GapMind for Amino acid biosynthesis

 

L-asparagine biosynthesis

Analysis of pathway asn in 206 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 aspS2, gatA, gatB, gatC
Acidithiobacillus ferrooxidans ATCC 23270 aspS2, gatA, gatB, gatC
Acidovorax sp. GW101-3H11 aspS2, gatA, gatB, gatC
Algiphilus aromaticivorans DG1253 aspS2, gatA, gatB, gatC
Alicycliphilus denitrificans K601 aspS2, gatA, gatB, gatC
Alkalihalobacterium alkalinitrilicum DSM 22532 aspS2, gatA, gatB, gatC
Allochromatium vinosum DSM 180 aspS2, gatA, gatB, gatC
Ammonifex degensii KC4 aspS2, gatA, gatB, gatC
Anaerobutyricum hallii DSM 3353 aspS2, gatA, gatB, gatC
Aquimarina longa SW024 asnB
Archaeoglobus veneficus SNP6 aspS2, gatA, gatB, gatC
Arcobacter nitrofigilis DSM 7299 aspS2, gatA, gatB, gatC
Azoarcus olearius BH72 aspS2, gatA, gatB, gatC
Azohydromonas australica DSM 1124 aspS2, gatA, gatB, gatC
Azorhizobium caulinodans ORS 571 aspS2, gatA, gatB, gatC
Azospirillum brasilense Sp245 aspS2, gatA, gatB, gatC
Azospirillum sp. B510 aspS2, gatA, gatB, gatC
Bacteroides thetaiotaomicron VPI-5482 asnB
Beijerinckia indica subsp. indica ATCC 9039 aspS2, gatA, gatB, gatC
Beijerinckia mobilis UQM 1969 aspS2, gatA, gatB, gatC
Bradyrhizobium sp. BTAi1 aspS2, gatA, gatB, gatC
Brevundimonas sp. GW460-12-10-14-LB2 aspS2, gatA, gatB, gatC
Burkholderia phytofirmans PsJN 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
Carboxydothermus pertinax Ug1 aspS2, gatA, gatB, gatC
Caulobacter crescentus NA1000 aspS2, gatA, gatB, gatC
Cereibacter sphaeroides ATCC 17029 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
Clostridium tyrobutyricum FAM22553 aspS2, gatA, gatB, gatC
Crocosphaera subtropica ATCC 51142 aspS2, gatA, gatB, gatC
Cupriavidus basilensis FW507-4G11 aspS2, gatA, gatB, gatC
Dechloromonas agitata is5 aspS2, gatA, gatB, gatC
Dechlorosoma suillum PS 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
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
Desulfogranum mediterraneum DSM 13871 aspS2, gatA, gatB, gatC
Desulforamulus ruminis DSM 2154 aspS2, gatA, gatB, gatC
Desulfoscipio geothermicus DSM 3669 aspS2, gatA, gatB, gatC
Desulfotalea psychrophila LSv54 aspS2, gatA, gatB, gatC
Desulfovibrio oxyclinae DSM 11498 aspS2, gatA, gatB, gatC
Desulfovibrio vulgaris Hildenborough JW710 aspS2, gatA, gatB, gatC
Desulfovibrio vulgaris Miyazaki F aspS2, gatA, gatB, gatC
Desulfurobacterium atlanticum DSM 15668 aspS2, gatA, gatB, gatC
Desulfuromonas acetexigens DSM 1397 aspS2, gatA, gatB, gatC
Desulfuromusa kysingii DSM 7343 aspS2, gatA, gatB, gatC
Dinoroseobacter shibae DFL-12 aspS2, gatA, gatB, gatC
Dyella japonica UNC79MFTsu3.2 asnB
Echinicola vietnamensis KMM 6221, DSM 17526 aspS2, gatA, gatB, gatC
Escherichia coli BW25113 asnB
Ferroglobus placidus DSM 10642 aspS2, gatA, gatB, gatC
Frankia alni ACN14a aspS2, gatA, gatB, gatC
Geobacter metallireducens GS-15 aspS2, gatA, gatB, gatC
Geotalea uraniireducens Rf4 aspS2, gatA, gatB, gatC
Halococcus hamelinensis 100A6 aspS2, gatA, gatB, gatC
Haloechinothrix alba DSM 45207 asnB
Haloferax volcanii DS2 aspS2, gatA, gatB, gatC
Haloglycomyces albus DSM 45210 aspS2, gatA, gatB, gatC
Halomonas desiderata SP1 aspS2, gatA, gatB, gatC
Halorhodospira halophila SL1 aspS2, gatA, gatB, gatC
Heliomicrobium modesticaldum Ice1 Ice1; ATCC 51547 aspS2, gatA, gatB, gatC
Herbaspirillum autotrophicum IAM 14942 aspS2, gatA, gatB, gatC
Herbaspirillum seropedicae SmR1 aspS2, gatA, gatB, gatC
Hippea alviniae EP5-r aspS2, gatA, gatB, gatC
Hydrogenophaga taeniospiralis CCUG 15921 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 michiganensis M5al asnB
Klebsiella variicola At-22 asnB
Kyrpidia tusciae DSM 2912 aspS2, gatA, gatB, gatC
Leptospirillum ferrooxidans C2-3 aspS2, gatA, gatB, gatC
Lysobacter soli OAE881 asnB
Magnetospirillum magneticum AMB-1 aspS2, gatA, gatB, gatC
Malonomonas rubra DSM 5091 aspS2, gatA, gatB, gatC
Maridesulfovibrio bastinii DSM 16055 aspS2, gatA, gatB, gatC
Maridesulfovibrio zosterae DSM 11974 aspS2, gatA, gatB, gatC
Marinobacter adhaerens HP15 aspS2, gatA, gatB, gatC
Mesorhizobium ciceri biovar biserrulae 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 mazei Go1 aspS2, gatA, gatB, gatC
Methanospirillum lacunae Ki8-1 aspS2, gatA, gatB, gatC
Methanothermobacter thermautotrophicus str. Delta H aspS2, gatA, gatB, gatC
Methylobacterium nodulans ORS 2060 aspS2, gatA, gatB, gatC
Methylobacterium sp. 4-46 Apr-46 aspS2, gatA, gatB, gatC
Methylocapsa acidiphila B2 asnB
Methylocapsa aurea KYG aspS2, gatA, gatB, gatC
Methylocella silvestris BL2 aspS2, gatA, gatB, gatC
Methylococcus capsulatus str. Bath aspS2, gatA, gatB, gatC
Methylocystis bryophila S285 aspS2, gatA, gatB, gatC
Methyloferula stellata AR4 AR4T aspS2, gatA, gatB, gatC
Methylohalobius crimeensis 10Ki aspS2, gatA, gatB, gatC
Methylomonas methanica MC09 aspS2, gatA, gatB, gatC
Methylosarcina fibrata AML-C10 aspS2, gatA, gatB, gatC
Methylotuvimicrobium alcaliphilum 20Z aspS2, gatA, gatB, gatC
Methylovulum miyakonense HT12 aspS2, gatA, gatB, gatC
Mucilaginibacter yixingensis DSM 26809 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 aspS2, gatA, gatB, gatC
Nitrosopumilus maritimus SCM1 aspS2, gatA, gatB, gatC?
Nocardioides dokdonensis FR1436 asnB
Nocardiopsis lucentensis DSM 44048 aspS2, gatA*, gatB, gatC
Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102 aspS2, gatA, gatB, gatC
Novosphingobium aromaticivorans DSM 12444 aspS2, gatA, gatB, gatC
Oleispira antarctica RB-8 aspS2, gatA, gatB, gatC
Paraburkholderia atlantica CCGE1002 aspS2, gatA, gatB, gatC
Paraburkholderia bryophila 376MFSha3.1 aspS2, gatA, gatB, gatC
Paraburkholderia phymatum STM815 aspS2, gatA, gatB, gatC
Paucidesulfovibrio gracilis DSM 16080 aspS2, gatA, gatB, gatC
Pedobacter sp. GW460-11-11-14-LB5 aspS2, gatA, gatB, gatC
Pelobacter propionicus DSM 2379 aspS2, gatA, gatB, gatC
Persephonella marina EX-H1 aspS2, gatA, gatB, gatC
Phaeacidiphilus oryzae TH49 aspS2, gatA, gatB, gatC
Phaeobacter inhibens BS107 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 fluorescens FW300-N1B4 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2C3 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2E2 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens FW300-N2E3 aspS2, gatA, gatB, gatC
Pseudomonas fluorescens GW456-L13 aspS2, gatA, gatB, gatC
Pseudomonas putida KT2440 aspS2, gatA, gatB, gatC
Pseudomonas simiae WCS417 aspS2, gatA, gatB, gatC
Pseudomonas stutzeri RCH2 aspS2, gatA, gatB, gatC
Pyrolobus fumarii 1A aspS2, gatA, gatB, gatC
Rhizobium etli CFN 42 aspS2, gatA, gatB, gatC
Rhizobium johnstonii 3841 aspS2, gatA, gatB, gatC
Rhizobium leguminosarum bv. trifolii WSM1325 aspS2, gatA, gatB, gatC
Rhizorhabdus wittichii RW1 aspS2, gatA, gatB, gatC
Rhodanobacter denitrificans FW104-10B01 asnB
Rhodomicrobium vannielii ATCC 17100 aspS2, gatA, gatB, gatC
Rhodopseudomonas palustris CGA009 aspS2, gatA, gatB, gatC
Rhodospirillum centenum SW SW; ATCC 51521 aspS2, gatA, gatB, gatC
Rhodospirillum rubrum ATCC 11170 aspS2, gatA, gatB, gatC
Roseburia faecis M72 aspS2, gatA, gatB, gatC
Saccharomonospora cyanea NA-134 aspS2, gatA, gatB, gatC
Sedimenticola selenatireducens DSM 17993 aspS2, gatA, gatB, gatC
Shewanella amazonensis SB2B asnB
Shewanella loihica PV-4 asnB
Shewanella oneidensis MR-1 asnB
Shewanella sp. ANA-3 asnB
Sinorhizobium fredii NGR234 aspS2, gatA, gatB, gatC
Sinorhizobium medicae WSM419 aspS2, gatA, gatB, gatC
Sinorhizobium meliloti 1021 aspS2, gatA, gatB, gatC
Sphingomonas koreensis DSMZ 15582 aspS2, gatA, gatB, gatC
Stenotrophomonas chelatiphaga DSM 21508 asnB
Steroidobacter denitrificans DSM 18526 aspS2, gatA, gatB, gatC
Stutzerimonas stutzeri A1501 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 sk43H DSM 22779 aspS2, gatA, gatB, gatC
Sulfurivirga caldicuralii DSM 17737 aspS2, gatA, gatB, gatC
Synechococcus elongatus PCC 7942 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
Thermoanaerobacter kivui LKT-1 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
Thermus aquaticus YT-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
Thiohalospira halophila DSM 15071 HL 3 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
Tistlia consotensis USBA 355 aspS2, gatA, gatB, gatC
Trichlorobacter lovleyi SZ aspS2, gatA, gatB, gatC
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome aspS2, gatA, gatB, gatC
Trichormus variabilis ATCC 29413 aspS2, gatA, gatB, gatC
Xanthobacter autotrophicus Py2 aspS2, gatA, gatB, gatC
Xanthomonas campestris pv. campestris strain 8004 asnB
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 Jul 25 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