GapMind for catabolism of small carbon sources

 

D-cellobiose catabolism

Analysis of pathway cellobiose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 bgl, ptsG-crr
Acidithiobacillus ferrooxidans ATCC 23270 cdt, cbp, pgmA, glk
Acidovorax sp. GW101-3H11 bgl, gtsA, gtsB, gtsC, gtsD, glk
Algiphilus aromaticivorans DG1253 bgl, SSS-glucose, glk
Alicycliphilus denitrificans K601 cdt, cbp, pgmA, glk
Alkalihalobacterium alkalinitrilicum DSM 22532 bgl, ptsG-crr
Allochromatium vinosum DSM 180 bgl, MFS-glucose, glk
Ammonifex degensii KC4 cdt, cbp, pgmA, glk
Anaerobutyricum hallii DSM 3353 bgl, manX, manY, manZ
Aquimarina longa SW024 bgl, ptsG-crr
Archaeoglobus veneficus SNP6 bgl, ptsG-crr
Arcobacter nitrofigilis DSM 7299 bgl, ptsG-crr
Azoarcus olearius BH72 cdt, cbp, pgmA, glk
Azohydromonas australica DSM 1124 bgl, gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571 bgl, MFS-glucose, glk
Azospirillum brasilense Sp245 bgl, mglA, mglB, mglC, glk
Azospirillum sp. B510 bgl, mglA, mglB, mglC, glk
Bacteroides thetaiotaomicron VPI-5482 bgl, SSS-glucose, glk
Beijerinckia indica ATCC 9039 bgl, mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969 bgl, MFS-glucose, glk
Billgrantia desiderata SP1 bgl, gtsA, gtsB, gtsC, gtsD, glk
Bradyrhizobium sp. BTAi1 bgl, mglA, mglB, mglC, glk
Brevundimonas sp. GW460-12-10-14-LB2 bgl, MFS-glucose, glk*
Burkholderia phytofirmans PsJN bgl, gtsA, gtsB, gtsC, gtsD, glk
Burkholderia vietnamiensis G4 bgl, gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672 cdt, cbp, pgmA, glk
Caminibacter mediatlanticus TB-2 bgl, ptsG-crr
Carboxydothermus pertinax Ug1 cdt, cbp, pgmA, glk
Caulobacter crescentus NA1000 bgl, MFS-glucose, glk
Cereibacter sphaeroides ATCC 17029 bgl, aglE', aglF', aglG', aglK', glk
Chlorobaculum parvum NCIB 8327 bgl, SemiSWEET, glk
Chlorobaculum tepidum TLS bgl, SemiSWEET, glk
Chlorobium limicola DSM 245 bgl, SemiSWEET, glk
Chlorobium phaeobacteroides BS1 bgl, SemiSWEET, glk
Clostridium acetobutylicum ATCC 824 bglG, ascB, glk
Clostridium kluyveri DSM 555 cdt, cbp, pgmA, glk
Clostridium tyrobutyricum FAM22553 bgl, ptsG-crr
Crocosphaera subtropica ATCC 51142 bgl, SemiSWEET, glk
Cupriavidus basilensis FW507-4G11 bgl, mglA, mglB, mglC, glk
Dechloromonas agitata is5 cdt, cbp, pgmA, glk
Dechlorosoma suillum PS cdt, cbp, pgmA, glk
Dehalococcoides mccartyi 195 bgl, ptsG-crr
Denitrovibrio acetiphilus DSM 12809 bgl, ptsG-crr
Derxia gummosa DSM 723 bgl, gtsA, gtsB, gtsC, gtsD, glk
Desulfacinum hydrothermale DSM 13146 cdt, cbp, pgmA, glk
Desulfacinum infernum DSM 9756 cdt, cbp, pgmA, glk
Desulfarculus baarsii DSM 2075 cdt, cbp, pgmA, glk
Desulfatibacillum aliphaticivorans DSM 15576 bgl, ptsG-crr
Desulfatiglans anilini DSM 4660 cdt, cbp, pgmA, glk
Desulfitobacterium hafniense DCB-2 cbpC, msdC1, msdC2, cbp, pgmA, glk
Desulfobacca acetoxidans DSM 11109 bgl, ptsG-crr
Desulfobacter vibrioformis DSM 8776 cdt, cbp, pgmA, glk
Desulfogranum mediterraneum DSM 13871 cdt, cbp, pgmA, glk
Desulforamulus ruminis DSM 2154 cbpC, msdC1, msdC2, bgl, glk
Desulfoscipio geothermicus DSM 3669 cdt, cbp, pgmA, glk
Desulfotalea psychrophila LSv54 bgl, MFS-glucose, glk
Desulfovibrio oxyclinae DSM 11498 cdt, cbp, pgmA, glk
Desulfovibrio vulgaris Hildenborough JW710 cdt, cbp, pgmA, glk
Desulfovibrio vulgaris Miyazaki F bgl, ptsG-crr
Desulfurobacterium atlanticum DSM 15668 bgl, ptsG-crr
Desulfuromonas acetexigens cdt, cbp, pgmA, glk
Desulfuromusa kysingii DSM 7343 bgl, ptsG-crr
Dinoroseobacter shibae DFL-12 bgl, aglE', aglF', aglG', aglK', glk
Dyella japonica UNC79MFTsu3.2 bgl, MFS-glucose, glk
Echinicola vietnamensis KMM 6221, DSM 17526 bgl, MFS-glucose, glk
Escherichia coli BW25113 bgl, mglA, mglB, mglC, glk
Ferroglobus placidus DSM 10642 bgl, ptsG-crr
Frankia alni ACN14a cdt, cbp, pgmA, glk
Geobacter metallireducens GS-15 bgl, MFS-glucose, glk
Geotalea uraniireducens Rf4 cdt, cbp, pgmA, glk
Halococcus hamelinensis 100A6 bgl, MFS-glucose, glk
Haloechinothrix alba DSM 45207 bgl, MFS-glucose, glk
Haloferax volcanii DS2 bgl, MFS-glucose, glk
Haloglycomyces albus DSM 45210 bgl, mglA, mglB, mglC, glk
Halorhodospira halophila SL1 cdt, cbp, pgmA, glk
Heliomicrobium modesticaldum Ice1; ATCC 51547 cdt, cbp, pgmA, glk
Herbaspirillum autotrophicum IAM 14942 cdt, cbp, pgmA, glk
Herbaspirillum seropedicae SmR1 bgl, mglA, mglB, mglC, glk
Hippea alviniae EP5-r bgl, ptsG-crr
Hydrogenophaga taeniospiralis NBRC 102512 bgl, gtsA, gtsB, gtsC, gtsD, glk
Hydrogenovibrio halophilus DSM 15072 cdt, cbp, pgmA, glk
Hydrogenovibrio kuenenii DSM 12350 cdt, cbp, pgmA, glk
Hydrogenovibrio marinus DSM 11271 cdt, cbp, pgmA, glk
Hyphomicrobium sulfonivorans WDL6 bgl, MFS-glucose, glk
Klebsiella michiganensis M5al bgl, mglA, mglB, mglC, glk
Klebsiella variicola At-22 bgl, mglA, mglB, mglC, glk
Kyrpidia tusciae DSM 2912 cdt, cbp, pgmA, glk
Leptospirillum ferrooxidans C2-3 bgl, SemiSWEET, glk
Magnetospirillum magneticum AMB-1 bgl, SemiSWEET, glk
Malonomonas rubra DSM 5091 bgl, MFS-glucose, glk
Maridesulfovibrio bastinii DSM 16055 cdt, cbp, pgmA, glk
Maridesulfovibrio zosterae DSM 11974 bgl, MFS-glucose, glk
Marinobacter adhaerens HP15 bgl, gtsA, gtsB, gtsC, gtsD, glk
Mesorhizobium ciceri WSM1271 SMc04256, SMc04257, SMc04258, SMc04259, cbp, pgmA, glk
Methanobacterium lacus AL-21 bgl, ptsG-crr
Methanococcus aeolicus Nankai-3 bgl, ptsG-crr
Methanococcus maripaludis C5 bgl, ptsG-crr
Methanosarcina acetivorans C2A bgl, ptsG-crr
Methanosarcina mazei Go1 bgl, ptsG-crr
Methanospirillum lacunae Ki8-1 bgl, SemiSWEET, glk
Methanothermobacter thermautotrophicus Delta H bgl, ptsG-crr
Methylobacterium nodulans ORS 2060 bgl, ptsG-crr
Methylobacterium sp. 4-46 Apr-46 cdt, cbp, pgmA, glk
Methylocapsa acidiphila B2 bgl, ptsG-crr
Methylocapsa aurea KYG bgl, MFS-glucose, glk
Methylocella silvestris BL2 bgl, ptsG-crr
Methylococcus capsulatus Bath bgl, MFS-glucose, glk
Methylocystis bryophila S285 bgl, SemiSWEET, glk
Methyloferula stellata AR4T bgl, ptsG-crr
Methylohalobius crimeensis 10Ki cdt, cbp, pgmA, glk
Methylomonas methanica MC09 bgl, MFS-glucose, glk
Methylosarcina fibrata AML-C10 bgl, MFS-glucose, glk
Methylotuvimicrobium alcaliphilum 20Z bgl, SSS-glucose, glk
Methylovulum miyakonense HT12 bgl, SemiSWEET, glk
Mycolicibacterium vanbaalenii PYR-1 bgl, MFS-glucose, glk
Nitratifractor salsuginis DSM 16511 bgl, ptsG-crr
Nitratiruptor tergarcus DSM 16512 bgl, ptsG-crr
Nitriliruptor alkaliphilus DSM 45188 bgl, mglA, mglB, mglC, glk
Nocardioides dokdonensis FR1436 bgl, MFS-glucose, glk
Nocardiopsis lucentensis DSM 44048 bgl, MFS-glucose, glk
Nostoc punctiforme ATCC 29133; PCC 73102 bgl, MFS-glucose, glk
Novosphingobium aromaticivorans DSM 12444 bgl, MFS-glucose, glk
Oleispira antarctica bgl, ptsG-crr
Paraburkholderia atlantica CCGE1002 bgl, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 bgl, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia phymatum STM815 bgl, gtsA, gtsB, gtsC, gtsD, glk
Paucidesulfovibrio gracilis DSM 16080 cdt, cbp, pgmA, glk
Pedobacter sp. GW460-11-11-14-LB5 bgl, SSS-glucose, glk
Pelobacter propionicus DSM 2379 bgl, SemiSWEET, glk
Persephonella marina EX-H1 bgl, ptsG-crr
Phaeacidiphilus oryzae TH49 bgl, MFS-glucose, glk
Phaeobacter inhibens BS107 bgl, aglE', aglF', aglG', aglK', glk
Polaromonas naphthalenivorans CJ2 bgl, gtsA, gtsB, gtsC, gtsD, glk
Prosthecochloris aestuarii DSM 271 bgl, SemiSWEET, glk
Pseudarthrobacter sulfonivorans Ar51 bgl, mglA, mglB, mglC, glk
Pseudomonas benzenivorans DSM 8628 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N1B4 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2C3 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E2 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E3 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens GW456-L13 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas putida KT2440 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas stutzeri RCH2 bgl, gtsA, gtsB, gtsC, gtsD, glk
Pyrolobus fumarii 1A bgl, ptsG-crr
Rhizobium etli CFN 42 bgl, gtsA, gtsB, gtsC, gtsD, glk
Rhizobium johnstonii 3841 bgl, aglE', aglF', aglG', aglK', glk
Rhizobium leguminosarum WSM1325 bgl, aglE', aglF', aglG', aglK', glk
Rhizorhabdus wittichii RW1 cdt, cbp, pgmA, glk
Rhodanobacter denitrificans FW104-10B01 bgl, MFS-glucose, glk
Rhodomicrobium vannielii ATCC 17100 bgl, ptsG-crr
Rhodopseudomonas palustris CGA009 bgl, ptsG-crr
Rhodospirillum centenum SW; ATCC 51521 bgl, SemiSWEET, glk
Rhodospirillum rubrum ATCC 11170 bgl, gtsA, gtsB, gtsC, gtsD, glk
Roseburia faecis M72 bgl, mglA, mglB, mglC, glk
Saccharomonospora cyanea NA-134 cebE, cebF, cebG, msiK, bgl, glk
Sedimenticola selenatireducens DSM 17993 cdt, cbp, pgmA, glk
Shewanella amazonensis SB2B bgl, MFS-glucose, glk
Shewanella loihica PV-4 bgl, MFS-glucose, glk
Shewanella oneidensis MR-1 bgl, ptsG, crr
Shewanella sp. ANA-3 bgl, MFS-glucose, glk
Sinorhizobium fredii NGR234 bgl, gtsA, gtsB, gtsC, gtsD, glk
Sinorhizobium medicae WSM419 bgl, aglE', aglF', aglG', aglK', glk
Sinorhizobium meliloti 1021 bgl, aglE', aglF', aglG', aglK', glk
Sphingomonas koreensis DSMZ 15582 bgl, MFS-glucose, glk
Stenotrophomonas chelatiphaga DSM 21508 bgl, MFS-glucose, glk
Steroidobacter denitrificans DSM 18526 cdt, cbp, pgmA, glk
Stutzerimonas stutzeri A1501 bgl, gtsA, gtsB, gtsC, gtsD, glk
Sulfuricurvum kujiense DSM 16994 bgl, ptsG-crr
Sulfurihydrogenibium azorense Az-Fu1 bgl, ptsG-crr
Sulfurihydrogenibium subterraneum DSM 15120 bgl, ptsG-crr
Sulfurimonas denitrificans DSM 1251 bgl, ptsG-crr
Sulfuritalea hydrogenivorans DSM 22779 cdt, cbp, pgmA, glk
Sulfurivirga caldicuralii DSM 17737 cdt, cbp, pgmA, glk
Synechococcus elongatus PCC 7942 bgl, MFS-glucose, glk
Teredinibacter turnerae T7901 bgl, MFS-glucose, glk
Thauera aminoaromatica S2 cdt, cbp, pgmA, glk
Thermithiobacillus tepidarius DSM 3134 cdt, cbp, pgmA, glk
Thermocrinis albus DSM 14484 bgl, ptsG-crr
Thermodesulforhabdus norvegica DSM 9990 cdt, cbp, pgmA, glk
Thermomonospora curvata DSM 43183 bgl, MFS-glucose, glk
Thermovibrio ammonificans HB-1 bgl, ptsG-crr
Thermus aquaticus YT-1 bgl, gtsA, gtsB, gtsC, gtsD, glk
Thioalkalivibrio denitrificans ALJD cdt, cbp, pgmA, glk
Thioalkalivibrio halophilus HL17 cdt, cbp, pgmA, glk
Thioalkalivibrio paradoxus ARh 1 cdt, cbp, pgmA, glk
Thioalkalivibrio thiocyanodenitrificans ARhD 1 cdt, cbp, pgmA, glk
Thiohalomonas denitrificans HLD2 cdt, cbp, pgmA, glk
Thiohalospira halophila HL 3 cdt, cbp, pgmA, glk
Thiomicrorhabdus arctica DSM 13458 cdt, cbp, pgmA, glk
Thiomicrorhabdus chilensis DSM 12352 cdt, cbp, pgmA, glk
Thiomicrospira cyclica ALM1 cdt, cbp, pgmA, glk
Thiomicrospira microaerophila ASL8-2 cdt, cbp, pgmA, glk
Thiomicrospira pelophila DSM 1534 cdt, cbp, pgmA, glk
Thiothrix lacustris DSM 21227 bgl, MFS-glucose, glk
Tistlia consotensis USBA 355 bgl, mglA, mglB, mglC, glk
Trichlorobacter lovleyi SZ bgl, ptsG-crr
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome bgl, mglA, mglB, mglC, glk
Trichormus variabilis ATCC 29413 bgl, SemiSWEET, glk
Xanthobacter autotrophicus Py2 bgl, MFS-glucose, glk
Xenophilus azovorans DSM 13620 bgl, ptsG-crr

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 Apr 09 2024. 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