GapMind for catabolism of small carbon sources

 

thymidine catabolism

Analysis of pathway thymidine in 276 genomes

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

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