GapMind for catabolism of small carbon sources

 

lactose catabolism

Analysis of pathway lactose in 276 genomes

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

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