The protein in the one of the diagrams is described here.
Note the identifier “P52737” is also in my diagram. It gives the same name as in the diagram. The website provides the same FASTA sequence as in the diagram.
The coordinates of the zinc fingers are also there at that website:
|Zinc fingeri|140 – 162|C2H2-type 1; degeneratePROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|168 – 190|C2H2-type 2PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|196 – 218|C2H2-type 3PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|224 – 246|C2H2-type 4PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|252 – 274|C2H2-type 5PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|280 – 302|C2H2-type 6PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|308 – 330|C2H2-type 7PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|336 – 358|C2H2-type 8PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|364 – 386|C2H2-type 9PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|392 – 414|C2H2-type 10PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|420 – 442|C2H2-type 11PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|448 – 470|C2H2-type 12PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|476 – 498|C2H2-type 13PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|504 – 526|C2H2-type 14PROSITE-ProRule annotationAdd BLAST||23|
One could add the amino acids between zinc fingers to make the rows in my diagram. The colored columns indicated conserved residues or conserved classes of residues (like aromatic residues).
The arrows point to a hierarchy generated by MEGA by taking the individual zinc finger rows. Note, I even put the FASTA coordinates in the tree, identifying the protein by name and the coordinates of the particular zinc finger and the ZF number as designated by UNIPROT.
Whether one uses rooted or unrooted neighbor joining, maximum likelihood, bootstrapped or not, …the point was all of these would be pretty much fictions because of the problem of creating a functional binding as the zinc finger array evolved.
Whatever hierarchical structure derived by supposed phylogenetic methods is only an imagination in the mind of the phylogeneticist unless he can justify the functional of the protein in each of the evolutionary phases it goes through.
The point is, making hierarchies isn’t proof of evolution, it’s proof things can be arranged hierarchically! The ZN136 protein is an example where it would be absurd to think this actually evolved because the protein would be functionally broken in almost every step of evolution.
The problem of hierarchy of domains in a single protein can be extended to paralogs in a single organism and then to orthologs across organisms. Just because one can make a hierarchical tree doesn’t mean that it can reasonably be evolved. Zinc finger proteins such as in the KRAB family are counter examples to that belief.