GapMind for catabolism of small carbon sources

 

L-histidine catabolism

Analysis of pathway histidine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Actinokineospora bangkokensis 44EHW permease, hutH, hutU, hutI, hutF, hutG'
Actinomyces timonensis 7400942 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Algiphilus aromaticivorans DG1253 permease, hutH, hutU, hutI, hutG
Algoriphagus aquaeductus T4 permease, hutH, hutU, hutI, hutG
Algoriphagus machipongonensis PR1 permease, hutH, hutU, hutI, hutG
Alicyclobacillus ferrooxydans TC-34 permease, hutH, hutU, hutI, hutG
Alishewanella agri BL06 permease, hutH, hutU, hutI, hutG
Alistipes indistinctus YIT 12060 permease, hutH, hutU, hutI, hutG
Alistipes shahii WAL 8301 permease, hutH, hutU, hutI, hutG
Alkalitalea saponilacus SC/BZ-SP2 LAT2, hutH, hutU, hutI, hutG
Amantichitinum ursilacus IGB-41 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Amphibacillus jilinensis Y1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Amphritea japonica JAMM 1866 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Amycolatopsis halophila YIM 93223 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
Amycolatopsis xylanica CPCC 202699 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Aquimarina agarilytica ZC1 permease, hutH, hutU, hutI, hutG
Aquimarina longa SW024 permease, hutH, hutU, hutI, hutF, hutG'
Aquimarina macrocephali JAMB N27 permease, hutH, hutU, hutI, hutF, hutG'
Archaeoglobus sulfaticallidus PM70-1 permease, hutH, hutU, hutI, hutG
Arcticibacter svalbardensis MN12-7 permease, hutH, hutU, hutI, hutG
Ardenticatena maritima 110S aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Arenimonas metalli CF5-1 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Arenitalea lutea P7-3-5 permease, hutH, hutU, hutI, hutG
Azospirillum humicireducens SgZ-5 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Azospirillum thiophilum BV-S braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Bacillus altitudinis 41KF2b LAT2, hutH, hutU, hutI, hutG
Bacillus coahuilensis m4-4 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Bacillus cytotoxicus NVH 391-98 LAT2, hutH, hutU, hutI, hutG
Bacillus horneckiae 1P01SC PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Bacillus okhensis Kh10-101 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Bacillus safensis FO-36b LAT2, hutH, hutU, hutI, hutG
Bacillus velezensis CBMB205 LAT2, hutH, hutU, hutI, hutG
Bacteroides clarus YIT 12056 permease, hutH, hutU, hutI, hutG
Bacteroides faecis MAJ27 permease, hutH, hutU, hutI, hutG
Bacteroides fluxus YIT 12057 permease, hutH, hutU, hutI, hutG
Bacteroides oleiciplenus YIT 12058 permease, hutH, hutU, hutI, hutG
Barnesiella intestinihominis YIT 11860 permease, hutH, hutU, hutI, hutG
Belnapia rosea CPCC 100156 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Bizionia argentinensis JUB59 permease, hutH, hutU, hutI, hutG
Bradyrhizobium diazoefficiens USDA110 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Brevibacterium jeotgali SJ5-8 permease, hutH, hutU, hutI, hutG
Brucella inopinata BO1 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Brucella microti CCM 4915 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Bryobacter aggregatus MPL3 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Caldicellulosiruptor hydrothermalis 108 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Caldicellulosiruptor kronotskyensis 2002 LAT2, hutH, hutU, hutI, hutG
Carboxydothermus pertinax Ug1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Catellicoccus marimammalium M35/04/3 LAT2, hutH, hutU, hutI, hutG
Chromobacterium vaccinii MWU205 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Chryseobacterium angstadtii KM permease, hutH, hutU, hutI, hutG
Chryseobacterium arthrosphaerae CC-VM-7 permease, hutH, hutU, hutI, hutG
Chryseobacterium viscerum 687B-08 permease, hutH, hutU, hutI, hutG
Cloacibacillus porcorum CL-84 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Cobetia crustatorum JO1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Collimonas arenae Ter10 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Collimonas pratensis Ter91 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Collinsella tanakaei YIT 12063 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Coprobacter fastidiosus NSB1 permease, hutH, hutU, hutI, hutG
Corynebacterium deserti GIMN1.010 permease, hutH, hutU, hutI, hutG
Corynebacterium frankenforstense ST18 permease, hutH, hutU, hutI, hutG
Corynebacterium lactis RW2-5 permease, hutH, hutU, hutI, hutG
Croceitalea dokdonensis DOKDO 023 permease, hutH, hutU, hutI, hutG
Cronobacter condimenti 1330 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Cronobacter muytjensii ATCC 51329 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Cronobacter universalis NCTC 9529 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Desulfatitalea tepidiphila S28bF LAT2, hutH, hutU, hutI, hutG
Desulfotomaculum hydrothermale Lam5 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Dethiosulfovibrio salsuginis USBA 82 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Devosia chinhatensis IPL18 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Devriesea agamarum IMP2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Dialister succinatiphilus YIT 11850 bgtA, bgtB*, hutH, hutU, hutI, hutG
Dietzia timorensis ID05-A0528 permease, hutH, hutU, hutI, hutG
Dokdonella koreensis DS-123 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Domibacillus robiginosus WS 4628 permease, hutH, hutU, hutI, hutG
Duganella sacchari Sac-22 permease, hutH, hutU, hutI, hutF, hutG'
Dyadobacter tibetensis Y620-1 permease, hutH, hutU, hutI, hutG
Dyella jiangningensis SBZ3-12 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Endozoicomonas montiporae CL-33 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Enterococcus termitis LMG 8895 LAT2, hutH, hutU, hutI, hutG
Enterorhabdus caecimuris B7 permease, hutH, hutU, hutI, hutG
Epibacterium ulvae U95 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Erythrobacter gangjinensis K7-2 permease, hutH, hutU, hutI, hutG
Erythrobacter marinus HWDM-33 Ga0059261_1577, hutH, hutU, hutI, hutG
Ethanoligenens harbinense YUAN-3 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Fervidicella metallireducens AeB LAT2, hutH, hutU, hutI, hutG
Fibrella aestuarina BUZ 2 permease, hutH, hutU, hutI, hutG
Flammeovirga pacifica WPAGA1 permease, hutH, hutU, hutI, hutG
Flaviramulus ichthyoenteri Th78 permease, hutH, hutU, hutI, hutG
Flavobacterium beibuense F44-8 permease, hutH, hutU, hutI, hutG
Flavobacterium glycines Gm-149 permease, hutH, hutU, hutI, hutG
Flavobacterium sp. LM5 LAT2, hutH, hutU, hutI, hutG
Flavobacterium ummariense DS-12 permease, hutH, hutU, hutI, hutG
Frischella perrara PEB0191 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Galbibacter marinus ck-I2-15 permease, hutH, hutU, hutI, hutG
Gallaecimonas xiamenensis 3-C-1 permease, hutH, hutU, hutI, hutG
Geobacter daltonii FRC-32 permease, hutH, hutU, hutI, hutG
Gillisia marina CBA3202 permease, hutH, hutU, hutI, hutG
Gracilibacillus halophilus YIM-C55.5 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Granulicella mallensis MP5ACTX8 LAT2, hutH, hutU, hutI, hutF, hutG'
Granulicella tundricola MP5ACTX9 permease, hutH, hutU, hutI, hutG
Hafnia paralvei ATCC 29927 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Haladaptatus cibarius D43 permease, hutH, hutU, hutI, hutG
Halioglobus japonicus S1-36 permease, hutH, hutU, hutI, hutG
Halobacillus alkaliphilus FP5 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Halococcus hamelinensis 100A6 permease, hutH, hutU, hutI, hutG
Halomonas salina B6 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Halomonas smyrnensis AAD6 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Halomonas stevensii S18214 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Halomonas titanicae BH1 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Halomonas xinjiangensis TRM 0175 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Halopiger salifodinae KCY07-B2 permease, hutH, hutU, hutI, hutG
Halostagnicola larsenii XH-48 permease, hutH, hutU, hutI, hutG
Haloterrigena daqingensis JX313 permease, hutH, hutU, hutI, hutG
Herbaspirillum aquaticum IEH 4430 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Hippea alviniae EP5-r permease, hutH, hutU, hutI, hutG
Hippea jasoniae Mar08-272r permease, hutH, hutU, hutI, hutG
Hoeflea phototrophica DFL-43 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Hyphomicrobium nitrativorans NL23 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Imtechella halotolerans K1 permease, hutH, hutU, hutI, hutG
Indibacter alkaliphilus LW1 permease, hutH, hutU, hutI, hutG
Jannaschia aquimarina GSW-M26 permease, hutH, hutU, hutI, hutG
Jeotgalibacillus soli P9 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Kangiella geojedonensis YCS-5 permease, hutH, hutU, hutI, hutF, hutG'
Knoellia flava TL1 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Kocuria flava HO-9041 permease, hutH, hutU, hutI, hutG
Kocuria turfanensis HO-9042 permease, hutH, hutU, hutI, hutG
Laceyella sediminis RHA1 LAT2, hutH, hutU, hutI, hutG
Lacinutrix algicola AKS293 permease, hutH, hutU, hutI, hutG
Lacinutrix himadriensis E4-9a permease, hutH, hutU, hutI, hutG
Lacinutrix mariniflava AKS432 permease, hutH, hutU, hutI, hutG
Lactobacillus curieae CCTCC M 2011381 LAT2, hutH, hutU, hutI, hutG
Lactobacillus delbrueckii ZN7a-9 LAT2, hutH, hutU, hutI, hutG
Lactobacillus hokkaidonensis LOOC260 LAT2, hutH, hutU, hutI, hutG
Lactobacillus oryzae SG293 LAT2, hutH, hutU, hutI, hutG
Lactobacillus pobuzihii E100301 permease, hutH, hutU, hutI, hutG
Lactobacillus shenzhenensis LY-73 bgtA, bgtB, hutH, hutU, hutI, hutG
Lactobacillus silagei IWT126 LAT2, hutH, hutU, hutI, hutG
Leeuwenhoekiella blandensis MED217 permease, hutH, hutU, hutI, hutG
Lentibacillus jeotgali Grbi PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Limnohabitans curvus MWH-C5 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Limnohabitans parvus II-B4 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Listeria fleischmannii LU2006-1 LAT2, hutH, hutU, hutI, hutG
Luteimonas huabeiensis HB2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Luteipulveratus mongoliensis MN07-A0370 bgtA, bgtB, hutH, hutU, hutI, hutF, hutG'
Lutibaculum baratangense AMV1 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Lysobacter daejeonensis GH1-9 permease, hutH, hutU, hutI, hutF, hutG'
Magnetovibrio blakemorei MV-1 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Marinicella litoralis KMM 3900 permease, hutH, hutU, hutI, hutF, hutG'
Mariniradius saccharolyticus AK6 permease, hutH, hutU, hutI, hutG
Marinobacter algicola DG893 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Marinobacter guineae M3B PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Marinobacter psychrophilus 20041 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Marinomonas arctica 328 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Marivita geojedonensis DPG-138 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Martelella endophytica YC6887 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Megamonas funiformis YIT 11815 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Mesorhizobium ciceri WSM1271 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Methanobacterium arcticum M2 permease, hutH, hutU, hutI, hutG
Methanobacterium veterum MK4 permease, hutH, hutU, hutI, hutG
Methanocella arvoryzae MRE50 permease, hutH, hutU, hutI, hutG
Methanococcus aeolicus Nankai-3 permease, hutH, hutU, hutI, hutG
Methanoculleus horonobensis T10 permease, hutH, hutU, hutI, hutG
Methanolinea tarda NOBI-1 permease, hutH, hutU, hutI, hutG
Methanosarcina soligelidi SMA-21 permease, hutH, hutU, hutI, hutG
Methanospirillum lacunae Ki8-1 permease, hutH, hutU, hutI, hutG
Methanospirillum stamsii Pt1 permease, hutH, hutU, hutI, hutG
Methylibium petroleiphilum PM1 bgtA, bgtB*, hutH, hutU, hutI, hutG
Methylobacterium gossipiicola Gh-105 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylocapsa aurea KYG braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Methylotenera versatilis 301 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Microbacterium profundi Shh49 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Microvirga lotononidis WSM3557 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Moritella dasanensis ArB 0140 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Mucilaginibacter gossypii Gh-67 LAT2, hutH, hutU, hutI, hutG
Mucilaginibacter gossypiicola Gh-48 LAT2, hutH, hutU, hutI, hutG
Mucilaginibacter mallensis MP1X4 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Nafulsella turpanensis ZLM-10 permease, hutH, hutU, hutI, hutG
Natronomonas moolapensis 8.8.11 permease, hutH, hutU, hutI, hutG
Nautilia profundicola AmH permease, hutH, hutU, hutI, hutG
Neiella marina J221 permease, hutH, hutU, hutI, hutG
Neptunomonas antarctica S3-22 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Nocardioides daejeonensis MJ31 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Nocardioides dokdonensis FR1436 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
Nocardiopsis baichengensis YIM 90130 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Nocardiopsis gilva YIM 90087 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Novosphingobium barchaimii LL02 Ga0059261_1577, hutH, hutU, hutI, hutG
Novosphingobium fuchskuhlense FNE08-7 Ga0059261_1577, hutH, hutU, hutI, hutG
Novosphingobium lindaniclasticum LE124 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Oceanisphaera arctica V1-41 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Ochrobactrum rhizosphaerae PR17 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Ochrobactrum thiophenivorans DSM 7216 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Oscillibacter ruminantium GH1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Paenisporosarcina indica PN2 permease, hutH, hutU, hutI, hutG
Palaeococcus pacificus DY20341 permease, hutH, hutU, hutI, hutG
Paludibacter propionicigenes WB4 permease, hutH, hutU, hutI, hutG
Pandoraea thiooxydans ATSB16 permease, hutH, hutU, hutI, hutF, hutG'
Pantoea rwandensis LMG 26275 BPHYT_RS24000, BPHYT_RS24005, BPHYT_RS24010, BPHYT_RS24015, hutH, hutU, hutI, hutF, hutG'
Pedobacter arcticus A12 permease, hutH, hutU, hutI, hutG
Photobacterium gaetbulicola Gung47 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Photobacterium jeanii R-40508 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Phyllobacterium brassicacearum STM 196 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Phyllobacterium endophyticum PEPV15 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Phyllobacterium leguminum ORS 1419 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Planktomarina temperata RCA23 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Planococcus halocryophilus Or1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Pleomorphomonas diazotrophica R5-392 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Polaribacter dokdonensis DSW-5 permease, hutH, hutU, hutI, hutG
Pontibacillus litoralis JSM 072002 permease, hutH, hutU, hutI, hutG
Pontibacter lucknowensis DM9 permease, hutH, hutU, hutI, hutG
Pontibacter ramchanderi LP43 permease, hutH, hutU, hutI, hutG
Pontimonas salivibrio CL-TW6 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutG
Porphyrobacter dokdonensis DSW-74 permease, hutH, hutU, hutI, hutG
Pseudoalteromonas arctica A 37-1-2 permease, hutH, hutU, hutI, hutG
Pseudomonas baetica a390 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudomonas litoralis 2SM5 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Pseudomonas taeanensis MS-3 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Pseudovibrio axinellae Ad2 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Psychrobacter arcticus 273-4 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Psychrobacter cryohalolentis K5 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Psychromonas ingrahamii 37 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Psychromonas ossibalaenae JAMM 0738 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Rhizobium freirei PRF 81 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhizobium grahamii CCGE 502 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhizobium subbaraonis JC85 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutF, hutG'
Rhodanobacter denitrificans 2APBS1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Rhodobacter johrii JA192 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Rhodobacter maris JA276 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutG
Rhodobacter ovatus JA234 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Rhodobacter viridis JA737 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutG
Rhodococcus qingshengii djl-6-2 permease, hutH, hutU, hutI, hutG
Rhodopseudomonas pseudopalustris DSM 123 braC, braD, braE, braF, braG, hutH, hutU, hutI, hutG
Roseateles aquatilis CCUG 48205 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Roseivirga spongicola UST030701-084 permease, hutH, hutU, hutI, hutG
Rubrivirga marina SAORIC-28 Ga0059261_1577, hutH, hutU, hutI, hutG
Ruegeria conchae TW15 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Saccharomonospora marina XMU15 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Salinicoccus carnicancri Crm PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Serinicoccus profundi MCCC 1A05965 natA, natB, natC, natD, natE, hutH, hutU, hutI, hutF, hutG'
Shewanella halifaxensis HAW-EB4 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Skermanella stibiiresistens SB22 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Snodgrassella alvi wkB2 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Sphaerochaeta globosa Buddy PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Sphaerochaeta pleomorpha Grapes PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Sphingobium baderi LL03 permease, hutH, hutU, hutI, hutF, hutG'
Sphingobium czechense LL01 Ga0059261_1577, hutH, hutU, hutI, hutG
Sphingobium quisquiliarum P25 permease, hutH, hutU, hutI, hutG
Sphingomonas histidinilytica UM2 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Sphingomonas indica Dd16 Ga0059261_1577, hutH, hutU, hutI, hutG
Sphingomonas laterariae LNB2 permease, hutH, hutU, hutI, hutF, hutG'
Sphingopyxis indica DS15 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Sphingopyxis terrae UI2 Ga0059261_1577, hutH, hutU, hutI, hutF, hutG'
Sporolactobacillus vineae SL153 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Streptacidiphilus oryzae TH49 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Streptococcus anginosus CCUG 39159 permease, hutH, hutU, hutI, hutG
Streptococcus massiliensis 4401825 bgtA, bgtB, hutH, hutU, hutI, hutG
Streptococcus oralis 7747 permease, hutH, hutU, hutI, hutG
Streptococcus oralis AZ_3a bgtA, bgtB, hutH, hutU, hutI, hutG
Streptomyces kebangsaanensis SUK12 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutF, hutG'
Succinatimonas hippei YIT 12066 bgtA, bgtB*, hutH, hutU, hutI, hutG
Sulfurimonas gotlandica GD1 permease, hutH, hutU, hutI, hutG
Tatumella morbirosei LMG 23360 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'
Thauera humireducens SgZ-1 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Thermoactinomyces daqus H-18 PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
Thermobifida halotolerans YIM 90462 Ga0059261_1577, hutH, hutU, hutI, hutG
Thermodesulfovibrio aggregans TGE-P1 permease, hutH, hutU, hutI, hutG
Thermophagus xiamenensis HS1 permease, hutH, hutU, hutI, hutG
Thermovenabulum gondwanense R270 permease, hutH, hutU, hutI, hutG
Thioclava dalianensis DLFJ1-1 hutV, hutW, hutX, hutH, hutU, hutI, hutG
Thiohalospira halophila HL 3 permease, hutH, hutU, hutI, hutG
Tistlia consotensis USBA 355 aapJ, aapQ, aapM, aapP, hutH, hutU, hutI, hutF, hutG'
Vagococcus penaei CD276 LAT2, hutH, hutU, hutI, hutG
Verminephrobacter eiseniae EF01-2 Ac3H11_2562, Ac3H11_2561, Ac3H11_2560, Ac3H11_2555, Ac3H11_2554, hutH, hutU, hutI, hutF, hutG'
Weissella oryzae SG25 LAT2, hutH, hutU, hutI, hutG
Williamsia sterculiae CPCC 203464 permease, hutH, hutU, hutI, hutG
Yersinia intermedia Y228 hisP, hisM, hisQ, hisJ, hutH, hutU, hutI, hutF, hutG'

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.

Links

Downloads

Related tools

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