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[[User:Michael_Strong|home]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1|H1N1]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/PB2|PB2]]<font color="blue">•</font> [[User:Michael_Strong/H1N1/PB1|PB1]]<font color="blue">•</font>  [[User:Michael_Strong/H1N1/PA|PA]]  <font color="blue">•</font> [[User:Michael_Strong/H1N1/HA|HA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NP|NP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NA|NA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/MP|MP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NS|NS]]  
[[User:Michael_Strong|home]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1|H1N1]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/PB2|PB2]]<font color="blue">•</font> [[User:Michael_Strong/H1N1/PB1|PB1]]<font color="blue">•</font>  [[User:Michael_Strong/H1N1/PA|PA]]  <font color="blue">•</font> [[User:Michael_Strong/H1N1/HA|HA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NP|NP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NA|NA]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/MP|MP]] <font color="blue">•</font>  [[User:Michael_Strong/H1N1/NS|NS]]  


<applet load='NS_m1.pdb' size='300' frame='true' align='right' caption='NS Homology Model' scene='User:Michael_Strong/H1N1/H1n1_ns_protein_homology_model/1'/>


<scene name='User:Michael_Strong/H1N1/H1n1_ns_protein_homology_model/1'>H1N1 NS protein homology model</scene>
Shown below are Clustal Multiple Sequence Alignmnents of the Protein Sequences from five strains of the recent 2009 H1N1 Swine Influenza Virus, including isolates from Mexico, California, Texas, New York, and Canada.  Protein sequences obtained from: http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html. Multiple sequence alignments of the PB2, PB1, PA, HA, NP, NA, MP, and NS proteins are provided.
== PB2 Protein Structural Homolgy Model ==
 
<applet load='MPB21.pdb' size='300' frame='true' align='center' caption='PB2 Homology Model, Mexico Strain, A/Mexico/InDRE4487/2009, residues 535-742, 95% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cw4 3cw4]' scene ='User:Michael_Strong/H1N1/PB2/MSA/1/1' />


Shown below are Clustal Multiple Sequence Alignmnents of the Protein Sequences from five strains of the recent 2009 H1N1 Swine Influenza Virus, including isolates from Mexico, California, Texas, New York, and Canada.  Protein sequences obtained from: http://www.ncbi.nlm.nih.gov/genomes/FLU/SwineFlu.html. Multiple sequence alignments of the PB2, PB1, PA, HA, NP, NA, MP, and NS proteins are provided.
=== PB2 Sequence Polymorphisms ===
<br><br>
Sequence Polymorphisms are given in relation to the Mexico/InDRE4487/2009 protein numbering system:<br>
PB2: S81 in Mexico strain (N in TX, CA, NY, and Canada)


{| class="wikitable"
{| class="wikitable"
|-
|Protein
|  Protein
|Polymorphism
| Position
|Strain with Polymorphism
!  Mexico
|Number of Strains with Polymorphism
!  California
|----
!  Texas
|PB2
!  New York
|I30V
!  Canada
|gi|229892696_A/Canada-AB/RV153
|-
|1
!  PB2
|----
| 82
|PB2
| S
|N82S
| N
|gi|229484025_A/Mexico/InDRE448
| N
|all others
| N
|----
|  N
|PB2
|-
|H151Q
!  PB1
|gi|237624321_A/swine/Alberta/O
| 678
|1
|  S
|----
|  S
|PB2
|  S
|D161N
|  N
|gi|227831783_A/California/06/2
|  S
|1
|-
|----
!  PA
|PB2
| 224
|V267I
| S
|gi|229783414_A/New_York/1682/2
| P
|1
| S
|----
| S
|PB2
|  S
|S324R
|-
|gi|237624321_A/swine/Alberta/O
!  PA
|1
| 275
|----
| I
|PB2
| L
|H432Y
| L
|gi|237624321_A/swine/Alberta/O
| L
|1
|  L
|----
|-
|PB2
!  HA
|L464M
| 100
|gi|229892692_A/Mexico/InDRE411
| S
|1
| P
|----
| S
|PB2
| S
|K526R
|  S
|gi|229892698_A/Canada-NS/RV153
|-
|5
!  HA
|----
| 263
|PB2
| A
|G698D
| T
|gi|227831783_A/California/06/2
| A
|1
| A
|<scene name='User:Michael_Strong/H1N1/PB2/MSA/2/1'>G698</scene>
|  A
|----
|-
|}
!  HA
| 269
| S
| S
| S
| T
|  T
|-
!  HA
| 338
| V
| I
| V
| V
|  V
|-
!  NP
| Start Site
| M1
| M7
| M7
| M7
|  M1
|-
!  NP
| 106
| V
| V
| V
| I
|  I
|-
!  NA
| 106
| V
| V
| V
| I
| I
|-
!  NA
|  248
|  N
|  N
|  N
|  D
|  D
|-
!  MP
|  Start Site
|  M1
|  T5
|  M1
|  M1
|  M1
|-
!  MP
|  227
|  A
|  A
|  A
|  A
|  T
|-
!  NS
|  123
|  I
|  I
|  I
|  V
|  V
|}  
 




===multiple sequence alignment of PB2===


CLUSTAL 2.0.10 multiple sequence alignment
CLUSTAL 2.0.10 multiple sequence alignment
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