                         SEQUENCE LISTING

<110>  Arad, Dorit
       Nevo, Yaniv
       Ezra, Assaf
 
<120>  METHODS AND COMPOSITIONS FOR DETECTION OF A PATHOGEN, DISEASE,
       MEDICAL CONDITION, OR BIOMARKER THEREOF 

<130>  11125.0002-00304

<150>  US 61/129,887
<151>  2008-07-28

<150>  US 61/136,143
<151>  2008-08-14

<150>  US 61/136,105
<151>  2008-08-12

<150>  US 61/159,485
<151>  2009-05-12

<160>  65    

<170>  PatentIn version 3.5

<210>  1
<211>  4
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  1

Gly Lys Lys Arg 
1               


<210>  2
<211>  4
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  2

Arg Arg Lys Lys 
1               


<210>  3
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  3

Arg Leu Ile Gln Lys Arg Ser Asp 
1               5               


<210>  4
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  4

Leu Ile Gln Lys Arg Ser Asp Val 
1               5               


<210>  5
<211>  6
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  5

Phe Val Asn Gln His Leu 
1               5       


<210>  6
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  6

Leu Val Glu Ala Leu Tyr Leu Val 
1               5               


<210>  7
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  7

Glu Ala Leu Tyr Leu Val Cys Gly 
1               5               


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

<220>
<223>  Substrate

<400>  8

Glu Arg Gly Phe Phe Tyr Thr Pro 
1               5               


<210>  9
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  9

Pro Ala Leu Phe Phe Arg Leu 
1               5           


<210>  10
<211>  5
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  10

Leu Val Ile His Thr 
1               5   


<210>  11
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  11

His Gln Val Tyr Phe Val Arg Lys 
1               5               


<210>  12
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  12

Pro Ala Arg Phe Phe Arg Leu 
1               5           


<210>  13
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  13

Pro Ala Glu Phe Phe Ala Leu 
1               5           


<210>  14
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  14

Pro Leu Glu Met Phe Ala Leu 
1               5           


<210>  15
<211>  6
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  15

His Ser Ser Lys Leu Gln 
1               5       


<210>  16
<211>  6
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  16

Gln Phe Tyr Ser Ser Asn 
1               5       


<210>  17
<211>  14
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  17

Gly Ala Gly Leu Arg Leu Ser Ser Tyr Tyr Ser Gly Ala Gly 
1               5                   10                  


<210>  18
<211>  10
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  18

Ser Ser Ile Tyr Ser Gln Thr Glu Glu Gln 
1               5                   10  


<210>  19
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  19

Gly Val Val Asn Ala Ser Cys Arg 
1               5               


<210>  20
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  20

Ser Tyr Val Leu Ala Ser Val Ser 
1               5               


<210>  21
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  21

Asn Asn Val Glu Ala Ala Thr Ser 
1               5               


<210>  22
<211>  8
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  22

Thr Ala Val Asn Ala Ser Gly Asn 
1               5               


<210>  23
<211>  4
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  X is any amino acid

<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is A or S

<400>  23

Val Xaa Ala Xaa 
1               


<210>  24
<211>  5
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (3)..(3)
<223>  X is any amino acid except K

<400>  24

Val Val Xaa Ala Ser 
1               5   


<210>  25
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  25

Val Val Asn Ala Ser Cys Arg 
1               5           


<210>  26
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  26

Arg Gly Val Val Asn Ala Ser Ser Arg Leu Ala 
1               5                   10      


<210>  27
<211>  12
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  27

Arg Gly Val Val Asn Ala Ser Ser Arg Leu Ala Cys 
1               5                   10          


<210>  28
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (1)..(1)
<223>  X is S or G

<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  X is Q, G, R, or K

<220>
<221>  MISC_FEATURE
<222>  (3)..(3)
<223>  X is N, C, or D

<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is Y, a hydrophobic amino acid, or an aromatic amino acid

<220>
<221>  MISC_FEATURE
<222>  (6)..(6)
<223>  X is I, V, or a hydrophobic amino acid

<220>
<221>  MISC_FEATURE
<222>  (7)..(7)
<223>  X is V or Q

<400>  28

Xaa Xaa Xaa Xaa Pro Xaa Xaa 
1               5           


<210>  29
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (1)..(1)
<223>  X is V, L, T, or P

<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  X is any amino acid

<220>
<221>  MISC_FEATURE
<222>  (3)..(3)
<223>  X is any hydrophobic amino acid

<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is F or L

<220>
<221>  MISC_FEATURE
<222>  (6)..(6)
<223>  X is any hydrophobic amino acid

<400>  29

Xaa Xaa Xaa Xaa Val Xaa Gln 
1               5           


<210>  30
<211>  10
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is F or L

<220>
<221>  misc_feature
<222>  (5)..(5)
<223>  Xaa can be any naturally occurring amino acid

<400>  30

Lys Val Lys Val Xaa Val Val Gln Pro Lys 
1               5                   10  


<210>  31
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate


<220>
<221>  MISC_FEATURE
<222>  (3)..(3)
<223>  X is any amino acid

<220>
<221>  MISC_FEATURE
<222>  (4)..(4)
<223>  X is any hydrophobic amino acid

<400>  31

Pro Pro Xaa Xaa Leu Pro Ile 
1               5           


<210>  32
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  32

Leu Glu Ala Leu Phe Gln Gly Pro Asp Ser Gln 
1               5                   10      


<210>  33
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  33

Leu Glu Ala Leu Phe Gln Gly Pro Pro Val Tyr 
1               5                   10      


<210>  34
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  34

Leu Glu Ala Leu Phe Gln Gly Pro Pro Ile Tyr 
1               5                   10      


<210>  35
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  35

Leu Glu Ala Leu Phe Gln Gly Pro Pro Ala Tyr 
1               5                   10      


<210>  36
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  36

Leu Glu Ala Leu Phe Gln Gly Pro Pro Gln Phe 
1               5                   10      


<210>  37
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  37

Leu Glu Ala Leu Phe Gln Gly Pro Pro Thr Phe 
1               5                   10      


<210>  38
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  38

Leu Glu Ala Leu Phe Gln Gly Pro Ile Glu Phe 
1               5                   10      


<210>  39
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  39

Met Glu Ala Leu Phe Gln Gly Pro Leu Gln Tyr 
1               5                   10      


<210>  40
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  40

Met Glu Ala Leu Phe Gln Gly Pro Ile Gln Tyr 
1               5                   10      


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

<220>
<223>  Substrate

<400>  41

Met Glu Ala Leu Phe Gln Gly Pro Leu Glu Phe 
1               5                   10      


<210>  42
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  42

Met Glu Ala Leu Phe Gln Gly Pro Leu Arg Tyr 
1               5                   10      


<210>  43
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  43

Ile Glu Ala Leu Phe Gln Gly Pro Pro Val Phe 
1               5                   10      


<210>  44
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  44

Ile Glu Ala Leu Phe Gln Gly Pro Pro Gln Phe 
1               5                   10      


<210>  45
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  45

Ile Glu Ala Leu Phe Gln Gly Pro Pro Lys Phe 
1               5                   10      


<210>  46
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  46

Ile Glu Ala Leu Phe Gln Gly Pro Leu Lys Phe 
1               5                   10      


<210>  47
<211>  116
<212>  PRT
<213>  Homo sapiens

<400>  47

Ala Pro Phe Arg Ser Ala Leu Glu Ser Ser Pro Ala Asp Pro Ala Thr 
1               5                   10                  15      


Leu Ser Glu Asp Glu Ala Arg Leu Leu Leu Ala Ala Leu Val Gln Asp 
            20                  25                  30          


Tyr Val Gln Met Lys Ala Ser Glu Leu Glu Gln Glu Gln Glu Arg Glu 
        35                  40                  45              


Gly Ser Ser Leu Asp Ser Pro Arg Ser Lys Arg Cys Gly Asn Leu Ser 
    50                  55                  60                  


Thr Cys Met Leu Gly Thr Tyr Thr Gln Asp Phe Asn Lys Phe His Thr 
65                  70                  75                  80  


Phe Pro Gln Thr Ala Ile Gly Val Gly Ala Pro Gly Lys Lys Arg Asp 
                85                  90                  95      


Met Ser Ser Asp Leu Glu Arg Asp His Arg Pro His Val Ser Met Pro 
            100                 105                 110         


Gln Asn Ala Asn 
        115     


<210>  48
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>  
<223>  Herpes simplex virus protease substrate consensus 

<220>  
<221>  misc_feature
<222>  (1)..(1)
<223>  can be any hydrophobic or aromatic amino acid

<220>
<221>  misc_feature
<222>  (2)..(2)
<223>  can be any hydrophobic amino acid

<220>
<221>  misc_feature
<222>  (3)..(3)
<223>  can be Q, N, E or D

<220>
<221>  misc_feature
<222>  (4)..(5)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be S, T, D, or E

<220>
<221>  misc_feature
<222>  (7)..(7)
<223>  can be any hydrophobic amino acid or HB donor

<400>  48

Xaa Xaa Xaa Ala Ser Xaa Xaa
1               5

<210>  49
<211>  7
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  West Nile virus protease substrate consensus

<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  can be A or a HB donor

<220>
<221>  misc_feature
<222>  (2)..(2)
<223>  can be any amino acid

<220>
<221>  misc_feature
<222>  (3)..(4)
<223>  can be any basic amino acid

<220>
<221>  misc_feature
<222>  (4)..(5)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (5)..(5)
<223>  can be S or G

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be any amino acid

<220>
<221>  misc_feature
<222>  (7)..(7)
<223>  can be any hydrophobic amino acid

<400>  49

Xaa Xaa Xaa Xaa Xaa Xaa Xaa
1               5

<210>  50
<211>  9
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  West Nile virus protease substrate consensus

<220>
<221>  misc_feature
<222>  (5)..(6)
<223>  protease cleavage point

<400>  50

Pro Asn Arg Lys Arg Gly Trp Pro Ala
1               5

<210>  51
<211>  11
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  West Nile virus protease substrate consensus

<220>
<221>  misc_feature
<222>  (6)..(7)
<223>  protease cleavage point

<400>  51

Phe Ala Ser Gly Lys Arg Ser Gln Ile Gly Val
1               5                   10

<210>  52
<211>  4
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Enterovirus 3C protease substrate consensus

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<400>  52

Phe Gln Gly Pro
1

<210>  53
<211>  8
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Coxsackievirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (4)..(5)
<223>  can be any amino acid

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  53

Thr Thr Gly Xaa Xaa Xaa Gln Gln
1               5

<210>  54
<211>  6
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Coxsackievirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (2)..(2)
<223>  can be any aromatic amino acid

<220>
<221>  misc_feature
<222>  (4)..(4)
<223>  can be H or Q

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  54

Ala Xaa Gly Xaa Gln Xaa
1               5

<210>  55
<211>  8
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Echovirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  can be T or N

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (4)..(4)
<223>  any amino acid

<220>
<221>  misc_feature
<222>  (5)..(5)
<223>  any aromatic amino acid

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  55

Xaa Thr Gly Xaa Xaa Xaa Gln Gln
1               5

<210>  56
<211>  8
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Echovirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  can be T or N

<220>
<221>  misc_feature
<222>  (2)..(2)
<223>  can be Y or H

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  56

Xaa Xaa Gly Ala Phe Xaa Gln Gln
1               5

<210>  57
<211>  6
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Echovirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  can be any naturally occurring amino acid

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  
protease cleavage point

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  57

Xaa Phe Gly Gln Gln Xaa
1               5

<210>  58
<211>  9
<212>  PRT
<213>  Artificial sequence

<220>  
<223>  Echovirus protease substrate consensus

<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  can be T or E

<220>
<221>  misc_feature
<222>  (2)..(2)
<223>  can be any amino acid

<220>
<221>  misc_feature
<222>  (2)..(3)
<223>  protease cleavage point

<220>
<221>  misc_feature
<222>  (4)..(4)
<223>  can be any amino acid

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  can be G or S

<400>  58

Xaa Xaa Gly Xaa Phe Xaa Gln Gln Ser
1               5


<210>  59
<211>  12
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  59

Leu Glu Ala Leu Phe Gln Gly Pro Pro Val Tyr Cys
1               5                   10


<210>  60
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Primer

<400>  60

caccatgacg atggacgagc ag                 22


<210>  61
<211>  4
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Primer extension

<400>  61

cacc                                      4


<210>  62
<211>  22
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Primer

<400>  62

tcacgccttg acgtatgact cg                 22


<210>  63
<211>  11
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  63

Leu Glu Ala Leu Phe Gln Gly Pro Asp Ser Gln
1               5                   10

<210>  64
<211>  14
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  64

Lys Leu Glu Ala Leu Phe Gln Gly Pro Pro Val Tyr Glu Ala
1               5                   10        

<210>  65
<211>  12
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Substrate

<400>  65

Thr Ser Ala Val Leu Gln Ser Gly Phe Arg Asp Lys
1               5                   10


















