GapMind for catabolism of small carbon sources

 

L-lysine catabolism

Analysis of pathway lysine in 201 genomes

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

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