NQ-NDH: NADH Dehydrogenases and Quinone Specificity in Bacterial Respiration

This repository contains supplementary data and analysis files associated with the study:

"Naphthoquinone preferentially pairs with non-proton-pumping NADH dehydrogenase for respiratory electron transport"

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📁 Repository Structure

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📂 Adaptive Laboratory Evolution

This folder contains information related to strains evolved under selection pressure:

• Sample code...: Internal codes and references to strains used
• List of mutated genes...: Mutations identified in endpoint isolates
• List of oligonucleotides...: Primers used for PCR amplification and gene complementation

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📂 CO-CONSERVATION Analysis

This folder includes analysis of gene conservation and respiratory trait distribution across bacteria:

• List of bacterial Genomes: Presence/absence of genes in ~9000 bacterial genomes, covering MQ/UQ biosynthesis and NADH dehydrogenases
• Co-conservation table: Presence/absence of MQ/UQ biosynthesis and NADH dehydrogenases(NDH-I and NDH-II)
• Gene specific e-values: Custom HMM search cutoffs used for each gene family
• Sequence similarity and kinetic parameters: Comparison of NDH-2 from different species

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📌 Notes

• All genomes used were publicly available (NCBI RefSeq or GenBank).
• Gene presence was predicted using HMM-based custom cutoffs.
• This repository supports reproducibility and transparency for downstream meta-analysis.