similarity of 3D and sequential structure of protein in three bacteria?

Question

[Samane]

how should I find outer membrane protein similarity of three micro organism (3D and sequential)?

I research on Aptamer, then I need to know outer membrane protein of three micro organism ....how many they have similarity? and how many percent in outer membrane protein of them are there?

for example one of that protein is Bap or OMP or Bau A ...how can I find ,how many similarity is there between them for exm in Acinetobacter baumannii ,A.lwoffii and A.Calcoaceticus?

thank you so much for helping me.

Answer 1

[João Rodrigues]

1. You can BLAST their sequences to get homologues: sequence identity and similarity scores give you information on how close they are.
2. You can go to PDBe and use the structural similarity search feature to look for structurally similar proteins (if you have a structure to start with): RMSD gives you information on how close they are.