For example Lys 305, which covalently binds retinal, is conserved between both vertebrate and cephalopod rhodopsin. Our result clearly shows that although some residues that co-ordinate the retinal moiety are conserved between vertebrate and cephalopod rhodopsin, this does not apply to all of them. It is not clear what the cause of the functional difference between these two rhodopsin families is. Whilst vertebrate rhodopsin activates the cyclic GMP signalling pathway, invertebrate rhodopsin activates the inositol-1,4,5-triphosphate signalling pathway via a G q-type G protein. Though related, they differ in their molecular properties and function. The second example has cephalopod rhodopsins as alignment A and vertebrate rhodopsins as alignment B. Because residues that are located at the interface of protein-protein interactions tend to be conserved, and because in this case most interface residues are of type 3 (specific for the STAT5a and the STAT4 alignment separately), the interaction between the subunits of the STAT5a dimer may be specific. By concentrating on the residues involved in the intermolecular contacts between STAT5a dimers, it is possible to see that they tend to be highly conserved within STAT5a orthologues, but not between STAT5a and STAT4. Unphosphorylated STAT5a dimerises in a way that is different to the dimerisation mode of STAT4 via Src-homology (SH2) domains. These are two families of the signal transducer and activator of transcription proteins. The first example has STAT5a as alignment A and STAT4 as alignment B. We have pre-computed two examples of Spial output. Positions 3, 4, 8, 9, and 10 had non-consensus amino acids that were present above this proportion in alignment B.įor more on what the numbers and letters in the two rows below the alignment mean, see position types. Positions 2, 3, 7, 8, and 10 had non-consensus amino acids that were present above this proportion in alignment A. In the example above, the specificity threshold was 0.35. This proportion can be specified by using the specificity threshold option. Next, Spial decides whether there are amino acids that are specific for any of the two alignments, but not for the consensus.įor this, a non-consensus amino acid has to be present above a certain proportion in either alignment. Positions 1, 2, 7, 9, and 10 had amino acids that were present above this proportion in both alignments. In the example below, the consensus threshold was 0.35. This proportion can be specified by using the consensus threshold option. In order for an amino acid to be consensus, it has to be present above a certain proportion in both alignments. The two input alignments have to be of the same length and the positions in both alignments have to correspond.įor each amino acid at each position in the two input alignments A and B, Spial decides whether the amino acid is consensus or not. Alternatively, Spial directly accepts two sets of alignments as input. The sequences input is aligned using MUSCLE and split to produce two alignments (hereon referred to as alignments A and B). Spial accepts two types of inputs: sequences and alignments.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |