GapMind for Amino acid biosynthesis

 

L-arginine biosynthesis

Analysis of pathway arg in 150 genomes

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

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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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