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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]]
 
 
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. 
 
== PB2 Protein Structural Homolgy Model ==
 
<applet load='MPB21.pdb' size='300' frame='true' align='center' caption='PB2 Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998206 A/Mexico/InDRE4487/2009 PB2], 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' />
 
=== PB2 Sequence Polymorphisms ===
 
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|PB2
|I30V
|gi|229892696_A/Canada-AB/RV153
|1
|----
|PB2
|N82S
|gi|229484025_A/Mexico/InDRE448
|all others
|----
|PB2
|H151Q
|gi|237624321_A/swine/Alberta/O
|1
|----
|PB2
|D161N
|gi|227831783_A/California/06/2
|1
|----
|PB2
|V267I
|gi|229783414_A/New_York/1682/2
|1
|----
|PB2
|S324R
|gi|237624321_A/swine/Alberta/O
|1
|----
|PB2
|H432Y
|gi|237624321_A/swine/Alberta/O
|1
|----
|PB2
|L464M
|gi|229892692_A/Mexico/InDRE411
|1
|----
|PB2
|K526R
|gi|229892698_A/Canada-NS/RV153
|5
|----
|PB2
|G698D
|gi|227831783_A/California/06/2
|1
|<scene name='User:Michael_Strong/H1N1/PB2/MSA/2/1'>G698</scene>
|----
|}
 
== PB1 Sequence Polymorphisms ==
 
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|PB1
|L10V
|gi|229396439_A/New_York/10/200
|1
|----
|PB1
|I12T
|gi|229536040_A/Arizona/02/2009
|1
|----
|PB1
|Q48R
|gi|229783391_A/New_York/1669/2
|1
|----
|PB1
|A157V
|gi|229487525_A/Canada-NS/RV153
|2
|----
|PB1
|A370G
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|F466S
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|V587A
|gi|229487525_A/Canada-NS/RV153
|3
|----
|PB1
|N641S
|gi|229892784_A/Canada-NS/RV153
|1
|----
|PB1
|M646V
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|S665F
|gi|237624323_A/swine/Alberta/O
|1
|----
|PB1
|S678N
|gi|229396395_A/New_York/18/200
|1
|----
|}
 
 
 
== PA Protein Structural Homolgy Model  ==
 
<applet load='MSPA1.pdb' size='300' frame='true' align='center' caption='PA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998223 A/Mexico/InDRE4487/2009 PA], residues 257-716, 97% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3cm8 3cm8]' scene ='User:Michael_Strong/H1N1/PA/MSA/1/1'/>
 
=== PA Sequence Polymorphisms ===
 
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|PA
|S224P
|gi|227977170_A/California/07/2
|6
|----
|PA
|R269K
|gi|229484063_A/Canada-NS/RV153
|2
|<scene name='User:Michael_Strong/H1N1/PA/MSA/269/2'>269</scene>
|----
|PA
|L275I
|gi|229484065_A/Mexico/InDRE448
|all others
|<scene name='User:Michael_Strong/H1N1/PA/MSA/275/3'>275</scene>
|----
|PA
|M581L
|gi|237511889_A/Mexico/4108/200
|11
|<scene name='User:Michael_Strong/H1N1/PA/MSA/581/2'>581</scene>
|----
|PA
|L702P
|gi|237624325_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/PA/MSA/702/1'>702</scene>
|----
|}
 
== HA Protein Structural Homolgy Model  ==
 
<applet load='MSHA2.pdb' size='300' frame='true' align='center' caption='HA Homology Model, Mexico Strain, [http://www.ncbi.nlm.nih.gov/nuccore/FJ998208 A/Mexico/InDRE4487/2009 HA], residues 16-341, 83% sequence identity to pdp template [http://proteopedia.org/wiki/index.php/3gbn 3gbn]' scene ='User:Michael_Strong/H1N1/HA/MSA/1/1'/>
 
=== HA Sequence Polymorphisms ===
 
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|HA
|V7I
|gi|237624327_A/swine/Alberta/O
|1
|----
|HA
|L8M
|gi|227831776_A/California/06/2
|5
|----
|HA
|A13T
|gi|229536010_A/Kansas/03/2009
|1
|----
|HA
|N48D
|gi|229536049_A/Arizona/02/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/48/1'>48</scene>
|----
|HA
|L49I
|gi|229535997_A/South_Carolina/
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/49/1'>49</scene>
|----
|HA
|I96V
|gi|229598877_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/96/1'>96</scene>
|----
|HA
|S100P
|gi|229535949_A/California/04/2
|5
|<scene name='User:Michael_Strong/H1N1/HA/MSA/100/1'>100</scene>
|----
|HA
|N104K
|gi|229892708_A/Canada-AB/RV153
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/104/1'>104</scene>
|----
|HA
|V125M
|gi|229598896_A/Texas/15/2009
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/125/1'>125</scene>
|----
|HA
|V149I
|gi|229536088_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/149/1'>149</scene>
|----
|HA
|A214T
|gi|229535949_A/California/04/2
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/214/1'>214</scene>
|----
|HA
|Y215N
|gi|237624327_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/215/1'>215</scene>
|----
|HA
|S220T
|gi|229396494_A/Ohio/07/2009
|21
|<scene name='User:Michael_Strong/H1N1/HA/MSA/220/1'>220</scene>
|----
|HA
|F227L
|gi|229598896_A/Texas/15/2009
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/227/1'>227</scene>
|----
|HA
|D239G
|gi|229892706A/Mexico/InDRE4114
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/239/2'>239</scene>
|----
|HA
|D291E
|gi|229535997_A/South_Carolina/
|2
|<scene name='User:Michael_Strong/H1N1/HA/MSA/291/1'>291</scene>
|----
|HA
|N293D
|gi|229783398_A/New_York/1682/2
|1
|<scene name='User:Michael_Strong/H1N1/HA/MSA/293/2'>293</scene>
|----
|HA
|V338I
|gi|229535949_A/California/04/2
|5
|<scene name='User:Michael_Strong/H1N1/HA/MSA/338/1'>338</scene>
|----
|HA
|A351V
|gi|237624327_A/swine/Alberta/O
|1
|----
|HA
|I400V
|gi|229484027_A/Canada-NS/RV153
|3
|----
|HA
|V428I
|gi|229598877_A/Ohio/07/2009
|4
|----
|HA
|V444I
|gi|237511819_A/Mexico/4108/200
|1
|----
|HA
|I527F
|gi|229892706A/Mexico/InDRE4114
|1
|----
|}
 
<scene name='User:Michael_Strong/H1N1/HA/MSA/All/1'>All Polymorphisms</scene>
 
== NP Protein Structural Homolgy Model  ==
 
<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 ===
 
{| class="wikitable"
|Protein
|Polymorphism
|Strain with Polymorphism
|Number of Strains with Polymorphism
|----
|NP
|G22D
|gi|229598884_A/Texas/15/2009
|1
|----
|NP
|V35A
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/35/1'>35</scene>
|----
|NP
|S90N
|gi|229536012_A/Arizona/01/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/90/1'>90</scene>
|----
|NP
|V106I
|gi|229892748_A/Canada-ON/RV152
|28
|<scene name='User:Michael_Strong/H1N1/NP/MSA/106/1'>106</scene>
|----
|NP
|Q128L
|gi|227977162_A/California/07/2
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/128/1'>128</scene>
|----
|NP
|L139I
|gi|229783384_A/New_York/1669/2
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/139/1'>139</scene>
|----
|NP
|E198K
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/198/1'>198</scene>
|----
|NP
|N208D
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/208/1'>208</scene>
|----
|NP
|V223I
|gi|229536102_A/Nebraska/02/200
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/223/1'>223</scene>
|----
|NP
|M228T
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/228/1'>228</scene>
|----
|NP
|A257T
|gi|229396492_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/257/1'>257</scene>
|----
|NP
|V349I
|gi|229536131_A/Colorado/03/200
|2
|<scene name='User:Michael_Strong/H1N1/NP/MSA/349/1'>349</scene>
|----
|NP
|V358M
|gi|229598873_A/Ohio/07/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/358/1'>358</scene>
|----
|NP
|V369I
|gi|229536077_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/369/1'>369</scene>
|----
|NP
|T379I
|gi|229536102_A/Nebraska/02/200
|18
|<scene name='User:Michael_Strong/H1N1/NP/MSA/379/1'>379</scene>
|----
|NP
|T379V
|gi|229892752_A/Canada-NS/RV153
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/379/1'>379</scene>
|----
|NP
|D381N
|gi|229396423_A/California/08/2
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/381/1'>381</scene>
|----
|NP
|D381Y
|gi|237624329_A/swine/Alberta/O
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/381/1'>381</scene>
|----
|NP
|T402A
|gi|237511901_A/Mexico/4516/200
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/402/1'>402</scene>
|----
|NP
|S456N
|gi|229536077_A/Indiana/09/2009
|1
|<scene name='User:Michael_Strong/H1N1/NP/MSA/456/1'>456</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>
|----
|}


[[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]]
<scene name='User:Michael_Strong/H1N1/NS2/MSA/All/1'>All Polymorphisms</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.
==Multiple Sequence Alignment of 5 H1N1 Strains==
<br><br>
===multiple sequence alignment of PB2===
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)


CLUSTAL 2.0.10 multiple sequence alignment
CLUSTAL 2.0.10 multiple sequence alignment
Line 132: Line 859:


--------------------
--------------------
===multiple sequence alignment of PB1===
'''PB1'''
'''PB1'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 251: Line 979:


--------------------
--------------------
===multiple sequence alignment of PA===
'''PA'''
'''PA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 365: Line 1,094:


--------------------
--------------------
===multiple sequence alignment of HA===
'''HA'''
'''HA'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 455: Line 1,185:


--------------------
--------------------
===multiple sequence alignment of NP===
'''NP'''
'''NP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 536: 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 614: Line 1,347:


--------------------
--------------------
===multiple sequence alignment of MP===
'''MP'''
'''MP'''
<PRE>CLUSTAL 2.0.10 =
<PRE>CLUSTAL 2.0.10 =
Line 662: Line 1,396:


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