# Align the HIV-1 Gag protein with the Gag protein of Visna virus

Align the HIV-1 Gag protein with the Gag protein of Visna virus

Background Visna virus is a lentivirus causing encephalitis in sheep

The problem is align the follow two protein Gag of viruses HIV-1 (GenBank KU749412.1) and Gag Visna virus (GenBank L06906.1) that are:

"MGARASILRGEKLDTWERIRLRPGGKKHYMLKHLVWASRELDRFALNPGLLETLEGCKQIIKQLQPALQTGTEELRSLFNTVATLYCVHAGIPVKDTKEALDKIEEEQNKCQQKAKQAEAAAAGKISLNYPIVQNLQGQMVHQAISPRTLNAWVKVIEEKAFSPEVIPMFTALSEGATPQDLNTMLNTVGGHQAAMQMLKDTINEEAAEWDRLHPVHAGPVAPGQMREPRGSDIAGTTSTLAEQIAWITGNPPVPVGEIYKRWIILGLNKIVRMYSPXSILDIRQGPKEPFRDYVDRFFKTLRAEQATQDVKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQTTNAIMMQRSNFKGPKRTIKCFNCGKEGHLARNCRAPRKKGCWKCGKEGHQMKDCNERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPAESFRFEETTPAPKQEQKDKEPLTSLKSLFGSDPLSQ"
"MAKQGSKEKKGYPELKEVIKATCKIRVGPGKETLTEGNCLWALKTIDFIFEDLKTEPWTITKMYTVWDRLKGLTPEETSKREFASLQATLACIMCSQMGMKPETVQAAKGIISMKEGLHENKEAKGEKVEQLYPNLEKHREVYPIVNLQAGGRSWKAVESVVFQQLQTVAMQHGLVSEDFERQLAYYATTWTSKDILEVLAMMPGNRAQKELIQGKLNEEAERWVRQNPPGPNVLTVDQIMGVGQTNQQASQANMDQARQICLQWVITALRSVRHMSHRPGNPMLVKQKNTESYEDFIARLLEAIDAEPVTDPIKTYLKVTLSYTNASTDCQKQMDRTLGTRVQQATVEEKMQACRDVGSEGFKMQLLAQALRPQGKAGQKGVNQKCYNCGKPGHLARQCRQGIICHHCGKRGHMQKDCRQKKQQGNNRRGPRVVPSAPPML"


I propose that the better alignment method is the one that maximize the function

f(string1, string2)=(number of letter equal between strign1 and string2)/(common length of strings).


With that definition I found f(s1,s2)=0.25760 (and 0.2949 between POL protein) for the two strings above.

• What score might others find?
• Is that definition one of biological significative?
• Is there is a better one, what definition for align proteins?
• Are Visna and HIV viruses relatives?
• There are a number of scoring methods. Maybe review this page for an overview and compare different scoring metrics: en.wikipedia.org/wiki/Sequence_alignment Dec 11 '20 at 22:48

Both are lentiviruses and env is a fast evolving gene. What you are looking at here is the location of indels and this will vary between alignment algorithms.