3D structures to the domains
We initiate the process using these sequences as input seed for Hmmer, then, after some iterations we obtain this seed .
The resulting complete sequences from uniprot can be download from here these sequences
The taxonomy of the search results are:
The domains of the search results are:
We made the same search but using only PDB databank instead of uniprot, these are the results
The taxonomy of the search results are:
The domains of the search results are:
Using pymol, we can observe that all the pdbs are trimer, the pdbs are here
1yu0 2c3f 2dp5 2iou 2yw0 6x3m 1yu1 1yu2 1yu3 1yu4 2yvv 3eka
Considering the species we have:
ARCHEA
Interpro L0KWD4, the alpha fold model as a trimer is in this link
EUKARIOT
Interpro B9TE92, the alpha fold model as a trimer is in this link
BACTERIA
The 128 bacterias present in this cluster have an AF model as a monomer, we took three small sequences and model them as trimers.
A0A0F2JLV1
A0A1H4DFS6.fasta A0A4S4BSN2.fasta
We also try to observe the amino acids present in all these sequences:
VIRUS
The 212 bacterias present in this cluster do not have an AF model as a monomer nor as trimer. We took two sequences and model them as trimers.
We also try to observe the amino acids present in all these sequences:
A SECOND DOMAIN
K6SYF0
Monomer AF model AF-K6SYF0-F1-model_v4.pdb
A THIRD DOMAIN
E9I2F2 (EUK)
