-----eLignin database Changelog----- --------------------------- ** 2018-12-20 ** --------------------------- During the autumn of 2018 the following was added to the database ORGANISMS Added 100 new strains: Acetobacterium woodii NZva16 Acinetobacter baumannii KMB1 Acinetobacter junii 5ga Acinetobacter tandoii Van Dexter isolate Agaricus bisporus NRRL-20762 Alcaligenes faecalis KD10 Aromatoleum aromaticum EbN1 Aspergillus flavus F10 Auricularia auricula-judae DSM 11326 Azoarcus anaerobius LuFRes1 Azotobacter vinelandii ATCC 12837 Bacillus cereus KD4 Bacillus sphaericus KD7 Bjerkandera adusta Zi47 Bjerkandera adusta FP-101809 Bjerkandera adusta NBRC 104974 Brettanomyces anomalus NCYC 615 Burkholderia cepacia KK01 Burkholderia cepacia KF12 Burkholderia cepacia Song isolate 1 Burkholderia sp. VE22 Ceriporiopsis subvermispora FP-105752 Citrobacter sp. VA53 Clostridium methoxybenzovorans SR3 Clostridium thermoaceticum ATCC 39073 Comamonas acidovorans KNB3 Comamonas testosteroni BR6020 Cupriavidus laharis 1263a Cupriavidus pinatubonensis 1245 Cyathus pallidus NRRL-6529 Cyathus stercoreus NRRL-6573 Daedalea flavida FR17 Desulfobacterium catecholicum NZva20 Desulfobacterium phenolicum Ph01 Emericella nidulans APF4 Enterobacter sp. DG-6 Flavimonas oryzihabitans Song isolate 4 Haloarcula sp. D1 Haloferax sp. D1227 Haloferax sp. C-24 Halorubrum ezzemoulense C-46 Holophaga foetida TMBS4 Hymenochaete yasudai MAFF420327 Irpex lacteus CD2 Irpex lacteus FP-101234 Klebsiella pneumoniae NX-1(1) Marasmius cryptomeriae TUFC100845 Microbacterium esteraromaticum Song isolate 5 Moraxella sp. GU2 Mycena haematopus Hin 5 Natrialba sp. C21 Nocardia sp. KD19 Ochrobactrum anthropi KD16 Ochrobactrum oryzae BMP03 Ochrobactrum tritici NX-1(3) Oudemansiella venosolamellata NBRC 104979 Pantoea agglomerans T71 Pantoea dispersa Song isolate 2 Papillibacter cinnamivorans CIN1 Pelobacter acidigallici Ma Gal2 (DSM 2377) Petriellidium boydii SP 31-4 Phanerochaete chrysosporium NRRL-6361 (ATCC 24725) Phialophora mutabilis 203-E-15-y-l Phlebia brevispora NRRL-13108 Phlebia radiata K 233 Phlebia tremellosa MAFF420690 Pleurotus eryngii DSM 9619 Polyporus compactus NRRL-A-2351 Pseudomonas citronellolis KMA4 Pseudomonas citronellolis T8 Pseudomonas fluorescens DSM 50090 Pseudomonas plecoglossicida G2 Pseudomonas putida PRS2000 Pseudomonas putida NX-1(2) Pseudomonas putida ORC Pycnoporus cinnabarinus ATCC 200478 Pycnoporus cinnabarinus FP-104138 Pycnoporus sanguineus FP-103506 Rhodococcus erythropolis TA421 Rhodococcus erythropolis 1CP Rhodococcus fascians Song isolate 3 Rhodococcus opacus PD630 (DSMZ 44193) Rhodococcus pyridinivorans CCZU-B16 Rhodococcus rhodochrous 116 Rhodococcus sp. UKMP-5M Rhodopseudomonas palustris CGA001 Rhodotorula glutinis Jain isolate Rhodotorula rubra IFO 889 Rigidoporus lineatus ES-500 Streptomyces sp. ZC2 Streptomyces sp. KS1025A Streptomyces sp. CA2 Stropharia rugosoannulata Zi297 Stropharia rugosoannulata TUFC30865 Sulfuritalea hydrogenivorans sk43H Thauera aromatica K172 Thauera sp. Cin3,4 Trametes gibbosa BEOFB 310 Trametes versicolor NBRC 104985 Trichosporon mucoides SBUG 80 SUBSTRATES Added 16 new substrates: Sawdust lignin Base-catalyzed depolymerized lignin o-cresol anisole maple lignin Agropyron repens grass lignin lignosulfonate Miscanthus grass lignin (Ionic liquid pretreated) Dealkaline lignin cis,cis-muconic acid syringol phenylacetic acid Soda lignin from Japanese cedar Wood chips PATHWAYS Added 3 new pathways: Funneling pathway: p-cresol Funneling pathway: guaiacol Funneling pathway: sinapic acid GENES: Added 16 new genes. Pp_benF (Pseudomonas putida KT2440) Pp_benE1 (Pseudomonas putida KT2440) Pp_benE2 (Pseudomonas putida KT2440) Pp_PcaK (Pseudomonas putida PRS2000) Cg_nagT (Corynebacterium glutamicum ATCC13032) Cg_pcaK (Corynebacterium glutamicum ATCC13032) Cg_vanK (Corynebacterium glutamicum ATCC13032) Cg_benE (Corynebacterium glutamicum ATCC13032) Cg_benK (Corynebacterium glutamicum ATCC13032) Ab_benK (Acinetobacter baylyi ADP1) Ab_mucK (Acinetobacter baylyi ADP1) Ab_vanK (Acinetobacter baylyi ADP1) Ab_pcaK (Acinetobacter baylyi ADP1) Kp_MhbT (Klebsiella pneumoniae M5a1) Am_GcoAB (Amycolatopsis sp. 75iv2 (ATCC 39116)) Str_vdcBCD (Streptomyces sp. D7) TRANSPORT PROTEINS Added 15 new transporters: Pp_benKp Pp_benFp Pp_benE1p Pp_benE2p Cg_nagTp Cg_pcaKp Cg_vanKp Cg_benEp Cg_benKp Pp_pcaKp Ab_benKp Ab_mucKp Ab_vanKp Ab_pcaKp Kp_MhbTp REACTIONS Added 4 new reactions. Guaiacol + O2 + H+ --> Catechol + Formaldehyde + H20 vanillic acid --> vanillic acid sinapic acid + H+ --> syringaldehyde +H2O Syringaldehyde + NAD+ + H2O --> Syringic acid +NADPH +H+ REFERENCES Added 101 new references, belonging to the new entries. --------------------------- ** 2018-06-29 ** --------------------------- During the late spring of 2018 we have made a big effort to add new content to all the section of the database, as well as some overall bug fixing. Below follows the new content that has been added during the last months. ORGANISMS Added 56 new strains: Acinetobacter calcoaceticus DSM 586 Acinetobacter sp. Vasudevan isolate Aeromonas formicans Gupta strain Arthrobacter sp. KB-1 Azotobacter vinelandii NBRC13581 Bacillus ligniniphilus L1 Brevibacillus agri RJH-1 Brevibacillus parabrevis MTCC 1210 Burkholderia cepacia ATCC 29351 Burkholderia sp. H1 Candida albicans CBS562 Candida dubliniensis CBS7987 Candida orthopsilosis MCO457 Candida tropicalis CBS94 Comamonas sp. E6 Comamonas testosteroni CNB-1 Cupriavidus necator ATCC 17697 Cyathus stercoreus ATCC 36910 Dichomitus squalens CBS 432.34 Dysgonomonas sp. WJDL-Y1 Flavobacterium lutescens NBRC3084 Fusarium oxysporum MUCL 30736 Fusarium solani MUCL 35071 Klebsiella sp. LLC-3 Klebsiella sp. BRL6-2 Marinobacterium georgiense KW-40 Microbulbifer hydrolyticus IRE-31 Nematoloma frowardii b19 Nocardia corallina A81 Novosphingobium taihuense T3-B9 Ochrobactrum sp. LLC-2 Pestalotia oxyanthi MUCL 35070 Phanerochaete chrysosporium BKM 1767 Phlebia radiata 79 Phlebia tremellosa 79-16 Pseudomonas alcaligenes NCIMB 9867 Pseudomonas fluorescens PU1 Pseudomonas mira V2 Pseudomonas ochraceae NGJ1 Pseudomonas putida F1 Pseudomonas putida Perestelo isolate 3 Pseudomonas putida mt-2 Pseudomonas putida NCIMB 9866 Pseudomonas sp. Isolate 9.1 Pseudomonas sp. SG-MS2 Pseudomonas sp. LLC-1 Pseudomonas sp. KF704 Pseudomonas sp. MT1 Pseudomonas sp. ITH-SA-1 Rhodosporidium toruloides IFO0880 Serratia liquefaciens LD-5 Serratia marcescens Perestelo isolate 2 Sphingomonas aromaticivorans F199 Sporotrichum pulverulentum ATCC 32629 Tolumonas lignolytica BRL6-1 Trichosporon oleaginosus ATCC 20509 SUBSTRATES Added 41 new substrates: (+)catechin 2,3-dihydroxybenzoic acid 2-hydroxy-2-phenylacetic acid 2-phenylethanol 3-aminophenol 3-hydroxyphenylacetic acid 3-methoxybenzoic acid 4-chloronitrobenzene 4-ethylphenol 4-hydroxyacetophenone 4-hydroxyphenylacetic acid 4-methyl-2,6-dimethoxyphenol 5-phenylvaleric acid acetovanillone aniline conidendrin dehydrodiisoeugenol di(2-ethylhexyl)phthalate (DEHP) ethyl-4-hydroxy-3-methoxycinnamate guaiacolglyceryl ether guaiacylglycerol-beta-guaiacyl ether HCl lignin L-3-phenyllactic acid maize straw m-coumaric acid methyl-vanillate milled wood lignin m-xylene naphthalene Nitrobenzene p-anisic acid p-benzyloxyphenol p-cresol peanut hull lignin phenanthrene phenylheptanoate phenylhexanoate phenyloctanoate phenylpyruvic acid pinoresinol veratrylglycerol-beta-guaiacyl ether PATHWAYS Added a theoretical superpathway map to the Browse Pathways page in order to facilitate for users to find (theoretically) connecting pathways. Added new pathway maps to every pathway. Added 5 new pathways: Funneling pathway: m-cresol Funneling pathway: p-cresol Funneling pathway: salicylic acid I Funneling pathway: syringic acid II Funneling pathway: syringic acid III GENES Added a suffix to each gene to denote the species/strain (e.g. PP_ for Pseudomonas putida KT2400, Ppmt2_ for Pseudomonas putida mt-2). Added 22 new genes. Pa_xylD (Pseudomonas alcaligenes NCIMB 9867) Pae_praC (Paenibacillus sp. JJ-1b) Pae_praD (Paenibacillus sp. JJ-1b) Pp_galB (Pseudomonas putida KT2440) Pp_galC (Pseudomonas putida KT2440) Pp_galD (Pseudomonas putida KT2440) Pp_pchC (Pseudomonas putida NCIMB 9866) Pp_pchF (Pseudomonas putida NCIMB 9866) Ppmt2_xylE (Pseudomonas putida mt-2) Ppmt2_xylG (Pseudomonas putida mt-2) Ppmt2_xylH (Pseudomonas putida mt-2) Psmt1_salA (Pseudomonas sp. MT1) Sph_desA (Sphingobium sp. SYK-6) Sph_desB (Sphingobium sp. SYK-6) Sph_desZ (Sphingobium sp. SYK-6) Sph_ligA (Sphingobium sp. SYK-6) Sph_ligB (Sphingobium sp. SYK-6) Sph_ligC (Sphingobium sp. SYK-6) Sph_ligI (Sphingobium sp. SYK-6) Sph_ligJ (Sphingobium sp. SYK-6) Sph_ligK (Sphingobium sp. SYK-6) Sph_pinZ (Sphingobium sp. SYK-6) ENZYMES Added 12 new enzymes (NB! some of these entries are still work-in-progress). 2-oxo-3-hexenedioate decarboxylase 2-pyrone-4,6-dicarboxylate hydrolase 3-O-methylgallate 3,4-dioxygenase 4-methylphenol methylhydroxylase 4-oxalmesaconate hydratase 4-oxalocrotonate tautomerase benzoate transporter gallate dioxygenase HMG aldolase oxaloacetate decarboxylase salicylate 1-hydroxylase syringate O-demethylase REACTIONS Added 20 new reactions. (2Z,4E)-2-hydroxyhexa-2,4-dienedioate --> (3E)-2-oxohex-3-enedioate (3E)-2-oxohex-3-enedioate + H+ --> (2Z)-2-hydroxypenta-2,4-dienoate + CO2 2-pyrone-4,6-dicarboxylate + H2O --> (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate + H+ 3-hydroxybenzaldehyde + NADP+ + H2O --> 3-hydroxybenzoate + NADPH + 2 H+ 3-hydroxybenzoate + NADPH + oxygen + H+ --> protocatechuate + NADP+ + H2O 3-hydroxybenzyl alcohol + NAD+ --> 3-hydroxybenzaldehyde + NADH + H+ 3-methylphenol + NADH + oxygen + H+ --> 3-hydroxybenzyl alcohol + NAD+ + H2O 3-O-methylgallate + tetrahydrofolate --> gallic acid + 5-methyltetrahydrofolate 3-O-methylgallate + oxygen --> 2-pyrone-4,6-dicarboxylate + methanol + H+ 3-O-methylgallate + oxygen --> 4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + H+ 4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate --> (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate 4-hydroxybenzyl alcohol + 2 azurin (oxidized) --> 4-hydroxybenzaldehyde + 2 azurin (reduced) + 2 H+ gallate + O2 --> (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate + 2 H+ oxaloacetate + H+ --> pyruvate + CO2 p-comaroyl-CoA + H2O --> 4-hydroxybenzaldehyde + acetyl-CoA p-coumaric acid + CoA + ATP --> p-coumaroyl-CoA + AMP + PPi p-cresol + 2 azurin (oxidized) + H2O --> 4-hydroxybenzyl alcohol + 2 azurin (reduced) + 2 H+ (+/-)-pinoresinol + NADPH --> (+/-)-lariciresinol NADP+ salicylic acid + NADH + 2 H+ + oxygen --> catechol + CO2 + NAD+ + H2O syringic acid + tetrahydrofolate --> 3-O-methylgallate + 5-methyltetrahydrofolate REFERENCES Added 78 new references, belonging to the new entries.