GapMind for catabolism of small carbon sources

 

D-xylose catabolism

Analysis of pathway xylose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 xylT, xylA, xylB
Actinokineospora bangkokensis 44EHW xylT, xylA, xylB
Actinomyces timonensis 7400942 xylT, xylA, xylB
Algiphilus aromaticivorans DG1253 xylT, xylA, xylB
Algoriphagus aquaeductus T4 Echvi_1871, xylA, xylB
Algoriphagus machipongonensis PR1 Echvi_1871, xylA, xylB
Alicyclobacillus ferrooxydans TC-34 xylT, xylA, xylB
Alishewanella agri BL06 xylT, xylA, xylB
Alistipes indistinctus YIT 12060 xylT, xylA, xylB
Alistipes shahii WAL 8301 xylT, xylA, xylB
Alkalitalea saponilacus SC/BZ-SP2 xylT, xylA, xylB
Amantichitinum ursilacus IGB-41 xylF, xylG, xylH, xylA, xylB
Amphibacillus jilinensis Y1 xylF, xylG, xylH, xylA, xylB
Amphritea japonica JAMM 1866 xylT, xylA, xylB
Amycolatopsis halophila YIM 93223 xylF, xylG, xylH, xylA, xylB
Amycolatopsis xylanica CPCC 202699 xylF, xylG, xylH, xylA, xylB
Aquimarina agarilytica ZC1 xylT, xylA, xylB
Aquimarina longa SW024 Echvi_1871, xylA, xylB
Aquimarina macrocephali JAMB N27 Echvi_1871, xylA, xylB
Archaeoglobus sulfaticallidus PM70-1 xylT, xylA, xylB
Arcticibacter svalbardensis MN12-7 Echvi_1871, xylA, xylB
Ardenticatena maritima 110S xylT, xylA, xylB
Arenimonas metalli CF5-1 xylT, xylA, xylB
Arenitalea lutea P7-3-5 xylT, xylA, xylB
Azospirillum humicireducens SgZ-5 xylF, xylG, xylH, xylA, xylB
Azospirillum thiophilum BV-S xylF, xylG, xylH, xylA, xylB
Bacillus altitudinis 41KF2b xylT, xylA, xylB
Bacillus coahuilensis m4-4 xylF, xylG, xylH, xylA, xylB
Bacillus cytotoxicus NVH 391-98 xylT, xylA, xylB
Bacillus horneckiae 1P01SC xylT, xylA, xylB
Bacillus okhensis Kh10-101 xylF, xylG, xylH, xdh, xylC, xad, DKDP-aldolase, aldA, gyaR, glcB
Bacillus safensis FO-36b xylT, xylA, xylB
Bacillus velezensis CBMB205 xylT, xylA, xylB
Bacteroides clarus YIT 12056 xylT, xylA, xylB
Bacteroides faecis MAJ27 xylT, xylA, xylB
Bacteroides fluxus YIT 12057 xylT, xylA, xylB
Bacteroides oleiciplenus YIT 12058 xylT, xylA, xylB
Barnesiella intestinihominis YIT 11860 xylT, xylA, xylB
Belnapia rosea CPCC 100156 xylT, xdh, xylC, xad, kdaD, dopDH
Bizionia argentinensis JUB59 xylT, xylA, xylB
Bradyrhizobium diazoefficiens USDA110 xylF, xylG, xylH, xylA, xylB
Brevibacterium jeotgali SJ5-8 xylT, xylA, xylB
Brucella inopinata BO1 xylF, xylG, xylH, xylA, xylB
Brucella microti CCM 4915 xylF, xylG, xylH, xylA, xylB
Bryobacter aggregatus MPL3 xylF_Tm, xylE_Tm, xylK_Tm, xylA, xylB
Caldicellulosiruptor hydrothermalis 108 xylF, xylG, xylH, xylA, xylB
Caldicellulosiruptor kronotskyensis 2002 xylF, xylG, xylH, xylA, xylB
Carboxydothermus pertinax Ug1 xylT, xylA, xylB
Catellicoccus marimammalium M35/04/3 xylT, xylA, xylB
Chromobacterium vaccinii MWU205 xylT, xylA, xylB
Chryseobacterium angstadtii KM xylT, xylA, xylB
Chryseobacterium arthrosphaerae CC-VM-7 Echvi_1871, xylA, xylB
Chryseobacterium viscerum 687B-08 xylT, xylA, xylB
Cloacibacillus porcorum CL-84 xylT, xylA, xylB
Cobetia crustatorum JO1 xylT, xdh, xylC, xad, kdaD, dopDH
Collimonas arenae Ter10 xylF, xylG, xylH, xylA, xylB
Collimonas pratensis Ter91 xylF, xylG, xylH, xylA, xylB
Collinsella tanakaei YIT 12063 xylT, xylA, xylB
Coprobacter fastidiosus NSB1 xylT, xylA, xylB
Corynebacterium deserti GIMN1.010 xylT, xylA, xylB
Corynebacterium frankenforstense ST18 xylT, xyrA, xdhA, xylB
Corynebacterium lactis RW2-5 xylT, xylA, xylB
Croceitalea dokdonensis DOKDO 023 xylT, xylA, xylB
Cronobacter condimenti 1330 xylF, xylG, xylH, xylA, xylB
Cronobacter muytjensii ATCC 51329 xylF, xylG, xylH, xylA, xylB
Cronobacter universalis NCTC 9529 xylF, xylG, xylH, xylA, xylB
Desulfatitalea tepidiphila S28bF xylT, xylA, xylB
Desulfotomaculum hydrothermale Lam5 xylT, xyrA, xdhA, xylB
Dethiosulfovibrio salsuginis USBA 82 xylT, xylA, xylB
Devosia chinhatensis IPL18 xylF, xylG, xylH, xylA, xylB
Devriesea agamarum IMP2 xylT, xylA, xylB
Dialister succinatiphilus YIT 11850 xylT, xylA, xylB
Dietzia timorensis ID05-A0528 xylT, xylA, xylB
Dokdonella koreensis DS-123 xylT, xylA, xylB
Domibacillus robiginosus WS 4628 xylF, xylG, xylH, xyrA, xdhA, xylB
Duganella sacchari Sac-22 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Dyadobacter tibetensis Y620-1 Echvi_1871, xylA, xylB
Dyella jiangningensis SBZ3-12 xylT, xylA, xylB
Endozoicomonas montiporae CL-33 xylF_Tm, xylE_Tm, xylK_Tm, xylA, xylB
Enterococcus termitis LMG 8895 xylT, xylA, xylB
Enterorhabdus caecimuris B7 xylT, xylA, xylB
Epibacterium ulvae U95 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-aldolase, aldA, gyaR, glcB
Erythrobacter gangjinensis K7-2 xylT, xylA, xylB
Erythrobacter marinus HWDM-33 xylT, xdh, xylC, xad, kdaD, dopDH
Ethanoligenens harbinense YUAN-3 xylT, xylA, xylB
Fervidicella metallireducens AeB xylF, xylG, xylH, xylA, xylB
Fibrella aestuarina BUZ 2 xylT, xylA, xylB
Flammeovirga pacifica WPAGA1 xylT, xylA, xylB
Flaviramulus ichthyoenteri Th78 xylT, xylA, xylB
Flavobacterium beibuense F44-8 xylT, xylA, xylB
Flavobacterium glycines Gm-149 xylT, xylA, xylB
Flavobacterium sp. LM5 xylT, xylA, xylB
Flavobacterium ummariense DS-12 xylT, xylA, xylB
Frischella perrara PEB0191 xylT, xylA, xylB
Galbibacter marinus ck-I2-15 xylT, xylA, xylB
Gallaecimonas xiamenensis 3-C-1 xylT, xdh, xylC, xad, kdaD, dopDH
Geobacter daltonii FRC-32 xylT, xylA, xylB
Gillisia marina CBA3202 xylT, xylA, xylB
Gracilibacillus halophilus YIM-C55.5 xylF, xylG, xylH, xylA, xylB
Granulicella mallensis MP5ACTX8 xylT, xylA, xylB
Granulicella tundricola MP5ACTX9 xylT, xylA, xylB
Hafnia paralvei ATCC 29927 xylT, xylA, xylB
Haladaptatus cibarius D43 xylT, xyrA, xdhA, xylB
Halioglobus japonicus S1-36 xylT, xylA, xylB
Halobacillus alkaliphilus FP5 xylT, xylA, xylB
Halococcus hamelinensis 100A6 xylT, xdh, xylC, xad, kdaD, dopDH
Halomonas salina B6 xylT, xylA, xylB
Halomonas smyrnensis AAD6 xylT, xylA, xylB
Halomonas stevensii S18214 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Halomonas titanicae BH1 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Halomonas xinjiangensis TRM 0175 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Halopiger salifodinae KCY07-B2 xylT, xdh, xylC, xad, kdaD, dopDH
Halostagnicola larsenii XH-48 xylT, xdh, xylC, xad, kdaD, dopDH
Haloterrigena daqingensis JX313 xylT, xdh, xylC, xad, kdaD, dopDH
Herbaspirillum aquaticum IEH 4430 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Hippea alviniae EP5-r xylT, xylA, xylB
Hippea jasoniae Mar08-272r xylT, xylA, xylB
Hoeflea phototrophica DFL-43 xylF, xylG, xylH, xylA, xylB
Hyphomicrobium nitrativorans NL23 xylT, xylA, xylB
Imtechella halotolerans K1 Echvi_1871, xylA, xylB
Indibacter alkaliphilus LW1 Echvi_1871, xylA, xylB
Jannaschia aquimarina GSW-M26 xylT, xylA, xylB
Jeotgalibacillus soli P9 xylT, xylA, xylB
Kangiella geojedonensis YCS-5 xylT, xylA, xylB
Knoellia flava TL1 xylF, xylG, xylH, xylA, xylB
Kocuria flava HO-9041 xylT, xylA, xylB
Kocuria turfanensis HO-9042 xylF, xylG, xylH, xylA, xylB
Laceyella sediminis RHA1 xylT, xylA, xylB
Lacinutrix algicola AKS293 Echvi_1871, xylA, xylB
Lacinutrix himadriensis E4-9a xylT, xylA, xylB
Lacinutrix mariniflava AKS432 xylT, xylA, xylB
Lactobacillus curieae CCTCC M 2011381 xylT, xylA, xylB
Lactobacillus delbrueckii ZN7a-9 xylT, xylA, xylB
Lactobacillus hokkaidonensis LOOC260 xylT, xylA, xylB
Lactobacillus oryzae SG293 xylT, xylA, xylB
Lactobacillus pobuzihii E100301 xylT, xylA, xylB
Lactobacillus shenzhenensis LY-73 xylT, xylA, xylB
Lactobacillus silagei IWT126 xylT, xylA, xylB
Leeuwenhoekiella blandensis MED217 Echvi_1871, xylA, xylB
Lentibacillus jeotgali Grbi xylT, xyrA, xdhA, xylB
Limnohabitans curvus MWH-C5 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Limnohabitans parvus II-B4 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Listeria fleischmannii LU2006-1 xylT, xylA, xylB
Luteimonas huabeiensis HB2 xylT, xylA, xylB
Luteipulveratus mongoliensis MN07-A0370 xylF, xylG, xylH, xyrA, xdhA, xylB
Lutibaculum baratangense AMV1 xylT, xylA, xylB
Lysobacter daejeonensis GH1-9 Echvi_1871, xylA, xylB
Magnetovibrio blakemorei MV-1 xylT, xylA, xylB
Marinicella litoralis KMM 3900 xylT, xylA, xylB
Mariniradius saccharolyticus AK6 Echvi_1871, xylA, xylB
Marinobacter algicola DG893 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Marinobacter guineae M3B gtsA, gtsB, gtsC, gtsD, xylA, xylB
Marinobacter psychrophilus 20041 xylT, xylA, xylB
Marinomonas arctica 328 xylF, xylG, xylH, xylA, xylB
Marivita geojedonensis DPG-138 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Martelella endophytica YC6887 xylF, xylG, xylH, xylA, xylB
Megamonas funiformis YIT 11815 xylT, xylA, xylB
Mesorhizobium ciceri WSM1271 xylF, xylG, xylH, xylA, xylB
Methanobacterium arcticum M2 xylT, xylA, xylB
Methanobacterium veterum MK4 xylT, xylA, xylB
Methanocella arvoryzae MRE50 xylT, xylA, xylB
Methanococcus aeolicus Nankai-3 xylT, xylA, xylB
Methanoculleus horonobensis T10 xylT, xylA, xylB
Methanolinea tarda NOBI-1 xylT, xylA, xylB
Methanosarcina soligelidi SMA-21 xylT, xylA, xylB
Methanospirillum lacunae Ki8-1 xylT, xylA, xylB
Methanospirillum stamsii Pt1 xylT, xylA, xylB
Methylibium petroleiphilum PM1 xylT, xylA, xylB
Methylobacterium gossipiicola Gh-105 xylT, xylA, xylB
Methylocapsa aurea KYG xylT, xylA, xylB
Methylotenera versatilis 301 xylT, xylA, xylB
Microbacterium profundi Shh49 xylF, xylG, xylH, xylA, xylB
Microvirga lotononidis WSM3557 xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Moritella dasanensis ArB 0140 xylT, xylA, xylB
Mucilaginibacter gossypii Gh-67 Echvi_1871, xylA, xylB
Mucilaginibacter gossypiicola Gh-48 Echvi_1871, xylA, xylB
Mucilaginibacter mallensis MP1X4 xylT, xylA, xylB
Nafulsella turpanensis ZLM-10 xylT, xylA, xylB
Natronomonas moolapensis 8.8.11 xylT, xylA, xylB
Nautilia profundicola AmH xylT, xylA, xylB
Neiella marina J221 xylF, xylG, xylH, xylA, xylB
Neptunomonas antarctica S3-22 xylT, xylA, xylB
Nocardioides daejeonensis MJ31 xylT, xylA, xylB
Nocardioides dokdonensis FR1436 xylT, xylA, xylB
Nocardiopsis baichengensis YIM 90130 xylF, xylG, xylH, xylA, xylB
Nocardiopsis gilva YIM 90087 xylT, xylA, xylB
Novosphingobium barchaimii LL02 xylT, xdh, xylC, xad, kdaD, dopDH
Novosphingobium fuchskuhlense FNE08-7 xylT, xylA, xylB
Novosphingobium lindaniclasticum LE124 xylT, xdh, xylC, xad, kdaD, dopDH
Oceanisphaera arctica V1-41 xylT, xylA, xylB
Ochrobactrum rhizosphaerae PR17 xylF, xylG, xylH, xylA, xylB
Ochrobactrum thiophenivorans DSM 7216 xylF, xylG, xylH, xylA, xylB
Oscillibacter ruminantium GH1 xylF, xylG, xylH, xylA, xylB
Paenisporosarcina indica PN2 xylT, xyrA, xdhA, xylB
Palaeococcus pacificus DY20341 xylT, xylA, xylB
Paludibacter propionicigenes WB4 xylT, xylA, xylB
Pandoraea thiooxydans ATSB16 xylT, xylA, xylB
Pantoea rwandensis LMG 26275 xylF, xylG, xylH, xylA, xylB
Pedobacter arcticus A12 Echvi_1871, xylA, xylB
Photobacterium gaetbulicola Gung47 xylT, xylA, xylB
Photobacterium jeanii R-40508 xylT, xylA, xylB
Phyllobacterium brassicacearum STM 196 xylF, xylG, xylH, xylA, xylB
Phyllobacterium endophyticum PEPV15 xylF, xylG, xylH, xylA, xylB
Phyllobacterium leguminum ORS 1419 xylF, xylG, xylH, xylA, xylB
Planktomarina temperata RCA23 xylT, xylA, xylB
Planococcus halocryophilus Or1 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Pleomorphomonas diazotrophica R5-392 xylF, xylG, xylH, xylA, xylB
Polaribacter dokdonensis DSW-5 xylT, xylA, xylB
Pontibacillus litoralis JSM 072002 xylT, xylA, xylB
Pontibacter lucknowensis DM9 xylT, xylA, xylB
Pontibacter ramchanderi LP43 Echvi_1871, xylA, xylB
Pontimonas salivibrio CL-TW6 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Porphyrobacter dokdonensis DSW-74 xylT, xylA, xylB
Pseudoalteromonas arctica A 37-1-2 xylT, xylA, xylB
Pseudomonas baetica a390 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudomonas litoralis 2SM5 xylT, xylA, xylB
Pseudomonas taeanensis MS-3 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Pseudovibrio axinellae Ad2 gtsA, gtsB, gtsC, gtsD, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Psychrobacter arcticus 273-4 xylT, xylA, xylB
Psychrobacter cryohalolentis K5 xylT, xylA, xylB
Psychromonas ingrahamii 37 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Psychromonas ossibalaenae JAMM 0738 xylT, xylA, xylB
Rhizobium freirei PRF 81 xylF, xylG, xylH, xylA, xylB
Rhizobium grahamii CCGE 502 xylF, xylG, xylH, xylA, xylB
Rhizobium subbaraonis JC85 xylF, xylG, xylH, xylA, xylB
Rhodanobacter denitrificans 2APBS1 xylT, xylA, xylB
Rhodobacter johrii JA192 xylT, xylA, xylB
Rhodobacter maris JA276 xylF, xylG, xylH, xylA, xylB
Rhodobacter ovatus JA234 xylT, xyrA, xdhA, xylB
Rhodobacter viridis JA737 xylT, xylA, xylB
Rhodococcus qingshengii djl-6-2 xylT, xylA, xylB
Rhodopseudomonas pseudopalustris DSM 123 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Roseateles aquatilis CCUG 48205 gtsA, gtsB, gtsC, gtsD, xylA, xylB
Roseivirga spongicola UST030701-084 xylT, xylA, xylB
Rubrivirga marina SAORIC-28 xylT, xylA, xylB
Ruegeria conchae TW15 xylF, xylG, xylH, xylA, xylB
Saccharomonospora marina XMU15 xylT, xylA, xylB
Salinicoccus carnicancri Crm xylT, xylA, xylB
Serinicoccus profundi MCCC 1A05965 xylT, xylA, xylB
Shewanella halifaxensis HAW-EB4 Echvi_1871, xyrA, xdhA, xylB
Skermanella stibiiresistens SB22 xylF, xylG, xylH, xylA, xylB
Snodgrassella alvi wkB2 xylT, xylA, xylB
Sphaerochaeta globosa Buddy xylF, xylG, xylH, xylA, xylB
Sphaerochaeta pleomorpha Grapes xylF, xylG, xylH, xylA, xylB
Sphingobium baderi LL03 xylT, xylA, xylB
Sphingobium czechense LL01 xylT, xdh, xylC, xad, kdaD, dopDH
Sphingobium quisquiliarum P25 xylT, xdh, xylC, xad, kdaD, dopDH
Sphingomonas histidinilytica UM2 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Sphingomonas indica Dd16 xylT, xylA, xylB
Sphingomonas laterariae LNB2 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Sphingopyxis indica DS15 xylT, xdh, xylC, xad, kdaD, dopDH
Sphingopyxis terrae UI2 xylT, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB
Sporolactobacillus vineae SL153 xylT, xylA, xylB
Streptacidiphilus oryzae TH49 xylT, xylA, xylB
Streptococcus anginosus CCUG 39159 xylT, xylA, xylB
Streptococcus massiliensis 4401825 xylT, xylA, xylB
Streptococcus oralis 7747 xylT, xylA, xylB
Streptococcus oralis AZ_3a xylT, xylA, xylB
Streptomyces kebangsaanensis SUK12 xylF, xylG, xylH, xylA, xylB
Succinatimonas hippei YIT 12066 xylF, xylG, xylH, xyrA, xdhA, xylB
Sulfurimonas gotlandica GD1 xylT, xylA, xylB
Tatumella morbirosei LMG 23360 xylT, xylA, xylB
Thauera humireducens SgZ-1 xylT, xylA, xylB
Thermoactinomyces daqus H-18 xylT, xylA, xylB
Thermobifida halotolerans YIM 90462 xylT, xylA, xylB
Thermodesulfovibrio aggregans TGE-P1 xylT, xylA, xylB
Thermophagus xiamenensis HS1 xylT, xylA, xylB
Thermovenabulum gondwanense R270 xylT, xylA, xylB
Thioclava dalianensis DLFJ1-1 xylF, xylG, xylH, xylA, xylB
Thiohalospira halophila HL 3 xylT, xylA, xylB
Tistlia consotensis USBA 355 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Vagococcus penaei CD276 xylT, xylA, xylB
Verminephrobacter eiseniae EF01-2 xylF, xylG, xylH, xdh, xylC, xad, kdaD, dopDH
Weissella oryzae SG25 xylT, xylA, xylB
Williamsia sterculiae CPCC 203464 xylT, xylA, xylB
Yersinia intermedia Y228 xylF, xylG, xylH, xylA, xylB

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