L-asparagine biosynthesis

GapMind for Amino acid biosynthesis

L-asparagine biosynthesis

Analysis of pathway asn in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	aspS2, gatA, gatB, gatC
Acidithiobacillus ferrooxidans ATCC 23270	aspS2, gatA, gatB, gatC
Alicycliphilus denitrificans K601	aspS2, gatA, gatB, gatC
Allochromatium vinosum DSM 180	aspS2, gatA, gatB, gatC
Ammonifex degensii KC4	aspS2, gatA, gatB, gatC
Archaeoglobus veneficus SNP6	aspS2, gatA, gatB, gatC
Arcobacter nitrofigilis DSM 7299	aspS2, gatA, gatB, gatC
Azoarcus sp. BH72	aspS2, gatA, gatB, gatC
Azohydromonas australica DSM 1124	aspS2, gatA, gatB, gatC
Azorhizobium caulinodans ORS 571	aspS2, gatA, gatB, gatC
Azospirillum lipoferum B510	aspS2, gatA, gatB, gatC
Bacillus alkalinitrilicus DSM 22532	aspS2, gatA, gatB, gatC
Beijerinckia indica ATCC 9039	aspS2, gatA, gatB, gatC
Beijerinckia mobilis UQM 1969	aspS2, gatA, gatB, gatC
Bradyrhizobium sp. BTAi1	aspS2, gatA, gatB, gatC
Burkholderia vietnamiensis G4	aspS2, gatA, gatB, gatC
Calditerrivibrio nitroreducens DSM 19672	aspS2, gatA, gatB, gatC
Caminibacter mediatlanticus TB-2	aspS2, gatA, gatB, gatC
Chlorobaculum parvum NCIB 8327	aspS2, gatA, gatB, gatC
Chlorobaculum tepidum TLS	aspS2, gatA, gatB, gatC
Chlorobium limicola DSM 245	aspS2, gatA, gatB, gatC
Chlorobium phaeobacteroides BS1	aspS2, gatA, gatB, gatC
Clostridium acetobutylicum ATCC 824	aspS2, gatA, gatB, gatC
Clostridium kluyveri DSM 555	aspS2, gatA, gatB, gatC
Crocosphaera subtropica ATCC 51142	aspS2, gatA, gatB, gatC
Dechloromonas agitata is5	aspS2, gatA, gatB, gatC
Dehalococcoides mccartyi 195	aspS2, gatA, gatB, gatC
Denitrovibrio acetiphilus DSM 12809	aspS2, gatA, gatB, gatC
Derxia gummosa DSM 723	aspS2, gatA, gatB, gatC
Desulfacinum hydrothermale DSM 13146	aspS2, gatA, gatB, gatC
Desulfacinum infernum DSM 9756	aspS2, gatA, gatB, gatC
Desulfallas geothermicus DSM 3669	aspS2, gatA, gatB, gatC
Desulfarculus baarsii DSM 2075	aspS2, gatA, gatB, gatC
Desulfatibacillum aliphaticivorans DSM 15576	aspS2, gatA, gatB, gatC
Desulfatiglans anilini DSM 4660	aspS2, gatA, gatB, gatC
Desulfitobacterium hafniense DCB-2	aspS2, gatA, gatB, gatC
Desulfobacca acetoxidans DSM 11109	aspS2, gatA, gatB, gatC
Desulfobacter vibrioformis DSM 8776	aspS2, gatA, gatB, gatC
Desulfobulbus mediterraneus DSM 13871	aspS2, gatA, gatB, gatC
Desulfotalea psychrophila LSv54	aspS2, gatA, gatB, gatC
Desulfotomaculum ruminis DSM 2154	aspS2, gatA, gatB, gatC
Desulfovibrio bastinii DSM 16055	aspS2, gatA, gatB, gatC
Desulfovibrio gracilis DSM 16080	aspS2, gatA, gatB, gatC
Desulfovibrio oxyclinae DSM 11498	aspS2, gatA, gatB, gatC
Desulfovibrio zosterae DSM 11974	aspS2, gatA, gatB, gatC
Desulfurobacterium atlanticum DSM 15668	aspS2, gatA, gatB, gatC
Desulfuromonas acetexigens	aspS2, gatA, gatB, gatC
Desulfuromusa kysingii DSM 7343	aspS2, gatA, gatB, gatC
Ferroglobus placidus DSM 10642	aspS2, gatA, gatB, gatC
Frankia alni ACN14A	aspS2, gatA, gatB, gatC
Geobacter lovleyi SZ	aspS2, gatA, gatB, gatC
Geobacter metallireducens GS-15	aspS2, gatA, gatB, gatC
Geobacter uraniireducens Rf4	aspS2, gatA, gatB, gatC
Haloechinothrix alba DSM 45207	asnB
Haloglycomyces albus DSM 45210	aspS2, gatA, gatB, gatC
Halomonas desiderata SP1	aspS2, gatA, gatB, gatC
Halorhodospira halophila SL1	aspS2, gatA, gatB, gatC
Heliobacterium modesticaldum Ice1; ATCC 51547	aspS2, gatA, gatB, gatC
Herbaspirillum autotrophicum IAM 14942	aspS2, gatA, gatB, gatC
Hydrogenophaga taeniospiralis NBRC 102512	aspS2, gatA, gatB, gatC
Hydrogenovibrio halophilus DSM 15072	aspS2, gatA, gatB, gatC
Hydrogenovibrio kuenenii DSM 12350	aspS2, gatA, gatB, gatC
Hydrogenovibrio marinus DSM 11271	aspS2, gatA, gatB, gatC
Hyphomicrobium sulfonivorans WDL6	aspS2, gatA, gatB, gatC
Klebsiella variicola At-22	asnB
Kyrpidia tusciae DSM 2912	aspS2, gatA, gatB, gatC
Leptospirillum ferrooxidans C2-3	aspS2, gatA, gatB, gatC
Malonomonas rubra DSM 5091	aspS2, gatA, gatB, gatC
Mesorhizobium ciceri WSM1271	asnB
Methanobacterium lacus AL-21	asnB
Methanococcus aeolicus Nankai-3	aspS2, gatA, gatB, gatC
Methanococcus maripaludis C5	asnB
Methanosarcina acetivorans C2A	aspS2, gatA, gatB, gatC
Methanosarcina barkeri Fusaro	aspS2, gatA, gatB, gatC
Methanosarcina mazei Go1	aspS2, gatA, gatB, gatC
Methanothermobacter thermautotrophicus Delta H	asnB
Methylobacterium nodulans ORS 2060	aspS2, gatA, gatB, gatC
Methylobacterium sp. 4-46	aspS2, gatA, gatB, gatC
Methylocapsa acidiphila B2	asnB
Methylocapsa aurea KYG T	aspS2, gatA, gatB, gatC
Methylocella silvestris BL2	aspS2, gatA, gatB, gatC
Methylococcus capsulatus Bath	aspS2, gatA, gatB, gatC
Methylocystis bryophila S285	aspS2, gatA, gatB, gatC
Methyloferula stellata AR4T	aspS2, gatA, gatB, gatC
Methylohalobius crimeensis 10Ki	aspS2, gatA, gatB, gatC
Methylomicrobium alcaliphilum 20Z	aspS2, gatA, gatB, gatC
Methylomonas methanica MC09	aspS2, gatA, gatB, gatC
Methylosarcina fibrata AML-C10	aspS2, gatA, gatB, gatC
Methylovulum miyakonense HT12	aspS2, gatA, gatB, gatC
Mycolicibacterium vanbaalenii PYR-1	asnB
Nitratifractor salsuginis DSM 16511	aspS2, gatA, gatB, gatC
Nitratiruptor tergarcus DSM 16512	aspS2, gatA, gatB, gatC
Nitriliruptor alkaliphilus DSM 45188	asnB
Nocardiopsis lucentensis DSM 44048	aspS2, gatA, gatB, gatC
Nostoc punctiforme ATCC 29133; PCC 73102	aspS2, gatA, gatB, gatC
Novosphingobium aromaticivorans DSM 12444	aspS2, gatA, gatB, gatC
Oleispira antarctica	aspS2, gatA, gatB, gatC
Paraburkholderia phymatum STM815	aspS2, gatA, gatB, gatC
Paraburkholderia sp. CCGE1002	aspS2, gatA, gatB, gatC
Pelobacter propionicus DSM 2379	aspS2, gatA, gatB, gatC
Persephonella marina EX-H1	aspS2, gatA, gatB, gatC
Polaromonas naphthalenivorans CJ2	aspS2, gatA, gatB, gatC
Prosthecochloris aestuarii DSM 271	aspS2, gatA, gatB, gatC
Pseudarthrobacter sulfonivorans Ar51	aspS2, gatA, gatB, gatC
Pseudomonas benzenivorans DSM 8628	aspS2, gatA, gatB, gatC
Pseudomonas stutzeri A1501	aspS2, gatA, gatB, gatC
Pyrolobus fumarii 1A	aspS2, gatA, gatB, gatC
Rhizobium etli CFN 42	aspS2, gatA, gatB, gatC
Rhizobium leguminosarum 3841	aspS2, gatA, gatB, gatC
Rhizobium leguminosarum WSM1325	aspS2, gatA, gatB, gatC
Rhodobacter sphaeroides ATCC 17029	aspS2, gatA, gatB, gatC
Rhodomicrobium vannielii ATCC 17100	aspS2, gatA, gatB, gatC
Rhodopseudomonas palustris CGA009	aspS2, gatA, gatB, gatC
Rhodospirillum centenum SW; ATCC 51521	aspS2, gatA, gatB, gatC
Rhodospirillum rubrum ATCC 11170	aspS2, gatA, gatB, gatC
Saccharomonospora cyanea NA-134	aspS2, gatA, gatB, gatC
Sedimenticola selenatireducens DSM 17993	aspS2, gatA, gatB, gatC
Sinorhizobium fredii NGR234	aspS2, gatA, gatB, gatC
Sinorhizobium medicae WSM419	aspS2, gatA, gatB, gatC
Sphingomonas wittichii RW1	aspS2, gatA, gatB, gatC
Stenotrophomonas chelatiphaga DSM 21508	asnB
Steroidobacter denitrificans DSM 18526	aspS2, gatA, gatB, gatC
Sulfuricurvum kujiense DSM 16994	aspS2, gatA, gatB, gatC
Sulfurihydrogenibium azorense Az-Fu1	aspS2, gatA, gatB, gatC
Sulfurihydrogenibium subterraneum DSM 15120	aspS2, gatA, gatB, gatC
Sulfurimonas denitrificans DSM 1251	aspS2, gatA, gatB, gatC
Sulfuritalea hydrogenivorans DSM 22779	aspS2, gatA, gatB, gatC
Sulfurivirga caldicuralii DSM 17737	aspS2, gatA, gatB, gatC
Teredinibacter turnerae T7901	aspS2, gatA, gatB, gatC
Thauera aminoaromatica S2	aspS2, gatA, gatB, gatC
Thermithiobacillus tepidarius DSM 3134	aspS2, gatA, gatB, gatC
Thermocrinis albus DSM 14484	aspS2, gatA, gatB, gatC
Thermodesulforhabdus norvegica DSM 9990	aspS2, gatA, gatB, gatC
Thermomonospora curvata DSM 43183	aspS2, gatA, gatB, gatC
Thermovibrio ammonificans HB-1	aspS2, gatA, gatB, gatC
Thioalkalivibrio denitrificans ALJD	aspS2, gatA, gatB, gatC
Thioalkalivibrio halophilus HL17	aspS2, gatA, gatB, gatC
Thioalkalivibrio paradoxus ARh 1	aspS2, gatA, gatB, gatC
Thioalkalivibrio thiocyanodenitrificans ARhD 1	aspS2, gatA, gatB, gatC
Thiohalomonas denitrificans HLD2	aspS2, gatA, gatB, gatC
Thiomicrorhabdus arctica DSM 13458	aspS2, gatA, gatB, gatC
Thiomicrorhabdus chilensis DSM 12352	aspS2, gatA, gatB, gatC
Thiomicrospira cyclica ALM1	aspS2, gatA, gatB, gatC
Thiomicrospira microaerophila ASL8-2	aspS2, gatA, gatB, gatC
Thiomicrospira pelophila DSM 1534	aspS2, gatA, gatB, gatC
Thiothrix lacustris DSM 21227	aspS2, gatA, gatB, gatC
Trichodesmium erythraeum IMS101	aspS2, gatA, gatB, gatC
Trichormus variabilis ATCC 29413	aspS2, gatA, gatB, gatC
Xanthobacter autotrophicus Py2	aspS2, gatA, gatB, gatC
Xenophilus azovorans DSM 13620	aspS2, gatA, gatB, gatC

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.

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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