GapMind for catabolism of small carbon sources

 

D-galactose catabolism

Analysis of pathway galactose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 galP, galK, galT, galE, pgmA
Acidithiobacillus ferrooxidans ATCC 23270 galP, galK, galT, galE, pgmA
Acidovorax sp. GW101-3H11 gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
Algiphilus aromaticivorans DG1253 galP, galK, galT, galE, pgmA
Alicycliphilus denitrificans K601 galP, galK, galT, galE, pgmA
Alkalihalobacterium alkalinitrilicum DSM 22532 galP, galK, galT, galE, pgmA
Allochromatium vinosum DSM 180 galP, galK, galT, galE, pgmA
Ammonifex degensii KC4 galP, galK, galT, galE, pgmA
Anaerobutyricum hallii DSM 3353 mglA, mglB, mglC, galK, galT, galE, pgmA
Aquimarina longa SW024 sglS, galK, galT, galE, pgmA
Archaeoglobus veneficus SNP6 galP, galK, galT, galE, pgmA
Arcobacter nitrofigilis DSM 7299 galP, galK, galT, galE, pgmA
Azoarcus olearius BH72 galP, galK, galT, galE, pgmA
Azohydromonas australica DSM 1124 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Azorhizobium caulinodans ORS 571 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Azospirillum brasilense Sp245 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Azospirillum sp. B510 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Bacteroides thetaiotaomicron VPI-5482 galP, galK, galT, galE, pgmA
Beijerinckia indica ATCC 9039 gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
Beijerinckia mobilis UQM 1969 HP1174, galK, galT, galE, pgmA
Billgrantia desiderata SP1 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Bradyrhizobium sp. BTAi1 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Brevundimonas sp. GW460-12-10-14-LB2 sglS, galdh, galactonolactonase, dgoD, dgoK, dgoA
Burkholderia phytofirmans PsJN ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Burkholderia vietnamiensis G4 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Calditerrivibrio nitroreducens DSM 19672 galP, galK, galT, galE, pgmA
Caminibacter mediatlanticus TB-2 galP, galK, galT, galE, pgmA
Carboxydothermus pertinax Ug1 galP, galK, galT, galE, pgmA
Caulobacter crescentus NA1000 HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
Cereibacter sphaeroides ATCC 17029 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Chlorobaculum parvum NCIB 8327 galP, galK, galT, galE, pgmA
Chlorobaculum tepidum TLS galP, galK, galT, galE, pgmA
Chlorobium limicola DSM 245 galP, galK, galT, galE, pgmA
Chlorobium phaeobacteroides BS1 galP, galK, galT, galE, pgmA
Clostridium acetobutylicum ATCC 824 galP, galK, galT, galE, pgmA
Clostridium kluyveri DSM 555 galP, galK, galT, galE, pgmA
Clostridium tyrobutyricum FAM22553 galP, galK, galT, galE, pgmA
Crocosphaera subtropica ATCC 51142 galP, galK, galT, galE, pgmA
Cupriavidus basilensis FW507-4G11 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Dechloromonas agitata is5 galP, galK, galT, galE, pgmA
Dechlorosoma suillum PS galP, galK, galT, galE, pgmA
Dehalococcoides mccartyi 195 galP, galK, galT, galE, pgmA
Denitrovibrio acetiphilus DSM 12809 galP, galK, galT, galE, pgmA
Derxia gummosa DSM 723 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Desulfacinum hydrothermale DSM 13146 galP, galK, galT, galE, pgmA
Desulfacinum infernum DSM 9756 galP, galK, galT, galE, pgmA
Desulfarculus baarsii DSM 2075 galP, galK, galT, galE, pgmA
Desulfatibacillum aliphaticivorans DSM 15576 galP, galK, galT, galE, pgmA
Desulfatiglans anilini DSM 4660 galP, galK, galT, galE, pgmA
Desulfitobacterium hafniense DCB-2 galP, galK, galT, galE, pgmA
Desulfobacca acetoxidans DSM 11109 galP, galK, galT, galE, pgmA
Desulfobacter vibrioformis DSM 8776 galP, galK, galT, galE, pgmA
Desulfogranum mediterraneum DSM 13871 galP, galK, galT, galE, pgmA
Desulforamulus ruminis DSM 2154 galP, galK, galT, galE, pgmA
Desulfoscipio geothermicus DSM 3669 galP, galK, galT, galE, pgmA
Desulfotalea psychrophila LSv54 galP, galK, galT, galE, pgmA
Desulfovibrio oxyclinae DSM 11498 galP, galK, galT, galE, pgmA
Desulfovibrio vulgaris Hildenborough JW710 galP, galK, galT, galE, pgmA
Desulfovibrio vulgaris Miyazaki F galP, galK, galT, galE, pgmA
Desulfurobacterium atlanticum DSM 15668 galP, galK, galT, galE, pgmA
Desulfuromonas acetexigens galP, galK, galT, galE, pgmA
Desulfuromusa kysingii DSM 7343 galP, galK, galT, galE, pgmA
Dinoroseobacter shibae DFL-12 SGLT1, galdh, galactonolactonase, dgoD, dgoK, dgoA
Dyella japonica UNC79MFTsu3.2 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Echinicola vietnamensis KMM 6221, DSM 17526 HP1174, galK, galT, galE, pgmA
Escherichia coli BW25113 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Ferroglobus placidus DSM 10642 galP, galK, galT, galE, pgmA
Frankia alni ACN14a galP, galK, galT, galE, pgmA
Geobacter metallireducens GS-15 galP, galK, galT, galE, pgmA
Geotalea uraniireducens Rf4 galP, galK, galT, galE, pgmA
Halococcus hamelinensis 100A6 galP, galK, galT, galE, pgmA
Haloechinothrix alba DSM 45207 galP, galK, galT, galE, pgmA
Haloferax volcanii DS2 galP, galK, galT, galE, pgmA
Haloglycomyces albus DSM 45210 gguA, gguB, chvE, galK, galT, galE, pgmA
Halorhodospira halophila SL1 galP, galK, galT, galE, pgmA
Heliomicrobium modesticaldum Ice1; ATCC 51547 galP, galK, galT, galE, pgmA
Herbaspirillum autotrophicum IAM 14942 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Herbaspirillum seropedicae SmR1 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Hippea alviniae EP5-r galP, galK, galT, galE, pgmA
Hydrogenophaga taeniospiralis NBRC 102512 gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
Hydrogenovibrio halophilus DSM 15072 galP, galK, galT, galE, pgmA
Hydrogenovibrio kuenenii DSM 12350 galP, galK, galT, galE, pgmA
Hydrogenovibrio marinus DSM 11271 galP, galK, galT, galE, pgmA
Hyphomicrobium sulfonivorans WDL6 galP, galK, galT, galE, pgmA
Klebsiella michiganensis M5al ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Klebsiella variicola At-22 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Kyrpidia tusciae DSM 2912 galP, galK, galT, galE, pgmA
Leptospirillum ferrooxidans C2-3 galP, galK, galT, galE, pgmA
Magnetospirillum magneticum AMB-1 galP, galK, galT, galE, pgmA
Malonomonas rubra DSM 5091 galP, galK, galT, galE, pgmA
Maridesulfovibrio bastinii DSM 16055 galP, galK, galT, galE, pgmA
Maridesulfovibrio zosterae DSM 11974 galP, galK, galT, galE, pgmA
Marinobacter adhaerens HP15 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Mesorhizobium ciceri WSM1271 gguA, gguB, chvE, galdh, galactonolactonase, dgoD, dgoK, dgoA
Methanobacterium lacus AL-21 galP, galK, galT, galE, pgmA
Methanococcus aeolicus Nankai-3 galP, galK, galT, galE, pgmA
Methanococcus maripaludis C5 galP, galK, galT, galE, pgmA
Methanosarcina acetivorans C2A galP, galK, galT, galE, pgmA
Methanosarcina mazei Go1 galP, galK, galT, galE, pgmA
Methanospirillum lacunae Ki8-1 galP, galK, galT, galE, pgmA
Methanothermobacter thermautotrophicus Delta H galP, galK, galT, galE, pgmA
Methylobacterium nodulans ORS 2060 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Methylobacterium sp. 4-46 Apr-46 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Methylocapsa acidiphila B2 galP, galK, galT, galE, pgmA
Methylocapsa aurea KYG galP, galK, galT, galE, pgmA
Methylocella silvestris BL2 galP, galK, galT, galE, pgmA
Methylococcus capsulatus Bath galP, galK, galT, galE, pgmA
Methylocystis bryophila S285 galP, galK, galT, galE, pgmA
Methyloferula stellata AR4T galP, galK, galT, galE, pgmA
Methylohalobius crimeensis 10Ki galP, galK, galT, galE, pgmA
Methylomonas methanica MC09 HP1174, galK, galT, galE, pgmA
Methylosarcina fibrata AML-C10 HP1174, galK, galT, galE, pgmA
Methylotuvimicrobium alcaliphilum 20Z galP, galK, galT, galE, pgmA
Methylovulum miyakonense HT12 galP, galK, galT, galE, pgmA
Mycolicibacterium vanbaalenii PYR-1 galP, galK, galT, galE, pgmA
Nitratifractor salsuginis DSM 16511 galP, galK, galT, galE, pgmA
Nitratiruptor tergarcus DSM 16512 galP, galK, galT, galE, pgmA
Nitriliruptor alkaliphilus DSM 45188 gguA, gguB, chvE, galK, galT, galE, pgmA
Nocardioides dokdonensis FR1436 galP, galK, galT, galE, pgmA
Nocardiopsis lucentensis DSM 44048 galP, galK, galT, galE, pgmA
Nostoc punctiforme ATCC 29133; PCC 73102 galP, galK, galT, galE, pgmA
Novosphingobium aromaticivorans DSM 12444 galP, galK, galT, galE, pgmA
Oleispira antarctica galP, galK, galT, galE, pgmA
Paraburkholderia atlantica CCGE1002 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Paraburkholderia bryophila 376MFSha3.1 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Paraburkholderia phymatum STM815 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Paucidesulfovibrio gracilis DSM 16080 galP, galK, galT, galE, pgmA
Pedobacter sp. GW460-11-11-14-LB5 galP, galK, galT, galE, pgmA
Pelobacter propionicus DSM 2379 galP, galK, galT, galE, pgmA
Persephonella marina EX-H1 galP, galK, galT, galE, pgmA
Phaeacidiphilus oryzae TH49 galP, galK, galT, galE, pgmA
Phaeobacter inhibens BS107 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA
Polaromonas naphthalenivorans CJ2 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Prosthecochloris aestuarii DSM 271 galP, galK, galT, galE, pgmA
Pseudarthrobacter sulfonivorans Ar51 gguA, gguB, chvE, galK, galT, galE, pgmA
Pseudomonas benzenivorans DSM 8628 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Pseudomonas fluorescens FW300-N1B4 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2C3 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2E2 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens FW300-N2E3 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas fluorescens GW456-L13 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas putida KT2440 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Pseudomonas simiae WCS417 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galdh, galactonolactonase, dgoD, dgoK, dgoA
Pseudomonas stutzeri RCH2 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Pyrolobus fumarii 1A galP, galK, galT, galE, pgmA
Rhizobium etli CFN 42 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Rhizobium johnstonii 3841 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Rhizobium leguminosarum WSM1325 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Rhizorhabdus wittichii RW1 galP, galK, galT, galE, pgmA
Rhodanobacter denitrificans FW104-10B01 HP1174, galK, galT, galE, pgmA
Rhodomicrobium vannielii ATCC 17100 galP, galK, galT, galE, pgmA
Rhodopseudomonas palustris CGA009 galP, galK, galT, galE, pgmA
Rhodospirillum centenum SW; ATCC 51521 galP, galK, galT, galE, pgmA
Rhodospirillum rubrum ATCC 11170 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Roseburia faecis M72 mglA, mglB, mglC, galK, galT, galE, pgmA
Saccharomonospora cyanea NA-134 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Sedimenticola selenatireducens DSM 17993 galP, galK, galT, galE, pgmA
Shewanella amazonensis SB2B HP1174, galK, galT, galE, pgmA
Shewanella loihica PV-4 HP1174, galK, galT, galE, pgmA
Shewanella oneidensis MR-1 galP, galK, galT, galE, pgmA
Shewanella sp. ANA-3 ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA
Sinorhizobium fredii NGR234 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Sinorhizobium medicae WSM419 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Sinorhizobium meliloti 1021 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Sphingomonas koreensis DSMZ 15582 HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
Stenotrophomonas chelatiphaga DSM 21508 HP1174, galdh, galactonolactonase, dgoD, dgoK, dgoA
Steroidobacter denitrificans DSM 18526 galP, galK, galT, galE, pgmA
Stutzerimonas stutzeri A1501 PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896, PfGW456L13_1897, galK, galT, galE, pgmA
Sulfuricurvum kujiense DSM 16994 galP, galK, galT, galE, pgmA
Sulfurihydrogenibium azorense Az-Fu1 galP, galK, galT, galE, pgmA
Sulfurihydrogenibium subterraneum DSM 15120 galP, galK, galT, galE, pgmA
Sulfurimonas denitrificans DSM 1251 galP, galK, galT, galE, pgmA
Sulfuritalea hydrogenivorans DSM 22779 galP, galK, galT, galE, pgmA
Sulfurivirga caldicuralii DSM 17737 galP, galK, galT, galE, pgmA
Synechococcus elongatus PCC 7942 galP, galK, galT, galE, pgmA
Teredinibacter turnerae T7901 sglS, galK, galT, galE, pgmA
Thauera aminoaromatica S2 galP, galK, galT, galE, pgmA
Thermithiobacillus tepidarius DSM 3134 galP, galK, galT, galE, pgmA
Thermocrinis albus DSM 14484 galP, galK, galT, galE, pgmA
Thermodesulforhabdus norvegica DSM 9990 galP, galK, galT, galE, pgmA
Thermomonospora curvata DSM 43183 galP, galK, galT, galE, pgmA
Thermovibrio ammonificans HB-1 galP, galK, galT, galE, pgmA
Thermus aquaticus YT-1 galP, galK, galT, galE, pgmA
Thioalkalivibrio denitrificans ALJD galP, galK, galT, galE, pgmA
Thioalkalivibrio halophilus HL17 galP, galK, galT, galE, pgmA
Thioalkalivibrio paradoxus ARh 1 galP, galK, galT, galE, pgmA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 galP, galK, galT, galE, pgmA
Thiohalomonas denitrificans HLD2 galP, galK, galT, galE, pgmA
Thiohalospira halophila HL 3 galP, galK, galT, galE, pgmA
Thiomicrorhabdus arctica DSM 13458 galP, galK, galT, galE, pgmA
Thiomicrorhabdus chilensis DSM 12352 galP, galK, galT, galE, pgmA
Thiomicrospira cyclica ALM1 galP, galK, galT, galE, pgmA
Thiomicrospira microaerophila ASL8-2 galP, galK, galT, galE, pgmA
Thiomicrospira pelophila DSM 1534 galP, galK, galT, galE, pgmA
Thiothrix lacustris DSM 21227 galP, galK, galT, galE, pgmA
Tistlia consotensis USBA 355 ytfQ, ytfR, ytfT, yjtF, galdh, galactonolactonase, dgoD, dgoK, dgoA
Trichlorobacter lovleyi SZ galP, galK, galT, galE, pgmA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome mglA, mglB, mglC, galK, galT, galE, pgmA
Trichormus variabilis ATCC 29413 galP, galK, galT, galE, pgmA
Xanthobacter autotrophicus Py2 galP, galK, galT, galE, pgmA
Xenophilus azovorans DSM 13620 galP, galdh, galactonolactonase, dgoD, dgoK, dgoA

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