GapMind for catabolism of small carbon sources

 

sucrose catabolism

Analysis of pathway sucrose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 sut, SUS, scrK, galU, pgmA
Actinokineospora bangkokensis 44EHW ams, MFS-glucose, glk
Actinomyces timonensis 7400942 ams, fruII-ABC, 1pfk, fba, tpi
Algiphilus aromaticivorans DG1253 sut, scrP, scrK, pgmA
Algoriphagus aquaeductus T4 ams, glcP, scrK
Algoriphagus machipongonensis PR1 ams, glcP, scrK
Alicyclobacillus ferrooxydans TC-34 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Alishewanella agri BL06 scrT, ams, scrK, glk
Alistipes indistinctus YIT 12060 ams, BT1758, scrK
Alistipes shahii WAL 8301 ams, MFS-glucose, glk
Alkalitalea saponilacus SC/BZ-SP2 ams, SSS-glucose, glk
Amantichitinum ursilacus IGB-41 ams, frcA, frcB, frcC, scrK
Amphibacillus jilinensis Y1 ams, mglA, mglB, mglC, glk
Amphritea japonica JAMM 1866 sut, SUS, scrK, galU, pgmA
Amycolatopsis halophila YIM 93223 ams, fruII-ABC*, 1pfk, fba, tpi
Amycolatopsis xylanica CPCC 202699 ams, mglA, mglB, mglC, glk
Aquimarina agarilytica ZC1 ams, SemiSWEET, glk
Aquimarina longa SW024 ams, fruII-ABC, 1pfk, fba, tpi
Aquimarina macrocephali JAMB N27 ams, MFS-glucose, glk
Archaeoglobus sulfaticallidus PM70-1 ams, fruII-ABC, 1pfk, fba, tpi
Arcticibacter svalbardensis MN12-7 ams, MFS-glucose, glk
Ardenticatena maritima 110S aglE, aglF, aglG, aglK, ams, scrK, glk
Arenimonas metalli CF5-1 sut, SUS, scrK, galU, pgmA
Arenitalea lutea P7-3-5 ams, glcP, scrK
Azospirillum humicireducens SgZ-5 ams, fruA, fruI, 1pfk, fba, tpi
Azospirillum thiophilum BV-S ams, fruA, fruI, 1pfk, fba, tpi
Bacillus altitudinis 41KF2b ams, fruII-ABC, 1pfk, fba, tpi
Bacillus coahuilensis m4-4 ams, ptsG-crr
Bacillus cytotoxicus NVH 391-98 ams, fruII-ABC, 1pfk, fba, tpi
Bacillus horneckiae 1P01SC ams, fruII-ABC, 1pfk, fba, tpi
Bacillus okhensis Kh10-101 ams, mglA, mglB, mglC, glk
Bacillus safensis FO-36b ams, fruII-ABC, 1pfk, fba, tpi
Bacillus velezensis CBMB205 ams, fruII-ABC, 1pfk, fba, tpi
Bacteroides clarus YIT 12056 ams, BT1758, scrK
Bacteroides faecis MAJ27 ams, BT1758, scrK
Bacteroides fluxus YIT 12057 ams, MFS-glucose, glk
Bacteroides oleiciplenus YIT 12058 ams, BT1758, scrK
Barnesiella intestinihominis YIT 11860 ams, MFS-glucose, glk
Belnapia rosea CPCC 100156 ams, fruA, fruI, 1pfk, fba, tpi
Bizionia argentinensis JUB59 ams, fruII-ABC, 1pfk, fba, tpi
Bradyrhizobium diazoefficiens USDA110 ams, mglA, mglB, mglC, glk
Brevibacterium jeotgali SJ5-8 sut, SUS, scrK, galU, pgmA
Brucella inopinata BO1 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Brucella microti CCM 4915 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Bryobacter aggregatus MPL3 sut, SUS, scrK, galU, pgmA
Caldicellulosiruptor hydrothermalis 108 ams, mglA, mglB, mglC, glk
Caldicellulosiruptor kronotskyensis 2002 ams, fruII-ABC, 1pfk, fba, tpi
Carboxydothermus pertinax Ug1 ams, fruII-ABC, 1pfk, fba, tpi
Catellicoccus marimammalium M35/04/3 ams, fruII-ABC, 1pfk, fba, tpi
Chromobacterium vaccinii MWU205 ams, frcA, frcB, frcC, scrK
Chryseobacterium angstadtii KM ams, SSS-glucose, glk
Chryseobacterium arthrosphaerae CC-VM-7 ams, MFS-glucose, glk
Chryseobacterium viscerum 687B-08 ams, MFS-glucose, glk
Cloacibacillus porcorum CL-84 sut, SUS, scrK, galU, pgmA
Cobetia crustatorum JO1 thuE, thuF, thuG, thuK, ams, scrK, glk
Collimonas arenae Ter10 ams, mglA, mglB, mglC, glk
Collimonas pratensis Ter91 ams, gtsA, gtsB, gtsC, gtsD, glk
Collinsella tanakaei YIT 12063 ams, manX, manY, manZ
Coprobacter fastidiosus NSB1 ams, BT1758, scrK
Corynebacterium deserti GIMN1.010 ams, MFS-glucose, glk
Corynebacterium frankenforstense ST18 ams, fruII-ABC, 1pfk, fba, tpi
Corynebacterium lactis RW2-5 ams, fruII-ABC, 1pfk, fba, tpi
Croceitalea dokdonensis DOKDO 023 ams, glcP, scrK
Cronobacter condimenti 1330 ams, fruA, fruB, 1pfk, fba, tpi
Cronobacter muytjensii ATCC 51329 ams, fruA, fruB, 1pfk, fba, tpi
Cronobacter universalis NCTC 9529 ams, fruA, fruB, 1pfk, fba, tpi
Desulfatitalea tepidiphila S28bF ams, MFS-glucose, glk
Desulfotomaculum hydrothermale Lam5 ams, fruII-ABC, 1pfk, fba, tpi
Dethiosulfovibrio salsuginis USBA 82 ams, mglA, mglB, mglC, glk
Devosia chinhatensis IPL18 ams, frcA, frcB, frcC, scrK
Devriesea agamarum IMP2 ams, fruII-ABC, 1pfk, fba, tpi
Dialister succinatiphilus YIT 11850 sut, SUS, scrK, galU, pgmA
Dietzia timorensis ID05-A0528 ams, fruII-ABC, 1pfk, fba, tpi
Dokdonella koreensis DS-123 sut, SUS, scrK, galU, pgmA
Domibacillus robiginosus WS 4628 ams, fruII-ABC, 1pfk, fba, tpi
Duganella sacchari Sac-22 ams, MFS-glucose, glk
Dyadobacter tibetensis Y620-1 ams, glcP, scrK
Dyella jiangningensis SBZ3-12 ams, MFS-glucose, glk
Endozoicomonas montiporae CL-33 ams, ptsG, crr
Enterococcus termitis LMG 8895 ams, fruII-ABC, 1pfk, fba, tpi
Enterorhabdus caecimuris B7 ams, fruII-ABC, 1pfk, fba, tpi
Epibacterium ulvae U95 aglE, aglF, aglG, aglK, ams, scrK, glk
Erythrobacter gangjinensis K7-2 ams, MFS-glucose, glk
Erythrobacter marinus HWDM-33 ams, glcP, scrK
Ethanoligenens harbinense YUAN-3 ams, fruII-ABC, 1pfk, fba, tpi
Fervidicella metallireducens AeB ams, ptsG-crr
Fibrella aestuarina BUZ 2 ams, glcP, scrK
Flammeovirga pacifica WPAGA1 ams, SSS-glucose, glk
Flaviramulus ichthyoenteri Th78 sut, scrP, scrK, pgmA
Flavobacterium beibuense F44-8 ams, fruII-ABC, 1pfk, fba, tpi
Flavobacterium glycines Gm-149 ams, glcP, scrK
Flavobacterium sp. LM5 ams, fruII-ABC, 1pfk, fba, tpi
Flavobacterium ummariense DS-12 ams, fruII-ABC, 1pfk, fba, tpi
Frischella perrara PEB0191 ams, fruA, fruB, 1pfk, fba, tpi
Galbibacter marinus ck-I2-15 ams, MFS-glucose, glk
Gallaecimonas xiamenensis 3-C-1 ams, MFS-glucose, glk
Geobacter daltonii FRC-32 ams, ptsG-crr
Gillisia marina CBA3202 ams, ptsG-crr
Gracilibacillus halophilus YIM-C55.5 ams, mglA, mglB, mglC, glk
Granulicella mallensis MP5ACTX8 ams, MFS-glucose, glk
Granulicella tundricola MP5ACTX9 ams, MFS-glucose, glk
Hafnia paralvei ATCC 29927 ams, fruA, fruB, 1pfk, fba, tpi
Haladaptatus cibarius D43 sut, SUS, scrK, galU, pgmA
Halioglobus japonicus S1-36 ams, MFS-glucose, glk
Halobacillus alkaliphilus FP5 ams, fruII-ABC, 1pfk, fba, tpi
Halococcus hamelinensis 100A6 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Halomonas salina B6 thuE, thuF, thuG, thuK, ams, scrK, glk
Halomonas smyrnensis AAD6 thuE, thuF, thuG, thuK, ams, scrK, glk
Halomonas stevensii S18214 thuE, thuF, thuG, thuK, ams, scrK, glk
Halomonas titanicae BH1 thuE, thuF, thuG, thuK, ams, scrK, glk
Halomonas xinjiangensis TRM 0175 ams, gtsA, gtsB, gtsC, gtsD, glk
Halopiger salifodinae KCY07-B2 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Halostagnicola larsenii XH-48 ams, fruII-A, fruII-B, fruII-C, 1pfk, fba, tpi
Haloterrigena daqingensis JX313 sut, SUS, scrK, galU, pgmA
Herbaspirillum aquaticum IEH 4430 ams, mglA, mglB, mglC, glk
Hippea alviniae EP5-r sut, SUS, scrK, galU, pgmA
Hippea jasoniae Mar08-272r ams, ptsG-crr
Hoeflea phototrophica DFL-43 aglE, aglF, aglG, aglK, ams, scrK, glk
Hyphomicrobium nitrativorans NL23 sut, SUS, scrK, galU, pgmA
Imtechella halotolerans K1 ams, MFS-glucose, glk
Indibacter alkaliphilus LW1 ams, glcP, scrK
Jannaschia aquimarina GSW-M26 aglE, aglF, aglG, aglK, ams, scrK, glk
Jeotgalibacillus soli P9 ams, fruII-ABC, 1pfk, fba, tpi
Kangiella geojedonensis YCS-5 sut, SUS, scrK, galU, pgmA
Knoellia flava TL1 ams, mglA, mglB, mglC, glk
Kocuria flava HO-9041 ams, fruII-ABC, 1pfk, fba, tpi
Kocuria turfanensis HO-9042 ams, fruII-ABC, 1pfk, fba, tpi
Laceyella sediminis RHA1 ams, fruII-ABC, 1pfk, fba, tpi
Lacinutrix algicola AKS293 sut, scrP, scrK, pgmA
Lacinutrix himadriensis E4-9a sut, scrP, scrK, pgmA
Lacinutrix mariniflava AKS432 ams, glcP, scrK
Lactobacillus curieae CCTCC M 2011381 sut, scrP, scrK, pgmA
Lactobacillus delbrueckii ZN7a-9 ams, fruII-ABC, 1pfk, fba, tpi
Lactobacillus hokkaidonensis LOOC260 ams, MFS-glucose, glk
Lactobacillus oryzae SG293 ams, glcU', glk
Lactobacillus pobuzihii E100301 ams, fruII-ABC, 1pfk, fba, tpi
Lactobacillus shenzhenensis LY-73 sacP, scrB, scrK
Lactobacillus silagei IWT126 ams, MFS-glucose, glk
Leeuwenhoekiella blandensis MED217 ams, SSS-glucose, glk
Lentibacillus jeotgali Grbi ams, MFS-glucose, glk
Limnohabitans curvus MWH-C5 ams, gtsA, gtsB, gtsC, gtsD, glk
Limnohabitans parvus II-B4 ams, gtsA, gtsB, gtsC, gtsD, glk
Listeria fleischmannii LU2006-1 ams, fruII-ABC, 1pfk, fba, tpi
Luteimonas huabeiensis HB2 ams, MFS-glucose, glk
Luteipulveratus mongoliensis MN07-A0370 ams, mglA, mglB, mglC, glk
Lutibaculum baratangense AMV1 sut, SUS, scrK, galU, pgmA
Lysobacter daejeonensis GH1-9 ams, SSS-glucose, glk
Magnetovibrio blakemorei MV-1 sut, ams, scrK, glk
Marinicella litoralis KMM 3900 sut, SUS, scrK, galU, pgmA
Mariniradius saccharolyticus AK6 ams, glcP, scrK
Marinobacter algicola DG893 ams, fruA, fruI, 1pfk, fba, tpi
Marinobacter guineae M3B ams, gtsA, gtsB, gtsC, gtsD, glk
Marinobacter psychrophilus 20041 sut, scrP, scrK, pgmA
Marinomonas arctica 328 aglE, aglF, aglG, aglK, ams, scrK, glk
Marivita geojedonensis DPG-138 aglE, aglF, aglG, aglK, ams, scrK, glk
Martelella endophytica YC6887 thuE, thuF, thuG, thuK, ams, scrK, glk
Megamonas funiformis YIT 11815 ams, fruII-ABC, 1pfk, fba, tpi
Mesorhizobium ciceri WSM1271 aglE, aglF, aglG, aglK, ams, scrK, glk
Methanobacterium arcticum M2 sut, SUS, scrK, galU, pgmA
Methanobacterium veterum MK4 sut, SUS, scrK, galU, pgmA
Methanocella arvoryzae MRE50 ams, fruII-ABC, 1pfk, fba, tpi
Methanococcus aeolicus Nankai-3 ams, fruII-ABC, 1pfk, fba, tpi
Methanoculleus horonobensis T10 ams, fruII-ABC, 1pfk, fba, tpi
Methanolinea tarda NOBI-1 ams, SemiSWEET, glk
Methanosarcina soligelidi SMA-21 sut, SUS, scrK, galU, pgmA
Methanospirillum lacunae Ki8-1 ams, SemiSWEET, glk
Methanospirillum stamsii Pt1 ams, SemiSWEET, glk
Methylibium petroleiphilum PM1 sut, SUS, scrK, galU, pgmA
Methylobacterium gossipiicola Gh-105 ams, fruA, fruI, 1pfk, fba, tpi
Methylocapsa aurea KYG ams, MFS-glucose, glk
Methylotenera versatilis 301 ams, fruA, fruI, 1pfk, fba, tpi
Microbacterium profundi Shh49 ams, mglA, mglB, mglC, glk
Microvirga lotononidis WSM3557 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Moritella dasanensis ArB 0140 ams, fruA, fruB, 1pfk, fba, tpi
Mucilaginibacter gossypii Gh-67 ams, glcP, scrK
Mucilaginibacter gossypiicola Gh-48 ams, glcP, scrK
Mucilaginibacter mallensis MP1X4 ams, glcP, scrK
Nafulsella turpanensis ZLM-10 ams, glcP, scrK
Natronomonas moolapensis 8.8.11 ams, fruII-ABC, 1pfk, fba, tpi
Nautilia profundicola AmH ams, fruII-ABC, 1pfk, fba, tpi
Neiella marina J221 ams, ptsG, crr
Neptunomonas antarctica S3-22 sut, SUS, scrK, galU, pgmA
Nocardioides daejeonensis MJ31 ams, MFS-glucose, glk
Nocardioides dokdonensis FR1436 ams, fruII-ABC, 1pfk, fba, tpi
Nocardiopsis baichengensis YIM 90130 ams, mglA, mglB, mglC, glk
Nocardiopsis gilva YIM 90087 ams, frcA, frcB, frcC, scrK
Novosphingobium barchaimii LL02 ams, MFS-glucose, glk
Novosphingobium fuchskuhlense FNE08-7 ams, MFS-glucose, glk
Novosphingobium lindaniclasticum LE124 ams, MFS-glucose, glk
Oceanisphaera arctica V1-41 ams, fruA, fruI, 1pfk, fba, tpi
Ochrobactrum rhizosphaerae PR17 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Ochrobactrum thiophenivorans DSM 7216 ams, mglA, mglB, mglC, glk
Oscillibacter ruminantium GH1 ams, mglA, mglB, mglC, glk
Paenisporosarcina indica PN2 sut, scrP, scrK, pgmA
Palaeococcus pacificus DY20341 ams, fruII-ABC, 1pfk, fba, tpi
Paludibacter propionicigenes WB4 ams, SemiSWEET, glk
Pandoraea thiooxydans ATSB16 ams, MFS-glucose, glk
Pantoea rwandensis LMG 26275 ams, mglA, mglB, mglC, glk
Pedobacter arcticus A12 ams, MFS-glucose, glk
Photobacterium gaetbulicola Gung47 ams, fruA, fruB, 1pfk, fba, tpi
Photobacterium jeanii R-40508 ams, fruA, fruB, 1pfk, fba, tpi
Phyllobacterium brassicacearum STM 196 thuE, thuF, thuG, thuK, SUS, scrK, galU, pgmA
Phyllobacterium endophyticum PEPV15 ams, gtsA, gtsB, gtsC, gtsD, glk
Phyllobacterium leguminum ORS 1419 aglE, aglF, aglG, aglK, SUS, scrK, galU, pgmA
Planktomarina temperata RCA23 ams, mglA, mglB, mglC, glk
Planococcus halocryophilus Or1 ams, fruII-ABC, 1pfk, fba, tpi
Pleomorphomonas diazotrophica R5-392 thuE, thuF, thuG, thuK, scrP, scrK, pgmA
Polaribacter dokdonensis DSW-5 ams, glcP, scrK
Pontibacillus litoralis JSM 072002 ams, ptsG-crr
Pontibacter lucknowensis DM9 ams, MFS-glucose, glk
Pontibacter ramchanderi LP43 ams, MFS-glucose, glk
Pontimonas salivibrio CL-TW6 ams, fruII-ABC, 1pfk, fba, tpi
Porphyrobacter dokdonensis DSW-74 ams, fruP, scrK
Pseudoalteromonas arctica A 37-1-2 scrT, scrP, scrK, pgmA
Pseudomonas baetica a390 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas litoralis 2SM5 sut, SUS, scrK, galU, pgmA
Pseudomonas taeanensis MS-3 ams, gtsA, gtsB, gtsC, gtsD, glk
Pseudovibrio axinellae Ad2 ams, gtsA, gtsB, gtsC, gtsD, glk
Psychrobacter arcticus 273-4 ams, fruII-ABC, 1pfk, fba, tpi
Psychrobacter cryohalolentis K5 ams, fruII-ABC, 1pfk, fba, tpi
Psychromonas ingrahamii 37 aglE, aglF, aglG, aglK, ams, scrK, glk
Psychromonas ossibalaenae JAMM 0738 ams, fruA, fruB, 1pfk, fba, tpi
Rhizobium freirei PRF 81 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhizobium grahamii CCGE 502 thuE, thuF, thuG, thuK, ams, scrK, glk
Rhizobium subbaraonis JC85 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhodanobacter denitrificans 2APBS1 ams, MFS-glucose, glk
Rhodobacter johrii JA192 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhodobacter maris JA276 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhodobacter ovatus JA234 ams, frcA, frcB, frcC, scrK
Rhodobacter viridis JA737 aglE, aglF, aglG, aglK, ams, scrK, glk
Rhodococcus qingshengii djl-6-2 ams, fruII-ABC, 1pfk, fba, tpi
Rhodopseudomonas pseudopalustris DSM 123 sut, SUS, scrK, galU, pgmA
Roseateles aquatilis CCUG 48205 ams, gtsA, gtsB, gtsC, gtsD, glk
Roseivirga spongicola UST030701-084 ams, MFS-glucose, glk
Rubrivirga marina SAORIC-28 ams, MFS-glucose, glk
Ruegeria conchae TW15 ams, frcA, frcB, frcC, scrK
Saccharomonospora marina XMU15 ams, fruII-ABC, 1pfk, fba, tpi
Salinicoccus carnicancri Crm ams, fruII-ABC, 1pfk, fba, tpi
Serinicoccus profundi MCCC 1A05965 ams, MFS-glucose, glk
Shewanella halifaxensis HAW-EB4 ams, SSS-glucose, glk
Skermanella stibiiresistens SB22 ams, fruA, fruI, 1pfk, fba, tpi
Snodgrassella alvi wkB2 sut, SUS, scrK, galU, pgmA
Sphaerochaeta globosa Buddy ams, fruE, fruF, fruG, fruK, scrK
Sphaerochaeta pleomorpha Grapes ams, mglA, mglB, mglC, glk
Sphingobium baderi LL03 ams, MFS-glucose, glk
Sphingobium czechense LL01 ams, MFS-glucose, glk
Sphingobium quisquiliarum P25 ams, MFS-glucose, glk
Sphingomonas histidinilytica UM2 sut, SUS, scrK, galU, pgmA
Sphingomonas indica Dd16 sut, SUS, scrK, galU, pgmA
Sphingomonas laterariae LNB2 ams, MFS-glucose, glk
Sphingopyxis indica DS15 ams, MFS-glucose, glk
Sphingopyxis terrae UI2 ams, MFS-glucose, glk
Sporolactobacillus vineae SL153 ams, manX, manY, manZ
Streptacidiphilus oryzae TH49 ams, fruII-ABC, 1pfk, fba, tpi
Streptococcus anginosus CCUG 39159 ams, fruII-ABC, 1pfk, fba, tpi
Streptococcus massiliensis 4401825 ams, fruII-ABC, 1pfk, fba, tpi
Streptococcus oralis 7747 ams, fruII-ABC, 1pfk, fba, tpi
Streptococcus oralis AZ_3a ams, fruII-ABC, 1pfk, fba, tpi
Streptomyces kebangsaanensis SUK12 ams, mglA, mglB, mglC, glk
Succinatimonas hippei YIT 12066 ams, mglA, mglB, mglC, glk
Sulfurimonas gotlandica GD1 ams, fruII-ABC, 1pfk, fba, tpi
Tatumella morbirosei LMG 23360 ams, fruA, fruB, 1pfk, fba, tpi
Thauera humireducens SgZ-1 sut, SUS, scrK, galU, pgmA
Thermoactinomyces daqus H-18 ams, fruII-ABC, 1pfk, fba, tpi
Thermobifida halotolerans YIM 90462 ams, MFS-glucose, glk
Thermodesulfovibrio aggregans TGE-P1 ams, SemiSWEET, glk
Thermophagus xiamenensis HS1 ams, SSS-glucose, glk
Thermovenabulum gondwanense R270 ams, ptsG-crr
Thioclava dalianensis DLFJ1-1 aglE, aglF, aglG, aglK, ams, scrK, glk
Thiohalospira halophila HL 3 sut, ams, scrK, glk
Tistlia consotensis USBA 355 ams, mglA, mglB, mglC, glk
Vagococcus penaei CD276 ams, fruII-ABC, 1pfk, fba, tpi
Verminephrobacter eiseniae EF01-2 ams, mglA, mglB, mglC, glk
Weissella oryzae SG25 ams, manX, manY, manZ
Williamsia sterculiae CPCC 203464 ams, fruII-ABC, 1pfk, fba, tpi
Yersinia intermedia Y228 ams, fruA, fruB, 1pfk, fba, 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