GapMind for catabolism of small carbon sources

 

L-rhamnose catabolism

Analysis of pathway rhamnose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Actinokineospora bangkokensis 44EHW rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Actinomyces timonensis 7400942 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Algiphilus aromaticivorans DG1253 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Algoriphagus aquaeductus T4 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Algoriphagus machipongonensis PR1 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Alicyclobacillus ferrooxydans TC-34 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Alishewanella agri BL06 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Alistipes indistinctus YIT 12060 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Alistipes shahii WAL 8301 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Alkalitalea saponilacus SC/BZ-SP2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Amantichitinum ursilacus IGB-41 rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
Amphibacillus jilinensis Y1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Amphritea japonica JAMM 1866 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Amycolatopsis halophila YIM 93223 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Amycolatopsis xylanica CPCC 202699 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Aquimarina agarilytica ZC1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Aquimarina longa SW024 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Aquimarina macrocephali JAMB N27 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Archaeoglobus sulfaticallidus PM70-1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Arcticibacter svalbardensis MN12-7 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ardenticatena maritima 110S rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Arenimonas metalli CF5-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Arenitalea lutea P7-3-5 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Azospirillum humicireducens SgZ-5 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Azospirillum thiophilum BV-S rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Bacillus altitudinis 41KF2b rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Bacillus coahuilensis m4-4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bacillus cytotoxicus NVH 391-98 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bacillus horneckiae 1P01SC rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Bacillus okhensis Kh10-101 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bacillus safensis FO-36b rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bacillus velezensis CBMB205 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Bacteroides clarus YIT 12056 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Bacteroides faecis MAJ27 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Bacteroides fluxus YIT 12057 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Bacteroides oleiciplenus YIT 12058 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Barnesiella intestinihominis YIT 11860 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Belnapia rosea CPCC 100156 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Bizionia argentinensis JUB59 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Bradyrhizobium diazoefficiens USDA110 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Brevibacterium jeotgali SJ5-8 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Brucella inopinata BO1 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Brucella microti CCM 4915 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Bryobacter aggregatus MPL3 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Caldicellulosiruptor hydrothermalis 108 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, fucO
Caldicellulosiruptor kronotskyensis 2002 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Carboxydothermus pertinax Ug1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Catellicoccus marimammalium M35/04/3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chromobacterium vaccinii MWU205 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chryseobacterium angstadtii KM rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chryseobacterium arthrosphaerae CC-VM-7 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Chryseobacterium viscerum 687B-08 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Cloacibacillus porcorum CL-84 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Cobetia crustatorum JO1 Echvi_1617, LRA1, LRA2, LRA3, LRA4, aldA
Collimonas arenae Ter10 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Collimonas pratensis Ter91 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Collinsella tanakaei YIT 12063 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Coprobacter fastidiosus NSB1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Corynebacterium deserti GIMN1.010 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Corynebacterium frankenforstense ST18 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Corynebacterium lactis RW2-5 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Croceitalea dokdonensis DOKDO 023 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Cronobacter condimenti 1330 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Cronobacter muytjensii ATCC 51329 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Cronobacter universalis NCTC 9529 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Desulfatitalea tepidiphila S28bF rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Desulfotomaculum hydrothermale Lam5 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Dethiosulfovibrio salsuginis USBA 82 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Devosia chinhatensis IPL18 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Devriesea agamarum IMP2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Dialister succinatiphilus YIT 11850 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dietzia timorensis ID05-A0528 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dokdonella koreensis DS-123 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Domibacillus robiginosus WS 4628 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Duganella sacchari Sac-22 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Dyadobacter tibetensis Y620-1 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Dyella jiangningensis SBZ3-12 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Endozoicomonas montiporae CL-33 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Enterococcus termitis LMG 8895 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Enterorhabdus caecimuris B7 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Epibacterium ulvae U95 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Erythrobacter gangjinensis K7-2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Erythrobacter marinus HWDM-33 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ethanoligenens harbinense YUAN-3 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Fervidicella metallireducens AeB rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Fibrella aestuarina BUZ 2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Flammeovirga pacifica WPAGA1 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Flaviramulus ichthyoenteri Th78 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Flavobacterium beibuense F44-8 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Flavobacterium glycines Gm-149 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Flavobacterium sp. LM5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Flavobacterium ummariense DS-12 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Frischella perrara PEB0191 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Galbibacter marinus ck-I2-15 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Gallaecimonas xiamenensis 3-C-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Geobacter daltonii FRC-32 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Gillisia marina CBA3202 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Gracilibacillus halophilus YIM-C55.5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Granulicella mallensis MP5ACTX8 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Granulicella tundricola MP5ACTX9 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Hafnia paralvei ATCC 29927 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Haladaptatus cibarius D43 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Halioglobus japonicus S1-36 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Halobacillus alkaliphilus FP5 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Halococcus hamelinensis 100A6 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Halomonas salina B6 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Halomonas smyrnensis AAD6 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Halomonas stevensii S18214 Echvi_1617, LRA1, LRA2, LRA3, LRA5, LRA6
Halomonas titanicae BH1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Halomonas xinjiangensis TRM 0175 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Halopiger salifodinae KCY07-B2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Halostagnicola larsenii XH-48 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Haloterrigena daqingensis JX313 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Herbaspirillum aquaticum IEH 4430 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Hippea alviniae EP5-r rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hippea jasoniae Mar08-272r rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Hoeflea phototrophica DFL-43 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Hyphomicrobium nitrativorans NL23 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Imtechella halotolerans K1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Indibacter alkaliphilus LW1 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Jannaschia aquimarina GSW-M26 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Jeotgalibacillus soli P9 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Kangiella geojedonensis YCS-5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Knoellia flava TL1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Kocuria flava HO-9041 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Kocuria turfanensis HO-9042 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Laceyella sediminis RHA1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lacinutrix algicola AKS293 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lacinutrix himadriensis E4-9a rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lacinutrix mariniflava AKS432 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Lactobacillus curieae CCTCC M 2011381 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Lactobacillus delbrueckii ZN7a-9 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lactobacillus hokkaidonensis LOOC260 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lactobacillus oryzae SG293 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Lactobacillus pobuzihii E100301 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lactobacillus shenzhenensis LY-73 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lactobacillus silagei IWT126 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Leeuwenhoekiella blandensis MED217 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lentibacillus jeotgali Grbi rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Limnohabitans curvus MWH-C5 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Limnohabitans parvus II-B4 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Listeria fleischmannii LU2006-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Luteimonas huabeiensis HB2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Luteipulveratus mongoliensis MN07-A0370 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Lutibaculum baratangense AMV1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Lysobacter daejeonensis GH1-9 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Magnetovibrio blakemorei MV-1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Marinicella litoralis KMM 3900 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Mariniradius saccharolyticus AK6 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Marinobacter algicola DG893 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Marinobacter guineae M3B rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Marinobacter psychrophilus 20041 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Marinomonas arctica 328 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Marivita geojedonensis DPG-138 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Martelella endophytica YC6887 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Megamonas funiformis YIT 11815 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Mesorhizobium ciceri WSM1271 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanobacterium arcticum M2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanobacterium veterum MK4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanocella arvoryzae MRE50 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methanococcus aeolicus Nankai-3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanoculleus horonobensis T10 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Methanolinea tarda NOBI-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanosarcina soligelidi SMA-21 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanospirillum lacunae Ki8-1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methanospirillum stamsii Pt1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Methylibium petroleiphilum PM1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Methylobacterium gossipiicola Gh-105 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Methylocapsa aurea KYG rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Methylotenera versatilis 301 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Microbacterium profundi Shh49 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Microvirga lotononidis WSM3557 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Moritella dasanensis ArB 0140 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Mucilaginibacter gossypii Gh-67 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Mucilaginibacter gossypiicola Gh-48 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Mucilaginibacter mallensis MP1X4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Nafulsella turpanensis ZLM-10 rhaT, LRA1, LRA2, LRA3, LRA4, fucO
Natronomonas moolapensis 8.8.11 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Nautilia profundicola AmH rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Neiella marina J221 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Neptunomonas antarctica S3-22 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Nocardioides daejeonensis MJ31 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Nocardioides dokdonensis FR1436 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Nocardiopsis baichengensis YIM 90130 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Nocardiopsis gilva YIM 90087 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Novosphingobium barchaimii LL02 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Novosphingobium fuchskuhlense FNE08-7 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Novosphingobium lindaniclasticum LE124 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Oceanisphaera arctica V1-41 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ochrobactrum rhizosphaerae PR17 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Ochrobactrum thiophenivorans DSM 7216 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Oscillibacter ruminantium GH1 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Paenisporosarcina indica PN2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Palaeococcus pacificus DY20341 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Paludibacter propionicigenes WB4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pandoraea thiooxydans ATSB16 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pantoea rwandensis LMG 26275 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pedobacter arcticus A12 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Photobacterium gaetbulicola Gung47 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Photobacterium jeanii R-40508 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Phyllobacterium brassicacearum STM 196 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Phyllobacterium endophyticum PEPV15 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Phyllobacterium leguminum ORS 1419 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Planktomarina temperata RCA23 rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
Planococcus halocryophilus Or1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pleomorphomonas diazotrophica R5-392 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Polaribacter dokdonensis DSW-5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pontibacillus litoralis JSM 072002 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pontibacter lucknowensis DM9 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pontibacter ramchanderi LP43 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Pontimonas salivibrio CL-TW6 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Porphyrobacter dokdonensis DSW-74 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Pseudoalteromonas arctica A 37-1-2 Echvi_1617, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas baetica a390 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas litoralis 2SM5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudomonas taeanensis MS-3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Pseudovibrio axinellae Ad2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Psychrobacter arcticus 273-4 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Psychrobacter cryohalolentis K5 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Psychromonas ingrahamii 37 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Psychromonas ossibalaenae JAMM 0738 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium freirei PRF 81 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium grahamii CCGE 502 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhizobium subbaraonis JC85 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodanobacter denitrificans 2APBS1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodobacter johrii JA192 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Rhodobacter maris JA276 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodobacter ovatus JA234 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Rhodobacter viridis JA737 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Rhodococcus qingshengii djl-6-2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Rhodopseudomonas pseudopalustris DSM 123 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Roseateles aquatilis CCUG 48205 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Roseivirga spongicola UST030701-084 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Rubrivirga marina SAORIC-28 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Ruegeria conchae TW15 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Saccharomonospora marina XMU15 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Salinicoccus carnicancri Crm rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Serinicoccus profundi MCCC 1A05965 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Shewanella halifaxensis HAW-EB4 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Skermanella stibiiresistens SB22 rhaP, rhaQ, rhaS, rhaT', LRA1, LRA2, LRA3, LRA5, LRA6
Snodgrassella alvi wkB2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphaerochaeta globosa Buddy rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphaerochaeta pleomorpha Grapes rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingobium baderi LL03 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Sphingobium czechense LL01 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Sphingobium quisquiliarum P25 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingomonas histidinilytica UM2 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Sphingomonas indica Dd16 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingomonas laterariae LNB2 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingopyxis indica DS15 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Sphingopyxis terrae UI2 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Sporolactobacillus vineae SL153 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Streptacidiphilus oryzae TH49 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Streptococcus anginosus CCUG 39159 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Streptococcus massiliensis 4401825 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Streptococcus oralis 7747 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Streptococcus oralis AZ_3a rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Streptomyces kebangsaanensis SUK12 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Succinatimonas hippei YIT 12066 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Sulfurimonas gotlandica GD1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Tatumella morbirosei LMG 23360 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Thauera humireducens SgZ-1 rhaT, LRA1, LRA2, LRA3, LRA4, aldA
Thermoactinomyces daqus H-18 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Thermobifida halotolerans YIM 90462 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermodesulfovibrio aggregans TGE-P1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermophagus xiamenensis HS1 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thermovenabulum gondwanense R270 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Thioclava dalianensis DLFJ1-1 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Thiohalospira halophila HL 3 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Tistlia consotensis USBA 355 rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
Vagococcus penaei CD276 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Verminephrobacter eiseniae EF01-2 rhaP, rhaQ, rhaS, rhaT', rhaM, rhaA, rhaB, rhaD, tpi, aldA
Weissella oryzae SG25 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, aldA
Williamsia sterculiae CPCC 203464 rhaT, rhaM, rhaA, rhaB, rhaD, tpi, fucO
Yersinia intermedia Y228 rhaT, rhaM, rhaA, rhaB, rhaD, 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