydromonas australica DSM 1124	tctA, tctB, tctC, acn, icd
Azorhizobium caulinodans ORS 571	citA, acn, icd
Azospirillum lipoferum B510	citW, citD, citE, citF
Bacillus alkalinitrilicus DSM 22532	citM, acn, icd
Beijerinckia indica ATCC 9039	SLC13A5, acn, icd
Beijerinckia mobilis UQM 1969	SLC13A5, acn, icd
Bradyrhizobium sp. BTAi1	citA, acn, icd
Burkholderia vietnamiensis G4	citA, acn, icd
Calditerrivibrio nitroreducens DSM 19672	SLC13A5, acn, icd
Caminibacter mediatlanticus TB-2	SLC13A5, 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
Crocosphaera subtropica ATCC 51142	SLC13A5, acn, icd
Dechloromonas agitata is5	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
Desulfallas geothermicus DSM 3669	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
Desulfobulbus mediterraneus DSM 13871	SLC13A5, acn, icd
Desulfotalea psychrophila LSv54	SLC13A5, acn, icd
Desulfotomaculum ruminis DSM 2154	SLC13A5, acn, icd
Desulfovibrio bastinii DSM 16055	citT, acn, icd
Desulfovibrio gracilis DSM 16080	SLC13A5, acn, icd
Desulfovibrio oxyclinae DSM 11498	SLC13A5, acn, icd
Desulfovibrio zosterae DSM 11974	cit1, acn, icd
Desulfurobacterium atlanticum DSM 15668	SLC13A5, acn, icd
Desulfuromonas acetexigens	SLC13A5, acn, icd
Desulfuromusa kysingii DSM 7343	tctA, tctB, tctC, acn, icd
Ferroglobus placidus DSM 10642	SLC13A5, acn, icd
Frankia alni ACN14A	SLC13A5, acn, icd
Geobacter lovleyi SZ	SLC13A5, acn, icd
Geobacter metallireducens GS-15	SLC13A5, acn, icd
Geobacter uraniireducens Rf4	SLC13A5, acn, icd
Haloechinothrix alba DSM 45207	tctA, tctB, tctC, acn, icd
Haloglycomyces albus DSM 45210	SLC13A5, acn, icd
Halomonas desiderata SP1	tctA, tctB, tctC, acn, icd
Halorhodospira halophila SL1	SLC13A5, acn, icd
Heliobacterium modesticaldum Ice1; ATCC 51547	SLC13A5, acn, icd
Herbaspirillum autotrophicum IAM 14942	citA, 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 variicola At-22	citA, citD, citE, citF
Kyrpidia tusciae DSM 2912	SLC13A5, acn, icd
Leptospirillum ferrooxidans C2-3	SLC13A5, acn, icd
Malonomonas rubra DSM 5091	SLC13A5, citD, citE, citF
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 barkeri Fusaro	SLC13A5, acn, icd
Methanosarcina mazei Go1	SLC13A5, acn, icd
Methanothermobacter thermautotrophicus Delta H	SLC13A5, acn, icd
Methylobacterium nodulans ORS 2060	citA, acn, icd
Methylobacterium sp. 4-46	citA, acn, icd
Methylocapsa acidiphila B2	SLC13A5, acn, icd
Methylocapsa aurea KYG T	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
Methylomicrobium alcaliphilum 20Z	SLC13A5, acn, icd
Methylomonas methanica MC09	SLC13A5, acn, icd
Methylosarcina fibrata AML-C10	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
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 phymatum STM815	citA, acn, icd
Paraburkholderia sp. CCGE1002	citA, acn, icd
Pelobacter propionicus DSM 2379	SLC13A5, citD, citE, citF
Persephonella marina EX-H1	SLC13A5, 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 stutzeri A1501	tctA, tctB, tctC, acn, icd
Pyrolobus fumarii 1A	SLC13A5, acn, icd
Rhizobium etli CFN 42	tctA, tctB, tctC, acn, icd
Rhizobium leguminosarum 3841	tctA, tctB, tctC, acn, icd
Rhizobium leguminosarum WSM1325	tctA, tctB, tctC, acn, icd
Rhodobacter sphaeroides ATCC 17029	tctA, tctB, tctC, 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
Saccharomonospora cyanea NA-134	citM, acn, icd
Sedimenticola selenatireducens DSM 17993	SLC13A5, acn, icd
Sinorhizobium fredii NGR234	tctA, tctB, tctC, acn, icd
Sinorhizobium medicae WSM419	tctA, tctB, tctC, acn, icd
Sphingomonas wittichii RW1	SLC13A5, acn, icd
Stenotrophomonas chelatiphaga DSM 21508	citM, acn, icd
Steroidobacter denitrificans DSM 18526	SLC13A5, 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
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
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
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
Trichodesmium erythraeum IMS101	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 Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources