LAB #4: Blast by Julio Gonzalez
rhodopsin [Plecoglossus altivelis]
1. I chose rhodopsin, which is a light protein receptor and it involved in visual photo transduction. So, it basically a protein that is found in the eye and helps with the visual system. The reason I chose this protein was because I wanted to search something that was in the human body, but we don't usually talk about.
2. I chose the rhodopsin protein in the Plecoglossus altivelis (ACCESSION AB074484.1), which is the fish ayu or sweetfish. I found one that was from Homo sapien, but it seem too boring.
3. Amino acid sequence that codes for the protein in Plecoglossus altivelis:
1 mngtegpffy vpmsnasgiv rspyeypqyy linpaayfml acymffliit gfpinfltly
61 vtiehkklrt alnyillnla vadlfmvigg ftttlytsmh gyfvfgrtgc niegfcatlg
121 geiamwslvv laierwvvvc kpmtnfrfge nhaimgvaft wvmaaacavp plfgwsryip
181 egmqcscgid yytrapgfnn esfvvymfiv hftlpltvvt fcygrllctv keaaaaqqes
241 ettqraerev trmvvlmeis ylvcwlpyas vawyifcnqg sefgpvfmta paffakssal
301 ynpliyvcmn kqfrhcmitt lccgknpfee eegasttask teassvssss vapa
3b. Translated amino acids for the first 10:
Methionine, Asparagine, Glycine, Threonine, Glutamic acid, Glutamine, Proline, Phenylalanine, Phenylalanine, Tyrosine
4. Citations:
AUTHORS : Minamoto,T. and Shimizu,I.
TITLE: A novel isoform of vertebrate ancient opsin in a smelt fish,
Plecoglossus altivelis
JOURNAL: Biochem. Biophys. Res. Commun. 290 (1), 280-286 (2002)
5. The 15 lines of the nucleotide sequence:
1 accgaaggct gattgcaacc gcaagaccgc aaccatgaac ggcacagagg gacccttttt
61 ctatgtccct atgtcaaatg cctccggcat tgtcaggagt ccttatgaat accctcagta
121 ctaccttatc aacccagcag catacttcat gctggcctgc tacatgttct ttctcatcat
181 caccggcttc cccatcaact tcctaacact gtacgtcacc atcgagcaca agaagctgag
241 gaccgcccta aactacatcc tgctgaacct ggctgtggct gacctcttca tggtgatcgg
301 tggcttcacc accacattgt acacatccat gcatggctac ttcgtcttcg gtaggactgg
361 ctgcaacatc gaaggatttt gtgccaccct cggtggtgag attgccatgt ggtccctggt
421 tgtcctggct attgagaggt gggtggttgt ctgcaagccc atgaccaact tccgctttgg
481 tgagaaccat gccatcatgg gtgttgcgtt cacctgggtg atggccgctg cctgtgctgt
541 gcccccactc ttcggctggt cccgctacat cccagagggc atgcagtgct catgcggaat
601 tgactattac acccgtgccc ccggctttaa caacgagtcc tttgtggtct acatgttcat
661 tgtccacttc acacttcctc tgaccgtcgt caccttctgc tatggccgtc tgctgtgcac
721 cgtcaaggag gcagctgctg cccagcagga gtccgagacc acccagaggg ccgagaggga
781 agttacccgc atggtcgtcc tgatggagat ctcctacctg gtgtgctggt tgccctatgc
841 cagcgtggcc tggtacatct tctgcaatca gggaagtgag tttggccctg tcttcatgac
Hi Julio,
ReplyDeleteThat seems like an interesting start of a sequence there. I was just learning in my biochemistry class that glycine often shows up in collagen and prolines allow for sharp bends, two of which proteins show up in your sequence. For it to be a collagen protein though, glycine would be every third amino acid, which this is not and I am guessing collagen in the eye ball would not be a good thing. Eye can see why you would think this is an important protein. Thanks for sharing! -Darsi
It is interesting that this protein is present in organisms as distinct from one another as humans and fish. I wonder if this is an example of a homologous trait or a homoplastic trait. It would be interesting to see which other groups of organisms share this protein, and how they all relate to one another.
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