2026 Metabolic Analyses

Putative napA-like nitrate reductase
Mol* Viewer alignment anchored by 4 cysteine residues coordinating a 4Fe-4S cluster. A central pocket accomodates a molybdenum atom bound by two molybdopterin guanine dinucleotide (MGD) molecules.
FJG1 nitrate reductase: alphafold AF-A0A126T3J1-F1 (prediction), pLDDT confidence >90%, blue
E. coli napA: PDB 2NYA (x-ray), emerald

Nitrogen Inventory - AMS
Gene regulatory network connections related to nitrogen cycling under oxygen limitation in Ammonium Mineral Salts (AMS) medium.

Nitrogen Inventory - NMS
Gene regulatory network connections related to nitrogen cycling under oxygen limitation in Nitrate Mineral Salts (NMS) medium.

2025 ProGRN_FJG1

Select a link below to view a subnetwork of the FJG1 GRN in a browser window.

ProGRN_FJG1_Subnetwork_1k
Top 1,000 network connections, determined by max differential expression between time points 24 h (oxic) and 48 h (hypoxic) experimental conditions. The smaller size of this network enables a search feature that is not possible with the larger networks. Also included on this page is an extended menu of customizable options.

ProGRN_FJG1_Subnetwork_10k
Top 10,000 network connections, determined by max differential expression between time points 24 h (oxic) and 48 h (hypoxic) experimental conditions.

Interactive visualization
Lines represent connections between regulator and target genes. Red circles denote regulator genes. Blue circles denote target genes linked under hypoxia with supplemental nitrate. Yellow circles denote target genes linked under hypoxia with supplemental ammonium. Green circles denote target genes with connections found under hypoxia in both nitrate and ammonium supplemented growth conditions. Nodes are labeled with the gene locus annotations from M. denitrificans FJG1 (GenBank ID CP014476).

In the visualization window
Hover over a gene node to see gene locus and functional information.
Click on a node to highlight subnetwork connections.
Click on a node and drag to reshape the visualization.

Below the visualization window, in the Physics menu
To stabilize the network view, uncheck the "enabled" box.
Experiment with the Physics settings to reorganize and customize the visualization.

All network visualizations were created using Pyvis 9.1.2 (Csardi and Nepusz 2001). Transcriptome from Kits KD, Klotz MG, Stein LY. 2015. Methane oxidation coupled to nitrate reduction under hypoxia by the Gammaproteobacterium Methylomonas denitrificans, sp. nov. type strain FJG1: Denitrifying metabolism in M. denitrificans FJG1. Environmental Microbiology. 17(9):3219–3232. doi:10.1111/1462-2920.12772. More information can be found at www.climatechangemicrobiology.com and source code can be downloaded from https://github.com/climatechangemicrobiology.

CC-BY-NC-SA-4.0 2025 Cerrise Weiblen.
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