GapMind for catabolism of small carbon sources

 

L-lysine catabolism

Analysis of pathway lysine in 276 genomes

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

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