GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis

Analysis of pathway met in 276 genomes

Genome Best path
Acidovorax caeni R-24608 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Actinokineospora bangkokensis 44EHW asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Actinomyces timonensis 7400942 asp-kinase, asd, hom, metX, metY, metE
Algiphilus aromaticivorans DG1253 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Algoriphagus aquaeductus T4 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Algoriphagus machipongonensis PR1 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Alicyclobacillus ferrooxydans TC-34 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Alishewanella agri BL06 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Alistipes indistinctus YIT 12060 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Alistipes shahii WAL 8301 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Alkalitalea saponilacus SC/BZ-SP2 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Amantichitinum ursilacus IGB-41 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Amphibacillus jilinensis Y1 asp-kinase, asd, hom, metX, metB, metC, metE
Amphritea japonica JAMM 1866 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Amycolatopsis halophila YIM 93223 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Amycolatopsis xylanica CPCC 202699 asp-kinase, asd, hom, metX, metY, metE
Aquimarina agarilytica ZC1 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Aquimarina longa SW024 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Aquimarina macrocephali JAMB N27 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Archaeoglobus sulfaticallidus PM70-1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Arcticibacter svalbardensis MN12-7 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Ardenticatena maritima 110S asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Arenimonas metalli CF5-1 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Arenitalea lutea P7-3-5 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Azospirillum humicireducens SgZ-5 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Azospirillum thiophilum BV-S asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Bacillus altitudinis 41KF2b asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Bacillus coahuilensis m4-4 asp-kinase, asd, hom, metX, metB, metC, metE
Bacillus cytotoxicus NVH 391-98 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Bacillus horneckiae 1P01SC asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Bacillus okhensis Kh10-101 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Bacillus safensis FO-36b asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Bacillus velezensis CBMB205 asp-kinase, asd, hom, metX, metB, metC, metE
Bacteroides clarus YIT 12056 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Bacteroides faecis MAJ27 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Bacteroides fluxus YIT 12057 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Bacteroides oleiciplenus YIT 12058 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Barnesiella intestinihominis YIT 11860 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Belnapia rosea CPCC 100156 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Bizionia argentinensis JUB59 asp-kinase, asd, hom, metX, metY, metE
Bradyrhizobium diazoefficiens USDA110 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Brevibacterium jeotgali SJ5-8 asp-kinase, asd, hom, metX, metY, metE
Brucella inopinata BO1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Brucella microti CCM 4915 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Bryobacter aggregatus MPL3 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Caldicellulosiruptor hydrothermalis 108 asp-kinase, asd, hom, metX, metY, metE
Caldicellulosiruptor kronotskyensis 2002 asp-kinase, asd, hom, metX, metY, metE
Carboxydothermus pertinax Ug1 asp-kinase, asd, hom, metX, metY, mesB
Catellicoccus marimammalium M35/04/3 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Chromobacterium vaccinii MWU205 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Chryseobacterium angstadtii KM asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Chryseobacterium arthrosphaerae CC-VM-7 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Chryseobacterium viscerum 687B-08 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Cloacibacillus porcorum CL-84 asp-kinase, asd, hom, metX, metY, metH, ramA
Cobetia crustatorum JO1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Collimonas arenae Ter10 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Collimonas pratensis Ter91 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Collinsella tanakaei YIT 12063 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Coprobacter fastidiosus NSB1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Corynebacterium deserti GIMN1.010 asp-kinase, asd, hom, metX, metB, metC, metE
Corynebacterium frankenforstense ST18 asp-kinase, asd, hom, metX, metB, metC, metE
Corynebacterium lactis RW2-5 asp-kinase, asd, hom, metX, metB, metC, metE
Croceitalea dokdonensis DOKDO 023 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Cronobacter condimenti 1330 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Cronobacter muytjensii ATCC 51329 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Cronobacter universalis NCTC 9529 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Desulfatitalea tepidiphila S28bF asp-kinase, asd, hom, metX, metY, mesB
Desulfotomaculum hydrothermale Lam5 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Dethiosulfovibrio salsuginis USBA 82 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, ramA
Devosia chinhatensis IPL18 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Devriesea agamarum IMP2 asp-kinase, asd, hom, metX, metY, metE
Dialister succinatiphilus YIT 11850 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Dietzia timorensis ID05-A0528 asp-kinase, asd, hom, metX, metY, metE
Dokdonella koreensis DS-123 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Domibacillus robiginosus WS 4628 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Duganella sacchari Sac-22 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Dyadobacter tibetensis Y620-1 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Dyella jiangningensis SBZ3-12 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Endozoicomonas montiporae CL-33 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Enterococcus termitis LMG 8895 asp-kinase, asd, hom, metX, metB, metC, metE
Enterorhabdus caecimuris B7 asp-kinase, asd, hom, metX, metY, metE
Epibacterium ulvae U95 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Erythrobacter gangjinensis K7-2 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Erythrobacter marinus HWDM-33 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Ethanoligenens harbinense YUAN-3 asp-kinase, asd, hom, metX, metY, metE
Fervidicella metallireducens AeB asp-kinase, asd, hom, metA, metB, metC, metE
Fibrella aestuarina BUZ 2 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Flammeovirga pacifica WPAGA1 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Flaviramulus ichthyoenteri Th78 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Flavobacterium beibuense F44-8 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Flavobacterium glycines Gm-149 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Flavobacterium sp. LM5 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Flavobacterium ummariense DS-12 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Frischella perrara PEB0191 asp-kinase, asd, hom, metA, metB, metC, metE
Galbibacter marinus ck-I2-15 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Gallaecimonas xiamenensis 3-C-1 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Geobacter daltonii FRC-32 asp-kinase, asd, hom, metX, metY, metH, ramA
Gillisia marina CBA3202 asp-kinase, asd, hom, metX, metY, metE
Gracilibacillus halophilus YIM-C55.5 asp-kinase, asd, hom, metX, metB, metC, metE
Granulicella mallensis MP5ACTX8 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Granulicella tundricola MP5ACTX9 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Hafnia paralvei ATCC 29927 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Haladaptatus cibarius D43 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Halioglobus japonicus S1-36 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Halobacillus alkaliphilus FP5 asp-kinase, asd, hom, metX, metB, metC, metE
Halococcus hamelinensis 100A6 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Halomonas salina B6 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Halomonas smyrnensis AAD6 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Halomonas stevensii S18214 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Halomonas titanicae BH1 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Halomonas xinjiangensis TRM 0175 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Halopiger salifodinae KCY07-B2 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Halostagnicola larsenii XH-48 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Haloterrigena daqingensis JX313 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Herbaspirillum aquaticum IEH 4430 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Hippea alviniae EP5-r asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Hippea jasoniae Mar08-272r asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Hoeflea phototrophica DFL-43 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Hyphomicrobium nitrativorans NL23 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Imtechella halotolerans K1 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Indibacter alkaliphilus LW1 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Jannaschia aquimarina GSW-M26 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Jeotgalibacillus soli P9 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Kangiella geojedonensis YCS-5 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Knoellia flava TL1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Kocuria flava HO-9041 asp-kinase, asd, hom, metX, metY, mesD, mesX
Kocuria turfanensis HO-9042 asp-kinase, asd, hom, metX, metY, mesD, mesX
Laceyella sediminis RHA1 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Lacinutrix algicola AKS293 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Lacinutrix himadriensis E4-9a asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Lacinutrix mariniflava AKS432 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Lactobacillus curieae CCTCC M 2011381 asp-kinase, asd, hom, metX, metB, metC, metE
Lactobacillus delbrueckii ZN7a-9 asp-kinase, asd, hom, metX, metB, metC, metE
Lactobacillus hokkaidonensis LOOC260 asp-kinase, asd, hom, metX, metY, metE
Lactobacillus oryzae SG293 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Lactobacillus pobuzihii E100301 asp-kinase, asd, hom, metX, metB, metC, metE
Lactobacillus shenzhenensis LY-73 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Lactobacillus silagei IWT126 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Leeuwenhoekiella blandensis MED217 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Lentibacillus jeotgali Grbi asp-kinase, asd, hom, metX, metB, metC, metE
Limnohabitans curvus MWH-C5 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Limnohabitans parvus II-B4 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Listeria fleischmannii LU2006-1 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Luteimonas huabeiensis HB2 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Luteipulveratus mongoliensis MN07-A0370 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Lutibaculum baratangense AMV1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Lysobacter daejeonensis GH1-9 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Magnetovibrio blakemorei MV-1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Marinicella litoralis KMM 3900 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Mariniradius saccharolyticus AK6 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Marinobacter algicola DG893 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Marinobacter guineae M3B asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Marinobacter psychrophilus 20041 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Marinomonas arctica 328 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Marivita geojedonensis DPG-138 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Martelella endophytica YC6887 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Megamonas funiformis YIT 11815 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Mesorhizobium ciceri WSM1271 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Methanobacterium arcticum M2 asp-kinase, asd, hom, metX, metY, mesA
Methanobacterium veterum MK4 asp-kinase, asd, hom, metX, metY, mesA
Methanocella arvoryzae MRE50 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanococcus aeolicus Nankai-3 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanoculleus horonobensis T10 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanolinea tarda NOBI-1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanosarcina soligelidi SMA-21 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Methanospirillum lacunae Ki8-1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanospirillum stamsii Pt1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methylibium petroleiphilum PM1 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Methylobacterium gossipiicola Gh-105 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methylocapsa aurea KYG asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methylotenera versatilis 301 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Microbacterium profundi Shh49 asp-kinase, asd, hom, metX, metB, metC, mesD, mesX
Microvirga lotononidis WSM3557 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Moritella dasanensis ArB 0140 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Mucilaginibacter gossypii Gh-67 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Mucilaginibacter gossypiicola Gh-48 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Mucilaginibacter mallensis MP1X4 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Nafulsella turpanensis ZLM-10 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Natronomonas moolapensis 8.8.11 asp-kinase, asd, hom, metX, metY, split_metE_1, split_metE_2
Nautilia profundicola AmH asp-kinase, asd, hom, metX, metY, metE
Neiella marina J221 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Neptunomonas antarctica S3-22 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Nocardioides daejeonensis MJ31 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Nocardioides dokdonensis FR1436 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Nocardiopsis baichengensis YIM 90130 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Nocardiopsis gilva YIM 90087 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Novosphingobium barchaimii LL02 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Novosphingobium fuchskuhlense FNE08-7 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Novosphingobium lindaniclasticum LE124 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Oceanisphaera arctica V1-41 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Ochrobactrum rhizosphaerae PR17 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Ochrobactrum thiophenivorans DSM 7216 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Oscillibacter ruminantium GH1 asp-kinase, asd, hom, metX, metY, metE
Paenisporosarcina indica PN2 asp-kinase, asd, hom, metX, metY, metE
Palaeococcus pacificus DY20341 asp-kinase, asd, hom, metX, metY, metE
Paludibacter propionicigenes WB4 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Pandoraea thiooxydans ATSB16 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Pantoea rwandensis LMG 26275 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Pedobacter arcticus A12 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Photobacterium gaetbulicola Gung47 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Photobacterium jeanii R-40508 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Phyllobacterium brassicacearum STM 196 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Phyllobacterium endophyticum PEPV15 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Phyllobacterium leguminum ORS 1419 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Planktomarina temperata RCA23 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Planococcus halocryophilus Or1 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Pleomorphomonas diazotrophica R5-392 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Polaribacter dokdonensis DSW-5 asp-kinase, asd, hom, hom_kinase, metB, metC, metH*, B12-reactivation-domain
Pontibacillus litoralis JSM 072002 asp-kinase, asd, hom, metX, metY, metE
Pontibacter lucknowensis DM9 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Pontibacter ramchanderi LP43 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Pontimonas salivibrio CL-TW6 asp-kinase, asd, hom, metX, metY, metE
Porphyrobacter dokdonensis DSW-74 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Pseudoalteromonas arctica A 37-1-2 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Pseudomonas baetica a390 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Pseudomonas litoralis 2SM5 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas taeanensis MS-3 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Pseudovibrio axinellae Ad2 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Psychrobacter arcticus 273-4 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Psychrobacter cryohalolentis K5 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Psychromonas ingrahamii 37 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Psychromonas ossibalaenae JAMM 0738 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Rhizobium freirei PRF 81 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhizobium grahamii CCGE 502 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhizobium subbaraonis JC85 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhodanobacter denitrificans 2APBS1 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Rhodobacter johrii JA192 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Rhodobacter maris JA276 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Rhodobacter ovatus JA234 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Rhodobacter viridis JA737 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Rhodococcus qingshengii djl-6-2 asp-kinase, asd, hom, metX, metY, metE
Rhodopseudomonas pseudopalustris DSM 123 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Roseateles aquatilis CCUG 48205 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Roseivirga spongicola UST030701-084 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rubrivirga marina SAORIC-28 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Ruegeria conchae TW15 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Saccharomonospora marina XMU15 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Salinicoccus carnicancri Crm asp-kinase, asd, hom, metX, metB, metC, metE
Serinicoccus profundi MCCC 1A05965 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Shewanella halifaxensis HAW-EB4 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Skermanella stibiiresistens SB22 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Snodgrassella alvi wkB2 asp-kinase, asd, hom, metA, metB, metC, metE
Sphaerochaeta globosa Buddy asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Sphaerochaeta pleomorpha Grapes asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Sphingobium baderi LL03 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sphingobium czechense LL01 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sphingobium quisquiliarum P25 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sphingomonas histidinilytica UM2 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Sphingomonas indica Dd16 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Sphingomonas laterariae LNB2 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sphingopyxis indica DS15 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sphingopyxis terrae UI2 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Sporolactobacillus vineae SL153 asp-kinase, asd, hom, metX, metY, metE
Streptacidiphilus oryzae TH49 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Streptococcus anginosus CCUG 39159 asp-kinase, asd, hom, metX, metB, metC, metE
Streptococcus massiliensis 4401825 asp-kinase, asd, hom, metX, metB, metC, metE
Streptococcus oralis 7747 asp-kinase, asd, hom, metX, metB, metC, metE
Streptococcus oralis AZ_3a asp-kinase, asd, hom, metX, metB, metC, metE
Streptomyces kebangsaanensis SUK12 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Succinatimonas hippei YIT 12066 asp-kinase, asd, hom, metX, metY, metE
Sulfurimonas gotlandica GD1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Tatumella morbirosei LMG 23360 asp-kinase, asd, hom, metA, metB, metC, mesD, mesX
Thauera humireducens SgZ-1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thermoactinomyces daqus H-18 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Thermobifida halotolerans YIM 90462 asp-kinase, asd, hom, metX, metY, metE
Thermodesulfovibrio aggregans TGE-P1 asp-kinase, asd, hom, metX, metY, metE
Thermophagus xiamenensis HS1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Thermovenabulum gondwanense R270 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Thioclava dalianensis DLFJ1-1 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Thiohalospira halophila HL 3 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Tistlia consotensis USBA 355 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Vagococcus penaei CD276 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Verminephrobacter eiseniae EF01-2 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Weissella oryzae SG25 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Williamsia sterculiae CPCC 203464 asp-kinase, asd, hom, metX, metY, metE
Yersinia intermedia Y228 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain

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 26 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