GapMind for catabolism of small carbon sources

 

L-fucose catabolism

Analysis of pathway fucose in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Acidithiobacillus ferrooxidans ATCC 23270 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Acidovorax sp. GW101-3H11 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Algiphilus aromaticivorans DG1253 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Alicycliphilus denitrificans K601 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Alkalihalobacterium alkalinitrilicum DSM 22532 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Allochromatium vinosum DSM 180 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Ammonifex degensii KC4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Anaerobutyricum hallii DSM 3353 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Aquimarina longa SW024 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Archaeoglobus veneficus SNP6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Arcobacter nitrofigilis DSM 7299 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Azoarcus olearius BH72 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Azohydromonas australica DSM 1124 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Azorhizobium caulinodans ORS 571 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Azospirillum brasilense Sp245 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Azospirillum sp. B510 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bacteroides thetaiotaomicron VPI-5482 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Beijerinckia indica ATCC 9039 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Beijerinckia mobilis UQM 1969 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Billgrantia desiderata SP1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bradyrhizobium sp. BTAi1 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Brevundimonas sp. GW460-12-10-14-LB2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Burkholderia phytofirmans PsJN BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Burkholderia vietnamiensis G4 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Calditerrivibrio nitroreducens DSM 19672 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Caminibacter mediatlanticus TB-2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Carboxydothermus pertinax Ug1 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Caulobacter crescentus NA1000 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cereibacter sphaeroides ATCC 17029 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Chlorobaculum parvum NCIB 8327 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chlorobaculum tepidum TLS fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chlorobium limicola DSM 245 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Chlorobium phaeobacteroides BS1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Clostridium acetobutylicum ATCC 824 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Clostridium kluyveri DSM 555 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Clostridium tyrobutyricum FAM22553 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Crocosphaera subtropica ATCC 51142 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cupriavidus basilensis FW507-4G11 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Dechloromonas agitata is5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dechlorosoma suillum PS fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dehalococcoides mccartyi 195 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Denitrovibrio acetiphilus DSM 12809 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Derxia gummosa DSM 723 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfacinum hydrothermale DSM 13146 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfacinum infernum DSM 9756 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfarculus baarsii DSM 2075 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfatibacillum aliphaticivorans DSM 15576 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfatiglans anilini DSM 4660 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfitobacterium hafniense DCB-2 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfobacca acetoxidans DSM 11109 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfobacter vibrioformis DSM 8776 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfogranum mediterraneum DSM 13871 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulforamulus ruminis DSM 2154 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfoscipio geothermicus DSM 3669 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfotalea psychrophila LSv54 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfovibrio oxyclinae DSM 11498 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfovibrio vulgaris Hildenborough JW710 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfovibrio vulgaris Miyazaki F fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfurobacterium atlanticum DSM 15668 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfuromonas acetexigens fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfuromusa kysingii DSM 7343 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dinoroseobacter shibae DFL-12 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dyella japonica UNC79MFTsu3.2 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Echinicola vietnamensis KMM 6221, DSM 17526 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Escherichia coli BW25113 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Ferroglobus placidus DSM 10642 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Frankia alni ACN14a fucP, fucU, fucI, fucK, fucA, tpi, fucO
Geobacter metallireducens GS-15 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Geotalea uraniireducens Rf4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halococcus hamelinensis 100A6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Haloechinothrix alba DSM 45207 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Haloferax volcanii DS2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Haloglycomyces albus DSM 45210 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Halorhodospira halophila SL1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Heliomicrobium modesticaldum Ice1; ATCC 51547 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Herbaspirillum autotrophicum IAM 14942 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Herbaspirillum seropedicae SmR1 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Hippea alviniae EP5-r fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hydrogenophaga taeniospiralis NBRC 102512 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Hydrogenovibrio halophilus DSM 15072 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hydrogenovibrio kuenenii DSM 12350 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hydrogenovibrio marinus DSM 11271 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Hyphomicrobium sulfonivorans WDL6 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Klebsiella michiganensis M5al fucP, fucU, fucI, fucK, fucA, tpi, aldA
Klebsiella variicola At-22 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Kyrpidia tusciae DSM 2912 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Leptospirillum ferrooxidans C2-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Magnetospirillum magneticum AMB-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Malonomonas rubra DSM 5091 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Maridesulfovibrio bastinii DSM 16055 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Maridesulfovibrio zosterae DSM 11974 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinobacter adhaerens HP15 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Mesorhizobium ciceri WSM1271 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Methanobacterium lacus AL-21 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanococcus aeolicus Nankai-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanococcus maripaludis C5 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanosarcina acetivorans C2A fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanosarcina mazei Go1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanospirillum lacunae Ki8-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methanothermobacter thermautotrophicus Delta H fucP, fucU, fucI, fucK, fucA, tpi, fucO
Methylobacterium nodulans ORS 2060 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylobacterium sp. 4-46 Apr-46 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylocapsa acidiphila B2 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Methylocapsa aurea KYG fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylocella silvestris BL2 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Methylococcus capsulatus Bath fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylocystis bryophila S285 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methyloferula stellata AR4T fucP, fucU, fucI, fucK, fucA, tpi, fucO
Methylohalobius crimeensis 10Ki fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylomonas methanica MC09 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylosarcina fibrata AML-C10 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylotuvimicrobium alcaliphilum 20Z fucP, fucU, fucI, fucK, fucA, tpi, aldA
Methylovulum miyakonense HT12 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Mycolicibacterium vanbaalenii PYR-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nitratifractor salsuginis DSM 16511 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nitratiruptor tergarcus DSM 16512 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nitriliruptor alkaliphilus DSM 45188 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Nocardioides dokdonensis FR1436 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nocardiopsis lucentensis DSM 44048 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Nostoc punctiforme ATCC 29133; PCC 73102 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Novosphingobium aromaticivorans DSM 12444 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Oleispira antarctica fucP, fucU, fucI, fucK, fucA, tpi, aldA
Paraburkholderia atlantica CCGE1002 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Paraburkholderia bryophila 376MFSha3.1 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Paraburkholderia phymatum STM815 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Paucidesulfovibrio gracilis DSM 16080 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Pedobacter sp. GW460-11-11-14-LB5 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pelobacter propionicus DSM 2379 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Persephonella marina EX-H1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Phaeacidiphilus oryzae TH49 BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Phaeobacter inhibens BS107 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Polaromonas naphthalenivorans CJ2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Prosthecochloris aestuarii DSM 271 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudarthrobacter sulfonivorans Ar51 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas benzenivorans DSM 8628 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N1B4 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N2C3 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pseudomonas fluorescens FW300-N2E2 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N2E3 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens GW456-L13 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas putida KT2440 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas simiae WCS417 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas stutzeri RCH2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pyrolobus fumarii 1A fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhizobium etli CFN 42 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhizobium johnstonii 3841 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhizobium leguminosarum WSM1325 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Rhizorhabdus wittichii RW1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodanobacter denitrificans FW104-10B01 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodomicrobium vannielii ATCC 17100 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodopseudomonas palustris CGA009 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Rhodospirillum centenum SW; ATCC 51521 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Rhodospirillum rubrum ATCC 11170 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Roseburia faecis M72 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Saccharomonospora cyanea NA-134 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sedimenticola selenatireducens DSM 17993 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella amazonensis SB2B fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella loihica PV-4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella oneidensis MR-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella sp. ANA-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sinorhizobium fredii NGR234 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sinorhizobium medicae WSM419 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sinorhizobium meliloti 1021 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sphingomonas koreensis DSMZ 15582 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Stenotrophomonas chelatiphaga DSM 21508 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Steroidobacter denitrificans DSM 18526 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Stutzerimonas stutzeri A1501 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfuricurvum kujiense DSM 16994 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfurihydrogenibium azorense Az-Fu1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfurihydrogenibium subterraneum DSM 15120 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfurimonas denitrificans DSM 1251 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfuritalea hydrogenivorans DSM 22779 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sulfurivirga caldicuralii DSM 17737 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Synechococcus elongatus PCC 7942 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Teredinibacter turnerae T7901 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Thauera aminoaromatica S2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermithiobacillus tepidarius DSM 3134 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermocrinis albus DSM 14484 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermodesulforhabdus norvegica DSM 9990 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Thermomonospora curvata DSM 43183 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermovibrio ammonificans HB-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thermus aquaticus YT-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thioalkalivibrio denitrificans ALJD fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thioalkalivibrio halophilus HL17 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thioalkalivibrio paradoxus ARh 1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thioalkalivibrio thiocyanodenitrificans ARhD 1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiohalomonas denitrificans HLD2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiohalospira halophila HL 3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiomicrorhabdus arctica DSM 13458 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiomicrorhabdus chilensis DSM 12352 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiomicrospira cyclica ALM1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiomicrospira microaerophila ASL8-2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiomicrospira pelophila DSM 1534 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Thiothrix lacustris DSM 21227 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Tistlia consotensis USBA 355 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Trichlorobacter lovleyi SZ fucP, fucU, fucI, fucK, fucA, tpi, aldA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome fucP, fucU, fucI, fucK, fucA, tpi, aldA
Trichormus variabilis ATCC 29413 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Xanthobacter autotrophicus Py2 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Xenophilus azovorans DSM 13620 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase

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