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'''2009 H1N1 swine flu genome and protein analysis'''
'''2009 H1N1 swine flu genome and protein analysis'''


This page was created by Michael Strong, other contributers include ...
[[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]]
Shown below are Protein Structural Homology Models of the PB2, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins from the 2009 Mexico [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=643780 A/Mexico/InDRE4487/2009] H1N1 Swine flu genome. Sequence polymorphisms of the PB2, PB1, PA, HA, NP, NA, MP1, MP2, NS1 and NS2 proteins are also indicated, as identified by comparison of subsequently sequenced 2009 H1N1 strains from around the globe. The "green links" next to the listed amino acids highlight the amino acid polymorphisms in the structural homology models. More detail on each protein, including Multiple Sequence Alignments of newly sequence H1N1 strains, Sequence Polymorphisms, and Related Sequence Homologs are provided on the individual protein pages (links above).  


Genome and 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 from 2009 H1N1 strains from Mexico, California, Texas, New York, and Canada are also provided below. 


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 ==
== PB2 Protein Structural Homolgy Model ==


Line 332: Line 333:
<applet load='MSNP1.pdb' size='300' frame='true' align='center' caption='NP Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998217 A/Mexico/InDRE4487/2009 NP], residues 28-502, 94% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2q06 2q06]' scene ='User:Michael_Strong/H1N1/NP/MSA/1/1'/>
<applet load='MSNP1.pdb' size='300' frame='true' align='center' caption='NP Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998217 A/Mexico/InDRE4487/2009 NP], residues 28-502, 94% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2q06 2q06]' scene ='User:Michael_Strong/H1N1/NP/MSA/1/1'/>


== NP Sequence Polymorphisms ==
=== NP Sequence Polymorphisms ===


{| class="wikitable"
{| class="wikitable"
Line 463: Line 464:
<scene name='User:Michael_Strong/H1N1/NP/MSA/All/1'>All Polymorphisms</scene>
<scene name='User:Michael_Strong/H1N1/NP/MSA/All/1'>All Polymorphisms</scene>


== NA Protein Structural Homolgy Model  ==
<applet load='MSNA1.pdb' size='300' frame='true' align='center' caption='NA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998214 A/Mexico/InDRE4487/2009 NA], residues 83-467, 89% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3b7e 3b7e]' scene ='User:Michael_Strong/H1N1/NA/MSA/1/1'/>
=== NA Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NA
|H36R
|gi|229892732_A/Mexico/InDRE411
|1
|----
|NA
|E57K
|gi|229536081_A/Indiana/09/2009
|1
|----
|NA
|V83M
|gi|229536111_A/Michigan/02/200
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/83/1'>83</scene>
|----
|NA
|S95G
|gi|228017756_A/California/06/2
|5
|<scene name='User:Michael_Strong/H1N1/NA/MSA/95/2'>95</scene>
|----
|NA
|G96E
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/96/2'>96</scene>
|----
|NA
|Y100H
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/100/1'>100</scene>
|----
|NA
|V106I
|gi|228481034_A/Auckland/3/2009
|30
|<scene name='User:Michael_Strong/H1N1/NA/MSA/106/1'>106</scene>
|----
|NA
|I108V
|gi|228860931_A/Netherlands/602
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/108/1'>108</scene>
|----
|NA
|P120S
|gi|229892684_A/Catalonia/P48/2
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/120/1'>120</scene>
|----
|NA
|S123L
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/123/1'>123</scene>
|----
|NA
|V241I
|gi|229535806_A/Texas/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/241/1'>241</scene>
|----
|NA
|N248D
|gi|229396353_A/New_York/12/200
|30
|<scene name='User:Michael_Strong/H1N1/NA/MSA/248/1'>248</scene>
|----
|NA
|N307T
|gi|228481034_A/Auckland/3/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/307/1'>307</scene>
|----
|NA
|S319R
|gi|229892682_A/Korea/01/2009
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/319/1'>319</scene>
|----
|NA
|S334C
|gi|237624331_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NA/MSA/334/1'>334</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NA/MSA/All/1'>All Polymorphisms</scene>
==MP1 Protein Structural Homolgy Model  ==
<applet load='MMP21.pdb' size='300' frame='true' align='center' caption='MP2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998211 A/Mexico/InDRE4487/2009 MP1], residues 23-60, 82% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2rlf 2rlf]' scene ='User:Michael_Strong/H1N1/MP/1/2'/>
===MP1 Sequence Polymorphisms===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|MP1
|L3P
|gi|227831763_A/California/05/2
|1
|<scene name='User:Michael_Strong/H1N1/MP/3/2'>3</scene>
|----
|MP1
|H222R
|gi|237624333_A/swine/Alberta/O
|1
|----
|MP1
|A227T
|gi|229484039_A/Canada-ON/RV152
|2
|----
|}
==MP2 Protein Structural Homolgy Model ==
<applet load='MMP21.pdb' size='300' frame='true' align='center' caption='MP2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998211 A/Mexico/InDRE4487/2009 MP2], residues 23-60, 82% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/2rlf 2rlf]' scene ='User:Michael_Strong/H1N1/MP2/MSA/1/1'/>
===MP2 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|MP2
|L3P
|gi|227831764_A/California/05/2
|1
|----
|MP2
|Y52H
|gi|229609551_A/Stockholm/28/20
|1
|<scene name='User:Michael_Strong/H1N1/MP2/MSA/52/1'>52</scene>
|----
|MP2
|T65M
|gi|229536073_A/Texas/07/2009
|1
|----
|MP2
|S82N
|gi|237511788_A/Mexico/4108/200
|1
|----
|}
== NS1 Protein Structural Homolgy Model  ==
<applet load='MNS21.pdb' size='300' frame='true' align='center' caption='NS1 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998220 A/Mexico/InDRE4487/2009 NS1], residues 5-202, 84% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3f5t 3f5t]' scene ='User:Michael_Strong/H1N1/NS1/MSA/1/1'/>


=== NS1 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NS1
|D12E
|gi|229536107_A/Nebraska/02/200
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/12/1'>12</scene>
|----
|NS1
|F32L
|gi|229535811_A/Texas/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/32/1'>32</scene>
|----
|NS1
|G45R
|gi|229598886_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/45/1'>45</scene>
|----
|NS1
|R88C
|gi|229536033_A/Minnesota/02/20
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/88/1'>88</scene>
|----
|NS1
|E97G
|gi|229892754_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/97/1'>97</scene>
|----
|NS1
|M104T
|gi|237624336_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/104/1'>104</scene>
|----
|NS1
|I123V
|gi|229892764_A/Canada-AB/RV153
|15
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/123/1'>123</scene>
|----
|NS1
|F134I
|gi|237624336_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NS1/MSA/134/1'>134</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NS1/MSA/All/2'>All Polymorphisms</scene>
== NS2 Protein Structural Homolgy Model ==
<applet load='MNS22.pdb' size='300' frame='true' align='center' caption='NS2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998220 A/Mexico/InDRE4487/2009 NS2], residues 64-116, 94% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/1pd3 1pd3]' scene ='User:Michael_Strong/H1N1/NS2/MSA/1/1'/>
=== NS2 Sequence Polymorphisms ===
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NS2
|E63K
|gi|229783374_A/Korea/01/2009
|1
|----
|NS2
|E67K
|gi|229598887_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/67/1'>67</scene>
|----
|NS2
|A89E
|gi|228017754_A/California/06/2
|3
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/89/1'>89</scene>
|----
|NS2
|A115T
|gi|229892755_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NS2/MSA/115/1'>115</scene>
|----
|}
<scene name='User:Michael_Strong/H1N1/NS2/MSA/All/1'>All Polymorphisms</scene>
==Multiple Sequence Alignment of 5 H1N1 Strains==
===multiple sequence alignment of PB2===
===multiple sequence alignment of PB2===


Line 587: Line 859:


--------------------
--------------------
===multiple sequence alignment of PB1===
'''PB1'''
'''PB1'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 706: Line 979:


--------------------
--------------------
===multiple sequence alignment of PA===
'''PA'''
'''PA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 820: Line 1,094:


--------------------
--------------------
===multiple sequence alignment of HA===
'''HA'''
'''HA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 910: Line 1,185:


--------------------
--------------------
===multiple sequence alignment of NP===
'''NP'''
'''NP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 991: Line 1,267:
                             ****
                             ****
</PRE><SPAN class=3Dpsmall>
</PRE><SPAN class=3Dpsmall>


--------------------
--------------------
===multiple sequence alignment of NA===
'''NA'''
'''NA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 1,069: Line 1,347:


--------------------
--------------------
===multiple sequence alignment of MP===
'''MP'''
'''MP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 1,117: Line 1,396:


--------------------
--------------------
===multiple sequence alignment of NS===
'''NS'''
'''NS'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
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