GapMind for catabolism of small carbon sources

 

trehalose catabolism

Analysis of pathway trehalose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 thuE, thuF, thuG, thuK, treF, glk
Acidithiobacillus ferrooxidans ATCC 23270 TRET1, PsTP, pgmA, glk
Acidovorax sp. GW101-3H11 treF, gtsA, gtsB, gtsC, gtsD, glk
Algiphilus aromaticivorans DG1253 treF, SSS-glucose, glk
Alicycliphilus denitrificans K601 treF, ptsG-crr
Alkalihalobacterium alkalinitrilicum DSM 22532 treEIIA, treB, treC, glk
Allochromatium vinosum DSM 180 TRET1, PsTP, pgmA, glk
Ammonifex degensii KC4 treF, MFS-glucose, glk
Anaerobutyricum hallii DSM 3353 treF, manX, manY, manZ
Aquimarina longa SW024 treF, ptsG-crr
Archaeoglobus veneficus SNP6 treF, ptsG-crr
Arcobacter nitrofigilis DSM 7299 treF, ptsG-crr
Azoarcus olearius BH72 TRET1, PsTP, pgmA, glk
Azohydromonas australica DSM 1124 treF, gtsA, gtsB, gtsC, gtsD, glk
Azorhizobium caulinodans ORS 571 treF, MFS-glucose, glk
Azospirillum brasilense Sp245 treF, mglA, mglB, mglC, glk
Azospirillum sp. B510 treF, mglA, mglB, mglC, glk
Bacteroides thetaiotaomicron VPI-5482 BT2158, klh, SSS-glucose, glk
Beijerinckia indica ATCC 9039 treF, mglA, mglB, mglC, glk
Beijerinckia mobilis UQM 1969 treF, MFS-glucose, glk
Billgrantia desiderata SP1 treF, gtsA, gtsB, gtsC, gtsD, glk
Bradyrhizobium sp. BTAi1 treF, mglA, mglB, mglC, glk
Brevundimonas sp. GW460-12-10-14-LB2 treF, MFS-glucose, glk*
Burkholderia phytofirmans PsJN treF, gtsA, gtsB, gtsC, gtsD, glk
Burkholderia vietnamiensis G4 treF, gtsA, gtsB, gtsC, gtsD, glk
Calditerrivibrio nitroreducens DSM 19672 TRET1, PsTP, pgmA, glk
Caminibacter mediatlanticus TB-2 treF, ptsG-crr
Carboxydothermus pertinax Ug1 treF, MFS-glucose, glk
Caulobacter crescentus NA1000 treF, MFS-glucose, glk
Cereibacter sphaeroides ATCC 17029 treF, aglE', aglF', aglG', aglK', glk
Chlorobaculum parvum NCIB 8327 treF, SemiSWEET, glk
Chlorobaculum tepidum TLS treF, SemiSWEET, glk
Chlorobium limicola DSM 245 treF, SemiSWEET, glk
Chlorobium phaeobacteroides BS1 treF, SemiSWEET, glk
Clostridium acetobutylicum ATCC 824 treF, manX, manY, manZ
Clostridium kluyveri DSM 555 treEIIA, treB, treC, glk
Clostridium tyrobutyricum FAM22553 treF, ptsG-crr
Crocosphaera subtropica ATCC 51142 thuE, thuF, thuG, thuK, treF, glk
Cupriavidus basilensis FW507-4G11 treF, mglA, mglB, mglC, glk
Dechloromonas agitata is5 TRET1, PsTP, pgmA, glk
Dechlorosoma suillum PS TRET1, PsTP, pgmA, glk
Dehalococcoides mccartyi 195 treF, ptsG-crr
Denitrovibrio acetiphilus DSM 12809 treF, ptsG-crr
Derxia gummosa DSM 723 treF, gtsA, gtsB, gtsC, gtsD, glk
Desulfacinum hydrothermale DSM 13146 TRET1, PsTP, pgmA, glk
Desulfacinum infernum DSM 9756 TRET1, PsTP, pgmA, glk
Desulfarculus baarsii DSM 2075 TRET1, PsTP, pgmA, glk
Desulfatibacillum aliphaticivorans DSM 15576 treF, ptsG-crr
Desulfatiglans anilini DSM 4660 TRET1, PsTP, pgmA, glk
Desulfitobacterium hafniense DCB-2 treF, MFS-glucose, glk
Desulfobacca acetoxidans DSM 11109 treF, ptsG-crr
Desulfobacter vibrioformis DSM 8776 TRET1, PsTP, pgmA, glk
Desulfogranum mediterraneum DSM 13871 treEIIA, treB, treC, glk
Desulforamulus ruminis DSM 2154 treF, ptsG-crr
Desulfoscipio geothermicus DSM 3669 TRET1, PsTP, pgmA, glk
Desulfotalea psychrophila LSv54 treF, MFS-glucose, glk
Desulfovibrio oxyclinae DSM 11498 TRET1, PsTP, pgmA, glk
Desulfovibrio vulgaris Hildenborough JW710 TRET1, PsTP, pgmA, glk
Desulfovibrio vulgaris Miyazaki F treF, ptsG-crr
Desulfurobacterium atlanticum DSM 15668 treF, ptsG-crr
Desulfuromonas acetexigens TRET1, PsTP, pgmA, glk
Desulfuromusa kysingii DSM 7343 treF, ptsG-crr
Dinoroseobacter shibae DFL-12 treF, aglE', aglF', aglG', aglK', glk
Dyella japonica UNC79MFTsu3.2 treF, MFS-glucose, glk
Echinicola vietnamensis KMM 6221, DSM 17526 lacA, lacC, lacB, klh, MFS-glucose, glk
Escherichia coli BW25113 treF, mglA, mglB, mglC, glk
Ferroglobus placidus DSM 10642 treF, ptsG-crr
Frankia alni ACN14a lpqY, thuF, thuG, thuK, treF, glk
Geobacter metallireducens GS-15 treF, MFS-glucose, glk
Geotalea uraniireducens Rf4 TRET1, PsTP, pgmA, glk
Halococcus hamelinensis 100A6 treF, MFS-glucose, glk
Haloechinothrix alba DSM 45207 treF, MFS-glucose, glk
Haloferax volcanii DS2 treF, MFS-glucose, glk
Haloglycomyces albus DSM 45210 treF, mglA, mglB, mglC, glk
Halorhodospira halophila SL1 TRET1, PsTP, pgmA, glk
Heliomicrobium modesticaldum Ice1; ATCC 51547 TRET1, PsTP, pgmA, glk
Herbaspirillum autotrophicum IAM 14942 TRET1, PsTP, pgmA, glk
Herbaspirillum seropedicae SmR1 treF, mglA, mglB, mglC, glk
Hippea alviniae EP5-r treF, ptsG-crr
Hydrogenophaga taeniospiralis NBRC 102512 treF, gtsA, gtsB, gtsC, gtsD, glk
Hydrogenovibrio halophilus DSM 15072 TRET1, PsTP, pgmA, glk
Hydrogenovibrio kuenenii DSM 12350 TRET1, PsTP, pgmA, glk
Hydrogenovibrio marinus DSM 11271 TRET1, PsTP, pgmA, glk
Hyphomicrobium sulfonivorans WDL6 treF, MFS-glucose, glk
Klebsiella michiganensis M5al treF, mglA, mglB, mglC, glk
Klebsiella variicola At-22 treF, mglA, mglB, mglC, glk
Kyrpidia tusciae DSM 2912 TRET1, PsTP, pgmA, glk
Leptospirillum ferrooxidans C2-3 treF, SemiSWEET, glk
Magnetospirillum magneticum AMB-1 treF, SemiSWEET, glk
Malonomonas rubra DSM 5091 treF, MFS-glucose, glk
Maridesulfovibrio bastinii DSM 16055 TRET1, PsTP, pgmA, glk
Maridesulfovibrio zosterae DSM 11974 treF, MFS-glucose, glk
Marinobacter adhaerens HP15 treF, gtsA, gtsB, gtsC, gtsD, glk
Mesorhizobium ciceri WSM1271 treF, aglE', aglF', aglG', aglK', glk
Methanobacterium lacus AL-21 treF, ptsG-crr
Methanococcus aeolicus Nankai-3 treF, ptsG-crr
Methanococcus maripaludis C5 treF, ptsG-crr
Methanosarcina acetivorans C2A treF, ptsG-crr
Methanosarcina mazei Go1 treF, ptsG-crr
Methanospirillum lacunae Ki8-1 treF, SemiSWEET, glk
Methanothermobacter thermautotrophicus Delta H treF, ptsG-crr
Methylobacterium nodulans ORS 2060 treF, ptsG-crr
Methylobacterium sp. 4-46 Apr-46 treF, ptsG-crr
Methylocapsa acidiphila B2 treF, ptsG-crr
Methylocapsa aurea KYG treF, MFS-glucose, glk
Methylocella silvestris BL2 treF, ptsG-crr
Methylococcus capsulatus Bath treF, MFS-glucose, glk
Methylocystis bryophila S285 treF, SemiSWEET, glk
Methyloferula stellata AR4T treF, ptsG-crr
Methylohalobius crimeensis 10Ki thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Methylomonas methanica MC09 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Methylosarcina fibrata AML-C10 lpqY, thuF, thuG, thuK, PsTP, pgmA, glk
Methylotuvimicrobium alcaliphilum 20Z treF, SSS-glucose, glk
Methylovulum miyakonense HT12 treF, SemiSWEET, glk
Mycolicibacterium vanbaalenii PYR-1 treF, MFS-glucose, glk
Nitratifractor salsuginis DSM 16511 treF, ptsG-crr
Nitratiruptor tergarcus DSM 16512 treF, ptsG-crr
Nitriliruptor alkaliphilus DSM 45188 treF, mglA, mglB, mglC, glk
Nocardioides dokdonensis FR1436 thuE, thuF, thuG, thuK, treF, glk
Nocardiopsis lucentensis DSM 44048 thuE, thuF, thuG, thuK, treF, glk
Nostoc punctiforme ATCC 29133; PCC 73102 treF, MFS-glucose, glk
Novosphingobium aromaticivorans DSM 12444 treF, MFS-glucose, glk
Oleispira antarctica treF, ptsG-crr
Paraburkholderia atlantica CCGE1002 treF, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia bryophila 376MFSha3.1 treF, gtsA, gtsB, gtsC, gtsD, glk
Paraburkholderia phymatum STM815 treF, gtsA, gtsB, gtsC, gtsD, glk
Paucidesulfovibrio gracilis DSM 16080 TRET1, PsTP, pgmA, glk
Pedobacter sp. GW460-11-11-14-LB5 lacA, lacC, lacB, klh, SSS-glucose, glk
Pelobacter propionicus DSM 2379 treF, SemiSWEET, glk
Persephonella marina EX-H1 treF, ptsG-crr
Phaeacidiphilus oryzae TH49 treF, MFS-glucose, glk
Phaeobacter inhibens BS107 treF, aglE', aglF', aglG', aglK', glk
Polaromonas naphthalenivorans CJ2 treF, gtsA, gtsB, gtsC, gtsD, glk
Prosthecochloris aestuarii DSM 271 treF, SemiSWEET, glk
Pseudarthrobacter sulfonivorans Ar51 treF, mglA, mglB, mglC, glk
Pseudomonas benzenivorans DSM 8628 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N1B4 treEIIA, treB, treC, glk
Pseudomonas fluorescens FW300-N2C3 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E2 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas fluorescens FW300-N2E3 treEIIA, treB, treC, glk
Pseudomonas fluorescens GW456-L13 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas putida KT2440 treF, gtsA, gtsB, gtsC, gtsD, glk
Pseudomonas simiae WCS417 treEIIA, treB, treC, glk
Pseudomonas stutzeri RCH2 treF, gtsA, gtsB, gtsC, gtsD, glk
Pyrolobus fumarii 1A treF, ptsG-crr
Rhizobium etli CFN 42 treF, gtsA, gtsB, gtsC, gtsD, glk
Rhizobium johnstonii 3841 treF, aglE', aglF', aglG', aglK', glk
Rhizobium leguminosarum WSM1325 treF, aglE', aglF', aglG', aglK', glk
Rhizorhabdus wittichii RW1 TRET1, PsTP, pgmA, glk
Rhodanobacter denitrificans FW104-10B01 treF, MFS-glucose, glk
Rhodomicrobium vannielii ATCC 17100 treF, ptsG-crr
Rhodopseudomonas palustris CGA009 treF, ptsG-crr
Rhodospirillum centenum SW; ATCC 51521 thuE, thuF, thuG, thuK, treF, glk
Rhodospirillum rubrum ATCC 11170 treF, gtsA, gtsB, gtsC, gtsD, glk
Roseburia faecis M72 malF, malG, malK, malX, PsTP, pgmA, glk
Saccharomonospora cyanea NA-134 thuE, thuF, thuG, thuK, treF, glk
Sedimenticola selenatireducens DSM 17993 TRET1, PsTP, pgmA, glk
Shewanella amazonensis SB2B treF, MFS-glucose, glk
Shewanella loihica PV-4 treF, MFS-glucose, glk
Shewanella oneidensis MR-1 treF, ptsG, crr
Shewanella sp. ANA-3 treF, MFS-glucose, glk
Sinorhizobium fredii NGR234 treF, gtsA, gtsB, gtsC, gtsD, glk
Sinorhizobium medicae WSM419 treF, aglE', aglF', aglG', aglK', glk
Sinorhizobium meliloti 1021 treF, aglE', aglF', aglG', aglK', glk
Sphingomonas koreensis DSMZ 15582 treF, MFS-glucose, glk
Stenotrophomonas chelatiphaga DSM 21508 treF, MFS-glucose, glk
Steroidobacter denitrificans DSM 18526 TRET1, PsTP, pgmA, glk
Stutzerimonas stutzeri A1501 treF, gtsA, gtsB, gtsC, gtsD, glk
Sulfuricurvum kujiense DSM 16994 treF, ptsG-crr
Sulfurihydrogenibium azorense Az-Fu1 treF, ptsG-crr
Sulfurihydrogenibium subterraneum DSM 15120 treF, ptsG-crr
Sulfurimonas denitrificans DSM 1251 treF, ptsG-crr
Sulfuritalea hydrogenivorans DSM 22779 treF, MFS-glucose, glk
Sulfurivirga caldicuralii DSM 17737 TRET1, PsTP, pgmA, glk
Synechococcus elongatus PCC 7942 thuE, thuF, thuG, thuK, PsTP, pgmA, glk
Teredinibacter turnerae T7901 treF, MFS-glucose, glk
Thauera aminoaromatica S2 treF, ptsG-crr
Thermithiobacillus tepidarius DSM 3134 TRET1, PsTP, pgmA, glk
Thermocrinis albus DSM 14484 treF, ptsG-crr
Thermodesulforhabdus norvegica DSM 9990 TRET1, PsTP, pgmA, glk
Thermomonospora curvata DSM 43183 treF, MFS-glucose, glk
Thermovibrio ammonificans HB-1 treF, ptsG-crr
Thermus aquaticus YT-1 treF, gtsA, gtsB, gtsC, gtsD, glk
Thioalkalivibrio denitrificans ALJD TRET1, PsTP, pgmA, glk
Thioalkalivibrio halophilus HL17 treF, ptsG-crr
Thioalkalivibrio paradoxus ARh 1 TRET1, PsTP, pgmA, glk
Thioalkalivibrio thiocyanodenitrificans ARhD 1 TRET1, PsTP, pgmA, glk
Thiohalomonas denitrificans HLD2 thuE, thuF, thuG, thuK, treF, glk
Thiohalospira halophila HL 3 TRET1, PsTP, pgmA, glk
Thiomicrorhabdus arctica DSM 13458 TRET1, PsTP, pgmA, glk
Thiomicrorhabdus chilensis DSM 12352 TRET1, PsTP, pgmA, glk
Thiomicrospira cyclica ALM1 TRET1, PsTP, pgmA, glk
Thiomicrospira microaerophila ASL8-2 TRET1, PsTP, pgmA, glk
Thiomicrospira pelophila DSM 1534 TRET1, PsTP, pgmA, glk
Thiothrix lacustris DSM 21227 TRET1, PsTP, pgmA, glk
Tistlia consotensis USBA 355 treF, mglA, mglB, mglC, glk
Trichlorobacter lovleyi SZ treF, ptsG-crr
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome treF, mglA, mglB, mglC, glk
Trichormus variabilis ATCC 29413 treF, SemiSWEET, glk
Xanthobacter autotrophicus Py2 treF, MFS-glucose, glk
Xenophilus azovorans DSM 13620 TRET1, PsTP, pgmA, 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 Apr 09 2024. 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