GapMind for catabolism of small carbon sources

 

L-citrulline catabolism

Analysis of pathway citrulline in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Acidithiobacillus ferrooxidans ATCC 23270 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Acidovorax sp. GW101-3H11 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Algiphilus aromaticivorans DG1253 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Alicycliphilus denitrificans K601 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Alkalihalobacterium alkalinitrilicum DSM 22532 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Allochromatium vinosum DSM 180 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Ammonifex degensii KC4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Anaerobutyricum hallii DSM 3353 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Aquimarina longa SW024 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Archaeoglobus veneficus SNP6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Arcobacter nitrofigilis DSM 7299 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Azoarcus olearius BH72 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Azohydromonas australica DSM 1124 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Azorhizobium caulinodans ORS 571 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Azospirillum brasilense Sp245 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Azospirillum sp. B510 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Bacteroides thetaiotaomicron VPI-5482 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Beijerinckia indica ATCC 9039 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Beijerinckia mobilis UQM 1969 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Billgrantia desiderata SP1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Bradyrhizobium sp. BTAi1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Brevundimonas sp. GW460-12-10-14-LB2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Burkholderia phytofirmans PsJN AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Burkholderia vietnamiensis G4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Calditerrivibrio nitroreducens DSM 19672 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Caminibacter mediatlanticus TB-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Carboxydothermus pertinax Ug1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Caulobacter crescentus NA1000 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Cereibacter sphaeroides ATCC 17029 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Chlorobaculum parvum NCIB 8327 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Chlorobaculum tepidum TLS AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Chlorobium limicola DSM 245 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Chlorobium phaeobacteroides BS1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Clostridium acetobutylicum ATCC 824 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Clostridium kluyveri DSM 555 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1*, putA
Clostridium tyrobutyricum FAM22553 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Crocosphaera subtropica ATCC 51142 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Cupriavidus basilensis FW507-4G11 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Dechloromonas agitata is5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Dechlorosoma suillum PS AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Dehalococcoides mccartyi 195 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Denitrovibrio acetiphilus DSM 12809 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Derxia gummosa DSM 723 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Desulfacinum hydrothermale DSM 13146 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfacinum infernum DSM 9756 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfarculus baarsii DSM 2075 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, rocA
Desulfatibacillum aliphaticivorans DSM 15576 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfatiglans anilini DSM 4660 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfitobacterium hafniense DCB-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfobacca acetoxidans DSM 11109 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfobacter vibrioformis DSM 8776 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, rocA
Desulfogranum mediterraneum DSM 13871 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulforamulus ruminis DSM 2154 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Desulfoscipio geothermicus DSM 3669 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Desulfotalea psychrophila LSv54 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Desulfovibrio oxyclinae DSM 11498 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfovibrio vulgaris Hildenborough JW710 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Desulfovibrio vulgaris Miyazaki F AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Desulfurobacterium atlanticum DSM 15668 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Desulfuromonas acetexigens AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Desulfuromusa kysingii DSM 7343 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Dinoroseobacter shibae DFL-12 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1, putA
Dyella japonica UNC79MFTsu3.2 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Echinicola vietnamensis KMM 6221, DSM 17526 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Escherichia coli BW25113 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Ferroglobus placidus DSM 10642 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Frankia alni ACN14a AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Geobacter metallireducens GS-15 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, rocA
Geotalea uraniireducens Rf4 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, PRO3, put1, putA
Halococcus hamelinensis 100A6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Haloechinothrix alba DSM 45207 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Haloferax volcanii DS2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Haloglycomyces albus DSM 45210 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Halorhodospira halophila SL1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Heliomicrobium modesticaldum Ice1; ATCC 51547 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Herbaspirillum autotrophicum IAM 14942 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Herbaspirillum seropedicae SmR1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Hippea alviniae EP5-r AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Hydrogenophaga taeniospiralis NBRC 102512 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Hydrogenovibrio halophilus DSM 15072 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Hydrogenovibrio kuenenii DSM 12350 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Hydrogenovibrio marinus DSM 11271 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Hyphomicrobium sulfonivorans WDL6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Klebsiella michiganensis M5al AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Klebsiella variicola At-22 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Kyrpidia tusciae DSM 2912 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Leptospirillum ferrooxidans C2-3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Magnetospirillum magneticum AMB-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Malonomonas rubra DSM 5091 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Maridesulfovibrio bastinii DSM 16055 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Maridesulfovibrio zosterae DSM 11974 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Marinobacter adhaerens HP15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Mesorhizobium ciceri WSM1271 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Methanobacterium lacus AL-21 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanococcus aeolicus Nankai-3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanococcus maripaludis C5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanosarcina acetivorans C2A AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanosarcina mazei Go1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanospirillum lacunae Ki8-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Methanothermobacter thermautotrophicus Delta H AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methylobacterium nodulans ORS 2060 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1, putA
Methylobacterium sp. 4-46 Apr-46 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Methylocapsa acidiphila B2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylocapsa aurea KYG AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylocella silvestris BL2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylococcus capsulatus Bath AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methylocystis bryophila S285 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methyloferula stellata AR4T AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylohalobius crimeensis 10Ki AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylomonas methanica MC09 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Methylosarcina fibrata AML-C10 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Methylotuvimicrobium alcaliphilum 20Z AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Methylovulum miyakonense HT12 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Mycolicibacterium vanbaalenii PYR-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nitratifractor salsuginis DSM 16511 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Nitratiruptor tergarcus DSM 16512 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Nitriliruptor alkaliphilus DSM 45188 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nocardioides dokdonensis FR1436 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis lucentensis DSM 44048 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nostoc punctiforme ATCC 29133; PCC 73102 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Novosphingobium aromaticivorans DSM 12444 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Oleispira antarctica AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Paraburkholderia atlantica CCGE1002 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Paraburkholderia bryophila 376MFSha3.1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Paraburkholderia phymatum STM815 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Paucidesulfovibrio gracilis DSM 16080 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Pedobacter sp. GW460-11-11-14-LB5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Pelobacter propionicus DSM 2379 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Persephonella marina EX-H1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Phaeacidiphilus oryzae TH49 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Phaeobacter inhibens BS107 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Polaromonas naphthalenivorans CJ2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Prosthecochloris aestuarii DSM 271 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Pseudarthrobacter sulfonivorans Ar51 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puo, patD, gabT, gabD
Pseudomonas benzenivorans DSM 8628 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N1B4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2C3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens FW300-N2E3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas fluorescens GW456-L13 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas putida KT2440 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas simiae WCS417 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas stutzeri RCH2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Pyrolobus fumarii 1A AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Rhizobium etli CFN 42 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Rhizobium johnstonii 3841 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Rhizobium leguminosarum WSM1325 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Rhizorhabdus wittichii RW1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Rhodanobacter denitrificans FW104-10B01 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Rhodomicrobium vannielii ATCC 17100 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Rhodopseudomonas palustris CGA009 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodospirillum centenum SW; ATCC 51521 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Rhodospirillum rubrum ATCC 11170 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, PRO3, put1, putA
Roseburia faecis M72 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1*, putA
Saccharomonospora cyanea NA-134 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Sedimenticola selenatireducens DSM 17993 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Shewanella amazonensis SB2B AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella loihica PV-4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella oneidensis MR-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Shewanella sp. ANA-3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Sinorhizobium fredii NGR234 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Sinorhizobium medicae WSM419 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Sinorhizobium meliloti 1021 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Sphingomonas koreensis DSMZ 15582 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Stenotrophomonas chelatiphaga DSM 21508 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Steroidobacter denitrificans DSM 18526 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Stutzerimonas stutzeri A1501 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Sulfuricurvum kujiense DSM 16994 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Sulfurihydrogenibium azorense Az-Fu1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Sulfurihydrogenibium subterraneum DSM 15120 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Sulfurimonas denitrificans DSM 1251 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Sulfuritalea hydrogenivorans DSM 22779 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Sulfurivirga caldicuralii DSM 17737 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Synechococcus elongatus PCC 7942 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Teredinibacter turnerae T7901 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, rocA
Thauera aminoaromatica S2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1*, putA
Thermithiobacillus tepidarius DSM 3134 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thermocrinis albus DSM 14484 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thermodesulforhabdus norvegica DSM 9990 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thermomonospora curvata DSM 43183 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thermovibrio ammonificans HB-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thermus aquaticus YT-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thioalkalivibrio denitrificans ALJD AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, orr, oraS, oraE, ord, ortA, ortB
Thioalkalivibrio halophilus HL17 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thioalkalivibrio paradoxus ARh 1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Thiohalomonas denitrificans HLD2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thiohalospira halophila HL 3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thiomicrorhabdus arctica DSM 13458 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Thiomicrorhabdus chilensis DSM 12352 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thiomicrospira cyclica ALM1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thiomicrospira microaerophila ASL8-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thiomicrospira pelophila DSM 1534 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thiothrix lacustris DSM 21227 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Tistlia consotensis USBA 355 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Trichlorobacter lovleyi SZ AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Trichormus variabilis ATCC 29413 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Xanthobacter autotrophicus Py2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Xenophilus azovorans DSM 13620 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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