GapMind for catabolism of small carbon sources

 

L-arabinose catabolism

Analysis of pathway arabinose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 araE, araA, araB, araD
Actinokineospora bangkokensis 44EHW araE, araA, araB, araD
Actinomyces timonensis 7400942 araE, araA, araB, araD
Algiphilus aromaticivorans DG1253 BT0355, araA, araB, araD
Algoriphagus aquaeductus T4 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Algoriphagus machipongonensis PR1 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Alicyclobacillus ferrooxydans TC-34 araE, araA, araB, araD
Alishewanella agri BL06 araE, araA, araB, araD
Alistipes indistinctus YIT 12060 araE, araA, araB, araD
Alistipes shahii WAL 8301 araE, araA, araB, araD
Alkalitalea saponilacus SC/BZ-SP2 Echvi_1880, araA, araB, araD
Amantichitinum ursilacus IGB-41 araF, araG, araH, araA, araB, araD
Amphibacillus jilinensis Y1 gguA, gguB, chvE, araA, araB, araD
Amphritea japonica JAMM 1866 araE, araA, araB, araD
Amycolatopsis halophila YIM 93223 araE, araA, araB, araD
Amycolatopsis xylanica CPCC 202699 gguA, gguB, chvE, araA, araB, araD
Aquimarina agarilytica ZC1 araE, araA, araB, araD
Aquimarina longa SW024 Echvi_1880, araA, araB, araD
Aquimarina macrocephali JAMB N27 Echvi_1880, araA, araB, araD
Archaeoglobus sulfaticallidus PM70-1 araE, araA, araB, araD
Arcticibacter svalbardensis MN12-7 Echvi_1880, araA, araB, araD
Ardenticatena maritima 110S araE, araA, araB, araD
Arenimonas metalli CF5-1 araE, araA, araB, araD
Arenitalea lutea P7-3-5 araE, araA, araB, araD
Azospirillum humicireducens SgZ-5 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Azospirillum thiophilum BV-S gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Bacillus altitudinis 41KF2b araE, araA, araB, araD
Bacillus coahuilensis m4-4 gguA, gguB, chvE, araA, araB, araD
Bacillus cytotoxicus NVH 391-98 araE, araA, araB, araD
Bacillus horneckiae 1P01SC araE, araA, araB, araD
Bacillus okhensis Kh10-101 gguA, gguB, chvE, araA, araB, araD
Bacillus safensis FO-36b araE, araA, araB, araD
Bacillus velezensis CBMB205 araE, araA, araB, araD
Bacteroides clarus YIT 12056 BT0355, araA, araB, araD
Bacteroides faecis MAJ27 BT0355, araA, araB, araD
Bacteroides fluxus YIT 12057 araE, araA, araB, araD
Bacteroides oleiciplenus YIT 12058 BT0355, araA, araB, araD
Barnesiella intestinihominis YIT 11860 BT0355, araA, araB, araD
Belnapia rosea CPCC 100156 araE, xacB, xacC, xacD, xacE, xacF
Bizionia argentinensis JUB59 araE, araA, araB, araD
Bradyrhizobium diazoefficiens USDA110 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Brevibacterium jeotgali SJ5-8 araE, araA, araB, araD
Brucella inopinata BO1 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Brucella microti CCM 4915 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Bryobacter aggregatus MPL3 araE, xacB, xacC, xacD, xacE, xacF
Caldicellulosiruptor hydrothermalis 108 araE, araA, araB, araD
Caldicellulosiruptor kronotskyensis 2002 araE, araA, araB, araD
Carboxydothermus pertinax Ug1 araE, araA, araB, araD
Catellicoccus marimammalium M35/04/3 araE, araA, araB, araD
Chromobacterium vaccinii MWU205 araE, araA, araB, araD
Chryseobacterium angstadtii KM araE, araA, araB, araD
Chryseobacterium arthrosphaerae CC-VM-7 Echvi_1880, araA, araB, araD
Chryseobacterium viscerum 687B-08 araE, araA, araB, araD
Cloacibacillus porcorum CL-84 araE, araA, araB, araD
Cobetia crustatorum JO1 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Collimonas arenae Ter10 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Collimonas pratensis Ter91 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Collinsella tanakaei YIT 12063 araE, araA, araB, araD
Coprobacter fastidiosus NSB1 araE, araA, araB, araD
Corynebacterium deserti GIMN1.010 araE, araA, araB, araD
Corynebacterium frankenforstense ST18 araE, araA, araB, araD
Corynebacterium lactis RW2-5 araE, araA, araB, araD
Croceitalea dokdonensis DOKDO 023 BT0355, araA, araB, araD
Cronobacter condimenti 1330 araF, araG, araH, araA, araB, araD
Cronobacter muytjensii ATCC 51329 araF, araG, araH, araA, araB, araD
Cronobacter universalis NCTC 9529 araF, araG, araH, araA, araB, araD
Desulfatitalea tepidiphila S28bF araE, araA, araB, araD
Desulfotomaculum hydrothermale Lam5 araE, araA, araB, araD
Dethiosulfovibrio salsuginis USBA 82 araE, araA, araB, araD
Devosia chinhatensis IPL18 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Devriesea agamarum IMP2 araE, araA, araB, araD
Dialister succinatiphilus YIT 11850 araE, araA, araB, araD
Dietzia timorensis ID05-A0528 araE, araA, araB, araD
Dokdonella koreensis DS-123 araE, araA, araB, araD
Domibacillus robiginosus WS 4628 araE, araA, araB, araD
Duganella sacchari Sac-22 araE, xacB, xacC, xacD, xacE, xacF
Dyadobacter tibetensis Y620-1 Echvi_1880, araA, araB, araD
Dyella jiangningensis SBZ3-12 araE, xacB, xacC, xacD, xacE, xacF
Endozoicomonas montiporae CL-33 araE, araA, araB, araD
Enterococcus termitis LMG 8895 araE, araA, araB, araD
Enterorhabdus caecimuris B7 araE, araA, araB, araD
Epibacterium ulvae U95 araE, xacB, xacC, xacD, xacE, xacF
Erythrobacter gangjinensis K7-2 araE, araA, araB, araD
Erythrobacter marinus HWDM-33 araE, xacB, xacC, xacD, xacE, xacF
Ethanoligenens harbinense YUAN-3 araE, araA, araB, araD
Fervidicella metallireducens AeB gguA, gguB, chvE, araA, araB, araD
Fibrella aestuarina BUZ 2 araE, araA, araB, araD
Flammeovirga pacifica WPAGA1 araE, araA, araB, araD
Flaviramulus ichthyoenteri Th78 araE, xacB, xacC, xacD, xacE, xacF
Flavobacterium beibuense F44-8 araE, araA, araB, araD
Flavobacterium glycines Gm-149 Echvi_1880, araA, araB, araD
Flavobacterium sp. LM5 araE, araA, araB, araD
Flavobacterium ummariense DS-12 araE, araA, araB, araD
Frischella perrara PEB0191 araE, araA, araB, araD
Galbibacter marinus ck-I2-15 BT0355, araA, araB, araD
Gallaecimonas xiamenensis 3-C-1 araUsh, araVsh, araWsh, araZsh, xacB, xacC, xacD, xacE, xacF
Geobacter daltonii FRC-32 araE, araA, araB, araD
Gillisia marina CBA3202 araE, araA, araB, araD
Gracilibacillus halophilus YIM-C55.5 gguA, gguB, chvE, araA, araB, araD
Granulicella mallensis MP5ACTX8 araE, araA, araB, araD
Granulicella tundricola MP5ACTX9 araE, araA, araB, araD
Hafnia paralvei ATCC 29927 araF, araG, araH, araA, araB, araD
Haladaptatus cibarius D43 araE, xacB, xacC, xacD, xacE, xacF
Halioglobus japonicus S1-36 araE, araA, araB, araD
Halobacillus alkaliphilus FP5 araE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Halococcus hamelinensis 100A6 xacG, xacH, xacI, xacJ, xacK, xacB, xacC, xacD, xacE, xacF
Halomonas salina B6 araE, xacB, xacC, xacD, xacE, xacF
Halomonas smyrnensis AAD6 araE, xacB, xacC, xacD, xacE, xacF
Halomonas stevensii S18214 Echvi_1880, araA, araB, araD
Halomonas titanicae BH1 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Halomonas xinjiangensis TRM 0175 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Halopiger salifodinae KCY07-B2 xacG, xacH, xacI, xacJ, xacK, xacB, xacC, xacD, xacE, xacF
Halostagnicola larsenii XH-48 xacG, xacH, xacI, xacJ, xacK, araA, araB, araD
Haloterrigena daqingensis JX313 araE, xacB, xacC, xacD, xacE, xacF
Herbaspirillum aquaticum IEH 4430 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Hippea alviniae EP5-r araE, araA, araB, araD
Hippea jasoniae Mar08-272r araE, araA, araB, araD
Hoeflea phototrophica DFL-43 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Hyphomicrobium nitrativorans NL23 araE, araA, araB, araD
Imtechella halotolerans K1 Echvi_1880, araA, araB, araD
Indibacter alkaliphilus LW1 BT0355, araA, araB, araD
Jannaschia aquimarina GSW-M26 araE, xacB, xacC, xacD, xacE, xacF
Jeotgalibacillus soli P9 araE, araA, araB, araD
Kangiella geojedonensis YCS-5 araE, araA, araB, araD
Knoellia flava TL1 gguA, gguB, chvE, araA, araB, araD
Kocuria flava HO-9041 araE, araA, araB, araD
Kocuria turfanensis HO-9042 gguA, gguB, chvE, araA, araB, araD
Laceyella sediminis RHA1 araE, araA, araB, araD
Lacinutrix algicola AKS293 araE, araA, araB, araD
Lacinutrix himadriensis E4-9a araE, araA, araB, araD
Lacinutrix mariniflava AKS432 araE, araA, araB, araD
Lactobacillus curieae CCTCC M 2011381 araE, araA, araB, araD
Lactobacillus delbrueckii ZN7a-9 araE, araA, araB, araD
Lactobacillus hokkaidonensis LOOC260 araE, araA, araB, araD
Lactobacillus oryzae SG293 araE, araA, araB, araD
Lactobacillus pobuzihii E100301 araE, araA, araB, araD
Lactobacillus shenzhenensis LY-73 araUsh, araVsh, araWsh, araZsh, araA, araB, araD
Lactobacillus silagei IWT126 araE, araA, araB, araD
Leeuwenhoekiella blandensis MED217 araE, araA, araB, araD
Lentibacillus jeotgali Grbi araE, araA, araB, araD
Limnohabitans curvus MWH-C5 araE, araA, araB, araD
Limnohabitans parvus II-B4 araE, xacB, xacC, xacD, xacE, xacF
Listeria fleischmannii LU2006-1 araE, araA, araB, araD
Luteimonas huabeiensis HB2 araE, xacB, xacC, xacD, xacE, xacF
Luteipulveratus mongoliensis MN07-A0370 gguA, gguB, chvE, araA, araB, araD
Lutibaculum baratangense AMV1 araE, xacB, xacC, xacD, xacE, xacF
Lysobacter daejeonensis GH1-9 Echvi_1880, araA, araB, araD
Magnetovibrio blakemorei MV-1 araE, araA, araB, araD
Marinicella litoralis KMM 3900 araE, araA, araB, araD
Mariniradius saccharolyticus AK6 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Marinobacter algicola DG893 araE, araA, araB, araD
Marinobacter guineae M3B araE, araA, araB, araD
Marinobacter psychrophilus 20041 araE, araA, araB, araD
Marinomonas arctica 328 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Marivita geojedonensis DPG-138 araE, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Martelella endophytica YC6887 gguA, gguB, chvE, araA, araB, araD
Megamonas funiformis YIT 11815 araE, araA, araB, araD
Mesorhizobium ciceri WSM1271 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Methanobacterium arcticum M2 araE, araA, araB, araD
Methanobacterium veterum MK4 araE, araA, araB, araD
Methanocella arvoryzae MRE50 araE, araA, araB, araD
Methanococcus aeolicus Nankai-3 araE, araA, araB, araD
Methanoculleus horonobensis T10 araE, araA, araB, araD
Methanolinea tarda NOBI-1 araE, araA, araB, araD
Methanosarcina soligelidi SMA-21 araE, araA, araB, araD
Methanospirillum lacunae Ki8-1 araE, araA, araB, araD
Methanospirillum stamsii Pt1 araE, araA, araB, araD
Methylibium petroleiphilum PM1 araE, araA, araB, araD
Methylobacterium gossipiicola Gh-105 araE, araA, araB, araD
Methylocapsa aurea KYG araE, araA, araB, araD
Methylotenera versatilis 301 araE, araA, araB, araD
Microbacterium profundi Shh49 gguA, gguB, chvE, araA, araB, araD
Microvirga lotononidis WSM3557 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Moritella dasanensis ArB 0140 araE, araA, araB, araD
Mucilaginibacter gossypii Gh-67 araE, araA, araB, araD
Mucilaginibacter gossypiicola Gh-48 Echvi_1880, araA, araB, araD
Mucilaginibacter mallensis MP1X4 araE, araA, araB, araD
Nafulsella turpanensis ZLM-10 araE, araA, araB, araD
Natronomonas moolapensis 8.8.11 araE, araA, araB, araD
Nautilia profundicola AmH araE, araA, araB, araD
Neiella marina J221 araE, xacB, xacC, xacD, xacE, xacF
Neptunomonas antarctica S3-22 araE, araA, araB, araD
Nocardioides daejeonensis MJ31 araE, araA, araB, araD
Nocardioides dokdonensis FR1436 araE, araA, araB, araD
Nocardiopsis baichengensis YIM 90130 gguA, gguB, chvE, araA, araB, araD
Nocardiopsis gilva YIM 90087 araE, xacB, xacC, xacD, xacE, xacF
Novosphingobium barchaimii LL02 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Novosphingobium fuchskuhlense FNE08-7 araE, xacB, xacC, xacD, xacE, xacF
Novosphingobium lindaniclasticum LE124 araE, xacB, xacC, xacD, xacE, xacF
Oceanisphaera arctica V1-41 araE, araA, araB, araD
Ochrobactrum rhizosphaerae PR17 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Ochrobactrum thiophenivorans DSM 7216 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Oscillibacter ruminantium GH1 gguA, gguB, chvE, araA, araB, araD
Paenisporosarcina indica PN2 araE, araA, araB, araD
Palaeococcus pacificus DY20341 araE, araA, araB, araD
Paludibacter propionicigenes WB4 BT0355, araA, araB, araD
Pandoraea thiooxydans ATSB16 araE, araA, araB, araD
Pantoea rwandensis LMG 26275 araE, araA, araB, araD
Pedobacter arcticus A12 Echvi_1880, araA, araB, araD
Photobacterium gaetbulicola Gung47 araE, araA, araB, araD
Photobacterium jeanii R-40508 araE, araA, araB, araD
Phyllobacterium brassicacearum STM 196 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Phyllobacterium endophyticum PEPV15 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Phyllobacterium leguminum ORS 1419 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Planktomarina temperata RCA23 araE, xacB, xacC, xacD, xacE, xacF
Planococcus halocryophilus Or1 gguA, gguB, chvE, araA, araB, araD
Pleomorphomonas diazotrophica R5-392 araF, araG, araH, araA, araB, araD
Polaribacter dokdonensis DSW-5 araE, araA, araB, araD
Pontibacillus litoralis JSM 072002 araE, araA, araB, araD
Pontibacter lucknowensis DM9 araE, xacB, xacC, xacD, xacE, xacF
Pontibacter ramchanderi LP43 Echvi_1880, xacB, xacC, xacD, xacE, xacF
Pontimonas salivibrio CL-TW6 araE, xacB, xacC, xacD, xacE, xacF
Porphyrobacter dokdonensis DSW-74 araE, araA, araB, araD
Pseudoalteromonas arctica A 37-1-2 Echvi_1880, xacB, xacC, xacD, KDG-aldolase, aldA, gyaR, glcB
Pseudomonas baetica a390 araF, araG, araH, xacB, xacC, xacD, xacE, xacF
Pseudomonas litoralis 2SM5 araE, araA, araB, araD
Pseudomonas taeanensis MS-3 araE, xacB, xacC, xacD, xacE, xacF
Pseudovibrio axinellae Ad2 araE, xacB, xacC, xacD, xacE, xacF
Psychrobacter arcticus 273-4 araE, araA, araB, araD
Psychrobacter cryohalolentis K5 araE, araA, araB, araD
Psychromonas ingrahamii 37 araE, araA, araB, araD
Psychromonas ossibalaenae JAMM 0738 araE, araA, araB, araD
Rhizobium freirei PRF 81 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium grahamii CCGE 502 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhizobium subbaraonis JC85 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Rhodanobacter denitrificans 2APBS1 araE, araA, araB, araD
Rhodobacter johrii JA192 araE, xacB, xacC, xacD, xacE, xacF
Rhodobacter maris JA276 araE, xacB, xacC, xacD, xacE, xacF
Rhodobacter ovatus JA234 araE, araA, araB, araD
Rhodobacter viridis JA737 araE, araA, araB, araD
Rhodococcus qingshengii djl-6-2 araE, araA, araB, araD
Rhodopseudomonas pseudopalustris DSM 123 araE, xacB, xacC, xacD, xacE, xacF
Roseateles aquatilis CCUG 48205 araE, xacB, xacC, xacD, xacE, xacF
Roseivirga spongicola UST030701-084 BT0355, araA, araB, araD
Rubrivirga marina SAORIC-28 BT0355, araA, araB, araD
Ruegeria conchae TW15 araE, xacB, xacC, xacD, xacE, xacF
Saccharomonospora marina XMU15 araE, xacB, xacC, xacD, xacE, xacF
Salinicoccus carnicancri Crm araE, araA, araB, araD
Serinicoccus profundi MCCC 1A05965 araE, araA, araB, araD
Shewanella halifaxensis HAW-EB4 araE, araA, araB, araD
Skermanella stibiiresistens SB22 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Snodgrassella alvi wkB2 araE, araA, araB, araD
Sphaerochaeta globosa Buddy gguA, gguB, chvE, araA, araB, araD
Sphaerochaeta pleomorpha Grapes gguA, gguB, chvE, araA, araB, araD
Sphingobium baderi LL03 araE, araA, araB, araD
Sphingobium czechense LL01 araE, xacB, xacC, xacD, xacE, xacF
Sphingobium quisquiliarum P25 araE, xacB, xacC, xacD, xacE, xacF
Sphingomonas histidinilytica UM2 araE, araA, araB, araD
Sphingomonas indica Dd16 araE, araA, araB, araD
Sphingomonas laterariae LNB2 araE, xacB, xacC, xacD, xacE, xacF
Sphingopyxis indica DS15 araE, xacB, xacC, xacD, xacE, xacF
Sphingopyxis terrae UI2 araE, araA, araB, araD
Sporolactobacillus vineae SL153 araE, araA, araB, araD
Streptacidiphilus oryzae TH49 xylFsa, xylGsa, xylHsa, araA, araB, araD
Streptococcus anginosus CCUG 39159 araE, araA, araB, araD
Streptococcus massiliensis 4401825 araE, araA, araB, araD
Streptococcus oralis 7747 araE, araA, araB, araD
Streptococcus oralis AZ_3a araE, araA, araB, araD
Streptomyces kebangsaanensis SUK12 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Succinatimonas hippei YIT 12066 gguA, gguB, chvE, araA, araB, araD
Sulfurimonas gotlandica GD1 araE, araA, araB, araD
Tatumella morbirosei LMG 23360 araF, araG, araH, araA, araB, araD
Thauera humireducens SgZ-1 araE, araA, araB, araD
Thermoactinomyces daqus H-18 araE, araA, araB, araD
Thermobifida halotolerans YIM 90462 araE, xacB, xacC, xacD, xacE, xacF
Thermodesulfovibrio aggregans TGE-P1 araE, araA, araB, araD
Thermophagus xiamenensis HS1 Echvi_1880, araA, araB, araD
Thermovenabulum gondwanense R270 araE, araA, araB, araD
Thioclava dalianensis DLFJ1-1 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Thiohalospira halophila HL 3 araE, araA, araB, araD
Tistlia consotensis USBA 355 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Vagococcus penaei CD276 araE, araA, araB, araD
Verminephrobacter eiseniae EF01-2 gguA, gguB, chvE, xacB, xacC, xacD, xacE, xacF
Weissella oryzae SG25 araE, araA, araB, araD
Williamsia sterculiae CPCC 203464 araE, araA, araB, araD
Yersinia intermedia Y228 araF, araG, araH, araA, araB, araD

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