Need help in Using BLAST for beginner - finding the paralog, ortholog and protein (Mar/15/2006 )

Hi,

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 ...
tttcttgaccccttcatgggactcccaacaggggtaccccatttactcag
cctgccctgctcaacctcttgcaggagggagcacacgagtgaacgagtgcaggaaccagc
tggctgctttagtgctgtgaggagtaaactccatgcaggccctgcagcag caaccagttt
ttccagatttgctcaaagcaatcccagtgagcatccacgtcaatgtcatt ctcttctctg
ccatccttattgtgttaaccatggtggggacagccttcttcatgtacaat gcttttggaa
aaccttttgaaactctgcatggtcccctagggctgtaccttttgagcttc atttcaggct
cctgtggctgtcttgtcatgatattgtttgcctctgaagtgaaaatccat cacctctcag
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.

::: gi|48425584|pdb|1S78|B
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

Length=624

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.

Hello,

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)

http://www.rcsb.org/pdb/navbarsearch.do?ne...=0&image=Search

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.