Homologuous Opsins BLAST Research

Bioinformatic Analyses - iGEM Evry Paris-Saclay 2023

Author

Samuel Ortion

Goals

Find other opsins (bacteria, fungi or archaea), which may be cloned in E. coli.
The main objective is to find out less characterized opsins with higher light sensitivity.

Constraints

No cysteine bridges (unavailable in E. coli chassis).

BLAST Analysis on TARA Ocean Gene Atlas

With E-value \(10E-10\) threshold.

Shareable results links: - CatCh: 3 Hits; - ChrimsonR: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/results?id=649fb4b1afd60 : 1 Hit; - Jaws: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/results?id=649fb55f90dce 6 Hits - NpHR: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/results?id=649fba11b3022 6 Hits

(Results links valid until 2023-07-16)

Downloaded Homolog sequences as zipped FASTA files, in tmp/.

Structure prediction with AlphaFold2

See if there is a disulfide bridge with ChimeraX

In ChimeraX:

to visualize S-S bonds by Favorites -> Command Line -> type <disp :cys> in Command: box. ref

In pyMol:

sel cysteines, resn cyc

Hidden Markov Model (HMM) Homologuous Protein Search

EBI InterPro https://www.ebi.ac.uk/interpro/

HMMER tool https://www.ebi.ac.uk/Tools/hmmer/

On `data/opsins/CatCh.fa`

FASTA matches from HMMER stored in ./tmp/hmmer/D12B9266-1A87-11EE-A6BA-8584F9E0C6C4.1.fa

grep -c ">" ./tmp/hmmer/D12B9266-1A87-11EE-A6BA-8584F9E0C6C4.1.fa

292 matches.

Filter out sequences with disulfide bond

python3 ./src/has_disulfide_bond.py ./tmp/hmmer/D12B9266-1A87-11EE-A6BA-8584F9E0C6C4.1.fa -o ./tmp/hmmer/D12B9266-1A87-11EE-A6BA-8584F9E0C6C4.1.disulfide.csv