U.S. patent application number 13/189765 was filed with the patent office on 2012-01-19 for plasmodium falciparum antigens and methods of use.
This patent application is currently assigned to U.S.A as Represented by the Secretary of the Navy, Office of Naval Research (Code 00CC). Invention is credited to Daniel J. Carucci, Denise L. Doolan, Alessandro Sette, John Sidney, Scott Southwood.
Application Number | 20120015401 13/189765 |
Document ID | / |
Family ID | 32507736 |
Filed Date | 2012-01-19 |
United States Patent
Application |
20120015401 |
Kind Code |
A1 |
Sette; Alessandro ; et
al. |
January 19, 2012 |
PLASMODIUM FALCIPARUM ANTIGENS AND METHODS OF USE
Abstract
The subject invention provides novel Plasmodium falciparum
antigens and novel polynucleotides encoding these antigens. Also
provided by the subject invention are methods of using these
antigens and polynucleotides.
Inventors: |
Sette; Alessandro; (La
Jolla, CA) ; Doolan; Denise L.; (Rockville, MD)
; Carucci; Daniel J.; (Washington, DC) ; Sidney;
John; (San Diego, CA) ; Southwood; Scott;
(Santee, CA) |
Assignee: |
U.S.A as Represented by the
Secretary of the Navy, Office of Naval Research (Code 00CC)
Arlington
VA
Epimmune Inc.
San Diego
CA
|
Family ID: |
32507736 |
Appl. No.: |
13/189765 |
Filed: |
July 25, 2011 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10537642 |
Dec 27, 2005 |
8017745 |
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PCT/US03/38966 |
Dec 8, 2003 |
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13189765 |
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60431494 |
Dec 6, 2002 |
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Current U.S.
Class: |
435/69.3 ;
435/252.3; 435/254.21; 435/254.23; 435/320.1; 435/348; 435/362;
435/419; 536/23.7 |
Current CPC
Class: |
C07K 14/445 20130101;
C12Q 1/6837 20130101; Y02A 50/30 20180101; Y02A 50/412 20180101;
A61K 39/00 20130101; Y10S 424/802 20130101 |
Class at
Publication: |
435/69.3 ;
536/23.7; 435/320.1; 435/252.3; 435/362; 435/348; 435/419;
435/254.21; 435/254.23 |
International
Class: |
C12P 21/02 20060101
C12P021/02; C12N 1/19 20060101 C12N001/19; C12N 1/21 20060101
C12N001/21; C12N 5/10 20060101 C12N005/10; C07H 21/00 20060101
C07H021/00; C12N 15/63 20060101 C12N015/63 |
Goverment Interests
[0003] This invention was made with government support under Grant
No. 1 R43AI49051-01 awarded by NIAID. The government has certain
rights in the invention.
Claims
1. An isolated or purified polynucleotide: a) encoding a
polypeptide comprising SEQ ID NO: 2; b) encoding a Human Leukocyte
Antigen (HLA) binding fragment of SEQ ID NO: 2, said fragment
comprising at least five consecutive amino acids of SEQ ID NO: 2;
or c) that is complementary along the full length of said
polynucleotide of a) or b).
2. The isolated or purified polynucleotide according to claim 1,
wherein said polynucleotide encodes said polypeptide comprising SEQ
ID NO: 2.
3. The isolated or purified polynucleotide according to claim 1,
wherein said polynucleotide encodes said FILA binding fragment.
4. The isolated or purified polynucleotide according to claim 1,
wherein said polynucleotide is complementary along the full length
of said polynucleotide of a).
5. The isolated or purified polynucleotide according to claim 1,
wherein said polynucleotide is complementary along the full length
of said polynucleotide of b).
6. A vector comprising a promoter operably linked to a
polynucleotide: a) encoding a polypeptide comprising SEQ ID NO: 2;
b) encoding a Human Leukocyte Antigen (HLA) binding fragment of SEQ
ID NO: 2, said fragment comprising at least five consecutive amino
acids of SEQ ID NO: 2; or c) that is complementary along the full
length of said polynucleotide of a) or b).
7. The vector according to claim 6, wherein said polynucleotide
encodes said polypeptide comprising SEQ ID NO: 2.
8. The vector according to claim 6, wherein said polynucleotide
encodes said HLA biding fragment.
9. The vector according to claim 6, wherein said polynucleotide is
complementary along the full length of said polynucleotide of
a).
10. The vector according to claim 6, wherein said polynucleotide is
complementary along the full length of said polynucleotide of
b).
11. An isolated transformed host cell comprising a polynucleotide:
a) encoding a polypeptide comprising SEQ ID NO: 2; b) encoding a
Human Leukocyte Antigen (HLA) binding fragment of SEQ ID NO: 2,
said fragment comprising at least five consecutive amino acids of
SEQ ID NO: 2; or c) that is complementary along the full length of
said polynucleotide of a) or b).
12. The isolated transformed host cell according to claim 11,
wherein said polynucleotide encodes said polypeptide comprising SEQ
ID NO: 2.
13. The isolated transformed host cell according to claim 11,
wherein said polynucleotide encodes said HLA binding fragment.
14. The isolated transformed host cell according to claim 11,
wherein said polynucleotide is complementary along the full length
of said polynucleotide of a).
15. The isolated transformed host cell according to claim 11,
wherein said polynucleotide is complementary along the full length
of the polynucleotide of b).
16. The isolated transformed host cell according to claim 11,
wherein said polynucleotide is a vector comprising a promoter
operably linked to a polynucleotide: a) encoding a polypeptide
comprising SEQ ID NO: 2; b) encoding a Human Leukocyte Antigen
(HLA) binding fragment of SEQ ID NO: 2, said fragment comprising at
least five consecutive amino acids of SEQ ID NO: 2; or c) that is
complementary along the full length of said polynucleotide of a) or
b).
17. The isolated transformed host cell according to claim 16,
wherein said polynucleotide encodes said polypeptide comprising SEQ
ID NO: 2.
18. The isolated transformed host cell according to claim 16,
wherein said polynucleotide encodes said HLA binding fragment.
19. The isolated transformed host cell according to claim 16,
wherein said polynucleotide is complementary along the full length
of said polynucleotide of a).
20. The isolated transformed host cell according to claim 16,
wherein said polynucleotide is complementary along the full length
of said polynucleotide of b).
21. A method of making a polypeptide, comprising culturing an
isolated transformed host cell according to claim 11 under
conditions that allow for the production of said polypeptide.
22. The isolated or purified polynucleotide according to claim 1,
wherein said HLA binding fragment has a length selected from the
group consisting of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, and 35
amino acids.
23. The vector according to claim 6, wherein said HLA binding
fragment has a length selected from the group consisting of 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
27, 28, 29, 30, 31, 32, 33, 34, and 35 amino acids.
24. The isolated transformed host cell according to claim 11,
wherein said HLA binding fragment has a length selected from the
group consisting of 8, 9, 10. 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, and 35
amino acids.
25. The isolated transformed host cell according to claim 16,
wherein said HLA binding fragment has a length selected from the
group consisting of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, and 35
amino acids.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 10/537,642, filed Dec. 27, 2005, which is the national stage of
PCT Application No. PCT/US2003/038966, filed Dec. 8, 2003, which
claims the benefit of U.S. Provisional Application Ser. No.
60/431,494, filed Dec. 6, 2002, the disclosure of each of which is
incorporated herein by reference in its entirety, including all
figures, tables, nucleic acid sequences, amino acid sequences, and
drawings.
[0002] The Sequence Listing for this application is labeled
"Seq-List.txt" which was created on Feb. 24, 2004 and is 566 KB.
The entire contents of the sequence listing is incorporated herein
by reference in its entirety.
BACKGROUND OF INVENTION
[0004] The recent explosion in genomic sequencing has deposited a
wealth of information in the hands of researchers. However, there
is not yet a means to efficiently analyze such data to identify
which antigens among many thousands are appropriate targets for
vaccine development.
[0005] More than 5000 proteins are expressed during the life cycle
of the Plasmodium spp. parasite. Subunit vaccines currently in
development are based on a single or few antigens and may
therefore, elicit too narrow a breadth of response, providing
neither optimal protection nor protection on genetically diverse
backgrounds. By contrast, to duplicate the protection induced by
whole organism vaccination (Good, M. F. & Doolan, D. L. Immune
effector mechanisms in malaria. Curr. Opin. Immunol. 11, 412-419
(1999)), a malaria vaccine targeting an unprecedented number of
parasite-derived proteins through inclusion of their minimal
CD8.sup.+ and CD4.sup.+ T cell epitopes in a multiepitope construct
appears to be required. However, the antigens mediating whole
organism induced protection are largely unknown.
[0006] Because of various factors, principally related to antigen
abundance and immunodominance, not all possible antigens are
recognized by natural immunity (Yewdell J W, Bennink J R.
Immunodominance in major histocompatibility complex class
I-restricted T lymphocyte responses. Annu. Rev. Immunol. 17, 51-88.
(1999)). Various approaches have been proposed for antigen
identification, including expression cloning (Kawakami, Y. &
Rosenberg, S. A. Immunobiology of human melanoma antigens MART-1
and gp100 and their use for immuno-gene therapy. Int. Rev. Immunol.
14, 173-192 (1997)), elution and mass spectrometry sequencing of
naturally processed MHC-bound peptides (Rotzschke, O. et al.
Isolation and analysis of naturally processed viral peptides as
recognized by cytotoxic T cells. Nature 348, 252-254 (1990); van
Bleek, G. M. & Nathenson, S. G. Isolation of an endogenously
processed immunodominant viral peptide from the class I H-2 Kb
molecule. Nature 348, 213-216 (1990); Hunt, D. F. et al. Peptides
presented to the immune system by the murine class II major
histocompatibility complex molecule 1-Ad. Science 256, 1817-1820
(1992); Cox, A. L. et al. Identification of a peptide recognized by
five melanoma-specific human cytotoxic T cell lines. Science 264,
716-719 (1994)), in vitro testing of pools of overlapping peptides
(Kern, F. et al. Cytomegalovirus (CMV) Phosphoprotein 65 Makes a
Large Contribution to Shaping the T Cell Repertoire in CMV-Exposed
Individuals. J. Infect. Dis. 185, 1709-1716 (2002)), and reverse
immunogenetics (Davenport, M. P. & Hill, A. V. Reverse
immunogenetics: from HLA-disease associations to vaccine
candidates. Mol. Med. Today 2, 38-45 (1996); Aidoo, M. et al.
Identification of conserved antigenic components for a cytotoxic T
lymphocyte-inducing vaccine against malaria. Lancet 345, 1003-1007
(1995)). However, these methods suffer from potential problems such
as the repeated identification of the same (frequent/dominant)
epitope, biases at the level of expansion of T cell populations,
and use of clonal/oligoclonal T cells. They also tend to
underestimate the complexity of responses, and are not able to
analyze a large number of potential targets in the context of
multiple HLA types. Finally, none of these approaches easily lends
itself towards the daunting task of efficiently analyzing large
amounts of genomic sequence data.
BRIEF SUMMARY
[0007] The subject invention also provides novel Plasmodium
falciparum antigens that are useful in therapeutic and diagnostic
applications. In various aspects, the subject invention provides
embodiments such as: [0008] A) isolated and/or purified
polynucleotide sequences comprising: [0009] a) a polynucleotide
sequence encoding a polypeptide sequence selected from the group
consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; [0010]
b) a complementary polynucleotide sequence to a polynucleotide
sequence encoding a polypeptide sequence selected from the group
consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; [0011]
c) a polynucleotide sequence having at least about 20% to 99.99%
identity to a polynucleotide sequence of A(a) or A(b); [0012] d) a
fragment of a polynucleotide sequence according to A(a) or A(b);
[0013] e) a polynucleotide sequence encoding a polypeptide as set
forth in Table 2, 3, 4, 5, or 6, or a polynucleotide sequence
encoding a polypeptide selected from the group consisting of SEQ ID
NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, and 27; [0014] f) a polynucleotide
sequence encoding a variant of a polypeptide (e.g., a variant
polypeptide) selected from the group consisting of SEQ ID NO: 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, and 27;
[0015] g) a polynucleotide sequence encoding a polypeptide fragment
of a polypeptide selected from the group consisting of SEQ ID NO:
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, and 27, wherein the fragment has
substantially the same serologic reactivity as the native
polypeptide and/or substantially the same T-cell reactivity as the
native polypeptide or fragment; [0016] h) a polynucleotide sequence
encoding a fragment of a variant polypeptide of a polypeptide
selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, and 27, wherein the fragment of the variant polypeptide
has substantially the same serologic activity as the native
polypeptide or substantially the same T-cell reactivity as the
native polypeptide or fragment; or [0017] i) a polynucleotide
sequence encoding a multi-epitope construct; [0018] B) primers or
detection probes (e.g., fragments of the disclosed polynucleotide
sequences) for hybridization with a target sequence or the amplicon
generated from the target sequence comprising a sequence of at
least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,
85, 90, 95, or 100 consecutive nucleotides of the polynucleotide
sequences set forth herein. Labeled probes or primers are labeled
with a radioactive compound or with another type of label as set
forth in embodiment C, below; [0019] C) isolated polynucleotides
according to embodiments A or B further comprising a label; labels
can include, and are not limited to 1) radioactive labels, 2)
enzyme labels, 3) chemiluminescent labels, 4) fluorescent labels,
5) magnetic labels, or other suitable labels. Exemplary labels
include, and are not limited to, .sup.32P, .sup.35S, .sup.3H,
.sup.125I, biotin, acetylaminofluorene, digoxigenin,
5-bromo-deoxyuridine, or fluorescein; [0020] D) methods of
detecting P. falciparum in biological samples comprising contacting
a biological sample with isolated polynucleotides of embodiments A,
B, or C. In this embodiment, P. falciparum cells, or cells
comprising (infected) by P. falciparum are recovered, lysed, and
DNA and/or RNA are extracted from the lysed cells. The extracted
DNA or RNA is then tested using polynucleotides and/or probes set
forth herein for the presence of P. falciparum. Typical assay
formats utilizing nucleic acid hybridization includes, and are not
limited to, 1) nuclear run-on assay, 2) slot blot assay, 3)
northern blot assay (Alwine, et al. Proc. Natl. Acad. Sci.
74:5350), 4) magnetic particle separation, 5) nucleic Acid or DNA
chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in
situ hybridization, 9) RNase protection assay (Melton, et al. Nuc.
Acids Res. 12:7035 and as described in the 1998 catalog of Ambion,
Inc., Austin, Tex.), 10) ligase chain reaction, 11) polymerase
chain reaction (PCR), 12) reverse transcriptase (RT)-PCR
(Berchtold, et al. Nuc. Acids. Res. 17:453), 13) differential
display RT-PCR (DDRT-PCR) or other suitable combinations of
techniques and assays; [0021] E) analytical systems, such as DNA
chips comprising polynucleotide sequences according to embodiments
A, B, or C; [0022] F) modified polynucleotide sequences comprising
polynucleotide sequences according to embodiments A or B; [0023] G)
a polynucleotide sequence according to embodiments A, B, or F,
further comprising regulatory sequences, such as promoters,
enhancer elements, or termination sequences, that are operably
linked to the polynucleotide sequences of embodiments A or B;
[0024] H) a vector comprising a promoter operably linked to a
nucleic acid sequence of the subject invention (e.g., as set forth
in embodiments A, B, or F), optionally, one or more origins of
replication, and, optionally, one or more selectable markers (e.g.,
an antibiotic resistance gene); [0025] I) host cells transformed by
a vector according embodiment G or H. The host cell may be chosen
from eukaryotic or prokaryotic systems, such as for example
bacterial cells, (Gram negative or Gram positive), yeast cells,
animal cells (such as Chinese hamster ovary (CHO) cells), plant
cells, and/or insect cells using baculovirus vectors. In some
embodiments, the host cells for expression of the polypeptides
include, and are not limited to, those taught in U.S. Pat. Nos.
6,319,691, 6,277,375, 5,643,570, or 5,565,335, each of which is
incorporated by reference in its entirety, including all references
cited within each respective patent; [0026] I) novel compositions
comprising a pharmaceutically acceptable carrier and a
polynucleotide according to embodiments A or B; [0027] J) methods
of inducing an immune response or protective immune response in an
individual comprising the administration of a composition
comprising a polynucleotide according to embodiments A and/or B and
a pharmaceutically acceptable carrier in an amount sufficient to
induce an immune response; [0028] K) the method according to
embodiment J, further comprising the administration of: 1) a viral
vector comprising a polynucleotide according to embodiment A and/or
B (or composition comprising the viral vector); and/or 2) a
polypeptide antigen (or composition thereof) of the invention; in a
preferred embodiment, the antigen is the polypeptide that is
encoded by the polynucleotide administered as the polynucleotide
vaccine. As a particularly preferred embodiment, the polypeptide
antigen is administered as a booster subsequent to the initial
administration of the polynucleotide vaccine. Exemplary viral
vectors suitable for use in this embodiment include, but are not
limited to, poxvirus such as vaccinia virus, avipox virus, fowlpox
virus, a highly attenuated vaccinia virus (such as Ankara or MVA
[Modified Vaccinia Ankara]), retrovirus, adenovirus, baculovirus
and the like. In a preferred embodiment, the viral vector is Ankara
or MVA; [0029] L) compositions comprising the polynucleotides of
embodiments A, B, or F inserted into nucleic acid vaccine vectors
(plasmids) or viral vectors and, optionally, a pharmaceutically
acceptable carrier, e.g., saline; [0030] M) one or more isolated
polypeptides comprising: [0031] a) a polypeptide encoded by a
polynucleotide sequence according to embodiment A(a); [0032] b) a
variant polypeptide encoded by a polynucleotide sequence having at
least about 20% to 99.99% identity to a polynucleotide according to
embodiment A(a); [0033] c) a fragment of a polypeptide or a variant
polypeptide, wherein said fragment or variant has substantially the
same serologic reactivity or substantially the same T-cell
reactivity as the native polypeptide (e.g., those polypeptides set
forth in SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and Tables 2, 3,
4, 5 or 6); [0034] d) a polypeptide sequence provided in Tables 2,
3, 4, 5 or 6 or selected from the group consisting of SEQ ID NO:
NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, and 27; [0035] e) a variant
polypeptide having at least about 20% to 99.99% identity to a
polypeptide provided in Tables 2, 3, 4, 5 or 6 or selected from the
group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and
27; [0036] f) a polypeptide (epitope) set forth in Table 2, 3, 4, 5
or 6; or [0037] g) a multi-epitope construct: 1) comprising at
least one epitope set forth in Table 2, 3, 4, 5 or 6; 2) comprising
a polypeptide selected from the group consisting of SEQ ID NO: NO:
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, and 27 and at least one epitope set
forth in Tables 2, 3, 4, 5 and/or 6; or 3) comprising and at least
one epitope set forth in Tables 2, 3, 4, 5 and/or 6 and one or more
polypeptide selected from the group consisting of SEQ ID NO: NO: 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, and 27; [0038] N) a polypeptide epitope
according to embodiment M(f), wherein the polypeptide epitope is a
CTL-inducing peptides of about 13 residues or less in length,
preferably between about 8 and about 11 residues (e.g., 8, 9, 10 or
all residues), and more preferably 9 or 10 residues; [0039] O) a
polypeptide epitope according to embodiment M(f), wherein the
polypeptide epitope is a HTL-inducing peptide of less than about 50
residues, preferably, between about 6 and about 30 residues, more
preferably, between about 12 and 25 residues (e.g., 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 residues), and most
preferably, between about 15 and 20 residues (e.g., 15, 16, 17, 18,
19, or 20 residues); [0040] P) methods for eliciting an immune
response in an individual comprising the administration of
compositions comprising polypeptides according to embodiment M or N
to an individual in amounts sufficient to induce an immune response
in the individual; [0041] Q) a composition comprising a
pharmaceutically acceptable carrier and a polypeptide according to
embodiment M or N, that can, optionally, contain an adjuvant;
[0042] R) diagnostic assays based upon Western blot formats, or
standard immunoassays known to the skilled artisan, comprising
contacting a biological sample obtained from an individual with a
polypeptide according to the embodiments M or N and detecting the
formation of an antibody-antigen complex or detecting the
stimulation of T-cells obtained from the individual (for example,
as set forth in the Examples herein); [0043] S) a "multi-epitope
construct" comprising: 1) polynucleotides that encode multiple
polypeptide epitopes (of any length) that can bind to one or more
molecules functioning in the immune system; or 2) polypeptides
comprising multiple polypeptide epitopes that can bind to one or
more molecules functioning in the immune system. Some embodiments
provide for "multi-epitope constructs" that comprise a combination
or series of different epitopes, optionally connected by "flanking"
residues. "Multi-epitope constructs" can include the full length
polypeptides from which the epitopes are obtained (e.g., the
polypeptides of SEQ ID NOs: 1-27); [0044] T) a multi-epitope
construct according to embodiment S, wherein the epitopes used in
the formation of the multi-epitope construct are selected from
those set forth in Table 2, Table, 3, Table 4, Table 5, and Table
6; [0045] U) a multi-epitope construct according to embodiments S
or T that is of "high affinity" or "intermediate affinity"; [0046]
V) a multi-epitope construct according to embodiments S, T, or U
that comprises five or more, ten or more, fifteen or more, twenty
or more, or twenty-five or more epitopes. Other embodiments provide
multi-epitope constructs that comprise at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, or 99 epitopes; [0047] W) a multi-epitope construct
according to embodiments S, T, U, or V wherein: a) all of the
epitopes in a multi-epitope construct are from one organism (e.g.,
the epitopes are obtained from P. falciparum); or b) or the
multi-epitope construct includes epitopes present in two or more
different organisms (e.g., some epitopes from P. falciparum and
some epitopes from another organism). Additionally, the same
epitope may be present in a multi-epitope construct at more than
one location in the construct. In some embodiments, novel epitopes
of the subject invention may be linked to known epitopes of an
organism (e.g., P. falciparum or another organism); [0048] X) a
multi-epitope construct according to embodiments S, T, U, V, or W,
wherein the individual epitopes interact with an antigen binding
site of an antibody molecule or fragment thereof, a class I HLA, a
T-cell receptor, and/or a class II HLA molecule; [0049] Y) a
multi-epitope construct according to embodiments S, T, U, V, W, or
X, wherein the construct further comprises, optionally, 1 to 5
"flanking" or "linking" residues positioned next to one or more
epitopes; [0050] Z) a multi-epitope construct according to
embodiments S, T, U, V, W, X, or Y that has, optionally, been
"optimized"; [0051] AA) an isolated antibody or fragment thereof
that specifically binds to a polypeptide as set forth in
embodiments M or N; [0052] BB) a viral vector comprising a
polynucleotide according to embodiment A or B. Exemplary viral
vectors suitable for use in this embodiment include, but are not
limited to, poxvirus such as vaccinia virus, avipox virus, fowlpox
virus, a highly attenuated vaccinia virus (such as Ankara or MVA
[Modified Vaccinia Ankara]), retrovirus, adenovirus, baculovirus
and the like. In a preferred embodiment, the viral vector is Ankara
or MVA; and/or [0053] CC) a viral vector according to embodiment
BB, wherein the viral vector further comprises nucleic acids
encoding immunostimulatory molecules such as IL-1, IL-2, IL-3,
IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-15, II-16,
II-18, IL-23, IL-24, erythropoietin, G-CSF, M-CSF, platelet derived
growth factor (PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth
factor (FGF; e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3, FGF-4, FGF-5,
FGF-6, or FGF-7), insulin-like growth factors (e.g., IGF-1, IGF-2);
vascular endothelial growth factor (VEGF); interferons (e.g.,
IFN-.gamma., IFN-.alpha.. IFN-.beta.); leukemia inhibitory factor
(LIF); ciliary neurotrophic factor (CNTF); oncostatin M; stem cell
factor (SCF); transforming growth factors (e.g., TGF-a,
TGF-.beta.1, TGF-.beta.1, TGF-.beta.1), or chemokines (such as, but
not limited to, BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX,
Eotaxin-1, Eotaxin-2/MPIF-2, Exodus-2/SLC,
Fractalkine/Neur7otactin, GROalpha/MGSA, HCC-1, I-TAC,
Lymphotactin/ATAC/SCM, MCP-1/MCAF, MCP-3, MCP-4, MDC/STCP-1,
ABCD-1, MIP-1.alpha., MIP-.beta.3, MIP-2.alpha./GRO.beta.,
MIP-3.alpha./Exodus/LARC, MIP-3.beta./Exodus-3/ELC,
MIP-4/PARC/DC-CK1, PF-4, RANTES, SDF1.alpha., TARC, or TECK).
BRIEF DESCRIPTION OF DRAWINGS AND TABLES
[0054] Table 1 presents a summary of immune reactivities of a panel
of 27 novel antigens and four known antigens.
[0055] Tables 2-6 provide peptide epitopes of P. falciparum.
BRIEF DESCRIPTION OF SEQUENCES
[0056] Sequence ID NOs: 1-27 are amino acid sequences of novel
malaria antigens.
DETAILED DISCLOSURE
[0057] The subject invention provides isolated and/or purified
novel P. falciparum polynucleotides and fragments of these novel
polynucleotides. Thus, the present invention provides isolated
and/or purified polynucleotide sequences comprising: [0058] a
polynucleotide sequence encoding a polypeptide sequence selected
from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
and 27; [0059] a complementary polynucleotide sequence to a
polynucleotide sequence encoding a polypeptide sequence selected
from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
and 27; [0060] a polynucleotide sequence having at least about 20%
to 99.99% identity to a polynucleotide sequence of (a) or (b);
[0061] a fragment of a polynucleotide sequence according to (a) or
(b); [0062] a polynucleotide sequence encoding a polypeptide as set
forth in Table 2, 3, 4, 5 or 6 or a polynucleotide sequence
encoding a polypeptide selected from the group consisting of SEQ ID
NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, and 27; [0063] a polynucleotide
sequence encoding variant of a polypeptide (e.g., a variant
polypeptide) selected from the group consisting of SEQ ID NO: 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, and 27; [0064] a polynucleotide sequence
encoding a polypeptide fragment of a polypeptide selected from the
group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27,
wherein the fragment has substantially the same serologic
reactivity as the native polypeptide or substantially the same
T-cell reactivity as the native polypeptide or fragment; [0065] a
polynucleotide sequence encoding a fragment of a variant
polypeptide of a polypeptide selected from the group consisting of
SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27, wherein the
fragment of the variant polypeptide has substantially the same
serologic activity as the native polypeptide or substantially the
same T-cell reactivity as the native polypeptide or fragment; or
[0066] a polynucleotide sequence encoding a multi-epitope
construct.
[0067] "Nucleotide sequence", "polynucleotide" or "nucleic acid"
can be used interchangeably and are understood to mean, according
to the present invention, either a double-stranded DNA, a
single-stranded DNA or products of transcription of the said DNAs
(e.g., RNA molecules). It should also be understood that the
present invention does not relate to genomic polynucleotide
sequences of P. falciparum in their natural environment or natural
state. The nucleic acid, polynucleotide, or nucleotide sequences of
the invention have been isolated, purified (or partially purified),
by separation methods including, but not limited to, ion-exchange
chromatography, molecular size exclusion chromatography, affinity
chromatography, or by genetic engineering methods such as
amplification, cloning, subcloning or chemical synthesis.
[0068] A homologous polynucleotide or polypeptide sequence, for the
purposes of the present invention, encompasses a sequence having a
percentage identity with the polynucleotide or polypeptide
sequences, set forth herein, of between at least (or at least
about) 20.00% to 99.99% (inclusive). The aforementioned range of
percent identity is to he taken as including, and providing written
description and support for, any fractional percentage, in
intervals of 0.01%, between 20.00% and, up to, including 99.99%.
These percentages are purely statistical and differences between
two nucleic acid sequences can be distributed randomly and over the
entire sequence length.
[0069] In various embodiments, homologous sequences can exhibit a
percent identity of 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,
49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82,
83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or
99 percent with the sequences of the instant invention. Typically,
the percent identity is calculated with reference to the full
length, native, and/or naturally occurring polypeptide or
polynucleotide (e.g., those polypeptides set forth in SEQ ID NOs:
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 26, 27 or those set forth in SEQ ID
NOs:28-81)). The terms "identical" or percent "identity", in the
context of two or more polynucleotide or polypeptide sequences,
refer to two or more sequences or subsequences that are the same or
have a specified percentage of amino acid residues that are the
same, when compared and aligned for maximum correspondence over a
comparison window, as measured using a sequence comparison
algorithm or by manual alignment and visual inspection. Preferably,
such a substitution is made in accordance with analoging principles
set forth, e.g., in co-pending U.S. Ser. No. 09/260,714 filed Mar.
1, 1999 and Ser. No. 09/226,775, filed Jan. 6, 1999 and PCT
application number PCT/US00/19774 each of which is hereby
incorporated by reference in its entirety.
[0070] Both protein and nucleic acid sequence homologies may be
evaluated using any of the variety of sequence comparison
algorithms and programs known in the art. Such algorithms and
programs include, but are by no means limited to, TBLASTN, BLASTP,
FASTA, TFASTA, and CLUSTALW (Pearson and Lipman, 1988, Proc. Natl.
Acad. Sci. USA 85(8):2444-2448; Altschul et al., 1990, J. Mol.
Biol. 215(3):403-410; Thompson et al., 1994, Nucleic Acids Res.
22(2):4673-4680; Higgins et al., 1996, Methods Enzymol.
266:383-402; Altschul et al., 1990, J. Mol. Biol. 215(3):403-410;
Altschul et al., 1993, Nature Genetics 3:266-272). Sequence
comparisons are, typically, conducted using default parameters
provided by the vendor or using those parameters set forth in the
above-identified references, which are hereby incorporated by
reference in their entireties. A "complementary" polynucleotide
sequence, as used herein, generally refers to a sequence arising
from the hydrogen bonding between a particular purine and a
particular pyrimidine in double-stranded nucleic acid molecules
(DNA-DNA, DNA-RNA, or RNA-RNA). The major specific pairings are
guanine with cytosine and adenine with thymine or uracil. A
"complementary" polynucleotide sequence may also be referred to as
an "antisense" polynucleotide sequence or an "antisense"
sequence.
[0071] Sequence homology and sequence identity can also be
determined by hybridization studies under high stringency,
intermediate stringency, and/or low stringency. Various degrees of
stringency of hybridization can be employed. The more severe the
conditions, the greater the complementarity that is required for
duplex formation. Severity of conditions can be controlled by
temperature, probe concentration, probe length, ionic strength,
time, and the like. Preferably, hybridization is conducted under
low, intermediate, or high stringency conditions by techniques well
known in the art, as described, for example, in Keller, G. H., M.
M. Manak [1987] DNA Probes, Stockton Press, New York, N.Y., pp.
169-170.
[0072] For example, hybridization of immobilized. DNA on Southern
blots with .sup.32P-labeled gene-specific probes can be performed
by standard methods (Maniatis et al. [1982] Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory, New York). In
general, hybridization and subsequent washes can be carried out
under intermediate to high stringency conditions that allow for
detection of target sequences with homology to the exemplified
polynucleotide sequence. For double-stranded DNA gene probes,
hybridization can be carried out overnight at 20-25.degree. C.
below the melting temperature (T.sub.m) of the DNA hybrid in
6.times.SSPE, 5.times.Denhardt's solution, 0.1% SDS, 0.1 mg/ml
denatured DNA. The melting temperature is described by the
following formula (Beltz et al. [1983] Methods of Enzymology, R.
Wu, L. Grossman and K. Moldave [eds.] Academic Press, New York
100:266-285).
Tm=81.5.degree. C.+16.6 Log [Na.sup.+]0.41(% G+C)-0.61(%
formamide)-600/length of duplex in base pairs.
[0073] Washes are typically carried out as follows: [0074] (1)
twice at room temperature for 15 minutes in 1.times.SSPE, 0.1% SDS
(low stringency wash); [0075] (2) once at T.sub.m-20.degree. C. for
15 minutes in 0.2.times.SSPE, 0.1% SDS (intermediate stringency
wash).
[0076] For oligonucleotide probes, hybridization can be carried out
overnight at 10-20.degree. C. below the melting temperature
(T.sub.m) of the hybrid in 6.times.SSPE, 5.times.Denhardt's
solution, 0.1% SDS, 0.1 mg/ml denatured DNA. T.sub.m for
oligonucleotide probes can be determined by the following
formula:
T.sub.m (.degree. C.)=2(number T/A base pairs).sup.+4(number G/C
base pairs) (Suggs et al. [1981] ICN-UCLA Symp. Dev. Biol. Using
Purified Genes, D. D. Brown [ed.], Academic Press, New York,
23:683-693).
[0077] Washes can be carried out as follows: [0078] (1) twice at
room temperature for 15 minutes 1.times.SSPE, 0.1% SDS (low
stringency wash); [0079] 2) once at the hybridization temperature
for 15 minutes in 1.times.SSPE, 0.1% SDS (intermediate stringency
wash).
[0080] In general, salt and/or temperature can be altered to change
stringency. With a labeled DNA fragment >70 or so bases in
length, the following conditions can be used:
[0081] Low: 1 or 2.times.SSPE, room temperature
[0082] Low: 1 or 2.times.SSPE, 42.degree. C.
[0083] Intermediate: 0.2.times. or 1.times.SSPE, 65.degree. C.
[0084] High: 0.1.times.SSPE, 65.degree. C.
[0085] By way of another non-limiting example, procedures using
conditions of high stringency can also be performed as follows:
Pre-hybridization of filters containing DNA is carried out for 8 h
to overnight at 65.degree. C. in buffer composed of 6.times.SSC, 50
mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02%
BSA, and 500 .mu.g/ml denatured salmon sperm DNA. Filters are
hybridized for 48 h at 65.degree. C., the preferred hybridization
temperature, in pre-hybridization mixture containing 100 .mu.g/ml
denatured salmon sperm DNA and 5-20.times.10.sup.6 cpm of
.sup.32P-labeled probe. Alternatively, the hybridization step can
be performed at 65.degree. C. in the presence of SSC buffer,
1.times.SSC corresponding to 0.15M NaCl and 0.05 M Na citrate.
Subsequently, filter washes can be done at 37.degree. C. for 1 h in
a solution containing 2.times.SSC, 0.01% PVP, 0.01% Ficoll, and
0.01% BSA, followed by a wash in 0.1.times.SSC at 50.degree. C. for
45 min. Alternatively, filter washes can be performed in a solution
containing 2.times.SSC and 0.1% SDS, or 0.5.times.SSC and 0.1% SDS,
or 0.1.times.SSC and 0.1% SDS at 68.degree. C. for 15 minute
intervals. Following the wash steps, the hybridized probes are
detectable by autoradiography. Other conditions of high stringency
which may be used are well known in the art and as cited in
Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual,
Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and
Ausubel et al., 1989, Current Protocols in Molecular Biology, Green
Publishing Associates and Wiley Interscience, N.Y. are incorporated
herein in their entirety.
[0086] Another non-limiting example of procedures using conditions
of intermediate stringency are as follows: Filters containing DNA
are pre-hybridized, and then hybridized at a temperature of
60.degree. C. in the presence of a 5.times.SSC buffer and labeled
probe. Subsequently, filters washes are performed in a solution
containing 2.times.SSC at 50.degree. C. and the hybridized probes
are detectable by autoradiography. Other conditions of intermediate
stringency which may he used are well known in the art and as cited
in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual,
Second Edition, Cold Spring Harbor Press, N.Y., pp. 9.47-9.57; and
Ausubel et al., 1989, Current Protocols in Molecular Biology, Green
Publishing Associates and Wiley Interscience, N.Y. are incorporated
herein in their entirety.
[0087] Duplex formation and stability depend on substantial
complementarity between the two strands of a hybrid and, as noted
above, a certain degree of mismatch can be tolerated. Therefore,
the probe sequences of the subject invention include mutations
(both single and multiple), deletions, insertions of the described
sequences, and combinations thereof, wherein said mutations,
insertions and deletions permit formation of stable hybrids with
the target polynucleotide of interest. Mutations, insertions and
deletions can be produced in a given polynucleotide sequence in
many ways, and these methods are known to an ordinarily skilled
artisan. Other methods may become known in the future. It is also
well known in the art that restriction enzymes can be used to
obtain functional fragments of the subject DNA sequences. For
example, Bal31 exonuclease can be conveniently used for
time-controlled limited digestion of DNA (commonly referred to as
"erase-a-base" procedures). See, for example, Maniatis et al.
[1982] Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratory, New York; Wei et al. [1983] J. Biol. Chem.
258:13006-13512.
[0088] The present invention further comprises fragments of the
polynucleotide sequences of the instant invention. Representative
fragments of the polynucleotide sequences according to the
invention will be understood to mean any nucleotide fragment having
at least 8 successive nucleotides, preferably at least 12
successive nucleotides, and still more preferably at least 15 or at
least 20 successive nucleotides of the sequence from which it is
derived. The upper limit for such fragments is the total number of
polynucleotides found in the full length sequence (or, in certain
embodiments, of the full length open reading frame (ORF) identified
herein).
[0089] In some embodiments, the subject invention includes those
fragments capable of hybridizing under various conditions of
stringency conditions (e.g., high or intermediate or low
stringency) with a nucleotide sequence according to the invention;
fragments that hybridize with a nucleotide sequence of the subject
invention can be, optionally, labeled as set forth below.
[0090] Other embodiments provide for nucleic acid fragments
corresponding to nucleotide sequences comprising full, or partial,
open reading frames (ORF sequences). Also within the scope of the
invention are those polynucleotide fragments encoding polypeptides
reactive with antibodies found in the serum of individuals infected
with P. falciparum. Fragments according to the subject invention
can be obtained, for example, by specific amplification (e.g., PCR
amplification), digestion with restriction enzymes, of nucleotide
sequences according to the invention. Such methodologies are
well-known in the art and are taught, for example, by Sambrook et
al., 1989. Nucleic acid fragments according to the invention can
also be obtained by chemical synthesis according to methods well
known to persons skilled in the art.
[0091] The subject invention also provides nucleic acid based
methods for the identification of the presence of an organism in a
sample. In these varied embodiments, the invention provides for the
detection of nucleic acids in a sample comprising contacting a
sample with a nucleic acid (polynucleotide) of the subject
invention (such as an RNA, mRNA, DNA, cDNA, or other nucleic acid).
In a preferred embodiment, the polynucleotide is a probe that is,
optionally, labeled and used in the detection system. Many methods
for detection of nucleic acids exist and any suitable method for
detection is encompassed by the instant invention. Typical assay
formats utilizing nucleic acid hybridization includes, and are not
limited to, 1) nuclear run-on assay, 2) slot blot assay, 3)
northern blot assay (Alwine, et al. Proc. Natl. Acad. Sci.
74:5350), 4) magnetic particle separation, 5) nucleic Acid or DNA
chips, 6) reverse Northern blot assay, 7) dot blot assay, 8) in
situ hybridization, 9) RNase protection assay (Melton, et al. Nuc.
Acids Res. 12:7035 and as described in the 1998 catalog of Ambion,
Inc., Austin, Tex.), 10) ligase chain reaction, 11) polymerase
chain reaction (PCR), 12) reverse transcriptase (RT)-PCR
(Berchtold, et al. Nuc. Acids. Res. 17:453), 13) differential
display RT-PCR (DDRT-PCR) or other suitable combinations of
techniques and assays. Labels suitable for use in these detection
methodologies include, and are not limited to 1) radioactive
labels, 2) enzyme labels, 3) chemiluminescent labels, 4)
fluorescent labels, 5) magnetic labels, or other suitable labels,
including those set forth below. These methodologies and labels are
well known in the art and widely available to the skilled artisan.
Likewise, methods of incorporating labels into the nucleic acids
are also well known to the skilled artisan.
[0092] Thus, the subject invention also provides detection probes
(e.g., fragments of the disclosed polynucleotide sequences) for
hybridization with a target sequence or the amplicon generated from
the target sequence. Such a detection probe will advantageously
have as sequence a sequence of at least 8, 9, 10, 11, 12, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45,
50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides. Labeled
probes or primers are labeled with a radioactive compound or with
another type of label as set forth above. Alternatively,
non-labeled nucleotide sequences may be used directly as probes or
primers; however, the sequences are generally labeled with a
radioactive element (.sup.32P, .sup.35.sub.S, .sup.3H, .sup.125I)
or w.sub.it.sub.h a molecule such as biotin, acetylaminofluorene,
digoxigenin, 5-bromo-deoxyuridine, or fluorescein to provide probes
that can be used in numerous applications.
[0093] The polynucleotide sequences according to the invention may
also he used in analytical systems, such as DNA chips. DNA chips
and their uses are well known in the art and (see for example, U.S.
Pat. Nos. 5,561,071; 5,753,439; 6,214,545; Schena et al.,
BioEssays, 1996, 18:427-431; Bianchi et al., Clin. Diagn. Virol.,
1997, 8:199-208; each of which is hereby incorporated by reference
in their entireties) and/or are provided by commercial vendors such
as Affymetrix, Inc. (Santa Clara, Calif.). In addition, the nucleic
acid sequences of the subject invention can be used as molecular
weight markers in nucleic acid analysis procedures.
[0094] The subject invention also provides for modified nucleotide
sequences. Modified nucleic acid sequences will be understood to
mean any nucleotide sequence that has been modified, according to
techniques well known to persons skilled in the art, and exhibiting
modifications in relation to the native, naturally occurring
nucleotide sequences. One non-limiting example of a "modified"
nucleotide sequences includes mutations in regulatory and/or
promoter sequences of a polynucleotide sequence that result in a
modification of the level of expression of the polypeptide. A
"modified" nucleotide sequence will also be understood to mean any
nucleotide sequence encoding a "modified" polypeptide as defined
below.
[0095] Another aspect of the invention provides vectors for the
cloning and/or the expression of a polynucleotide sequence taught
herein. Vectors of this invention, including vaccine vectors, can
also comprise elements necessary to allow the expression and/or the
secretion of the said nucleotide sequences in a given host cell.
The vector can contain a promoter, signals for initiation and for
termination of translation, as well as appropriate regions for
regulation of transcription. In certain embodiments, the vectors
can be stably maintained in the host cell and can, optionally,
contain signal sequences directing the secretion of translated
protein. These different elements are chosen according to the host
cell used. Vectors can integrate into the host genome or,
optionally, be autonomously-replicating vectors.
[0096] The subject invention also provides for the expression of a
polypeptide, peptide, derivative, or variant encoded by a
polynucleotide sequence disclosed herein comprising the culture of
an organism transformed with a polynucleotide of the subject
invention under conditions that allow for the expression of the
polypeptide, peptide, derivative, or analog and, optionally,
recovering the expressed polypeptide, peptide, derivative, or
analog.
[0097] The disclosed polynucleotide sequences can also be regulated
by a second nucleic acid sequence so that the protein or peptide is
expressed in a host transformed with the recombinant DNA molecule.
For example, expression of a protein or peptide may be controlled
by any promoter/enhancer element known in the art. Promoters which
may be used to control expression include, but are not limited to,
the CMV-IE promoter, the SV40 early promoter region (Bernoist and
Chambon, 1981, Nature 290:304-310), the promoter contained in the
3' long terminal repeat of Rous sarcoma virus (Yamamoto, et al.,
1980, Cell 22:787-797), the herpes simplex thymidine kinase
promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. U.S.A.
78:1441-1445), the regulatory sequences of the metallothionein gene
(Brinster et al., 1982, Nature 296:39-42); prokaryotic vectors
containing promoters such as the .beta.-lactamase promoter
(Villa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. U.S.A.
75:3727-3731), or the tac promoter (DeBoer, et al., 1983, Proc.
Natl. Acad. Sci. U.S.A. 80:21-25); see also "Useful proteins from
recombinant bacteria" in Scientific American, 1980, 242:74-94;
plant expression vectors comprising the nopaline synthetase
promoter region (Herrera-Estrella et al., 1983, Nature 303:209-213)
or the cauliflower mosaic virus 35S RNA promoter (Gardner, et al.,
1981, Nucl. Acids Res. 9:2871), and the promoter of the
photosynthetic enzyme ribulose biphosphate carboxylase
(Herrera-Estrella et al., 1984, Nature 310:115-120); promoter
elements from yeast or fungi such as the Gal 4 promoter, the ADC
(alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase)
promoter, and/or the alkaline phosphatase promoter.
[0098] The vectors according to the invention are, for example,
vectors of plasmid or viral origin. In a specific embodiment, a
vector is used that comprises a promoter operably linked to a
protein or peptide-encoding nucleic acid sequence contained within
the disclosed polynucleotide sequences, one or more origins of
replication, and, optionally, one or more selectable markers (e.g.,
an antibiotic resistance gene). Expression vectors comprise
regulatory sequences that control gene expression, including gene
expression in a desired host cell. Exemplary vectors for the
expression of the polypeptides of the invention include the
pET-type plasmid vectors (Promega) or pBAD plasmid vectors
(Invitrogen) or those provided in the examples below. Furthermore,
the vectors according to the invention are useful for transforming
host cells so as to clone or express the polynucleotide sequences
of the invention.
[0099] The invention also encompasses the host cells transformed by
a vector according to the invention. These cells may be obtained by
introducing into host cells a nucleotide sequence inserted into a
vector as defined above, and then culturing the said cells under
conditions allowing the replication and/or the expression of the
polynucleotide sequences of the subject invention.
[0100] The host cell may be chosen from eukaryotic or prokaryotic
systems, such as for example bacterial cells, (Gram negative or
Gram positive), yeast cells (for example, Saccharomyces cereviseae
or Pichia pastoris), animal cells (such as Chinese hamster ovary
(CHO) cells), plant cells, and/or insect cells using baculovirus
vectors. In some embodiments, the host cells for expression of the
polypeptides include, and are not limited to, those taught in U.S.
Pat. Nos. 6,319,691, 6,277,375, 5,643,570, or 5,565,335, each of
which is incorporated by reference in its entirety, including all
references cited within each respective patent.
[0101] Furthermore, a host cell strain may be chosen which
modulates the expression of the inserted sequences, or modifies and
processes the gene product in the specific fashion desired.
Expression from certain promoters can be elevated in the presence
of certain inducers; thus, expression of the genetically engineered
polypeptide may be controlled. Furthermore, different host cells
have characteristic and specific mechanisms for the translational
and post-translational processing and modification (e.g.,
glycosylation, phosphorylation) of proteins. Appropriate cell lines
or host systems can be chosen to ensure the desired modification
and processing of the foreign protein expressed. For example,
expression in a bacterial system can be used to produce an
unglycosylated core protein product. Expression in yeast will
produce a glycosylated product. Expression in mammalian cells can
be used to ensure "native" glycosylation of a heterologous protein.
Furthermore, different vector/host expression systems may effect
processing reactions to different extents.
[0102] The subject invention also concerns novel compositions that
can be employed to elicit an immune response or a protective immune
response. In this aspect of the invention, an amount of a
composition comprising recombinant DNA or mRNA encoding an
polynucleotide of the subject invention sufficient to elicit an
immune response or protective immune response is administered to an
individual. Signal sequences may be deleted from the nucleic acid
encoding an antigen of interest and the individual may be monitored
for the induction of an immune response according to methods known
in the art. A "protective immune response" or "therapeutic immune
response" refers to a CTL (or CD8.sup.+ T cell) and/or an HTL (or
CD4.sup.+ T cell) response to an antigen that, in some way,
prevents or at least partially arrests disease symptoms, side
effects or progression. The immune response may also include an
antibody response that has been facilitated by the stimulation of
helper T cells.
[0103] In another embodiment, the subject invention further
comprises the administration of polynucleotide vaccines in
conjunction with a polypeptide antigen, or composition thereof, of
the invention. In a preferred embodiment, the antigen is the
polypeptide that is encoded by the polynucleotide administered as
the polynucleotide vaccine. As a particularly preferred embodiment,
the polypeptide antigen is administered as a booster subsequent to
the initial administration of the polynucleotide vaccine.
[0104] A further embodiment of the subject invention provides for
the induction of an immune response to the novel Plasmodium
falciparum antigens disclosed herein (see, for example, the
antigens and peptides set forth in the Tables and Sequence Listing
attached hereto) using a "prime-boost" vaccination regimen known to
those skilled in the art. In this aspect of the invention, a DNA
vaccine is administered to an individual in an amount sufficient to
"prime" the immune response of the individual, provided that the
DNA vaccine comprises nucleic acids encoding the antigens,
multi-epitope constructs, and/or peptide antigens set forth herein.
The immune response of the individual is then "boosted" via the
administration of: 1) one or a combination of: a peptide,
polypeptide, and/or full length polypeptide antigen (e.g., SEQ ID
NOs: 1-27) of the subject invention (optionally in conjunction with
a immunostimulatory molecule and/or an adjuvant); or 2) a viral
vector that contains nucleic acid encoding one, or more, of the
same or, optionally, different, antigens, multi-epitope constructs,
and/or peptide antigens set forth in the Tables or Sequence Listing
of the subject application. In some alternative embodiments of the
invention, a gene encoding an immunostimulatory molecule may be
incorporated into the viral vector used to "boost the immune
response of the individual. Exemplary immunostimulatory molecules
include, and are not limited to, IL-1, IL-2, IL-3, IL-4, IL-5,
IL-6, IL-7, IL-8, 1L-9, IL-10, IL-11, IL-15, 11-16, 11-18, IL-23,
IL-24, erythropoietin, G-CSF, M-CSF, platelet derived growth factor
(PDGF), MSF, FLT-3 ligand, EGF, fibroblast growth factor (FGF;
e.g., aFGF (FGF-1), bFGF (FGF-2), FGF-3, FGF-4, FGF-5, FGF-6, or
FGF-7), insulin-like growth factors (e.g., IGF-1, IGF-2); vascular
endothelial growth factor (VEGF); interferons (e.g., IFN-.gamma.,
IFN-.alpha., IFN-.beta.); leukemia inhibitory factor (LIF); ciliary
neurotrophic factor (CNTF); oncostatin M; stem cell factor (SCF);
transforming growth factors (e.g., TGF-a, TGF-.beta.1, TGF-.beta.1,
TGF-.beta.1), or chemokines (such as, but not limited to,
BCA-1/BLC-1, BRAK/Kec, CXCL16, CXCR3, ENA-78/LIX, Eotaxin-1,
Eotaxin-2/MPIF-2, Exodus-2/SLC, Fractalkine/Neurotactin,
GROalpha/MGSA, HCC-1, I-TAC, Lymphotactin/ATAC/SCM, MCP-1/MCAF,
MCP-3, MCP-4, MDC/STCP-1, ABCD-1, MIP-1.alpha., MIP-1.beta.,
MIP-2.alpha./GRO.beta., MIP-3.alpha./Exodus/LARC,
MIP-3.beta./Exodus-3/ELC, MIP-4/PARC/DC-CK1, PF-4, RANTES,
SDF1.alpha., TARC, or TECK). Genes encoding these immunostimulatory
molecules are known to those skilled in the art and coding
sequences may be obtained from a variety of sources, including
various patents databases, publicly available databases (such as
the nucleic acid and protein databases found at the National
Library of Medicine or the European Molecular Biology Laboratory),
the scientific literature, or scientific literature cited in
catalogs produced by companies such as Genzyme, Inc., R&D
Systems, Inc, or InvivoGen, Inc. [see, for example, the 1995
Cytokine Research Products catalog, Genzyme Diagnostics, Genzyme
Corporation, Cambridge Mass.; 2002 or 1995 Catalog of R&D
Systems, Inc (Minneapolis, Minn.); or 2002 Catalog of InvivoGen,
Inc (San Diego, Calif.) each of which is incorporated by reference
in its entirety, including all references cited therein].
[0105] Methods of introducing DNA vaccines into individuals are
well-known to the skilled artisan. For example, DNA can be injected
into skeletal muscle or other somatic tissues (e.g., intramuscular
injection). Cationic liposomes or biolistic devices, such as a gene
gun, can be used to deliver DNA vaccines. Alternatively,
iontophoresis and other means for transdermal transmission can be
used for the introduction of DNA vaccines into an individual.
[0106] Viral vectors for use in the subject invention can have a
portion of the viral genome deleted to introduce new genes without
destroying infectivity of the virus. The viral vector of the
present invention is, typically, a non-pathogenic virus. At the
option of the practitioner, the viral vector can be selected so as
to infect a specific cell type, such as professional antigen
presenting cells (e.g., macrophage or dendritic cells).
Alternatively, a viral vector can be selected that is able to
infect any cell in the individual. Exemplary viral vectors suitable
for use in the present invention include, but are not limited to
poxvirus such as vaccinia virus, avipox virus, fowlpox virus, a
highly attenuated vaccinia virus (such as Ankara or MVA [Modified
Vaccinia Ankara]), retrovirus, adenovirus, baculovirus and the
like. In a preferred embodiment, the viral vector is Ankara or MVA.
General strategies for construction of vaccinia virus expression
vectors are known in the art (see, for example, Smith and Moss Bio
Techniques November/December, 306-312, 1984; U.S. Pat. No.
4,738,846 (hereby incorporated by reference in its entirety).
Sutter and Moss (Proc. Nat'l. Acad. Sci U.S.A. 89:10847-10851,
1992) and Sutter et al. (Vaccine, 12(11):1032-40, 1994) disclose
the construction and use as a vector, a non-replicating recombinant
Ankara virus (MVA) which can be used as a viral vector in the
present invention. Other versions of the Modified Vaccinia Ankara
strain can also be used in the practice of the subject invention
(such as the MVA-BN strain produced by Bavarian Nordic S/A
(Copenhagen, Denmark).
[0107] Compositions comprising the subject polynucleotides can
include appropriate nucleic acid vaccine vectors (plasmids), which
are commercially available (e.g., Vical, San Diego, Calif.) or
other nucleic acid vectors (plasmids), which are also commercially
available (e.g., Valenti, Burlingame, Calif.). Alternatively,
compositions comprising viral vectors and polynucleotides according
to the subject invention are provided by the subject invention. In
addition, the compositions can include a pharmaceutically
acceptable carrier, e.g., saline. The pharmaceutically acceptable
carriers are well known in the art and also are commercially
available. For example, such acceptable carriers are described in
E. W. Martin's Remington's Pharmaceutical Science, Mack Publishing
Company, Easton, Pa.
[0108] The subject invention also provides one or more isolated
polypeptides comprising: [0109] a) a polypeptide encoded by a
polynucleotide sequence according to embodiment A(a) (set forth
above); [0110] b) a variant polypeptide encoded by a polynucleotide
sequence having at least about 20% to 99.99% identity to a
polynucleotide according to embodiment A(a) (as set forth above);
[0111] c) a fragment of a polypeptide or a variant polypeptide,
wherein said fragment or variant has substantially the same
serologic reactivity or substantially the same T-cell reactivity as
the native polypeptide (e.g., those polypeptides set forth in SEQ
ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27 and Table 2, 3, 4, 5 or 6);
[0112] d) a polypeptide sequence provided in Table 2, 3, 4, 5 or 6
or selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 26, and 27; [0113] e) a variant polypeptide having at
least about 20% to 99.99% identity to a polypeptide provided in
Table 2, 3, 4, 5 or 6 or selected from the group consisting of SEQ
ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27; [0114] f) a
polypeptide (epitope) set forth in Table 2, 3, 4, 5 or 6; or [0115]
g) a multi-epitope construct: 1) comprising at least one epitope
set forth in Table 2, 3, 4, 5 or 6; 2) comprising a polypeptide
selected from the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, and 27 and at least one epitope set forth in Tables 2,
3, 4, 5 or 6; or 3) comprising and at least one epitope set forth
in Tables 2, 3, 4, 5 or 6 and one or more polypeptide selected from
the group consisting of SEQ ID NO: NO: 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
and 27.
[0116] The term "peptide" may be used interchangeably with
"oligopeptide" or "polypeptide" or "epitope" in the present
specification to designate a series of residues, typically L-amino
acids, connected one to the other, typically by peptide bonds
between the .alpha.-amino and carboxyl groups of adjacent amino
acids. The preferred CTL (or CD8.sup.+ T cell)-inducing peptides of
the invention are 13 residues or less in length and usually consist
of between about 8 and about 11 residues (e.g., 8, 9, 10 or 11
residues), preferably 9 or 10 residues. The preferred HTL (or
CD4.sup.+ T cell)-inducing peptides are less than about 50 residues
in length and usually consist of between about 6 and about 30
residues, more usually between about 12 and 25 (e.g., 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25), and often between
about 15 and 20 residues (e.g., 15, 16, 17, 18, 19 or 20).
[0117] According to the subject invention, a "fragment" is a
polypeptide of at least 3 consecutive, preferably 4 consecutive,
and even more preferably 5 consecutive amino acids. In some
embodiments, the polypeptide fragments are reactive with antibodies
found in the serum of an individual. In other embodiments, a
fragment is an "epitope" as described supra. In the context of the
instant invention, the terms polypeptide, peptide and protein can
be used interchangeably; however, it should be understood that the
invention does not relate to the polypeptides in natural form, that
is to say that they are not in their natural environment but that
the polypeptides may have been isolated or obtained by purification
from natural sources, obtained from host cells prepared by genetic
manipulation (e.g., the polypeptides, or fragments thereof, are
recombinantly produced by host cells, or by chemical synthesis).
Polypeptides according to the instant invention may also contain
non-natural amino acids, as will be described below.
[0118] A "variant" or "modified" polypeptide (or polypeptide
variant) is to be understood to designate polypeptides exhibiting,
in relation to the natural polypeptide, certain modifications.
These modifications can include a deletion, addition, or
substitution of at least one amino acid, a truncation, an
extension, a chimeric fusion, a mutation, or polypeptides
exhibiting post-translational modifications. Among the homologous
polypeptides, those whose amino acid sequences exhibit between at
least (or at least about) 20.00% to 99.99% (inclusive) identity to
the full length, native, or naturally occurring polypeptide are
another aspect of the invention. The aforementioned range of
percent identity is to be taken as including, and providing written
description and support for, any fractional percentage, in
intervals of 0.01%, between 20.00% and, up to, including 99.99%.
These percentages are purely statistical and differences between
two polypeptide sequences can be distributed randomly and over the
entire sequence length.
[0119] Variant peptides (epitopes) can also be created by altering
the presence or absence of particular residues in these primary
anchor positions. Such analogs are used to modulate the binding
affinity of a peptide comprising a particular motif or supermotif.
The term "motif' refers to the pattern of residues in a peptide of
defined length, usually a peptide of from about 8 to about 13 amino
acids for a class I HLA motif (e.g., 8, 9, 10, 11, 12 or 13 aa) and
from about 6 to about 25 amino acids for a class II HLA motif
(e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
22, 23, 24 or 25 amino acids), which is recognized by a particular
HLA molecule. Peptide motifs are typically different for each
protein encoded by each human HLA allele and differ in the pattern
of the primary and secondary anchor residues. Optionally, variant
peptides or polypeptides can also comprise one or more heterologous
polypeptide sequences (e.g., tags that facilitate purification of
the polypeptides of the invention (see, for example, U.S. Pat. No.
6,342,362, hereby incorporated by reference in its entirety;
Altendorf et al. [1999-WWW, 2000] "Structure and Function of the
F.sub.o Complex of the ATP Synthase from Escherichia Coli," J. of
Experimental Biology 203:19-28, The Co. of Biologists, Ltd., G. B.;
Baneyx [1999] "Recombinant Protein Expression in Escherichia coli,"
Biotechnology 10:411-21, Elsevier Science Ltd.; Eihauer et al.
[2001] "The FLAG.TM. Peptide, a Versatile Fusion Tag for the
Purification of Recombinant Proteins," J. Biochem Biophys Methods
49:455-65; Jones et al. [1995] J. Chromatography 707:3-22; Jones et
al. [1995] "Current Trends in Molecular Recognition and
Bioseparation," J. of Chromatography A. 707:3-22, Elsevier Science
B. V.; Margolin [2000] "Green Fluorescent Protein as a Reporter for
Macromolecular Localization in Bacterial Cells," Methods 20:62-72,
Academic Press; Puig et al. [2001] "The Tandem Affinity
Purification (TAP) Method: A General Procedure of Protein Complex
Purification," Methods 24:218-29, Academic Press; Sassenfeld [1990]
"Engineering Proteins for Purification," TibTech 8:88-93; Sheibani
[1999] "Prokaryotic Gene Fusion Expression Systems and Their Use in
Structural and Functional Studies of Proteins," Prep. Biochem.
& Biotechnol. 29(1):77-90, Marcel Dekker, Inc.; Skerra et al.
[1999] "Applications of a Peptide Ligand for Streptavidin: the
Strep-tag", Biomolecular Engineering 16:79-86, Elsevier Science, B.
V.; Smith [1998] "Cookbook for Eukaryotic Protein Expression:
Yeast, Insect, and Plant Expression Systems," The Scientist
12(22):20; Smyth et al. [200] "Eukaryotic Expression and
Purification of Recombinant Extracellular Matrix Proteins Carrying
the Strep II Tag", Methods in Molecular Biology, 139:49-57; Unger
[1997] "Show Me the Money: Prokaryotic Expression Vectors and
Purification Systems," The Scientist 11(17):20, each of which is
hereby incorporated by reference in their entireties), or
commercially available tags from vendors such as such as STRATAGENE
(La Jolla, Calif.), NOVAGEN (Madison, Wis.), QIAGEN, Inc.,
(Valencia, Calif.), or InVitrogen (San Diego, Calif.).
[0120] Variant polypeptides can, alternatively, have 20, 21, 22,
23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,
57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 94, 95, 96, 97, 98, or 99 percent identity with the
polypeptide sequences of the instant invention. In a preferred
embodiment, a variant or modified polypeptide exhibits
approximately 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,
95%, 96%, 97%, 98%, or 99% identity to a natural polypeptic of the
invention. Typically, the percent identity is calculated with
reference to the full length, native, and/or naturally occurring
polypeptide (e.g., those polypeptides set forth in SEQ ID NOs: 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, or 27).
[0121] The nomenclature used to describe peptide compounds follows
the conventional practice wherein the amino group is presented to
the left (the N-terminus) and the carboxyl group to the right (the
C-terminus) of each amino acid residue. When amino acid residue
positions are referred to in an epitope, they are numbered in an
amino to carboxyl direction with position one being the position
closest to the amino terminal end of the epitope, or the peptide or
protein of which it may be a part. In the formulae representing
selected specific embodiments of the present invention, the amino-
and carboxyl-tenninal groups, although not specifically shown, are
in the form they would assume at physiologic pH values, unless
otherwise specified. In the amino acid structure formulae, each
residue is generally represented by standard three-letter or
single-letter designations (e.g., as set forth infra). By way of
example, amino acid substitutions can be carried out without
resulting in a substantial modification of the biological activity
of the corresponding modified polypeptides; for example, the
replacement of leucine with valine or isoleucine, of aspartic acid
with glutamic acid, of glutamine with asparagine, of arginine with
lysine, and the like, the reverse substitutions can be performed
without substantial modification of the biological activity of the
polypeptides.
[0122] The L-form of an amino acid residue is represented by a
capital single letter or a capital first letter of a three-letter
symbol, and the D-form, for those amino acids having D-forms, is
represented by a lower case single letter or a lower case three
letter symbol. Glycine has no asymmetric carbon atom and is simply
referred to as "Gly" or G. Symbols for the amino acids are as
follows: (Single Letter Symbol; Three Letter Symbol Amino Acid) A;
Ala; Alanine: C; Cys; Cysteine: D; Asp; Aspartic Acid: E; Glu;
Glutamic Acid: F; Phe; Phenylalanine: G; Gly; Glycine: H; His;
Histidine: I; Ile; Isoleucine: K; Lys; Lysine: L; Leu; Leucine: M;
Met; Methionine: N; Asn; Asparagine: P; Pro; Proline: Q; Gln;
Glutamine: R; Arg; Arginine: S; Ser; Serine: T; Thr; Threonine: V;
Val; Valine: W; Trp; Tryptophan: Y; Tyr; Tyrosine.
[0123] Amino acid "chemical characteristics" are defined as:
Aromatic (F, W, Y); Aliphatic-hydrophobic (L, I, V, M); Small polar
(S, T, C); Large polar (Q, N); Acidic (D, E); Basic (R, H, K);
Non-polar: Proline; Alanine; and Glycine.
[0124] In order to extend the life of the polypeptides according to
the invention, it may be advantageous to use non-natural amino
acids, for example in the D-form, or alternatively amino acid
analogs, for example sulfur-containing forms of amino acids in the
production of "variant polypeptides". Alternative means for
increasing the life of polypeptides can also he used in the
practice of the instant invention. For example, polypeptides of the
invention, and fragments thereof, can be recombinantly modified to
include elements that increase the plasma, or serum half-life of
the polypeptides of the invention. These elements include, and are
not limited to, antibody constant regions (see for example, U.S.
Pat. No. 5,565,335, hereby incorporated by reference in its
entirety, including all references cited therein), or other
elements such as those disclosed in U.S. Pat. Nos. 6,319,691,
6,277,375, or 5,643,570, each of which is incorporated by reference
in its entirety, including all references cited within each
respective patent. Alternatively, the polynucleotides and genes of
the instant invention can be recombinantly fused to elements, well
known to the skilled artisan, that are useful in the preparation of
immunogenic constructs for the purposes of vaccine formulation.
[0125] The subject invention also provides biologically active
fragments (epitopes) of a polypeptide according to the invention
and includes those peptides capable of eliciting an immune response
directed against P. falciparum, said immune response providing
components (B-cells, antibodies, and/or or components of the
cellular immune response (e.g., helper, cytotoxic, and/or
suppressor T-cells)) reactive with the biologically active fragment
of a polypeptide; the intact, full length, unmodified polypeptide
disclosed herein; or both the biologically active fragment of a
polypeptide and the intact, full length, unmodified polypeptides
disclosed herein.
[0126] Fragments, as described herein, can be obtained by cleaving
the polypeptides of the invention with a proteolytic enzyme (such
as trypsin, chymotrypsin, or collagenase) or with a chemical
reagent, such as cyanogen bromide (CNBr). Alternatively,
polypeptide fragments can be generated in a highly acidic
environment, for example at pH 2.5. Such polypeptide fragments may
be equally well prepared by chemical synthesis or using hosts
transformed with an expression vector according to the invention.
The transformed host cells contain a nucleic acid, allowing the
expression of these fragments, under the control of appropriate
elements for regulation and/or expression of the polypeptide
fragments.
[0127] In one embodiment, the subject invention provides methods
for eliciting an immune response in an individual comprising the
administration of compositions comprising polypeptides according to
the subject invention to an individual in amounts sufficient to
induce an immune response in the individual. In some embodiments, a
"protective" or "therapeutic immune response" is induced in the
individual. A "protective immune response" or "therapeutic immune
response" refers to a CTL (or CD8.sup.+ T cell) and/or an HTL (or
CD4.sup.+ T cell), and/or an antibody response to an antigen
derived from an infectious agent or a tumor antigen, which in some
way prevents or at least partially arrests disease symptoms, side
effects or progression. The protective immune response may also
include an antibody response that has been facilitated by the
stimulation of helper T cells (or CD4.sup.+ T cells). Additional
methods of inducing an immune response in an individual are taught
in U.S. Pat. No. 6,419,931, hereby incorporated by reference in its
entirety. The term CTL can be used interchangeably with CD8.sup.+
T-cell(s) and the term HTL can be used interchangeably with
CD4.sup.+ T-cell(s) throughout the subject application.
[0128] The term "individual" includes mammals which include, and
are not limited to, apes, chimpanzees, orangutans, humans, monkeys
or domesticated animals (pets) such as dogs, cats, guinea pigs,
hamsters, Vietnamese pot-bellied pigs, rabbits, ferrets, cows,
horses, goats and sheep. In a preferred embodiment, the methods of
inducing an immune response contemplated herein are practiced on
humans.
[0129] Another embodiment of the subject invention provides methods
of inducing an immune response in an individual comprising the
administration of a composition comprising polypeptides encoded by
the polynucleotides of the subject invention in amounts sufficient
to induce an immune response. In some embodiments of the invention,
the immune response provides protective immunity. The composition
administered to the individual may, optionally, contain an adjuvant
and may be delivered in any manner known in the art for the
delivery of immunogen to a subject. Compositions may also be
formulated in any carriers, including for example, pharmaceutically
acceptable carriers such as those described in E. W. Martin's
Remington's Pharmaceutical Science, Mack Publishing Company,
Easton, Pa. In a preferred embodiment, compositions may be
formulated in incomplete Freund's adjuvant. In various embodiments,
the subject invention provides for diagnostic assays based upon
Western blot formats or standard immunoassays known to the skilled
artisan. For example, antibody-based assays such as enzyme linked
immunosorbent assays (ELISAs), radioimmunoassays (RIAs), lateral
flow assays, immunochromatographic strip assays, automated flow
assays, and assays utilizing antibody-containing biosensors may be
employed for the detection of the polypeptides, and fragments
thereof, provided by the subject invention. The assays and methods
for conducting the assays are well-known in the art and the methods
may test biological samples qualitatively (presence or absence of
polypeptide) or quantitatively (comparison of a sample against a
standard curve prepared using a polypeptide of the subject
invention) for the presence of one or more polypeptide of the
subject invention. Thus, the subject invention provides a method of
detecting a P. falciparum polypeptide, or fragment thereof,
comprising contacting a sample with an antibody that specifically
binds to a polypeptide, or fragment thereof, comprising SEQ ID NOs:
1-26, or 27 and detecting the presence of an antibody-antigen
complex.
[0130] The antibody-based assays can be considered to be of four
types: direct binding assays, sandwich assays, competition assays,
and displacement assays. In a direct binding assay, either the
antibody or antigen is labeled, and there is a means of measuring
the number of complexes formed. In a sandwich assay, the formation
of a complex of at least three components (e.g.,
antibody-antigen-antibody) is measured. In a competition assay,
labeled antigen and unlabelled antigen compete for binding to the
antibody, and either the bound or the free component is measured.
In a displacement assay, the labeled antigen is pre-bound to the
antibody, and a change in signal is measured as the unlabelled
antigen displaces the bound, labeled antigen from the receptor.
[0131] Lateral flow assays can be conducted according to the
teachings of U.S. Pat. No. 5,712,170 and the references cited
therein. U.S. Pat. No. 5,712,170 and the references cited therein
are hereby incorporated by reference in their entireties.
Displacement assays and flow immunosensors useful for carrying out
displacement assays are described in: (1) Kusterbeck et al.,
"Antibody-Based Biosensor for Continuous Monitoring", in Biosensor
Technology, R. P. Buck et al., eds., Marcel Dekker, N.Y. pp.
345-350 (1990); Kusterbeck et al., "A Continuous Flow Immunoassay
for Rapid and Sensitive Detection of Small Molecules", Journal of
Immunological Methods, vol. 135, pp. 191-197 (1990); Ligler et al.,
"Drug Detection Using the Flow Immunosensor", in Biosensor Design
and Application, J. Findley et al., eds., American Chemical Society
Press, pp. 73-80 (1992); and Ogert et al., "Detection of Cocaine
Using the Flow Immunosensor", Analytical Letters, vol. 25, pp.
1999-2019 (1992), all of which are incorporated herein by reference
in their entireties. Displacement assays and flow immunosensors are
also described in U.S. Pat. No. 5,183,740, which is also
incorporated herein by reference in its entirety. The displacement
immunoassay, unlike most of the competitive immunoassays used to
detect small molecules, can generate a positive signal with
increasing antigen concentration. One aspect of the invention
allows for the exclusion of Western blots as a diagnostic assay,
particularly where the Western blot is a screen of whole cell
lysates of P. falciparum, or related organisms, against immune
serum of infected individuals. In another aspect of the invention,
peptide, or polypeptide, based diagnostic assays utilize P.
falciparum peptides or polypeptides that have been produce either
by chemical peptide synthesis or by recombinant methodologies that
utilize non-plasmodium host cells for the production of peptides or
polypeptides.
[0132] Another aspect of the invention provides for the use of
peptides, polypeptides, and multi-epitope constructs in assays such
as those taught in U.S. Pat. No. 5,635,363, which is hereby
incorporated by reference in its entirety. Briefly, peptides,
polypeptides, and multi-epitope constructs of the subject invention
can be used to form stable multimeric complexes that comprise
prepared major histocompatibility complex (MHC) protein subunits
having a substantially homogeneous bound peptide population. The
multimeric MHC-antigen complex forms a stable structure with T
cells recognizing the complex through their antigen receptor,
thereby allowing for the labeling, identification and separation of
specific T cells. The multimeric binding complex has the formula
(.alpha.-.beta.-P).sub.n, where n.gtoreq.2, usually n.gtoreq.4, and
usually n.gtoreq.10; .alpha. is an .alpha. chain of a class I or
class II MHC protein. .beta. is a .beta. chain, (the .beta. chain
of a class II MHC protein or .beta..sub.2microglobulin for a MHC
class I protein; and P is a peptide antigen. The multimeric complex
stably binds through non-covalent interactions to a T cell receptor
having the appropriate antigenic specificity. The MHC proteins may
be from any individual. Of particular interest are the human HLA
proteins. Included in the HLA proteins are the class II subunits
HLA-DP.alpha., HLA-DP.beta., HLA-DQ.alpha., HLA-DQ.beta.,
HLA-DR.alpha. and HLA-DR.beta., and the class I proteins HLA-A,
HLA-B, HLA-C, and .beta..sub.2-microglobulin. In a preferred
embodiment, the MHC protein subunits are a soluble foim of the
normally membrane-bound protein. The soluble form is derived from
the native form by deletion of the transmembrane domain.
Conveniently, the protein is truncated, removing both the
cytoplasmic and transmembrane domains. The protein may be truncated
by proteolytic cleavage, or by expressing a genetically engineered
truncated form. For class I proteins, the soluble form will include
the .alpha.1, .alpha.2 and .alpha.3 domain. Not more than about 10,
usually not more than about 5, preferably none of the amino acids
of the transmembrane domain will be included. The deletion may
extend as much as about 10 amino acids into the .alpha.3 domain,
preferably none of the amino acids of the .alpha.3 domain will be
deleted. The deletion will be such that it does not interfere with
the ability of the .alpha.3 domain to fold into a disulfide bonded
structure. The class I .beta. chain, .beta..sub.2-microglobulin,
lacks a transmembrane domain in its native form, and need not be
truncated. Generally, no Class II subunits will be used in
conjunction with Class I subunits. Soluble class II subunits will
include the .alpha.1 and .alpha.2 domains for the .alpha. subunit,
and the .beta.1 and .beta.2 domains for the .beta. subunit. Not
more than about 10, usually not more than about 5, preferably none
of the amino acids of the transmembrane domain will be included.
The deletion may extend as much as about 10 amino acids into the
.alpha.2 or .beta.2 domain, preferably none of the amino acids of
the .beta.2 or .beta.2 domain will be deleted. The deletion will be
such that it does not interfere with the ability of the .alpha.2 or
.beta.2 domain to fold into a disulfide bonded structure. The
monomeric complex (.alpha.-.beta.-P) (monomer) is multimerized. The
resulting multimer will be stable over long periods of time.
Usually not more than about 10% of the multimer will be dissociated
after storage at 4.degree. C. for about one day, more usually after
about one week. Preferably, the multimer will be formed by binding
the monomers to a multivalent entity through specific attachment
sites on the .alpha. or .beta. subunit, as described below in
detail. The multimer may also be formed by chemical cross-linking
of the monomers. A number of reagents capable of cross-linking
proteins are known in the art, illustrative entities include:
azidobenzoyl hydrazide,
N-[4-(p-azidosalicylamino)butyl]-3'-[2'-pyridyldithio]propionamide),
bis-sulfosuccinimidyl suberate, dimethyladipimidate,
disuccinimidyltartrate, N-.gamma.-maleimidobutyryloxysuccinimide
ester, N-hydroxy sulfosuccinimidyl-4-azidobenzoate, N-succinimidyl
[4-azidophenyl]-1,3'-dithiopropionate, N-succinimidyl
[4-iodoacetyl]aminobenzoate, glutaraldehyde, formaldehyde and
succinimidyl 4-[N-maleimidomethyl]cyclohexane-1 -carboxylate.
[0133] The attachment site for binding to a multivalent entity may
be naturally occurring, or may be introduced through genetic
engineering. The site will be a specific binding pair member or one
that is modified to provide a specific binding pair member, where
the complementary pair has a multiplicity of specific binding
sites. Binding to the complementary binding member can be a
chemical reaction, epitope-receptor binding or hapten-receptor
binding where a hapten is linked to the subunit chain. In a
preferred embodiment, one of the subunits is fused to an amino acid
sequence providing a recognition site for a modifying enzyme. The
recognition sequence will usually be fused proximal to the carboxy
terminus of one of the subunit to avoid potential hindrance at the
antigenic peptide binding site. Conveniently, an expression
cassette will include the sequence encoding the recognition
site.
[0134] Modifying enzymes of interest include BirA, various
glycosylases, farnesyl protein transferase, protein kinases and the
like. The subunit may be reacted with the modifying enzyme at any
convenient time, usually after formation of the monomer. The group
introduced by the modifying enzyme, e.g. biotin, sugar, phosphate,
farnesyl, etc. provides a complementary binding pair member, or a
unique site for further modification, such as chemical
cross-linking, biotinylation, etc. that will provide a
complementary binding pair member. An alternative strategy is to
introduce an unpaired cysteine residue to the subunit, thereby
introducing a unique and chemically reactive site for binding. The
attachment site may also be a naturally occurring or introduced
epitope, where the multivalent binding partner will be an antibody,
e.g. IgG, IgM, etc. Any modification will be at a site, e.g.
C-terminal proximal, that will not interfere with binding.
[0135] Exemplary of multimer formation is the introduction of the
recognition sequence for the enzyme BirA, which catalyzes
biotinylation of the protein substrate. The monomer with a
biotinylated subunit is then bound to a multivalent binding
partner, e.g. streptavidin or avidin, to which biotin binds with
extremely high affinity. Streptavidin has a valency of 4, providing
a multimer of (.alpha.-.beta.-P).sub.4.
[0136] The multivalent binding partner may be free in solution, or
may be attached to an insoluble support. Examples of suitable
insoluble supports include beads, e.g. magnetic beads, membranes
and microtiter plates. These are typically made of glass, plastic
(e.g. polystyrene), polysaccharides, nylon or nitrocellulose.
Attachment to an insoluble support is useful when the binding
complex is to be used for separation of T cells.
[0137] Frequently, the multimeric complex will be labeled, so as to
be directly detectable, or will be used in conjunction with
secondary labeled immunoreagents which will specifically bind the
complex. In general the label will have a light detectable
characteristic. Preferred labels are fluorophors, such as
fluorescein isothiocyanate (FITC), rhodamine, Texas Red,
phycoerythrin and allophycocyanin. Other labels of interest may
include dyes, enzymes, chemiluminescers, particles, radioisotopes,
or other directly or indirectly detectable agent. Conveniently, the
multivalent binding partner will have the labeling group.
Alternatively, a second stage label may be used, e.g. labeled
antibody directed to one of the peptide constituents, and the
like.
[0138] The binding complex will be used to detect and/or separate
antigen specific T cells. The T cells may be from any source,
usually having the same species of origin as the MHC heterodimer.
The T cells may be from an in vitro culture, or a physiologic
sample. For the most part, the physiologic samples employed will be
blood or lymph, but samples may also involve other sources oft
cells, particularly where T cells may be invasive. Thus other sites
of interest are tissues, or associated fluids, as in the brain,
lymph node, neoplasms, spleen, liver, kidney, pancreas, tonsil,
thymus, joints, synovia, and the like. The sample may be used as
obtained or may be subject to modification, as in the case of
dilution, concentration, or the like. Prior treatments may involve
removal of cells by various techniques, including centrifugation,
using Ficoll-Hypaque, panning, affinity separation, using
antibodies specific for one or more markers present as surface
membrane proteins on the surface of cells, or any other technique
that provides enrichment of the set or subset of cells of
interest.
[0139] The binding complex is added to a suspension comprising T
cells of interest, and incubated at about 4.degree. C. for a period
of time sufficient to bind the available cell surface receptor. The
incubation will usually be at least about 5 minutes and usually
less than about 30 minutes. It is desirable to have a sufficient
concentration of labeling reagent in the reaction mixture, so that
labeling reaction is not limited by lack of labeling reagent. The
appropriate concentration is determined by titration. The medium in
which the cells are labeled will be any suitable medium as known in
the art. If live cells are desired a medium will be chosen that
maintains the viability of the cells. A preferred medium is
phosphate buffered saline containing from 0.1 to 0.5% BSA. Various
media are commercially available and may be used according to the
nature of the cells, including Dulbecco's Modified Eagle Medium
(dMEM), Hank's Basic Salt Solution (HBSS), Dulbecco's phosphate
buffered saline (dPBS), RPMI, Iscove's medium, PBS with 5 mM EDTA,
etc., frequently supplemented with fetal calf serum, BSA, HSA,
etc.
[0140] Where a second stage labeling reagent is used, the cell
suspension may be washed and resuspended in medium as described
above prior to incubation with the second stage reagent.
Alternatively, the second stage reagent may be added directly into
the reaction mix.
[0141] A number of methods for detection and quantitation of
labeled cells are known in the art. Flow cytometry is a convenient
means of enumerating cells that are a small percent of the total
population. Fluorescent microscopy may also be used. Various
immunoassays, e.g. ELISA, RIA, etc. may used to quantitate the
number of cells present after binding to an insoluble support.
[0142] Flow cyometry may also be used for the separation of a
labeled subset of T cells from a complex mixture of cells. The
cells may be collected in any appropriate medium which maintains
the viability of the cells, usually having a cushion of serum at
the bottom of the collection tube. Various media are commercially
available as described above. The cells may then be used as
appropriate.
[0143] Alternative means of separation utilize the binding complex
bound directly or indirectly to an insoluble support, e.g. column,
microtiter plate, magnetic beads, etc. The cell sample is added to
the binding complex. The complex may be bound to the support by any
convenient means. After incubation, the insoluble support is washed
to remove non-bound components. From one to six washes may be
employed, with sufficient volume to thoroughly wash
non-specifically bound cells present in the sample. The desired
cells are then eluted from the binding complex. In particular the
use of magnetic particles to separate cell subsets from complex
mixtures is described in Miltenyi et al. (1990) Cytometry
11:231-238.
[0144] Detecting and/or quantitating specific T cells in a sample
or fraction thereof may be accomplished by a variety of specific
assays. In general, the assay will measure the binding between a
patient sample, usually blood derived, generally in the fol in of
plasma or serum and the subject multimeric binding complexes. The
patient sample may be used directly, or diluted as appropriate,
usually about 1:10 and usually not more than about 1:10,000. Assays
may be perfoinied in any physiological buffer, e.g. PBS, normal
saline, HBSS, dPBS, etc.
[0145] A sandwich assay is perfoli zied by first attaching the
multimeric binding complex to an insoluble surface or support. The
multimeric binding complex may be bound to the surface by any
convenient means, depending upon the nature of the surface, either
directly or through specific antibodies. The particular manner of
binding is not crucial so long as it is compatible with the
reagents and overall methods of the invention. They may be bound to
the plates covalently or non-covalently, preferably
non-covalently.
[0146] The insoluble supports may be any compositions to which the
multimeric binding complex can be bound, which is readily separated
from soluble material, and which is otherwise compatible with the
overall method of measuring T cells. The surface of such supports
may be solid or porous and of any convenient shape. Examples of
suitable insoluble supports to which the receptor is bound include
beads, e.g. magnetic beads, membranes and microtiter plates. These
are typically made of glass, plastic (e.g. polystyrene),
polysaccharides, nylon or nitrocellulose. Microtiter plates are
especially convenient because a large number of assays can be
carried out simultaneously, using small amounts of reagents and
samples.
[0147] Before adding patient samples or fractions thereof, the
non-specific binding sites on the insoluble support i.e. those not
occupied by the multimeric binding complex, are generally blocked.
Preferred blocking agents include non-interfering proteins such as
bovine serum albumin, casein, gelatin, and the like. Samples,
fractions or aliquots thereof are then added to separately
assayable supports (for example, separate wells of a microtiter
plate) containing support-hound multimeric binding complex.
[0148] Generally from about 0.001 to 1 ml of sample, diluted or
otherwise, is sufficient, usually about 0.01 ml sufficing.
Preferably, each sample and standard will be added to multiple
wells so that mean values can be obtained for each. The incubation
time should be sufficient for T cells to bind the insoluble binding
complex. Generally, from about 0.1 to 3 hr is sufficient, usually 1
hr sufficing.
[0149] After incubation, the insoluble support is generally washed
of non-bound components. Generally, a dilute physiologic buffer at
an appropriate pH, generally 7-8, is used as a wash medium. From
one to six washes may be employed, with sufficient volume to
thoroughly wash non-specifically bound T cells present in the
sample. After washing, a solution containing specific second
receptor is applied. The receptor may be any compound that binds
patient T cells with sufficient specificity such that they can be
distinguished from other components present. In a preferred
embodiment, second receptors are antibodies specific for common T
cell antigens, either monoclonal or polyclonal sera, e.g.
anti-thy-1, anti-CD45, etc.
[0150] T cell specific antibodies may be labeled to facilitate
direct or indirect quantification of binding. Examples of labels
that permit direct measurement include radiolabels, such as .sup.3H
or .sup.125I, fluorescers, dyes, beads, chemilumninescers,
colloidal particles, and the like. Examples of labels which permit
indirect measurement of binding include enzymes where the substrate
may provide for a colored or fluorescent product. Examples of
suitable enzymes for use in conjugates include horseradish
peroxidase, alkaline phosphatase, malate dehydrogenase and the
like. Where not commercially available, such antibody-enzyme
conjugates are readily produced by techniques known to those
skilled in the art.
[0151] Alternatively, the second receptor may be unlabeled. In this
case, a labeled second receptor-specific compound is employed which
hinds to the bound second receptor. Such a second receptor-specific
compound can be labelled in any of the above manners. It is
possible to select such compounds such that multiple compounds bind
each molecule of bound second receptor. Examples of second
receptor/second receptor-specific molecule pairs include
antibody/anti-antibody and avidin (or streptavidin)/biotin. Since
the resultant signal is thus amplified, this technique may be
advantageous where only a small number oft cells are present. An
example is the use of a labeled antibody specific to the second
receptor. More specifically, where the second receptor is a rabbit
anti-allotypic antibody, an antibody directed against the constant
region of rabbit antibodies provides a suitable second receptor
specific molecule. The anti-immunoglobulin will usually come from
any source other than human, such as ovine, rodentia, particularly
mouse, or bovine. The volume, composition and concentration of T
cell specific receptor solution provides for measurable binding to
the T cells already bound to the insoluble substrate. Generally,
the same volume as that of the sample is used: from about 0.001 to
1 ml is sufficient, usually about 0.1 ml sufficing. When antibody
ligands are used, the concentration generally will be about 0.1 to
50 .mu.g/ml, preferably about 1 .mu.g/ml. The solution containing
the second receptor is generally buffered in the range of about pH
6.5-9.5. The solution may also contain an innocuous protein as
previously described. The incubation time should be sufficient for
the labeled ligand to bind available molecules. Generally, from
about 0.1 to 3 hr is sufficient, usually 1 hr sufficing.
[0152] After the second receptor or second receptor-conjugate has
bound, the insoluble support is generally again washed free of
non-specifically bound second receptor, essentially as described
for prior washes. After non-specifically bound material has been
cleared, the signal produced by the bound conjugate is detected by
conventional means. Where an enzyme conjugate is used, an
appropriate enzyme substrate is provided so a detectable product is
formed. More specifically, where a peroxidase is the selected
enzyme conjugate, a preferred substrate combination is
H.sub.2O.sub.2 and O-phenylenediamine which yields a colored
product under appropriate reaction conditions. Appropriate
substrates for other enzyme conjugates such as those disclosed
above are known to those skilled in the art. Suitable reaction
conditions as well as means for detecting the various useful
conjugates or their products are also known to those skilled in the
art. For the product of the substrate O-phenylenediamine for
example, light absorbance at 490-495 nm is conveniently measured
with a spectrophotometer.
[0153] Generally the number of bound T cells detected will be
compared to control samples from samples having a different MHC
context, e.g. T cells from an animal that does not express the MHC
molecule used to make the binding complex.
[0154] An alternative protocol is to provide anti-T cell reagent,
e.g. anti-thy-1, anti-CD45, etc. bound to the insoluble surface.
After adding the sample and washing away non-specifically bound T
cells, one or a combination of the subject binding complexes are
added, where the binding complexes are labeled so as not to
interfere with the binding to T cells.
[0155] It is particularly convenient in a clinical setting to
perform the assays in a self-contained apparatus. A number of such
methods are known in the art. The apparatus will generally employ a
continuous flow-path of a suitable filter or membrane, having at
least three regions, a fluid transport region, a sample region, and
a measuring region. The sample region is prevented from fluid
transfer contact with the other portions of the flow path prior to
receiving the sample. After the sample region receives the sample,
it is brought into fluid transfer relationship with the other
regions, and the fluid transfer region contacted with fluid to
permit a reagent solution to pass through the sample region and
into the measuring region. The measuring region may have bound to
it the multimeric binding complex, with a conjugate of an enzyme
with T cell specific antibody employed as a reagent, generally
added to the sample before application. Alternatively, the binding
complex may be conjugated to an enzyme, with T cell specific
antibody bound to the measurement region.
[0156] Detection of T cells is of interest in connection with a
variety of conditions associated with T cell activation. Such
conditions include autoimmune diseases, e.g. multiple sclerosis,
myasthenia gravis, rheumatoid arthritis, type 1 diabetes, graft vs.
host disease, Grave's disease, etc.; various forms of cancer, e.g.
carcinomas, melanomas, sarcomas, lymphomas and leukemias. Various
infectious diseases such as those caused by viruses, e.g. HIV-1,
hepatitis, herpesviruses, enteric viruses, respiratory viruses,
rhabdovirus, rubeola, poxvirus, paramyxovirus, morbillivirus, etc.
are of interest. Infectious agents of interest also include
bacteria, such as Pneumococcus, Staphylococcus, Bacillus.
Streptococcus, Meningococcus, Gonococcus, Eschericia, Klebsiella,
Proteus, Pseudomonas, Salmonella, Shigella, Hemophilus, Yersinia,
Listeria, Corynebacterium, Vibrio, Clostridia, Chlamydia,
Mycobacterium, Helicobacter and Treponema; protozoan pathogens, and
the like. T cell associated allergic responses may also be
monitored, e.g. delayed type hypersensitivity or contact
hypersensitivity involving T cells.
[0157] Of particular interest are conditions having an association
with a specific peptide or MHC haplotype, where the subject binding
complexes may be used to track the T cell response with respect to
the haplotype and antigen. A large number of associations have been
made in disease states that suggest that specific MHC haplotypes,
or specific protein antigens are responsible for disease
states.
[0158] Polypeptide fragments, including immunogenic fragments, for
each of SEQ ID NOs: 1-27 can be any length from at least 5
consecutive amino acids to 1 amino acid less than a full length
polypeptide of any given SEQ ID NO:. Thus, for SEQ ID NO: 1 (used
here as a non-limiting example) the polypeptide fragment can
contain any number of consecutive amino acids from 5 to 1903 (for
example, 5, 6, 7, . . . , 1901, 1902, 1903). For the sake of
brevity, the individual integers between 5 and 1903 have not been
reproduced herein but are, in fact, specifically contemplated. In
one embodiment, the immunogenic fragments of the invention induce
immunity or protective immunity from disease.
[0159] The present invention also provides for the exclusion of any
individual fragment (of any given SEQ ID NO:) specified by
N-terminal to C-terminal positions, actual sequence, or of any
fragment specified by size (in amino acid residues) as described
above. In addition, any number of fragments specified by N-terminal
and C-terminal positions, actual sequence, or by size (in amino
acid residues) as described above may be excluded as individual
species. Further, any number of fragments specified by N-terminal
and C-terminal positions or by size (in amino acid residues) as
described above may be combined to provide a polypeptide fragment.
These types of fragments may, optionally, include polypeptide
sequences such as linkers, described below.
[0160] Where a claim recites "a polypeptide comprising SEQ ID NO:
X, or fragments or immunogenic fragments or epitopes of SEQ ID
NO:X", the language "fragments or immunogenic fragments or epitopes
of SEQ ID NO:X" specifically excludes identical sub-sequences found
within other longer naturally occurring prior art polypeptide or
protein sequences that are not identical to sequence from which the
claimed sequence was derived. This does not include instances where
such sub-sequences are a part of a larger molecule specifically
modified by the hand of man to enhance the immunogenicity of the
fragments of the subject invention. Thus, fragments or immunogenic
fragments or epitopes of SEQ ID NO:X specifically exclude, and are
not to be considered anticipated, where the fragment is a
sub-sequence of another naturally occurring non-malarial peptide,
polypeptide, or protein isolated from a bacterial, viral,
reptilian, insect, avian, or mammalian source and is identified in
a search of protein sequence databases.
[0161] Fragments or immunogenic fragments or epitopes of the
invention may further contain linkers that facilitate the
attachment of the fragments to a carrier molecule for the
stimulation of an immune response or diagnostic purposes. The
linkers can also be used to attach fragments according to the
invention to solid support matrices for use in affinity
purification protocols. In this aspect of the invention, the
linkers specifically exclude, and are not to be considered
anticipated, where the fragment is a subsequence of another
peptide, polypeptide, or protein as identified in a search of
protein sequence databases as indicated in the preceding paragraph.
In other words, the non-identical portions of the other peptide,
polypeptide, of protein are not considered to be a "linker" in this
aspect of the invention. Non-limiting examples of "linkers"
suitable for the practice of the invention include chemical linkers
(such as those sold by Pierce, Rockford, Ill.) and peptides that
allow for the connection of the immunogenic fragment to a carrier
molecule (see, for example, linkers disclosed in U.S. Pat. Nos.
6,121,424, 5,843,464, 5,750,352, and 5,990,275, hereby incorporated
by reference in their entirety). In various embodiments, the
linkers can be up to 50 amino acids in length, up to 40 amino acids
in length, up to 30 amino acids in length, up to 20 amino acids in
length, up to 10 amino acids in length, or up to 5 amino acids in
length. Of course, the linker may be any pre-selected number of
amino acids (up to 50 amino acids) in length.
[0162] In various embodiments, polypeptides suitable for use in
various disclosed methods of the subject invention can be selected
from the group consisting of: a) a polypeptide comprising a
polypeptide sequence selected from the group consisting of SEQ ID
NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18,
19, 20, 21 ,22, 23, 24, 25, 26, and 27; b) a variant polypeptide
having at least about 20% to 99.99% identity to a polypeptide
selected from the group consisting of SEQ ID NO: 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17, 18, 19, 20, 21, 22, 23,
24, 25, 26, and 27; c) a fragment of a polypeptide or a variant
polypeptide of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27,
wherein said fragment or variant has substantially the same
serologic reactivity or substantially the same T-cell reactivity as
the native polypeptide; d) a multi-epitope construct; and e)
combinations thereof.
Multi-Epitope Constructs
[0163] As indicated supra, the subject invention provides for
"multi-epitope constructs". A "multi-epitope construct" comprises:
1) nucleic acids that encode multiple polypeptide epitopes (of any
length) that can bind to one or more molecules functioning in the
immune system; or 2) polypeptides comprising multiple polypeptide
epitopes that can bind to one or more molecules functioning in the
immune system. "Multi-epitope constructs" can, optionally, contain
"flanking" or "spacing" residues between each epitope. Some
embodiments provide for "multi-epitope constructs" that comprise a
series of the same epitope (termed "homopolymers"). Other
embodiments provide for "multi-epitope constructs" that comprise a
combination or series of different epitopes, optionally connected
by "flanking" or "spacing" residues (termed "heteropolymers"). In
some embodiments, "multi-epitope constructs" may exclude
full-length polypeptides from which the epitopes are obtained
(e.g., the polypeptides of SEQ ID NOs: 1-27). In certain preferred
embodiments, the epitopes used in the formation of the
multi-epitope construct are selected from those set forth in Table
2, Table 3, Table 4, Table 5, and/or Table 6 and any epitope set
forth in these Tables 2-6 can be mixed and/or matched any other
epitope set forth in any of the aforementioned Tables 2-6.
[0164] Multi-epitope constructs may be of "high affinity" or
"intermediate affinity". As used herein, "high affinity" with
respect to HLA class I molecules is defined as binding with an
IC.sub.50, or KD value, of 50 nM or less; "intermediate affinity"
with respect to HLA class I molecules is defined as binding with an
IC.sub.50 or KD value of between about 50 and about 500 nM. "High
affinity" with respect to binding to HLA class II molecules is
defined as binding with an IC.sub.50 or KD value of 100 nM or less;
"intermediate affinity" with respect to binding to HLA class II
molecules is defined as binding with an IC.sub.50 or KD value of
between about 100 and about 1000 nM.
[0165] The multi-epitope constructs described herein preferably
include five or more, ten or more, fifteen or more, twenty or more,
or twenty-five or more epitopes. Other embodiments provide
multi-epitope constructs that comprise at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,
45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, or 99 epitopes. All of the epitopes in a multi-epitope
construct may be from one organism (e.g., the epitopes are obtained
from P. falciparum), or the multi-epitope construct may include
epitopes present in two or more different organisms (e.g., some
epitopes from P. falciparum and some epitopes from another
organism). Additionally, the same epitope may be present in a
multi-epitope construct at more than one location in the construct.
In some embodiments, novel epitopes of the subject invention may be
linked to known epitopes of an organism (e.g., P. falciparum or
another organism).
[0166] A "multi-epitope vaccine," is a vaccine comprising multiple
epitopes. A multi-epitope vaccine can induce an immune response and
is administered to an individual in an amount sufficient to induce
an immune response in the individual. In sonic embodiments, the
immune response induced by the multi-epitope vaccine is a
protective immune response against a given organism, pathogen, or
pathologic condition (e.g., P. falciparum).
[0167] In certain embodiments, the epitopes of a multi-epitope
construct or the polypeptides disclosed herein interact with an
antigen binding site of an antibody molecule, a class I HLA, a
T-cell receptor, and/or a class II HLA molecule. In certain
preferred embodiments, the epitopes interact with an FILA molecule
(e.g., class I or class II) or a T-cell receptor. In an even more
preferred embodiment, the epitope interacts with both an HLA
molecule (e.g., class I or class II) and a T-cell receptor. In
various embodiments, all of the nucleic acids in a multi-epitope
construct can encode class I HLA epitopes or class II HLA epitopes.
Multi-epitope constructs comprising epitopes that interact
exclusively with class I HLA molecules may be referred to as "CTL
multi-epitope constructs" (or "CD8.sup.+ T cell multi-epitope
constructs"). Multi-epitope constructs comprising epitopes that
interact exclusively with class II HLA molecules may be referred to
as "HTL multi-epitope constructs" (or "CD4.sup.+ T cell multi
epitope constructs"). Some multi-epitope constructs (designated "TL
multi-epitope constructs") can have a subset of the multi-epitope
nucleic acids encoding class I HLA epitopes and another subset of
the multi-epitope nucleic acids encoding class II HLA epitopes
(e.g., the constructs stimulate both CTL (i.e., CD8.sup.+ T cell)
and HTL (i.e., CD4.sup.+ T cell) of the immune system). Other
multi-epitope constructs can provide epitopes that interact
exclusively with B-cells or immunoglobulin molecules and are
designated "BL multi-epitope constructs". Multi-epitope constructs
that provide epitopes that interact with B-cells (and/or
immunoglobulin molecules) and further provide class I HLA epitopes
and class II HLA epitopes are designated "immune system (IMS)
multi-epitope constructs". In certain embodiments, multi-epitope
constructs can provide class I or class II epitopes (e.g., CTL
(i.e., CD8.sup.+ T cell) epitopes or HTL (i.e., CD4.sup.+ T cell)
epitopes) and BL epitopes. "Human Leukocyte Antigen" or "HLA" is a
human class I or class II Major Histocompatibility Complex (MHC)
protein (see, e.g., Stites, et al., IMMUNOLOGY, 8.sup.TH ED., Lange
Publishing, Los Altos, Calif. (1994)).
[0168] CTL epitope (class I epitope) (i.e., CD8.sup.+ T cell
epitope) encoding nucleic acids preferably provide an epitope
peptide of about eight to about thirteen amino acids in length
(e.g., 8, 9, 10, 11, 12 or 13), more preferably about eight to
about eleven amino acids in length, and most preferably about nine
amino acids in length. HTL (CD4.sup.+ T-cell) epitope nucleic acids
can provide an epitope peptide of about seven to about twenty three
(e.g., 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22
or 23) preferably about seven to about seventeen (e.g., 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, or 17, more preferably about eleven to
about fifteen (e.g., 11, 12, 13, 14 or 15), and most preferably
about thirteen amino acids in length.
[0169] "Degenerate binding" indicates that a peptide is bound by
more than one HLA molecule; a synonym is "cross reactive binding."
"Cross reactive binding" may also be used to define the interaction
of an antigen with multiple populations of antibodies. In certain
preferred embodiments, epitopes disclosed herein do not exhibit
cross reactive or degenerate binding. Other embodiments encompass
degenerate or cross reactive binding of antigens or epitopes.
[0170] With regard to a particular amino acid sequence, an
"epitope" is a set of amino acid residues that is involved in
recognition by a particular immunoglobulin, or in the context of T
cells, those residues necessary for recognition by T cell receptor
proteins and/or Major Histocompatibility Complex (MHC) receptors.
In an immune system setting, in vitro or in vivo, an epitope is the
collective features of a molecule, such as primary, secondary and
tertiary peptide structure, and charge, that together form a site
recognized by an immunoglobulin, T cell receptor or HLA molecule.
Throughout this disclosure epitope and peptide are often used
interchangeably. It is to be appreciated, however, that isolated or
purified protein or peptide molecules larger than and comprising an
epitope of the invention are still within the bounds of the
invention.
[0171] A "flanking" or "linking" residue is a residue that is
positioned next to an epitope. A flanking residue can be introduced
or inserted at a position adjacent to the N-terminus or the
C-terminus of an epitope. Flanking residues suitable for use in the
subject invention are disclosed, for example, in U.S. Pat. No.
6,419,931, which is hereby incorporated by reference in its
entirety, including all sequences, figures, references, and
tables.
[0172] An "immunogenic peptide" or "peptide epitope" is a peptide
that comprises an allele-specific motif or supermotif such that the
peptide will bind an HLA molecule and induce a CTL (or CD8.sup.+ T
cell) and/or HTL (or CD4.sup.+ T cell) response. An "immunogenic
peptide" or "peptide epitope" can also be a peptide that comprises
a motif that binds to antibody molecules or B-cells found in the
immune system of an individual. Thus, immunogenic peptides of the
invention are capable of binding to an antibody molecule, a B-cell,
or appropriate HLA molecule and thereafter inducing an immune
response (e.g., the induction of antibody production, a cytotoxic T
cell response, or a helper T cell response) to the antigen from
which the immunogenic peptide is derived.
[0173] The term "residue" refers to an amino acid or amino acid
mimetic incorporated into a peptide or protein by an amide bond or
amide bond mimetic.
[0174] A "spacer" or "linker" refers to a sequence that is inserted
between two epitopes in a multi-epitope construct to prevent the
occurrence of junctional epitopes and/or to increase the efficiency
of processing. A multi-epitope construct may have one or more
spacer nucleic acids. A spacer nucleic acid may flank each epitope
nucleic acid in a construct, or the spacer nucleic acid to epitope
nucleic acid ratio may be about 2 to 10, about 5 to 10, about 6 to
10, about 7 to 10, about 8 to 10, or about 9 to 10, where a ratio
of about 8 to 10 has been determined to yield favorable results for
some constructs. The spacer nucleic acid may encode one or more
amino acids. A spacer nucleic acid flanking a class I HLA epitope
in a multi-epitope construct is preferably between one and about
eight amino acids in length. A spacer nucleic acid flanking a class
II HLA epitope in a multi-epitope construct is preferably greater
than five, six, seven, or more amino acids in length, and more
preferably five or six amino acids in length. The number of spacers
in a construct, the number of amino acids in a spacer, and the
amino acid composition of a spacer can be selected to optimize
epitope processing and/or minimize junctional epitopes. It is
preferred that spacers are selected by concomitantly optimizing
epitope processing and junctional motifs. Suitable amino acids for
optimizing epitope processing are described herein. Also, suitable
amino acid spacing for minimizing the number of junctional epitopes
in a construct are described herein for class I and class II HLAs.
For example, spacers flanking class II HLA epitopes preferably
include G, P, and/or N residues as these are not generally known to
be primary anchor residues (see, e.g., PCT/US00/19774). A
particularly preferred spacer for flanking a class II HLA epitope
includes alternating G and P residues, for example, (GP).sub.n,
(PG).sub.n, (GP).sub.nG, or (PG).sub.nP, and so forth, where n is
an integer between one and ten, preferably two or about two, and
where a specific example of such a spacer is GPGPG.
[0175] In some multi-epitope constructs, it is sufficient that each
spacer nucleic acid encodes the same amino acid sequence. In
multi-epitope constructs having two spacer nucleic acids encoding
the same amino acid sequence, the spacer nucleic acids encoding
those spacers may have the same or different nucleotide sequences,
where different nucleotide sequences may be preferred to decrease
the likelihood of unintended recombination events when the
multi-epitope construct is inserted into cells.
[0176] In other multi-epitope constructs, one or more of the spacer
nucleic acids may encode different amino acid sequences. While many
of the spacer nucleic acids may encode the same amino acid sequence
in a multi-epitope construct, one, two, three, four, five or more
spacer nucleic acids may encode different amino acid sequences, and
it is possible that all of the spacer nucleic acids in a
multi-epitope construct encode different amino acid sequences.
Spacer nucleic acids may be optimized with respect to the epitope
nucleic acids they flank by determining whether a spacer sequence
will maximize epitope processing and/or minimize junctional
epitopes, as described herein.
[0177] Multi-epitope constructs may be distinguished from one
another according to whether the spacers in one construct optimize
epitope processing or minimize junctional epitopes over another
construct, and preferably, constructs may be distinguished where
one construct is concomitantly optimized for epitope processing and
junctional epitopes over the other. Computer assisted methods and
in vitro and in vivo laboratory methods for determining whether a
construct is optimized for epitope processing and junctional motifs
are described herein.
[0178] "Multi-epitope constructs of the invention may also be
"optimized". The term "optimized" or "optimizing" refers to
increasing the immunogenicity or antigenicity of a multi-epitope
construct having at least one epitope pair by sorting epitopes to
minimize the occurrence of junctional epitopes, inserting flanking
residues that flank the C-terminus or N-terminus of an epitope, and
inserting spacer residue to further prevent the occurrence of
junctional epitopes or to provide a flanking residue. An increase
in immunogenicity or antigenicity of an optimized multi-epitope
construct is measured relative to a multi-epitope construct that
has not been constructed based on the optimization parameters and
is using assays known to those of skill in the art, e.g.,
assessment of immunogenicity in HLA transgenic mice, ELISPOT,
interferon-gamma release assays, tetramer staining, chromium
release assays, and presentation on dendritic cells.
[0179] The subject invention also concerns antibodies that bind to
polypeptides of the invention. Antibodies that are immunospecific
for the malarial polypeptides set forth herein are specifically
contemplated. In various embodiments, antibodies which do not cross
react with other proteins or malarial proteins are also
specifically contemplated. The antibodies of the subject invention
can be prepared using standard materials and methods known in the
art (see, for example, Monoclonal Antibodies: Principles and
Practice, 1983; Monoclonal Hybridoma Antibodies: Techniques and
Applications, 1982; Selected Methods in Cellular Immunology, 1980;
Immunological Methods, Vol. II, 1981; Practical Immunology, and
Kohler et al. [1975] Nature 256:495).
[0180] The term "antibody" is used in the broadest sense and
specifically covers monoclonal antibodies (including full length
monoclonal antibodies), polyclonal antibodies, multispecific
antibodies (e.g., bispecific antibodies), and antibody fragments so
long as they exhibit the desired biological activity, particularly
neutralizing activity. "Antibody fragments" comprise a portion of a
full length antibody, generally the antigen binding or variable
region thereof. Examples of antibody fragments include Fab, Fab',
F(ab').sub.2, and Fv fragments; diabodies; linear antibodies;
single-chain antibody molecules; and multi-specific antibodies
formed from antibody fragments.
[0181] The term "monoclonal antibody" as used herein refers to an
antibody obtained from a population of substantially homogeneous
antibodies, i.e., the individual antibodies comprising the
population are identical except for possible naturally occurring
mutations that may be present in minor amounts. Monoclonal
antibodies are highly specific, being directed against a single
antigenic site. Furthermore, in contrast to conventional
(polyclonal) antibody preparations that typically include different
antibodies directed against different determinants (epitopes), each
monoclonal antibody is directed against a single determinant on the
antigen. The modifier "monoclonal" indicates the character of the
antibody as being obtained from a substantially homogeneous
population of antibodies, and is not to be construed as requiring
production of the antibody by any particular method. For example,
the monoclonal antibodies to be used in accordance with the present
invention may be made by the hybridoma method first described by
Kohler et al. [1975] Nature 256: 495, or may be made by recombinant
DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The "monoclonal
antibodies" may also be isolated from phage antibody libraries
using the techniques described in Clackson et al. [1991] Nature
352: 624-628 and Marks et al. [1991]J. Mol. Biol. 222: 581-597, for
example.
[0182] The monoclonal antibodies described herein specifically
include "chimeric" antibodies (immunoglobulins) in which a portion
of the heavy and/or light chain is identical with or homologous to
corresponding sequences in antibodies derived from a particular
species or belonging to a particular antibody class or subclass,
while the remainder of the chain(s) is identical with or homologous
to corresponding sequences in antibodies derived from another
species or belonging to another antibody class or subclass, as well
as fragments of such antibodies, so long as they exhibit the
desired biological activity (U.S. Pat. No. 4,816,567; and Morrison
et al. [1984] Proc. Natl. Acad Sci. USA 81: 6851-6855). Also
included are humanized antibodies, such as those taught in U.S.
Pat. Nos. 6,407,213 or 6,417,337 which are hereby incorporated by
reference in their entirety.
[0183] "Single-chain Fv" or "sFv" antibody fragments comprise the
V.sub.H and V.sub.L domains of an antibody, wherein these domains
are present in a single polypeptide chain. Generally, the Fv
polypeptide further comprises a polypeptide linker between the
V.sub.H and V.sub.L domains which enables the sFv to form the
desired structure for antigen binding. For a review of sFv see
Pluckthun in The Pharmacology of Monoclonal Antibodies [1994] Vol.
113:269-315, Rosenburg and Moore eds. Springer-Verlag, New
York.
[0184] The term "diabodies" refers to small antibody fragments with
two antigen-binding sites, which fragments comprise a heavy chain
variable domain (V.sub.H) connected to a light chain variable
domain (V.sub.L) in the same polypeptide chain (V.sub.H-V.sub.L).
Diabodies are described more fully in, for example, EP 404,097; WO
93/11161; and Hollinger et al. [1993] Proc. Natl. Acad. Sci. USA
90: 6444-6448. The term "linear antibodies" refers to the
antibodies described in Zapata et al. [1995] Protein Eng.
8(10):1057-1062.
[0185] An "isolated" antibody is one which has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials which would interfere with diagnostic or therapeutic uses
for the antibody, and may include enzymes, hormones, and other
proteinaceous or nonproteinaceous solutes. In preferred
embodiments, the antibody will be purified (1) to greater than 95%
by weight of antibody as determined by the Lowry method, and most
preferably more than 99% by weight, (2) to a degree sufficient to
obtain at least 15 residues of N-terminal or internal amino acid
sequence by use of a spinning cup sequenator, or (3) to homogeneity
by SDS-PAGE under reducing or nonreducing conditions using
Coomassie blue or, preferably, silver stain. Isolated antibody
includes the antibody in situ within recombinant cells since at
least one component of the antibody's natural environment will not
be present. Ordinarily, however, isolated antibody will be prepared
by at least one purification step.
[0186] The terms "comprising", "consisting of" and "consisting
essentially of" are defined according to their standard meaning.
The terms may be substituted for one another throughout the instant
application in order to attach the specific meaning associated with
each term. The phrases "isolated" or "biologically pure" refer to
material that is substantially or essentially free from components
which normally accompany the material as it is found in its native
state. Thus, isolated peptides in accordance with the invention
preferably do not contain materials normally associated with the
peptides in their in situ environment. "Link" or "join" refers to
any method known in the art for functionally connecting peptides,
including, without limitation, recombinant fusion, covalent
bonding, disulfide bonding, ionic bonding, hydrogen bonding, and
electrostatic bonding.
[0187] Following are examples which illustrate procedures for
practicing the invention. These examples should not be construed as
limiting. All percentages are by weight and all solvent mixture
proportions are by volume unless otherwise noted.
[0188] In this disclosure, "binding data" results are often
expressed in terms of "IC.sub.50's." IC.sub.50 is the concentration
of peptide in a binding assay at which 50% inhibition of binding of
a reference peptide is observed. Given the conditions in which the
assays are run (i.e., limiting HLA proteins and labeled peptide
concentrations), these values approximate KD values. Assays for
deteimining binding are described in detail, e.g., in PCT
publications WO 94/20127 and WO 94/03205 (each of which is hereby
incorporated by reference in its entirety). It should be noted that
IC.sub.50 values can change, often dramatically, if the assay
conditions are varied, and depending on the particular reagents
used (e.g., HLA preparation, etc.). For example, excessive
concentrations of HLA molecules will increase the apparent measured
IC.sub.50 of a given ligand. Alternatively, binding is expressed
relative to a reference peptide. Although as a particular assay
becomes more, or less, sensitive, the IC.sub.50's of the peptides
tested may change somewhat, the binding relative to the reference
peptide will not significantly change. For example, in an assay run
under conditions such that the IC.sub.50 of the reference peptide
increases 10-fold, the IC.sub.50 values of the test peptides will
also shift approximately 10-fold. Therefore, to avoid ambiguities,
the assessment of whether a peptide is a good, intermediate, weak,
or negative binder is generally based on its IC.sub.50, relative to
the IC.sub.50 of a standard peptide. Binding may also be determined
using other assay systems including those using: live cells (e.g.,
Ceppellini et al., Nature 339:392, 1989; Christnick et al., Nature
352:67, 1991; Busch et al., Int. Immunol. 2:443, 19990; Hill et
al., J. Immunol. 147:189,1991; del Guercio et al., J. Immunol.
154:685, 1995), cell free systems using detergent lysates (e.g.,
Cerundolo et al., J Immunol. 21:2069, 1991), immobilized purified
MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et
al., J Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al.,
EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et
al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase
assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and
measurement of class I MHC stabilization or assembly (e.g.,
Ljunggren et al., Nature 346:476, 1990; Schumacher et al, Cell
62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J.
lmmunol. 149:1896, 1992). Predicted IC.sub.50 values may be
referred to as PIC values and measured IC.sub.50 values may be
referred to a MIC values.
EXAMPLE 1
[0189] Starting with 27 open reading frames defined by
Multidimensional Protein Identification Technology, 9 highly
antigenic proteins were identified. These highly antigenic proteins
were recognized by volunteers immunized with irradiated
sporozoites; mock immunized individuals (controls) failed to
recognize these proteins. Several of these nine proteins were more
antigenic than previously well-characterized proteins.
[0190] To identify and prioritize a set of ORFs representing
antigens potentially expressed in the sporozoite and intrahepatic
stage of the parasite life cycle, MS/MS spectra of peptide
sequences generated by Multidimensional Protein Identification
Technology (MudPIT) (Washburn, M. P., Wolters, D., & Yates, J.
R. 3.sup.rd. Large-scale analysis of the yeast proteome by
multidimensional protein identification technology. Nat.
Biotechnol. 19, 242-247 (2001)) of P. falciparum sporozoite
preparations were scanned against the P. falciparum genomic
sequence database using SEQUEST.TM. software (Florens, L. et al. A
proteomic view of the Plasmodium falciparum life cycle. Submitted).
A panel of 27 ORF's (10 expressed only in sporozoites, and 17
common to other stages of the parasite life cycle) were selected.
Their size ranged between 96-4544 amino acids (mean 1252), the
percentage of the protein covered by identified peptides ranged
between 0.5-49.5%, and the frequency of recognition in the P.
falciparum proteome dataset ranged between 16 peptide hits from 6
different sporozoite runs (antigen 2) to single peptide hits
(antigens 1, 11, 14, 16, 19 and 25. When searched against the final
P. falciparum database using refined gene model predictions, and
taking into consideration genomic sequence information from the
Anopheles (vector) and human (host) databases, 19 of the 27
antigens could be identified using stringent selection criteria and
six others could be identified only with relaxed criteria.
[0191] Amino acid sequences from the 27 ORFs were scanned with
HLA-A1, A2, A3/A11, A24 and DR supertype PIC algorithms; a total of
3241 peptides were identified (range=14-435; mean=120 sequences per
antigen). A set of 1142 sequences was synthesized (range=13-50;
mean=42), selecting the top 10 scorers per supertype per antigen
for larger ORFs. Control sets of peptides were synthesized from 4
known antigens (PfCSP, PfSSP2, PfLSA1 and PfEXP1). Next, predicted
epitopes were tested for their capacity to induce recall
IFN-.gamma. immune responses using PBMC from volunteers immunized
with irradiated P. falciparum sporozoites and either protected
(n=4) or not protected (n=4) against challenge with infectious
sporozoites, or control volunteers mock immunized in parallel (n=4)
(see Table 1). Peptides were tested as pools, at 1 .mu.g/ml each
peptide with each antigen represented by a separate pool, by
IFN-.gamma. ELIspot (Washburn, M. P., Wolters, D., & Yates, J.
R. 3.sup.rd. Large-scale analysis of the yeast proteome by
multidimensional protein identification technology. Nat.
Biotechnol. 19, 242-247 (2001)). Positive and negative control
epitopes from well characterized antigens (CMV, Influenza, EBV,
HIV) were also included.
[0192] Considering a stimulation index (ratio test
response/control) >2.0 as positive, 19 of the 27 unknown
antigens were recognized by at least 1 of 8 irradiated sporozoite
immunized volunteers, but not by any of the 4 mock immunized
controls (Table 1). Nine of the 27 antigens (#2, 5, 3, 18, 22, 21,
13, 11, 20) were recognized by at least 50% of irradiated
sporozoite volunteers in at least 25% of assays, 3 antigens (#1,
12, 17) were recognized by at least 25% of volunteers in at least
15% of assays, and 7 antigens (#6, 7, 9, 14, 15, 16, 19) were
recognized by at least 10% volunteers in at least 5% of assays.
Eight of the 27 unknown antigens (#4, 8, 10, 23, 24, 25, 26, 27)
failed to induce IFN-.gamma. responses of sufficient magnitude to
meet our criteria of positivity. Pools of predicted epitopes from
the known antigens, PfCSP, PfSSP2, PfLSA1 and PfEXP1, were also
recognized by irradiated sporozoite volunteers although the
frequency of response to those pools was somewhat lower than that
to pools of peptides representing previously validated epitopes
derived from the same antigens (Doolan, D. L. et al. Degenerate
cytotoxic T cell epitopes from P. falciparum restricted by multiple
HLA-A and HLA-B supertype alleles. Immunity. 7, 97-112 (1997);
Doolan, D. L. et al. HLA-DR-promiscuous T cell epitopes from
Plasmodium flaciparum pre-erthrocytic-stage antigens restricted by
multiple HLA class II alleles. J Immunol. 165:1123-1137 (2000);
Wang, R., et al. Induction of CD4(+) T cell-dependent CD8(+) type 1
responses in humans by a malaria DNA vaccine. Proc. Natl. Acad.
Sci. U.S.A. 98, 10817-10822 (2001)) (Table 1). Particularly
noteworthy, the reactivity against several of the newly identified
antigens greatly exceeded the reactivities observed against all 4
known antigens For example, both antigens 2 and 5 were recognized
by 7/8 irradiated sporozoite volunteers in 9/16 assays, and
antigens 3 and 18 were recognized by 6/8 irradiated sporozoite
volunteers in 6/16 assays.
[0193] Results show that HLA-A2 peptide pools from antigens 2, 5
and 13, and HLA-A1 and HLA-DR peptide pools from antigens 2 and 5,
are recognized by irradiated sporozoite volunteers who express the
respective HLA alleles, but not by mock immunized controls.
Deconvolution at the level of individual epitopes is in progress.
Additionally, a comprehensive analysis of HLA binding against the
A1, A2, A3/11, A24, and DR1 supertypes has been completed for
selected antigens. Several degenerate binders have been identified
for each supertype/antigen combination, and 50 to 70% of the
predicted peptides have been identified as degenerate HLA
binders.Further analysis also revealed that the antigenicity
results correlate to a large degree with the proteomic data. For
example, of 9 antigens associated with high immune reactivity, 7
were identified by multiple peptide hits in multiple MudPIT
runs
[0194] All patents, patent applications, provisional applications,
polynucleotide sequences, amino acid sequences, tables and
publications referred to or cited herein are incorporated by
reference in their entirety, including all figures, to the extent
they are not inconsistent with the explicit teachings of this
specification. It should be understood that the examples and
embodiments described herein are for illustrative purposes only and
that various modifications or changes in light thereof will be
suggested to persons skilled in the art and are to be included
within the spirit and purview of this application.
TABLE-US-00001 TABLE 1 Summary of immune reactivities against the
panel of 27 putative antigens and 4 known antigens. MOCK IRRADIATED
SPOROZOITE IMMUNIZED IMMUNIZED # vol % vol # % SI SFC # vol #
Antigen respond respond assays assays respond respond respond
assays 1 3 37.5 3 18.75 2.5 59.3 0 0 2 8 100 9 56.25 2.9 110.4 0 0
3 6 75 6 37.5 2.6 119.1 0 0 4 0 -- -- -- -- -- 0 0 5 7 87.5 9 56.25
2.8 101.8 0 0 6 1 12.5 1 6.25 2.4 88.3 0 0 7 1 12.5 1 6.25 2.1 43.3
0 0 8 0 -- -- -- -- -- 0 0 9 2 25 2 12.5 2.5 32.0 0 0 10 0 -- -- --
-- -- 0 0 11 4 50 4 25 3.1 81.3 0 0 12 3 37.5 3 18.75 2.2 48.2 0 0
13 4 50 5 31.25 2.9 92.2 0 0 14 1 12.5 1 6.25 2.2 55.3 0 0 15 2 25
2 12.5 2.5 28.8 0 0 16 2 25 2 12.5 2.2 27.2 0 0 17 3 37.5 3 18.75
2.4 57.6 0 0 18 6 75 6 37.5 2.2 58.4 0 0 19 2 25 2 12.5 2.7 31.3 0
0 20 4 50 4 25 2.5 74.8 0 0 21 4 50 5 31.25 2.3 48.2 0 0 22 5 62.5
5 31.25 2.9 108.4 0 0 23 0 -- -- -- -- -- 0 0 24 0 -- -- -- -- -- 0
0 25 0 -- -- -- -- -- 0 0 26 0 -- -- -- -- -- 0 0 27 0 -- -- -- --
-- 0 0 TOTAL UNKNOWNS 1-8 44.7 3.8 24.0 2.5 66.6 "HIGH" 4-8 66.7
5.9 36.8 2.7 88.3 "INTERMEDIATE" 3 37.5 3.0 18.8 2.4 55.0 "LOW" 1-2
19.6 1.6 9.8 2.4 43.8 Range 1-8 12.5-100 1-9 6.25-56.25 2.1-3.1
27.2-110.4 KNOWNS (@1 ug/ml) predicted 1.4 17.2 1.4 8.6 2.9 57.3
Range 1-3 12.5-37.5 1-3 6.25-18.75 2.0-3.4 30.5-137.4 KNOWNS (@1
ug/ml) validated 4.0 50.0 3.8 23.4 3.5 64.0 Range 3-5 37.5-62.5 3-6
18.75-37.5 3.5-3.6 46.6-91.4 TOTAL KNOWNS (@1 ug/ml) 2.3 28.1 2.2
13.5 3.2 60.0 Range 1-5 12.5-62.5 1-6 6.25-37.5 2.0-3.6 30.5-137.4
TOTAL KNOWNS (@10 ug/ml) 4-8 81.3 7.8 60.9 11.1 588.2 CMV/EBV/Flu 7
87.5 12.0 50.0 4.0 59.0 4 100
TABLE-US-00002 TABLE 2 Pf-derived A1 supertype peptides with PIC
<20 nM Addn Malaria Source Accession Peptide locus info No.
Position No. Sequence 331.t00003 Chromosome10 216 98.0038 KTNKWEDIY
331.t00003 Chromosome10 790 98.0039 KSIYIFYTY 331.t00003
Chromosome10 986 98.0040 GTFTFQNMY 331.t00003 Chromosome10 1298
98.0041 CNDGNILYY 331.t00003 Chromosome10 1379 98.0042 YFECIMKLY
331.t00003 Chromosome10 1389 98.0043 VYEGKLKKY 331.t00003
Chromosome10 1650 98.0001 VVDLFCGVGY 331.t00003 Chromosome10 1770
98.0044 FSSINTYDY 331.t00003 Chromosome10 1803 98.0045 VSNVEDSNY
331.t00003 Chromosome10 1831 98.0046 NSNYNKKLY 18.000811
Chr12Contig18 182 98.0047 KVSDEIWNY MY924Fe3.p1t1 92 98.0048
ISGEGLIIY MY924Fe3.p1t1 215 98.0002 FVEDSSSFLY MY924Fe3.p1t1 384
98.0049 DSDSSNVLY MY924Fe3.p1t1 561 98.0050 SQDVFIIEY MY924Fe3.p1t1
1028 98.0051 NSMFHIIMY MY924Fe3.p1t1 1093 98.0052 SSYNLFEEY
MY924Fe3.p1t1 1258 98.0053 SSGKTFICY MY924Fe3.p1t1 1340 98.0054
ILENILLSY MY924Fe3.p1t1 1439 98.0055 FSDLILYVY MY924Fe3.p1t1 2318
98.0056 HIENILLKY MP03001 MAL3P2.11 CAB38998 14 98.0057 FVEALFQEY
MP03001 MAL3P2.11 CAB38998 310 98.0058 PSDKHIKEY 1369.t00001
Chromosome 11 38 98.0059 IMNHLMTLY 1369.t00001 Chromosome 11 149
98.0060 LIENELMNY 1369.t00001 Chromosome 11 182 98.0061 NVDQQNDMY
1369.t00001 Chromosome 11 309 98.0062 SSFFMNRFY 1369.t00001
Chromosome 11 342 98.0063 NHEQKLSEY 1369.t00001 Chromosome 11 347
98.0003 LSEYYDXDIY 1369.t00001 Chromosome 11 363 98.0064 QEEQKKYIY
699.t00001 Chromosome I1 313 98.0065 DSQNELTNY 699.t00001
Chromosome 11 441 98.0004 FSFFFSLIDY 699.t00001 Chromosome 11 480
98.0066 CHEMKAEFY 699.t00001 Chromosome 11 548 98.0067 MFSSIFENY
699.t00001 Chromosome 11 749 98.0068 NSLILLNLY 699.t00001
Chromosome 11 859 98.0069 YIDNDINIY 699.t00001 Chromosome 11 919
98.0070 EEDKTYELY 699.t00001 Chromosome 11 922 98.0071 KTYELYQKY
699.t00001 Chromosome 11 1013 98.0072 CTHISYYKY 699.t00001
Chromosome 11 1046 98.0005 FVDEEGEQLY M13Hg2.q1t3 8 98.0073
NSLYNKIEY M13Hg2.q1t3 46 98.0006 YSSASESNFY M13Hg2.q1t3 49 98.0074
ASESNFYKY M13Hg2.q1t3 196 98.0075 ASGKLFSLY M13Hg2.q1t3 237 98.0076
GSNKVSDWY M13Hg2.q1t3 511 98.0007 FQDNYLKLDY M13Hg2.q1t3 597
98.0008 FFDYNSQYYY M13Hg2.q1t3 597 98.0077 FFDYNSQYY M13Hg2.q1t3
699 98.0078 MLEQKLSNY M13Hg2.q1t3 882 98.0079 NSFNNSNIY
Mal_5L10c4.q1t6 8 98.0080 CSSTKDLNY Mal_5L10c4.q1t6 263 98.0081
YDDDKYNKY Mal_5L10c4.q1t6 638 98.0082 GTYGNMENY Mal_5L10c4.q1t6 690
98.0083 FTYYSCKNY Mal_5L10c4.q1t6 1022 98.0084 YDERNTLVY
Mal_5L10c4.q1t6 1387 98.0085 STDDSKNVY Mal_5L10c4.q1t6 1451 98.0086
FSDDNKNLY Mal_5L10c4.q1t6 1508 98.0009 YLDNELTINY Mal_5L10c4.q1t6
1709 98.0087 STTSLNYHY Mal_5L10c4.q1t6 1907 98.0088 GLDLKMTLY
571.t00003 Chromosome11 1044 98.0010 YTFQNNNDFY 571.t00003
Chromosome11 1080 98.0089 HTNNKTSIY 571.t00003 Chromosome11 1710
98.0090 FVDPNKYIY 571.t00003 Chromosome11 1827 98.0011 NVEAYHNDNY
571.t00003 Chromosome11 1858 98.0091 YSNNSHAEY 571.t00003
Chromosome11 1905 98.0092 LTNNSSYIY 571.t00003 Chromosome11 2211
98.0093 SSSIYNQNY 571.t00003 Chromosome11 2476 98.0094 GSYGTFLKY
571.t00003 Chromosome11 2532 98.0095 DIDKTVLHY 571.t00003
Chromosome11 2571 98.0012 FNDTQKKGTY MP03072 PFC0450w CAA15614 95
98.0013 LSASDEYEQY MP03072 PFC0450w CAA15614 96 98.0096 SASDEYEQY
45.t00001 Chromosomel4 13 98.0014 FQAAESNERY 45.t00001 Chromosomel4
14 98.0097 QAAESNERY 45.t00001 Chromosomel4 81 98.0015 ELEASISGKY
45.t00001 Chromosomel4 82 98.0098 LEASISGKY 45.t00001 Chromosomel4
188 98.0099 NLALLYGEY MP03137 PFC0700c CAB11150 14 98.0100
SSPLFNNFY MP03137 PFC0700c CAB11150 69 98.0101 LNEQLIYTY MP03137
PFC0700c CAB11150 145 98.0102 QNADKNFLY MP03137 PFC0700c CAB11150
255 98.0016 FVSSIFISFY MP03137 PFC0700c CAB11150 256 98.0103
VSSIFISFY 12.t00018 Chromosome14 112 98.0104 YSYYEPLRY 12.t00018
Chromosome14 250 98.0017 KSNNIIPLLY 12.t00018 Chromosome14 467
98.0105 SSSDEENLY 12.t00018 Chromosome14 468 98.0106 SSDEENLYY
12.t00018 Chromosome14 607 98.0107 KSNMNNNLY 12.t00018 Chromosome14
626 98.0108 FYDKRFIFY 12.t00018 Chromosome14 696 98.0018 NVEKNFLLYY
12.t00018 Chromosome14 696 98.0109 NVEKNFLLY 12.t00018 Chromosome14
949 98.0110 KMDSFLNVY 12.t00018 Chromosome14 1042 98.0111 NSLIEFLFY
mal_BU121g9.q1c1 80 98.0112 ATYKNGNIY mal_9A57b11.q1t2 226 98.0113
DEEKIFVKY mal_BL50e8.p1ca_5 86 98.0114 HTSNDSGSY mal_BL50e8.p1ca_5
136 98.0019 FSFTVGEGKY mal_BL50e8.p1ca_5 186 98.0115 ETNNNLFIY
mal_BL50e8.p1ca_5 319 98.0116 HVSKHAFEY mal_BL50e8.p1ca_5 387
98.0117 MSGYSSNNY mal_BL50e8.p1ca_5 460 98.0118 FMESAFVNY
mal_BL50e8.p1ca_5 650 98.0119 RSPCSHKLY mal_BL50e8.p1ca_5 679
98.0020 FTGENNIERY mal_BL50e8.p1ca_5 777 98.0120 NTLMLKADY
mal_BL50e8.p1ca_5 880 98.0121 VSSKPANEY M13S8h6.p1t_3 57 98.0122
ITYSFTVSY M13S8h6.p1t_3 233 98.0123 LVETLDNLY M13S8h6.p1t_3 235
98.0124 ETLDNLYLY M13S8h6.p1t_3 295 98.0125 LSAKYYISY M13S8h6.p1t_3
551 98.0126 HSDIHLLNY M13S8h6.p1t_3 676 98.0021 FTSPVNIKEY
M13S8h6.p1t_3 746 98.0127 YSSYSSPKY M13S8h6.p1t_3 898 98.0128
GMERNKTKY M13S8h6.p1t_3 1268 98.0129 YSNIDSGKY M13S8h6.p1t_3 1488
98.0130 LIDLSCIHY 585.t00002 Chromosome11 297 98.0131 CSDSSLNIY
585.t00002 Chromosome11 381 98.0132 VSFDNNENY 585.t00002
Chromosome11 465 98.0022 YTDIIINIRY 585.t00002 Chromosome11 575
98.0023 LSNIRKPLFY 585.t00002 Chromosome11 741 98.0133 NVDANYCKY
585.t00002 Chromosome11 1021 98.0134 CVEKNNMSY 585.t00002
Chromosome11 1161 98.0135 SSDGKKSEY
585.t00002 Chromosome11 1219 98.0136 RSNNFFFSY 585.t00002
Chromosome11 1361 98.0024 FTMVYEKIKY 585.t00002 Chromosome11 1739
98.0137 NVDIFLHYY 1223.t00015 mal_9A21f9.q1t_4 387 98.0138
SSNEIHNFY 1223.t00015 mal_9A21f9.q1t_4 1065 98.0139 GTKLNRTKY
1223.t00015 mal_9A21f9.q1t_4 1583 98.0025 ATVSRAGIVY 1223.t00015
mal_9A21f9.q1t_4 1833 98.0140 YTLSSGTKY 1223.t00015
mal_9A21f9.q1t_4 2309 98.0141 VSEKEQQLY 1223.t00015
mal_9A21f9.q1t_4 2426 98.0142 VVDFERLRY 1223.t00015
mal_9A21f9.q1t_4 2778 98.0143 FIDLYKQMY 1223.t00015
mal_9A21f9.q1t_4 3445 98.0144 IVDITNVNY 1223.t00015
mal_9A21f9.q1t_4 4163 98.0145 LEDVKKILY 1223.t00015
mal_9A21f9.q1t_4 4267 98.0146 SLDIPDIAY 599.t00001 Chromosome11 26
98.0147 SSCQNSLNY 599.t00001 Chromosome11 183 98.0148 KSDITNLNY
599.t00001 Chromosome11 304 98.0149 ETNNGDLKY 599.t00001
Chromosome11 430 98.0150 LSEDNKNRY 599.t00001 Chromosome11 1018
98.0026 LLDLRKNGLY 599.t00001 Chromosome11 1412 98.0027 GVDKSLKIMY
599.t00001 Chromosome11 1427 98.0151 YTPTNKEMY 599.t00001
Chromosome11 1516 98.0028 ESANDSTNYY 599.t00001 Chromosome11 1662
98.0152 LSNSITVSY 599.t00001 Chromosome11 1902 98.0153 GTTQSNNIY
MP01072 M1045c5.p1c.C_6 27 98.0154 SDDEIIIIY MP01072
M1045c5.p1c.C_6 41 98.0155 ISSNGKLNY MP01072 M1045c5.p1c.C_6 60
98.0156 GSIQNAYLY MP01072 M1045c5.p1c.C_6 381 98.0157 GTMRNRKKY
MP01072 M1045c5.p1c.C_6 707 98.0158 KSLLKNYNY MP01072
M1045c5.p1c.C_6 725 98.0159 NVEDTNMLY MP01072 M1045c5.p1c.C_6 1065
98.0029 NTDNKDVLNY MP01072 M1045c5.p1c.C_6 1253 98.0160 HTITISQKY
MP01072 M1045c5.p1c.C_6 1257 98.0161 ISQKYTSSY MP01072
M1045c5.p1c.C_6 1336 98.0030 KTFHRILAVY PIR2 T28161 228 98.0162
KTNGAEERY PIR2 T28161 293 98.0163 GTVPTNLDY PIR2 T28161 403 98.0031
ESSQNSPKNY PIR2 T28161 639 98.0032 QTDFQGWGHY PIR2 T28161 899
98.0164 EADFIKKMY PIR2 T28161 917 98.0165 ATICRAMKY PIR2 T28161
1192 98.0033 KTDEQYNENY PIR2 T28161 1201 98.0034 YTFKNPPPQY PIR2
T28161 1884 98.0166 WLEYFLDDY PIR2 T28161 2221 98.0167 ITSSSESEY
55.t00004 Chromosome14 45 98.0168 YVDIGSNIY 55.t00004 Chromosome14
457 98.0169 DTCKNIWNY 55.t00004 Chromosome14 563 98.0170 LSQGKKNTY
55.t00004 Chromosome14 928 98.0171 NIDCVISPY 55.t00004 Chromosome14
953 98.0172 NMDNLLFTY 55.t00004 Chromosome14 1105 98.0035
FVDHNYNYNY 55.t00004 Chromosome14 1261 98.0173 HSKENQQKY 55.t00004
Chromosome14 1339 98.0174 VSEGYTSTY 55.t00004 Chromosome14 1358
98.0175 FMDSQNGMY 55.t00004 Chromosome14 1537 98.0036 NSYNDSLINY
13.t00011 Chromosome14 27 98.0176 STGINEENY 13.t00011 Chromosome14
44 98.0177 MNETVFLDY 13.t00011 Chromosome14 77 98.0178 LTSKVWDTY
37.t00002 Chromosome14 10 98.0179 KHDALTYMY 37.t00002 Chromosome14
14 98.0180 LTYMYCVYY 674.t00001 Chromosome11 201 98.0181 NIDINDLGY
674.t00001 Chromosome11 260 98.0182 ISSNQFNNY 674.t00001
Chromosome11 400 98.0183 DIEPLISSY 674.t00001 Chromosome11 453
98.0037 VTNNDSINNY 674.t00001 Chromosome11 772 98.0184 ESGKNMEHY
674.t00001 Chromosome11 868 98.0185 LKDFDMLLY 674.t00001
Chromosome11 936 98.0186 YIDVEDDDY 674.t00001 Chromosome11 1001
98.0187 DMDDNYYLY 674.t00001 Chromosome11 1224 98.0188 YGDNNKDCY
674.t00001 Chromosome11 1239 98.0189 IYDFNNNSY PIC Malaria A*0101
A*2402 locus AA PIC A*0201 A*1101 PIC 331.t00003 9 15.962 1000000.0
1475.7 1000000.0 331.t00003 9 10.624 1000000.0 34.6 1000000.0
331.t00003 9 6.439 1000000.0 51.0 1000000.0 331.t00003 9 5.246
1000000.0 1000000.0 1000000.0 331.t00003 9 8.786 1000000.0 39035.2
242.6 331.t00003 9 18.802 1000000.0 1000000.0 1753.1 331.t00003 10
9.498 1000000.0 153.7 1000000.0 331.t00003 9 4.161 1000000.0 4680.1
1000000.0 331.t00003 9 18.299 1000000.0 11308.4 1000000.0
331.t00003 9 19.200 1000000.0 4533.0 1000000.0 18.000811 9 6.117
1000000.0 40.5 1000000.0 MY924Fe3.p1t1 9 4.901 1000000.0 2464.4
1000000.0 MY924Fe3.p1t1 10 8.740 1000000.0 445.2 1000000.0
MY924Fe3.p1t1 9 7.960 1000000.0 22156.1 1000000.0 MY924Fe3.p1t1 9
6.978 1000000.0 117.2 1000000.0 MY924Fe3.p1t1 9 4.429 1000000.0
243.3 1000000.0 MY924Fe3.p1t1 9 6.022 1000000.0 82.2 1000000.0
MY924Fe3.p1t1 9 2:145 1000000.0 264.3 1000000.0 MY924Fe3.p1t1 9
3.307 1000000.0 8368.7 1000000.0 MY924Fe3.p1t1 9 2.218 1000000.0
4308.8 1000000.0 MY924Fe3.p1t1 9 2.560 1000000.0 10911.0 1000000.0
MP03001 9 1.370 1000000.0 698.4 1000000.0 MP03001 9 18.149
1000000.0 150075.4 1000000.0 1369.t00001 9 9.966 1000000.0 224.2
1019.1 1369.t00001 9 18.117 1000000.0 15763.1 1000000.0 1369.t00001
9 6.934 1000000.0 6419.6 1000000.0 1369.t00001 9 17.546 1000000.0
48.4 1000000.0 1369.t00001 9 16.912 1000000.0 1000000.0 1000000.0
1369.t00001 10 18.838 1000000.0 3608.2 1000000.0 1369.t00001 9
19.642 1000000.0 1000000.0 1000000.0 699.t00001 9 19.647 1000000.0
97274.6 1000000.0 699.t00001 10 1.491 1000000.0 319.3 1000000.0
699.t00001 9 15.998 1000000 0 1000000.0 1000000.0 699.t00001 9
6.908 1000000.0 1357.8 2826.7 699.t00001 9 11.791 1000000.0 4626.8
1000000.0 699.t00001 9 12.867 1000000.0 52350.4 1000000.0
699.t00001 9 13.159 1000000.0 1000000.0 1000000.0 699.t00001 9
7.495 1000000.0 22.4 1000000.0 699.t00001 9 14.092 1000000.0 406.1
1000000.0 699.t00001 10 6.559 1000000.0 5771.7 1000000.0
M13Hg2.q1t3 9 19.553 1000000.0 3889.9 1000000.0 M13Hg2.q1t3 10
12.365 1000000.0 5058.0 1000000.0 M13Hg2.q1t3 9 1.848 1000000.0
630.5 1000000.0 M13Hg2.q1t3 9 2.466 1000000.0 266.9 1000000.0
M13Hg2.q1t3 9 16.782 1000000.0 1646.1 1000000.0 M13Hg2.q1t3 10
7.493 1000000.0 19742.1 1000000.0 M13Hg2.q1t3 10 19.854 1000000.1
2749.2 1043.1 M13Hg2.q1t3 9 11.735 1000000.0 3766.2 160.3
M13Hg2.q1t3 9 1.204 1000000.0 13925.8 1000000.0 M13Hg2.q1t3 9
16.821 1000000.0 5231.6 1000000.0 Mal_5L10c4.q1t6 9 2.097 1000000.0
16168.9 1000000.0 Ma1_5L10c4.q1t6 9 7.997 1000000.0 98918.2
1000000.0 Mal_5L10c4.q1t6 9 2.825 1000000.0 209.0 1000000.0
Mal_5L10c4.q1t6 9 6.979 1000000.0 257.7 1000000.0 Mal_5L10c4.q1t6 9
5.181 1000000.0 47876.1 1000000.0
Mal_5L10c4.q1t6 9 4.783 1000000.0 2220.4 1000000.0 Mal_5L10c4.q1t6
9 2.622 1000000.0 56737.7 1000000.0 Mal_5L10c4.q1t6 10 6.162
1000000.0 7177.6 1000000 0 Mal_5L10c4.q1t6 9 7.670 1000000.0 19.1
1000000.0 Mal_5L10e4.q1t6 9 2.747 1000000.0 5170.0 1000000.0
571.t00003 10 2.179 1000000.0 93.5 1000000.0 571.t00003 9 4.189
1000000.0 1677.3 1000000.0 571.t00003 9 2.171 1000000.0 6898.3
1000000.0 571.t00003 10 5.835 1000000.0 1804.6 1000000.0 571.t00003
9 7.282 1000000.0 662.3 1000000.0 571.t00003 9 7.415 1000000.0
186.2 1000000.0 571.t00003 9 6.330 1000000.0 318.5 1000000.0
571.t00003 9 1.127 1000000.0 151.7 1000000.0 571.t00003 9 4.678
1000000.0 10960.5 1000000.0 571.t00003 10 7.668 1000000.0 1000000.0
1000000.0 MP03072 10 14.664 1000000.0 11938.7 1000000.0 MP03072 9
16.603 1000000.0 163.8 1000000.0 45.t00001 10 13.667 1000000.0
5804.6 1000000.0 45.t00001 9 7.537 1000000.0 4581.2 1000000.0
45.t00001 10 17.550 1000000.0 30954.5 1000000.0 45.t00001 9 18.208
1000000.0 1000000.0 1000000.0 45.t00001 9 12.836 1000000.0 4104.6
1000000.0 MP03137 9 20.002 1000000.0 464.0 1000000.0 MP03137 9
10.436 1000000.0 1000000.0 1000000.0 MP03137 9 10.234 1000000.0
1000000.0 1000000.0 MP03137 10 10.460 1000000.0 44.6 1000000.0
MP03137 9 15.732 1000000.0 544.5 1000000.0 12.t00018 9 4.229
1000000.0 560.9 1000000.0 12.t00018 10 8.533 1000000.0 967.3
1000000.0 12.t00018 9 8.006 1000000.0 2243.6 1000000.0 12.t00018 9
6.105 1000000.0 64.6 1000000.0 12.t00018 9 6.927 1000000.0 923.1
1000000.0 12.t00018 9 4.639 1000000.0 1000000.0 18.3 12.t00018 10
7.724 1000000.0 328.7 1000000.0 12.t00018 9 0.789 1000000.0 1330.7
1000000.0 12.t00018 9 6.016 1000000.0 1384.3 151.9 12.t00018 9
9.105 1000000.0 774.9 1000000.0 mal_BU121g9.q1c1 9 3.423 1000000.0
290.6 1000000.0 mal_9A57b11.q1t2 9 18.436 1000000.0 1000000.0
1000000.0 mal_BL50e8.p1ca_5 9 7.801 1000000.0 10632.6 1000000.0
mal_BL50e8.p1ca_5 10 4.464 1000000.0 4191.1 1000000.0
mal_BL50e8.p1ca_5 9 3.940 1000000.0 574.3 1000000.0
mal_BL50e8.p1ca_5 9 3.473 1000000.0 286.4 1000000.0
mal_BL50e8.p1ca_5 9 4.983 1000000.0 1178.7 1000000.0
mal_BL50e8.p1ca_5 9 2.609 1000000.0 3568.1 1208.1 mal_BL50e8.p1ca_5
9 6.243 1000000.0 805.6 1000000.0 mal_BL50e8.p1ca_5 10 15.909
1000000.0 1908.1 1000000.0 mal_BL50e8.p1ca_5 9 15.648 1000000.0
6774.7 1000000.0 mal_BL50e8.p1ca_5 9 15.176 1000000.0 3405.9
1000000.0 M13S8h6.p1t_3 9 10.960 1000000.0 25.1 1000000.0
M13S8h6.p1t_3 9 3.907 1000000.0 24044.7 1000000.0 M13S8h6.p1t_3 9
2.901 1000000.0 801.6 1000000.0 M13S8h6.p1t_3 9 4.669 1000000.0
635.7 1000000.0 M13S8h6.p1t_3 9 1.423 1000000.0 5008.9 1000000.0
M13S8h6.p1t_3 10 10.972 1000000.0 1911.2 1000000.0 M13S8h6.p1t_3 9
5.286 1000000.0 6184.9 1000000.0 M13S8h6.p1t_3 9 7.244 1000000.0
88038.7 24764.5 M13S8h6.p1t_3 9 11.517 1000000.0 14325.6 1000000.0
M13S8h6.p1t_3 9 3.960 1000000.0 1722.8 1000000.0 585.t00002 9 2.643
1000000.0 44436.7 1000000.0 585.t00002 9 7.080 1000000.0 824.4
1000000.0 585.t00002 10 1.851 1000000.0 1716.6 1000000.0 585.t00002
10 5.132 1000000.0 3669.8 1000000.0 585.t00002 9 3.822 1000000.0
813.1 1000000.0 585.t00002 9 6.497 1000000.0 33246.6 1000000 0
585.t00002 9 5.530 1000000.0 8369.5 1000000.0 585.t00002 9 6.117
1000000.0 11.9 1000000.0 585.t00002 10 2.669 1000000.0 726.8
1000000.0 585.t00002 9 3.691 1000000.0 42.6 1000000.0 1223.t00015 9
7.488 1000000.0 19.5 1000000.0 1223.t00015 9 6.438 1000000.0 9805.4
1000000.0 1223.t00015 10 9.716 1000000.0 351.9 1000000.0
1223.t00015 9 4.847 1000000.0 1878.1 1000000.0 1223.t00015 9 6.585
1000000.0 56024.7 1000000.0 1223.t00015 9 3.185 1000000.0 457.2
1000000.0 1223.t00015 9 5.792 1000000.0 14889.5 1000000.0
1223.t00015 9 6.389 1000000.0 1065.1 1000000.0 1223.t00015 9 9.183
1000000.0 1000000.0 1000000.0 1223.t00015 9 9.566 1000000.0 1095.4
1000000.0 599.t00001 9 1.030 1000000.0 86.7 1000000.0 599.t00001 9
4.923 1000000.0 947.1 1000000.0 599.t00001 9 6.392 1000000.0 6561.2
1000000.0 599.t00001 9 7.171 1000000.0 178412.8 1000000.0
599.t00001 10 3.696 1000000.0 12286.3 1000000.0 599.t00001 10 8.185
1000000.0 3010.4 1000000.0 599.t00001 9 6.553 1000000.0 73406.9
1000000.0 599.t00001 10 6.672 1000000.0 2007.1 1000000.0 599.t00001
9 9.278 1000000.0 771.6 1000000.0 599.t00001 9 3.444 1000000.0
4003.2 1000000.0 MP01072 9 11.359 1000000.0 1265.6 1000000.0
MP01072 9 6.926 1000000.0 2877.4 1000000.0 MP01072 9 2.697
1000000.0 389.5 1000000.0 MP01072 9 1.998 1000000.0 249.1 1000000.0
MP01072 9 15.958 1000000.0 419.1 1000000.0 MP01072 9 9.314
1000000.0 3255.4 1000000.0 MP01072 10 6.923 1000000.0 6127.0
1000000.0 MP01072 9 3.528 1000000.0 4947.2 1000000.0 MP01072 9
13.157 1000000.0 5019.1 1000000.0 MP01072 10 13.836 1000000.0 85.1
1000000.0 PIR2 9 8.691 1000000.0 326.3 1000000.0 PIR2 9 3.979
I000000.0 793.4 1000000.0 PIR2 10 8.536 1000000.0 24883.8 1000000.0
PIR2 10 2.601 1000000.0 1349.4 1000000.0 PIR2 9 9.348 1000000.0
113941.0 1000000.0 PIR2 9 5.412 1000000.0 112.4 1000000.0 PIR2 10
5.386 1000000.0 1911.8 1000000.0 PIR2 10 8.064 1000000.0 918.8
1000000.0 PIR2 9 8.602 1000000.0 35096.0 1000000.0 PIR2 9 9.299
1000000.0 1168.0 1000000.0 55.t00004 9 3.352 1000000.0 18704.2
1000000.0 55.t00004 9 3.842 1000000.0 878.3 1000000.0 55.t00004 9
10.561 1000000.0 40514.9 1000000.0 55.t00004 9 8.449 1000000.0
3464.1 1000000.0 55.t00004 9 5.144 1000000.0 413.3 6464.5 55.t00004
10 6.601 1000000.0 687.9 1000000.0 55.t00004 9 3.798 1000000.0
41445.3 1000000.0 55.t00004 9 7.735 1000000.0 4760.1 1000000.0
55.t00004 9 8.455 1000000.0 21913.6 2720.6 55.t00004 10 12.536
1000000.0 1846.9 1000000.0 13.t00011 9 6.590 1000000.0 838.9
1000000.0 13.t00011 9 5.456 1000000.0 1000000.0 1000000.0 13.t00011
9 6.496 1000000.0 616.6 1000000.0 37.t00002 9 23.541 1000000.0
1000000.0 1000000.0 37.t00002 9 10.044 1000000.0 20.3 1000000.0
674.t00001 9 10.069 1000000.0 23874.2 1000000.0 674.t00001 9 6.099
1000000.0 2575.9 1000000.0
674.t00001 9 14.646 1000000.0 183727.1 1000000.0 674.t00001 10
17.920 1000000.0 1310.7 1000000.0 674.t00001 9 8.198 1000000.0
75390.5 1000000.0 674.t00001 9 12.047 1000000.0 1000000.0 1000000.0
674.t00001 9 13.870 1000000.0 377275.0 1000000.0 674.t00001 9 3.056
1000000.0 2478.6 45380.9 674.t00001 9 19.772 1000000.0 368191.0
1000000.0 674.t00001 9 17.735 1000000.0 1000000.0 365.4
TABLE-US-00003 TABLE 3 Pf-derived A24 supertype peptides with PIC
< 100 nM PIC Malaria locus Addn Source info Accession No.
Position Peptide No. Sequence AA A*0101 PIC A*0201 A*1101 A*2402
PIC 331.t00003 Chromosome10 10 98.0206 FYKKKRNVL 9 67134.0
1000000.0 1000000.0 1.708 331.t00003 Chromosome10 110 98.0207
VYEINKNEF 9 84.1 1000000.0 1000000.0 2.011 331.t00003 Chromosome10
604 98.0208 FFVWGIIDMF 9 221.0 1000000.0 1000000.0 3.642 331.t00003
Chromosome10 684 98.0209 VYNIKENFW 9 123239.4 1000000.0 1000000.0
2.687 331.t00003 Chromosome10 1108 98.0210 KYNLCIINML 9 147073.6
1000000.0 1000000.0 0.324 331.t00003 Chromosome10 1268 98.0211
FYVPIKKKL 9 172677.3 1000000.0 1000000.0 2.705 331.t00003
Chromosome10 1365 98.0212 KYEIIGNIL 9 89209.4 1000000.0 1000000.0
1.961 331.t00003 Chromosome10 1449 98.0213 FWLAIKDIF 9 173.9
1000000.0 1000000.0 1.093 331.t00003 Chromosome10 1515 98.0214
LYRRRKNLF 9 113.5 1000000.0 1000000.0 1.220 331.t00003 Chromosome10
1704 98.0215 IYIIKQNSF 9 111.6 1000000.0 1000000.0 0.256 18.000811
Chr12Contig18 5 98.0190 LFVCFLIFHF 10 672.3 1000000.0 1000000.0
19.783 18.000811 Chr12Contig18 8 98.0191 CFLIFHFFLF 10 1385.7
1000000.0 1000000.0 18.444 18.000811 Chr12Contig18 8 98.0216
CFLIFHFFL 9 106491.6 1000000.0 1000000.0 0.321 18.000811
Chr12Contig18 11 98.0217 IFHFFLFLL 9 53306.2 1000000.0 1000000.0
38.527 18.000811 Chr12Contig18 13 98.0192 HFFLFLLYIL 10 1000000.0
1000000.0 1000000.0 35.659 18.000811 Chr12Contig18 13 98.0218
HFFLFLLYI 9 24845.8 1000000.0 1000000.0 26.159 18.000811
Chr12Contig18 14 98.0219 FFLFLLYIL 9 62569.1 1000000.0 1000000.0
32.471 18.000811 Chr12Contig18 19 98.0220 LYILFLVKM 9 90645.8
1000000.0 1000000.0 63.051 18.000811 Chr12Contig18 41 98.0221
VFLVFSNVL 9 178682.3 1000000.0 1000000.0 5.555 18.000811
Chr12Contig18 160 98.0222 TYGIIVPVL 9 123562.9 1000000.0 1000000.0
3.015 MY924Fe3.p1t1 153 98.0223 FFNVINIFF 9 45.6 1000000.0
1000000.0 0.470 MY924Fe3.p1t1 1412 98.0224 FYSWLQNVL 9 83170.3
1000000.0 1000000.0 2.428 MY924Fe3.p1t1 1435 98.0225 FYERFSDLI 9
46149.1 1000000.0 1000000.0 0.625 MY924Fe3.p1t1 1534 98.0226
VYLIQNNYI 9 615175.4 1000000.0 1000000.0 0.632 MY924Fe3.p1t1 1557
98.0227 NYMKNSFYI 9 24802.7 1000000.0 1000000.0 2.200 MY924Fe3.p1t1
1800 98.0228 VYCNYVTEI 9 160654.7 1000000.0 1000000.0 3.071
MY924Fe3.p1t1 1839 98.0229 HYEVLPYKF 9 14.6 1000000.0 1000000.0
2.621 MY924Fe3.p1t1 1846 98.0230 KFTIIVESL 9 181796.5 1000000.0
1000000.0 1.946 MY924Fe3.p1t1 2159 98.0231 FMTRAHFHI 9 9020.6 52.2
1000000.0 1.455 MY924Fc3.p1t1 2380 98.0232 FYKSKVIII 9 53263.7
1000000.0 1000000.0 0.928 MP03001 MAL3P2.11 CAB38998 11 98.0233
SFLFVEALF 9 80.3 1000000.0 1000000.0 53.045 MP03001 MAL3P2.11
CAB38998 54 98.0234 YYGKQENWY 9 73.1 1000000.0 1000000.0 49.750
MP03001 MAL3P2.11 CAB38998 369 98.0235 KMEKCSSVF 9 34.0 1000000.0
1000000.0 39.989 MP03001 MAL3P2.11 CAB38998 376 98.0236 VFNVVNSSI 9
231723.3 1000000.0 1000000.0 82.506 1369.t00001 Chromosome11 34
98.0237 NYMKIMNHL 9 37582.2 1000000.0 1000000.0 4.875 1369.t00001
Chromosome11 225 98.0193 SYKSSKRDKF 10 1632.7 1000000.0 1000000.0
46.746 1369.t00001 Chromosome11 264 98.0238 TYKKKNNHI 9 90904.7
1000000.0 1000000.0 12.042 1369.t00001 Chromosome11 277 98.0239
VYYNILIVL 9 59837A 1000000.0 1000000.0 11.637 1369.t00001
Chromosome11 285 98.0240 LYYLFNQHI 9 56431.2 1000000.0 1000000.0
5.598 1369.t00001 Chromosome11 310 98.0241 SFFMNRFYI 9 56480.3
1000000.0 1000000.0 80.940 1369.t00001 Chromosome11 316 98.0242
FYITTRYKY 9 45.2 1000000.0 1000000.0 3.968 1369.t00001 Chromosome11
328 98.0243 KYINFINFI 9 289163.4 1000000.0 1000000.0 0.095
1369.t00001 Chromosome11 331 98.0244 NFINFIKVL 9 610070.5 1000000.0
1000000.0 37.188 1369.t00001 Chromosome11 380 98.0245 KYEALIKLL 9
105887.8 1000000.0 1000000.0 9.605 699.t00001 Chromosome11 443
98.0246 FFFSLIDYF 9 118.9 1000000.0 1000000.0 1.331 699.t00001
Chromosome11 460 98.0247 KYNIKVCEL 9 98354.1 1000000.0 1000000.0
0.429 699.t00001 Chromosome11 487 98.0248 FYLYISFLL 9 34312.8
1000000.0 1000000.0 0.417 699.t00001 Chromosome11 664 98.0249
FYTNNANLL 9 42910.8 1000000.0 1000000.0 0.639 699.t00001
Chromosome11 766 98.0250 EYNPSFFYL 9 22929.4 1000000.0 1000000.0
1.772 699.t00001 Chromosome11 845 98.0251 SFIIFKNIF 9 249.9
1000000.0 1000000.0 3.449 699.t00001 Chromosome11 881 98.0252
LYMNFLKFI 9 34148.2 1000000.0 1000000.0 4.363 699.t00001
Chromosome11 929 98.0253 KYLIILLYI 9 93640.1 1000000.0 1000000.0
1.034 699.100001 Chromosome11 1020 98.0254 KYIYIYIYI 9 215740.5
1000000.0 1000000.0 0.296 699.100001 Chromosome11 1024 98.0255
IYIYIFIYL 9 52331.1 1000000.0 1000000.0 2.300 M13Hg2.q1t3 135
98.0256 IYINKLSFF 9 67.4 1000000.0 1000000.0 3.329 M13Hg2.q1t3 142
98.0257 FFSIKDELF 9 27.2 1000000.0 1000000.0 14.276 M13Hg2.q1t3 156
98.0258 EFLKNNSYF 9 164.9 1000000.0 1000000.0 20.204 M13Hg2.q1t3
163 98.0259 YFNIIQQKI 9 45274.1 1000000.0 1000000.0 13.888
M13Hg2.q1t3 244 98.0260 WYCSACNFL 9 56993.5 1000000.0 1000000.0
7.339 M13Hg2.q1t3 296 98.0261 LYLINNKNL 9 150801.1 1000000.0
1000000.0 28.854 M13Hg2.q1t3 345 98.0262 TYKDANNNI 9 71978.1
1000000.0 1000000.0 29.035 M13Hg2.q113 521 98.0263 VYEKEKQYF 9
103.6 1000000.0 1000000.0 3.963 M13Hg2.q1t3 553 98.0194 PYFNFFVNYF
10 185.8 1000000.0 1000000.0 33.503 M13Hg2.q1t3 889 98.0264
IYNNNNEHI 9 77962.6 1000000.0 1000000.0 24.919 Mal_5L10c4.q1t6 78
98.0265 EYNKYNEYF 9 90.4 1000000.0 1000000.0 3.130 Mal_5L10c4.q1t6
137 98.0266 NYVNNNNVF 9 220.5 1000000.0 1000000.0 3.441
Mal_5L10c4.q1t6 321 98.0267 KYPIKYCEL 9 183114.8 1000000.0
1000000.0 0.364 Mal_5L10c4.q1t6 416 98.0268 AYHDLIKLF 9 66.8
1000000.0 1000000.0 4.671 Mal_5L10c4.q116 533 98.0269 KYISSVNYF 9
194.8 1000000.0 1000000.0 0.018 Mal_5L10c4.q1t6 773 98.0270
KYDWFFNSF 9 34.0 1000000.0 1000000.0 0.374 Mal_5L10c4.q1t6 1183
98.0271 HYVIKKYII 9 133499.1 1000000.0 1000000.0 1.507
Mal_5L10c4.q1t6 1259 98.0272 LYLHIHKLF 9 72.0 1000000.0 1000000.0
0.343 Mal_5L10c4.q1t6 1323 98.0273 YYRTNYGYI 9 165642.6 1000000.0
1000000.0 4.072 Mal_5L10c4.q1t6 2054 98.0274 KYLRYHSQL 9 421667.1
1000000.0 1000000.0 0.655 571.t00003 Cluomosome11 74 98.0275
FYIDKCIHF 9 23.2 1000000.0 1000000.0 0.120 571.t00003 Chromosome11
162 98.0276 FYTNYYQSF 9 48.3 1000000.0 1000000.0 0.186 571.t00003
Chromosome11 177 98.0277 PYINQTNIF 9 228.9 1000000.0 1000000.0
0.527 571.t00003 Chromosome11 807 98.0278 NYPNNANHI 9 176667.0
1000000.0 1000000.0 3.103 571.t00003 Chromosome11 834 98.0279
TYNNFHNSY 9 52.4 1000000.0 1000000.0 0.776 571.t00003 Chromosome11
1917 98.0280 YMNNNTYSF 9 7.7 1000000.0 1000000.0 2.132 571.t00003
Chromosome11 2026 98.0281 KYTEGATNF 9 74.8 1000000.0 1000000.0
1.964 571.t00003 Chromosome11 2450 98.0282 FYISIIDII 9 150563.0
1000000.0 1000000.0 1.632 571.t00003 Chromosome11 2540 98.0283
YYKEHISEF 9 96.3 1000000.0 1000000.0 3.143 571.t00003 Chromosome11
2914 98.0284 YYNRANNEI 9 46291.4 1000000.0 1000000.0 3.342 MP03072
PFC0450w CAA15614 17 98.0285 AFLLITFLM 9 37258.4 1000000.0
1000000.0 17.525 MP03072 PFC0450w CAA15614 53 98.0195 LYVIFLVLLF 10
174.0 1000000.0 1000000.0 16.581 MP03072 PFC0450w CAA15614 53
98.0286 LYVIFLVLL 9 107336.6 1000000.0 1000000.0 5.089 MP03072
PFC0450w CAA15614 86 98.0287 KYVQLASTY 9 65.1 1000000.0 1000000.0
70.547 45.t00001 Chromosome14 21 98.0196 RYQDPQNYEL 10 1000000.0
1000000.0 1000000.0 46.471 45.t00001 Chromosome14 40 98.0288
IYYEDGNSW 9 97026.0 1000000.0 1000000.0 15.493 45.t00001
Chromosome14 94 98.0289 VYRHCEYIL 9 560574.8 1000000.0 1000000.0
27.538 45.t00001 Chromosome14 135 98.0290 TWKPTIFLL 9 34068.5
1000000.0 1000000.0 26.741 45.t00001 Chromosome14 168 9830291
SYKVNCINF 9 25.3 1000000.0 1000000.0 63.592 45.t00001 Chromosome14
216 98.0292 KYNYFIHFF 9 39.1 1000000.0 1000000.0 0.380 45.t00001
Chromosome14 218 98.0293 NYFIHFFTW 9 95820.5 1000000.0 1000000.0
2.156 45.t00001 Chromosome14 222 98.0294 HFFTWGTMF 9 17.4 1000000.0
1000000.0 6.418 45.t00001 Chromosome14 229 98.0295 MFVPKYFEL 9
57423.3 1000000.0 1000000.0 28.589 45.t00001 Chromosome14 295
98.0296 IYTIIQDQL 9 334935.0 1000000.0 1000000.0 9.774 MP03137
PFC0700c CAB11150 3 98.0197 DFFLKSKFNI 10 1000000.0 1000000.0
1000000.0 79.527 MP03137 PFC0700c CAB11150 4 98.0297 FFLKSKFNI 9
80470.7 1000000.0 1000000.0 10.043 MP03137 PFC0700c CAB11150 9
98.0298 KFNILSSPL 9 275819.0 1000000.0 1000000.0 48.661 MP03137
PFC0700c CAB11150 61 98.0299 RMTSLKNEL 9 45471.5 1089.6 1000000.0
50.292 MP03137 PFC0700c CAB11150 77 98.0300 YYNNFNNNY 9 29.9
1000000.0 1000000.0 2.802 MP03137 PFC0700c CAB11150 87 98.0301
YYNKSTEKL 9 25069.1 1000000.0 1000000.0 6.131 MP03137 PFC0700c
CAB11150 109 98.0302 EYEPTANLL 9 29899.8 1000000.0 1000000.0 9.359
12.t00018 Chromosome14 479 98.0303 PYEEVENYF 9 118.2 1000000.0
1000000.0 3.525 12.t00018 Chromosome14 506 98.0304 KFILHMTLL 9
418744.3 1000000.0 1000000.0 7.942 12.t00018 Chromosome14 544
98.0305 NFLNIYASL 9 309896.9 1000000.0 1000000.0 7.653 12.t00018
Chromosome14 594 98.0306 VWKKLIEYF 9 120.2 1000000.0 1000000.0
7.058 12.t00018 Chromosome14 614 98.0307 LYVSMYIPF 9 113.5
1000000.0 1000000.0 6.679 12.t00018 Chromosome14 618 98.0308
MYIPFIKKF 9 62.3 1000000.0 1000000.0 2.663 12.t00018 Chromosome14
625 98.0309 KFYDKRFIF 9 53.3 1000000.0 1000000.0 1.395 12.t00018
Chromosome14 675 98.0310 IYNMYHNNF 9 27.2 1000000.0 1000000.0 0.737
12.t00018 Chromosome14 678 98.0311 MYHNNFSYF 9 61.8 1000000.0
1000000.0 5.105 12.t00018 Chromosome14 815 98.0312 KYDITKNLI 9
86746.4 1000000.0 1000000.0 2.983 mal_BU121g9.q1c1 61 98.0313
GYFKRIFKL 9 39278.5 1000000.0 1000000.0 64.889 mal_BU121g9.q1c1 81
98.0314 TYKNGNIYI 9 240142.1 1000000.0 1000000.0 20.110
mal_BU121g9.q1c1 87 98.0315 IYIYIYIYI 9 133656.3 1000000.0
1000000.0 2.246 mal_BU121g9.q1c1 89 98.0198 IYIYIYIYFL 10 1000000.0
1000000.0 1000000.0 72.026 mal_BU121g9.q1c1 89 98.0316 IYIYIYIYF 9
89.8 1000000.0 1000000.0 0.543 mal_9A57b11.q1t2 75 98.0317
IFKNDNNTF 9 290.7 1000000.0 1000000.0 11.568 mal_9A57b11.q1t2 103
98.0318 KYGNICHHI 9 61693.1 1000000.0 1000000.0 4.552
mal_9A57b11.q1t2 139 98.0319 QYTDIPSLI 9 41835.9 1000000.0
1000000.0 24.727 mal_9A57b11.q1t2 159 98.0320 VFCYEYFIF 9 98.9
1000000.0 1000000.0 69.226 mal_9A57b11.q1t2 161 98.0199 CYEYFIFDIF
10 811.1 1000000.0 1000000.0
61.974 mal_9A57b11.q1t2 161 98.0321 CYEYFIFDI 9 32300.1 1000000.0
1000000.0 79.659 mal_9A57b11.q1t2 171 98.0322 KYARNILSL 9 27927.9
1000000.0 1000000.0 3.398 mal_9A57b11.q1t2 230 98.0323 IFVKYLPLF 9
68.2 1000000.0 1000000.0 30.518 mal_9A57b11.q1t2 233 98.0324
KYLPLFLMM 9 16925.5 1000000.0 1000000.0 15.776 mal_9A5tb11.q1t2 237
98.0325 LFLMMEIISF 9 51.0 1000000.0 1000000.0 70.804
mal_BL50e8.p1ca_5 116 98.0326 QYSNYFDYL 9 103941.7 1000000.0
1000000.0 17.499 mal_BL50e8.p1ca_5 184 98.0327 PYETNNNLF 9 37.2
1000000.0 1000000.0 4.367 mal_BL50e8.p1ca_5 341 98.0328 YYSRRVEKI 9
33168.4 1000000.0 1000000.0 6.349 mal_BL50e8.p1ca_5 555 98.0329
KFKWIQDNL 9 453346.6 1000000.0 1000000.0 30.007 mal_BL50e8.p1ca_5
687 98.0200 RYVGLGSFHF 10 1143.3 1000000.0 1000000.0 33.267
mal_BL50e8.p1ca_5 768 98.0330 TYKMYPPEF 9 68.2 1000000.0 1000000.0
7.746 mal_BL50e8.p1ca_5 771 98.0331 MYPPEFNTL 9 37286.8 1000000.0
1000000.0 14.291 mal_BL50e8.p1ca_5 827 98.0332 KYCIGSTYF 9 184.3
1000000.0 1000000.0 0.261 mal_BL50e8.plca_5 833 98.0333 TYFLRQVSI 9
163553.3 1000000.0 1000000.0 31.623 mal_BL50e8.p1ca_5 857 98.0334
KYSARLHPI 9 52609.1 1000000.0 1000000.0 33.171 M13S8h6.p1t_3 152
98.0335 FYLKKKFLF 9 30.5 1000000.0 1000000.0 0.091 M13S8h6.p1t_3
298 98.0336 KYYISYKVL 9 328554.4 1000000.0 1000000.0 3.468
M13S8h6.p1t_3 321 98.0337 KYINKNISL 9 213679.4 1000000.0 1000000.0
0.395 M13S8h6.p1t_3 380 98.0338 KYLKEDNTF 9 189.5 1000000.0
1000000.0 2.580 M13S8h6.p1t_3 753 98.0339 KYGDNENNF 9 50.4
1000000.0 1000000.0 2.048 M13S8h6.p1t_3 1208 98.0340 VFTKINNLF 9
55.7 1000000.0 1000000.0 4.101 M13S8h6.p1t_3 1438 98.0341 IWLIRSIYL
9 175087.7 1000000.0 1000000.0 2.659 M13S8h6.p1t_3 1444 98.0342
IYLFIITYI 9 153399.4 1000000.0 1000000.0 4.385 M13S8h6.p1t_3 1536
98.0343 FFFVFFYIF 9 26.2 1000000.0 1000000.0 0.631 M13S8h6.p1t_3
1541 98.0344 FYIFLIYSF 9 60.5 1000000.0 1000000.0 0.315 585.t00002
Chromosome11 1 98.0345 MYIFFFILF 9 12.6 1000000.0 1000000.0 1.911
585.t00002 Chromosome11 11 98.0346 FYVMSTYTF 9 45.7 1000000.0
1000000.0 0.144 585.t00002 Chromosome11 512 98.0347 RYCTKCFLW 9
31357.1 1000000.0 1000000.0 1.726 585.t00002 Chromosome11 605
98.0348 VYAKNIPLW 9 36459.4 1000000.0 1000000.0 1.882 585.t00002
Chromosome11 663 98.0349 FFCTFFISL 9 35177.1 1000000.0 1000000.0
1.436 585.t00002 Chromosome11 681 98.0350 PYYKKKNLF 9 53.3
1000000.0 1000000.0 2.732 585.t00002 Chromosome11 1378 98.0351
FYTLVNILI 9 40959.2 1000000.0 1000000.0 2.113 585.t00002
Chromosome11 1419 98.0352 YFIIRSYEL 9 135598.6 1000000.0 1000000.0
2.721 585.t00002 Chromosome11 1483 98.0353 KYICLTCAF 9 30.1
1000000.0 1000000.0 0.435 585.t00002 Chromosome11 1752 98.0354
KYDLFNNFI 9 83062.5 1000000.0 1000000.0 1.355 1223.t00015
mal_9A21f9.q1t_4 1202 98.0355 KYKDMAKIF 9 215.2 1000000.0 1000000.0
0.315 1223.t00015 mal_9A21f9.q1t_4 1599 98.0356 GYRPFIYSW 9 83421.5
1000000.0 1000000.0 3.292 1223.t00015 mal_9A21f9.q1t_4 1621 98.0357
LYAIFNKLF 9 57.9 1000000.0 1000000.0 0.212 1223.t00015
mal_9A21f9.q1t_4 1631 98.0358 FYLDKIQIL 9 36632.3 1000000.0
1000000.0 0.942 1223.t00015 mal_9A21f9.q1t_4 2272 98.0359 RMEDKTFSL
9 8870.6 143.4 1000000.0 4.349 1223.t00015 mal_9A21f9.q1t_4 2702
98.0360 IYNCVTINW 9 10684.6 1000000.0 1000000.0 2.727 1223.t00015
mal_9A21f9.q1t_4 3109 98.0361 RWTDDSNNF 9 60.4 1000000.0 1000000.0
1.600 1223.t00015 mal_9A21f9.q1t_4 3735 98.0362 FFYDILNVI 9 40209.1
1000000.0 1000000.0 5.095 1223.t00015 mal_9A21f9.q1t_4 3968 98.0363
KYRKIIYSL 9 215862.1 1000000.0 1000000.0 0.665 1223.t00015
mal_9A21f9.q1t_4 4515 98.0364 KYFIFRIHL 9 114989.5 1000000.0
1000000.0 0.325 599.t00001 Chromosome11 8 98.0365 KYLTINFFI 9
160943.0 1000000.0 1000000.0 0.123 599.t00001 Chromosome11 14
98.0366 FFILLTLVF 9 30.5 1000000.0 1000000.0 3.495 599.t00001
Chromosome11 24 98.0367 KYSSCQNSL 9 213208.8 1000000.0 1000000.0
0.906 599.t00001 Chromosome11 955 98.0368 KFIEHINEF 9 278.8
1000000.0 1000000.0 1.175 599.t00001 Chromosome11 1118 98.0369
KYIELNDLI 9 231736.4 1000000.0 1000000.0 1.464 599.t00001
Chromosome11 1194 98.0370 PYSNVTYVI 9 97127.6 1000000.0 1000000.0
1.861 599.t00001 Chromosome11 1434 98.0371 MYDILNAYF 9 42.0
1000000.0 1000000.0 1.204 599.t00001 Chromosome11 1769 98.0372
IIYIMNNTIF 9 38.3 1000000.0 1000000.0 1.389 599.t00001 Chromosome11
1929 98.0373 FFKYIISYF 9 126.1 1000000.0 1000000.0 3.000 599.t00001
Chromosome11 1943 98.0374 KYLNDDNYL 9 679247.8 1000000.0 1000000.0
0.368 MP01072 M1045c5.p1c.C_6 67 98.0375 LYKSIFKAF 9 52.5 1000000.0
1000000.0 21.749 MP01072 M1045c5.p1c.C_6 107 98.0376 SYRIVNAGF 9
268.7 1000000.0 1000000.0 7.480 MP01072 M1045c5.p1c.C_6 319 98.0377
KYTFRSLSI 9 63496.4 1000000.0 1000000.0 7.958 MP01072
M1045c5.p1c.C_6 388 98.0378 KYKNDSNRI 9 401700.0 1000000.0
1000000.0 6.170 MP01072 M1045c5.p1c.C_6 612 98.0379 SYIYNKNIF 9
105.6 1000000.0 1000000.0 13.043 MP01072 M1045c5.p1c.C_6 1042
98.0380 FMKNNTTLF 9 117 1000000.0 1000000.0 2.141 MP01072
M1045c5.p1c.C_6 1123 98.0381 HYVMINNNL 9 52910.4 1000000.0
1000000.0 3.607 MP01072 M1045c5.p1c.C_6 1163 98.0382 FFLFFSIFI 9
69264.3 1000000.0 1000000.0 2.646 MP01072 M1045c5.p1c.C_6 1249
98.0383 RYFLHTITI 9 101443.4 1000000.0 1000000.0 2.834 MP01072
M1045c5.p1c.C_6 1260 98.0384 KYTSSYDSL 9 230897.9 1000000.0
1000000.0 1.533 PIR2 T28161 243 98.0385 YYKLREDWW 9 283854.6
1000000.0 1000000.0 8.617 PIR2 T28161 304 98.0386 QYLRWFEEW 9
35188.7 1000000.0 1000000.0 14.859 PIR2 T28161 628 98.0387
HWTQIKKIIF 9 30.8 1000000.0 1000000.0 11.497 PIR2 T28161 647
98.0388 HYFVLETVL 9 65432.8 1000000.0 1000000.0 12.976 PIR2 T28161
833 98.0389 RWMDTAGFI 9 32693.4 1000000.0 1000000.0 6.822 PIR2
T28161 848 98.0201 IYMPPRRQHF 10 391.2 1000000.0 1000000.0 14.666
PIR2 T28161 1024 98.0390 RWMTEWAEW 9 39609.0 1000000.0 1000000.0
3.877 PIR2 T28161 1574 98.0391 KYQYDKVKL 9 515925.0 1000000.0
1000000.0 6.877 PIR2 T28161 1681 98.0392 KYCRFYKRW 9 239673.9
1000000.0 1000000.0 3.433 PIR2 T28161 1887 98.0393 YFLDDYNKI 9
114991.6 1000000.0 1000000.0 7.588 55.t00004 Chromosome14 223
98.0394 KYELRKTSI 9 226076.9 1000000.0 1000000.0 3.213 55.t00004
Chromosome14 339 98.0395 MYKNKVDPL 9 208222.7 1000000.0 1000000.0
31.490 55.t00004 Chromosome14 455 98.0396 YYDTCKNIW 9 80910.8
1000000.0 1000000.0 11.820 55.t00004 Chromosome14 686 98.0397
KYINNMSFI 9 317672.0 1000000.0 1000000.0 1.757 55.t00004
Chromosome14 896 98.0398 LYPWKENKF 9 99.5 1000000.0 1000000.0 6.128
55.t00004 Chromosome14 973 98.0399 KWNVFNNSI 9 191824.8 1000000.0
1000000.0 0.536 55.t00004 Chromosome14 1027 98.0400 KFKIINSYI 9
648818.6 1000000.0 1000000.0 2.246 55.t00004 Chromosome14 1123
98.0401 NYAYDNIEL 9 113781.7 1000000.0 1000000.0 8.937 55.t00004
Chromosome14 1155 98.0402 IYTSTNNII 9 105468.3 1000000.0 1000000.0
7.723 55.t00004 Chromosome14 1268 98.0403 KYTYNINNL 9 65476.9
1000000.0 1000000.0 7.681 13.t00011 Chromosome14 68 98.0202
RYNVINHIYL 10 1000000.0 1000000.0 1000000.0 74.419 13.t00011
Chromosome14 68 98.0404 RYNVINHIY 9 26.0 1000000.0 1000000.0 55.779
13.t00011 Chromosome14 84 98.0405 TYNYLTPTL 9 75416.9 1000000.0
1000000.0 7.874 13.t00011 Chromosome14 96 98.0203 RFRVFKDYSF 10
3387.1 1000000.0 1000000.0 29.344 13.t00011 Chromosome14 99 98.0406
VFKDYSPFI 9 99598.3 1000000.0 1000000.0 7.373 13.t00011
Chromosome14 105 98.0407 FFIDEVKKI 9 230004.2 1000000.0 1000000.0
12.686 37.t00002 Chromosome14 20 98.0408 VYYDNYESL 9 72350.5
1000000.0 1000000.0 10.652 674.t00001 Chromosome11 68 98.0409
RFVEKIYYL 9 228887.0 1000000.0 1000000.0 8.045 674.t00001
Chromosomell 114 98.0410 IYINVQKNL 9 306183.0 1000000.0 1000000.0
14.033 674.t00001 Chromosome11 140 98.0411 KFYYYFKEF 9 92.8
1000000.0 1000000.0 14.487 674.t00001 Chromosome11 141 98.0204
EYYYFKEFLL 10 1000000.0 1000000.0 1000000.0 13.628 674.t00001
Chromosome11 141 98.0412 FYYYFKEFL 9 104311.6 1000000.0 1000000.0
1.300 674.t00001 Chromosome11 418 98.0413 TYIPDKKLL 9 209801.1
1000000.0 1000000.0 17.181 674.t00001 Chromosome11 461 98.0414
NYLYNKYYI 9 288938.1 1000000.0 1000000.0 5.750 674.t00001
Chromosome11 579 98.0415 NFKEQHLLF 9 72.4 1000000.0 1000000.0
38.780 674.t00001 Chromosome11 649 98.0416 FIYINNKHNL 9 41447.1
1000000.0 1000000.0 10.887 674.100001 Chromosome11 800 98.0417
LYREIISREL 9 274526.6 1000000.0 1000000.0 38.601 674.t00001
Chromosome11 1095 98.0418 NYINNNIYL 9 268777.1 1000000.0 1000000.0
3.259 674.t00001 Chromosome11 1117 98.0419 NYNQKENSF 9 40.2
1000000.0 1000000.0 27.868 674.t00001 Chromosome11 1396 98.0205
QYKVKIKPVF 10 5076.8 1000000.0 1000000.0 42.788
TABLE-US-00004 TABLE 4 Pf-derived A2 supertype peptides with PIC
< 100 nM PIC Malaria locus Addn Source info Position Accession
No. Peptide No. Sequence AA A*0101 A*0201 PIC A*1101 A*2402
331.t00003 Chromosome10 105 99.0042 LIYPCVYEI 9 38050.5 43.8
1000000.0 1000000.0 331.t00003 Chromosome10 598 99.0043 NMNVQNFFV 9
50979.5 35.3 1000000.0 1000000.0 331.t00003 Chromosome10 605
99.0044 FVWGHDMFM 9 25516.6 18.5 1000000.0 1000000.0 331.t00003
Chromosome10 660 99.0045 QLDDKFAFI 9 3138.5 43.0 1000000.0
1000000.0 331.t00003 Chromosome10 950 99.0046 CLINHNFFM 9 63467.3
65.7 1000000.0 1000000.0 331.t00003 Chromosome10 957 99.0047
FMLVGGINI 9 11445.4 72.5 1000000.0 399.0 331.t00003 Chromosome10
1007 99.0048 YIIGGGCTV 9 19833.9 77.9 1000000.0 1000000.0
331.t00003 Chromosome10 1016 99.0049 FTFGSFPDV 9 2705.2 14.1
1000000.0 1000000.0 331.t00003 Chromosome10 1847 99.0050 NLSFAQYTL
9 22775.6 52.7 1000000.0 1000000.0 331.t00003 Chromosome10 1889
99.0051 RMYHYVVDI 9 47589.4 49.4 1000000.0 890.2 18.000811
Chr12Contig18 2 99.0001 VLRLFVCFLI 10 1000000.0 72.4 1000000.0
1000000.0 18.000811 Chr12Contig18 9 99.0002 FLIFHFFLFL 10 1000000.0
10.9 1000000.0 1000000.0 18.000811 Chr12Contig18 10 99.0003
LIFHFFLFLL 10 1000000.0 29.1 1000000.0 1000000.0 18.000811
Chr12Contig18 15 99.0004 FLFLLYILFL 10 404264.4 19.6 1000000.0
1000000.0 18.000811 Chr12Contig18 32 99.0005 RLPVICSFLV 10
1000000.0 99.3 1000000.0 1000000.0 18.000811 Chr12Contig18 35
99.0006 VICSFLVFLV 10 1000000.0 71.5 1000000.0 1000000.0 18.000811
Chr12Contig18 39 99.0007 FLVFLVFSNV 10 1000000.0 45.6 1000000.0
1000000.0 18.000811 Chr12Contig18 10 99.0052 LIFHFFLFL 9 8592.7 9.8
1000000.0 1000000.0 18.000811 Chr12Contig18 17 99.0053 FLLYILFLV 9
6742.1 1.9 1000000.0 1000000.0 18.000811 Chr12Contig18 35 99.0054
VICSFLVFL 9 43080.6 76.0 1000000.0 1000000.0 18.000811
Chr12Contig18 159 99.0055 ATYGIIVPV 9 18077.0 45.4 1000000.0
1000000.0 MY924Fe3.p1t1 222 99.0008 FLYAFNKYYV 10 538964.2 15.2
1000000.0 1000000.0 MY924Fe3.p1t1 127 99.0056 NMISVVYYI 9 97099.2
14.5 1000000.0 8.2 MY924Fe3.p1t1 299 99.0057 SLCFYFLLL 9 2719.7
20.9 1000000.0 1000000.0 MY924Fe3.p1t1 470 99.0058 ILFLHNYLL 9
31359.3 26.7 1000000.0 1000000.0 MY924Fe3.p1t1 512 99.0059
YLDVYNFLL 9 4353.0 7.2 1000000.0 1000000.0 MY924Fc3.p1t1 1209
99.0060 FQLYYMYYL 9 91212.8 4.0 1000000.0 1000000.0 MY924Fe3.p1t1
1267 99.0061 YVMDKVLKL 9 984.8 45.3 1000000.0 1000000.0
MY924Fe3.p1t1 2260 99.0062 LLFILSHFI 9 11073.4 23.7 1000000.0
1000000.0 MY924Fe3.p1t1 2326 99.0063 YLVNYCLVV 9 16842.3 10.9
1000000.0 1000000.0 MY924Fe3.p1t1 2395 99.0064 KIYVCIYYL 9 157982.7
39.3 1000000.0 1000000.0 MP03001 MAL3P2.11 6 CAB38998 99.0009
ILSVSSFLFV 10 1000000.0 94.9 1000000.0 1000000.0 MP03001 MAL3P2.11
386 CAB38998 99.0010 LIMVLSFLFL 10 1000000.0 38.4 1000000.0
1000000.0 MP03001 MAL3P2.11 318 CAB38998 99.0065 YLNKIQNSL 9
13496.2 78.4 1000000.0 1000000.0 MP03001 MAL3P2.11 387 CAB38998
99.0066 IMVLSFLFL 9 8739.3 36.0 1000000.0 2608.6 1369.t00001
Chromosome11 60 99.0011 VQMMIMIKFM 10 1000000.0 96.6 1000000.0
1000000.0 1369.t00001 Chromosome11 62 99.0012 MMIMIKFMGV 10
1000000.0 47.1 1000000.0 1000000.0 1369.t00001 Chromosome11 9
99.0067 KlYKIIIWI 9 56576.0 72.2 1000000.0 1000000.0 1369.t00001
Chromosome11 23 99.0068 YMIKKLLKI 9 4324.7 52.7 1000000.0 788.9
1369.t10001 Chromosome11 42 99.0069 LMTLYQIQV 9 32880.1 41.7
1000000.0 1000000.0 1369.100001 Chromosome11 68 99.0070 FMGVIYIMI 9
10136.0 91.9 1000000.0 58.6 1369.t00001 Chromosome11 280 99.0071
NILIVLYYL 9 117610.0 42.8 1000000.0 1000000.0 1369.t00001
Chromosome11 312 99.0072 FMNRFYITT 9 14073.8 47.8 1000000.0
1000000.0 699.t00001 Chromosome11 488 99.0013 YLYISFLLLI 10
311433.0 34.2 1000000.0 1000000.0 699.t00001 Chromosome11 1025
99.0014 YIYIFIYLFI 10 1000000.0 19.8 1000000.0 1000000.0 699.t00001
Chromosome11 408 99.0073 LLDDYHFET 9 5923.7 39.5 1000000.0
1000000.0 699.t00001 Chromosome11 488 99.0074 YIYISFLLL 9 2547.9
11.2 1000000.0 1000000.0 699.t00001 Chromosome11 572 99.0075
FLTLTVYPI 9 22535.9 28.3 1000000.0 1000000.0 699.t00001
Chromosome11 651 99.0076 FHEILELL 9 15575.2 47.0 1000000.0
1000000.0 699.t00001 Chromosome11 782 99.0077 LLYNIIITSI 9 62668.0
50.4 1000000.0 1000000.0 699.t00001 Chromosome11 882 99.0078
YMNFLKFTV 9 14215.9 50.3 1000000.0 1000000.0 699.t00001
Chromosome11 1033 99.0079 FIYIWLHLI 9 6243.9 15.6 1000000.0
1000000.0 699.t00001 Chromosome11 1039 99.0080 HLIIIFIFV 9 6908.2
11.5 1000000.0 1000000.0 M13Hg2.q1t3 576 99.0015 FLMWSSQIII 10
96042.7 91.8 1000000.0 I000000.0 M13Hg2.q1t3 96 99.0081 ILLSRFIFI 9
11278.3 22.9 1000000.0 1000000.0 M13Hg2.q1t3 508 99.0082 YLNFQDNYL
9 34942.8 80.6 1000000.0 1000000.0 M13Hg2.q1t3 551 99.0083
NIPYFNFFV 9 86593.7 41.8 1000000.0 1000000 0 M13Hg2.q1t3 558
99.0084 FVNYFEAVV 9 15474.4 100.0 1000000.0 1000000.0 M13Hg2.q1t3
569 99.0085 NIHCYTYFL 9 27934.2 25.6 1000000.0 1000000.0
M13Hg2.q1t3 576 99.0086 FLMWSSQII 9 5275.5 31.9 1000000.0 1000000.0
M13Hg2.q1t3 577 99.0087 LMWSSQIII 9 15320.6 46.4 1000000.0 614.0
M13Hg2.q1t3 723 99.0088 ILNKISSFV 9 17591.1 89.9 1000000.0
1000000.0 Mal_5L10c4.q1t6 334 99.0089 FVFFIIKNV 9 13366.7 53.5
1000000.0 1000000.0 Mal_5L10c4.q1t6 366 99.0090 IQICKLYHV 9 8534.4
35.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 534 99.0091 YISSVNYFL 9
25585.7 24.2 1000000.0 1000000.0 Mal_5L10c4.q1t6 1205 99.0092
YLFQLVQSL 9 4424.1 26.3 1000000.0 1000000.0 Mal_5L10c4.q1t6 1240
99.0093 SIYFYWFLL 9 13813.9 27.2 1000000.0 1000000.0
Mal_5L10c4.q1t6 1260 99.0094 YLHIHKLFI 9 46175.4 47.6 1000000.0
1000000.0 Mal_5L10c4.q1t6 1596 99.0095 ILDDSINFV 9 8148.9 41.5
1000000.0 1000000.0 Mal_5L10c4.q1t6 1629 99.0096 FLPEQSYVL 9
36294.8 55.0 1000000.0 1000000.0 Mal_5L10c4.q1t6 1890 99.0097
ITLVIQIIYV 9 52344.4 36.6 1000000.0 1000000.0 Mal_5L10c4.q1t6 2106
99.0098 FLSVINASV 9 15607.8 17.1 1000000.0 1000000.0 571.t00003
Chromosome11 105 99.0016 ILYPSLMPYV 10 1000000.0 81.0 1000000.0
1000000.0 571.t00003 Chromosome11 2443 99.0017 YLFGKVKFYI 10
821413.1 47.5 1000000.0 1000000.0 571.t00003 Chromosome11 68
99.0099 KLINTNFYI 9 109718.5 49.2 1000000.0 1000000.0 571.t00003
Chromosome11 92 99.0100 KTFIYSNFL 9 34260.6 95.5 1000000.0
1000000.0 571.t00003 Chromosome11 109 99.0101 SLMPYVECI 9 3307.6
80.4 1000000.0 1000000.0 571.t00003 Chromosome11 163 99.0102
YTNYYQSFI 9 14053.9 63.6 1000000.0 1000000.0 571.t00003
Chromosome11 1224 99.0103 FQWEKSNKI 9 17731.1 88.1 1000000.0
1000000.0 571.t00003 Chromosome11 1330 99.0104 FLIKLNNE1 9 32980.5
73.6 1000000.0 1000000.0 571.t00003 Chromosome11 1478 99.0105
YMYTNYLNM 9 5105.1 65.8 1000000.0 4545.4 571.t00003 Chromosome11
2286 99.0106 FQGEYVSNL 9 28240.4 61.4 1000000.0 1000000.0 MP03072
PFC0450w 7 CAA15614 99.0018 ILILIDAASV 10 1000000.0 88.5 1000000.0
1000000.0 MP03072 PFC0450w 19 CAA15614 99.0019 LLITFLMINL 10
1000000.0 82.3 1000000.0 1000000.0 MP03072 PFC0450w 46 CAA15614
99.0020 ALVVAIILYV 10 599232.7 38.0 1000000.0 1000000.0 MP03072
PFC0450w 50 CAA15614 99.0021 ATILYVIFLV 10 1000000.0 58.1 1000000.0
1000000.0 MP03072 PFC0450w 52 CAA15614 99.0022 ILYVIFLVLL 10
1000000.0 33.8 1000000.0 1000000.0 MP03072 PFC0450w 54 CAA15614
99.0023 YVIFLVLLFI 10 656413.8 20.3 1000000.0 1000000.0 MP03072
PFC0450w 57 CAA15614 99.0024 FLVLLFIYKA 10 139.6 80.7 498.9
1000000.0 MP03072 PFC0450w 18 CAA15614 99.0107 FLLITFLMI 9 5377.9
28.0 1000000.0 1000000.0 MP03072 PFC0450w 47 CAA15614 99.0108
LVVAIILYV 9 17753.4 20.8 1000000.0 1000000.0 MP03072 PFC0450w 50
CAA15614 99.0109 AIILYVIFL 9 35558.1 23.3 1000000.0 1000000.0
MP03072 PFC0450w 51 CAA15614 99.0110 IILYVIFLV 9 29081.2 23.4
1000000.0 1000000.0 MP03072 PFC0450w 52 CAA15614 99.0111 ILYVIFLVL
9 4626.7 49.4 1000000.0 1000000.0 MP03072 PFC0450w 55 CAA15614
99.0112 VIFLVLLFT 9 17063.1 28.6 1000000 0 1000000.0 45.t00001
Chromosome14 22 99.0113 YQDPQNYEL 9 17446.7 62.2 1000000.0
1000000.0 45.t00001 Chromosome14 134 99.0114 KTWKPTIFL 9 18939.7
82.8 1000000.0 1000000.0 45.t00001 Chromosome14 142 99.0115
LLNESNIFL 9 13381.3 66.8 1000000.0 1000000.0 45.t00001 Chromosome14
220 99.0116 FIHFFTWGT 9 54429.1 69.2 1000000.0 1000000.0 MP03137
PFC0700c 180 CAB11150 99.0117 VLFLQMMNV 9 71815.8 72.3 1000000.0
1000000.0 MP03137 PFC0700c 251 CAB11150 99.0118 NQMIFVSSI 9 39082.0
99.1 1000000.0 1000000.0 MP03137 PFC0700c 253 CAB11150 99.0119
MIFVSSIFI 9 17820.1 95.9 1000000.0 1000000.0 MP03137 PFC0700c 258
CAB11150 99.0120 SIFISFYLI 9 13357.1 72.3 1000000.0 1000000.0
MP03137 PFC0700c 293 CAB11150 99.0121 RLFEESLGI 9 22704.6 90.4
1000000.0 1000000.0 12.t00018 Chromosome14 870 99.0025 YLCLYNGLLL
10 294216.7 79.1 1000000.0 1000000.0 12.t00018 Chromosome14 1018
99.0026 YLLFFREKFL 10 1000000.0 57.8 1000000.0 1000000.0 12.t00018
Chromosome14 597 99.0122 KLIEYFLNM 9 8556.1 30.0 1000000.0
1000000.0 12.t00018 Chromosome14 615 99 0123 YVSMYIPFI 9 7367.7
57.9 1000000.0 1000000.0 12.t00018 Chromosome14 870 99.0124
YLCLYNGLL 9 12899.1 68.8 1000000.0 1000000.0 12.t00018 Chromosome14
893 99.0125 NIISSIFYI 9 94922.9 77.9 1000000.0 1000000.0 12.t00018
Chromosome14 907 99.0126 YLYDNYSHL 9 11094.9 55.2 1000000 0
1000000.0 12.t00018 Chromosome14 953 99.0127 FLNVYENFL 9 23398.0
34.3 1000000.0 1000000.0 12.t00018 Chromosome14 1037 99.0128
LIFGYNSLI 9 26493.2 50.1 1000000.0 1000000.0 12.t00018 Chromosome14
1047 99.0129 FLEYOCREV 9 24096.2 30.4 1000000.0 1000000.0
mal_BU12129.q1c1 90 99.0130 YIYIYIYFL 9 32096.6 3.8 1000000.0
1000000.0 mal_BU121g9.q1c1 92 99.0131 YIYINFLQI 9 15022.6 13.6
1000000.0 1000000.0 mal_9A57b11.q1t2 138 99.0132 KQYTDIPSL 9
184531.0 81.9 1000000.0 1000000.0 mal_9A57h11.q1t2 158 99.0133
KVFCYEYFI 9 10650.1 18.0 1000000.0 1000000.0 mal_9A57611.q1t2 165
99.0134 FIFDIFKYA 9 21.1 20.2 44.0 1000000.0 mal_BL50e8.p1ca_5 6
99.0027 ALLSFLVVLV 10 1000000.0 42.5 1000000.0 1000000.0
mal_BL50c8.p1ca_5 65 99.0028 RQINFMETFV 10 1000000.0 54.6 1000000.0
1000000.0 mal_BL50c8.p1ca_5 4 99.0135 FVALLSFLV 9 3130.0 26.0
1000000.0 1000000.0 mal_BL50e8.p1ca_5 7 99.0136 LLSFLVVLV 9 11579.5
36.2 1000000.0 1000000.0 mal_BL50e8.p1ca_5 192 99.0137 FIYNWVLQT 9
30528.1 55.9 1000000.0 1000000.0 mal_BL50e8.p1ca_5 349 99.0138
ILIRALLSL 9 8963.2 44.4 1000000.0
1000000.0 mal_BL50e8.p1ca_5 353 99.0139 ALLSLDFSL 9 22110.4 36.6
1000000.0 1000000.0 mal_BL50e8.p1ca_5 562 99.0140 NLFGGGFYI 9
22065.3 23.4 1000000.0 1000000.0 mal_BL50e8.p1ca_5 779 99.0141
LMLKADYFT 9 22456.0 21.9 1000000.0 444.0 mal_BL50e8.p1ca_5 973
99.0142 NIYTHSVYV 9 245555.5 53.7 1000000.0 1000000.0 M13S8h6.p1t_3
7 99.0143 FVLACVLLI 9 10293.7 14.2 1000000.0 1000000.0
M13S8h6.p1t_3 23 99.0144 ATSTEFFFL 9 3703.8 20.0 1000000.0
1000000.0 M13S8h6.p1t_3 34 99.0145 FLLICGFCI 9 23058.3 21.3
1000000.0 1000000.0 M13S8h6.p1t_3 55 99.0146 VLITYSFTV 9 35516.3
7.8 1000000.0 1000000.0 M13S8h6.p1t_3 61 99.0147 FIVSYIFFM 9
18627.5 9.0 1000000.0 1000000.0 M13S8h6.p1t_3 77 99.0148 LLVCISILL
9 4378.4 24.2 1000000.0 1000000.0 M13S8h6.p1t_3 1447 99.0149
FIITYIWII 9 50315.1 20.9 1000000.0 1000000.0 M13S8h6.p1t_3 1469
99.0150 KMMWTIFIL 9 13621.2 14.7 1000000.0 35.6 M13S8h6.p1t_3 1538
99.0151 FVFFYIFLI 9 5681.7 3.2 1000000.0 1000000.0 M13S8h6.p1t_3
1582 99.0152 YLDRIQFLV 9 3212.4 6.0 1000000.0 1000000.0 585.t00002
Chromosome11 651 99.0029 VLSPFSLIFV 10 236320.1 33.8 1000000.0
1000000.0 585.t00002 Chromosome11 1380 99.0030 TLVNILILFL 10
1000000.0 25.5 1000000.0 1000000.0 585.t00002 Chromosome11 1406
99.0031 FVFFRFLFFV 10 132657.2 16.7 1000000.0 1000000.0 585.t00002
Chromosome11 6 99.0153 FILFYFYVM 9 18702.2 16.8 1000000.0 1000000.0
585.t00002 Chromosome11 17 99.0154 YTFCFLPVL 9 3159.4 24.6
1000000.0 1000000.0 585.t00002 Chromosome11 643 99.0155 WLFFFDLVV 9
13858.2 39.1 1000000.0 1000000.0 585.t00002 Chromosome11 661
99.0156 FILFFCIFFI 9 13336.6 6.4 1000000.0 1000000.0 585.t00002
Chromosome11 1386 99.0157 ILFLICYSI 9 18185.7 17.8 1000000.0
1000000.0 585.t00002 Chromosome11 1399 99.0158 YMFSYIPFV 9 20964.1
1.1 1000000.0 1000000.0 585.t00002 Chromosome11 1507 99.0159
YILFILFFI 9 12765.9 4.2 1000000.0 1000000.0 1223.t00015
mal_9A21f9.q1t_4 1387 99.0032 LIHDDVLLFL 10 1000000.0 32.2
1000000.0 1000000.0 1223.t00015 mal_9A2119.q1t_4 270 99.0160
FVSFYKFEV 9 10792.4 28.2 1000000.0 1000000.0 1223.t00015
ma1_9A2110.q1t_4 811 99.0161 MLWCSMESV 9 5755.3 27.5 1000000.0
1000000.0 1223.t00015 ma1_9A21f9.q1t_4 924 99.0162 KLFDAINYL 9
35603.1 20.5 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1648
99.0163 FVMDITDSI 9 4215.8 44.1 1000000.0 1000000.0 1223.t00015
mal_9A2119.q1t_4 1853 99.0164 MLYSIVWGL 9 18338.7 24.8 1000000.0
1000000.0 1223.t00015 mal_9A21f9.q1t_4 2301 99.0165 NIYFSYFYV 9
68948.8 41.1 1000000.0 1000000.0 1223.t00015 mal_9A21f9.q1t_4 2548
99.0166 FILEHVNSI 9 80628.8 42.2 1000000.0 1000000.0 1223.t00015
mal_9A21f9.q1t_4 3057 99.0167 SLLKAQLFV 9 12372.4 15.7 1000000.0
1000000.0 1223.t00015 mal_9A21f9.q1t_4 4419 99.0168 SLDEVVLYT 9
8137.8 46.3 1000000.0 1000000.0 599.t00001 Chromosome11 1069
99.0033 HLMHIINVFI 10 1000000.0 56.9 1000000.0 1000000.0 599.t00001
Chromosome11 1341 99.0034 FLSDYTTCSV 10 93945.4 72.2 1000000.0
1000000.0 599.t00001 Chromosome11 1458 99.0035 FLRNYVVIFI 10
615882.5 83.6 1000000.0 1000000.0 599.t00001 Chromosome11 9 99.0169
YLTINFFIL 9 4373.8 64.1 1000000.0 1000000.0 599.t00001 Chromosome11
883 99.0170 NMNDIENFV 9 32886.3 78.0 1000000.0 1000000.0 599.t00001
Chromosome11 1013 99.0171 FIHDILLDL 9 11903.4 46.8 1000000 0
1000000.0 599.t00001 Chromosome11 1034 99.0172 NQYAYDLKI 9 38604.8
81.2 1000000.0 1000000.0 599.t00001 Chromosome11 1718 99.0173
GLGGLLFII 9 5216.8 74.2 1000000.0 1000000.0 599.t00001 Chromosome11
1770 99.0174 YIMNNTIFT 9 4444.5 75.2 1000000.0 1000000.0 599.t00001
Chromosome11 1914 99.0175 HLFNFSNFV 9 16629.7 25.5 1000000.0
1000000.0 MP01072 M1045c5.p1c.C_6 1138 99.0036 YLIRNILMSI 10
819635.3 75.5 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 66
99.0176 YLYKSIFKA 9 6.2 29.5 1755.3 1000000.0 MP01072
M1045c5.p1c.C_6 82 99.0177 YLDFYEFCV 9 5138.7 6.7 1000000.0
1000000.0 MP01072 M1045c5.p1c.C_6 1161 99.0178 KIPPLFFSI 9 19713.1
22.7 1000000.0 1000000.0 MP01072 M1045c5.p1c.C_6 1281 99.0179
KLNEINILL 9 15599.8 69.4 1000000.0 1000000.0 PIR2 T28161 577
99.0037 FLMFWVAHM 10 60152.9 33.4 1000000.0 1000000.0 PIR2 T28161
142 99.0180 LLAEVCYAA 9 9.8 35.1 4774.0 1000000.0 PIR2 T28161 369
99.0181 CLYVCDPYV 9 78244.5 58.0 1000000.0 1000000.0 PIR2 T28161
577 99.0182 FLMFWVAIIM 9 3061.0 5.7 1000000.0 1000000.0 PIR2 128161
642 99.0183 FQGWGHYFV 9 53546.0 13.8 1000000.0 1000000.0 PIR2
128161 888 99.0184 FLGDVLFAA 9 6.7 8.3 2549.7 1000000.0 PIR2 T28161
892 99.0185 VLFAANYEA 9 25.8 20.9 100.0 1000000.0 PIR2 T28161 1098
99.0186 YLQAQTTAA 9 26.9 64.0 17290.2 1000000.0 PIR2 T28161 1461
99.0187 FLRQMFYTL 9 8779.8 60.8 1000000.0 1000000.0 PIR2 T28161
2149 99.0188 FAAFTYFYL 9 11639.0 45.5 1000000.0 1000000.0 55.t00004
Chromosome14 1358 99.0038 FMDSQNGMYI 10 26503.4 87.2 1000000.0
4109.6 55.t00004 Chromosome14 1542 99.0039 SLINYNKYFV 10 1000000.0
43.5 1000000.0 1000000.0 55.t00004 Chromosome14 84 99.0189
FVVAQLYEL 9 27995.5 19.7 1000000.0 1000000.0 55.t00004 Chromosome14
480 99.0190 KTFFFFSNV 9 10931.8 72.4 1000000.0 1000000.0 55.t00004
Chromosome14 1098 99.0191 IINSDDYFV 9 58940.8 86.9 1000000.0
1000000.0 55.t00004 Chromosome14 1364 99.0192 GMYILPQYV 9 18255.9
74.7 1000000.0 1000000.0 674.t00001 Chromosome11 89 99.0040
ELVEFIFLLL 10 1000000.0 97.4 1000000.0 1000000.0 674.t00001
Chromosome11 281 99.0041 FLYKDVLMDI 10 358012.1 50.4 1000000.0
1000000.0 674.t00001 Chromosome11 89 99.0193 ELVEFIFLL 9 21772.0
47.1 1000000.0 1000000.0 674.t00001 Chromosome11 1102 99.0194
YLNKANPNI 9 12319.8 91.3 1000000.0 1000000.0 674.t00001
Chromosome11 1353 99.0195 FLQYRIPHM 9 33178.8 81.0 1000000.0
1000000.0 674.t00001 Chromosome11 1430 99.0196 YIVDIFCKI 9 11720.4
48.5 1000000.0 1000000.0
TABLE-US-00005 TABLE 5 Pf-derived A3, 11 supertype peptides scoring
positive on PIC algorithm PIC Malaria locus Addn Source info
Position Accession No. Peptide No. Sequence AA A*0101 A*0201 PIC
A*1101 PIC A*2402 331.t00003 Chromosome10 354 99.0197 KFEPFIIHVK 10
1000000.0 1000000.0 26.5 1000000.0 331.t00003 Chromosome10 5
99.0294 KTMDTFYKK 9 2654.1 1000000.0 0.4 1000000.0 331.t00003
Chromosome10 208 99.0295 SFFDVSKKK 9 130857.6 1000000.0 16.4
1000000.0 331.t00003 Chromosome10 435 99.0296 LSQLVHFYK 9 29656.2
1000000.0 0.6 1000000.0 331.t00003 Chromosome10 779 99.0297
SVFVRRYIK 9 18991.0 1000000.0 0.7 1000000.0 331.t00003 Chromosome10
988 99.0298 FTFQNMYVR 9 5834.2 1000000.0 22.0 1000000.0 331.t00003
Chromosome10 1324 99.0299 SQNSNTFLK 9 10099.5 1000000.0 0.4
1000000.0 331.t00003 Chromosome10 1337 99.0300 ILFHKFLNK 9 3064.6
1000000.0 2.4 1000000.0 331.t00003 Chromosome10 1521 99.0301
NLFDENFCR 9 30418.9 1000000.0 165.9 1000000.0 331.t00003
Chromosome10 1551 99.0302 ALYEKVHGK 9 9346.6 1000000.0 4.4
1000000.0 18.000811 Chr12Contig18 17 99.0198 FLLYILFLVK 10 1000000
0 1000000.0 82.1 1000000.0 18.000811 Chr12Contig18 43 99.0199
LVFSNVLCFR 10 365585.5 1000000.0 14.5 1000000.0 18.000811
Chr12Contig18 80 99.0200 AFLESQSMNK 10 1000000.0 1000000.0 65.8
1000000.0 18.000811 Chr12Contig18 112 99.0201 TFLESSFDIK 10
1000000.0 1000000.0 323.9 1000000.0 18.000811 Chr12Contig18 116
99.0202 SSFDIKSEVK 10 1000000.0 1000000.0 34.1 1000000.0 18.000811
Chr12Contig18 18 99.0303 LLYILFLVK 9 5498.6 1000000.0 10.1
1000000.0 18.000811 Chr12Contin18 129 99.0304 KSMLKELIK 9 5942.8
1000000.0 12.7 1000000.0 18.000811 Chr12Contig18 166 99.0305
PVLTSLFNK 9 10202.9 1000000.0 10.1 1000000.0 MY924Fe3.p1t1 1262
99.0203 TFICYYVMDK 10 1000000.0 1000000.0 23.0 1000000.0
MY924Fe3.p1t1 155 99.0306 NVFNIFFEK 9 10371.8 1000000.0 0.2
1000000.0 MY924Fe3.p1t1 220 99.0307 SSFLYAFNK 9 12434.3 1000000.0
0.1 1000000.0 MY924Fe3.p1t1 1030 99.0308 MFHIIMYTK 9 208352.1
1000000.0 18.2 1000000.0 MY924Fe3.p1t1 1181 99.0309 SLDDIYKYK 9
22644.9 1000000.0 2.9 1000000.0 MY924Fe3.p1t1 1613 99.0310
KVVVKNLYK 9 34654.1 1000000.0 0.9 1000000.0 MY924Fe3.p1t1 1853
99.0311 SLFRLGFVK 9 10283.0 1000000.0 0.2 1000000.0 MY924Fe3.p1t1
2012 99.0312 SLFFNSLYY 9 4.6 1000000.0 2.6 1000000.0 MY924Fe3.p1t1
2238 99.0313 ITFEKNYYR 9 21591.6 1000000.0 1.5 1000000.0
MY924Fe3.p1t1 2285 99.0314 SQYEENKSK 9 139775.3 1000000.0 39.1
1000000.0 MP03001 MAL3P2.11 57 CAB38998 99.0204 KQENWYSLKK 10
1000000.0 1000000.0 50.6 1000000.0 MP03001 MAL3P2.11 335 CAB38998
99.0205 VTCGNGIQVR 10 1000000.0 1000000.0 170.6 1000000.0 MP03001
MAL3P2.11 17 CAB38998 99.0315 ALFQEYQCY 9 3.4 1000000.0 72.7
1000000.0 MP03001 MAL3P2.11 57 CAB38998 99.0316 KQENWYSLK 9 44996.2
1000000.0 173.7 1000000.0 1369.t00001 Chromosome11 44 99.0206
TLYQIQVMKR 10 1000000.0 1000000.0 52.0 1000000.0 1369.t00001
Chromosome11 58 99.0207 KQVQMMIMIK 10 1000000.0 1000000.0 8.7
1000000.0 1369.t00001 Chromosome11 70 99.0208 GVIYIMIISK 10
1000000.0 1000000.0 10.6 1000000.0 1369.t00001 Chromosome11 158
99.0209 ELFDKDTFFK 10 1000000.0 1000000.0 14.2 1000000.0
1369.t00001 Chromosome11 18 99.0317 KTMNNYMIK 9 16730.1 1000000.0
1.1 1000000.0 1369.t00001 Chromosome11 159 99.0318 LFDKDTFFK 9
32977.1 1000000.0 126.3 1000000.0 1369.t00001 Chromosome11 287
99.0319 YLFNQHIKK 9 21347.4 1000000.0 8.2 1000000.0 1369.t00001
Chromosome11 307 99.0320 MQSSFEVINR 9 12685.3 1000000.0 25.4
1000000.0 1369.t00001 Chromosome11 315 99.0321 RFYITTRYK 9 258367.4
1000000.0 21.4 1000000.0 1369.t00001 Chromosome11 319 99.0322
TTRYKYLNK 9 10429.2 1000000.0 4.5 1000000.0 699.t00001 Chromosome11
464 99.0210 KVCELLGYYK 10 1000000.0 1000000.0 1.1 1000000.0
699.t00001 Chromosome11 492 99.0211 SFLLLIVFSK 10 1000000.0
1000000.0 21.9 1000000.0 699.t00001 Chromosome11 623 99.0212
KLLYKMNYLK 10 1000000.0 1000000.0 15.0 1000000.0 699.t00001
Chromosome11 764 99.0213 TLEYNPSFFY 10 91.9 1000000.0 219.0
1000000.0 699.t00001 Chromosome11 782 99.0214 LLYNHITSIK 10
1000000.0 1000000.0 12.1 1000000.0 699.t00001 Chromosome11 878
99.0215 LFYLYMNFLK 10 1000000.0 1000000.0 8.2 1000000.0 699.100001
Chromosome11 386 99.0323 KQNIPIYIY 9 57.8 1000000.0 175.4 1000000.0
699.100001 Chromosome11 507 99.0324 KTNIFFKKK 9 23058.6 1000000.0
1.5 1000000.0 699.t00001 Chromosome11 734 99.0325 1VNDLGIFY 9 2.4
1000000.0 16.6 1000000.0 699.t00001 Chromosome11 769 99.0326
PSFFYLSFK 9 22074.6 1000000.0 20.1 1000000.0 mal4T2c4.p1t1 15
99.0216 ILLIRPMLVK 10 1000000.0 1000000.0 95.1 1000000.0
mal442c4.p1t1 29 99.0217 LVKLRPMLVK 10 1000000.0 1000000.0 22.3
1000000.0 mal4T2c4.p1t1 36 99.0218 LVKLGPILVK 10 1000000.0
1000000.0 15.0 1000000.0 mal4T2c4.p1t1 16 99.0327 LLIRPMLVK 9
29115.0 1000000.0 16.1 1000000.0 M13Hg2.q1t3 97 99.0219 LLSRFIFIYK
10 1000000.0 1000000.0 12.9 1000000.0 M13Hg2.q1t3 267 99.0220
KTSDAKLVDK 10 543207.5 1000000.0 21.8 1000000.0 M13Hg2.q1t3 277
99.0221 ETSTISTFIK 10 714638.7 1000000.0 21.8 1000000.0 M13Hg2.q1t3
406 99.0222 IFFSYNPFHK 10 1000000.0 1000000 0 18.5 1000000.0
M13Hg2.q1t3 528 99.0223 YFFNCIQMAK 10 1000000.0 1000000.0 48.6
1000000.0 M13Hg2.q1t3 9 99.0328 SLYNKIEYR 9 32837.9 1000000.0 36.8
1000000.0 M13Hg2.q1t3 48 99.0329 SASESNFYK 9 17208.3 1000000.0 0.2
1000000.0 M13Hg2.q113 216 99.0330 ISYIFPLFK 9 12671.6 1000000.0 2.2
1000000.0 M13Hg2.q1t3 420 99.0331 SQNYENINK 9 36248.0 1000000.0 3.6
1000000.0 M13Hg2.q1t3 661 99.0332 SLMDASKNK 9 5327.4 1000000.0 3.2
1000000.0 Mal_5L10c4.q1t6 21 99.0333 KLGFFVCYK 9 42997.2 1000000.0
3.5 1000000.0 Mal_5L10c4.q1t6 36 99.0334 SFKNKILQK 9 139254.7
1000000.0 14.9 1000000.0 Mal_5L10c4.q1t6 56 99.0335 KFMYLRKKK 9
74875.0 1000000.0 33.4 1000000.0 Mal_5L10c4.q1t6 381 99.0336
KQIIFEALK 9 120283.5 1000000.0 38.9 1000000.0 Mal_5L10c4.q1t6 519
99.0337 ETFYKELYK 9 14646.9 1000000.0 1.2 1000000.0 Mal_5L10c4.q1t6
537 99.0338 SVNYFLLER 9 4574.8 1000000.0 0.4 1000000.0
Mal_5L10c4.q1t6 724 99.0339 ILNFLNFNK 9 12039.7 1000000.0 2.7
1000000.0 Mal_5L10c4.q1t6 897 99.0340 NTCSKEIYK 9 26259.6 1000000.0
4.6 1000000.0 Mal_5110c4.q1t6 1316 99.0341 KLRNFLFYY 9 34.8
1000000.0 27.7 1000000.0 Mal_5L10c4.q1t6 1722 99.0342 CSNNNIFYK 9
16887.2 1000000.0 2.7 1000000 0 571.t00003 Chromosome11 1059
99.0224 MQYNHDNIYK 10 1000000.0 1000000.0 6.8 1000000.0 571.t00003
Chromosome11 2438 99.0225 SFSMLYLFGK 10 1000000.0 1000000.0 20.1
1000000.0 571.t00003 Chromosome11 675 99.0343 ALNPKYQNH 9 4302.1
1000000.0 149.6 1000000.0 571.t00003 Chromosome11 749 99.0344
TLNSFQHNK 9 9140.5 1000000.0 4.0 1000000.0 571.t00003 Chromosome11
1220 99.0345 KINEFQWEK 9 55899.8 1000000.0 0.3 1000000.0 571.t00003
Chromosome11 1368 99.0346 RSDYFHNTK 9 15625.8 1000000.0 5.2
1000000.0 571.t00003 Chromosome11 1429 99.0347 STNSQQLIK 9 14992.1
1000000.0 1.1 1000000.0 571.t00003 Chromosome11 1552 99.0348
KFMTPTTLK 9 54389.6 1000000.0 8.1 1000000.0 571.t00003 Cluomosome11
1684 99.0349 TTNSTPHFK 9 5905.8 1000000.0 3.8 1000000.0 571.t00003
Chromosome11 2509 99.0350 KLMETRFSK 9 8313.3 1000000.0 2.8
1000000.0 MP03072 PFC0450w 36 CAA15614 99.0226 SQAHRENGKK 10
1000000.0 1000000.0 109.2 1000000.0 MP03072 PFC0450w 45 CAA15614
99.0227 KALVVAIILY 10 220.1 1000000.0 237.1 1000000.0 MP03072
PFC0450w 55 CAA15614 99.0228 VIFLVLLFIY 10 137.2 1000000.0 61.8
1000000.0 MP03072 PFC0450w 56 CAA15614 99.0229 IFLVLLFIYK 10
1000000.0 1000000.0 44.3 1000000.0 MP03072 PFC0450w 58 CAA15614
99.0230 LVLLFIYKAY 10 371.7 1000000.0 207.5 1000000.0 MP03072
PFC0450w 59 CAA15614 99.0231 VLLFIYKAYK 10 1000000.0 1000000.0 31.2
1000000.0 MP03072 PFC0450w 61 CAA15614 99.0232 LFIYKAYKNK 10
1000000.0 1000000.0 434.4 1000000.0 MP03072 PFC0450w 72 CAA15614
99.0233 KLYTNFFMKK 10 1000000.0 1000000.0 5.8 1000000.0 MP03072
PFC0450w 92 CAA15614 99.0234 STYLSASDEY 10 57.2 1000000.0 85.1
1000000.0 MP03072 PFC0450w 36 CAA15614 99.0351 SQAHRENGK 9 65339.9
1000000.0 230.0 1000000.0 MP03072 PFC0450w 46 CAA15614 99.0352
ALVVAIILY 9 6.0 1000000.0 95.4 1000000.0 MP03072 PFC0450w 57
CAA15614 99.0353 FLVLLFIYK 9 14940.5 1000000.0 5.0 1000000.0
MP03072 PFC0450w 58 CAA15614 99.0354 LVLLFIYKA 9 13.1 102.2 132.5
1000000.0 MP03072 PFC0450w 60 CAA15614 99.0355 LLFIYKAYK 9 59055.3
1000000.0 9.6 1000000.0 MP03072 PFC0450w 62 CAA15614 99.0356
FTYKAYKNK 9 35013.8 1000000.0 22.0 1000000.0 MP03072 PFC0450w 72
CAA15614 99.0357 KLYTNFFMK 9 7491.5 1000000.0 2.3 1000000.0 MP03072
PFC0450w 74 CAA15614 99.0358 YTNFFM KKR 9 18478.3 1000000.0 48.4
1000000.0 45.t00001 Chromosome14 50 99.0235 ALERLLSLKK 10 1000000.0
1000000.0 149.5 1000000.0 45.t00001 Chromosome14 109 99.0236
KILIKIPVTK 10 1000000.0 1000000.0 30.2 1000000.0 45.t00001
Chromosome14 128 99.0237 RLPLLPKTWK 10 1000000.0 1000000.0 19.6
1000000.0 45.t00001 Chromosome14 147 99.0238 NIFLRFIPDK 10
1000000.0 1000000.0 24.9 1000000.0 45.t00001 Chromosome14 161
99.0239 SQVSNSDSYK 10 1000000.0 1000000.0 36.0 1000000.0 45.t00001
Chromosome14 197 99.0240 QQNQESKIMK 10 928526.9 1000000.0 431.5
1000000.0 45.t00001 Chromosome14 249 99.0241 IIALLIIPPK 10
1000000.0 1000000.0 19.3 1000000.0 45.t00001 Chromosome14 374
99.0242 SQDLACIFDA 10 226.7 389.1 400.3 1000000.0 45.t00001
Chromosome14 34 99.0359 AVIFTPIYY 9 7.6 1000000.0 4.7 1000000.0
45.t00001 Chromosome14 50 99.0360 ALER LLSLK 9 6245.7 1000000.0
55.5 1000000.0 45.t00001 Chromosome14 85 99.0361 SISGKYDIK 9
29562.3 1000000.0 25.1 1000000.0 45.t00001 Chromosome14 101 99.0362
ILCIEGEQK 9 519431 1000000.0 162.5 1000000.0 45.t00001 Chromosome14
126 99.0363 EQRLPLLPK 9 66848.0 1000000.0 244.3 1000000.0 45.t00001
Chromosome14 148 99.0364 IFLRFIPDK 9 170326.8 1000000.0 112.0
1000000.0 45.t00001 Chromosome14 250 99.0365 IALLIIPPK 9 47443.5
1000000.0 25.2 1000000.0 45.t00001 Chromosome14 270 99.0366
PVVCSMEYK 9 20870.3 1000000.0 23.1 1000000.0 45.t00001 Chromosome14
271 99.0367 VVCSMEYKK 9 24792.5 1000000.0 8.3 1000000.0 45.t00001
Chromosome14 308 99.0368 FSYDLRLNK 9 5228.9 1000000.0 13.4
1000000.0 45.t00001 Chromosome14 323 99.0369 HLNIPIGFK 9 25082.0
1000000.0 98.3 1000000.0 MP03137 PFC0700c 14 CAB11150 99.0243
SSPLFNNFYK 10 1000000.0 1000000.0 0.5 1000000.0 MP03137 PFC0700c
151 CAB11150 99.0244 FLYLLNKKNK 10 1000000.0 1000000.0 139.2
1000000.0 MP03137 PFC0700c 183 CAB11150 99.0245 LQMMNVNLQK 10
1000000.0 1000000.0 83.6 1000000.0 MP03137 PFC0700c 195 CAB11150
99.0246 LTNHLINTPK 10 427675.0 1000000.0 20.8 1000000.0 MP03137
PFC0700c 259 CAB11150 99.0247 IFISFYLINK 10 1000000.0 1000000.0
102.0 1000000.0
MP03137 PFC0700c 293 CAB11150 99.0248 RLFEESLGIR 10 923199.1
1000000.0 420.0 1000000.0 MP03137 PFC0700c 16 CAB11150 99.0370
PLFNNFYKR 9 11760.5 1000000.0 383.0 1000000.0 MP03137 PFC0700c 141
CAB11150 99.0371 YQNFQNADK 9 40121.5 1000000.0 637.4 1000000.0
MP03137 PFC0700c 184 CAB11150 99.0372 QMMNVNLQK 9 17662.1 1000000.0
1.4 1000000.0 MP03137 PFC0700c 222 CAB11150 99.0373 AVSEIQNNK 9
6991.0 1000000.0 3.1 1000000.0 MP03137 PFC0700c 236 CAB11150
99.0374 GTMYILLKK 9 986.2 1000000.0 0.5 1000000.0 MP03137 PFC0700c
260 CAB11150 99.0375 FISFYLINK 9 7376.0 1000000.0 12.2 1000000.0
MP03137 PFC0700c 264 CAB11150 99.0376 YLINKHWQR 9 39562.3 1000000.0
41.6 1000000.0 MP03137 PFC0700c 273 CAB11150 99.0377 ALKISQLQK 9
37884.8 1000000.0 5.1 1000000.0 MP03137 PFC0700c 282 CAB11150
99.0378 KINSNFLLK 9 5732.3 1000000.0 1.0 1000000.0 12.t00018
Chromosome14 89 99.0249 QLKHFFNSNK 10 1000000.0 1000000.0 33.5
1000000.0 12.t00018 Chromosome14 615 99.0250 YVSMYIPFIK 10 301060.0
1000000.0 2.6 1000000.0 12.t00018 Chromosome14 671 99.0251
VLFYIYNMYH 10 900700.0 1000000.0 13.6 1000000.0 12.t00018
Chromosome14 705 99.0252 YTYIFFNYDK 10 742244.6 1000000.0 2.1
1000000.0 12.t00018 Chromosome14 1140 99.0253 SFFITYSYWK 10
1000000.0 1000000.0 5.7 1000000.0 12.t00018 Chromosome14 195
99.0379 STSNKH1NR 9 6609.8 1000000.0 3.8 1000000.0 12.t00018
Chromosome14 687 99.0380 SQCNDYYIK 9 95255.3 1000000.0 6.3
1000000.0 12.t00018 Chromosome14 896 99.0381 SSIFYIKNK 9 41588.5
1000000.0 8.4 1000000.0 12.t00018 Chromosome14 1020 99.0382
LFFREKFLK 9 89243.3 1000000.0 14.3 1000000.0 12.t00018 Chromosome14
1160 99.0383 ILDNVSFLK 9 7621.1 1000000.0 21.0 1000000.0
mal_BU121g9.q1c1 10 99.0254 ILVLDIPGFK 10 1000000.0 1000000.0 55.0
1000000.0 mal_BU121g9.q1c1 45 99.0255 ETYGDSLVLH 10 453286.5
1000000.0 386.1 1000000 0 mal_BU121g9.q1c1 59 99.0256 EVGYFKRIFK 10
1000000.0 1000000.0 20.4 1000000.0 mal_BU121g9.q1c1 11 99.0384
LVLDIPGFK 9 13172.2 1000000.0 26.7 1000000.0 mal_BU121g9.q1c1 30
99.0385 GMLTVAGPR 9 54761.5 1000000.0 326.1 1000000.0
mal_BU121g9.q1c1 39 99.0386 SQTELFETY 9 6.7 1000000.0 254.2
1000000.0 mal_BU121g9.q1c1 48 99.0387 GDSLVLIIAK 9 19504.9
1000000.0 306.8 1000000.0 mal_BU121g9.q1c1 50 99.0388 SLVLHAKER 9
133501.5 1000000.0 487.4 1000000.0 mal_BU121g9.q1c1 60 99.0389
VGYFKRIFK 9 44416.3 1000000.0 27.9 1000000.0 mal_BU121g9.q1c1 86
99.0390 NIYIYIYIY 9 40.2 1000000.0 322.7 1000000.0 mal_BU121g9.q1c1
88 99.0391 YIYIYIYIY 9 16.2 1000000.0 310.0 1000000.0
mal_9A57b11.q1t2 31 99.0257 SSFNCDIANK 10 1000000.0 1000000.0 8.4
1000000.0 mal_9A57b11.q1t2 49 99.0258 SMGVFCLKEK 10 1000000.0
1000000.0 24.6 1000000.0 mal_9A57b11.q1t2 119 99.0259 HIVKNRIYNK 10
1000000.0 1000000.0 51.7 1000000.0 mal_9A57b11.q1t2 128 99.0260
KLKLHKIIRK 10 1000000.0 1000000.0 64.9 1000000.0 mal_9A57b11.q1t2
165 99.0261 FIFDIFKYAR 10 1000000.0 1000000.0 148.8 1000000.0
mal_9A57b11.q1t2 202 99.0262 AQKALSNLHK 10 1000000.0 1000000.0
113.8 1000000.0 mal_9A57b11.q1t2 208 99.0263 NLHKSWLQYK 10 507559.4
1000000.0 199.6 1000000.0 mal_9A57b11.q1t2 234 99.0264 YLPLFLMMEH
10 1000000.0 1000000.0 147.3 1000000.0 mal_9A57b11.q1t2 32 99.0392
SFNCDIANK 9 27329.1 1000000.0 35.4 1000000.0 mal_9A57b11.q1t2 62
99.0393 KINKKYNKK 9 40379.4 1000000.0 56.4 1000000.0
mal_9A57b11.q1t2 95 99.0394 ILNNKELFK 9 13663.7 1000000.0 29.6
1000000.0 mal_9A57b11.q1t2 120 99.0395 IVKNRIYNK 9 25949.5
1000000.0 17.8 1000000.0 mal_9A57b11.q1t2 154 99.0396 LINSKVFCY 9
6.1 1000000.0 113.8 1000000.0 mal_9A57b11.q1t2 183 99.0397
RQKEFYPIK 9 127059.4 1000000.0 38.7 1000000.0 mal_BL50e8.p1ca_5 9
99.0265 SFLVVLVFNK 10 1000000.0 1000000.0 33.6 1000000.0
mal_BL50e8.p1ca_5 152 99.0266 STYMTPSAIK 10 1000000.0 1000000.0 2.8
1000000.0 mal_BL50e8.p1ca_5 656 99.0267 KLYGEFTMNK 10 1000000.0
1000000.0 1.3 1000000.0 mal_BL50e8.p1ca_5 907 99.0268 GVYYIFVYLR 10
1000000.0 1000000.0 3.7 1000000.0 mal_BL50e8.p1ca_5 115 99.0398
SQYSNYFDY 9 11.0 1000000.0 15.2 1000000.0 mal_BL50e8.p1ca_5 361
99.0399 LFITYFQQK 9 90294.9 1000000.0 50.9 1000000.0
mal_BL50e8.p1ca_5 409 99.0400 ATSWDEYPK 9 44148.4 1000000.0 0.8
1000000.0 mal_BL50e8.p1ca_5 752 99.0401 ASFAAHENK 9 11256.9
1000000.0 0.2 1000000.0 mal_BL50e8.p1ca_5 780 99.0402 MLKADYFIR 9
35925.9 1000000.0 61.1 1000000.0 mal_BL50e8.p1ca_5 819 99.0403
VLNPVTIPK 9 14931.7 1000000.0 5.6 1000000.0 M13S8h6.p1t_3 63
99.0269 VSYIFFMSFK 10 1000000.0 1000000.0 0.4 1000000.0
M13S8h6.p1t_3 937 99.0270 MQKYFLHISK 10 1000000.0 1000000.0 37.5
1000000.0 M13S8h6.p1t_3 25 99.0404 STFFFFLSR 9 3848.4 1000000.0 0.1
1000000.0 M13S8h6.p1t_3 84 99.0405 LLLTFGVYY 9 22.7 1000000.0 157.5
1000000.0 M13S8h6.p1t_3 157 99.0406 KFLFRYKQK 9 941796.8 1000000.0
16.1 1000000.0 M13S8h6.p1t_3 394 99.0407 KVFIKGKGK 9 43309.1
1000000.0 3.8 1000000.0 M13S8h6.p1t_3 1449 99.0408 ITYIWIILK 9
6990.4 1000000.0 1.6 1000000.0 M13S8h6.p1t_3 1534 99.0409 KFFFFVFFY
9 51.8 1000000.0 3.5 2.2 M13S8h6.p1t_3 1655 99.0410 KLLQKLISK 9
8661.9 1000000.0 53.4 1000000.0 M13S8h6.p1t_3 1703 99.0411
ILNILKLAK 9 21447.1 1000000.0 55.0 1000000.0 585.t00002
Chromosome11 193 99.0412 SQNNFSKIK 9 90378.2 1000000.0 9.1
1000000.0 585.t00002 Chromosome11 300 99.0413 SSLNIYNTK 9 46908.8
1000000.0 5.2 1000000.0 585.t00002 Chromosome11 529 99.0414
KLFNYKFFK 9 60297.3 1000000.0 1.0 1000000.0 585.t00002 Chromosome11
572 99.0415 LTFLSNIRK 9 13099.9 1000000.0 1.3 1000000.0 585.t00002
Chromosome11 616 99.0416 KFFYIFHYK 9 49030.6 1000000.0 0.2
1000000.0 585.t00002 Chromosome11 1415 99.0417 VTCSYFIIR 9 6831.4
1000000.0 16.8 1000000.0 585.t00002 Chromosome11 1487 99.0418
LTCAFKIYK 9 25752.8 1000000.0 0.3 1000000.0 585.t00002 Chromosome11
1508 99.0419 ILFILFFIK 9 9492.2 1000000.0 1.2 1000000.0 585.t00002
Chromosome11 1541 99.0420 NLYFFIHNR 9 13239.8 1000000.0 59.3
1000000.0 585.t00002 Chromosome11 1742 99.0421 IFLHYYFKK 9 118461.5
1000000.0 7.6 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4294 99.0271
QVFFLQEMER 10 544655.4 1000000.0 27.6 1000000.0 1223.t00015
mal_9A21f9.q1t_4 272 99.0422 SFYKFEVEK 9 193104.9 1000000.0 16.1
1000000.0 1223.t00015 mal_9A21f9.q1t_4 325 99.0423 KTFREHFLK 9
17344.2 1000000.0 0.022 1000000.0 1223.t00015 mal_9A21f9.q1t_4 992
99.0424 VSNSSQLFK 9 13528.2 1000000.0 5.1 1000000.0 1223.t00015
mal_9A21f9.q1t_4 1397 99.0425 SLLNDVFPK 9 67376.3 1000000.0 1.2
1000000.0 1223.t00015 mal_9A21f9.q1t_4 1627 99.0426 KLFIFYLDK 9
25288.3 1000000.0 0.67 1000000.0 1223.t00015 mal_9A21f9.q1t_4 1664
99.0427 LLNSQIIQY 9 18.6 1000000.0 160.0 1000000.0 1223.t00015
mal_9A21f9.q1t_4 2115 99.0428 FQGFYFLDK 9 6204.2 1000000.0 44.3
1000000.0 1223.t00015 mal_9A21f9.q1t_4 2412 99.0429 NTFSFSWMK 9
16414.9 1000000.0 0.20 1000000.0 1223.t00015 mal_9A21f9.q1t_4 4500
99.0430 MFYNCPVYK 9 327575.1 1000000.0 10.3 1000000.0 599.t00001
Chromosome11 723 99.0272 NLLRHATFYK 10 1000000.0 1000000.0 7.4
1000000.0 599.t00001 Chromosome11 1288 99.0273 SSYGYNIYFK 10
1000000.0 1000000.0 0.3 1000000.0 599.t00001 Chromosome11 1451
99.0274 RTYVNEYFLR 10 1000000.0 1000000.0 25.4 1000000.0 599.t00001
Chromosome11 16 99.0431 ILLTLVFQK 9 46527.3 1000000.0 2.9 1000000.0
599.t00001 Chromosome11 28 99.0432 CQNSLNYSK 9 38238.7 1000000.0
63.2 1000000.0 599.t00001 Chromosome11 211 99.0433 IVNNTELNK 9
9493.8 1000000.0 3.6 1000000.0 599.t00001 Chromosome11 776 99.0434
TLFSQNLFY 9 10.5 1000000.0 75.0 1000000.0 599.t00001 Chromosome11
1320 99.0435 TFYESVFIR 9 63945.9 1000000.0 27.9 1000000.0
599.t00001 Chromosome11 1370 99.0436 YFFEEFFNK 9 19717.0 1000000.0
4.6 1000000.0 599.t00001 Chromosome11 1903 99.0437 TTQSNNIYK 9
20011.8 1000000.0 2.1 1000000.0 MP01072 M1045c5.p1c.C_6 1451
99.0275 SLFYFTSNGK 10 1000000.0 1000000.0 8.0 1000000.0 MP01072
M1045c5.p1c.C_6 46 99.0438 KLNYDNFEK 9 48445.0 1000000.0 3.4
1000000.0 MP01072 M1045c5.p1c.C_6 327 99.0439 ILCDDGIYR 9 19413.7
1000000.0 65.3 1000000.0 MP01072 M1045c5.p1c.C_6 359 99.0440
KVADVFLQII 9 6428.6 1000000.0 4.4 1000000.0 MP01072 M1045c5.p1c.C_6
419 99.0441 STSFLFLRK 9 2370.1 1000000.0 0.2 1000000.0 MP01072
M1045c5.p1c.C_6 421 99.0442 SFLFLRKQK 9 408258.6 1000000.0 12.7
1000000.0 MP01072 M1045c5.p1c.C_6 558 99.0443 SFFSSCENK 9 55537.2
1000000.0 17.7 1000000.0 MP01072 M1045c5.p1c.C_6 609 99.0444
AQSSYIYNK 9 18056.8 1000000.0 2.5 1000000.0 MP01072 M1045c5.p1c.C_6
1027 99.0445 MSAKYLYHK 9 5370.6 1000000.0 8.8 1000000.0 MP01072
M1045c5.p1c.C_6 1047 99.0446 TTLFSHFNK 9 10524.0 1000000.0 0.2
1000000.0 MP01072 M1045c5.p1c.C_6 1215 99.0447 SVYYNTMLR 9 9856.9
1000000.0 1.2 1000000.0 PIR2 T28161 1124 99.0276 VVNFLFELYK 10
408697.6 1000000.0 3.5 1000000.0 PIR2 T28161 1403 99.0277
TFFLWDRYKK 10 1000000.0 1000000.0 9.0 1000000.0 PIR2 T28161 108
99.0448 SVGACAPYR 9 59804.6 1000000.0 2.1 1000000.0 PIR2 T28161 204
99.0449 KQLEDNLRK 9 87893.1 1000000.0 16.9 1000000.0 PIR2 T28161
758 99.0450 KVASNMHHK 9 6948.7 1000000.0 1.6 1000000.0 PIR2 T28161
760 99.0451 ASNMHHKKK 9 32965.2 1000000.0 4.3 1000000.0 PIR2 T28161
838 99.0452 AGFISNTYK 9 154161.8 1000000.0 2.2 1000000.0 PIR2
T28161 965 99.0453 ILAFKEIYK 9 14274.5 1000000.0 12.6 1000000.0
PIR2 T28161 1879 99.0454 ALFKRWLEY 9 3.4 1000000.0 27.4 1000000.0
PIR2 T28161 2151 99.0455 AFTYFYLKK 9 40565.6 1000000.0 1.6
1000000.0 55.t00004 Chromosome14 483 99.0278 FFFSNVNNNK 10 409139.5
1000000.0 408.4 1000000.0 55.t00004 Chromosome14 564 99.0279
SQGKKNTYLK 10 1000000.0 1000000.0 13.0 1000000.0 55.100004
Chromosome14 976 99.0280 VFNNSIILEK 10 1000000.0 1000000.0 372.4
1000000.0 55.t00004 Chromosome14 1338 99.0281 SVSEGYTSTY 10 67.8
1000000.0 33.5 1000000.0 55.t00004 Chromosome14 229 99.0456
TSICKYWIK 9 8242.3 1000000.0 14.6 1000000.0 55.t00004 Chromosome14
263 99.0457 TTICKHWKK 9 4558.7 1000000.0 1.7 1000000.0 55.t00004
Chromosome14 537 99.0458 KVTNVHIYK 9 41321.8 1000000.0 0.2
1000000.0 55.t00004 Chromosome14 866 99.0459 ITNMNNINR 9 5371.8
1000000.0 37.6 1000000.0 55.t00004 Chromosome14 909 99.0460
MLNIYKINK 9 17179.3 1000000.0 13.6 1000000.0 55.t00004 Chromosome14
1030 99.0461 IINSYIDYK 9 84561.6 1000000.0 2.0 1000000.0 55.t00004
Chromosome14 1141 99.0462 NLYTYVVNK 9 45076.1 1000000.0 54.8
1000000.0 55.t00004 Chromosome14 1665 99.0463 KMIYSIFIK 9 42191.9
1000000.0 4.1 1000000.0 13.t00011 Chromosome14 8 99.0282 ISMDKSLFFK
10 1000000.0 1000000.0 16.7 1000000.0 13.t00011 Chromosome14 47
99.0283 TVFLDYVKGK 10 1000000.0 1000000.0 7.8 1000000.0 13.t00011
Chromosome14 59 99.0284 DVYKETNMNR 10 1000000.0 1000000.0 64.9
1000000.0
13.t00011 Chromosome14 117 99.0285 KLKKSTICNK 10 1000000.0
1000000.0 59.9 1000000.0 13.t00011 Chromosome14 9 99.0464 SMDKSLFFK
9 4208.2 1000000.0 3.5 1000000.0 13.t00011 Chromosome14 12 99.0465
KSLFFKSLK 9 64105.1 1000000.0 17.4 1000000.0 13.t00011 Chromosome14
48 99.0466 VFLDYVKGK 9 347222.4 1000000.0 216.7 1000000.0 13.t00011
Chromosome14 93 99.0467 KVKRFRVFK 9 52490.3 1000000.0 3.3 1000000.0
13.t00011 Chromosome14 104 99.0468 SFFIDEVKK 9 352606.0 1000000.0
37.8 1000000.0 13.t00011 Chromosome14 112 99.0469 KIYENKLKK 9
30696.4 1000000.0 14.5 1000000.0 37.t00002 Chromosome14 13 99.0286
ALTYMYCVYY 10 249.1 1000000.0 112.8 1000000.0 37.t00002
Chromosome14 31 99.0287 SQISIFCNLR 10 1000000.0 1000000.0 226.6
1000000.0 37.t00002 Chromosome14 32 99.0288 QISIFCNLRR 10 301919.5
1000000.0 80.8 1000000 0 37.t00002 Chromosome14 62 99.0289
VCNNETYYNK 10 1000000.0 1000000.0 186.8 1000000.0 37.t00002
Chromosome14 71 99.0290 KAHEENDKVK 10 1000000.0 1000000.0 956.7
1000000.0 37.t00002 Chromosome14 13 99.0470 ALTYMYCVY 9 9.1
1000000.0 279.6 1000000.0 37.t00002 Chromosome14 32 99.0471
QISIFCNLR 9 26897.2 1000000.0 855.0 1000000.0 37.t00002
Chromosome14 33 99.0472 ISIFCNLRR 9 37287.9 1000000.0 255.9
1000000.0 37.t00002 Chromosome14 61 99.0473 NVCNNETYY 9 25.3
1000000.0 514.8 1000000.0 674.t00001 Chromosome11 90 99.0291
LVEFIFLLLK 10 304423.1 1000000.0 13.7 1000000.0 674.t00001
Chromosome11 218 99.0292 SVFYNKEIIK 10 993500.3 1000000.0 4.5
1000000.0 674.t00001 Chromosome11 867 99.0293 SLKDFDMLLY 10 199.3
1000000.0 214.4 1000000.0 674.t00001 Chromosome11 64 99.0474
NVNDRFVEK 9 13728.8 1000000.0 11.8 1000000.0 674.t00001
Chromosome11 662 99.0475 TLSNSLPQK 9 36834.4 1000000.0 47.0
1000000.0 674.t00001 Chromosome11 673 99.0476 YQINNFIHK 9 12103.7
1000000.0 59.8 1000000.0 674.t00001 Chromosome11 689 99.0477
NLTINNFQK 9 59129.2 1000000.0 40.3 1000000.0 674.t00001
Chromosome11 1035 99.0478 KFNRDMLQK 9 254779.4 1000000.0 1.9
1000000.0 674.t00001 Chromosome11 1126 99.0479 NQSDFLLLK 9 8015.9
1000000.0 15.2 1000000.0 674.t00001 Chromosome11 1256 99.0480
SFHHFNIDK 9 178323.3 1000000.0 26.2 1000000.0 674.t00001
Chromosome11 1288 99.0481 KSKELLLQK 9 27230.7 1000000.0 4.4
1000000.0
TABLE-US-00006 TABLE 6 Pf-derived 15mer peptides with nonamer core
sequences scoring DR1 PIC <4 nM Addn Peptide Antigen Source info
Position No. Sequence AA DR1 PIC 331.t00003 Chromosome10 182
100.0001 LSHFKKNFILQNNEE 15 0.447 331.t00003 Chromosome10 365
100.0002 TTFLSALKLLKIAQY 15 0.400 331.t00003 Chromosome10 428
100.0003 NNKLSKNLSQLVHFY 15 0.130 331.t00003 Chromosome10 617
100.0004 KIYMFGGFSKGVRNN 15 0.061 331.t00003 Chromosome10 894
100.0005 DDMIGMPNLSSTVVC 15 0.337 331.t00003 Chromosome10 987
100.0006 TFTFQNMYVRSKVVS 15 0.400 331.t00003 Cluumosome10 1365
100.0007 KYEIIGNILIFHYKY 15 0.435 331.t00003 Chromosome10 1601
100.0008 KERMKNMYIVSNNDD 15 0.013 331.t00003 Chromosome10 1656
100.0009 GVGYFTLPLLKCIEA 15 0.302 331.t00003 Chromosome10 1725
100.0010 HRIILGLLPHSQPAW 15 0.167 Chr12Contig18 18.000811 13
100.0011 HFFLFLLYILFLVKM 15 1.826 Chr12Contig18 18.000811 16
100.0012 LFLLYILFLVKMNAL 15 0.593 Chr12Contig18 18.000811 21
100.0013 ILFLVKMNALRRLPV 15 0.035 Chr12Contig18 18.000811 27
100.0014 MNALRRLPVICSFLV 15 3.206 Chr12Contig18 18.000811 79
100.0015 SAFLESQSMNKIGDD 15 3.392 Chr12Contig18 18.000811 132
100.0016 LKELIKVGLPSFENL 15 0.785 Chr12Contig18 18.000811 143
100.0017 FENLVAENVKPPKVD 15 0.854 Chr12Contig18 18.000811 148
100.0018 AENVKPPKVDPATYG 15 3.392 Chr12Contia18 18.000811 158
100.0019 PATYGIIVPVLTSLF 15 0.221 Chr12Contig18 18.000811 161
100.0020 YGIIVPVLTSLFNKV 15 0.956 MY924Fe3.p1t1 1015 100.0021
SVDLQIKISMKVLNS 15 0.103 MY924Fe3.p1t1 1021 100.0022
KISMKVLNSMFHIIM 15 0.234 MY924Fc3.p1t1 1076 100.0023
KDVVQIQTVLLSLGT 15 0.066 MY924Fe3.p1t1 1331 100.0024
SQIIIILPSILENIL 15 0.092 MY924Fc3.p1t1 1526 100.0025
MHSVKFMIVYLIQNN 15 0.262 MY924Fe3.p1t1 1703 100.0026
TINLINELMKRQHDK 15 0.192 MY924Fe3.p1t1 1746 100.0027
REMLLKMKSMSRNQR 15 0.130 MY924Fe3.p1t1 1878 100.0028
RSIIFAGHTIELNSL 15 0.248 MY924Fe3.p1t1 1890 100.0029
NSLMFKQTSGRAGRR 15 0.061 MY924Fe3.p1t1 2201 100.0030
NLIITYLLIKKVLHN 15 0.162 MP03001 MAL3P2.11 1 100.0031
MRKLAILSVSSFLFV 15 2.786 MP03001 MAL3P2.11 36 100.0032
ELNYDNAGTNLYNEL 15 1.040 MP03001 MAL3P2.11 342 100.0033
QVRIKPGSANKPKDE 15 0.460 1369.t00001 Chromosome11 28 100.0034
LLKIWKNYMKIMNHL 15 0.328 1369.t00001 Chromosome11 43 100.0035
MTLYQIQVMKRNQKQ 15 0.056 1369.t00001 Chromosome11 57 100.0036
QKQVQMMIMIKFMGV 15 0.016 1369.t00001 Chromosome11 63 100.0037
MIMIKFMGVIYIMII 15 0.545 1369.t00001 Chromosome11 70 100.0038
GVIYIMIISKKMMRK 15 0.076 1369.t00001 Chromosome11 285 100.0039
LYYLFNQHIKKEINH 15 0.742 1369.t00001 Chromosome11 299 100.0040
HFNMLKNKMQSSEEM 15 0.560 1369.t00001 Chromosome11 353 100.0041
XDIYQKLYIKQEEQK 15 0.807 1369.t00001 Chromosome11 366 100.0042
QKKYIYNLIMNTQNK 15 0.167 1369.t00001 Chromosome11 381 100.0043
YEALIKLLPFSKRIR 15 0.701 699.t00001 Chromosome11 565 100.0044
NIHFAVLFLTLTVYP 15 0.347 699.t00001 Chromosome11 569 100.0045
AVLFLTLTVYPINNF 15 0.255 699.t00001 Chromosome11 623 100.0046
KLLYKMNYLKQDINN 15 0.545 699.t00001 Chromosome11 744 100.0047
KKEFKNSLILLNLYN 15 0.576 699.t00001 Chromosome11 773 100.0048
YLSFKILNTLLYNHI 15 0.234 699.t00001 Chromosome11 866 100.0049
IYILINHVIIPSITY 15 0.400 699.t00001 Chromosome11 875 100.0050
IPSLFYLYMNFLKFI 15 0.347 699.t00001 Chromosome11 929 100.0051
KYLIILLYIFKLIEY 15 0.701 699.t00001 Chromosome11 978 100.0052
FIFMQNNQTKLAEMK 15 0.039 699.t00001 Chromosome11 1032 100.0053
LFIYIWLHLIIIFIF 15 0.423 mal_4T2c4.p1t1 15 100.0054 ILLIRPMLVKLRPKL
15 0.221 mal_4T2c4.p1t1 19 100.0055 RPMLVKLRPKLVKLR 15 0.083
mal_4T2c4.p1t1 26 100.0056 RPKLVKLRPMLVKLG 15 0.010 mal_4T2c4.p1t1
33 100.0057 RPMLVKLGPILVKLR 15 0.004 mal_4T2c4.p1t1 40 100.0058
GPILVKLRPMLVKLR 15 0.010 mal_4T2c4.p1t1 47 100.0059 RPMLVKLRPMLAKLR
15 0.016 mal_4T2c4.p1t1 54 100.0060 RPMLAKLRPMLAKLR 15 0.027
mal_4T2c4.p1t1 61 100.0061 RPMLAKLRPKLVKLR 15 0.137
mal.sub.--4T2c4.p1t1 68 100.0062 RPKLVKLRPKLVKLR 15 0.083
mal_4T2c4.p1t1 75 100.0063 RPKLVKLRPISVNAK 15 0.076 M13Hg2.q1t3 89
100.0064 ILEMKPNILLSREIF 15 0.742 M13Hg2.q1t3 122 100.0065
NISINNAFSLPVNIY 15 0.663 M13Hg2.q1t3 163 100.0066 YFNIIQQKIQSNFLL
15 0.487 M13Hg2.q1t3 281 100.0067 ISTFIKNNINHQENN 15 0.682
M13Hg2.q1t3 442 100.0068 LKNMDGNILIKDFIQ 15 0.378 M13Hg2.q1t3 488
100.0069 IEFYNINMAKKVMNN 15 0.285 M13Hg2.q1t3 492 100.0070
NINMAKKVMNNMEKN 15 0.145 M13Hg2.q1t3 558 100.0071 FVNYFEAVVHMNIHC
15 0.831 M13Hg2.q1t3 691 100.0072 NNNIINGHMLEQKLS 15 0.123
M13Hg2.q1t3 869 100.0073 NNDMKKGYTNVSNNS 15 0.162 Mal_5L10c4.q1t6
154 100.0074 NNEFFGYPLQFVCET 15 0.255 Mal_5L10c4.q1t6 336 100.0075
FFIIKNVGVHKITYY 15 0.388 Mal_5L10c4.q1t6 1090 100.0076
KIEYISMLSPTINEI 15 0.113 Mal_5L10c4.q1t6 1101 100.0077
INEIKTLNTILTIPL 15 0.018 Mal_5L10c4.q1t6 1107 100.0078
LNTILTIPLIKMNEY 15 0.042 Mal_5L10c4.q1t6 1264 100.0079
HKLFINKLMTSNIRK 15 0.203 Mal_5L10c4.q1t6 1289 100.0080
QNRERNQLLYLTKIA 15 0.050 Mal_5L10c4.q1t6 1609 100.0081
IKKIKTPLILPIDPN 15 0.035 Mal_5L10c4.q1t6 1888 100.0082
QDHLVIQIIYVMDNI 15 0.133 Mal_5L10c4.q1t6 2031 100.0083
IEAMGOAHSIGYEQF 15 0.068 571.t00003 Chromosome11 33 100.0084
FDDFKINYSYKTKNH 15 0.182 571.t00003 Chromosome11 462 100.0085
ITDLNNMNVNQSNMK 15 0.500 571.t00003 Chromosome11 960 100.0086
TNNFNNNVMMLMNTS 15 0.007 571.t00003 Chromosome11 1124 100.0087
EQNVAQNVAQNVAQN 15 0.460 571.t00003 Chromosome11 1128 100.0088
AQNVAQNVAQNVEQN 15 0.460 571.t00003 Chromosome11 1550 100.0089
SNKFMTPTTLKEKYQ 15 0.255 571.t00003 Chromosome11 1941 100.0090
NIHMINDVATKLNQH 15 0.285 571.t00003 Chromosome11 2112 100.0091
HIHMMNQQIQKETNT 15 0.576 571.t00003 Chromosome11 2255 100.0092
NNVFQQPLSYSNGSE 15 0.347 571.t00003 Chromosome11 2738 100.0093
NNTINMNGMNKTESI 15 0.198 MP03072 PFC0450w 5 100.0094
LNILILIDAASVAFL 15 0.722 MP03072 PFC0450w 8 100.0095
LILIDAASVAFLLIT 15 1.340 MP03072 PFC0450w 17 100.0096
AFLLITFLMINLNEE 15 1.197 MP03072 PFC0450w 44 100.0097
KKALVVAIILYVIEL 15 0.302 MP03072 PFC0450w 48 100.0098
VVAIILYVIFLVLLF 15 0.609 MP03072 PFC0450w 52 100.0099
ILYVIFLVLLFIYKA 15 0.831 MP03072 PFC0450w 55 100.0100
VIFLVLLFIYKAYKN 15 0.956 MP03072 PFC0450w 58 100.0101
LVLLFIYKAYKNKRK 15 4.016 MP03072 PFC0450w 76 100.0102
NFFMKKRNAPKYVQL 15 0.593 MP03072 PEC0450w 85 100.0103
PKYVQLASTYLSASD 15 2.865 45.t00001 Chromosome14 2 100.0104
ENEYATGAVRPFQAA 15 0.722 45.t00001 Chromosome14 27 100.0105
NYELSKKAVIFTPIY 15 1.197 45.t00001 Chromosome14 108 100.0106
QKILIKIPVTKNIIT 15 0.085 45.t00001 Chromosome14 156 100.0107
KCLVISQVSNSDSYK 15 2.044 45.t00001 Chromosome14 202 100.0108
SKIMKLPKLPISNGK 15 0.742 45.t00001 Chromosome14 220 100.0109
FIHFFTWGTMFVPKY 15 0.026 45.t00001 Chromosome14 242 100.0110
LCNFKKNIIALLIIP 15 0.203 45.t00001 Chromosome14 246 100.0111
KKNIIALLIIPPKIH 15 0.010 45.t00001 Chromosome14 251 100.0112
ALLIIPPKIHISIEL 15 1.267 45.t00001 Chromosome14 274 100.0113
SMEYKKDFLITARKP 15 1.826 MP03137 PFC0700c 7 100.0114
KSKFNILSSPLFNNF 15 1.987 MP03137 PFC0700c 173 100.0115
FKKLKNHVLFLQMMN 15 0.785 MP03137 PFC0700c 177 100.0116
KNHVLFLQMMNVNLQ 15 0.095 MP03137 PFC0700c 180 100.0117
VLFLQMMNVNLQKQL 15 0.068 MP03137 PFC0700c 187 100.0118
NVNLQKQLLTNHLIN 15 0.956 MP03137 PFC0700c 191 100.0119
QKQLLTNHLINTPKI 15 1.132 MP03137 PFC0700c 197 100.0120
NHLINTPKIMPHHII 15 0.576 MP03137 PFC0700c 239 100.0121
YILLKKILSSRFNQM 15 1.100 MP03137 PFC0700c 250 100.0122
FNQMIFVSSIFISFY 15 2.420 12.t00018 Chromosome14 36 100.0123
CNILKENNTYKQKKH 15 4.016 12.t00018 Chromosome14 133 100.0124
TNELKKMDTKKDVHM 15 1.011 12.t00018 Chromosome14 504 100.0125
EVKFILHMTLLTLYK 15 0.269 12.t00018 Chromosome14 542 100.0126
KYNFLNIYASLRNEY 15 0.328 12.t00018 Chromosome14 583 100.0127
TRCFKNSYPKKVWKK 15 0.293 12.t00018 Chromosome14 612 100.0128
NNLYVSMYIPFIKKF 15 0.411 12.t00018 Chromosome14 1000 100.0129
EAKFKIERLLKSSYK 15 3.298 12.t00018 Chromosome14 1057 100.0130
KIYILNNNLLIVHLS 15 1.543 12.t00018 Chromosome14 1184 100.0131
KCSFDKTNPIQQSGK 15 2.044 12.t00018 Chromosome14 1212 100.0132
TGIFNMPNLVQINNY 15 0.078 mal_BU121g9.q1c1 29 100.0133
EGMLTVAGPRSQTEL 15 3.298 mal_9A57b11.q1t2 3 100.0134
KQNIKYTQIISIDNI 15 2.633 mal_9A57b11.q1t2 18 100.0135
LNKIADPILIGFSSS 15 0.929 mal_9A57b11.q1t2 123 100.0136
NRIYNKLKLHKIIRK 15 1.267 mal_9A57b11.q1t2 194 100.0137
NNEYGILNAQKALSN 15 0.098 mal_9A57b11.q1t2 197 100.0138
YGILNAQKALSNLHK 15 0.141 mal_9A57b11.q1t2 229 100.0139
KIFVKYLPLFLMMEH 15 0.042 mal_9A57b11.q1t2 236 100.0140
PLFLMMEHSFLNCHK 15 3.031 mal_BL50e8.p1ca_5 1 100.0141
MEGFVALLSFLVVLV 15 0.004 mal_BL50e8.p1ca_5 100 100.0142
VDGMKIGHPISVALG 15 0.010 mal_BL50e8.p1ca_5 151 100.0143
GSTYMTPSAIKIKVP 15 0.057 mal_BL50e8.p1ca_5 189 100.0144
NNLFIYNWVLQTSSP 15 0.560 mal_BL50e8.p1ca_5 347 100.0145
EKILIRALLSLDFSL 15 0.722 mal_BL50e8.p1ca_5 437 100.0146
HPVYPTAPAVAFPAG 15 0.187 mal_BL50e8.p1ca_5 585 100.0147
EVYYFPGKVTRVRAK 15 0.357 mal_BL50e8.p1ca_5 606 100.0148
EDKLVKIYISLLSSD 15 0.423 mal_BL50e8.p1ca_5 685 100.0149
IERYVGLGSFHFYLY 15 0.423 mal_BL50e8.p1ca_5 816 100.0150
CFQVLNPVTIPKYCI 15 0.285 M13S8h6.p1t_3 68 100.0151 FMSFKILEALLVCIS
15 0.006 M13S8h6.p1t_3 127 100.0152 KQIVIFLISLLSFFL 15 0.473
M13S8h6.p1t_3 169 100.0153 AKQIEILHTMLPNFL 15 0.095 M13S8h6.p1t_3
218 100.0154 IDDFQNMVSTLQPHV 15 0.034 M13S8h6.p1t_3 285 100.0155
KCAIKLAIAQLSAKY 15 0.130 M13S8h6.p1t_3 343 100.0156 IGSVKPQYALFGDTV
15 0.228 M13S8h6.p1t_3 871 100.0157 KIYIKKKRLLQMNNY 15 0.411
M13S8h6.p1t_3 1350 100.0158 KKLLKKLTSNLQLNK 15 0.076 M13S8h6.p1t_3
1602 100.0159 QDFLTKILPRQVLEF 15 0.241 M13S846.p1t_3 1754 100.0160
MWGLDVLIANKIESN 15 0.423 585.t00002 Chromosome11 5 100.0161
FFILFYFYVMSTYTF 15 0.500 585.t00002 Chromosome11 16 100.0162
TYTFCFLPVLQTQLG 15 0.515 585.t00002 Chromosome11 349 100.0163
KKKYKNKKMPKTIDG 15 0.473 585.t00002 Chromosome11 487 100.0164
GRAIIPLFLILNTYK 15 0.269 585.t00002 Chromosome11 562 100.0165
KIIFKRNPLFLTFLS 15 0.367 585.t00002 Chromosome11 643 100.0166
WLFFFDLVVLSPFSL 15 0.500 585.t00002 Chromosome11 774 100.0167
KNIIKGKNMMTRGGG 15 0.106 585.t00002 Chromosome11 796 100.0168
KMFIKGDTVMKANII 15 0.038 585.t00002 Chromosome11 1093 100.0169
VGSYKLMISQEAEFE 15 0.487 585.t00002 Chromosome11 1344 100.0170
LNRFITLITWTQHVS 15 0.095 1223.t00015 mal9A21f9.q1t4 1070 100.0171
RTKYETLVTIHVHQR 15 0.087 1223.t00015 mal9A21f9.qlt4 1162 100.0172
GLCYGGAPAGPAGTG 15 0.059 1223.t00015 mal9A21f9.q1t4 1654 100.0173
DSILILQTINLLNSQ 15 0.177 1223.t00015 mal9A21f9.q1t4 2461 100.0174
KHLIIINRVMQTPNG 15 0.043 1223.t00015 mal9A21f9.q1t4 2779 100.0175
IDLYKQMYVKKYDEI 15 0.158 1223.t00015 mal9A21f9.q1t4 2878 100.0176
DKDLKAALPYLHEAE 15 0.103 1223.t00015 mal9A21f9.q1L4 2985 100.0177
TIELLKPYIQSTFFK 15 0.145 1223.t00015 mal9A21f9.q1t4 2995 100.0178
STFFKTQIAKKASVA 15 0.002 1223.t00015 mal9A21f9.91t44 3014 100.0179
CKWVGAMAMYNQASK 15 0.145 1223.t00015 mal9A21f9.q1t4 3019 100.0180
AMAMYNQASKIVKPK 15 0.116 599.t00001 Chromosome11 12 100.0181
INFFILLTLVFQKYS 15 0.177 599.t00001 Chromosome11 364 100.0182
NNNLGIPTLIKKEVH 15 0.234 599.t00001 Chromosome11 519 100.0183
EEDIKNAYLPENKNF 15 0.435 599.t00001 Chromosome11 1074 100.0184
INVFIKEISKLFDHD 15 0.529 599.t00001 Chromosome11 1414 100.0185
DKSLKIMYSLFNKYT 15 0.098 599.t00001 Chromosome11 1463 100.0186
VVIFIYGNIIISDLK 15 0.645 599.t00001 Chromosome11 1621 100.0187
CESFISKVTNKVIKK 15 0.215 599.t00001 Chromosome11 1740 100.0188
ICTFVKYITFQLLNI 15 0.854 599.t00001 Chromosome11 1767 100.0189
KEHYIMNNTIFTFNQ 15 0.141 599.t00001 Chromosome11 1892 100.0190
KKKYKYIPSNGTTQS 15 0.500 M1045c5.p1c.C_6 53 100.0191
EKSLGILGSIQNAYL 15 0.085 M1045c5.plc.C_6 59 100.0192
LGSIQNAYLYKSIFK 15 0.388 M1045c5.p1c.C_6 588 100.0193
SCIMNNMIVTKESNE 15 0.473 M1045c5.p1c.C_6 1040 100.0194
KDFMKNNTTLFSHFN 15 0.241 M1045c5.p1c.C_6 1136 100.0195
MLYLIRNILMSIEDY 15 0.435 M1045c5.p1c.C_6 1229 100.0196
KKKYIKLNIFKNIIL 15 0.378 M1045c5.p1c.C_6 1350 100.0197
RWDLVMNMMIGIRIS 15 0.054 M1045c5.p1c.C_6 1380 100.0198
HKDVIQLPTSNAQHK 15 0.167 M1045e5.p1c.C_6 1393 100.0199
HKVIFKNYAPIIFKN 15 0.262 M1045c5.p1c.C_6 1430 100.0200
SNMVLGNLSTLSELL 15 0.423 PIR2 T28161 46 100.0201 AKFYNGGEIMQPNSK 15
0.153 PIR2 T28161 319 100.0202 KRNLKLQNAIKNCRG 15 0.043 PIR2 T28161
1072 100.0203 HVKIIKNLLIHGKEQ 15 0.302 PIR2 T28161 1093 100.0204
KYKLLYLQAQTTAAN 15 0.141 PIR2 T28161 1096 100.0205 LLYLQAQTTAANGGP
15 0.047 PIR2 T28161 1589 100.0206 SPKIVVPAPKVITTF 15 0.119 PIR2
T28161 1951 100.0207 FVDLIRQIAATIDKG 15 0.047 PIR2 T28161 2065
100.0208 QERLVKNPLVQPTLK 15 0.028 PIR2 T28161 2129 100.0209
HPAVIPALVTSTLAW 15 0.072 PIR2 T28161 2419 100.0210 NELMTNHVKQTSIEI
15 0.098 55.t00004 Chromosome14 81 100.0211 NNEFVVAQLYELNNY 15
1.340 55.t00004 Chromosome14 117 100.0212 DNNMKKYLIQKCGKK 15 1.776
55.t00004 Chromosome14 218 100.0213 SCSIIKYELRKTSIC 15 1.878
55.t00004 Chromosome14 385 100.0214 RNHMDKPPPHNINNN 15 1.228
55.t00004 Chromosome14 613 100.0215 NNNLIFQNSRENDHT 15 0.423
55.t00004 Chromosome14 754 100.0216 THDIIKNVSNNMKRF 15 0.357
55.t00004 Chromosome14 904 100.0217 FKNVDMLNIYKINKD 15 1.987
55.t00004 Chromosome14 1136 100.0218 MKDVINLYTYVVNKK 15 0.092
55.t00004 Chromosome14 1364 100.0219 GMYILPQYVTRECIN 15 1.500
55.t00004 Chromosome14 1510 100.0220 GDDVIYEETKKTDNI 15 1.587
13.t00011 Chromosome14 16 100.0221 FKSLKNNNMLESTGI 15 1.587
13.t00011 Chromosome14 49 100.0222 FTDYVKGKMMDVYKE 15 0.126
13.t00011 Chromosome14 84 100.0223 TYNYLTPTLKVKKEN 15 3.589
37.t00002 Chromosome14 50 100.0224 NDLIDQNIVYLNVCN 15 2.560
674.t00001 Chromosome11 30 100.0225 LKKLKKILLNLDVLI 15 0.742
674.t00001 Chromosome11 54 100.0226 NENFDMELLNNVNDR 15 1.378
674.t00001 Chromosome11 124 100.0227 NCPIKNEVTTLIQKI 15 0.367
674.t00001 Chromosome11 296 100.0228 EKNMTSQKSITSEKN 15 0.854
674.t00001 Chromosome11 577 100.0229 NSNFKEQHLLFCNNL 15 1.418
674.t00001 Chromosome11 752 100.0230 NNNIKTHIANFNIIH 15 1.040
674.t00001 Chromosome11 986 100.0231 NNLYKTYEMIQGDND 15 0.956
674.t00001 Chromosome11 1093 100.0232 NDNYINNNIYLNKAN 15 1.340
674.t00001 Chromosnme11 1353 100.0233 FLQYRIPHMNNNGNI 15 0.983
674.t00001 Chromosome11 1432 100.0234 VDIFCKIHALKNENK 15 0.854
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20120015401A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20120015401A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References