GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism

Analysis of pathway cellobiose in 276 genomes

Genome Best path
Acidovorax caeni R-24608 bgl, ptsG-crr
Actinokineospora bangkokensis 44EHW cebE, cebF, cebG, msiK, bgl, glk
Actinomyces timonensis 7400942 bglG, ascB, glk
Algiphilus aromaticivorans DG1253 bgl, SSS-glucose, glk
Algoriphagus aquaeductus T4 bgl, SSS-glucose, glk
Algoriphagus machipongonensis PR1 bgl, SSS-glucose, glk
Alicyclobacillus ferrooxydans TC-34 bgl, gtsA, gtsB, gtsC, gtsD, glk
Alishewanella agri BL06 bgl, MFS-glucose, glk
Alistipes indistinctus YIT 12060 bgl, MFS-glucose, glk
Alistipes shahii WAL 8301 bgl, MFS-glucose, glk
Alkalitalea saponilacus SC/BZ-SP2 bgl, SSS-glucose, glk
Amantichitinum ursilacus IGB-41 bgl, gtsA, gtsB, gtsC, gtsD, glk
Amphibacillus jilinensis Y1 bgl, mglA, mglB, mglC, glk
Amphritea japonica JAMM 1866 bgl, ptsG-crr
Amycolatopsis halophila YIM 93223 bgl, MFS-glucose, glk
Amycolatopsis xylanica CPCC 202699 cebE, cebF, cebG, msiK, bgl, glk
Aquimarina agarilytica ZC1 bgl, SemiSWEET, glk
Aquimarina longa SW024 bgl, ptsG-crr
Aquimarina macrocephali JAMB N27 bgl, MFS-glucose, glk
Archaeoglobus sulfaticallidus PM70-1 bgl, ptsG-crr
Arcticibacter svalbardensis MN12-7 bgl, MFS-glucose, glk
Ardenticatena maritima 110S bgl, aglE', aglF', aglG', aglK', glk
Arenimonas metalli CF5-1 bgl, ptsG-crr
Arenitalea lutea P7-3-5 bgl, ptsG-crr
Azospirillum humicireducens SgZ-5 bgl, mglA, mglB, mglC, glk
Azospirillum thiophilum BV-S bgl, mglA, mglB, mglC, glk
Bacillus altitudinis 41KF2b bgl, glcU', glk
Bacillus coahuilensis m4-4 bgl, ptsG-crr
Bacillus cytotoxicus NVH 391-98 bglG, ascB, glk
Bacillus horneckiae 1P01SC cdt, cbp, pgmA, glk
Bacillus okhensis Kh10-101 bgl, mglA, mglB, mglC, glk
Bacillus safensis FO-36b bgl, glcU', glk
Bacillus velezensis CBMB205 bgl, glcU', glk
Bacteroides clarus YIT 12056 bgl, SSS-glucose, glk
Bacteroides faecis MAJ27 bgl, SSS-glucose, glk
Bacteroides fluxus YIT 12057 bgl, MFS-glucose, glk
Bacteroides oleiciplenus YIT 12058 bgl, MFS-glucose, glk
Barnesiella intestinihominis YIT 11860 bgl, MFS-glucose, glk
Belnapia rosea CPCC 100156 cdt, cbp, pgmA, glk
Bizionia argentinensis JUB59 bgl, ptsG-crr
Bradyrhizobium diazoefficiens USDA110 bgl, mglA, mglB, mglC, glk
Brevibacterium jeotgali SJ5-8 cdt, cbp, pgmA, glk
Brucella inopinata BO1 bgl, mglA, mglB, mglC, glk
Brucella microti CCM 4915 bgl, gtsA, gtsB, gtsC, gtsD, glk
Bryobacter aggregatus MPL3 cdt, cbp, pgmA, glk
Caldicellulosiruptor hydrothermalis 108 bgl, mglA, mglB, mglC, glk
Caldicellulosiruptor kronotskyensis 2002 bgl, ptsG-crr
Carboxydothermus pertinax Ug1 cdt, cbp, pgmA, glk
Catellicoccus marimammalium M35/04/3 bgl, manX, manY, manZ
Chromobacterium vaccinii MWU205 bgl, ptsG, crr
Chryseobacterium angstadtii KM bgl, SSS-glucose, glk
Chryseobacterium arthrosphaerae CC-VM-7 bgl, MFS-glucose, glk
Chryseobacterium viscerum 687B-08 bgl, MFS-glucose, glk
Cloacibacillus porcorum CL-84 cdt, cbp, pgmA, glk
Cobetia crustatorum JO1 bgl, MFS-glucose, glk
Collimonas arenae Ter10 bgl, mglA, mglB, mglC, glk
Collimonas pratensis Ter91 bgl, gtsA, gtsB, gtsC, gtsD, glk
Collinsella tanakaei YIT 12063 bgl, manX, manY, manZ
Coprobacter fastidiosus NSB1 bgl, MFS-glucose, glk
Corynebacterium deserti GIMN1.010 bglG, ascB, glk
Corynebacterium frankenforstense ST18 bgl, MFS-glucose, glk
Corynebacterium lactis RW2-5 bgl, MFS-glucose, glk
Croceitalea dokdonensis DOKDO 023 bgl, SSS-glucose, glk
Cronobacter condimenti 1330 bgl, mglA, mglB, mglC, glk
Cronobacter muytjensii ATCC 51329 bgl, mglA, mglB, mglC, glk
Cronobacter universalis NCTC 9529 bgl, mglA, mglB, mglC, glk
Desulfatitalea tepidiphila S28bF cdt, cbp, pgmA, glk
Desulfotomaculum hydrothermale Lam5 bgl, ptsG-crr
Dethiosulfovibrio salsuginis USBA 82 bgl, mglA, mglB, mglC, glk
Devosia chinhatensis IPL18 SMc04256, SMc04257, SMc04258, SMc04259, bgl, glk
Devriesea agamarum IMP2 bgl, MFS-glucose, glk
Dialister succinatiphilus YIT 11850 bgl, ptsG-crr
Dietzia timorensis ID05-A0528 bgl, MFS-glucose, glk
Dokdonella koreensis DS-123 bgl, ptsG-crr
Domibacillus robiginosus WS 4628 bglG, ascB, glk
Duganella sacchari Sac-22 SMc04256, SMc04257, SMc04258, SMc04259, bgl, glk
Dyadobacter tibetensis Y620-1 bgl, SSS-glucose, glk
Dyella jiangningensis SBZ3-12 bgl, MFS-glucose, glk
Endozoicomonas montiporae CL-33 bgl, ptsG, crr
Enterococcus termitis LMG 8895 bgl, manX, manY, manZ
Enterorhabdus caecimuris B7 bgl, ptsG-crr
Epibacterium ulvae U95 bgl, gtsA, gtsB, gtsC, gtsD, glk
Erythrobacter gangjinensis K7-2 bgl, MFS-glucose, glk
Erythrobacter marinus HWDM-33 bgl, MFS-glucose, glk
Ethanoligenens harbinense YUAN-3 bgl, ptsG-crr
Fervidicella metallireducens AeB bgl, ptsG-crr
Fibrella aestuarina BUZ 2 bgl, SSS-glucose, glk
Flammeovirga pacifica WPAGA1 bgl, SSS-glucose, glk
Flaviramulus ichthyoenteri Th78 bgl, SSS-glucose, glk
Flavobacterium beibuense F44-8 bgl, ptsG-crr
Flavobacterium glycines Gm-149 bgl, SSS-glucose, glk
Flavobacterium sp. LM5 bgl, ptsG-crr
Flavobacterium ummariense DS-12 bgl, ptsG-crr
Frischella perrara PEB0191 bgl, manX, manY, manZ
Galbibacter marinus ck-I2-15 bgl, MFS-glucose, glk
Gallaecimonas xiamenensis 3-C-1 bgl, MFS-glucose, glk
Geobacter daltonii FRC-32 bgl, ptsG-crr
Gillisia marina CBA3202 bgl, ptsG-crr
Gracilibacillus halophilus YIM-C55.5 bgl, mglA, mglB, mglC, glk
Granulicella mallensis MP5ACTX8 bgl, MFS-glucose, glk
Granulicella tundricola MP5ACTX9 bgl, MFS-glucose, glk
Hafnia paralvei ATCC 29927 bgl, mglA, mglB, mglC, glk
Haladaptatus cibarius D43 cdt, cbp, pgmA, glk
Halioglobus japonicus S1-36 cdt, cbp, pgmA, glk
Halobacillus alkaliphilus FP5 bgl, ptsG-crr
Halococcus hamelinensis 100A6 bgl, MFS-glucose, glk
Halomonas salina B6 cdt, cbp, pgmA, glk
Halomonas smyrnensis AAD6 bgl, SSS-glucose, glk
Halomonas stevensii S18214 bgl, gtsA, gtsB, gtsC, gtsD, glk
Halomonas titanicae BH1 bgl, gtsA, gtsB, gtsC, gtsD, glk
Halomonas xinjiangensis TRM 0175 bgl, gtsA, gtsB, gtsC, gtsD, glk
Halopiger salifodinae KCY07-B2 bgl, gtsA, gtsB, gtsC, gtsD, glk
Halostagnicola larsenii XH-48 bgl, MFS-glucose, glk
Haloterrigena daqingensis JX313 cdt, cbp, pgmA, glk
Herbaspirillum aquaticum IEH 4430 bgl, mglA, mglB, mglC, glk
Hippea alviniae EP5-r bgl, ptsG-crr
Hippea jasoniae Mar08-272r bgl, ptsG-crr
Hoeflea phototrophica DFL-43 SMc04256, SMc04257, SMc04258, SMc04259, bgl, glk
Hyphomicrobium nitrativorans NL23 bgl, ptsG-crr
Imtechella halotolerans K1 bgl, MFS-glucose, glk
Indibacter alkaliphilus LW1 bgl, SSS-glucose, glk
Jannaschia aquimarina GSW-M26 bgl, aglE', aglF', aglG', aglK', glk
Jeotgalibacillus soli P9 bgl, ptsG-crr
Kangiella geojedonensis YCS-5 bgl, ptsG-crr
Knoellia flava TL1 bgl, mglA, mglB, mglC, glk
Kocuria flava HO-9041 bgl, MFS-glucose, glk
Kocuria turfanensis HO-9042 cebE, cebF, cebG, msiK, bgl, glk
Laceyella sediminis RHA1 bglG, ascB, glk
Lacinutrix algicola AKS293 bgl, ptsG-crr
Lacinutrix himadriensis E4-9a bgl, ptsG-crr
Lacinutrix mariniflava AKS432 bgl, ptsG-crr
Lactobacillus curieae CCTCC M 2011381 bgl, MFS-glucose, glk
Lactobacillus delbrueckii ZN7a-9 bgl, manX, manY, manZ
Lactobacillus hokkaidonensis LOOC260 bgl, MFS-glucose, glk
Lactobacillus oryzae SG293 bgl, glcU', glk
Lactobacillus pobuzihii E100301 bglG, ascB, glk
Lactobacillus shenzhenensis LY-73 bglG, ascB, glk
Lactobacillus silagei IWT126 bgl, MFS-glucose, glk
Leeuwenhoekiella blandensis MED217 bgl, SSS-glucose, glk
Lentibacillus jeotgali Grbi bgl, MFS-glucose, glk
Limnohabitans curvus MWH-C5 bgl, gtsA, gtsB, gtsC, gtsD, glk
Limnohabitans parvus II-B4 bgl, gtsA, gtsB, gtsC, gtsD, glk
Listeria fleischmannii LU2006-1 bgl, manX, manY, manZ
Luteimonas huabeiensis HB2 bgl, MFS-glucose, glk
Luteipulveratus mongoliensis MN07-A0370 bgl, mglA, mglB, mglC, glk
Lutibaculum baratangense AMV1 cdt, cbp, pgmA, glk
Lysobacter daejeonensis GH1-9 bgl, SSS-glucose, glk
Magnetovibrio blakemorei MV-1 cdt, cbp, pgmA, glk
Marinicella litoralis KMM 3900 bgl, ptsG-crr
Mariniradius saccharolyticus AK6 bgl, SSS-glucose, glk
Marinobacter algicola DG893 bgl, gtsA, gtsB, gtsC, gtsD, glk
Marinobacter guineae M3B bgl, gtsA, gtsB, gtsC, gtsD, glk
Marinobacter psychrophilus 20041 cdt, cbp, pgmA, glk
Marinomonas arctica 328 bgl, gtsA, gtsB, gtsC, gtsD, glk
Marivita geojedonensis DPG-138 bgl, gtsA, gtsB, gtsC, gtsD, glk
Martelella endophytica YC6887 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Megamonas funiformis YIT 11815 bgl, MFS-glucose, glk
Mesorhizobium ciceri WSM1271 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Methanobacterium arcticum M2 bgl, ptsG-crr
Methanobacterium veterum MK4 bgl, ptsG-crr
Methanocella arvoryzae MRE50 bgl, ptsG-crr
Methanococcus aeolicus Nankai-3 bgl, ptsG-crr
Methanoculleus horonobensis T10 cdt, cbp, pgmA, glk
Methanolinea tarda NOBI-1 bgl, SemiSWEET, glk
Methanosarcina soligelidi SMA-21 bgl, ptsG-crr
Methanospirillum lacunae Ki8-1 bgl, SemiSWEET, glk
Methanospirillum stamsii Pt1 bgl, SemiSWEET, glk
Methylibium petroleiphilum PM1 cdt, cbp, pgmA, glk
Methylobacterium gossipiicola Gh-105 cdt, cbp, pgmA, glk
Methylocapsa aurea KYG bgl, MFS-glucose, glk
Methylotenera versatilis 301 bgl, SemiSWEET, glk
Microbacterium profundi Shh49 bgl, mglA, mglB, mglC, glk
Microvirga lotononidis WSM3557 bgl, mglA, mglB, mglC, glk
Moritella dasanensis ArB 0140 bgl, ptsG, crr
Mucilaginibacter gossypii Gh-67 bgl, SSS-glucose, glk
Mucilaginibacter gossypiicola Gh-48 bgl, SSS-glucose, glk
Mucilaginibacter mallensis MP1X4 bgl, SSS-glucose, glk
Nafulsella turpanensis ZLM-10 bgl, MFS-glucose, glk
Natronomonas moolapensis 8.8.11 bgl, ptsG-crr
Nautilia profundicola AmH bgl, ptsG-crr
Neiella marina J221 bglT, cbp, pgmA, glk
Neptunomonas antarctica S3-22 bgl, ptsG-crr
Nocardioides daejeonensis MJ31 bgl, MFS-glucose, glk
Nocardioides dokdonensis FR1436 bgl, MFS-glucose, glk
Nocardiopsis baichengensis YIM 90130 bgl, mglA, mglB, mglC, glk
Nocardiopsis gilva YIM 90087 bgl, MFS-glucose, glk
Novosphingobium barchaimii LL02 bgl, MFS-glucose, glk
Novosphingobium fuchskuhlense FNE08-7 bgl, MFS-glucose, glk
Novosphingobium lindaniclasticum LE124 bgl, MFS-glucose, glk
Oceanisphaera arctica V1-41 bgl, ptsG, crr
Ochrobactrum rhizosphaerae PR17 bgl, mglA, mglB, mglC, glk
Ochrobactrum thiophenivorans DSM 7216 bgl, mglA, mglB, mglC, glk
Oscillibacter ruminantium GH1 bgl, mglA, mglB, mglC, glk
Paenisporosarcina indica PN2 bgl, ptsG-crr
Palaeococcus pacificus DY20341 bgl, ptsG-crr
Paludibacter propionicigenes WB4 bglT, cbp, pgmA, glk
Pandoraea thiooxydans ATSB16 cdt, cbp, pgmA, glk
Pantoea rwandensis LMG 26275 bgl, mglA, mglB, mglC, glk
Pedobacter arcticus A12 bgl, MFS-glucose, glk
Photobacterium gaetbulicola Gung47 bgl, SemiSWEET, glk
Photobacterium jeanii R-40508 bgl, ptsG, crr
Phyllobacterium brassicacearum STM 196 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Phyllobacterium endophyticum PEPV15 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Phyllobacterium leguminum ORS 1419 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Planktomarina temperata RCA23 bgl, mglA, mglB, mglC, glk
Planococcus halocryophilus Or1 bgl, ptsG-crr
Pleomorphomonas diazotrophica R5-392 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Polaribacter dokdonensis DSW-5 bgl, MFS-glucose, glk
Pontibacillus litoralis JSM 072002 bglG, ascB, glk
Pontibacter lucknowensis DM9 bgl, MFS-glucose, glk
Pontibacter ramchanderi LP43 bgl, MFS-glucose, glk
Pontimonas salivibrio CL-TW6 bgl, mglA, mglB, mglC, glk
Porphyrobacter dokdonensis DSW-74 bgl, MFS-glucose, glk
Pseudoalteromonas arctica A 37-1-2 bgl, MFS-glucose, glk
Pseudomonas baetica a390 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas litoralis 2SM5 bgl, ptsG-crr
Pseudomonas taeanensis MS-3 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudovibrio axinellae Ad2 bgl, gtsA, gtsB, gtsC, gtsD, glk
Psychrobacter arcticus 273-4 bgl, ptsG-crr
Psychrobacter cryohalolentis K5 bgl, ptsG-crr
Psychromonas ingrahamii 37 bgl, gtsA, gtsB, gtsC, gtsD, glk
Psychromonas ossibalaenae JAMM 0738 bgl, MFS-glucose, glk
Rhizobium freirei PRF 81 bgl, gtsA, gtsB, gtsC, gtsD, glk
Rhizobium grahamii CCGE 502 bgl, aglE', aglF', aglG', aglK', glk
Rhizobium subbaraonis JC85 bgl, aglE', aglF', aglG', aglK', glk
Rhodanobacter denitrificans 2APBS1 bgl, MFS-glucose, glk
Rhodobacter johrii JA192 bgl, aglE', aglF', aglG', aglK', glk
Rhodobacter maris JA276 bgl, aglE', aglF', aglG', aglK', glk
Rhodobacter ovatus JA234 cdt, cbp, pgmA, glk
Rhodobacter viridis JA737 bgl, aglE', aglF', aglG', aglK', glk
Rhodococcus qingshengii djl-6-2 bgl, MFS-glucose, glk
Rhodopseudomonas pseudopalustris DSM 123 bgl, ptsG-crr
Roseateles aquatilis CCUG 48205 bgl, gtsA, gtsB, gtsC, gtsD, glk
Roseivirga spongicola UST030701-084 bgl, MFS-glucose, glk
Rubrivirga marina SAORIC-28 bgl, MFS-glucose, glk
Ruegeria conchae TW15 bgl, gtsA, gtsB, gtsC, gtsD, glk
Saccharomonospora marina XMU15 cebE, cebF, cebG, msiK, bgl, glk
Salinicoccus carnicancri Crm bglG, ascB, glk
Serinicoccus profundi MCCC 1A05965 bgl, MFS-glucose, glk
Shewanella halifaxensis HAW-EB4 bgl, SSS-glucose, glk
Skermanella stibiiresistens SB22 bgl, mglA, mglB, mglC, glk
Snodgrassella alvi wkB2 bgl, ptsG-crr
Sphaerochaeta globosa Buddy bgl, mglA, mglB, mglC, glk
Sphaerochaeta pleomorpha Grapes bgl, mglA, mglB, mglC, glk
Sphingobium baderi LL03 bgl, MFS-glucose, glk
Sphingobium czechense LL01 bgl, MFS-glucose, glk
Sphingobium quisquiliarum P25 bgl, MFS-glucose, glk
Sphingomonas histidinilytica UM2 cdt, cbp, pgmA, glk
Sphingomonas indica Dd16 cdt, cbp, pgmA, glk
Sphingomonas laterariae LNB2 bgl, MFS-glucose, glk
Sphingopyxis indica DS15 bgl, MFS-glucose, glk
Sphingopyxis terrae UI2 bgl, MFS-glucose, glk
Sporolactobacillus vineae SL153 bgl, manX, manY, manZ
Streptacidiphilus oryzae TH49 bgl, MFS-glucose, glk
Streptococcus anginosus CCUG 39159 celEIIA, celEIIB, celEIIC, ascB, glk
Streptococcus massiliensis 4401825 celEIIA, celEIIB, celEIIC, ascB, glk
Streptococcus oralis 7747 bgl, manX, manY, manZ
Streptococcus oralis AZ_3a bgl, manX, manY, manZ
Streptomyces kebangsaanensis SUK12 bgl, mglA, mglB, mglC, glk
Succinatimonas hippei YIT 12066 bgl, mglA, mglB, mglC, glk
Sulfurimonas gotlandica GD1 bgl, ptsG-crr
Tatumella morbirosei LMG 23360 bgl, mglA, mglB, mglC, glk
Thauera humireducens SgZ-1 cdt, cbp, pgmA, glk
Thermoactinomyces daqus H-18 bglG, ascB, glk
Thermobifida halotolerans YIM 90462 bgl, MFS-glucose, glk
Thermodesulfovibrio aggregans TGE-P1 bgl, SemiSWEET, glk
Thermophagus xiamenensis HS1 bgl, SSS-glucose, glk
Thermovenabulum gondwanense R270 cdt, cbp, pgmA, glk
Thioclava dalianensis DLFJ1-1 bgl, aglE', aglF', aglG', aglK', glk
Thiohalospira halophila HL 3 cdt, cbp, pgmA, glk
Tistlia consotensis USBA 355 bgl, mglA, mglB, mglC, glk
Vagococcus penaei CD276 bglG, ascB, glk
Verminephrobacter eiseniae EF01-2 bgl, mglA, mglB, mglC, glk
Weissella oryzae SG25 bgl, manX, manY, manZ
Williamsia sterculiae CPCC 203464 bgl, MFS-glucose, glk
Yersinia intermedia Y228 bgl, mglA, mglB, mglC, glk

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