Need help in Using BLAST for beginner - finding the paralog, ortholog and protein (Mar/15/2006 )
I've some question due to my assignment. I tried to use BLAST to search the given unknown sequence. Then I got the name and the organism that are gi|7767146|pdb|1C2W|B, Escherichia coli.
the given unknown sequence is ...
aaaaaattgaaattataaagaagggacttatgtctacaa aacgcaaagt gaaaaatata
ccacctcattctggctgactaaaggccacagctgagcctg gaactgaccc ttccttcatc
ctcaacctgctgtcctccagaaagcaccaaggaaaaagca gagaatgaca gcaaacagat
cactaggcctctgaccacaggtgctgagtactcagcagcc ctcatataat aggtttgaaa
1. Is the gi|7767146|pdb|1C2W|B the name of this gene?
2. To find the human homologs of this gene, how can I do that? Which BLAST do I have to search?
3. Also the same question for ortholog.
4. How can I find name of the protein that is obtained from the gene? I've tried the Translation BLAST by pasting the given unknown sequence and the result come out as below but I can't understand it.
Chain B, Insights Into Erbb Signaling From The Structure Of The Erbb2-Pertuzumab Complex
::: gi|48425583|pdb|1S78|A Chain A, Insights Into Erbb Signaling From The Structure Of The Erbb2-Pertuzumab Complex
Score = 26.2 bits (56), Expect = 6.2
Identities = 14/37 (37%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Frame = +1
Query 175 RFAQSNPSEHPRQCHSLLCHPYCVNHGGDSLLHVQCF 285
R Q P E+ H L CHP C G V CF
Sbjct 523 RVLQGLPREYVNARHCLPCHPECQPQNGS----VTCF 555
Am I using the correct way? Please give me some guidance. I'm just learn to use BLAST for the first time. Thank you so much for your help.
gi|7767146|pdb|1C2W|B is not the gene name
the pdb code is 1C2W perhaps (look in the pdb (type pdb beta into google)
to find paralogs and homology use blast on the EBI site or use the ensembl database - I would use the later as it will explicitly tell you the homologs.