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app:lfmpro:sample-serthrkinases [2010/01/09 23:33] (current)
Ahmet Sacan
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 +====== Mining Ser/Thr Kinases Family ======  
 +  
 +The dataset and experiment setup is same as described in the [[sample-globins|Mining Globins Family page]]. The setup was the following set of proteins:  
 +  
 +<code>  
 +>> globals_set();  
 +>> [ptns,fams]=data_prepare_experiment('experimentFile','families.globins.kinases.txt');  
 +  1- 10 a.1.1.2 - (Globins)  
 + 11- 28 a.1.1.* - (Globin-like)  
 + 29- 38 d.144.1.7 - (Ser/Thr Kinases)  
 + 39-227 _except_a.1.1.* - (except Globins)  
 +228-424 _except_d.144.1.7 - (except Ser/Thr Kinases)  
 +</code>  
 +  
 +For this experiment, we will use the third and 5th groups of proteins, which are Ser/Thr Kinases in one group, and the remaining background proteins in the other. We again use ''mine_family_represent'' function for extracting representative feature set of the family:  
 +  
 +<code>  
 +>> rep=mine_family_represent('ser-thr-kinases', 'ptns',ptns([29:38]), 'rand',ptns([228:424]));  
 +</code>  
 +  
 +and then, for visualization, we map these features to any of the family members (e.g.,  
 +[[http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=ACV1B_HUMAN&pager.offset=5|protein 1b6cb]]).  
 +  
 +<code>  
 +>> signatures_show('1b6cb_', 'familyName','ser-thr-kinases','numHits',3,'pretty',1)  
 + 1: 1  -->431. score=0.024 dist=0.012 count=38  
 +  residues:  TYR402 ARG482 PRO381 GLU382 TYR476 ALA477 ALA380 TRP475 GLY479 ARG398 CYS474  
 +  atoms:  TYR402(CG,CD1,CA,CB,CD2,CE2) ARG482(CG,CD,NE,CZ,NH1,NH2) PRO381(CG,CD,N,CB) GLU382(CD,OE1,OE2) TYR476(N,C,O) ALA477(O,CA,C) ALA380(CA,CB) TRP475(O,C) GLY479(N,CA) ARG398(O) CYS474(O)  
 + 2: 7  -->147. score=0.000 dist=0.014 count=23  
 +  residues:  TRP242 TRP277 LEU278 PHE234 LEU276  
 +  atoms:  TRP242(CB,CG,CD1,CD2,NE1,CE2,CA) TRP277(N,CA,C,O) LEU278(N,CA,CB,CD1) PHE234(CG,CD1,CE1) LEU276(C,O)  
 + 3: 20 -->473. score=0.000 dist=0.000 count=7  
 +  residues:  PHE408 MET404 ILE488 ALA306 ILE470 ALA310 GLY405 MET467 CYS474 LEU492  
 +  atoms:  PHE408(CA,CG,CD1,CE1,CE2,CZ,CB,CD2) MET404(CB,CG,SD,CE,C,O,CA) ILE488(CB,CG1,CG2,CD1,CA) ALA306(O,CA,C,CB) ILE470(CG2,CB,CG1,CD1) ALA310(N,CA,CB) GLY405(N,CA) MET467(CE) CYS474(SG) LEU492(CD2)  
 +drawing the protein...  
 +drawing the local sites found...  
 +</code>  
 +  
 +<style center>  
 +{{1b6cb.kinases.3sites.jpg|Ser/Thr Kinases:1b6cb - top 3scoring site}}  
 +\\  
 +Figure. mapping of top scoring representative feature of Ser/Thr Kinases family onto protein 1b6cb.  
 +</style>  
 +  
 +In the mapped features, the 1st and 3rd features are responsible for the Protein Kinase activity and the 2nd site is an ATP biding domain. Through mapping the features onto other Ser/Thr Kinases proteins, we can find the corresponding sites. This gives us a powerful method of transferring information from one protein to another. Below, for instance, we can predict the ATP binding site (2nd site) on the other proteins. The Phenylalanine is the binding site for ATP which have been replaced by Leu in 1apme and by Arg in 1csn. The residues are listed in the order of number of atoms they contribute into the significant site:  
 +  
 +  
 +**1st Site:**  
 +<code>  
 +1a06__  
 +  TRP202 ARG264 PRO187 GLU188 LYS259 ALA186 GLU258 PRO261 ALA198 LEU256  
 +1apme_  
 +  TRP222 ARG280 PRO207 GLU208 VAL275 LEU277 ALA206 GLN274 ALA218 LEU272  
 +1b6cb_  
 +  TYR402 ARG482 PRO381 GLU382 TYR476 ALA477 ALA380 TRP475 GLY479 ARG398 CYS474  
 +1csn__  
 +  LEU242 ARG261 ILE187 GLU202 LYS237 GLN238 THR240 MET257  
 +1f3mc_  
 +  TRP448 ARG509 PRO433 GLU434 MET504 ALA432 LYS444 ASP503 VAL506 CYS501  
 +1h8fa_  
 +  TRP241 ARG328 PRO225 GLU226 GLU322 TYR323 ALA224 LEU320 PRO325  
 +1howa_  
 +  TRP588 ARG694 PRO573 GLU574 SER572 LEU689 PRO691 GLN688 GLY584 MET686  
 +1jvpp_  
 +  TRP187 ARG274 PRO171 GLU172 TYR269 ALA170 HIS268 PRO271 ALA183 MET266  
 +1phk__  
 +  TRP213 ARG275 PRO192 GLU193 VAL270 PRO272 ALA191 VAL269 GLU209  
 +1tkia_  
 +  TRP204 ARG266 PRO189 GLU190 LYS261 VAL260 ALA188 GLU262 ARG263 ALA200 LEU258  
 +</code>  
 +  
 +**2nd Site**  
 +<code>  
 +1a06__  
 +  HIS273 PHE252 TRP275  
 +1apme_  
 +  HIS294 LEU268 TRP296 LYS295  
 +1b6cb_  
 +  TRP242 PHE234 TRP277 LEU278 LEU276  
 +1csn__  
 +  HIS123 ARG197  
 +1f3mc_  
 +  HIS518 PHE497 PHE520 GLN519  
 +1h8fa_  
 +  HIS337 PHE339 LEU316 GLU312  
 +1howa_  
 +  HIS703 PHE682 TRP705  
 +1jvpp_  
 +  HIS283 PHE285 LEU262 ASP258  
 +1phk__  
 +  HIS284 PHE286 LEU263 PRO285  
 +1tkia_  
 +  HIS275 PHE254 TRP277 GLU250  
 +</code>  
 +  
 +**3rd Site**  
 +<code>  
 +1a06__  
 +  PHE218 TRP202 ILE230 MET257 PRO187 GLY183 VAL185 VAL206 ALA233 TYR184 ALA186  
 +1apme_  
 +  TYR146 ILE150 LEU172 LEU227 LEU167 ILE180 MET231 MET128 ALA147 LYS168 PRO169 LEU224  
 +1b6cb_  
 +  PHE408 MET404 ILE488 ALA306 ILE470 ALA310 GLY405 MET467 CYS474 LEU492  
 +1csn__  
 +  PHE253 VAL108 LEU212 VAL105 PHE208 MET209 PHE249 ALA109 PRO250  
 +1f3mc_  
 +  PHE497 LEU515 LEU450 CYS370 LEU374 CYS501 ILE447 GLY451 LEU521 PHE520  
 +1h8fa_  
 +  PHE201 LEU104 ILE109 ILE172 ILE100 MET101 LEU198 VAL110 ILE177 HIS179 ALA204  
 +1howa_  
 +  ILE225 MET284 LEU551 VAL209 ILE290 LEU206 ILE548 LEU205 LEU226 HIS292 ALA554  
 +1jvpp_  
 +  PHE90 TYR107 LEU103 LEU87 ILE99 ILE135 ILE141 PRO294 ILE104 MET196  
 +1phk__  
 +  PHE267 LEU263 MET130 MET219 THR215 LEU134 GLY216 VAL264 ALA281 PHE287  
 +1tkia_  
 +  PHE254 LEU206 VAL125 LEU258 VAL210 ALA272 TRP277 LEU278 CYS129 GLY207 MET203 VAL255 MET267  
 +</code>
app/lfmpro/sample-serthrkinases.txt · Last modified: 2010/01/09 23:33 by Ahmet Sacan