GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis

Analysis of pathway lys in 276 genomes

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

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 Apr 09 2024. The underlying query database was built on Apr 09 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