| Genome | Best path |
|---|
| Acidovorax caeni R-24608 | dctQ, dctM, dctP |
| Actinokineospora bangkokensis 44EHW | dctA |
| Actinomyces timonensis 7400942 | sdc |
| Algiphilus aromaticivorans DG1253 | sdc |
| Algoriphagus aquaeductus T4 | sdc |
| Algoriphagus machipongonensis PR1 | sdc |
| Alicyclobacillus ferrooxydans TC-34 | satP |
| Alishewanella agri BL06 | sdc |
| Alistipes indistinctus YIT 12060 | sdc |
| Alistipes shahii WAL 8301 | sdc |
| Alkalitalea saponilacus SC/BZ-SP2 | sdc |
| Amantichitinum ursilacus IGB-41 | dctA |
| Amphibacillus jilinensis Y1 | satP |
| Amphritea japonica JAMM 1866 | dctQ, dctM, dctP |
| Amycolatopsis halophila YIM 93223 | sdc |
| Amycolatopsis xylanica CPCC 202699 | dctA |
| Aquimarina agarilytica ZC1 | sdc |
| Aquimarina longa SW024 | sdc |
| Aquimarina macrocephali JAMB N27 | sdc |
| Archaeoglobus sulfaticallidus PM70-1 | sdc |
| Arcticibacter svalbardensis MN12-7 | dctA |
| Ardenticatena maritima 110S | sdc |
| Arenimonas metalli CF5-1 | sdc |
| Arenitalea lutea P7-3-5 | sdc |
| Azospirillum humicireducens SgZ-5 | dctA |
| Azospirillum thiophilum BV-S | dctA |
| Bacillus altitudinis 41KF2b | sdc |
| Bacillus coahuilensis m4-4 | satP |
| Bacillus cytotoxicus NVH 391-98 | dctA |
| Bacillus horneckiae 1P01SC | sdc |
| Bacillus okhensis Kh10-101 | sdc |
| Bacillus safensis FO-36b | dctA |
| Bacillus velezensis CBMB205 | dctA |
| Bacteroides clarus YIT 12056 | dauA |
| Bacteroides faecis MAJ27 | dauA |
| Bacteroides fluxus YIT 12057 | sdc |
| Bacteroides oleiciplenus YIT 12058 | dauA |
| Barnesiella intestinihominis YIT 11860 | dauA |
| Belnapia rosea CPCC 100156 | dctA |
| Bizionia argentinensis JUB59 | sdc |
| Bradyrhizobium diazoefficiens USDA110 | dctQ, dctM, dctP |
| Brevibacterium jeotgali SJ5-8 | dauA |
| Brucella inopinata BO1 | sdc |
| Brucella microti CCM 4915 | sdc |
| Bryobacter aggregatus MPL3 | dctA |
| Caldicellulosiruptor hydrothermalis 108 | sdc |
| Caldicellulosiruptor kronotskyensis 2002 | sdc |
| Carboxydothermus pertinax Ug1 | dctA |
| Catellicoccus marimammalium M35/04/3 | sdc |
| Chromobacterium vaccinii MWU205 | dctQ, dctM, dctP |
| Chryseobacterium angstadtii KM | dctA |
| Chryseobacterium arthrosphaerae CC-VM-7 | dctA |
| Chryseobacterium viscerum 687B-08 | dctA |
| Cloacibacillus porcorum CL-84 | dauA |
| Cobetia crustatorum JO1 | sdc |
| Collimonas arenae Ter10 | dctA |
| Collimonas pratensis Ter91 | dctA |
| Collinsella tanakaei YIT 12063 | dauA |
| Coprobacter fastidiosus NSB1 | dauA |
| Corynebacterium deserti GIMN1.010 | sdc |
| Corynebacterium frankenforstense ST18 | sdc |
| Corynebacterium lactis RW2-5 | sdc |
| Croceitalea dokdonensis DOKDO 023 | sdc |
| Cronobacter condimenti 1330 | dctA |
| Cronobacter muytjensii ATCC 51329 | dctA |
| Cronobacter universalis NCTC 9529 | dctA |
| Desulfatitalea tepidiphila S28bF | satP |
| Desulfotomaculum hydrothermale Lam5 | dctA |
| Dethiosulfovibrio salsuginis USBA 82 | sdc |
| Devosia chinhatensis IPL18 | sdc |
| Devriesea agamarum IMP2 | sdc |
| Dialister succinatiphilus YIT 11850 | sdc |
| Dietzia timorensis ID05-A0528 | sdc |
| Dokdonella koreensis DS-123 | dauA |
| Domibacillus robiginosus WS 4628 | dctA |
| Duganella sacchari Sac-22 | dctQ, dctM, dctP |
| Dyadobacter tibetensis Y620-1 | dctA |
| Dyella jiangningensis SBZ3-12 | sdc |
| Endozoicomonas montiporae CL-33 | sdc |
| Enterococcus termitis LMG 8895 | sdc |
| Enterorhabdus caecimuris B7 | dauA |
| Epibacterium ulvae U95 | dctQ, dctM, dctP |
| Erythrobacter gangjinensis K7-2 | sdc |
| Erythrobacter marinus HWDM-33 | sdc |
| Ethanoligenens harbinense YUAN-3 | sdc |
| Fervidicella metallireducens AeB | sdc |
| Fibrella aestuarina BUZ 2 | dctA |
| Flammeovirga pacifica WPAGA1 | satP |
| Flaviramulus ichthyoenteri Th78 | sdc |
| Flavobacterium beibuense F44-8 | sdc |
| Flavobacterium glycines Gm-149 | satP |
| Flavobacterium sp. LM5 | satP |
| Flavobacterium ummariense DS-12 | dctA |
| Frischella perrara PEB0191 | dauA |
| Galbibacter marinus ck-I2-15 | sdc |
| Gallaecimonas xiamenensis 3-C-1 | dctQ, dctM, dctP |
| Geobacter daltonii FRC-32 | satP |
| Gillisia marina CBA3202 | sdc |
| Gracilibacillus halophilus YIM-C55.5 | sdc |
| Granulicella mallensis MP5ACTX8 | dctA |
| Granulicella tundricola MP5ACTX9 | dctA |
| Hafnia paralvei ATCC 29927 | dctA |
| Haladaptatus cibarius D43 | sdc |
| Halioglobus japonicus S1-36 | sdc |
| Halobacillus alkaliphilus FP5 | sdc |
| Halococcus hamelinensis 100A6 | satP |
| Halomonas salina B6 | Dshi_1194, Dshi_1195 |
| Halomonas smyrnensis AAD6 | Dshi_1194, Dshi_1195 |
| Halomonas stevensii S18214 | Dshi_1194, Dshi_1195 |
| Halomonas titanicae BH1 | Dshi_1194, Dshi_1195 |
| Halomonas xinjiangensis TRM 0175 | Dshi_1194, Dshi_1195 |
| Halopiger salifodinae KCY07-B2 | sdc |
| Halostagnicola larsenii XH-48 | sdc |
| Haloterrigena daqingensis JX313 | sdc |
| Herbaspirillum aquaticum IEH 4430 | dctQ, dctM, dctP |
| Hippea alviniae EP5-r | satP |
| Hippea jasoniae Mar08-272r | satP |
| Hoeflea phototrophica DFL-43 | Dshi_1194, Dshi_1195 |
| Hyphomicrobium nitrativorans NL23 | dctQ, dctM, dctP |
| Imtechella halotolerans K1 | sdc |
| Indibacter alkaliphilus LW1 | sdc |
| Jannaschia aquimarina GSW-M26 | dctQ, dctM, dctP |
| Jeotgalibacillus soli P9 | sdc |
| Kangiella geojedonensis YCS-5 | sdc |
| Knoellia flava TL1 | dctA |
| Kocuria flava HO-9041 | sdc |
| Kocuria turfanensis HO-9042 | sdc |
| Laceyella sediminis RHA1 | dctA |
| Lacinutrix algicola AKS293 | sdc |
| Lacinutrix himadriensis E4-9a | sdc |
| Lacinutrix mariniflava AKS432 | sdc |
| Lactobacillus curieae CCTCC M 2011381 | dctA |
| Lactobacillus delbrueckii ZN7a-9 | sdc |
| Lactobacillus hokkaidonensis LOOC260 | dctA |
| Lactobacillus oryzae SG293 | dctA |
| Lactobacillus pobuzihii E100301 | sdc |
| Lactobacillus shenzhenensis LY-73 | sdc |
| Lactobacillus silagei IWT126 | dctA |
| Leeuwenhoekiella blandensis MED217 | sdc |
| Lentibacillus jeotgali Grbi | sdc |
| Limnohabitans curvus MWH-C5 | dctA |
| Limnohabitans parvus II-B4 | dauA |
| Listeria fleischmannii LU2006-1 | sdc |
| Luteimonas huabeiensis HB2 | dctA |
| Luteipulveratus mongoliensis MN07-A0370 | dctA |
| Lutibaculum baratangense AMV1 | Dshi_1194, Dshi_1195 |
| Lysobacter daejeonensis GH1-9 | sdc |
| Magnetovibrio blakemorei MV-1 | dauA |
| Marinicella litoralis KMM 3900 | sdc |
| Mariniradius saccharolyticus AK6 | sdc |
| Marinobacter algicola DG893 | Dshi_1194, Dshi_1195 |
| Marinobacter guineae M3B | Dshi_1194, Dshi_1195 |
| Marinobacter psychrophilus 20041 | Dshi_1194, Dshi_1195 |
| Marinomonas arctica 328 | dctQ, dctM, dctP |
| Marivita geojedonensis DPG-138 | Dshi_1194, Dshi_1195 |
| Martelella endophytica YC6887 | dauA |
| Megamonas funiformis YIT 11815 | sdc |
| Mesorhizobium ciceri WSM1271 | dctA |
| Methanobacterium arcticum M2 | satP |
| Methanobacterium veterum MK4 | satP |
| Methanocella arvoryzae MRE50 | satP |
| Methanococcus aeolicus Nankai-3 | sdc |
| Methanoculleus horonobensis T10 | sdc |
| Methanolinea tarda NOBI-1 | sdc |
| Methanosarcina soligelidi SMA-21 | satP |
| Methanospirillum lacunae Ki8-1 | satP |
| Methanospirillum stamsii Pt1 | sdc |
| Methylibium petroleiphilum PM1 | dctA |
| Methylobacterium gossipiicola Gh-105 | dctA |
| Methylocapsa aurea KYG | dctA |
| Methylotenera versatilis 301 | dauA |
| Microbacterium profundi Shh49 | dctA |
| Microvirga lotononidis WSM3557 | dctA |
| Moritella dasanensis ArB 0140 | dctQ, dctM, dctP |
| Mucilaginibacter gossypii Gh-67 | dctA |
| Mucilaginibacter gossypiicola Gh-48 | dctA |
| Mucilaginibacter mallensis MP1X4 | dctA |
| Nafulsella turpanensis ZLM-10 | sdc |
| Natronomonas moolapensis 8.8.11 | sdc |
| Nautilia profundicola AmH | dctQ, dctM, dctP |
| Neiella marina J221 | sdc |
| Neptunomonas antarctica S3-22 | dctQ, dctM, dctP |
| Nocardioides daejeonensis MJ31 | dauA |
| Nocardioides dokdonensis FR1436 | sdc |
| Nocardiopsis baichengensis YIM 90130 | sdc |
| Nocardiopsis gilva YIM 90087 | sdc |
| Novosphingobium barchaimii LL02 | dctA |
| Novosphingobium fuchskuhlense FNE08-7 | sdc |
| Novosphingobium lindaniclasticum LE124 | dctA |
| Oceanisphaera arctica V1-41 | sdc |
| Ochrobactrum rhizosphaerae PR17 | dctA |
| Ochrobactrum thiophenivorans DSM 7216 | dctA |
| Oscillibacter ruminantium GH1 | dauA |
| Paenisporosarcina indica PN2 | dctA |
| Palaeococcus pacificus DY20341 | sdc |
| Paludibacter propionicigenes WB4 | dauA |
| Pandoraea thiooxydans ATSB16 | dctA |
| Pantoea rwandensis LMG 26275 | dctA |
| Pedobacter arcticus A12 | sdc |
| Photobacterium gaetbulicola Gung47 | sdc |
| Photobacterium jeanii R-40508 | sdc |
| Phyllobacterium brassicacearum STM 196 | dctA |
| Phyllobacterium endophyticum PEPV15 | dctA |
| Phyllobacterium leguminum ORS 1419 | sdc |
| Planktomarina temperata RCA23 | dctQ, dctM, dctP |
| Planococcus halocryophilus Or1 | sdc |
| Pleomorphomonas diazotrophica R5-392 | satP |
| Polaribacter dokdonensis DSW-5 | sdc |
| Pontibacillus litoralis JSM 072002 | sdc |
| Pontibacter lucknowensis DM9 | dctA |
| Pontibacter ramchanderi LP43 | dctA |
| Pontimonas salivibrio CL-TW6 | sdc |
| Porphyrobacter dokdonensis DSW-74 | dctA |
| Pseudoalteromonas arctica A 37-1-2 | sdc |
| Pseudomonas baetica a390 | dctA |
| Pseudomonas litoralis 2SM5 | sdc |
| Pseudomonas taeanensis MS-3 | dctQ, dctM, dctP |
| Pseudovibrio axinellae Ad2 | dctQ, dctM, dctP |
| Psychrobacter arcticus 273-4 | sdc |
| Psychrobacter cryohalolentis K5 | sdc |
| Psychromonas ingrahamii 37 | dctQ, dctM, dctP |
| Psychromonas ossibalaenae JAMM 0738 | dctQ, dctM, dctP |
| Rhizobium freirei PRF 81 | dctA |
| Rhizobium grahamii CCGE 502 | dctA |
| Rhizobium subbaraonis JC85 | dctA |
| Rhodanobacter denitrificans 2APBS1 | sdc |
| Rhodobacter johrii JA192 | dctQ, dctM, dctP |
| Rhodobacter maris JA276 | dctQ, dctM, dctP |
| Rhodobacter ovatus JA234 | sdc |
| Rhodobacter viridis JA737 | dctQ, dctM, dctP |
| Rhodococcus qingshengii djl-6-2 | dctA |
| Rhodopseudomonas pseudopalustris DSM 123 | dctQ, dctM, dctP |
| Roseateles aquatilis CCUG 48205 | dctQ, dctM, dctP |
| Roseivirga spongicola UST030701-084 | sdc |
| Rubrivirga marina SAORIC-28 | sdc |
| Ruegeria conchae TW15 | dctQ, dctM, dctP |
| Saccharomonospora marina XMU15 | sdc |
| Salinicoccus carnicancri Crm | sdc |
| Serinicoccus profundi MCCC 1A05965 | sdc |
| Shewanella halifaxensis HAW-EB4 | sdc |
| Skermanella stibiiresistens SB22 | sdc |
| Snodgrassella alvi wkB2 | dctA |
| Sphaerochaeta globosa Buddy | dauA |
| Sphaerochaeta pleomorpha Grapes | dauA |
| Sphingobium baderi LL03 | dctA |
| Sphingobium czechense LL01 | dctA |
| Sphingobium quisquiliarum P25 | dctA |
| Sphingomonas histidinilytica UM2 | dctA |
| Sphingomonas indica Dd16 | dctA |
| Sphingomonas laterariae LNB2 | dctA |
| Sphingopyxis indica DS15 | dctA |
| Sphingopyxis terrae UI2 | dctA |
| Sporolactobacillus vineae SL153 | dctA |
| Streptacidiphilus oryzae TH49 | dctA |
| Streptococcus anginosus CCUG 39159 | sdc |
| Streptococcus massiliensis 4401825 | sdc |
| Streptococcus oralis 7747 | sdc |
| Streptococcus oralis AZ_3a | sdc |
| Streptomyces kebangsaanensis SUK12 | dctA |
| Succinatimonas hippei YIT 12066 | dauA |
| Sulfurimonas gotlandica GD1 | sdc |
| Tatumella morbirosei LMG 23360 | dctA |
| Thauera humireducens SgZ-1 | dctQ, dctM, dctP |
| Thermoactinomyces daqus H-18 | dctA |
| Thermobifida halotolerans YIM 90462 | dauA |
| Thermodesulfovibrio aggregans TGE-P1 | sdc |
| Thermophagus xiamenensis HS1 | sdc |
| Thermovenabulum gondwanense R270 | dctQ, dctM, dctP |
| Thioclava dalianensis DLFJ1-1 | dctQ, dctM, dctP |
| Thiohalospira halophila HL 3 | dauA |
| Tistlia consotensis USBA 355 | dctQ, dctM, dctP |
| Vagococcus penaei CD276 | sdc |
| Verminephrobacter eiseniae EF01-2 | dctA |
| Weissella oryzae SG25 | sdc |
| Williamsia sterculiae CPCC 203464 | dctA |
| Yersinia intermedia Y228 | dctA |
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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.
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).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know