BLASTP - What is the difference between identities and positives? How can I identify mismatch?

Question

[Kédina]

help me please

Answer 1

[Mensur Dlakic]

Look at the BLASTP alignment below:

Score           Expect  Method                          Identities  Positives   Gaps
32.0 bits(71)   0.023   Compositional matrix adjust.    15/39(38%)  26/39(66%)  0/39(0%)

Query  1   MQVISFKLPPALNAKLEQIAIKEKKSKSEIIRIALARYV  39
           M++I+FK+P      L+  AIK   ++SE+IR+A+ + V
Sbjct  2   MKIITFKIPEETLLLLDAYAIKHNMNRSEVIRLAIEKLV  40

Any position where query and subject have the same residue is an identity. Notice that the middle line between them will have the same residue. If you count the number of letters on the middle line, you will see that there are 15 of them. That is why the percent of identity is 38% (15/39, where 39 is total alignment length). Any time the residues are similar but not identical there will be a + sign on the middle line, which is for similar matches. The number of positives is (identical+similar / total length) which ends up being 66%. Finally, for mismatches there is an empty space on the middle line.

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