GapMind for Amino acid biosynthesis

 

L-lysine biosynthesis

Analysis of pathway lys in 150 genomes

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

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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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