GapMind for catabolism of small carbon sources

 

D-glucuronate catabolism

Analysis of pathway glucuronate in 201 genomes

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

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