GapMind for Amino acid biosynthesis

 

chorismate biosynthesis

Analysis of pathway chorismate in 206 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Acidithiobacillus ferrooxidans ATCC 23270 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Acidovorax sp. GW101-3H11 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Algiphilus aromaticivorans DG1253 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Alicycliphilus denitrificans K601 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Alkalihalobacterium alkalinitrilicum DSM 22532 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Allochromatium vinosum DSM 180 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Ammonifex degensii KC4 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Anaerobutyricum hallii DSM 3353 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Aquimarina longa SW024 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Archaeoglobus veneficus SNP6 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Arcobacter nitrofigilis DSM 7299 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Azoarcus olearius BH72 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Azohydromonas australica DSM 1124 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Azorhizobium caulinodans ORS 571 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Azospirillum brasilense Sp245 aroG, aroB, aroD, aroE, aroL?, aroA, aroC
Azospirillum sp. B510 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Bacteroides thetaiotaomicron VPI-5482 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Beijerinckia indica subsp. indica ATCC 9039 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Beijerinckia mobilis UQM 1969 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Bradyrhizobium sp. BTAi1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Brevundimonas sp. GW460-12-10-14-LB2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Burkholderia phytofirmans PsJN aroG, aroB, aroD, aroE, aroL, aroA, aroC
Burkholderia vietnamiensis G4 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Calditerrivibrio nitroreducens DSM 19672 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Caminibacter mediatlanticus TB-2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Carboxydothermus pertinax Ug1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Caulobacter crescentus NA1000 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Cereibacter sphaeroides ATCC 17029 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Chlorobaculum parvum NCIB 8327 aroG, aroB, aroD, aroE, aroL, aroA, aroC?
Chlorobaculum tepidum TLS aroG, aroB, aroD, aroE, aroL, aroA, aroC
Chlorobium limicola DSM 245 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Chlorobium phaeobacteroides BS1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Clostridium acetobutylicum ATCC 824 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Clostridium kluyveri DSM 555 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Clostridium tyrobutyricum FAM22553 aroG, aroB, aroD, aroE, aroL?, aroA, aroC
Crocosphaera subtropica ATCC 51142 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Cupriavidus basilensis FW507-4G11 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Dechloromonas agitata is5 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Dechlorosoma suillum PS aroG, aroB, aroD, aroE, aroL, aroA, aroC
Dehalococcoides mccartyi 195 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Denitrovibrio acetiphilus DSM 12809 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Derxia gummosa DSM 723 tpiA, fbp, asp-kinase, asd, aroA'?, aroB'?, aroD, aroE, aroL, aroA, aroC
Desulfacinum hydrothermale DSM 13146 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfacinum infernum DSM 9756 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfarculus baarsii DSM 2075 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfatibacillum aliphaticivorans DSM 15576 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfatiglans anilini DSM 4660 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfitobacterium hafniense DCB-2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfobacca acetoxidans DSM 11109 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfobacter vibrioformis DSM 8776 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfogranum mediterraneum DSM 13871 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulforamulus ruminis DSM 2154 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfoscipio geothermicus DSM 3669 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfotalea psychrophila LSv54 tpiA, fbp, asp-kinase, asd, aroA'?, aroB'?, aroD, aroE, aroL, aroA, aroC
Desulfovibrio oxyclinae DSM 11498 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfovibrio vulgaris Hildenborough JW710 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfovibrio vulgaris Miyazaki F tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfurobacterium atlanticum DSM 15668 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Desulfuromonas acetexigens DSM 1397 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Desulfuromusa kysingii DSM 7343 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Dinoroseobacter shibae DFL-12 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Dyella japonica UNC79MFTsu3.2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Echinicola vietnamensis KMM 6221, DSM 17526 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Escherichia coli BW25113 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Ferroglobus placidus DSM 10642 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Frankia alni ACN14a aroG, aroB, aroD, aroE, aroL, aroA, aroC
Geobacter metallireducens GS-15 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Geotalea uraniireducens Rf4 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Halococcus hamelinensis 100A6 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD?, aroE, aroL, aroA, aroC
Haloechinothrix alba DSM 45207 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Haloferax volcanii DS2 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Haloglycomyces albus DSM 45210 aroG, aroB, aroD?, aroE, aroL, aroA, aroC
Halomonas desiderata SP1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Halorhodospira halophila SL1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Herbaspirillum autotrophicum IAM 14942 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Herbaspirillum seropedicae SmR1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hippea alviniae EP5-r aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hydrogenovibrio halophilus DSM 15072 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hydrogenovibrio kuenenii DSM 12350 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hydrogenovibrio marinus DSM 11271 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Hyphomicrobium sulfonivorans WDL6 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Klebsiella michiganensis M5al aroG, aroB, aroD, aroE, aroL, aroA, aroC
Klebsiella variicola At-22 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Kyrpidia tusciae DSM 2912 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Leptospirillum ferrooxidans C2-3 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Lysobacter soli OAE881 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Magnetospirillum magneticum AMB-1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Malonomonas rubra DSM 5091 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Maridesulfovibrio bastinii DSM 16055 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Maridesulfovibrio zosterae DSM 11974 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Marinobacter adhaerens HP15 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Mesorhizobium ciceri biovar biserrulae WSM1271 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methanobacterium lacus AL-21 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanococcus aeolicus Nankai-3 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanococcus maripaludis C5 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanosarcina acetivorans C2A tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanosarcina mazei Go1 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanospirillum lacunae Ki8-1 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Methanothermobacter thermautotrophicus str. Delta H tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE?, aroL, aroA, aroC
Methylobacterium nodulans ORS 2060 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylobacterium sp. 4-46 Apr-46 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylocapsa acidiphila B2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylocapsa aurea KYG aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylocella silvestris BL2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylococcus capsulatus str. Bath aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylocystis bryophila S285 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methyloferula stellata AR4 AR4T aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylohalobius crimeensis 10Ki aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylomonas methanica MC09 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylosarcina fibrata AML-C10 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylotuvimicrobium alcaliphilum 20Z aroG, aroB, aroD, aroE, aroL, aroA, aroC
Methylovulum miyakonense HT12 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Mucilaginibacter yixingensis DSM 26809 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Mycolicibacterium vanbaalenii PYR-1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nitratifractor salsuginis DSM 16511 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nitratiruptor tergarcus DSM 16512 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nitriliruptor alkaliphilus DSM 45188 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nitrosopumilus maritimus SCM1 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Nocardioides dokdonensis FR1436 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nocardiopsis lucentensis DSM 44048 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Novosphingobium aromaticivorans DSM 12444 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Oleispira antarctica RB-8 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Paraburkholderia atlantica CCGE1002 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Paraburkholderia bryophila 376MFSha3.1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Paraburkholderia phymatum STM815 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Paucidesulfovibrio gracilis DSM 16080 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Pedobacter sp. GW460-11-11-14-LB5 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pelobacter propionicus DSM 2379 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Persephonella marina EX-H1 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Phaeacidiphilus oryzae TH49 aroG, aroB, aroD, aroE, aroL, aroA, aroC?
Phaeobacter inhibens BS107 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Polaromonas naphthalenivorans CJ2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Prosthecochloris aestuarii DSM 271 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudarthrobacter sulfonivorans Ar51 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas benzenivorans DSM 8628 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas fluorescens FW300-N1B4 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas fluorescens FW300-N2C3 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas fluorescens FW300-N2E2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas fluorescens FW300-N2E3 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas fluorescens GW456-L13 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas putida KT2440 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas simiae WCS417 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pseudomonas stutzeri RCH2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Pyrolobus fumarii 1A aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhizobium etli CFN 42 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhizobium johnstonii 3841 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhizobium leguminosarum bv. trifolii WSM1325 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhizorhabdus wittichii RW1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhodanobacter denitrificans FW104-10B01 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhodomicrobium vannielii ATCC 17100 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhodopseudomonas palustris CGA009 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhodospirillum centenum SW SW; ATCC 51521 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Rhodospirillum rubrum ATCC 11170 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Roseburia faecis M72 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Saccharomonospora cyanea NA-134 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sedimenticola selenatireducens DSM 17993 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Shewanella amazonensis SB2B aroG, aroB, aroD, aroE, aroL, aroA, aroC
Shewanella loihica PV-4 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Shewanella oneidensis MR-1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Shewanella sp. ANA-3 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sinorhizobium fredii NGR234 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sinorhizobium medicae WSM419 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sinorhizobium meliloti 1021 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sphingomonas koreensis DSMZ 15582 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Stenotrophomonas chelatiphaga DSM 21508 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Steroidobacter denitrificans DSM 18526 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Stutzerimonas stutzeri A1501 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sulfuricurvum kujiense DSM 16994 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sulfurihydrogenibium azorense Az-Fu1 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Sulfurihydrogenibium subterraneum DSM 15120 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Sulfurimonas denitrificans DSM 1251 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sulfuritalea hydrogenivorans sk43H DSM 22779 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Sulfurivirga caldicuralii DSM 17737 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Synechococcus elongatus PCC 7942 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Teredinibacter turnerae T7901 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thauera aminoaromatica S2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thermithiobacillus tepidarius DSM 3134 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thermoanaerobacter kivui LKT-1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thermocrinis albus DSM 14484 tpiA, fbp, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Thermodesulforhabdus norvegica DSM 9990 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thermomonospora curvata DSM 43183 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thermovibrio ammonificans HB-1 tpiA, fbp?, asp-kinase, asd, aroA', aroB', aroD, aroE, aroL, aroA, aroC
Thermus aquaticus YT-1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thioalkalivibrio denitrificans ALJD aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thioalkalivibrio halophilus HL17 aroG, aroB, aroD, aroE, aroL, aroA, aroC?
Thioalkalivibrio paradoxus ARh 1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thioalkalivibrio thiocyanodenitrificans ARhD 1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiohalomonas denitrificans HLD2 aroG, aroB, aroD, aroE, aroL, aroA?, aroC
Thiohalospira halophila DSM 15071 HL 3 aroG, aroB, aroD, aroE, aroL, aroA?, aroC
Thiomicrorhabdus arctica DSM 13458 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiomicrorhabdus chilensis DSM 12352 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiomicrospira cyclica ALM1 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiomicrospira microaerophila ASL8-2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiomicrospira pelophila DSM 1534 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Thiothrix lacustris DSM 21227 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Tistlia consotensis USBA 355 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Trichlorobacter lovleyi SZ aroG, aroB, aroD, aroE, aroL, aroA, aroC
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome aroG, aroB, aroD, aroE, aroL, aroA, aroC
Trichormus variabilis ATCC 29413 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Xanthobacter autotrophicus Py2 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Xanthomonas campestris pv. campestris strain 8004 aroG, aroB, aroD, aroE, aroL, aroA, aroC
Xenophilus azovorans DSM 13620 aroG, aroB, aroD, aroE, aroL, aroA, aroC

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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