GapMind for catabolism of small carbon sources

 

citrate catabolism

Analysis of pathway citrate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 citA, acn, icd
Actinokineospora bangkokensis 44EHW tctA, tctB, tctC, acn, icd
Actinomyces timonensis 7400942 SLC13A5, acn, icd
Algiphilus aromaticivorans DG1253 SLC13A5, acn, icd
Algoriphagus aquaeductus T4 citM, acn, icd
Algoriphagus machipongonensis PR1 citM, acn, icd
Alicyclobacillus ferrooxydans TC-34 SLC13A5, acn, icd
Alishewanella agri BL06 SLC13A5, acn, icd
Alistipes indistinctus YIT 12060 SLC13A5, acn, icd
Alistipes shahii WAL 8301 SLC13A5, acn, icd
Alkalitalea saponilacus SC/BZ-SP2 SLC13A5, acn, icd
Amantichitinum ursilacus IGB-41 citA, acn, icd
Amphibacillus jilinensis Y1 citM, acn, icd
Amphritea japonica JAMM 1866 SLC13A5, acn, icd
Amycolatopsis halophila YIM 93223 SLC13A5, acn, icd
Amycolatopsis xylanica CPCC 202699 SLC13A5, acn, icd
Aquimarina agarilytica ZC1 SLC13A5, acn, icd
Aquimarina longa SW024 SLC13A5, acn, icd
Aquimarina macrocephali JAMB N27 SLC13A5, acn, icd
Archaeoglobus sulfaticallidus PM70-1 SLC13A5, acn, icd
Arcticibacter svalbardensis MN12-7 SLC13A5, acn, icd
Ardenticatena maritima 110S SLC13A5, acn, icd
Arenimonas metalli CF5-1 SLC13A5, acn, icd
Arenitalea lutea P7-3-5 SLC13A5, acn, icd
Azospirillum humicireducens SgZ-5 citW, citD, citE, citF
Azospirillum thiophilum BV-S citM, acn, icd
Bacillus altitudinis 41KF2b citM, acn, icd
Bacillus coahuilensis m4-4 SLC13A5, acn, icd
Bacillus cytotoxicus NVH 391-98 cimH, acn, icd
Bacillus horneckiae 1P01SC citM, acn, icd
Bacillus okhensis Kh10-101 citM, acn, icd
Bacillus safensis FO-36b citM, acn, icd
Bacillus velezensis CBMB205 cimH, acn, icd
Bacteroides clarus YIT 12056 SLC13A5, acn, icd
Bacteroides faecis MAJ27 SLC13A5, acn, icd
Bacteroides fluxus YIT 12057 SLC13A5, acn, icd
Bacteroides oleiciplenus YIT 12058 SLC13A5, acn, icd
Barnesiella intestinihominis YIT 11860 SLC13A5, acn, icd
Belnapia rosea CPCC 100156 tctA, tctB, tctC, acn, icd
Bizionia argentinensis JUB59 SLC13A5, acn, icd
Bradyrhizobium diazoefficiens USDA110 citA, acn, icd
Brevibacterium jeotgali SJ5-8 SLC13A5, acn, icd
Brucella inopinata BO1 SLC13A5, acn, icd
Brucella microti CCM 4915 SLC13A5, acn, icd
Bryobacter aggregatus MPL3 SLC13A5, acn, icd
Caldicellulosiruptor hydrothermalis 108 SLC13A5, acn, icd
Caldicellulosiruptor kronotskyensis 2002 SLC13A5, acn, icd
Carboxydothermus pertinax Ug1 cit1, acn, icd
Catellicoccus marimammalium M35/04/3 SLC13A5, acn, icd
Chromobacterium vaccinii MWU205 SLC13A5, acn, icd
Chryseobacterium angstadtii KM citM, acn, icd
Chryseobacterium arthrosphaerae CC-VM-7 citM, acn, icd
Chryseobacterium viscerum 687B-08 citM, acn, icd
Cloacibacillus porcorum CL-84 tctA, tctB, tctC, citD, citE, citF
Cobetia crustatorum JO1 tctA, tctB, tctC, acn, icd
Collimonas arenae Ter10 citA, acn, icd
Collimonas pratensis Ter91 citA, acn, icd
Collinsella tanakaei YIT 12063 SLC13A5, acn, icd
Coprobacter fastidiosus NSB1 SLC13A5, acn, icd
Corynebacterium deserti GIMN1.010 tctA, tctB, tctC, acn, icd
Corynebacterium frankenforstense ST18 cit1, acn, icd
Corynebacterium lactis RW2-5 SLC13A5, acn, icd
Croceitalea dokdonensis DOKDO 023 SLC13A5, acn, icd
Cronobacter condimenti 1330 tctA, tctB, tctC, acn, icd
Cronobacter muytjensii ATCC 51329 tctA, tctB, tctC, citD, citE, citF
Cronobacter universalis NCTC 9529 tctA, tctB, tctC, citD, citE, citF
Desulfatitalea tepidiphila S28bF SLC13A5, acn, icd
Desulfotomaculum hydrothermale Lam5 SLC13A5, acn, icd
Dethiosulfovibrio salsuginis USBA 82 tctA, tctB, tctC, citD, citE, citF
Devosia chinhatensis IPL18 tctA, tctB, tctC, acn, icd
Devriesea agamarum IMP2 cit1, acn, icd
Dialister succinatiphilus YIT 11850 SLC13A5, acn, icd
Dietzia timorensis ID05-A0528 citM, acn, icd
Dokdonella koreensis DS-123 SLC13A5, acn, icd
Domibacillus robiginosus WS 4628 citM, acn, icd
Duganella sacchari Sac-22 citA, acn, icd
Dyadobacter tibetensis Y620-1 SLC13A5, acn, icd
Dyella jiangningensis SBZ3-12 SLC13A5, acn, icd
Endozoicomonas montiporae CL-33 cit1, acn, icd
Enterococcus termitis LMG 8895 citM, citD, citE, citF
Enterorhabdus caecimuris B7 SLC13A5, acn, icd
Epibacterium ulvae U95 tctA, tctB, tctC, acn, icd
Erythrobacter gangjinensis K7-2 SLC13A5, acn, icd
Erythrobacter marinus HWDM-33 SLC13A5, acn, icd
Ethanoligenens harbinense YUAN-3 SLC13A5, acn, icd
Fervidicella metallireducens AeB SLC13A5, citD, citE, citF
Fibrella aestuarina BUZ 2 citM, acn, icd
Flammeovirga pacifica WPAGA1 SLC13A5, acn, icd
Flaviramulus ichthyoenteri Th78 SLC13A5, acn, icd
Flavobacterium beibuense F44-8 SLC13A5, acn, icd
Flavobacterium glycines Gm-149 SLC13A5, acn, icd
Flavobacterium sp. LM5 SLC13A5, acn, icd
Flavobacterium ummariense DS-12 SLC13A5, acn, icd
Frischella perrara PEB0191 citW, citD, citE, citF
Galbibacter marinus ck-I2-15 SLC13A5, acn, icd
Gallaecimonas xiamenensis 3-C-1 tctA, tctB, tctC, acn, icd
Geobacter daltonii FRC-32 SLC13A5, acn, icd
Gillisia marina CBA3202 SLC13A5, acn, icd
Gracilibacillus halophilus YIM-C55.5 SLC13A5, acn, icd
Granulicella mallensis MP5ACTX8 cimH, acn, icd
Granulicella tundricola MP5ACTX9 SLC13A5, acn, icd
Hafnia paralvei ATCC 29927 citA, citD, citE, citF
Haladaptatus cibarius D43 SLC13A5, acn, icd
Halioglobus japonicus S1-36 SLC13A5, acn, icd
Halobacillus alkaliphilus FP5 tctA, tctB, tctC, acn, icd
Halococcus hamelinensis 100A6 SLC13A5, acn, icd
Halomonas salina B6 tctA, tctB, tctC, acn, icd
Halomonas smyrnensis AAD6 tctA, tctB, tctC, acn, icd
Halomonas stevensii S18214 cit1, acn, icd
Halomonas titanicae BH1 tctA, tctB, tctC, acn, icd
Halomonas xinjiangensis TRM 0175 tctA, tctB, tctC, acn, icd
Halopiger salifodinae KCY07-B2 citM, acn, icd
Halostagnicola larsenii XH-48 SLC13A5, acn, icd
Haloterrigena daqingensis JX313 SLC13A5, acn, icd
Herbaspirillum aquaticum IEH 4430 citA, acn, icd
Hippea alviniae EP5-r SLC13A5, acn, icd
Hippea jasoniae Mar08-272r SLC13A5, acn, icd
Hoeflea phototrophica DFL-43 tctA, tctB, tctC, acn, icd
Hyphomicrobium nitrativorans NL23 SLC13A5, acn, icd
Imtechella halotolerans K1 SLC13A5, acn, icd
Indibacter alkaliphilus LW1 citM, acn, icd
Jannaschia aquimarina GSW-M26 tctA, tctB, tctC, acn, icd
Jeotgalibacillus soli P9 SLC13A5, acn, icd
Kangiella geojedonensis YCS-5 SLC13A5, acn, icd
Knoellia flava TL1 tctA, tctB, tctC, acn, icd
Kocuria flava HO-9041 tctA, tctB, tctC, acn, icd
Kocuria turfanensis HO-9042 tctA, tctB, tctC, acn, icd
Laceyella sediminis RHA1 tctA, tctB, tctC, acn, icd
Lacinutrix algicola AKS293 SLC13A5, acn, icd
Lacinutrix himadriensis E4-9a SLC13A5, acn, icd
Lacinutrix mariniflava AKS432 SLC13A5, acn, icd
Lactobacillus curieae CCTCC M 2011381 cit1, acn, icd
Lactobacillus delbrueckii ZN7a-9 cit1, acn, icd
Lactobacillus hokkaidonensis LOOC260 SLC13A5, acn, icd
Lactobacillus oryzae SG293 cit1, citD, citE, citF
Lactobacillus pobuzihii E100301 cit1, acn, icd
Lactobacillus shenzhenensis LY-73 SLC13A5, citD, citE, citF
Lactobacillus silagei IWT126 cit1, citD, citE, citF
Leeuwenhoekiella blandensis MED217 SLC13A5, acn, icd
Lentibacillus jeotgali Grbi citM, acn, icd
Limnohabitans curvus MWH-C5 SLC13A5, acn, icd
Limnohabitans parvus II-B4 SLC13A5, acn, icd
Listeria fleischmannii LU2006-1 SLC13A5, acn, icd
Luteimonas huabeiensis HB2 cit1, acn, icd
Luteipulveratus mongoliensis MN07-A0370 tctA, tctB, tctC, acn, icd
Lutibaculum baratangense AMV1 tctA, tctB, tctC, acn, icd
Lysobacter daejeonensis GH1-9 SLC13A5, acn, icd
Magnetovibrio blakemorei MV-1 SLC13A5, acn, icd
Marinicella litoralis KMM 3900 SLC13A5, acn, icd
Mariniradius saccharolyticus AK6 citM, acn, icd
Marinobacter algicola DG893 tctA, tctB, tctC, acn, icd
Marinobacter guineae M3B tctA, tctB, tctC, acn, icd
Marinobacter psychrophilus 20041 tctA, tctB, tctC, acn, icd
Marinomonas arctica 328 tctA, tctB, tctC, acn, icd
Marivita geojedonensis DPG-138 tctA, tctB, tctC, acn, icd
Martelella endophytica YC6887 SLC13A5, acn, icd
Megamonas funiformis YIT 11815 SLC13A5, acn, icd
Mesorhizobium ciceri WSM1271 tctA, tctB, tctC, acn, icd
Methanobacterium arcticum M2 SLC13A5, acn, icd
Methanobacterium veterum MK4 SLC13A5, acn, icd
Methanocella arvoryzae MRE50 SLC13A5, acn, icd
Methanococcus aeolicus Nankai-3 SLC13A5, acn, icd
Methanoculleus horonobensis T10 SLC13A5, acn, icd
Methanolinea tarda NOBI-1 SLC13A5, acn, icd
Methanosarcina soligelidi SMA-21 SLC13A5, acn, icd
Methanospirillum lacunae Ki8-1 SLC13A5, acn, icd
Methanospirillum stamsii Pt1 SLC13A5, acn, icd
Methylibium petroleiphilum PM1 SLC13A5, acn, icd
Methylobacterium gossipiicola Gh-105 citA, acn, icd
Methylocapsa aurea KYG SLC13A5, acn, icd
Methylotenera versatilis 301 SLC13A5, acn, icd
Microbacterium profundi Shh49 tctA, tctB, tctC, acn, icd
Microvirga lotononidis WSM3557 tctA, tctB, tctC, acn, icd
Moritella dasanensis ArB 0140 fecB, fecC, fecD, fecE, acn, icd
Mucilaginibacter gossypii Gh-67 SLC13A5, acn, icd
Mucilaginibacter gossypiicola Gh-48 SLC13A5, acn, icd
Mucilaginibacter mallensis MP1X4 SLC13A5, acn, icd
Nafulsella turpanensis ZLM-10 SLC13A5, acn, icd
Natronomonas moolapensis 8.8.11 SLC13A5, acn, icd
Nautilia profundicola AmH SLC13A5, acn, icd
Neiella marina J221 SLC13A5, acn, icd
Neptunomonas antarctica S3-22 tctA, tctB, tctC, acn, icd
Nocardioides daejeonensis MJ31 tctA, tctB, tctC, acn, icd
Nocardioides dokdonensis FR1436 SLC13A5, acn, icd
Nocardiopsis baichengensis YIM 90130 tctA, tctB, tctC, acn, icd
Nocardiopsis gilva YIM 90087 tctA, tctB, tctC, acn, icd
Novosphingobium barchaimii LL02 citM, acn, icd
Novosphingobium fuchskuhlense FNE08-7 SLC13A5, acn, icd
Novosphingobium lindaniclasticum LE124 SLC13A5, acn, icd
Oceanisphaera arctica V1-41 tctA, tctB, tctC, acn, icd
Ochrobactrum rhizosphaerae PR17 SLC13A5, acn, icd
Ochrobactrum thiophenivorans DSM 7216 cimH, acn, icd
Oscillibacter ruminantium GH1 SLC13A5, acn, icd
Paenisporosarcina indica PN2 citM, acn, icd
Palaeococcus pacificus DY20341 SLC13A5, acn, icd
Paludibacter propionicigenes WB4 SLC13A5, acn, icd
Pandoraea thiooxydans ATSB16 citA, acn, icd
Pantoea rwandensis LMG 26275 citA, acn, icd
Pedobacter arcticus A12 SLC13A5, acn, icd
Photobacterium gaetbulicola Gung47 cit1, acn, icd
Photobacterium jeanii R-40508 SLC13A5, acn, icd
Phyllobacterium brassicacearum STM 196 tctA, tctB, tctC, acn, icd
Phyllobacterium endophyticum PEPV15 tctA, tctB, tctC, acn, icd
Phyllobacterium leguminum ORS 1419 citA, acn, icd
Planktomarina temperata RCA23 tctA, tctB, tctC, acn, icd
Planococcus halocryophilus Or1 tctA, tctB, tctC, acn, icd
Pleomorphomonas diazotrophica R5-392 cimH, acn, icd
Polaribacter dokdonensis DSW-5 SLC13A5, acn, icd
Pontibacillus litoralis JSM 072002 SLC13A5, acn, icd
Pontibacter lucknowensis DM9 SLC13A5, acn, icd
Pontibacter ramchanderi LP43 SLC13A5, acn, icd
Pontimonas salivibrio CL-TW6 SLC13A5, acn, icd
Porphyrobacter dokdonensis DSW-74 SLC13A5, acn, icd
Pseudoalteromonas arctica A 37-1-2 cit1, acn, icd
Pseudomonas baetica a390 citA, acn, icd
Pseudomonas litoralis 2SM5 SLC13A5, acn, icd
Pseudomonas taeanensis MS-3 tctA, tctB, tctC, acn, icd
Pseudovibrio axinellae Ad2 tctA, tctB, tctC, acn, icd
Psychrobacter arcticus 273-4 SLC13A5, acn, icd
Psychrobacter cryohalolentis K5 tctA, tctB, tctC, acn, icd
Psychromonas ingrahamii 37 tctA, tctB, tctC, acn, icd
Psychromonas ossibalaenae JAMM 0738 SLC13A5, acn, icd
Rhizobium freirei PRF 81 SLC13A5, acn, icd
Rhizobium grahamii CCGE 502 tctA, tctB, tctC, acn, icd
Rhizobium subbaraonis JC85 citM, acn, icd
Rhodanobacter denitrificans 2APBS1 SLC13A5, acn, icd
Rhodobacter johrii JA192 tctA, tctB, tctC, acn, icd
Rhodobacter maris JA276 SLC13A5, acn, icd
Rhodobacter ovatus JA234 SLC13A5, acn, icd
Rhodobacter viridis JA737 SLC13A5, acn, icd
Rhodococcus qingshengii djl-6-2 citM, acn, icd
Rhodopseudomonas pseudopalustris DSM 123 SLC13A5, acn, icd
Roseateles aquatilis CCUG 48205 citA, acn, icd
Roseivirga spongicola UST030701-084 SLC13A5, acn, icd
Rubrivirga marina SAORIC-28 SLC13A5, acn, icd
Ruegeria conchae TW15 tctA, tctB, tctC, acn, icd
Saccharomonospora marina XMU15 tctA, tctB, tctC, acn, icd
Salinicoccus carnicancri Crm citM, acn, icd
Serinicoccus profundi MCCC 1A05965 tctA, tctB, tctC, acn, icd
Shewanella halifaxensis HAW-EB4 SLC13A5, acn, icd
Skermanella stibiiresistens SB22 citM, acn, icd
Snodgrassella alvi wkB2 citA, acn, icd
Sphaerochaeta globosa Buddy SLC13A5, acn, icd
Sphaerochaeta pleomorpha Grapes tctA, tctB, tctC, citD, citE, citF
Sphingobium baderi LL03 SLC13A5, acn, icd
Sphingobium czechense LL01 SLC13A5, acn, icd
Sphingobium quisquiliarum P25 SLC13A5, acn, icd
Sphingomonas histidinilytica UM2 SLC13A5, acn, icd
Sphingomonas indica Dd16 SLC13A5, acn, icd
Sphingomonas laterariae LNB2 SLC13A5, acn, icd
Sphingopyxis indica DS15 SLC13A5, acn, icd
Sphingopyxis terrae UI2 SLC13A5, acn, icd
Sporolactobacillus vineae SL153 citM, acn, icd
Streptacidiphilus oryzae TH49 SLC13A5, acn, icd
Streptococcus anginosus CCUG 39159 SLC13A5, acn, icd
Streptococcus massiliensis 4401825 citW, acn, icd
Streptococcus oralis 7747 SLC13A5, acn, icd
Streptococcus oralis AZ_3a SLC13A5, acn, icd
Streptomyces kebangsaanensis SUK12 SLC13A5, acn, icd
Succinatimonas hippei YIT 12066 SLC13A5, acn, icd
Sulfurimonas gotlandica GD1 SLC13A5, acn, icd
Tatumella morbirosei LMG 23360 citA, acn, icd
Thauera humireducens SgZ-1 SLC13A5, acn, icd
Thermoactinomyces daqus H-18 SLC13A5, acn, icd
Thermobifida halotolerans YIM 90462 SLC13A5, acn, icd
Thermodesulfovibrio aggregans TGE-P1 SLC13A5, acn, icd
Thermophagus xiamenensis HS1 SLC13A5, acn, icd
Thermovenabulum gondwanense R270 tctA, tctB, tctC, acn, icd
Thioclava dalianensis DLFJ1-1 tctA, tctB, tctC, acn, icd
Thiohalospira halophila HL 3 SLC13A5, acn, icd
Tistlia consotensis USBA 355 tctA, tctB, tctC, acn, icd
Vagococcus penaei CD276 citM, citD, citE, citF
Verminephrobacter eiseniae EF01-2 tctA, tctB, tctC, acn, icd
Weissella oryzae SG25 SLC13A5, citD, citE, citF
Williamsia sterculiae CPCC 203464 citM, acn, icd
Yersinia intermedia Y228 tctA, tctB, tctC, citD, citE, citF

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