MCB/EEB372 Exam 1
(take home exam, honors code applies, i.e., no help from and discussions with
other course participants; books, notes and help-pages on the www are ok, except
for the ones where you start an email exchange with some other person)
Return by March 28, 5pm. Please hand in in person, not through campus mail or mailboxes.
Please do not send your answers per email. We appreciate high resolution graphics, but please submit them in a printed version.
An electronic copy of this exam is available on the MCB372 - homepage.
1) Assume that the following protein sequence were obtained from the translation of a putative ORF of a cyanobacterial genome:
>ORF with unknown function
MHLSELKSLHVSELIEMANGLEIENANRLRKQELMFAILKKRAKTGETIFGDGTLEVLPDGF
GFLRSPEMSYLASTDDIYISPSQIRRFNLHTGDTIEGEVRTPKDGERYFALVKVDKVNGQPP
EASKHKIMFENLTPLHPNKPLSLEREMRGEENVTGRIIDMIAPIGKGQRGLLVASPKSGKCL TSDFHTVLTTRGFIPIADVTLDDKVAVLDNNTGDMSYQNPQKVHKYDYDGPMYDVKTAGVEL
FVTPNHRMYVNTTNNTTNQNGYNLVEASSIFGKKVRYKNDAIWNKTDYQFILPDTATLTGHT NKISSTPAIQPDMNAFLFGLWIANGKIADKTAENNQQKQRWKVILTQVKEDVCEIIEQTLNK
LGFNFIRSGKDYTIENKQLFSYLNPFENGALNKYLPDFADLTTCKILTKASNKAYYFSTSER FANDVSRLALSASHAGTTSTGGLDAAPSNLYDTIIGLPTMERVTEYRVIVNQSSFFSYSTDK
TTVLNLSAQSALSLEQNSQKINKNTLVLTKNNVKSQTHSQRAERWDTALLTQKELDNSLNHD ILINKNPGTSQLECVVNPEVNNTSTNDRFVYWKGPVYSLTGPNNVFYVQRGKAVWTHNTVML
QHIAHAIKQNHPDVILFVLLIDERPEEVTEMQRSVAGEVIASTFDEPATRHVQVAEMVIEKA KRLVEMKHDVVILLDSITRLARAYNTVIPASGKVLTGGVDANALQRPKRFFGAARNIEEGGS
LTIIGTALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPSINLNKSGTRREEMLIKP EILQKIWVLRKFIHDMDEVEAMEFLLDKIRQTKNNAEFFDLMRR
What might be the function(s) of this protein?
Is there a common functional or structural feature among the homologous proteins?
What does this tell you about the protein encoded by this ORF?
Which catalytic activity(/ies) would you expect for the encoded protein?
Briefly describe how you went about to find homologs to this sequence.
2) The following file (here) contains amino acid sequences of several vacuolar ATPase A-subunits and prokaryotic V/A-ATPase (ATPsynthases, and ATP driven Sodium pumps) catalytic subunit. Using the tools of bootstrapping, ml-mapping and/or ml-ratio tests address the following question:
Do all of the bacterial sequences (Chlamydia, Chlamydiophila, Enterococcus (f and hirae), Thermus, Deinococcus, pnStreptococcus (pneumoniae), pyStreptococcus (pyogenes), Clostridium, Treponema (1&2) and Borrelia) group together?
Can you confidently exclude this possibility?
Does the answer change, if one removes the sequences associated with very long branches?
Does your answer change, if you consider among site rate variation?
(Also, describe any modifications you did to the datafile? How did you treat gaps? How did you reformat the data. The description of your work should be complete, i.e., given the information you provide, we should be able to duplicate your analysis.)
It is not sufficient to only do a bootstrap analysis of the data in clustalw! I am looking for at least three different approaches to address the question: Do all of the bacterial sequences group in a single group?
What is the implication of your analysis? ;-)