L-glutamine biosynthesis

GapMind for Amino acid biosynthesis

L-glutamine biosynthesis

Analysis of pathway gln in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	glnA
Acidithiobacillus ferrooxidans ATCC 23270	glnA
Alicycliphilus denitrificans K601	glnA
Allochromatium vinosum DSM 180	glnA
Ammonifex degensii KC4	gltX, glnA, gatA, gatB, gatC
Archaeoglobus veneficus SNP6	glnA
Arcobacter nitrofigilis DSM 7299	glnA
Azoarcus sp. BH72	glnA
Azohydromonas australica DSM 1124	glnA
Azorhizobium caulinodans ORS 571	gltX, glnA, gatA, gatB, gatC
Azospirillum lipoferum B510	gltX, glnA, gatA, gatB, gatC
Bacillus alkalinitrilicus DSM 22532	gltX, glnA, gatA, gatB, gatC
Beijerinckia indica ATCC 9039	gltX, glnA, gatA, gatB, gatC
Beijerinckia mobilis UQM 1969	gltX, glnA, gatA, gatB, gatC
Bradyrhizobium sp. BTAi1	gltX, glnA, gatA, gatB, gatC
Burkholderia vietnamiensis G4	glnA
Calditerrivibrio nitroreducens DSM 19672	gltX, glnA, gatA, gatB, gatC
Caminibacter mediatlanticus TB-2	glnA
Chlorobaculum parvum NCIB 8327	gltX, glnA, gatA, gatB, gatC
Chlorobaculum tepidum TLS	gltX, glnA, gatA, gatB, gatC
Chlorobium limicola DSM 245	glnA
Chlorobium phaeobacteroides BS1	glnA
Clostridium acetobutylicum ATCC 824	glnA
Clostridium kluyveri DSM 555	gltX, glnA, gatA, gatB, gatC
Crocosphaera subtropica ATCC 51142	gltX, glnA, gatA, gatB, gatC
Dechloromonas agitata is5	glnA
Dehalococcoides mccartyi 195	gltX, glnA, gatA, gatB, gatC
Denitrovibrio acetiphilus DSM 12809	glnA
Derxia gummosa DSM 723	glnA
Desulfacinum hydrothermale DSM 13146	glnA
Desulfacinum infernum DSM 9756	glnA
Desulfallas geothermicus DSM 3669	gltX, glnA, gatA, gatB, gatC
Desulfarculus baarsii DSM 2075	gltX, glnA, gatA, gatB, gatC
Desulfatibacillum aliphaticivorans DSM 15576	glnA
Desulfatiglans anilini DSM 4660	gltX, glnA, gatA, gatB, gatC
Desulfitobacterium hafniense DCB-2	gltX, glnA, gatA, gatB, gatC
Desulfobacca acetoxidans DSM 11109	gltX, glnA, gatA, gatB, gatC
Desulfobacter vibrioformis DSM 8776	glnA
Desulfobulbus mediterraneus DSM 13871	glnA
Desulfotalea psychrophila LSv54	glnA
Desulfotomaculum ruminis DSM 2154	gltX, glnA, gatA, gatB, gatC
Desulfovibrio bastinii DSM 16055	glnA
Desulfovibrio gracilis DSM 16080	gltX, glnA, gatA, gatB, gatC
Desulfovibrio oxyclinae DSM 11498	gltX, glnA, gatA, gatB, gatC
Desulfovibrio zosterae DSM 11974	glnA
Desulfurobacterium atlanticum DSM 15668	gltX, glnA, gatA, gatB, gatC
Desulfuromonas acetexigens	glnA
Desulfuromusa kysingii DSM 7343	glnA
Ferroglobus placidus DSM 10642	glnA
Frankia alni ACN14A	glnA
Geobacter lovleyi SZ	glnA
Geobacter metallireducens GS-15	glnA
Geobacter uraniireducens Rf4	glnA
Haloechinothrix alba DSM 45207	glnA
Haloglycomyces albus DSM 45210	glnA
Halomonas desiderata SP1	glnA
Halorhodospira halophila SL1	glnA
Heliobacterium modesticaldum Ice1; ATCC 51547	gltX, glnA, gatA, gatB, gatC
Herbaspirillum autotrophicum IAM 14942	glnA
Hydrogenophaga taeniospiralis NBRC 102512	glnA
Hydrogenovibrio halophilus DSM 15072	glnA
Hydrogenovibrio kuenenii DSM 12350	glnA
Hydrogenovibrio marinus DSM 11271	glnA
Hyphomicrobium sulfonivorans WDL6	gltX, glnA, gatA, gatB, gatC
Klebsiella variicola At-22	glnA
Kyrpidia tusciae DSM 2912	gltX, glnA, gatA, gatB, gatC
Leptospirillum ferrooxidans C2-3	glnA
Malonomonas rubra DSM 5091	glnA
Mesorhizobium ciceri WSM1271	glnA
Methanobacterium lacus AL-21	glnA
Methanococcus aeolicus Nankai-3	glnA
Methanococcus maripaludis C5	glnA
Methanosarcina acetivorans C2A	glnA
Methanosarcina barkeri Fusaro	glnA
Methanosarcina mazei Go1	glnA
Methanothermobacter thermautotrophicus Delta H	glnA
Methylobacterium nodulans ORS 2060	gltX, glnA, gatA, gatB, gatC
Methylobacterium sp. 4-46	gltX, glnA, gatA, gatB, gatC
Methylocapsa acidiphila B2	gltX, glnA, gatA, gatB, gatC
Methylocapsa aurea KYG T	gltX, glnA, gatA, gatB, gatC
Methylocella silvestris BL2	gltX, glnA, gatA, gatB, gatC
Methylococcus capsulatus Bath	glnA
Methylocystis bryophila S285	gltX, glnA, gatA, gatB, gatC
Methyloferula stellata AR4T	gltX, glnA, gatA, gatB, gatC
Methylohalobius crimeensis 10Ki	glnA
Methylomicrobium alcaliphilum 20Z	glnA
Methylomonas methanica MC09	glnA
Methylosarcina fibrata AML-C10	glnA
Methylovulum miyakonense HT12	glnA
Mycolicibacterium vanbaalenii PYR-1	glnA
Nitratifractor salsuginis DSM 16511	glnA
Nitratiruptor tergarcus DSM 16512	glnA
Nitriliruptor alkaliphilus DSM 45188	glnA
Nocardiopsis lucentensis DSM 44048	glnA
Nostoc punctiforme ATCC 29133; PCC 73102	gltX, glnA, gatA, gatB, gatC
Novosphingobium aromaticivorans DSM 12444	gltX, glnA, gatA, gatB, gatC
Oleispira antarctica	glnA
Paraburkholderia phymatum STM815	glnA
Paraburkholderia sp. CCGE1002	glnA
Pelobacter propionicus DSM 2379	glnA
Persephonella marina EX-H1	gltX, glnA, gatA, gatB, gatC
Polaromonas naphthalenivorans CJ2	glnA
Prosthecochloris aestuarii DSM 271	glnA
Pseudarthrobacter sulfonivorans Ar51	glnA
Pseudomonas benzenivorans DSM 8628	glnA
Pseudomonas stutzeri A1501	glnA
Pyrolobus fumarii 1A	glnA
Rhizobium etli CFN 42	glnA
Rhizobium leguminosarum 3841	glnA
Rhizobium leguminosarum WSM1325	glnA
Rhodobacter sphaeroides ATCC 17029	gltX, glnA, gatA, gatB, gatC
Rhodomicrobium vannielii ATCC 17100	glnA
Rhodopseudomonas palustris CGA009	gltX, glnA, gatA, gatB, gatC
Rhodospirillum centenum SW; ATCC 51521	gltX, glnA, gatA, gatB, gatC
Rhodospirillum rubrum ATCC 11170	gltX, glnA, gatA, gatB, gatC
Saccharomonospora cyanea NA-134	glnA
Sedimenticola selenatireducens DSM 17993	glnA
Sinorhizobium fredii NGR234	glnA
Sinorhizobium medicae WSM419	glnA
Sphingomonas wittichii RW1	gltX, glnA, gatA, gatB, gatC
Stenotrophomonas chelatiphaga DSM 21508	glnA
Steroidobacter denitrificans DSM 18526	glnA
Sulfuricurvum kujiense DSM 16994	glnA
Sulfurihydrogenibium azorense Az-Fu1	gltX, glnA, gatA, gatB, gatC
Sulfurihydrogenibium subterraneum DSM 15120	gltX, glnA, gatA, gatB, gatC
Sulfurimonas denitrificans DSM 1251	glnA
Sulfuritalea hydrogenivorans DSM 22779	glnA
Sulfurivirga caldicuralii DSM 17737	glnA
Teredinibacter turnerae T7901	glnA
Thauera aminoaromatica S2	glnA
Thermithiobacillus tepidarius DSM 3134	gltX, glnA, gatA, gatB, gatC
Thermocrinis albus DSM 14484	gltX, glnA, gatA, gatB, gatC
Thermodesulforhabdus norvegica DSM 9990	glnA
Thermomonospora curvata DSM 43183	glnA
Thermovibrio ammonificans HB-1	gltX, glnA, gatA, gatB, gatC
Thioalkalivibrio denitrificans ALJD	glnA
Thioalkalivibrio halophilus HL17	glnA
Thioalkalivibrio paradoxus ARh 1	glnA
Thioalkalivibrio thiocyanodenitrificans ARhD 1	glnA
Thiohalomonas denitrificans HLD2	glnA
Thiomicrorhabdus arctica DSM 13458	glnA
Thiomicrorhabdus chilensis DSM 12352	glnA
Thiomicrospira cyclica ALM1	glnA
Thiomicrospira microaerophila ASL8-2	glnA
Thiomicrospira pelophila DSM 1534	glnA
Thiothrix lacustris DSM 21227	glnA
Trichodesmium erythraeum IMS101	gltX, glnA, gatA, gatB, gatC
Trichormus variabilis ATCC 29413	gltX, glnA, gatA, gatB, gatC
Xanthobacter autotrophicus Py2	gltX, glnA, gatA, gatB, gatC
Xenophilus azovorans DSM 13620	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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis