BCH 261 Lecture Notes - Lecture 8: Sequence Alignment, Myoglobin, Valine

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30 Nov 2020
Department
Course
Lecture 8
Bioinformatics:
Proteins with similar structure & functions can have similar primary
structure
Law of evolution proteins w/ similar structure & functions
Proteins are constantly made differently b/c their genes are getting
mutated
Similar a.a. = a.a that fall under same classification (ex. (+)ly charged; ex.
Leucince & Valine are similar a.a b/c they’re both non-polar)
Can predict that they have similar functions, thus switching Leu to
Val wouldn’t change protein function
BLAST Alignment
BLAST alignment between human myoglobin and human a globin
sequences. The sequence of myoglobin (Mb) appears above that for the a
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globin. Between them are shown the identical amino acids (blue) and
those that are considered similar (green “+”). Gaps in the alignment are
shown by red text and red dashes. In this alignment there is 25%
sequence identity, suggesting a high degree of structural similarity
between the proteins. The expect score in this case is very low (6 * 10-6),
indicating that the alignment is statistically significant.
can find nucleotide-by-nucleotide comparisons between your query
sequence and similar database sequences by alignments
E values get larger from top to bottom
E values for alignments with the human genome are much
larger than they were for the Fusarium redolens sequences.
Recall that the smaller the E value, the more statistically
significant the similarity. This divergence between fungal and
human sequences is expected because of the large
evolutionary distance between these groups of organisms.
Other than the genus and species information, top hit sequences
share similar characteristics of rRNA seqeunce & internal
transcribed spacer (ITS)
structure of ribosomal RNA genes is conserved throughout
all eukaryotes, it is not surprising that there is some similarity
between your query sequence and sequences in the human
genome.
normal BCR and ABL genes are located on chromosomes 22 and
9, respectively. The only type of mutation that can lead to the fusion
of genes from two different (nonhomologous) chromosomes is a
translocation
Proteins found in diff species w/ similar functions often have similar a.a.
Seqeuence
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Sequence alignment & phylogentic tree for cyotchrome c from diff
organisms
Nomenclature for describing related or similar proteins
Homolog
Gene related to another gene from diff species by evolving from
common ancestor
Ortholog
Gene related to another gene from diff species by evolving from
common ancestor AND has similar function in each organism
Paralog
Gene related to another gene by gene duplication in same
organism
Consensus Sequences
Bits refers to frequency of events of which the a.a is conserved
Sequence logo = visual aid to look at which a.a. are conserved
Same gene that gives rise to diff proteins are NOT paralogs they
are known as isologs
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