GapMind for catabolism of small carbon sources

 

D-galacturonate catabolism

Analysis of pathway galacturonate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 exuT, udh, gli, gci, kdgD, dopDH
Acidithiobacillus ferrooxidans ATCC 23270 exuT, uxaC, uxaB, uxaA, kdgK, eda
Acidovorax sp. GW101-3H11 exuT, udh, uxuL, garD, kdgD, dopDH
Algiphilus aromaticivorans DG1253 exuT, udh, gli, gci, kdgD, dopDH
Alicycliphilus denitrificans K601 exuT, udh, uxuL, garD, kdgD, dopDH
Alkalihalobacterium alkalinitrilicum DSM 22532 exuT, uxaC, uxaB, uxaA, kdgK, eda
Allochromatium vinosum DSM 180 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ammonifex degensii KC4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Anaerobutyricum hallii DSM 3353 exuT, uxaC, uxaB, uxaA, kdgK, eda
Aquimarina longa SW024 exuT, udh, gli, gci, kdgD, dopDH
Archaeoglobus veneficus SNP6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Arcobacter nitrofigilis DSM 7299 exuT, udh, uxuL, garD, kdgD, dopDH
Azoarcus olearius BH72 exuT, udh, gli, gci, kdgD, dopDH
Azohydromonas australica DSM 1124 exuT, udh, uxuL, garD, kdgD, dopDH
Azorhizobium caulinodans ORS 571 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Azospirillum brasilense Sp245 exuT, uxaC, uxaB, uxaA, kdgK, eda
Azospirillum sp. B510 exuT, udh, uxuL, garD, kdgD, dopDH
Bacteroides thetaiotaomicron VPI-5482 exuT, uxaC, uxaB, uxaA, kdgK, eda
Beijerinckia indica ATCC 9039 exuT, uxaC, uxaB, uxaA, kdgK, eda
Beijerinckia mobilis UQM 1969 exuT, uxaC, uxaB, uxaA, kdgK, eda
Billgrantia desiderata SP1 exuT, udh, gli, gci, kdgD, dopDH
Bradyrhizobium sp. BTAi1 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Brevundimonas sp. GW460-12-10-14-LB2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Burkholderia phytofirmans PsJN exuT, udh, uxuL, garD, kdgD, dopDH
Burkholderia vietnamiensis G4 exuT, udh, uxuL, garD, kdgD, dopDH
Calditerrivibrio nitroreducens DSM 19672 exuT, uxaC, uxaB, uxaA, kdgK, eda
Caminibacter mediatlanticus TB-2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Carboxydothermus pertinax Ug1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Caulobacter crescentus NA1000 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cereibacter sphaeroides ATCC 17029 exuT, udh, gli, gci, kdgD, dopDH
Chlorobaculum parvum NCIB 8327 exuT, uxaC, uxaB, uxaA, kdgK, eda
Chlorobaculum tepidum TLS exuT, uxaC, uxaB, uxaA, kdgK, eda
Chlorobium limicola DSM 245 exuT, uxaC, uxaB, uxaA, kdgK, eda
Chlorobium phaeobacteroides BS1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Clostridium acetobutylicum ATCC 824 exuT, uxaC, uxaB, uxaA, kdgK, eda
Clostridium kluyveri DSM 555 exuT, uxaC, uxaB, uxaA, kdgK, eda
Clostridium tyrobutyricum FAM22553 exuT, uxaC, uxaB, uxaA, kdgK, eda
Crocosphaera subtropica ATCC 51142 exuT, uxaC, uxaB, uxaA, kdgK, eda
Cupriavidus basilensis FW507-4G11 exuT, udh, uxuL, garD, kdgD, dopDH
Dechloromonas agitata is5 exuT, udh, gli, gci, kdgD, dopDH
Dechlorosoma suillum PS exuT, udh, gli, gci, kdgD, dopDH
Dehalococcoides mccartyi 195 exuT, uxaC, uxaB, uxaA, kdgK, eda
Denitrovibrio acetiphilus DSM 12809 exuT, uxaC, uxaB, uxaA, kdgK, eda
Derxia gummosa DSM 723 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfacinum hydrothermale DSM 13146 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfacinum infernum DSM 9756 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfarculus baarsii DSM 2075 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfatibacillum aliphaticivorans DSM 15576 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfatiglans anilini DSM 4660 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfitobacterium hafniense DCB-2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfobacca acetoxidans DSM 11109 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfobacter vibrioformis DSM 8776 exuT, udh, gli, gci, kdgD, dopDH
Desulfogranum mediterraneum DSM 13871 exuT, udh, gli, gci, kdgD, dopDH
Desulforamulus ruminis DSM 2154 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfoscipio geothermicus DSM 3669 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfotalea psychrophila LSv54 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfovibrio oxyclinae DSM 11498 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfovibrio vulgaris Hildenborough JW710 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfovibrio vulgaris Miyazaki F exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfurobacterium atlanticum DSM 15668 exuT, uxaC, uxaB, uxaA, kdgK, eda
Desulfuromonas acetexigens exuT, udh, gli, gci, kdgD, dopDH
Desulfuromusa kysingii DSM 7343 exuT, udh, gli, gci, kdgD, dopDH
Dinoroseobacter shibae DFL-12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Dyella japonica UNC79MFTsu3.2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Echinicola vietnamensis KMM 6221, DSM 17526 exuT, uxaC, uxaB, uxaA, kdgK, eda
Escherichia coli BW25113 exuT, uxaC, uxaB, uxaA, kdgK, eda
Ferroglobus placidus DSM 10642 exuT, uxaC, uxaB, uxaA, kdgK, eda
Frankia alni ACN14a exuT, udh, gli, gci, kdgD, dopDH
Geobacter metallireducens GS-15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Geotalea uraniireducens Rf4 exuT, udh, gli, gci, kdgD, dopDH
Halococcus hamelinensis 100A6 exuT, uxaC, uxaB, uxaA, kdgK, eda
Haloechinothrix alba DSM 45207 exuT, udh, gli, gci, kdgD, dopDH
Haloferax volcanii DS2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Haloglycomyces albus DSM 45210 exuT, uxaC, uxaB, uxaA, kdgK, eda
Halorhodospira halophila SL1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Heliomicrobium modesticaldum Ice1; ATCC 51547 exuT, uxaC, uxaB, uxaA, kdgK, eda
Herbaspirillum autotrophicum IAM 14942 exuT, uxaC, uxaB, uxaA, kdgK, eda
Herbaspirillum seropedicae SmR1 exuT, udh, uxuL, garD, kdgD, dopDH
Hippea alviniae EP5-r exuT, uxaC, uxaB, uxaA, kdgK, eda
Hydrogenophaga taeniospiralis NBRC 102512 exuT, udh, uxuL, garD, kdgD, dopDH
Hydrogenovibrio halophilus DSM 15072 exuT, uxaC, uxaB, uxaA, kdgK, eda
Hydrogenovibrio kuenenii DSM 12350 exuT, uxaC, uxaB, uxaA, kdgK, eda
Hydrogenovibrio marinus DSM 11271 exuT, uxaC, uxaB, uxaA, kdgK, eda
Hyphomicrobium sulfonivorans WDL6 exuT, udh, gli, gci, kdgD, dopDH
Klebsiella michiganensis M5al exuT, uxaC, uxaB, uxaA, kdgK, eda
Klebsiella variicola At-22 exuT, uxaC, uxaB, uxaA, kdgK, eda
Kyrpidia tusciae DSM 2912 exuT, udh, gli, gci, kdgD, dopDH
Leptospirillum ferrooxidans C2-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Magnetospirillum magneticum AMB-1 exuT, udh, gli, gci, kdgD, dopDH
Malonomonas rubra DSM 5091 exuT, udh, gli, gci, kdgD, dopDH
Maridesulfovibrio bastinii DSM 16055 exuT, uxaC, uxaB, uxaA, kdgK, eda
Maridesulfovibrio zosterae DSM 11974 exuT, uxaC, uxaB, uxaA, kdgK, eda
Marinobacter adhaerens HP15 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mesorhizobium ciceri WSM1271 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanobacterium lacus AL-21 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanococcus aeolicus Nankai-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanococcus maripaludis C5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanosarcina acetivorans C2A exuT, udh, gli, gci, kdgD, dopDH
Methanosarcina mazei Go1 exuT, udh, gli, gci, kdgD, dopDH
Methanospirillum lacunae Ki8-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methanothermobacter thermautotrophicus Delta H exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylobacterium nodulans ORS 2060 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Methylobacterium sp. 4-46 Apr-46 exuT, udh, uxuL, garD, kdgD, dopDH
Methylocapsa acidiphila B2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylocapsa aurea KYG exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylocella silvestris BL2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylococcus capsulatus Bath exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylocystis bryophila S285 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methyloferula stellata AR4T exuT, udh, gli, gci, kdgD, dopDH
Methylohalobius crimeensis 10Ki exuT, udh, gli, gci, kdgD, dopDH
Methylomonas methanica MC09 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylosarcina fibrata AML-C10 exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylotuvimicrobium alcaliphilum 20Z exuT, uxaC, uxaB, uxaA, kdgK, eda
Methylovulum miyakonense HT12 exuT, uxaC, uxaB, uxaA, kdgK, eda
Mycolicibacterium vanbaalenii PYR-1 exuT, udh, gli, gci, kdgD, dopDH
Nitratifractor salsuginis DSM 16511 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nitratiruptor tergarcus DSM 16512 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nitriliruptor alkaliphilus DSM 45188 exuT, udh, gli, gci, kdgD, dopDH
Nocardioides dokdonensis FR1436 exuT, uxaC, uxaB, uxaA, kdgK, eda
Nocardiopsis lucentensis DSM 44048 exuT, udh, gli, gci, kdgD, dopDH
Nostoc punctiforme ATCC 29133; PCC 73102 exuT, uxaC, uxaB, uxaA, kdgK, eda
Novosphingobium aromaticivorans DSM 12444 exuT, uxaC, uxaB, uxaA, kdgK, eda
Oleispira antarctica exuT, uxaC, uxaB, uxaA, kdgK, eda
Paraburkholderia atlantica CCGE1002 exuT, udh, uxuL, garD, kdgD, dopDH
Paraburkholderia bryophila 376MFSha3.1 exuT, udh, uxuL, garD, kdgD, dopDH
Paraburkholderia phymatum STM815 exuT, udh, uxuL, garD, kdgD, dopDH
Paucidesulfovibrio gracilis DSM 16080 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pedobacter sp. GW460-11-11-14-LB5 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pelobacter propionicus DSM 2379 exuT, udh, gli, gci, kdgD, dopDH
Persephonella marina EX-H1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Phaeacidiphilus oryzae TH49 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Phaeobacter inhibens BS107 exuT, uxaC, uxaB, uxaA, kdgK, eda
Polaromonas naphthalenivorans CJ2 exuT, udh, uxuL, garD, kdgD, dopDH
Prosthecochloris aestuarii DSM 271 exuT, uxaC, uxaB, uxaA, kdgK, eda
Pseudarthrobacter sulfonivorans Ar51 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas benzenivorans DSM 8628 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N1B4 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2C3 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E2 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens FW300-N2E3 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas fluorescens GW456-L13 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas putida KT2440 PS417_04205, udh, uxuL, garD, kdgD, dopDH
Pseudomonas simiae WCS417 exuT, udh, uxuL, garD, kdgD, dopDH
Pseudomonas stutzeri RCH2 exuT, udh, uxuL, garD, kdgD, dopDH
Pyrolobus fumarii 1A exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhizobium etli CFN 42 exuT, udh, gli, gci, kdgD, dopDH
Rhizobium johnstonii 3841 exuT, udh, uxuL, garD, kdgD, dopDH
Rhizobium leguminosarum WSM1325 exuT, udh, uxuL, garD, kdgD, dopDH
Rhizorhabdus wittichii RW1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodanobacter denitrificans FW104-10B01 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodomicrobium vannielii ATCC 17100 exuT, uxaC, uxaB, uxaA, kdgK, eda
Rhodopseudomonas palustris CGA009 exuT, udh, gli, gci, kdgD, dopDH
Rhodospirillum centenum SW; ATCC 51521 exuT, udh, gli, gci, kdgD, dopDH
Rhodospirillum rubrum ATCC 11170 exuT, udh, gli, gci, kdgD, dopDH
Roseburia faecis M72 exuT, uxaC, uxaB, uxaA, kdgK, eda
Saccharomonospora cyanea NA-134 exuT, udh, uxuL, garD, kdgD, dopDH
Sedimenticola selenatireducens DSM 17993 exuT, udh, gli, gci, kdgD, dopDH
Shewanella amazonensis SB2B exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella loihica PV-4 exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella oneidensis MR-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Shewanella sp. ANA-3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sinorhizobium fredii NGR234 exuT, udh, gli, gci, kdgD, dopDH
Sinorhizobium medicae WSM419 exuT, udh, gli, gci, kdgD, dopDH
Sinorhizobium meliloti 1021 exuT, udh, gli, gci, kdgD, dopDH
Sphingomonas koreensis DSMZ 15582 exuT, uxaC, uxaB, uxaA, kdgK, eda
Stenotrophomonas chelatiphaga DSM 21508 exuT, uxaC, uxaB, uxaA, kdgK, eda
Steroidobacter denitrificans DSM 18526 exuT, udh, gli, gci, kdgD, dopDH
Stutzerimonas stutzeri A1501 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfuricurvum kujiense DSM 16994 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfurihydrogenibium azorense Az-Fu1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfurihydrogenibium subterraneum DSM 15120 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfurimonas denitrificans DSM 1251 exuT, uxaC, uxaB, uxaA, kdgK, eda
Sulfuritalea hydrogenivorans DSM 22779 exuT, udh, gli, gci, kdgD, dopDH
Sulfurivirga caldicuralii DSM 17737 exuT, uxaC, uxaB, uxaA, kdgK, eda
Synechococcus elongatus PCC 7942 exuT, uxaC, uxaB, uxaA, kdgK, eda
Teredinibacter turnerae T7901 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thauera aminoaromatica S2 exuT, udh, gli, gci, kdgD, dopDH
Thermithiobacillus tepidarius DSM 3134 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermocrinis albus DSM 14484 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermodesulforhabdus norvegica DSM 9990 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermomonospora curvata DSM 43183 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermovibrio ammonificans HB-1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thermus aquaticus YT-1 exuT, udh, gli, gci, kdgD, dopDH
Thioalkalivibrio denitrificans ALJD exuT, uxaC, uxaB, uxaA, kdgK, eda
Thioalkalivibrio halophilus HL17 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thioalkalivibrio paradoxus ARh 1 exuT, udh, gli, gci, kdgD, dopDH
Thioalkalivibrio thiocyanodenitrificans ARhD 1 exuT, udh, gli, gci, kdgD, dopDH
Thiohalomonas denitrificans HLD2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiohalospira halophila HL 3 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiomicrorhabdus arctica DSM 13458 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiomicrorhabdus chilensis DSM 12352 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiomicrospira cyclica ALM1 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiomicrospira microaerophila ASL8-2 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiomicrospira pelophila DSM 1534 exuT, uxaC, uxaB, uxaA, kdgK, eda
Thiothrix lacustris DSM 21227 exuT, uxaC, uxaB, uxaA, kdgK, eda
Tistlia consotensis USBA 355 exuT, udh, gli, gci, kdgD, dopDH
Trichlorobacter lovleyi SZ exuT, udh, gli, gci, kdgD, dopDH
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome exuT, uxaC, uxaB, uxaA, kdgK, eda
Trichormus variabilis ATCC 29413 exuT, udh, gli, gci, kdgD, dopDH
Xanthobacter autotrophicus Py2 exuT, udh, gli, gci, kdgD, dopDH
Xenophilus azovorans DSM 13620 exuT, udh, uxuL, garD, 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.

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