Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia

Proposed metabolic pathway for Fe(III)-mediated methanotrophic BNF by the methanotroph/methylotroph; Ru-5P: ribulose 5-phosphate, H6P: hexose 6-phosphate, F6P: fructose 6-phosphate, F1,6P: fructose 1,6-bisphosphate, GAP: glyceraldehyde 3-phosphate, 1,3-BPG: 1,3-bisphosphoglycerate, 3PG: 3-phosphoglycerate, 2PG: 2-phosphoglycerate, PEP: phosphoenolpyruvate, G6P: glucose-6-phosphate, 6PGL: 6-phosphogluconolactone, 6PG: 6-phosphogluconate, KDPG: 2-keto-3-deoxy-6-phosphogluconate, DHBP: 3,4-dihydroxy-2-butanone 4-phosphate, DMRL: 6,7-dimethyl-8-ribityllumazine, FMN: flavin mononucleotide, FAD: flavin adenine dinucleotide, FldHq/FldSq: flavodoxin hydroquinone/semiquinone, RFox/RFred: oxidized/reduced riboflavin, H4F: tetrahydrofolate, H4MPT: methenyltetrahydromethanopterin, Fe-Mbn: Fe-bound methanobactin
Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia
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Publication

Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia (2024) Linpeng Yu, et al. ISME Commun. 2024 Jan;4(1). Figure: F5.

Gene mentions


Organism Group Word Match Source NCBI Symbol NCBI ID
Homo sapiens Primates pyk PYK ncbigene_synonym PHKA2 5256
Homo sapiens Primates eno ENO famplex_relations ENO1 2023
Homo sapiens Primates eno ENO famplex_relations ENO2 2026
Homo sapiens Primates eno ENO famplex_relations ENO3 2027
Homo sapiens Primates eno ENO famplex_relations ENO4 387712
Homo sapiens Primates PEP PEP ncbigene_synonym PAEP 5047
Homo sapiens Primates PEP PEP ncbigene_synonym PREP 5550
Homo sapiens Primates PEP PEP ncbigene_synonym PTPN22 26191
Homo sapiens Primates eda EDA ncbigene_symbol EDA 1896
Homo sapiens Primates edd EDD ncbigene_synonym UBR5 51366
Homo sapiens Primates ace ACE ncbigene_symbol ACE 1636
Homo sapiens Primates GAP GAP ncbigene_synonym RASA1 5921
Homo sapiens Primates GAP GAP ncbigene_synonym RGS6 9628
Homo sapiens Primates FAD FAD ncbigene_synonym BRCA2 675
Homo sapiens Primates FAD FAD ncbigene_synonym FANCD2 2177
Homo sapiens Primates FAD FAD ncbigene_synonym PSEN1 5663
Homo sapiens Primates FMN FMN ncbigene_synonym FMN1 342184
Homo sapiens Primates fba FBA ncbigene_synonym FBXO3 26273
Homo sapiens Primates pgl PGL ncbigene_synonym SDHD 6392
Homo sapiens Primates pgl PGI ncbigene_synonym BGN 633
Homo sapiens Primates pgl PGI ncbigene_synonym GPI 2821
Homo sapiens Primates pgl PGI ncbigene_synonym PGPEP1 54858
Homo sapiens Primates pfk PFK famplex_relations PFKL 5211
Homo sapiens Primates pfk PFK famplex_relations PFKM 5213
Homo sapiens Primates pfk PFK famplex_relations PFKP 5214
Homo sapiens Primates 6PGL 6PGL ncbigene_synonym PGLS 25796
Homo sapiens Primates hps HPS ncbigene_synonym FGL1 2267
Homo sapiens Primates hps HPS ncbigene_synonym HPS1 3257
Homo sapiens Primates hps HPS ncbigene_synonym AP3B1 8546
Homo sapiens Primates mdh MDH ncbigene_synonym MDH2 4191
Homo sapiens Primates mxa MXA ncbigene_synonym MX1 4599
Homo sapiens Primates HCHO HCHO ncbigene_synonym BAAT 570
Homo sapiens Primates cyc CYC ncbigene_synonym CYCS 54205
Homo sapiens Primates UQCR UQCR ncbigene_synonym UQCR11 10975
Homo sapiens Primates fae FAE ncbigene_synonym FANCE 2178
Homo sapiens Primates fae FAE ncbigene_synonym ELOVL6 79071
Homo sapiens Primates glyA GLYA ncbigene_synonym SHMT2 6472
Homo sapiens Primates mtd MTD ncbigene_synonym MT1E 4493
Homo sapiens Primates hpr HPR ncbigene_symbol HPR 3250
Homo sapiens Primates CHH CHH ncbigene_synonym RMRP 6023
Homo sapiens Primates mch MCH ncbigene_synonym PMCH 5367
Homo sapiens Primates gck GCK ncbigene_symbol GCK 2645
Homo sapiens Primates gck GCK ncbigene_synonym MAP4K2 5871
Homo sapiens Primates gck GCK ncbigene_synonym FAM20C 56975
Homo sapiens Primates mcl MCL ncbigene_synonym FH 2271
Homo sapiens Primates mcl MCL ncbigene_synonym CLEC4D 338339
Homo sapiens Primates mcl MCI ncbigene_synonym MCIDAS 345643
Homo sapiens Primates ●●fix FIX ncbigene_synonym F9 2158
Homo sapiens Primates ●●fix FIX ncbigene_synonym AK3 50808
Homo sapiens Primates ppo PPO ncbigene_synonym PPOX 5498
Homo sapiens Primates fdh FDH ncbigene_synonym ADH5 128
Homo sapiens Primates fdh FDH ncbigene_synonym ALDH1L1 10840
Homo sapiens Primates nif NIF ncbigene_synonym S100A8 6279
Homo sapiens Primates nif NIF ncbigene_synonym S100A9 6280

Chemical mentions

Word Match MeSH Name ChEBI
Pyruvate pyruvate pyruvate chebi:15361
PEP PEP 2-(phosphonooxy)prop-2-enoic acid chebi:44897
Lactate lactate lactate chebi:24996
Riboflavin riboflavin 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-D-ribitol chebi:57986
edd EDD L-alpha-glutamyl-L-alpha-aspartyl-L-aspartic acid chebi:156328
GAP GAP 2-hydroxy-3-oxopropyl dihydrogen phosphate chebi:17138
FAD FAD L-phenylalanyl-L-alanyl-L-aspartic acid chebi:73627
FMN FMN 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-2H-benzo[g]pteridin-3-id-10(4H)-yl)-5-O-phosphonato-D-ribitol chebi:58210
Acetate acetate acetate chebi:30089
hps HPS chebi:85516
Fe(III) Fe(III) iron(3+) ion chebi:29034
amo AMO (2R)-2-{[(2R)-2-amino-2-(4-hydroxyphenyl)acetyl]amino}-2-[(2R,4S)-4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl]acetyl chebi:53705
NAD NAD adenosine 5'-{3-[1-(3-carbamoylpyridinio)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} chebi:15846
Quinone Quinone cyclohexa-2,5-diene-1,4-dione chebi:16509
Fe(II) Fe(II) iron(2+) chebi:29033
Glycine glycine 2-azaniumylacetate chebi:57305
NADH NADH adenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] diphosphate} chebi:57945
Glyoxylate glyoxylate glyoxylate chebi:36655
mch MCH chebi:88428
Fe(II) Fe(II) iron(2+) chebi:29033
Serine Serine L-serine chebi:17115
PEP PEP 2-(phosphonooxy)prop-2-enoic acid chebi:44897
L-malate L-malate (2S)-2-hydroxybutanedioate chebi:15589
Pyruvate pyruvate pyruvate chebi:15361
acetyl-CoA acetyl-CoA 3'-phosphonatoadenosine 5'-(3-{(3R)-4-[(3-{[2-(acetylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl} diphosphate) chebi:57288
HCOOH HCOOH formic acid chebi:30751
Nitrogen nitrogen nitrogen chebi:25555
NAD NAD adenosine 5'-{3-[1-(3-carbamoylpyridinio)-1,4-anhydro-D-ribitol-5-yl] dihydrogen diphosphate} chebi:15846
NADH NADH adenosine 5'-{3-[1-(3-carbamoyl-1,4-dihydropyridin-1-yl)-1,4-anhydro-D-ribitol-5-yl] diphosphate} chebi:57945

Disease mentions

Word Match MeSH Name DOID