All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.
ID: zAqktrSK
Submitter: Shu-Ching Ou
Submission Date: March 1, 2019, 5:26 p.m.
Version: 1
Number of data points | 9464 |
Proteins | Nucleoprotein |
Unique complexes | 9463 |
Assays/Quantities/Protocols | Experimental Assay: Preference |
Libraries | Variants for Nucleoprotein |
Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
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Structure ID | Release Date | Resolution | Structure Title |
---|---|---|---|
7NT8 | 2021-03-09T00:00:00+0000 | 2.22 | Influenza virus H3N2 nucleoprotein - R416A mutant |
Percent Identity | Matching Chains | Protein | Accession | Entry Name |
---|---|---|---|---|
99.6 | Nucleoprotein | P22435 | NCAP_I68A4 | |
99.4 | Nucleoprotein | P03467 | NCAP_I68A6 | |
98.4 | Nucleoprotein | P16986 | NCAP_I76AA | |
98.4 | Nucleoprotein | P26073 | NCAP_I68A2 | |
98.0 | Nucleoprotein | P06827 | NCAP_I72A2 | |
97.8 | Nucleoprotein | Q08041 | NCAP_I72A4 | |
97.8 | Nucleoprotein | Q1PUD5 | NCAP_I73A5 | |
97.2 | Nucleoprotein | Q3YPZ1 | NCAP_I71A1 | |
97.4 | Nucleoprotein | P16314 | NCAP_I79A4 | |
97.6 | Nucleoprotein | Q08033 | NCAP_I76A6 | |
97.8 | Nucleoprotein | A4K147 | NCAP_I54A2 | |
97.8 | Nucleoprotein | P26071 | NCAP_I55A0 | |
97.6 | Nucleoprotein | Q08031 | NCAP_I73A3 | |
97.4 | Nucleoprotein | Q08034 | NCAP_I78A7 | |
97.4 | Nucleoprotein | Q08035 | NCAP_I78A8 | |
97.6 | Nucleoprotein | A4U7B0 | NCAP_I51A0 | |
97.4 | Nucleoprotein | Q08028 | NCAP_I75A0 | |
97.4 | Nucleoprotein | P18072 | NCAP_I77AH | |
97.2 | Nucleoprotein | Q9E5Y8 | NCAP_I77A4 | |
97.6 | Nucleoprotein | P26072 | NCAP_I57A5 | |
97.4 | Nucleoprotein | P21433 | NCAP_I60A0 | |
97.2 | Nucleoprotein | Q07531 | NCAP_I73A2 | |
96.8 | Nucleoprotein | P18070 | NCAP_I78A6 | |
96.6 | Nucleoprotein | Q08036 | NCAP_I80A4 | |
96.6 | Nucleoprotein | P16982 | NCAP_I83A8 | |
97.2 | Nucleoprotein | P18071 | NCAP_I50A0 | |
96.6 | Nucleoprotein | Q09159 | NCAP_I77A5 | |
96.4 | Nucleoprotein | Q07546 | NCAP_I86A1 | |
96.4 | Nucleoprotein | O91743 | NCAP_I93A0 | |
96.2 | Nucleoprotein | Q07548 | NCAP_I80A3 | |
96.6 | Nucleoprotein | P26069 | NCAP_I40A0 | |
96.0 | Nucleoprotein | Q07550 | NCAP_I87A0 | |
96.0 | Nucleoprotein | P69294 | NCAP_I85A0 | |
96.0 | Nucleoprotein | P69293 | NCAP_I87A2 | |
96.0 | Nucleoprotein | P69295 | NCAP_I88A3 | |
96.0 | Nucleoprotein | P69289 | NCAP_I89A0 | |
96.0 | Nucleoprotein | P69290 | NCAP_I89A1 | |
96.0 | Nucleoprotein | P69291 | NCAP_I89A2 | |
96.0 | Nucleoprotein | P69292 | NCAP_I89A3 | |
96.0 | Nucleoprotein | P69296 | NCAP_I89A4 | |
96.6 | Nucleoprotein | P18073 | NCAP_I77AB | |
96.0 | Nucleoprotein | Q07545 | NCAP_I88A2 | |
95.8 | Nucleoprotein | Q07552 | NCAP_I80A0 | |
95.8 | Nucleoprotein | P26070 | NCAP_I47A0 | |
96.6 | Nucleoprotein | P18069 | NCAP_I77AA | |
95.8 | Nucleoprotein | Q08042 | NCAP_I90A0 | |
95.8 | Nucleoprotein | P26090 | NCAP_I83A0 | |
96.0 | Nucleoprotein | P23997 | NCAP_I83A2 | |
95.8 | Nucleoprotein | A4GCK1 | NCAP_I80AA | |
95.6 | Nucleoprotein | A4GCH9 | NCAP_I83A1 | |
95.2 | Nucleoprotein | Q289M3 | NCAP_I00A1 | |
95.0 | Nucleoprotein | A4GCL2 | NCAP_I43A0 | |
95.2 | Nucleoprotein | A3DRP4 | NCAP_I96A2 | |
94.8 | Nucleoprotein | A4U6V6 | NCAP_I45A0 | |
95.0 | Nucleoprotein | A8C8J8 | NCAP_I07A0 | |
95.0 | Nucleoprotein | Q07FI1 | NCAP_I96A3 | |
94.2 | Nucleoprotein | A4GCJ0 | NCAP_I36A0 | |
94.4 | Nucleoprotein | A4GCM3 | NCAP_I35A3 | |
94.0 | Nucleoprotein | P15682 | NCAP_I33A0 | |
94.0 | Nucleoprotein | P03466 | NCAP_I34A1 | |
93.8 | Nucleoprotein | P31609 | NCAP_I54A0 | |
93.8 | Nucleoprotein | P26089 | NCAP_I35A1 | |
93.8 | Nucleoprotein | B4URE0 | NCAP_I06A0 | |
93.6 | Nucleoprotein | Q5UEW0 | NCAP_I18A0 | |
92.6 | Nucleoprotein | P07381 | NCAP_I73A0 | |
92.6 | Nucleoprotein | P69299 | NCAP_I77A3 | |
92.6 | Nucleoprotein | P69297 | NCAP_I82A0 | |
92.6 | Nucleoprotein | P69298 | NCAP_I82A1 | |
92.4 | Nucleoprotein | Q0A2G1 | NCAP_I83A4 | |
92.4 | Nucleoprotein | Q9Q0U8 | NCAP_I96A0 | |
92.6 | Nucleoprotein | P26054 | NCAP_I72A6 | |
92.2 | Nucleoprotein | P26055 | NCAP_I53A0 | |
92.4 | Nucleoprotein | O90385 | NCAP_I80A6 | |
92.2 | Nucleoprotein | Q6DPD2 | NCAP_I02A7 | |
92.4 | Nucleoprotein | P68881 | NCAP_I69A1 | |
92.4 | Nucleoprotein | P68880 | NCAP_I74A2 | |
92.4 | Nucleoprotein | P15664 | NCAP_I76AK | |
92.4 | Nucleoprotein | P68882 | NCAP_I80A8 | |
92.2 | Nucleoprotein | P26062 | NCAP_I56A2 | |
92.4 | Nucleoprotein | P26064 | NCAP_I78A5 | |
92.4 | Nucleoprotein | P26091 | NCAP_I82A4 | |
92.6 | Nucleoprotein | P15678 | NCAP_I85A4 | |
92.4 | Nucleoprotein | P26052 | NCAP_I76AE | |
92.4 | Nucleoprotein | Q0A444 | NCAP_I49A1 | |
92.2 | Nucleoprotein | P15662 | NCAP_I56A1 | |
92.4 | Nucleoprotein | P15681 | NCAP_I61A0 | |
92.4 | Nucleoprotein | Q20P01 | NCAP_I68A3 | |
92.0 | Nucleoprotein | Q809S1 | NCAP_I01A3 | |
92.0 | Nucleoprotein | Q6J8B1 | NCAP_I02A5 | |
92.0 | Nucleoprotein | Q6DPE5 | NCAP_I02A6 | |
92.0 | Nucleoprotein | Q6J8C0 | NCAP_I03A0 | |
91.8 | Nucleoprotein | Q6DPE9 | NCAP_I02A1 | |
91.8 | Nucleoprotein | Q6DPE8 | NCAP_I02A2 | |
92.2 | Nucleoprotein | Q3SBF2 | NCAP_I66A1 | |
92.2 | Nucleoprotein | P21931 | NCAP_I72A5 | |
92.2 | Nucleoprotein | P26065 | NCAP_I80A1 | |
92.2 | Nucleoprotein | P15663 | NCAP_I60A2 | |
92.0 | Nucleoprotein | P06826 | NCAP_I78A3 | |
92.0 | Nucleoprotein | P26066 | NCAP_I80A5 | |
92.2 | Nucleoprotein | P15676 | NCAP_I85A7 | |
91.8 | Nucleoprotein | Q6DPC7 | NCAP_I03A1 | |
92.2 | Nucleoprotein | P16984 | NCAP_I49A0 | |
91.8 | Nucleoprotein | Q809S5 | NCAP_I01A0 | |
92.0 | Nucleoprotein | P26078 | NCAP_I42A0 | |
92.0 | Nucleoprotein | P16985 | NCAP_I81A0 | |
91.8 | Nucleoprotein | P15661 | NCAP_I83A5 | |
92.2 | Nucleoprotein | P26063 | NCAP_I62A0 | |
91.8 | Nucleoprotein | Q8QPJ5 | NCAP_I00A0 | |
91.8 | Nucleoprotein | P26060 | NCAP_I81A3 | |
91.6 | Nucleoprotein | Q809S9 | NCAP_I01A1 | |
92.2 | Nucleoprotein | P16978 | NCAP_I75A2 | |
92.0 | Nucleoprotein | P18277 | NCAP_I76A0 | |
91.8 | Nucleoprotein | P26059 | NCAP_I77AE | |
91.4 | Nucleoprotein | P15660 | NCAP_I77AG | |
92.0 | Nucleoprotein | P16983 | NCAP_I84A3 | |
91.6 | Nucleoprotein | Q6DPE6 | NCAP_I02A4 | |
91.8 | Nucleoprotein | P26080 | NCAP_I49A2 | |
91.8 | Nucleoprotein | P26053 | NCAP_I80A2 | |
91.8 | Nucleoprotein | P12604 | NCAP_I34A0 | |
91.4 | Nucleoprotein | Q6DPE7 | NCAP_I02A3 | |
91.6 | Nucleoprotein | Q0A2H2 | NCAP_I59A0 | |
91.6 | Nucleoprotein | P68042 | NCAP_I88A5 | |
91.6 | Nucleoprotein | P68043 | NCAP_I88A7 | |
91.6 | Nucleoprotein | P26082 | NCAP_I57A7 | |
91.6 | Nucleoprotein | P26068 | NCAP_I89A7 | |
91.8 | Nucleoprotein | P26056 | NCAP_I66A0 | |
92.0 | Nucleoprotein | P15671 | NCAP_I79A7 | |
91.4 | Nucleoprotein | P26076 | NCAP_I35A2 | |
91.4 | Nucleoprotein | O92784 | NCAP_I97A1 | |
91.4 | Nucleoprotein | P15677 | NCAP_I30A0 | |
91.4 | Nucleoprotein | P26085 | NCAP_I79A5 | |
91.2 | Nucleoprotein | P26061 | NCAP_I27A0 | |
91.6 | Nucleoprotein | P26092 | NCAP_I89A6 | |
91.6 | Nucleoprotein | P26077 | NCAP_I37A0 | |
91.2 | Nucleoprotein | Q67356 | NCAP_I67A2 | |
91.4 | Nucleoprotein | P15679 | NCAP_I77AC | |
91.4 | Nucleoprotein | P16988 | NCAP_I76AF | |
91.2 | Nucleoprotein | P26084 | NCAP_I76AG | |
91.4 | Nucleoprotein | P26087 | NCAP_I81A4 | |
91.0 | Nucleoprotein | P26081 | NCAP_I54A1 | |
91.0 | Nucleoprotein | P26083 | NCAP_I61A1 | |
91.0 | Nucleoprotein | P26079 | NCAP_I46A1 | |
91.0 | Nucleoprotein | P26086 | NCAP_I81A1 | |
91.2 | Nucleoprotein | Q809S7 | NCAP_I01A2 | |
90.8 | Nucleoprotein | P16987 | NCAP_I82A7 | |
90.8 | Nucleoprotein | P16979 | NCAP_I63A2 | |
90.8 | Nucleoprotein | P15673 | NCAP_I73A4 | |
90.4 | Nucleoprotein | P15667 | NCAP_I79A8 | |
90.4 | Nucleoprotein | P15683 | NCAP_I84A2 | |
90.6 | Nucleoprotein | Q6TXC0 | NCAP_I85A5 | |
90.6 | Nucleoprotein | P26074 | NCAP_I76A7 | |
90.2 | Nucleoprotein | P15670 | NCAP_I80AD | |
90.2 | Nucleoprotein | P15665 | NCAP_I77AF | |
90.2 | Nucleoprotein | P15669 | NCAP_I80AC | |
90.4 | Nucleoprotein | P67914 | NCAP_I86A2 | |
90.4 | Nucleoprotein | P67915 | NCAP_I86A3 | |
90.2 | Nucleoprotein | P15666 | NCAP_I78AF | |
91.3 | Nucleoprotein | Q2LFN9 | NCAP_I05A1 |