GapMind for Amino acid biosynthesis

 

L-histidine biosynthesis

Analysis of pathway his in 150 genomes

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

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