GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis

Analysis of pathway met in 150 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 asp-kinase, asd, hom, hom_kinase, metB?, metC, metH, B12-reactivation-domain
Acidithiobacillus ferrooxidans ATCC 23270 asp-kinase, asd, hom, metA, metB, metC, metE
Alicycliphilus denitrificans K601 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Allochromatium vinosum DSM 180 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Ammonifex degensii KC4 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Archaeoglobus veneficus SNP6 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Arcobacter nitrofigilis DSM 7299 asp-kinase, asd, hom, metX, metY, metE
Azoarcus sp. BH72 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Azohydromonas australica DSM 1124 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Azorhizobium caulinodans ORS 571 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Azospirillum lipoferum B510 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Bacillus alkalinitrilicus DSM 22532 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Beijerinckia indica ATCC 9039 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Beijerinckia mobilis UQM 1969 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Bradyrhizobium sp. BTAi1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Burkholderia vietnamiensis G4 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Calditerrivibrio nitroreducens DSM 19672 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Caminibacter mediatlanticus TB-2 asp-kinase, asd, hom, metX, metY, metE
Chlorobaculum parvum NCIB 8327 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Chlorobaculum tepidum TLS asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Chlorobium limicola DSM 245 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Chlorobium phaeobacteroides BS1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Clostridium acetobutylicum ATCC 824 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Clostridium kluyveri DSM 555 asp-kinase, asd, hom, metX, metY, metE
Crocosphaera subtropica ATCC 51142 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS?, metH, B12-reactivation-domain
Dechloromonas agitata is5 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Dehalococcoides mccartyi 195 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Denitrovibrio acetiphilus DSM 12809 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Derxia gummosa DSM 723 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Desulfacinum hydrothermale DSM 13146 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfacinum infernum DSM 9756 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfallas geothermicus DSM 3669 asp-kinase, asd, hom, metX, metY, mesB
Desulfarculus baarsii DSM 2075 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfatibacillum aliphaticivorans DSM 15576 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfatiglans anilini DSM 4660 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfitobacterium hafniense DCB-2 asp-kinase, asd, hom, metX, metY, mesB
Desulfobacca acetoxidans DSM 11109 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Desulfobacter vibrioformis DSM 8776 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Desulfobulbus mediterraneus DSM 13871 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Desulfotalea psychrophila LSv54 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Desulfotomaculum ruminis DSM 2154 asp-kinase, asd, hom, metX, metY, metH, ramA
Desulfovibrio bastinii DSM 16055 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Desulfovibrio gracilis DSM 16080 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Desulfovibrio oxyclinae DSM 11498 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Desulfovibrio zosterae DSM 11974 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Desulfurobacterium atlanticum DSM 15668 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE
Desulfuromonas acetexigens asp-kinase, asd, hom, metX, metY, metH, ramA
Desulfuromusa kysingii DSM 7343 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Ferroglobus placidus DSM 10642 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Frankia alni ACN14A asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Geobacter lovleyi SZ asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Geobacter metallireducens GS-15 asp-kinase, asd, hom, metX, metY, metH, ramA
Geobacter uraniireducens Rf4 asp-kinase, asd, hom, metX, metY, metH, ramA
Haloechinothrix alba DSM 45207 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Haloglycomyces albus DSM 45210 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Halomonas desiderata SP1 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Halorhodospira halophila SL1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Heliobacterium modesticaldum Ice1; ATCC 51547 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Herbaspirillum autotrophicum IAM 14942 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Hydrogenophaga taeniospiralis NBRC 102512 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Hydrogenovibrio halophilus DSM 15072 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Hydrogenovibrio kuenenii DSM 12350 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Hydrogenovibrio marinus DSM 11271 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Hyphomicrobium sulfonivorans WDL6 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Klebsiella variicola At-22 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Kyrpidia tusciae DSM 2912 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Leptospirillum ferrooxidans C2-3 asp-kinase, asd, hom, hom_kinase, metB, metC, metH, B12-reactivation-domain
Malonomonas rubra DSM 5091 asp-kinase, asd, hom, metX, metY, metH, ramA
Mesorhizobium ciceri WSM1271 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Methanobacterium lacus AL-21 asp-kinase, asd, hom, metX, metY, mesA
Methanococcus aeolicus Nankai-3 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanococcus maripaludis C5 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methanosarcina acetivorans C2A asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Methanosarcina barkeri Fusaro asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Methanosarcina mazei Go1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesC
Methanothermobacter thermautotrophicus Delta H asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesA
Methylobacterium nodulans ORS 2060 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Methylobacterium sp. 4-46 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Methylocapsa acidiphila B2 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methylocapsa aurea KYG T asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methylocella silvestris BL2 asp-kinase, asd, hom, metX, metB, metC, metH, B12-reactivation-domain
Methylococcus capsulatus Bath asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Methylocystis bryophila S285 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methyloferula stellata AR4T asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Methylohalobius crimeensis 10Ki asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Methylomicrobium alcaliphilum 20Z asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Methylomonas methanica MC09 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Methylosarcina fibrata AML-C10 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Methylovulum miyakonense HT12 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Mycolicibacterium vanbaalenii PYR-1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Nitratifractor salsuginis DSM 16511 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Nitratiruptor tergarcus DSM 16512 asp-kinase, asd, hom, metX, metY, metE
Nitriliruptor alkaliphilus DSM 45188 asp-kinase, asd, hom, metA, metZ, metH, ramA
Nocardiopsis lucentensis DSM 44048 asp-kinase, asd, hom, hom_kinase, metB, metC, metE
Nostoc punctiforme ATCC 29133; PCC 73102 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Novosphingobium aromaticivorans DSM 12444 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Oleispira antarctica asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Paraburkholderia phymatum STM815 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Paraburkholderia sp. CCGE1002 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Pelobacter propionicus DSM 2379 asp-kinase, asd, hom, metX, metY, metH, ramA
Persephonella marina EX-H1 asp-kinase, asd, hom, hom_kinase, metB?, metC?, metE
Polaromonas naphthalenivorans CJ2 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Prosthecochloris aestuarii DSM 271 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Pseudarthrobacter sulfonivorans Ar51 asp-kinase, asd, hom, metX, metY, metE
Pseudomonas benzenivorans DSM 8628 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Pseudomonas stutzeri A1501 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pyrolobus fumarii 1A asp-kinase, asd, hom?, hom_kinase, metB, metC, split_metE_1, split_metE_2
Rhizobium etli CFN 42 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhizobium leguminosarum 3841 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhizobium leguminosarum WSM1325 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhodobacter sphaeroides ATCC 17029 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Rhodomicrobium vannielii ATCC 17100 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Rhodopseudomonas palustris CGA009 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Rhodospirillum centenum SW; ATCC 51521 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Rhodospirillum rubrum ATCC 11170 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Saccharomonospora cyanea NA-134 asp-kinase, asd, hom, metX, metB, metC, metE
Sedimenticola selenatireducens DSM 17993 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Sinorhizobium fredii NGR234 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Sinorhizobium medicae WSM419 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Sphingomonas wittichii RW1 asp-kinase, asd, hom, metX, metB, metC, metH*, B12-reactivation-domain
Stenotrophomonas chelatiphaga DSM 21508 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain
Steroidobacter denitrificans DSM 18526 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Sulfuricurvum kujiense DSM 16994 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Sulfurihydrogenibium azorense Az-Fu1 asp-kinase, asd, hom, hom_kinase, metB?, metC?, metE
Sulfurihydrogenibium subterraneum DSM 15120 asp-kinase, asd, hom, hom_kinase, metB?, metC?, metE
Sulfurimonas denitrificans DSM 1251 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Sulfuritalea hydrogenivorans DSM 22779 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Sulfurivirga caldicuralii DSM 17737 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Teredinibacter turnerae T7901 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thauera aminoaromatica S2 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thermithiobacillus tepidarius DSM 3134 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Thermocrinis albus DSM 14484 asp-kinase, asd, hom, hom_kinase, metB?, metC?, metE
Thermodesulforhabdus norvegica DSM 9990 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, mesB
Thermomonospora curvata DSM 43183 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Thermovibrio ammonificans HB-1 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Thioalkalivibrio denitrificans ALJD asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thioalkalivibrio halophilus HL17 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thioalkalivibrio paradoxus ARh 1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thioalkalivibrio thiocyanodenitrificans ARhD 1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thiohalomonas denitrificans HLD2 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thiomicrorhabdus arctica DSM 13458 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Thiomicrorhabdus chilensis DSM 12352 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Thiomicrospira cyclica ALM1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Thiomicrospira microaerophila ASL8-2 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Thiomicrospira pelophila DSM 1534 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Thiothrix lacustris DSM 21227 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Trichodesmium erythraeum IMS101 asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS?, metH, B12-reactivation-domain
Trichormus variabilis ATCC 29413 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Xanthobacter autotrophicus Py2 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Xenophilus azovorans DSM 13620 asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain

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