GapMind for catabolism of small carbon sources

 

L-arginine catabolism

Analysis of pathway arginine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 artJ, artM, artP, artQ, rocF, rocD, PRO3, put1, putA
Actinokineospora bangkokensis 44EHW rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Actinomyces timonensis 7400942 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Algiphilus aromaticivorans DG1253 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Algoriphagus aquaeductus T4 rocE, rocF, rocD, PRO3, put1, putA
Algoriphagus machipongonensis PR1 rocE, rocF, rocD, PRO3, put1, putA
Alicyclobacillus ferrooxydans TC-34 rocE, rocF, rocD, PRO3, put1, putA
Alishewanella agri BL06 rocE, astA, astB, astC, astD, astE
Alistipes indistinctus YIT 12060 rocE, rocF, rocD, rocA
Alistipes shahii WAL 8301 rocE, rocF, rocD, rocA
Alkalitalea saponilacus SC/BZ-SP2 rocE, rocF, rocD, PRO3, put1, putA
Amantichitinum ursilacus IGB-41 braC, braD, braE, braF, braG, astA, astB, astC, astD, astE
Amphibacillus jilinensis Y1 bgtB, artP, adiA, speB, patA, patD, gabT, gabD
Amphritea japonica JAMM 1866 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Amycolatopsis halophila YIM 93223 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Amycolatopsis xylanica CPCC 202699 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Aquimarina agarilytica ZC1 rocE, rocF, rocD, PRO3, put1, putA
Aquimarina longa SW024 rocE, rocF, rocD, PRO3, put1, putA
Aquimarina macrocephali JAMB N27 rocE, rocF, rocD, PRO3, put1, putA
Archaeoglobus sulfaticallidus PM70-1 rocE, adiA, speB, patA, patD, gabT, gabD
Arcticibacter svalbardensis MN12-7 rocE, rocF, rocD, PRO3, put1, putA
Ardenticatena maritima 110S rocE, arcA, arcB, arcC, rocD, rocA
Arenimonas metalli CF5-1 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Arenitalea lutea P7-3-5 rocE, rocF, rocD, PRO3, put1, putA
Azospirillum humicireducens SgZ-5 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Azospirillum thiophilum BV-S braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Bacillus altitudinis 41KF2b rocE, rocF, rocD, PRO3, put1, putA
Bacillus coahuilensis m4-4 bgtB, artP, rocF, rocD, PRO3, put1, putA
Bacillus cytotoxicus NVH 391-98 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Bacillus horneckiae 1P01SC bgtB, artP, rocF, rocD, PRO3, put1, putA
Bacillus okhensis Kh10-101 bgtB, artP, rocF, rocD, PRO3, put1, putA
Bacillus safensis FO-36b rocE, rocF, rocD, PRO3, put1, putA
Bacillus velezensis CBMB205 rocE, rocF, rocD, PRO3, put1, putA
Bacteroides clarus YIT 12056 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Bacteroides faecis MAJ27 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Bacteroides fluxus YIT 12057 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Bacteroides oleiciplenus YIT 12058 rocE, rocF, rocD, rocA
Barnesiella intestinihominis YIT 11860 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Belnapia rosea CPCC 100156 braC, braD, braE, braF, braG, rocF, odc, patA, patD, gabT, gabD
Bizionia argentinensis JUB59 rocE, rocF, rocD, PRO3, put1, putA
Bradyrhizobium diazoefficiens USDA110 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Brevibacterium jeotgali SJ5-8 bgtB, artP, aruH, aruI, kauB, gbuA, gabT, gabD
Brucella inopinata BO1 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Brucella microti CCM 4915 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Bryobacter aggregatus MPL3 rocE, rocF, rocD, PRO3, put1, putA
Caldicellulosiruptor hydrothermalis 108 rocE, adiA, speB, patA, patD, gabT, gabD
Caldicellulosiruptor kronotskyensis 2002 rocE, adiA, speB, patA, patD, gabT, gabD
Carboxydothermus pertinax Ug1 rocE, adiA, speB, patA, patD, gabT, gabD
Catellicoccus marimammalium M35/04/3 rocE, arcA, arcB, arcC, rocD, rocA
Chromobacterium vaccinii MWU205 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Chryseobacterium angstadtii KM rocE, rocF, rocD, PRO3, put1, putA
Chryseobacterium arthrosphaerae CC-VM-7 rocE, rocF, rocD, PRO3, put1, putA
Chryseobacterium viscerum 687B-08 rocE, rocF, rocD, PRO3, put1, putA
Cloacibacillus porcorum CL-84 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Cobetia crustatorum JO1 artJ, artM, artP, artQ, aruH, aruI, kauB, gbuA, gabT, gabD
Collimonas arenae Ter10 rocE, rocF, rocD, PRO3, put1, putA
Collimonas pratensis Ter91 rocE, rocF, rocD, PRO3, put1, putA
Collinsella tanakaei YIT 12063 rocE, arcA, arcB, arcC, rocD, rocA
Coprobacter fastidiosus NSB1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Corynebacterium deserti GIMN1.010 rocE, rocF, odc, patA, patD, gabT, gabD
Corynebacterium frankenforstense ST18 rocE, rocF, odc, patA, patD, gabT, gabD
Corynebacterium lactis RW2-5 rocE, rocF, odc, patA, patD, gabT, gabD
Croceitalea dokdonensis DOKDO 023 rocE, rocF, rocD, PRO3, put1, putA
Cronobacter condimenti 1330 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Cronobacter muytjensii ATCC 51329 artJ, artM, artP, artQ, arcA, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Cronobacter universalis NCTC 9529 artJ, artM, artP, artQ, arcA, arcB, arcC, odc, puuA, puuB, puuC, puuD, gabT, gabD
Desulfatitalea tepidiphila S28bF rocE, adiA, speB, patA, patD, gabT, gabD
Desulfotomaculum hydrothermale Lam5 rocE, rocF, rocD, PRO3, put1*, putA
Dethiosulfovibrio salsuginis USBA 82 bgtB, artP, arcA, arcB, arcC, orr, oraS, oraE, ord, ortA, ortB
Devosia chinhatensis IPL18 bgtB, artP, rocF, rocD, PRO3, put1, putA
Devriesea agamarum IMP2 rocE, arcA, arcB, arcC, rocD, rocA
Dialister succinatiphilus YIT 11850 bgtB*, artP, rocF, odc, patA, patD, gabT, gabD
Dietzia timorensis ID05-A0528 rocE, rocF, rocD, rocA
Dokdonella koreensis DS-123 rocE, rocF, rocD, PRO3, put1, putA
Domibacillus robiginosus WS 4628 rocE, rocF, rocD, PRO3, put1, putA
Duganella sacchari Sac-22 braC, braD, braE, braF, braG, astA, astB, astC, astD, astE
Dyadobacter tibetensis Y620-1 rocE, rocF, rocD, PRO3, put1, putA
Dyella jiangningensis SBZ3-12 rocE, rocF, rocD, PRO3, put1, putA
Endozoicomonas montiporae CL-33 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Enterococcus termitis LMG 8895 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Enterorhabdus caecimuris B7 rocE, arcA, arcB, arcC, rocD, rocA
Epibacterium ulvae U95 artJ, artM, artP, artQ, adiA, speB, patA, patD, gabT, gabD
Erythrobacter gangjinensis K7-2 rocE, astA, astB, astC, astD, astE
Erythrobacter marinus HWDM-33 rocE, astA, astB, astC, astD, astE
Ethanoligenens harbinense YUAN-3 rocE, adiA, speB, patA, patD, gabT, gabD
Fervidicella metallireducens AeB rocE, arcA, arcB, arcC, orr, oraS, oraE, ord, ortA, ortB
Fibrella aestuarina BUZ 2 rocE, rocF, rocD, PRO3, put1, putA
Flammeovirga pacifica WPAGA1 rocE, rocF, rocD, PRO3, put1, putA
Flaviramulus ichthyoenteri Th78 rocE, rocF, rocD, PRO3, put1, putA
Flavobacterium beibuense F44-8 rocE, rocF, rocD, rocA
Flavobacterium glycines Gm-149 rocE, rocF, rocD, PRO3, put1, putA
Flavobacterium sp. LM5 rocE, rocF, rocD, PRO3, put1, putA
Flavobacterium ummariense DS-12 rocE, rocF, rocD, rocA
Frischella perrara PEB0191 artJ, artM, artP, artQ, rocF, rocD, rocA
Galbibacter marinus ck-I2-15 rocE, rocF, rocD, PRO3, put1, putA
Gallaecimonas xiamenensis 3-C-1 rocE, astA, astB, astC, astD, astE
Geobacter daltonii FRC-32 rocE, rocF, rocD, rocA
Gillisia marina CBA3202 rocE, rocF, rocD, PRO3, put1, putA
Gracilibacillus halophilus YIM-C55.5 rocE, rocF, rocD, rocA
Granulicella mallensis MP5ACTX8 rocE, rocF, rocD, PRO3, put1, putA
Granulicella tundricola MP5ACTX9 rocE, rocF, rocD, PRO3, put1, putA
Hafnia paralvei ATCC 29927 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Haladaptatus cibarius D43 rocE, rocF, rocD, rocA
Halioglobus japonicus S1-36 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Halobacillus alkaliphilus FP5 rocE, rocF, rocD, PRO3, put1, putA
Halococcus hamelinensis 100A6 rocE, adiA, speB, patA, patD, gabT, gabD
Halomonas salina B6 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Halomonas smyrnensis AAD6 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Halomonas stevensii S18214 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Halomonas titanicae BH1 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Halomonas xinjiangensis TRM 0175 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Halopiger salifodinae KCY07-B2 rocE, adiA, speB, patA, patD, gabT, gabD
Halostagnicola larsenii XH-48 rocE, adiA, speB, patA, patD, gabT, gabD
Haloterrigena daqingensis JX313 rocE, adiA, speB, patA, patD, gabT, gabD
Herbaspirillum aquaticum IEH 4430 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Hippea alviniae EP5-r rocE, rocF, rocD, PRO3, put1, putA
Hippea jasoniae Mar08-272r rocE, rocF, rocD, PRO3, put1, putA
Hoeflea phototrophica DFL-43 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Hyphomicrobium nitrativorans NL23 braC, braD, braE, braF, braG, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Imtechella halotolerans K1 rocE, rocF, rocD, PRO3, put1, putA
Indibacter alkaliphilus LW1 rocE, rocF, rocD, PRO3, put1, putA
Jannaschia aquimarina GSW-M26 artJ, artM, artP, artQ, aruH, aruI, kauB, gbuA, gabT, gabD
Jeotgalibacillus soli P9 bgtB, artP, rocF, rocD, PRO3, put1, putA
Kangiella geojedonensis YCS-5 rocE, astA, astB, astC, astD, astE
Knoellia flava TL1 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Kocuria flava HO-9041 rocE, adiA, speB, puo, patD, gabT, gabD
Kocuria turfanensis HO-9042 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Laceyella sediminis RHA1 rocE, rocF, rocD, PRO3, put1, putA
Lacinutrix algicola AKS293 rocE, rocF, rocD, PRO3, put1, putA
Lacinutrix himadriensis E4-9a rocE, rocF, rocD, PRO3, put1, putA
Lacinutrix mariniflava AKS432 rocE, rocF, rocD, PRO3, put1, putA
Lactobacillus curieae CCTCC M 2011381 rocE, arcA, arcB, arcC, rocD, rocA
Lactobacillus delbrueckii ZN7a-9 rocE, arcA, arcB, arcC, odc, patA, patD, gabT, gabD
Lactobacillus hokkaidonensis LOOC260 bgtB, artP, rocF, rocD, rocA
Lactobacillus oryzae SG293 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Lactobacillus pobuzihii E100301 rocE, rocF, odc, patA, patD, gabT, gabD
Lactobacillus shenzhenensis LY-73 bgtB, artP, rocF, odc, patA, patD, gabT, gabD
Lactobacillus silagei IWT126 rocE, arcA, arcB, arcC, rocD, rocA
Leeuwenhoekiella blandensis MED217 rocE, rocF, rocD, PRO3, put1, putA
Lentibacillus jeotgali Grbi rocE, rocF, rocD, PRO3, put1, putA
Limnohabitans curvus MWH-C5 braC, braD, braE, braF, braG, rocF, rocD, rocA
Limnohabitans parvus II-B4 rocE, rocF, ocd, put1, putA
Listeria fleischmannii LU2006-1 rocE, arcA, arcB, arcC, rocD, rocA
Luteimonas huabeiensis HB2 rocE, rocF, rocD, PRO3, put1, putA
Luteipulveratus mongoliensis MN07-A0370 bgtB, artP, adiA, aguA, aguB, patA, patD, gabT, gabD
Lutibaculum baratangense AMV1 braC, braD, braE, braF, braG, aruH, aruI, kauB, gbuA, gabT, gabD
Lysobacter daejeonensis GH1-9 rocE, rocF, ocd, put1, putA
Magnetovibrio blakemorei MV-1 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Marinicella litoralis KMM 3900 rocE, rocF, rocD, PRO3, put1, putA
Mariniradius saccharolyticus AK6 rocE, rocF, rocD, PRO3, put1, putA
Marinobacter algicola DG893 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Marinobacter guineae M3B artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Marinobacter psychrophilus 20041 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Marinomonas arctica 328 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Marivita geojedonensis DPG-138 artJ, artM, artP, artQ, aruH, aruI, kauB, gbuA, gabT, gabD
Martelella endophytica YC6887 artJ, artM, artP, artQ, arcA, arcB, arcC, ocd, put1, putA
Megamonas funiformis YIT 11815 rocE, adiA, speB, patA, patD, gabT, gabD
Mesorhizobium ciceri WSM1271 braC, braD, braE, braF, braG, aruH, aruI, kauB, gbuA, gabT, gabD
Methanobacterium arcticum M2 rocE, rocF, rocD, rocA
Methanobacterium veterum MK4 rocE, rocF, rocD, rocA
Methanocella arvoryzae MRE50 rocE, adiA, speB, patA, patD, gabT, gabD
Methanococcus aeolicus Nankai-3 rocE, rocF, rocD, rocA
Methanoculleus horonobensis T10 rocE, arcA, arcB, arcC, rocD, rocA
Methanolinea tarda NOBI-1 rocE, arcA, arcB, arcC, rocD, rocA
Methanosarcina soligelidi SMA-21 rocE, adiA, speB, patA, patD, gabT, gabD
Methanospirillum lacunae Ki8-1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Methanospirillum stamsii Pt1 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Methylibium petroleiphilum PM1 artJ, artM, artP, artQ, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Methylobacterium gossipiicola Gh-105 braC, braD, braE, braF, braG, rocF, odc, patA, patD, gabT, gabD
Methylocapsa aurea KYG braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Methylotenera versatilis 301 rocE, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Microbacterium profundi Shh49 rocE, rocF, odc, puo, patD, gabT, gabD
Microvirga lotononidis WSM3557 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Moritella dasanensis ArB 0140 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Mucilaginibacter gossypii Gh-67 rocE, rocF, rocD, PRO3, put1, putA
Mucilaginibacter gossypiicola Gh-48 rocE, rocF, rocD, PRO3, put1, putA
Mucilaginibacter mallensis MP1X4 rocE, rocF, rocD, PRO3, put1, putA
Nafulsella turpanensis ZLM-10 rocE, rocF, rocD, PRO3, put1, putA
Natronomonas moolapensis 8.8.11 rocE, adiA, speB, patA, patD, gabT, gabD
Nautilia profundicola AmH rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Neiella marina J221 rocE, astA, astB, astC, astD, astE
Neptunomonas antarctica S3-22 artJ, artM, artP, artQ, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nocardioides daejeonensis MJ31 rocE, arcA, arcB, arcC, rocD, rocA
Nocardioides dokdonensis FR1436 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis baichengensis YIM 90130 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Nocardiopsis gilva YIM 90087 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Novosphingobium barchaimii LL02 rocE, astA, astB, astC, astD, astE
Novosphingobium fuchskuhlense FNE08-7 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Novosphingobium lindaniclasticum LE124 rocE, astA, astB, astC, astD, astE
Oceanisphaera arctica V1-41 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Ochrobactrum rhizosphaerae PR17 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Ochrobactrum thiophenivorans DSM 7216 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Oscillibacter ruminantium GH1 rocE, arcA, arcB, arcC, rocD, rocA
Paenisporosarcina indica PN2 bgtB, artP, rocF, rocD, PRO3, put1, putA
Palaeococcus pacificus DY20341 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Paludibacter propionicigenes WB4 rocE, rocF, rocD, rocA
Pandoraea thiooxydans ATSB16 rocE, arcA, arcB, arcC, ocd, put1, putA
Pantoea rwandensis LMG 26275 artJ, artM, artP, artQ, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Pedobacter arcticus A12 rocE, rocF, rocD, PRO3, put1, putA
Photobacterium gaetbulicola Gung47 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Photobacterium jeanii R-40508 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Phyllobacterium brassicacearum STM 196 braC, braD, braE, braF, braG, rocF, rocD, rocA
Phyllobacterium endophyticum PEPV15 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Phyllobacterium leguminum ORS 1419 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Planktomarina temperata RCA23 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Planococcus halocryophilus Or1 rocE, rocF, rocD, PRO3, put1, putA
Pleomorphomonas diazotrophica R5-392 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Polaribacter dokdonensis DSW-5 rocE, rocF, rocD, PRO3, put1, putA
Pontibacillus litoralis JSM 072002 rocE, rocF, rocD, PRO3, put1, putA
Pontibacter lucknowensis DM9 rocE, rocF, rocD, rocA
Pontibacter ramchanderi LP43 rocE, rocF, rocD, rocA
Pontimonas salivibrio CL-TW6 rocE, rocF, rocD, rocA
Porphyrobacter dokdonensis DSW-74 rocE, astA, astB, astC, astD, astE
Pseudoalteromonas arctica A 37-1-2 rocE, astA, astB, astC, astD, astE
Pseudomonas baetica a390 artJ, artM, artP, artQ, arcA, arcB, arcC, aruF, aruG, astC, astD, astE
Pseudomonas litoralis 2SM5 artJ, artM, artP, artQ, adiA, aguA, aguB, patA, patD, gabT, gabD
Pseudomonas taeanensis MS-3 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Pseudovibrio axinellae Ad2 braC, braD, braE, braF, braG, arcA, arcB, arcC, ocd, put1, putA
Psychrobacter arcticus 273-4 artJ, artM, artP, artQ, rocF, rocD, PRO3, put1, putA
Psychrobacter cryohalolentis K5 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Psychromonas ingrahamii 37 artJ, artM, artP, artQ, adiA, speB, patA, patD, gabT, gabD
Psychromonas ossibalaenae JAMM 0738 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Rhizobium freirei PRF 81 braC, braD, braE, braF, braG, rocF, ocd, put1, putA
Rhizobium grahamii CCGE 502 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Rhizobium subbaraonis JC85 braC, braD, braE, braF, braG, arcA, arcB, arcC, rocD, PRO3, put1, putA
Rhodanobacter denitrificans 2APBS1 rocE, rocF, rocD, PRO3, put1, putA
Rhodobacter johrii JA192 bgtB, artP, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodobacter maris JA276 artJ, artM, artP, artQ, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodobacter ovatus JA234 bgtB, artP, rocF, rocD, PRO3, put1, putA
Rhodobacter viridis JA737 artJ, artM, artP, artQ, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Rhodococcus qingshengii djl-6-2 bgtB, artP, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Rhodopseudomonas pseudopalustris DSM 123 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Roseateles aquatilis CCUG 48205 artJ, artM, artP, artQ, rocF, ocd, put1, putA
Roseivirga spongicola UST030701-084 rocE, rocF, rocD, PRO3, put1, putA
Rubrivirga marina SAORIC-28 rocE, rocF, rocD, PRO3, put1, putA
Ruegeria conchae TW15 bgtB, artP, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Saccharomonospora marina XMU15 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Salinicoccus carnicancri Crm rocE, rocF, rocD, PRO3, put1, putA
Serinicoccus profundi MCCC 1A05965 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Shewanella halifaxensis HAW-EB4 rocE, adiA, speB, puuA, puuB, puuC, puuD, gabT, gabD
Skermanella stibiiresistens SB22 braC, braD, braE, braF, braG, rocF, rocD, PRO3, put1, putA
Snodgrassella alvi wkB2 rocE, rocF, odc, puuA, puuB, puuC, puuD, gabT, gabD
Sphaerochaeta globosa Buddy rocE, arcA, arcB, arcC, rocD, PRO3, put1*, putA
Sphaerochaeta pleomorpha Grapes rocE, arcA, arcB, arcC, rocD, rocA
Sphingobium baderi LL03 rocE, astA, astB, astC, astD, astE
Sphingobium czechense LL01 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Sphingobium quisquiliarum P25 rocE, astA, astB, astC, astD, astE
Sphingomonas histidinilytica UM2 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Sphingomonas indica Dd16 rocE, rocF, rocD, PRO3, put1, putA
Sphingomonas laterariae LNB2 rocE, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Sphingopyxis indica DS15 rocE, astA, astB, astC, astD, astE
Sphingopyxis terrae UI2 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Sporolactobacillus vineae SL153 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Streptacidiphilus oryzae TH49 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Streptococcus anginosus CCUG 39159 rocE, arcA, arcB, arcC, rocD, rocA
Streptococcus massiliensis 4401825 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Streptococcus oralis 7747 rocE, arcA, arcB, arcC, rocD, rocA
Streptococcus oralis AZ_3a bgtB, artP, rocF, rocD, rocA
Streptomyces kebangsaanensis SUK12 rocE, arg-monooxygenase, gbamidase, kauB, gbuA, gabT, gabD
Succinatimonas hippei YIT 12066 bgtB*, artP, rocF, rocD, rocA
Sulfurimonas gotlandica GD1 rocE, rocF, rocD, rocA
Tatumella morbirosei LMG 23360 artJ, artM, artP, artQ, astA, astB, astC, astD, astE
Thauera humireducens SgZ-1 artJ, artM, artP, artQ, rocF, rocD, PRO3, put1, putA
Thermoactinomyces daqus H-18 rocE, rocF, rocD, PRO3, put1, putA
Thermobifida halotolerans YIM 90462 rocE, arcA, arcB, arcC, rocD, PRO3, put1, putA
Thermodesulfovibrio aggregans TGE-P1 rocE, rocF, rocD, rocA
Thermophagus xiamenensis HS1 rocE, arcA, arcB, arcC, rocD, rocA
Thermovenabulum gondwanense R270 rocE, arcA, arcB, arcC, rocD, PRO3, prdF, prdA, prdB, prdC, davT, davD, gcdG, gcdH, ech, fadB, atoB
Thioclava dalianensis DLFJ1-1 artJ, artM, artP, artQ, rocF, ocd, put1*, putA*
Thiohalospira halophila HL 3 rocE, adiA, aguA, aguB, patA, patD, gabT, gabD
Tistlia consotensis USBA 355 artJ, artM, artP, artQ, adiA, aguA, aguB, puuA, puuB, puuC, puuD, gabT, gabD
Vagococcus penaei CD276 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Verminephrobacter eiseniae EF01-2 artJ, artM, artP, artQ, rocF, odc, patA, patD, gabT, gabD
Weissella oryzae SG25 rocE, arcA, arcB, arcC, rocD, rocA
Williamsia sterculiae CPCC 203464 bgtB, artP, arcA, arcB, arcC, rocD, rocA
Yersinia intermedia Y228 artJ, artM, artP, artQ, astA, astB, astC, astD, astE

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