GapMind for Amino acid biosynthesis

 

L-glutamine biosynthesis

Analysis of pathway gln in 276 genomes

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

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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