LOC56985 Evolution Main: Difference between revisions
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'''CLUSTALX alignement''' | '''CLUSTALX alignement''' | ||
The results for the CLUSTALX alignment can be viewed | The results for the CLUSTALX alignment can be viewed [[clustal alignment| here]]. | ||
"The line above the ruler is used to mark strongly conserved positions. Three characters ('*', ':' and | "The line above the ruler is used to mark strongly conserved positions. Three characters ('*', ':' and | ||
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[[Hypothetical Protein LOC56985| Back To Main hypothetical protein LOC56985 page]] | [[Hypothetical Protein LOC56985| Back To Main hypothetical protein LOC56985 page]] | ||
Revision as of 20:52, 3 June 2008
BLASTP Search Results
The initial top 60 blast search results, given in FASTA format, can be found in the link below.
For the purpose of creating a phylogenetic tree, sequences from the same species were removed and any sequences containing large gaps in the intial CLUSTAL alignment were also removed. The edited version of the blast search results used for the final clustal alignment can be seen below. Please note that {H} stands for hypothetical protein and {P} stands for predicted protein.
CLUSTALX alignement
The results for the CLUSTALX alignment can be viewed here.
"The line above the ruler is used to mark strongly conserved positions. Three characters ('*', ':' and '.') are used: '*' indicates positions which have a single, fully conserved residue
':' indicates that one of the following 'strong' groups is fully conserved:- STA, NEQK, NHQK, NDEQ, QHRK, MILV, MILF, HY, FYW
'.' indicates that one of the following 'weaker' groups is fully conserved:- CSA, ATV, SAG, STNK, STPA, SGND, SNDEQK, NDEQHK, NEQHRK, FVLIM, HFY
These are all the positively scoring groups that occur in the Gonnet Pam250 matrix. The strong and weak groups are defined as strong score 0.5 and weak score =<0.5 respectively." (Thompson, J.D. et. al. 1997)
