Question: What does + stand for in sequence alignment (blastp)?
0
gravatar for reddishvilla_12
11 months ago by
reddishvilla_120 wrote:

Currently using blastp to compare primary sequences of proteins between organisms, here is one of the sequence alignments:

Query  116  THKTVGQQ  123
            T KT+G Q
Sbjct  96   TVKTMGHQ  103

Confused as to what the + represents. Help appreciated.

ADD COMMENTlink modified 11 months ago • written 11 months ago by reddishvilla_120

I thought it might have something to do with the amino acids. Valine is interchangeable with methionine so I thought it might represent that. Not 100% sure though.

ADD REPLYlink modified 11 months ago • written 11 months ago by reddishvilla_120
3
gravatar for WouterDeCoster
11 months ago by
Belgium
WouterDeCoster14k wrote:

It means this sequence is found on the forward strand of the chromosome/contig.

(nevermind, disregard this, see comment of genomax2)

ADD COMMENTlink modified 11 months ago • written 11 months ago by WouterDeCoster14k
3
gravatar for genomax2
11 months ago by
genomax224k
United States
genomax224k wrote:

Having edited the OP to correct the display format: the + sign in this case means functional equivalence (even though those two AA are not identical as some others in that alignment).
@decosterwouter responded when the sequences looked as if they were tab formatted blast output.

ADD COMMENTlink modified 11 months ago • written 11 months ago by genomax224k

Thanks a lot! So because valine and methionine are both non-polar aliphatic amino acids they both function the same?

ADD REPLYlink written 11 months ago by reddishvilla_120

They are the the same general class and can possibly replace each other (context would be important) and not affect the overall function/structure. Remember the AA substitution matrices (PAM, BLOSUM etc).

ADD REPLYlink written 11 months ago by genomax224k
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