GapMind for catabolism of small carbon sources

 

L-citrulline catabolism

Analysis of pathway citrulline in 276 genomes

Genome Best path
Acidovorax caeni R-24608 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Actinokineospora bangkokensis 44EHW AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Actinomyces timonensis 7400942 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Algiphilus aromaticivorans DG1253 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Algoriphagus aquaeductus T4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Algoriphagus machipongonensis PR1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Alicyclobacillus ferrooxydans TC-34 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Alishewanella agri BL06 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
Alistipes indistinctus YIT 12060 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Alistipes shahii WAL 8301 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Alkalitalea saponilacus SC/BZ-SP2 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, PRO3, put1, putA
Amantichitinum ursilacus IGB-41 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Amphibacillus jilinensis Y1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Amphritea japonica JAMM 1866 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Amycolatopsis halophila YIM 93223 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Amycolatopsis xylanica CPCC 202699 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Aquimarina agarilytica ZC1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Aquimarina longa SW024 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Aquimarina macrocephali JAMB N27 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Archaeoglobus sulfaticallidus PM70-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Arcticibacter svalbardensis MN12-7 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Ardenticatena maritima 110S AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Arenimonas metalli CF5-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Arenitalea lutea P7-3-5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Azospirillum humicireducens SgZ-5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Azospirillum thiophilum BV-S AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Bacillus altitudinis 41KF2b AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Bacillus coahuilensis m4-4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Bacillus cytotoxicus NVH 391-98 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Bacillus horneckiae 1P01SC AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Bacillus okhensis Kh10-101 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Bacillus safensis FO-36b AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Bacillus velezensis CBMB205 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Bacteroides clarus YIT 12056 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, rocA
Bacteroides faecis MAJ27 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Bacteroides fluxus YIT 12057 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Bacteroides oleiciplenus YIT 12058 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Barnesiella intestinihominis YIT 11860 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Belnapia rosea CPCC 100156 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Bizionia argentinensis JUB59 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Bradyrhizobium diazoefficiens USDA110 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Brevibacterium jeotgali SJ5-8 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Brucella inopinata BO1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Brucella microti CCM 4915 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1, putA
Bryobacter aggregatus MPL3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Caldicellulosiruptor hydrothermalis 108 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Caldicellulosiruptor kronotskyensis 2002 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
Catellicoccus marimammalium M35/04/3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Chromobacterium vaccinii MWU205 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Chryseobacterium angstadtii KM AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Chryseobacterium arthrosphaerae CC-VM-7 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Chryseobacterium viscerum 687B-08 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Cloacibacillus porcorum CL-84 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Cobetia crustatorum JO1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Collimonas arenae Ter10 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Collimonas pratensis Ter91 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Collinsella tanakaei YIT 12063 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Coprobacter fastidiosus NSB1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Corynebacterium deserti GIMN1.010 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Corynebacterium frankenforstense ST18 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Corynebacterium lactis RW2-5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Croceitalea dokdonensis DOKDO 023 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Cronobacter condimenti 1330 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Cronobacter muytjensii ATCC 51329 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Cronobacter universalis NCTC 9529 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Desulfatitalea tepidiphila S28bF AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Desulfotomaculum hydrothermale Lam5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1*, putA
Dethiosulfovibrio salsuginis USBA 82 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, orr, oraS, oraE, ord, ortA, ortB
Devosia chinhatensis IPL18 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Devriesea agamarum IMP2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Dialister succinatiphilus YIT 11850 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Dietzia timorensis ID05-A0528 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Dokdonella koreensis DS-123 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Domibacillus robiginosus WS 4628 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Duganella sacchari Sac-22 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Dyadobacter tibetensis Y620-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Dyella jiangningensis SBZ3-12 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Endozoicomonas montiporae CL-33 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Enterococcus termitis LMG 8895 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Enterorhabdus caecimuris B7 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Epibacterium ulvae U95 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Erythrobacter gangjinensis K7-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Erythrobacter marinus HWDM-33 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
Ethanoligenens harbinense YUAN-3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Fervidicella metallireducens AeB AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, orr, oraS, oraE, ord, ortA, ortB
Fibrella aestuarina BUZ 2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Flammeovirga pacifica WPAGA1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Flaviramulus ichthyoenteri Th78 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Flavobacterium beibuense F44-8 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Flavobacterium glycines Gm-149 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Flavobacterium sp. LM5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Flavobacterium ummariense DS-12 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Frischella perrara PEB0191 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, rocA
Galbibacter marinus ck-I2-15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Gallaecimonas xiamenensis 3-C-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
Geobacter daltonii FRC-32 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Gillisia marina CBA3202 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Gracilibacillus halophilus YIM-C55.5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Granulicella mallensis MP5ACTX8 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Granulicella tundricola MP5ACTX9 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Hafnia paralvei ATCC 29927 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Haladaptatus cibarius D43 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Halioglobus japonicus S1-36 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Halobacillus alkaliphilus FP5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Halococcus hamelinensis 100A6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Halomonas salina B6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Halomonas smyrnensis AAD6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Halomonas stevensii S18214 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Halomonas titanicae BH1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Halomonas xinjiangensis TRM 0175 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
Halopiger salifodinae KCY07-B2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Halostagnicola larsenii XH-48 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Haloterrigena daqingensis JX313 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Herbaspirillum aquaticum IEH 4430 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
Hippea jasoniae Mar08-272r AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Hoeflea phototrophica DFL-43 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Hyphomicrobium nitrativorans NL23 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Imtechella halotolerans K1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Indibacter alkaliphilus LW1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Jannaschia aquimarina GSW-M26 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Jeotgalibacillus soli P9 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Kangiella geojedonensis YCS-5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Knoellia flava TL1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Kocuria flava HO-9041 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puo, patD, gabT, gabD
Kocuria turfanensis HO-9042 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Laceyella sediminis RHA1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Lacinutrix algicola AKS293 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Lacinutrix himadriensis E4-9a AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Lacinutrix mariniflava AKS432 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Lactobacillus curieae CCTCC M 2011381 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Lactobacillus delbrueckii ZN7a-9 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Lactobacillus hokkaidonensis LOOC260 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Lactobacillus oryzae SG293 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Lactobacillus pobuzihii E100301 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, patA, patD, gabT, gabD
Lactobacillus shenzhenensis LY-73 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, patA, patD, gabT, gabD
Lactobacillus silagei IWT126 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Leeuwenhoekiella blandensis MED217 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Lentibacillus jeotgali Grbi AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Limnohabitans curvus MWH-C5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Limnohabitans parvus II-B4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Listeria fleischmannii LU2006-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Luteimonas huabeiensis HB2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Luteipulveratus mongoliensis MN07-A0370 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Lutibaculum baratangense AMV1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Lysobacter daejeonensis GH1-9 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Magnetovibrio blakemorei MV-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Marinicella litoralis KMM 3900 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Mariniradius saccharolyticus AK6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Marinobacter algicola DG893 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Marinobacter guineae M3B AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Marinobacter psychrophilus 20041 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Marinomonas arctica 328 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
Marivita geojedonensis DPG-138 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Martelella endophytica YC6887 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Megamonas funiformis YIT 11815 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Mesorhizobium ciceri WSM1271 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Methanobacterium arcticum M2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanobacterium veterum MK4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanocella arvoryzae MRE50 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
Methanoculleus horonobensis T10 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanolinea tarda NOBI-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Methanosarcina soligelidi SMA-21 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
Methanospirillum stamsii Pt1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Methylibium petroleiphilum PM1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Methylobacterium gossipiicola Gh-105 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Methylocapsa aurea KYG AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Methylotenera versatilis 301 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Microbacterium profundi Shh49 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puo, patD, gabT, gabD
Microvirga lotononidis WSM3557 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Moritella dasanensis ArB 0140 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Mucilaginibacter gossypii Gh-67 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Mucilaginibacter gossypiicola Gh-48 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Mucilaginibacter mallensis MP1X4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Nafulsella turpanensis ZLM-10 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Natronomonas moolapensis 8.8.11 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Nautilia profundicola AmH AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Neiella marina J221 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Neptunomonas antarctica S3-22 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nocardioides daejeonensis MJ31 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Nocardioides dokdonensis FR1436 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis baichengensis YIM 90130 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis gilva YIM 90087 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Novosphingobium barchaimii LL02 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Novosphingobium fuchskuhlense FNE08-7 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Novosphingobium lindaniclasticum LE124 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
Oceanisphaera arctica V1-41 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Ochrobactrum rhizosphaerae PR17 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Ochrobactrum thiophenivorans DSM 7216 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
Oscillibacter ruminantium GH1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Paenisporosarcina indica PN2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Palaeococcus pacificus DY20341 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Paludibacter propionicigenes WB4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Pandoraea thiooxydans ATSB16 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Pantoea rwandensis LMG 26275 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Pedobacter arcticus A12 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Photobacterium gaetbulicola Gung47 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Photobacterium jeanii R-40508 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Phyllobacterium brassicacearum STM 196 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Phyllobacterium endophyticum PEPV15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Phyllobacterium leguminum ORS 1419 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Planktomarina temperata RCA23 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1, putA
Planococcus halocryophilus Or1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Pleomorphomonas diazotrophica R5-392 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Polaribacter dokdonensis DSW-5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Pontibacillus litoralis JSM 072002 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Pontibacter lucknowensis DM9 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Pontibacter ramchanderi LP43 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Pontimonas salivibrio CL-TW6 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Porphyrobacter dokdonensis DSW-74 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, ocd, put1, putA
Pseudoalteromonas arctica A 37-1-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Pseudomonas baetica a390 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas litoralis 2SM5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, patA, patD, gabT, gabD
Pseudomonas taeanensis MS-3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, aruF, aruG, astC, astD, astE
Pseudovibrio axinellae Ad2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Psychrobacter arcticus 273-4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Psychrobacter cryohalolentis K5 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Psychromonas ingrahamii 37 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Psychromonas ossibalaenae JAMM 0738 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Rhizobium freirei PRF 81 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Rhizobium grahamii CCGE 502 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Rhizobium subbaraonis JC85 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Rhodanobacter denitrificans 2APBS1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Rhodobacter johrii JA192 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodobacter maris JA276 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodobacter ovatus JA234 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, rocD, PRO3, put1, putA
Rhodobacter viridis JA737 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodococcus qingshengii djl-6-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puo, patD, gabT, gabD
Rhodopseudomonas pseudopalustris DSM 123 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Roseateles aquatilis CCUG 48205 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, ocd, put1, putA
Roseivirga spongicola UST030701-084 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Rubrivirga marina SAORIC-28 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Ruegeria conchae TW15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Saccharomonospora marina XMU15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Salinicoccus carnicancri Crm AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Serinicoccus profundi MCCC 1A05965 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Shewanella halifaxensis HAW-EB4 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Skermanella stibiiresistens SB22 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Snodgrassella alvi wkB2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Sphaerochaeta globosa Buddy AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1*, putA
Sphaerochaeta pleomorpha Grapes AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Sphingobium baderi LL03 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Sphingobium czechense LL01 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, ocd, put1, putA
Sphingobium quisquiliarum P25 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Sphingomonas histidinilytica UM2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Sphingomonas indica Dd16 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Sphingomonas laterariae LNB2 PS417_17590, PS417_17595, PS417_17600, PS417_17605, citrullinase, rocD, PRO3, put1, putA
Sphingopyxis indica DS15 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, PRO3, put1, putA
Sphingopyxis terrae UI2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Sporolactobacillus vineae SL153 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Streptacidiphilus oryzae TH49 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Streptococcus anginosus CCUG 39159 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Streptococcus massiliensis 4401825 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Streptococcus oralis 7747 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Streptococcus oralis AZ_3a AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Streptomyces kebangsaanensis SUK12 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Succinatimonas hippei YIT 12066 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Sulfurimonas gotlandica GD1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, rocD, rocA
Tatumella morbirosei LMG 23360 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Thauera humireducens SgZ-1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thermoactinomyces daqus H-18 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thermobifida halotolerans YIM 90462 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
Thermodesulfovibrio aggregans TGE-P1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thermophagus xiamenensis HS1 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Thermovenabulum gondwanense R270 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Thioclava dalianensis DLFJ1-1 PS417_17590, PS417_17595, PS417_17600, PS417_17605, arcB, arcC, ocd, put1*, putA*
Thiohalospira halophila HL 3 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Tistlia consotensis USBA 355 AO353_03055, AO353_03050, AO353_03045, AO353_03040, citrullinase, odc, puuA, puuB, puuC, puuD, gabT, gabD
Vagococcus penaei CD276 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Verminephrobacter eiseniae EF01-2 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, odc, patA, patD, gabT, gabD
Weissella oryzae SG25 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Williamsia sterculiae CPCC 203464 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, rocA
Yersinia intermedia Y228 AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, 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 Sep 24 2021. 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