Scripts, data, and analyses for extending flavoprotein (FLX) domains C-terminally to form extended FLX domains (eFLX) & performing structural predictions & alignments using AlphaFold2, RoseTTAFold, FoldSeek, and DALI

See associated manuscript for more details. 
To capture unannotated regions of the FLX domains for structural modeling, an extended flavin oxygenase domain (eFLX) was annotated by extending the C-terminus of the G3DSA:3.50.50.60 InterProScan FLX annotation to the N-terminus of the downstream annotation, using bedtools closest [1] and awk. Next, the annotation was expanded by 50 residues both upstream and downstream to account for potential inaccuracy in the domain annotations. The peptide FASTA representation of these eFLX domains were extracted, and subjected to 3D modelling using RoseTTAFold via the Robetta server [2], and AlphaFold2 (ColabFold v1.5.2-patch: AlphaFold2 using MMseqs2) using the ColabFold Google Collaboratory notebooks [3], [4]. After modeling, the rank 1 model and model 1 model from AlphaFold2 and RoseTTAFold, respectively, were used for structural similarity searches with FoldSeek via the FoldSeek server [5]. The DALI webserver was used for the structural similarity search to establish structural homology [6]. 
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