GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism

Analysis of pathway galacturonate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 exuT, uxaC, uxaB, uxaA, kdgK, eda
Actinokineospora bangkokensis 44EHW exuT, uxaC, uxaB, uxaA, kdgK, eda
Actinomyces timonensis 7400942 exuT, uxaC, uxaB, uxaA, kdgK, eda
Algiphilus aromaticivorans DG1253 exuT, udh, gli, gci, kdgD, dopDH
Algoriphagus aquaeductus T4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Algoriphagus machipongonensis PR1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Alicyclobacillus ferrooxydans TC-34 exuT, uxaC, uxaB, uxaA, kdgK, eda
Alishewanella agri BL06 exuT, uxaC, uxaB, uxaA, kdgK, eda
Alistipes indistinctus YIT 12060 exuT, uxaC, uxaB, uxaA, kdgK, eda
Alistipes shahii WAL 8301 exuT, uxaC, uxaB, uxaA, kdgK, eda
Alkalitalea saponilacus SC/BZ-SP2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Amantichitinum ursilacus IGB-41 exuT, uxaC, uxaB, uxaA, kdgK, eda
Amphibacillus jilinensis Y1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Amphritea japonica JAMM 1866 exuT, udh, gli, gci, kdgD, dopDH
Amycolatopsis halophila YIM 93223 exuT, uxaC, uxaB, uxaA, kdgK, eda
Amycolatopsis xylanica CPCC 202699 exuT, udh, uxuL, garD, kdgD, dopDH
Aquimarina agarilytica ZC1 PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
Aquimarina longa SW024 exuT, udh, gli, gci, kdgD, dopDH
Aquimarina macrocephali JAMB N27 exuT, udh, gli, gci, kdgD, dopDH
Archaeoglobus sulfaticallidus PM70-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Arcticibacter svalbardensis MN12-7 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ardenticatena maritima 110S exuT, uxaC, uxaB, uxaA, kdgK, eda
Arenimonas metalli CF5-1 exuT, udh, gli, gci, kdgD, dopDH
Arenitalea lutea P7-3-5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Azospirillum humicireducens SgZ-5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Azospirillum thiophilum BV-S exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacillus altitudinis 41KF2b PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
Bacillus coahuilensis m4-4 exuT, udh, gli, gci, kdgD, dopDH
Bacillus cytotoxicus NVH 391-98 exuT, udh, gli, gci, kdgD, dopDH
Bacillus horneckiae 1P01SC exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacillus okhensis Kh10-101 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacillus safensis FO-36b PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
Bacillus velezensis CBMB205 PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
Bacteroides clarus YIT 12056 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacteroides faecis MAJ27 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacteroides fluxus YIT 12057 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bacteroides oleiciplenus YIT 12058 exuT, uxaC, uxaB, uxaA, kdgK, eda
Barnesiella intestinihominis YIT 11860 exuT, uxaC, uxaB, uxaA, kdgK, eda
Belnapia rosea CPCC 100156 exuT, udh, gli, gci, kdgD, dopDH
Bizionia argentinensis JUB59 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bradyrhizobium diazoefficiens USDA110 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Brevibacterium jeotgali SJ5-8 exuT, udh, gli, gci, kdgD, dopDH
Brucella inopinata BO1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Brucella microti CCM 4915 exuT, uxaC, uxaB, uxaA, kdgK, eda
Bryobacter aggregatus MPL3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Caldicellulosiruptor hydrothermalis 108 exuT, uxaC, uxaB, uxaA, kdgK, eda
Caldicellulosiruptor kronotskyensis 2002 exuT, uxaC, uxaB, uxaA, kdgK, eda
Carboxydothermus pertinax Ug1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Catellicoccus marimammalium M35/04/3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Chromobacterium vaccinii MWU205 exuT, uxaC, uxaB, uxaA, kdgK, eda
Chryseobacterium angstadtii KM exuT, uxaC, uxaB, uxaA, kdgK, eda
Chryseobacterium arthrosphaerae CC-VM-7 exuT, uxaC, uxaB, uxaA, kdgK, eda
Chryseobacterium viscerum 687B-08 exuT, udh, gli, gci, kdgD, dopDH
Cloacibacillus porcorum CL-84 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cobetia crustatorum JO1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Collimonas arenae Ter10 exuT, udh, uxuL, garD, kdgD, dopDH
Collimonas pratensis Ter91 exuT, udh, uxuL, garD, kdgD, dopDH
Collinsella tanakaei YIT 12063 exuT, uxaC, uxaB, uxaA, kdgK, eda
Coprobacter fastidiosus NSB1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Corynebacterium deserti GIMN1.010 exuT, udh, gli, gci, kdgD, dopDH
Corynebacterium frankenforstense ST18 exuT, uxaC, uxaB, uxaA, kdgK, eda
Corynebacterium lactis RW2-5 exuT, udh, gli, gci, kdgD, dopDH
Croceitalea dokdonensis DOKDO 023 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cronobacter condimenti 1330 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cronobacter muytjensii ATCC 51329 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cronobacter universalis NCTC 9529 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfatitalea tepidiphila S28bF exuT, udh, gli, gci, kdgD, dopDH
Desulfotomaculum hydrothermale Lam5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dethiosulfovibrio salsuginis USBA 82 exuT, uxaC, uxaB, uxaA, kdgK, eda
Devosia chinhatensis IPL18 exuT, uxaC, uxaB, uxaA, kdgK, eda
Devriesea agamarum IMP2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dialister succinatiphilus YIT 11850 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dietzia timorensis ID05-A0528 exuT, udh, gli, gci, kdgD, dopDH
Dokdonella koreensis DS-123 exuT, uxaC, uxaB, uxaA, kdgK, eda
Domibacillus robiginosus WS 4628 PS417_04205, uxaC, uxaB, uxaA, kdgK, eda
Duganella sacchari Sac-22 exuT, udh, uxuL, garD, kdgD, dopDH
Dyadobacter tibetensis Y620-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dyella jiangningensis SBZ3-12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Endozoicomonas montiporae CL-33 exuT, uxaC, uxaB, uxaA, kdgK, eda
Enterococcus termitis LMG 8895 exuT, uxaC, uxaB, uxaA, kdgK, eda
Enterorhabdus caecimuris B7 exuT, uxaC, uxaB, uxaA, kdgK, eda
Epibacterium ulvae U95 exuT, uxaC, uxaB, uxaA, kdgK, eda
Erythrobacter gangjinensis K7-2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Erythrobacter marinus HWDM-33 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ethanoligenens harbinense YUAN-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Fervidicella metallireducens AeB exuT, uxaC, uxaB, uxaA, kdgK, eda
Fibrella aestuarina BUZ 2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flammeovirga pacifica WPAGA1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flaviramulus ichthyoenteri Th78 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flavobacterium beibuense F44-8 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flavobacterium glycines Gm-149 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flavobacterium sp. LM5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Flavobacterium ummariense DS-12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Frischella perrara PEB0191 exuT, uxaC, uxaB, uxaA, kdgK, eda
Galbibacter marinus ck-I2-15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Gallaecimonas xiamenensis 3-C-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Geobacter daltonii FRC-32 exuT, uxaC, uxaB, uxaA, kdgK, eda
Gillisia marina CBA3202 exuT, uxaC, uxaB, uxaA, kdgK, eda
Gracilibacillus halophilus YIM-C55.5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Granulicella mallensis MP5ACTX8 exuT, uxaC, uxaB, uxaA, kdgK, eda
Granulicella tundricola MP5ACTX9 exuT, uxaC, uxaB, uxaA, kdgK, eda
Hafnia paralvei ATCC 29927 exuT, uxaC, uxaB, uxaA, kdgK, eda
Haladaptatus cibarius D43 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halioglobus japonicus S1-36 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halobacillus alkaliphilus FP5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halococcus hamelinensis 100A6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halomonas salina B6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halomonas smyrnensis AAD6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halomonas stevensii S18214 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halomonas titanicae BH1 exuT, udh, uxuL, garD, kdgD, dopDH
Halomonas xinjiangensis TRM 0175 exuT, udh, gli, gci, kdgD, dopDH
Halopiger salifodinae KCY07-B2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halostagnicola larsenii XH-48 exuT, uxaC, uxaB, uxaA, kdgK, eda
Haloterrigena daqingensis JX313 exuT, uxaC, uxaB, uxaA, kdgK, eda
Herbaspirillum aquaticum IEH 4430 exuT, udh, uxuL, garD, kdgD, dopDH
Hippea alviniae EP5-r exuT, uxaC, uxaB, uxaA, kdgK, eda
Hippea jasoniae Mar08-272r exuT, uxaC, uxaB, uxaA, kdgK, eda
Hoeflea phototrophica DFL-43 exuT, uxaC, uxaB, uxaA, kdgK, eda
Hyphomicrobium nitrativorans NL23 exuT, udh, gli, gci, kdgD, dopDH
Imtechella halotolerans K1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Indibacter alkaliphilus LW1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Jannaschia aquimarina GSW-M26 exuT, uxaC, uxaB, uxaA, kdgK, eda
Jeotgalibacillus soli P9 exuT, uxaC, uxaB, uxaA, kdgK, eda
Kangiella geojedonensis YCS-5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Knoellia flava TL1 exuT, udh, gli, gci, kdgD, dopDH
Kocuria flava HO-9041 exuT, udh, uxuL, garD, kdgD, dopDH
Kocuria turfanensis HO-9042 exuT, udh, uxuL, garD, kdgD, dopDH
Laceyella sediminis RHA1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lacinutrix algicola AKS293 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lacinutrix himadriensis E4-9a exuT, uxaC, uxaB, uxaA, kdgK, eda
Lacinutrix mariniflava AKS432 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus curieae CCTCC M 2011381 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus delbrueckii ZN7a-9 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus hokkaidonensis LOOC260 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus oryzae SG293 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus pobuzihii E100301 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus shenzhenensis LY-73 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lactobacillus silagei IWT126 exuT, uxaC, uxaB, uxaA, kdgK, eda
Leeuwenhoekiella blandensis MED217 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lentibacillus jeotgali Grbi exuT, uxaC, uxaB, uxaA, kdgK, eda
Limnohabitans curvus MWH-C5 exuT, udh, uxuL, garD, kdgD, dopDH
Limnohabitans parvus II-B4 exuT, udh, uxuL, garD, kdgD, dopDH
Listeria fleischmannii LU2006-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Luteimonas huabeiensis HB2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Luteipulveratus mongoliensis MN07-A0370 exuT, udh, uxuL, garD, kdgD, dopDH
Lutibaculum baratangense AMV1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Lysobacter daejeonensis GH1-9 exuT, uxaC, uxaB, uxaA, kdgK, eda
Magnetovibrio blakemorei MV-1 exuT, udh, gli, gci, kdgD, dopDH
Marinicella litoralis KMM 3900 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mariniradius saccharolyticus AK6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Marinobacter algicola DG893 exuT, udh, gli, gci, kdgD, dopDH
Marinobacter guineae M3B exuT, uxaC, uxaB, uxaA, kdgK, eda
Marinobacter psychrophilus 20041 exuT, uxaC, uxaB, uxaA, kdgK, eda
Marinomonas arctica 328 exuT, udh, uxuL, garD, kdgD, dopDH
Marivita geojedonensis DPG-138 exuT, uxaC, uxaB, uxaA, kdgK, eda
Martelella endophytica YC6887 exuT, uxaC, uxaB, uxaA, kdgK, eda
Megamonas funiformis YIT 11815 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mesorhizobium ciceri WSM1271 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanobacterium arcticum M2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanobacterium veterum MK4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanocella arvoryzae MRE50 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanococcus aeolicus Nankai-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanoculleus horonobensis T10 exuT, udh, gli, gci, kdgD, dopDH
Methanolinea tarda NOBI-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanosarcina soligelidi SMA-21 exuT, udh, gli, gci, kdgD, dopDH
Methanospirillum lacunae Ki8-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanospirillum stamsii Pt1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylibium petroleiphilum PM1 exuT, udh, gli, gci, kdgD, dopDH
Methylobacterium gossipiicola Gh-105 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylocapsa aurea KYG exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylotenera versatilis 301 exuT, uxaC, uxaB, uxaA, kdgK, eda
Microbacterium profundi Shh49 exuT, udh, uxuL, garD, kdgD, dopDH
Microvirga lotononidis WSM3557 exuT, udh, gli, gci, kdgD, dopDH
Moritella dasanensis ArB 0140 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mucilaginibacter gossypii Gh-67 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mucilaginibacter gossypiicola Gh-48 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mucilaginibacter mallensis MP1X4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nafulsella turpanensis ZLM-10 exuT, uxaC, uxaB, uxaA, kdgK, eda
Natronomonas moolapensis 8.8.11 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nautilia profundicola AmH exuT, uxaC, uxaB, uxaA, kdgK, eda
Neiella marina J221 exuT, uxaC, uxaB, uxaA, kdgK, eda
Neptunomonas antarctica S3-22 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nocardioides daejeonensis MJ31 exuT, udh, gli, gci, kdgD, dopDH
Nocardioides dokdonensis FR1436 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nocardiopsis baichengensis YIM 90130 exuT, udh, gli, gci, kdgD, dopDH
Nocardiopsis gilva YIM 90087 exuT, udh, gli, gci, kdgD, dopDH
Novosphingobium barchaimii LL02 exuT, uxaC, uxaB, uxaA, kdgK, eda
Novosphingobium fuchskuhlense FNE08-7 exuT, uxaC, uxaB, uxaA, kdgK, eda
Novosphingobium lindaniclasticum LE124 exuT, uxaC, uxaB, uxaA, kdgK, eda
Oceanisphaera arctica V1-41 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ochrobactrum rhizosphaerae PR17 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ochrobactrum thiophenivorans DSM 7216 exuT, udh, gli, gci, kdgD, dopDH
Oscillibacter ruminantium GH1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Paenisporosarcina indica PN2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Palaeococcus pacificus DY20341 exuT, uxaC, uxaB, uxaA, kdgK, eda
Paludibacter propionicigenes WB4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pandoraea thiooxydans ATSB16 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pantoea rwandensis LMG 26275 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pedobacter arcticus A12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Photobacterium gaetbulicola Gung47 exuT, uxaC, uxaB, uxaA, kdgK, eda
Photobacterium jeanii R-40508 exuT, uxaC, uxaB, uxaA, kdgK, eda
Phyllobacterium brassicacearum STM 196 exuT, uxaC, uxaB, uxaA, kdgK, eda
Phyllobacterium endophyticum PEPV15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Phyllobacterium leguminum ORS 1419 exuT, udh, gli, gci, kdgD, dopDH
Planktomarina temperata RCA23 exuT, uxaC, uxaB, uxaA, kdgK, eda
Planococcus halocryophilus Or1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pleomorphomonas diazotrophica R5-392 exuT, uxaC, uxaB, uxaA, kdgK, eda
Polaribacter dokdonensis DSW-5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pontibacillus litoralis JSM 072002 exuT, udh, gli, gci, kdgD, dopDH
Pontibacter lucknowensis DM9 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pontibacter ramchanderi LP43 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pontimonas salivibrio CL-TW6 exuT, udh, uxuL, garD, kdgD, dopDH
Porphyrobacter dokdonensis DSW-74 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pseudoalteromonas arctica A 37-1-2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pseudomonas baetica a390 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas litoralis 2SM5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pseudomonas taeanensis MS-3 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudovibrio axinellae Ad2 exuT, udh, uxuL, garD, kdgD, dopDH
Psychrobacter arcticus 273-4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Psychrobacter cryohalolentis K5 exuT, udh, gli, gci, kdgD, dopDH
Psychromonas ingrahamii 37 exuT, uxaC, uxaB, uxaA, kdgK, eda
Psychromonas ossibalaenae JAMM 0738 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhizobium freirei PRF 81 exuT, udh, uxuL, garD, kdgD, dopDH
Rhizobium grahamii CCGE 502 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhizobium subbaraonis JC85 exuT, udh, gli, gci, kdgD, dopDH
Rhodanobacter denitrificans 2APBS1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodobacter johrii JA192 exuT, udh, gli, gci, kdgD, dopDH
Rhodobacter maris JA276 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodobacter ovatus JA234 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodobacter viridis JA737 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodococcus qingshengii djl-6-2 exuT, udh, gli, gci, kdgD, dopDH
Rhodopseudomonas pseudopalustris DSM 123 exuT, udh, gli, gci, kdgD, dopDH
Roseateles aquatilis CCUG 48205 exuT, uxaC, uxaB, uxaA, kdgK, eda
Roseivirga spongicola UST030701-084 exuT, udh, gli, gci, kdgD, dopDH
Rubrivirga marina SAORIC-28 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ruegeria conchae TW15 exuT, udh, gli, gci, kdgD, dopDH
Saccharomonospora marina XMU15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Salinicoccus carnicancri Crm exuT, uxaC, uxaB, uxaA, kdgK, eda
Serinicoccus profundi MCCC 1A05965 exuT, udh, uxuL, garD, kdgD, dopDH
Shewanella halifaxensis HAW-EB4 exuT, udh, gli, gci, kdgD, dopDH
Skermanella stibiiresistens SB22 exuT, udh, uxuL, garD, kdgD, dopDH
Snodgrassella alvi wkB2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphaerochaeta globosa Buddy exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphaerochaeta pleomorpha Grapes exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingobium baderi LL03 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingobium czechense LL01 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingobium quisquiliarum P25 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingomonas histidinilytica UM2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingomonas indica Dd16 exuT, udh, gli, gci, kdgD, dopDH
Sphingomonas laterariae LNB2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingopyxis indica DS15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sphingopyxis terrae UI2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sporolactobacillus vineae SL153 exuT, udh, gli, gci, kdgD, dopDH
Streptacidiphilus oryzae TH49 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Streptococcus anginosus CCUG 39159 exuT, uxaC, uxaB, uxaA, kdgK, eda
Streptococcus massiliensis 4401825 exuT, uxaC, uxaB, uxaA, kdgK, eda
Streptococcus oralis 7747 exuT, uxaC, uxaB, uxaA, kdgK, eda
Streptococcus oralis AZ_3a exuT, uxaC, uxaB, uxaA, kdgK, eda
Streptomyces kebangsaanensis SUK12 exuT, udh, gli, gci, kdgD, dopDH
Succinatimonas hippei YIT 12066 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfurimonas gotlandica GD1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Tatumella morbirosei LMG 23360 exuT, udh, uxuL, garD, kdgD, dopDH
Thauera humireducens SgZ-1 exuT, udh, uxuL, garD, kdgD, dopDH
Thermoactinomyces daqus H-18 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermobifida halotolerans YIM 90462 exuT, udh, gli, gci, kdgD, dopDH
Thermodesulfovibrio aggregans TGE-P1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermophagus xiamenensis HS1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermovenabulum gondwanense R270 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thioclava dalianensis DLFJ1-1 exuT, udh, gli, gci, kdgD, dopDH
Thiohalospira halophila HL 3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Tistlia consotensis USBA 355 exuT, udh, gli, gci, kdgD, dopDH
Vagococcus penaei CD276 exuT, uxaC, uxaB, uxaA, kdgK, eda
Verminephrobacter eiseniae EF01-2 exuT, udh, uxuL, garD, kdgD, dopDH
Weissella oryzae SG25 exuT, uxaC, uxaB, uxaA, kdgK, eda
Williamsia sterculiae CPCC 203464 exuT, uxaC, uxaB, uxaA, kdgK, eda
Yersinia intermedia Y228 exuT, uxaC, uxaB, uxaA, kdgK, eda

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