Difference between revisions of "Task 6 (MSUD)"

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(→‎BCKDHA)
(→‎BCKDHA)
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=== BCKDHA ===
  
=== BCKDHA ===
   
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==== Freecontact ====
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From the output of freecontact, only those residue pairs were extracted, that are separated by at least 5 residues. Pairs that are near in sequence are natually coupled, but this isn't interesting because it doesn't help to predict the 3D structure, where residues intereact, which are far away from each other in the 1D sequence. The CN score values of these extracted pairs range between -0.87 and 5.28. The following diagram shows the distribution of the scores:
  
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From the output of freecontact, only those residue pairs were extracted, that are separated by at least 5 residues. Pairs that are near in sequence are natually coupled, but this isn't interesting because it doesn't help to predict the 3D structure, where residues intereact, which are far away from each other in the 1D sequence. The CN (corrected norm contact) score values of these extracted pairs range between -0.87 and 5.28. The following diagram shows the distribution of the scores:
   
 
[[File:MSUD_BCKDHA_freecontact_CN_score_distribution.png]]
  
[[File:MSUD_BCKDHA_freecontact_CN_score_distribution.png]]
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In a second step, the highest scoring 300 (= alignment length) couplings were taken, scores for each residue were summed and normalized by the average score of these couplings. The residues with the highest values (with a gap to the others) are: Thr 338, Phe 130 and Tyr 158. Interestingly, according to Uniprot, Tyr 158 is in the thiamine pyrophosphate binding region, and near position 338 there are some modified residues (phosphoserine).
  
In a second step, the highest scoring 300 (= alignment length) couplings were taken, scores for each residue were summed and normalized by the average score of these couplings. The residues with the highest values (with a gap to the others) are: Thr 338, Phe 130 and Tyr 158. Interestingly, according to Uniprot, Tyr 158 is in the thiamine pyrophosphate binding region, and near position 338 there are some modified residues (phosphoserine).
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==== EVcouplings ====
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The following table shows the ten residue pairs with highest DI (direct information) scores:
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{| class="wikitable" border="1" style="text-align:center;width:450px"
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! 1. residue # !! 1. aa !! 2. residue # !! 2. aa !! MI score !! DI score
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|-
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|209 ||L ||243 ||E ||0.81 ||0.22
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|-
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|266 ||N ||327 ||E ||0.64 ||0.17
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|-
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|247 ||H ||291 ||Y ||0.42 ||0.13
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|-
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|192 ||P ||200 ||R ||0.61 ||0.11
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|-
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|296 ||I ||312 ||E ||0.22 ||0.10
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|-
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|242 ||S ||291 ||Y ||0.34 ||0.09
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|-
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|190 ||Q ||196 ||G ||0.72 ||0.09
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|-
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|236 ||F ||264 ||C ||0.39 ||0.09
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|-
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|250 ||F ||288 ||G ||0.34 ||0.08
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|-
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|210 ||A ||218 ||G ||0.11 ||0.08
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|}
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The pairs that are also in top ten for freecontact are: 266/327, 247/291, 296/312, 236/264. The evolutionary contraint (EC) hotspots identified by EVcouplings, which have the highest EC strength (with a gap to the others) are residues Glu 243 and Leu 209. According to UniProt, near residue 209 there is a potassium binding region, and according to PBD, 243 is a thiamine pyrophosphate binding residue. It has to be noted, that the residues identified as important by freecontact are not included in the calculation of EVcouplings (probably they are not part of the alignment generated by it).
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==== EVfold ====
   
 
== Discussion ==
  
== Discussion ==

Revision as of 12:34, 15 June 2013

Results

Lab journal

H-Ras

BCKDHA

Freecontact

From the output of freecontact, only those residue pairs were extracted, that are separated by at least 5 residues. Pairs that are near in sequence are natually coupled, but this isn't interesting because it doesn't help to predict the 3D structure, where residues intereact, which are far away from each other in the 1D sequence. The CN (corrected norm contact) score values of these extracted pairs range between -0.87 and 5.28. The following diagram shows the distribution of the scores:

MSUD BCKDHA freecontact CN score distribution.png

Most scores are between -1 and 1. So those pairs, which have a score greater than 1 are considered high scoring and used for further analyses. High scoring pairs were regarded as true positive (TP), if their distance (between any pair of atoms) in the reference structure is below 5 Å. There are 94 TPs among 194 high scoring pairs, and this has a correlation to CN score of 0.31 (for a pair with higher CN score it is more likely that it is TP). This table shows the ten highest scoring pairs:

1. residue # 1. aa 2. residue # 2. aa MI score CN score true/false positive
247 H 291 Y 0.69 5.28 TP
236 F 264 C 0.45 4.02 TP
266 N 327 E 0.31 3.67 TP
239 G 270 A 0.35 3.48 TP
296 I 312 E 0.44 3.37 FP
316 R 324 F 0.60 3.34 TP
144 S 235 Y 0.48 3.17 TP
300 G 330 T 0.27 3.13 TP
261 I 317 A 0.25 3.06 TP
301 N 333 I 0.87 2.77 FP


In a second step, the highest scoring 300 (= alignment length) couplings were taken, scores for each residue were summed and normalized by the average score of these couplings. The residues with the highest values (with a gap to the others) are: Thr 338, Phe 130 and Tyr 158. Interestingly, according to Uniprot, Tyr 158 is in the thiamine pyrophosphate binding region, and near position 338 there are some modified residues (phosphoserine).

EVcouplings

The following table shows the ten residue pairs with highest DI (direct information) scores:

1. residue # 1. aa 2. residue # 2. aa MI score DI score
209 L 243 E 0.81 0.22
266 N 327 E 0.64 0.17
247 H 291 Y 0.42 0.13
192 P 200 R 0.61 0.11
296 I 312 E 0.22 0.10
242 S 291 Y 0.34 0.09
190 Q 196 G 0.72 0.09
236 F 264 C 0.39 0.09
250 F 288 G 0.34 0.08
210 A 218 G 0.11 0.08


The pairs that are also in top ten for freecontact are: 266/327, 247/291, 296/312, 236/264. The evolutionary contraint (EC) hotspots identified by EVcouplings, which have the highest EC strength (with a gap to the others) are residues Glu 243 and Leu 209. According to UniProt, near residue 209 there is a potassium binding region, and according to PBD, 243 is a thiamine pyrophosphate binding residue. It has to be noted, that the residues identified as important by freecontact are not included in the calculation of EVcouplings (probably they are not part of the alignment generated by it).

EVfold

Discussion

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