Difference between revisions of "Structural Alignments (Phenylketonuria)"

From Bioinformatikpedia
(→‎Evaluate sequence alignments)
(→‎Evaluate sequence alignments)
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{| border="1" cellpadding="5" cellspacing="0" align="center"
  
{| border="1" cellpadding="5" cellspacing="0" align="center"
 
|-
  
|-
−
! colspan="8" style="background:#32CD32;" | RMSD results
 +
! colspan="8" style="background:#32CD32;" | LGA and hhsearch results
  +
|-
  +
! colspan="1" style="background:#32CD32;"
  +
! colspan="4" style="background:#32CD32;" | LGA
  +
! colspan="3" style="background:#32CD32;" | hhsearch
 
|-
  
|-
 
! style="background:#90EE90;" align="center" | pdb
  
! style="background:#90EE90;" align="center" | pdb
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! style="background:#90EE90;" align="center" | LGA_S
  
! style="background:#90EE90;" align="center" | LGA_S
 
! style="background:#90EE90;" align="center" | LGA_Q
  
! style="background:#90EE90;" align="center" | LGA_Q
−
! style="background:#90EE90;" align="center" | Seq_id
 +
! style="background:#90EE90;" align="center" | seq_id
  +
! style="background:#90EE90;" align="center" | probability
  +
! style="background:#90EE90;" align="center" | e-value
  +
! style="background:#90EE90;" align="center" | identities (%)
 
|-
  
|-
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| 1phz || 0.83 || 90.65 || 32.44 || 99.34
 +
| 1phz || 0.83 || 90.65 || 32.44 || 99.34 || 100.00 || 6.9e-165 || 92
 
|-
  
|-
−
| 1j8u || 0.73 || 90.29 || 35.83 || 99.67
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| 1j8u || 0.73 || 90.29 || 35.83 || 99.67 || 100.00 || 3.1e-135 || 100
 
|-
  
|-
−
| 2v27 || 1.70 || 62.77 || 12.55 || 96.02
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| 2v27 || 1.70 || 62.77 || 12.55 || 96.02 || 100.00 || 3.6e-74 || 32
 
|-
  
|-
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| 2qmx || 3.18 || 7.46 || 1.25 || 4.88
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| 2qmx || 3.18 || 7.46 || 1.25 || 4.88 || 98.20 || 1.1e-09 || 36
 
|-
  
|-
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| 3luy || 2.82 || 7.17 || 1.24 || 13.89
 +
| 3luy || 2.82 || 7.17 || 1.24 || 13.89 || 98.07 || 3.3e-09 || 22
 
|-
  
|-
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| 1qey || 0.64 || 3.65 || 1.63 || 0.00
 +
| 1qey || 0.64 || 3.65 || 1.63 || 0.00 || 54.00 || 3.4 || 67
 
|-
  
|-
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| 1wyp || 2.67 || 8.43 || 1.37 || 0.00
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| 1wyp || 2.67 || 8.43 || 1.37 || 0.00 || 29.42 || 15 || 19
 
|-
  
|-
−
| 1a6s || 3.15 || 6.93 || 1.08 || 11.43
 +
| 1a6s || 3.15 || 6.93 || 1.08 || 11.43 || 20.59 || 29 || 36
 
|-
  
|-
 
|}
  
|}

Revision as of 15:26, 1 June 2013

Summary

...

Explore structural alignments

Lab journal

Dataset generation

Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase)

  • reference structure of PAH: 2PAH (96,41% identity)
  • identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI)
  • identical sequence with unfilled binding site: not found anyone
  • low sequence identity: 3LUY (32,2% - no pdb ID under 30%)
  • high sequence identity: pdb ID: 2PHM (89,7%)
  • CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT
  • CA: 2B5U (CATH Code: 1.10.287.620)
  • C: 3BQO (CATH Code: 1.25.40.210)
  • other CATH category: 1V8H (CATH Code: 2.60.40.10)

Pymol

...

LGA

LGA ...

SSAP / CATHEDRAL (used by CATH)

SSAP ...
uses Cβ

TopMatch

TopMatch ...
uses Cα

SAP or CE

SAP? ->Error!
->
CE
CE-PDB ...

Modelling scores

To compare the different models, the RMSDs (root-mean-square deviation) are compared. In TopMatch the same formular is taken but called Er (root-mean-square error). The RMSD gives the squared distance between corresponding positions of two superimposed proteins in Ångström. The results are shown in <xr id="rmsd"/>. <figtable id="rmsd">

RMSD results
Method 1lrm 3luy 2phm 1j8u 2b5u 3bqo 1vh8
LGA-RMSD 0.81 3.30 0.88 0.73 3.07 3.59 3.42
SSAP-RMSD 0.99 18.77 1.24 1.02 39.16 22.39 7.27
TopMatch-Er 0.60 1.98 0.81 0.63 1.21 1.12 3.25
CE-RMSD 0.65 5.13 0.95 0.68 4.06 4.68 5.92
Root-mean-square deviation/error in Ångström for the four protein structure alignment predictors LGA, SSAP, TopMatch and CE.

</figtable>

  • lowest RMSDs: TopMatch
  • LGA and CE sometimes the one sometimes the other is better. For very similar structures CE better, otherwise LGA???
  • worst/highest RMSDs: SSAP, maybe the Cβ are more distant???


  • careful about the sidechains: here always 2pah.A as query is taken and xx.A as target

...

Evaluate sequence alignments

Lab journal
<figtable id="model_rmsd">

LGA and hhsearch results
colspan="1" style="background:#32CD32;" LGA hhsearch
pdb RMSD LGA_S LGA_Q seq_id probability e-value identities (%)
1phz 0.83 90.65 32.44 99.34 100.00 6.9e-165 92
1j8u 0.73 90.29 35.83 99.67 100.00 3.1e-135 100
2v27 1.70 62.77 12.55 96.02 100.00 3.6e-74 32
2qmx 3.18 7.46 1.25 4.88 98.20 1.1e-09 36
3luy 2.82 7.17 1.24 13.89 98.07 3.3e-09 22
1qey 0.64 3.65 1.63 0.00 54.00 3.4 67
1wyp 2.67 8.43 1.37 0.00 29.42 15 19
1a6s 3.15 6.93 1.08 11.43 20.59 29 36
...

</figtable>

References

<references/>

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