GapMind for catabolism of small carbon sources

 

L-fucose catabolism

Analysis of pathway fucose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Actinokineospora bangkokensis 44EHW fucP, fucU, fucI, fucK, fucA, tpi, fucO
Actinomyces timonensis 7400942 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Algiphilus aromaticivorans DG1253 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Algoriphagus aquaeductus T4 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Algoriphagus machipongonensis PR1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Alicyclobacillus ferrooxydans TC-34 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Alishewanella agri BL06 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Alistipes indistinctus YIT 12060 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Alistipes shahii WAL 8301 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Alkalitalea saponilacus SC/BZ-SP2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Amantichitinum ursilacus IGB-41 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Amphibacillus jilinensis Y1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Amphritea japonica JAMM 1866 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Amycolatopsis halophila YIM 93223 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Amycolatopsis xylanica CPCC 202699 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Aquimarina agarilytica ZC1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Aquimarina longa SW024 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Aquimarina macrocephali JAMB N27 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Archaeoglobus sulfaticallidus PM70-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Arcticibacter svalbardensis MN12-7 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Ardenticatena maritima 110S fucP, fucU, fucI, fucK, fucA, tpi, aldA
Arenimonas metalli CF5-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Arenitalea lutea P7-3-5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Azospirillum humicireducens SgZ-5 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Azospirillum thiophilum BV-S fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bacillus altitudinis 41KF2b fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus coahuilensis m4-4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus cytotoxicus NVH 391-98 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus horneckiae 1P01SC fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus okhensis Kh10-101 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus safensis FO-36b fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacillus velezensis CBMB205 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bacteroides clarus YIT 12056 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Bacteroides faecis MAJ27 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Bacteroides fluxus YIT 12057 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Bacteroides oleiciplenus YIT 12058 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Barnesiella intestinihominis YIT 11860 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Belnapia rosea CPCC 100156 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bizionia argentinensis JUB59 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Bradyrhizobium diazoefficiens USDA110 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Brevibacterium jeotgali SJ5-8 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Brucella inopinata BO1 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Brucella microti CCM 4915 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bryobacter aggregatus MPL3 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Caldicellulosiruptor hydrothermalis 108 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, fucO
Caldicellulosiruptor kronotskyensis 2002 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Carboxydothermus pertinax Ug1 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Catellicoccus marimammalium M35/04/3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chromobacterium vaccinii MWU205 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chryseobacterium angstadtii KM fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chryseobacterium arthrosphaerae CC-VM-7 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chryseobacterium viscerum 687B-08 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cloacibacillus porcorum CL-84 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cobetia crustatorum JO1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Collimonas arenae Ter10 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Collimonas pratensis Ter91 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Collinsella tanakaei YIT 12063 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Coprobacter fastidiosus NSB1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Corynebacterium deserti GIMN1.010 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Corynebacterium frankenforstense ST18 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Corynebacterium lactis RW2-5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Croceitalea dokdonensis DOKDO 023 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cronobacter condimenti 1330 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Cronobacter muytjensii ATCC 51329 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cronobacter universalis NCTC 9529 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfatitalea tepidiphila S28bF fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfotomaculum hydrothermale Lam5 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Dethiosulfovibrio salsuginis USBA 82 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Devosia chinhatensis IPL18 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Devriesea agamarum IMP2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dialister succinatiphilus YIT 11850 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dietzia timorensis ID05-A0528 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dokdonella koreensis DS-123 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Domibacillus robiginosus WS 4628 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Duganella sacchari Sac-22 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Dyadobacter tibetensis Y620-1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Dyella jiangningensis SBZ3-12 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Endozoicomonas montiporae CL-33 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, fucO
Enterococcus termitis LMG 8895 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Enterorhabdus caecimuris B7 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Epibacterium ulvae U95 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Erythrobacter gangjinensis K7-2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Erythrobacter marinus HWDM-33 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Ethanoligenens harbinense YUAN-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Fervidicella metallireducens AeB fucP, fucU, fucI, fucK, fucA, tpi, aldA
Fibrella aestuarina BUZ 2 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Flammeovirga pacifica WPAGA1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Flaviramulus ichthyoenteri Th78 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Flavobacterium beibuense F44-8 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Flavobacterium glycines Gm-149 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Flavobacterium sp. LM5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Flavobacterium ummariense DS-12 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Frischella perrara PEB0191 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Galbibacter marinus ck-I2-15 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Gallaecimonas xiamenensis 3-C-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Geobacter daltonii FRC-32 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Gillisia marina CBA3202 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Gracilibacillus halophilus YIM-C55.5 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Granulicella mallensis MP5ACTX8 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Granulicella tundricola MP5ACTX9 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Hafnia paralvei ATCC 29927 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Haladaptatus cibarius D43 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halioglobus japonicus S1-36 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Halobacillus alkaliphilus FP5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halococcus hamelinensis 100A6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halomonas salina B6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halomonas smyrnensis AAD6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halomonas stevensii S18214 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Halomonas titanicae BH1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Halomonas xinjiangensis TRM 0175 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Halopiger salifodinae KCY07-B2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halostagnicola larsenii XH-48 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Haloterrigena daqingensis JX313 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Herbaspirillum aquaticum IEH 4430 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Hippea alviniae EP5-r fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hippea jasoniae Mar08-272r fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hoeflea phototrophica DFL-43 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Hyphomicrobium nitrativorans NL23 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Imtechella halotolerans K1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Indibacter alkaliphilus LW1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Jannaschia aquimarina GSW-M26 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Jeotgalibacillus soli P9 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Kangiella geojedonensis YCS-5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Knoellia flava TL1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Kocuria flava HO-9041 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Kocuria turfanensis HO-9042 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Laceyella sediminis RHA1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lacinutrix algicola AKS293 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lacinutrix himadriensis E4-9a fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lacinutrix mariniflava AKS432 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus curieae CCTCC M 2011381 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus delbrueckii ZN7a-9 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus hokkaidonensis LOOC260 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus oryzae SG293 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Lactobacillus pobuzihii E100301 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus shenzhenensis LY-73 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lactobacillus silagei IWT126 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Leeuwenhoekiella blandensis MED217 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lentibacillus jeotgali Grbi fucP, fucU, fucI, fucK, fucA, tpi, aldA
Limnohabitans curvus MWH-C5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Limnohabitans parvus II-B4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Listeria fleischmannii LU2006-1 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Luteimonas huabeiensis HB2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Luteipulveratus mongoliensis MN07-A0370 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Lutibaculum baratangense AMV1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Lysobacter daejeonensis GH1-9 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Magnetovibrio blakemorei MV-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinicella litoralis KMM 3900 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Mariniradius saccharolyticus AK6 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Marinobacter algicola DG893 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinobacter guineae M3B fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinobacter psychrophilus 20041 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinomonas arctica 328 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marivita geojedonensis DPG-138 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Martelella endophytica YC6887 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Megamonas funiformis YIT 11815 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Mesorhizobium ciceri WSM1271 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Methanobacterium arcticum M2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanobacterium veterum MK4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanocella arvoryzae MRE50 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanococcus aeolicus Nankai-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanoculleus horonobensis T10 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanolinea tarda NOBI-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanosarcina soligelidi SMA-21 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanospirillum lacunae Ki8-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanospirillum stamsii Pt1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylibium petroleiphilum PM1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylobacterium gossipiicola Gh-105 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylocapsa aurea KYG fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylotenera versatilis 301 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Microbacterium profundi Shh49 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Microvirga lotononidis WSM3557 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Moritella dasanensis ArB 0140 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Mucilaginibacter gossypii Gh-67 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Mucilaginibacter gossypiicola Gh-48 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Mucilaginibacter mallensis MP1X4 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Nafulsella turpanensis ZLM-10 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Natronomonas moolapensis 8.8.11 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nautilia profundicola AmH fucP, fucU, fucI, fucK, fucA, tpi, aldA
Neiella marina J221 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Neptunomonas antarctica S3-22 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nocardioides daejeonensis MJ31 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nocardioides dokdonensis FR1436 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nocardiopsis baichengensis YIM 90130 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nocardiopsis gilva YIM 90087 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Novosphingobium barchaimii LL02 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Novosphingobium fuchskuhlense FNE08-7 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Novosphingobium lindaniclasticum LE124 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Oceanisphaera arctica V1-41 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Ochrobactrum rhizosphaerae PR17 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Ochrobactrum thiophenivorans DSM 7216 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Oscillibacter ruminantium GH1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Paenisporosarcina indica PN2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Palaeococcus pacificus DY20341 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Paludibacter propionicigenes WB4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pandoraea thiooxydans ATSB16 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pantoea rwandensis LMG 26275 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pedobacter arcticus A12 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Photobacterium gaetbulicola Gung47 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Photobacterium jeanii R-40508 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Phyllobacterium brassicacearum STM 196 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Phyllobacterium endophyticum PEPV15 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Phyllobacterium leguminum ORS 1419 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Planktomarina temperata RCA23 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Planococcus halocryophilus Or1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pleomorphomonas diazotrophica R5-392 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Polaribacter dokdonensis DSW-5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pontibacillus litoralis JSM 072002 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pontibacter lucknowensis DM9 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pontibacter ramchanderi LP43 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pontimonas salivibrio CL-TW6 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Porphyrobacter dokdonensis DSW-74 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudoalteromonas arctica A 37-1-2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas baetica a390 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas litoralis 2SM5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas taeanensis MS-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudovibrio axinellae Ad2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Psychrobacter arcticus 273-4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Psychrobacter cryohalolentis K5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Psychromonas ingrahamii 37 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Psychromonas ossibalaenae JAMM 0738 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhizobium freirei PRF 81 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhizobium grahamii CCGE 502 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhizobium subbaraonis JC85 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhodanobacter denitrificans 2APBS1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodobacter johrii JA192 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhodobacter maris JA276 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodobacter ovatus JA234 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodobacter viridis JA737 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodococcus qingshengii djl-6-2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodopseudomonas pseudopalustris DSM 123 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Roseateles aquatilis CCUG 48205 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Roseivirga spongicola UST030701-084 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rubrivirga marina SAORIC-28 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Ruegeria conchae TW15 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Saccharomonospora marina XMU15 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Salinicoccus carnicancri Crm fucP, fucU, fucI, fucK, fucA, tpi, aldA
Serinicoccus profundi MCCC 1A05965 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella halifaxensis HAW-EB4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Skermanella stibiiresistens SB22 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Snodgrassella alvi wkB2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphaerochaeta globosa Buddy HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Sphaerochaeta pleomorpha Grapes HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Sphingobium baderi LL03 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingobium czechense LL01 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sphingobium quisquiliarum P25 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingomonas histidinilytica UM2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingomonas indica Dd16 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingomonas laterariae LNB2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingopyxis indica DS15 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sphingopyxis terrae UI2 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sporolactobacillus vineae SL153 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Streptacidiphilus oryzae TH49 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Streptococcus anginosus CCUG 39159 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Streptococcus massiliensis 4401825 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Streptococcus oralis 7747 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Streptococcus oralis AZ_3a fucP, fucU, fucI, fucK, fucA, tpi, fucO
Streptomyces kebangsaanensis SUK12 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Succinatimonas hippei YIT 12066 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfurimonas gotlandica GD1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Tatumella morbirosei LMG 23360 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Thauera humireducens SgZ-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermoactinomyces daqus H-18 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermobifida halotolerans YIM 90462 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermodesulfovibrio aggregans TGE-P1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermophagus xiamenensis HS1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermovenabulum gondwanense R270 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thioclava dalianensis DLFJ1-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiohalospira halophila HL 3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Tistlia consotensis USBA 355 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Vagococcus penaei CD276 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Verminephrobacter eiseniae EF01-2 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Weissella oryzae SG25 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Williamsia sterculiae CPCC 203464 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Yersinia intermedia Y228 fucP, fucU, fucI, fucK, fucA, tpi, fucO

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.

Links

Downloads

Related tools

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