GapMind for catabolism of small carbon sources

 

glycerol catabolism

Analysis of pathway glycerol in 276 genomes

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

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