                         SEQUENCE LISTING

<110>  The University of Chicago
 
<120>  METHOD AND APPARATUS USING MACHINE LEARNING FOR EVOLUTIONARY 
       DATA-DRIVEN DESIGN OF PROTEINS AND OTHER SEQUENCE DEFINED 
       BIOMOLECULES

<130>  33300/55940

<150>  US 62/900,420
<151>  2019-09-13

<150>  US 63/020,083
<151>  2020-05-05

<160>  23    

<170>  PatentIn version 3.5

<210>  1
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (27)..(27)
<223>  Xaa can be any naturally occurring amino acid

<400>  1

Thr Val Gly Gly Tyr Thr Cys Gln Arg Asn Ser Val Pro Val Gln Val 
1               5                   10                  15      


Ser Leu Asn Ser Pro Gly Val Tyr Thr Lys Xaa Cys Met Lys Val Asp 
            20                  25                  30          


Trp Thr Gln Asp Thr Thr Ala Asn 
        35                  40  


<210>  2
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  2

Ile Val Gly Gly Arg Arg Ala Arg Pro Ile Ala Trp Pro Asx Met Val 
1               5                   10                  15      


Ser Leu Gln Leu Pro Asp Ala Phe Ala Pro Val Ala Gln Phe Val Asn 
            20                  25                  30          


Trp Ile Asp Ser Ile Ile Gln 
        35                  


<210>  3
<211>  41
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (27)..(27)
<223>  Xaa can be any naturally occurring amino acid

<400>  3

Thr Tyr Gly Gly His Asx Ala Lys Arg His Ser Arg Pro Tyr Met Ala 
1               5                   10                  15      


Tyr Leu Gln Ile Asp Arg Ala His Thr Lys Xaa Ser Thr Pro Leu Ser 
            20                  25                  30          


Trp Ile Lys Lys Thr Met Lys Lys Ser 
        35                  40      


<210>  4
<211>  41
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  4

Thr Val Glu Gly Ser Asp Ala Glu Thr Cys Met Ser Pro Met Gln Val 
1               5                   10                  15      


Met Leu Phe Arg Tyr Gly Phe Tyr Thr His Val Phe Arg Leu Lys Lys 
            20                  25                  30          


Trp Thr Gln Lys Val Thr Asp Gln Phe 
        35                  40      


<210>  5
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (13)..(13)
<223>  Xaa can be any naturally occurring amino acid

<400>  5

Ile Thr Asn Gly Ala Tyr Asp Gly Gln Ala Asx Val Xaa Val Gly Met 
1               5                   10                  15      


Ala Phe Pro Ala Gly Phe Asp Arg Ile Thr Ser Gln Leu Met Trp Ile 
            20                  25                  30          


Arg Gln His Thr Gly Leu Tyr 
        35                  


<210>  6
<211>  41
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  6

Val Asn Gly Asn Phe Asp Cys Gly Val Arg Gly Trp Pro Phe His Val 
1               5                   10                  15      


Gly Leu Tyr Asp Cys Gly Val Asn Thr Leu Thr Gly Leu Tyr Ser Gly 
            20                  25                  30          


Trp Ile Gln Gln Gln Leu Gln Leu Phe 
        35                  40      


<210>  7
<211>  41
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  7

Ile Thr Gly Gly Tyr Arg Ala Lys Pro Tyr Thr Ile Ile Tyr Leu Val 
1               5                   10                  15      


Gly Ile Val Tyr Pro Gly Val His Ile Arg Val Ser Asp Asp Ile Lys 
            20                  25                  30          


Trp Ile Lys Asp Val Ser Gly Val Gly 
        35                  40      


<210>  8
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  8

Ser Leu Arg Glu Glu Pro Asx Ile Ile Thr Val Thr Leu Lys Lys Gln 
1               5                   10                  15      


Gly Met Gly Leu Ser Ile Val Thr Arg Thr Ser Ser Val Val Thr Leu 
            20                  25                  30          


Glu Val Ala Lys Gln Gly Ala Ile 
        35                  40  


<210>  9
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  9

Met Lys Glu Pro Glu Ile Ile Thr Val Thr Leu Lys Lys Gln Asn Gly 
1               5                   10                  15      


Met Gly Leu Ser Ile Val Thr Arg Thr Ser Ser Val Val Thr Leu Glu 
            20                  25                  30          


Val Ala Lys Gln Gly Ala Leu 
        35                  


<210>  10
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  10

Ser Ser Gly Leu Glu Leu Phe Pro Val Glu Leu Glu Lys Asp Glu Asp 
1               5                   10                  15      


Gly Leu Gly Ile Ser Thr Ile Arg Asn Thr Lys Gly Asn Val Arg Phe 
            20                  25                  30          


Val Ile Gly Arg Glu Lys Pro Ser 
        35                  40  


<210>  11
<211>  41
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  11

Phe Gln Ser Met Thr Val Val Glu Ile Lys Leu Phe Lys Gly Pro Lys 
1               5                   10                  15      


Gly Leu Gly Phe Ser Thr Ala Lys Asn Thr Ser Ser Glu Val Val Tyr 
            20                  25                  30          


Leu Lys Val Gly Lys Pro Thr Thr Ile 
        35                  40      


<210>  12
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  12

Glu Val Ile Trp Glu Gln Tyr Thr Trp Thr Leu Gln Lys Asp Ser Lys 
1               5                   10                  15      


Gly Phe Gly Ile Ala Val Ser Arg Lys Ser Gly Lys Ile Ala Ala Ile 
            20                  25                  30          


Val Val Lys Pro Arg Lys Val 
        35                  


<210>  13
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  13

Leu Gln Gly Gly Asp Glu Lys Lys Val Asn Leu Val Leu Gly Asp Gly 
1               5                   10                  15      


Ser Leu Gly Leu Thr Ile Arg Lys Ser Ser Arg His Leu Ile Leu Thr 
            20                  25                  30          


Val Lys Asp Val Gly Arg Leu 
        35                  


<210>  14
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  14

Ser Ser Gly Pro Gly Leu Arg Glu Leu Cys Ile Gln Lys Ala Pro Gly 
1               5                   10                  15      


Arg Leu Gly Ile Ser Ile Arg Arg Ser Val Gly Asp Thr Leu Thr Val 
            20                  25                  30          


Leu Val Cys Asp Gly Phe Glu Ser 
        35                  40  


<210>  15
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  15

Gly Gln Asp Arg Asp Tyr Pro Thr Val Asp Met Glu Lys Gly Ala Lys 
1               5                   10                  15      


Gly Phe Gly Pro Ser Ile Arg Lys Ser Gly Gly Arg Arg Val Arg Leu 
            20                  25                  30          


Leu Leu Lys Arg Gly Thr Gly Ser 
        35                  40  


<210>  16
<211>  40
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  16

Glu Gly Ser Ser Gly Arg His Val Ala Cys Leu Ala Arg Ser Glu Arg 
1               5                   10                  15      


Gly Leu Gly Phe Ser Thr Ala Thr Ala Ala Ser Pro Thr Ile Ala Leu 
            20                  25                  30          


Leu Leu Glu Arg Glu Ala Gly Ser 
        35                  40  


<210>  17
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  17

Ile Ala Gly Met Asp Val Arg Leu Leu Arg Ile Lys Lys Glu Gly Ser 
1               5                   10                  15      


Leu Asp Leu Ala Leu Glu Gln Lys Ala Trp Asn Trp Ile Asp Leu Val 
            20                  25                  30          


Val Ala Val Cys Pro Pro Lys 
        35                  


<210>  18
<211>  39
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  18

Asp Arg Asp Pro Ala Phe Arg Val Ile Thr Val Thr Lys Glu Thr Gly 
1               5                   10                  15      


Leu Gly Leu Lys Ile Leu Thr Arg Ala Lys Leu Pro Trp Glu Ile Ala 
            20                  25                  30          


Phe Ile Arg Ser Gly Pro Ser 
        35                  


<210>  19
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  19
agcgatctcg gtgacgatgg                                                   20


<210>  20
<211>  23
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  20
cattaacgat gcaagtctcg tgg                                               23


<210>  21
<211>  59
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (34)..(39)
<223>  n is a, c, g, or t

<400>  21
tgactggagt tcagacgtgt gctcttccga tctnnnnnna cgactcacta tagggagac        59


<210>  22
<211>  58
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic


<220>
<221>  misc_feature
<222>  (33)..(38)
<223>  n is a, c, g, or t

<400>  22
cactctttcc ctacacgacg ctcttccgat ctnnnnnntg actagtcatt attagtgg         58


<210>  23
<211>  52
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Synthetic

<400>  23
caagcagaag acggcatacg agatcgagta atgtgactgg agttcagacg tg               52


