DETAILED ACTION
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicants ‘response 9/29/2025 is acknowledged.
Status of the Claims
3. Claims 1-20 are pending in this application.
Drawings
4. The drawings in this application filed 10/4/2022 are accepted by the examiner.
Information Disclosure Statement
5. The information disclosure statement filed 10/4/2022 has been considered. Initialed copies are enclosed. However, the listing of references in the specification (pages 38-39) is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Election/Restrictions
6. Applicants’ election without traverse of 9/29/2025 is acknowledged. Applicants elected invention I (claims 1-6) drawn to a lipoprotein. The traversal is on the ground(s) that applicant provisionally elects claims 1-10 (Group I, drawn to a method of treating) for prosecution. For election of species applicants have elected SEQ ID NO:13. Claims 7-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1-6 are under consideration.
Claim Rejections - 35 USC § 101
7. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
8. Claims 1-6 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, claims do not recite something significantly different than a judicial exception. The claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because the claims do not recite something significantly more. The claims are drawn to:
A method for treating or preventing a condition in a subject, wherein the method comprises: administering to the subject a lipoprotein obtainable from Bordetella pertussis; wherein the lipoprotein comprises an N terminal signal peptide of less than 40 amino acids in length; wherein the N terminal signal peptide comprises a lipobox comprising an amino acid sequence X1, X2, X3, X4; wherein X1 is selected from the group consisting of Leucine, Valine and isoleucine; wherein X2 is selected from the group consisting of Alanine, Serine, Threonine, Valine and isoleucine; wherein X3 is selected from the group consisting of Glycine, Alanine, and Serine; wherein X4 is Cysteine; wherein X4 is capable of being acylated; wherein the lipoprotein is a Toll-like receptor 2 agonist; wherein the lipoprotein is selected from the group consisting of a lipoprotein comprising the amino acid sequence of SEQ ID NO:1, a lipopeptide comprising the amino acid sequence of SEQ ID NO:13, and a lipopeptide comprising the amino acid sequence of SEQ ID NO:14; and wherein the condition to be treated or prevented comprises a condition caused by a pathogen, a cancer, or an allergic disease.
Based on instant specification in general, the lipopeptides derived from the bacteria Bordetella pertussis.
The instant method claim recites use of something that appears to be a natural product that is not markedly different in structure and function from naturally occurring products. There is no structural difference because each of the components of the claimed invention is not markedly different. The instantly claimed lipoproteins are naturally occurring as evidenced by Parkhill et al., "Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica."; Nat. Genet. 35:32-40(2003). Additionally, the mere recitation of a recombinant protein does not change the components from what exists in nature.
Using the December 16, 2014 Eligibility Guidelines and broadest reasonable interpretation of the instant claims as outlined above, the answer to question 1 is YES, the claimed invention is directed to a composition of matter.
With regard to Step2A, the answer to Step 2A is YES, the claimed invention is directed to a judicially recognized exception. When the nature-based product is produced by combining multiple components, the markedly different characteristics analysis should be applied to the resultant nature-based combination, rather than its component parts. The markedly different characteristics analysis compares the nature-based product limitation to its naturally occurring counterpart in its natural state. (To show a marked difference, a characteristic must be changed as compared to nature, and cannot be an inherent or innate characteristic of the naturally occurring counterpart.) and will be evaluated based on what is recited in the claim on a case-by-case basis. As seen by the examples that are being released in conjunction with this Interim Eligibility Guidance, even a small change can result in markedly different characteristics from the product's naturally. As stated above, the claims do not recite any markedly different characteristics or properties. The structural and functional characteristics are the same.
With regard to Step 2B, the answer to the question--Does the claim as a whole amount to significantly more than the judicial exception, is NO. To determine whether any element, or combination of elements, in the claim is sufficient to ensure that the claim amounts to significantly more than the judicial exception, examiners will: - Consider the additional elements claimed with the exception, both individually and as an ordered combination, to ensure that the claim as a whole describes a product or process that applies the exception in a meaningful way. It is noted that claims do not recite any additional elements that can be applied with the exception in a meaningful way. Simply appending well-understood, routine and conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception is not enough to qualify as "significantly more" when recited in a claim. In view of the foregoing eligibility analysis, the claims are not drawn to eligible subject matter.
Claim Rejections - 35 USC § 112
9. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
10. Claims 1-6 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The claims recite:
Claim 1. A method for treating or preventing a condition in a subject, wherein the method comprises: administering to the subject a lipoprotein obtainable from Bordetella pertussis; wherein the lipoprotein comprises an N terminal signal peptide of less than 40 amino acids in length; wherein the N terminal signal peptide comprises a lipobox comprising an amino acid sequence X1, X2, X3, X4; wherein X1is selected from the group consisting of Leucine, Valine and isoleucine; wherein X2 is selected from the group consisting of Alanine, Serine, Threonine, Valine and isoleucine; wherein X3 is selected from the group consisting of Glycine, Alanine, and Serine; wherein X4 is Cysteine; wherein X4 is capable of being acylated; wherein the lipoprotein is a Toll-like receptor 2 agonist; wherein the lipoprotein is selected from the group consisting of a lipoprotein comprising the amino acid sequence of SEQ ID NO:1, a lipopeptide comprising the amino acid sequence of SEQ ID NO:13, and a lipopeptide comprising the amino acid sequence of SEQ ID NO:14; and wherein the condition to be treated or prevented comprises a condition caused by a pathogen, a cancer, or an allergic disease.
Claim 3. The method as claimed in claim 1, wherein the condition to be treated or prevented is caused by a pathogen, wherein the pathogen is a bacterium, a virus, a fungus or a parasite.
The specification fails to describe has not described or enabled any condition caused by any pathogen being treated or prevented. It is not clear from the specification what is the method of treatment, what is being treated, in what type of subject, which infectious disease, what condition is being prevented and is any condition caused by any pathogen being treated or prevented? In general, the specification lacks a method of prevention, lacks what is claimed subject, lacks of what is being treated and lack of conditions being prevented.
Specification mentions therapeutic or as a vaccine composition in treatment and prevention of cancer and therapeutic or as a vaccine composition in the treatment and/or prevention of allergic diseases such as asthma. None of these are infectious disease or caused by a pathogen.
The examples are mostly Identification, Cloning, Expression and Purification of TLR2-Activating Lipoproteins from B. pertussis and Cytokine Production in a TLR2 Dependent Manner. Example 7 recites LP1569 is an Effective Adjuvant for Promoting Protective Cellular Immunity against B. pertussis. None of the examples recites a method of treatment or prevention of a condition caused by a pathogen.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter later claimed by him. The courts have stated:
“To fulfill the written description requirement, a patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude "the inventor invented the claimed invention." Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (1997); In re Gostelli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using “such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2d at 1966.” Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the Application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient.” MPEP 2163.
Further, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California v. Eli Lilly & Co., the court stated:
“A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials. Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284-85 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or sub-combinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus. . . ."). Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
The MPEP further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the sequence, it is “not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence.” MPEP 2163. The MPEP does state that for generic claim the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. MPEP 2163. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. See MPEP 2163. Although the MPEP does not define what constitute a sufficient number of representatives, the Courts have indicated what do not constitute a representative number species to adequately describe a broad generic. In Gostelli, the Court determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus. In re Gostelli, 872 F.2d at 1012, 10 USPQ2d at 1618.
The written description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate."). Accordingly, it is deemed that the specification fails to provide adequate written description for the genus of the claims and does not reasonably convey to one skilled in the relevant art that the inventor(s), at the time the application was filed, had possession of the entire scope of the claimed invention.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 USC 112 is severable from its enablement provision (see page 115). The skilled artisan cannot envision the detailed structure of the peptide fragments thereof; thus, conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. An adequate description requires more than a mere statement that it is part of the invention and a reference to a potential method of isolating it. Furthermore, In The Reagents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412), the court held that a generic statement which defines a genus of by only their functional activity does not provide an adequate description of the genus. The court indicated that while Applicants are not required to disclose every species encompassed by a genus, the description of a genus is achieved by the recitation of a representative number of molecules falling within the scope of the claimed genus.
Without describing the specifically named disease, pathogen and type of subject and condition is being prevented, the skilled artisan cannot envision the detailed structure of the fragments thereof, thus conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. An adequate description requires more than a mere statement that it is part of the invention and a reference to a potential method of isolating it. Furthermore, In The Reagents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412), the court held that a generic statement which defines a genus of by only their functional activity does not provide an adequate description of the genus. The court indicated that while Applicants are not required to disclose every species encompassed by a genus, the description of a genus is achieved by the recitation of a representative number of molecules falling within the scope of the claimed genus. Therefore, only the recited Th1 response and not the full breadth of the claims meets the written description provision of 35 USC 112, first paragraph.
Claim Rejections - 35 USC § 103
11. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
12. Claims 1 -6 is/are rejected under 35 U.S.C. 103 as being un-patentable over Castado et al. (US Pat Pub. 20070116711) in view of Parkhill et al. Nature Genetics, vol. 31, no.1, pp.32-40, 2003 (art of record applicants’1449).
The claims are drawn to:
Claim 1. A method for treating or preventing a condition in a subject, wherein the method comprises: administering to the subject a lipoprotein obtainable from Bordetella pertussis; wherein the lipoprotein comprises an N terminal signal peptide of less than 40 amino acids in length; wherein the N terminal signal peptide comprises a lipobox comprising an amino acid sequence X1, X2, X3, X4; wherein X1 is selected from the group consisting of Leucine, Valine and isoleucine; wherein X2 is selected from the group consisting of Alanine, Serine, Threonine, Valine and isoleucine; wherein X3 is selected from the group consisting of Glycine, Alanine, and Serine; wherein X4 is Cysteine; wherein X4 is capable of being acylated; wherein the lipoprotein is a Toll-like receptor 2 agonist; wherein the lipoprotein is selected from the group consisting of a lipoprotein comprising the amino acid sequence of SEQ ID NO:1, a lipopeptide comprising the amino acid sequence of SEQ ID NO:13, and a lipopeptide comprising the amino acid sequence of SEQ ID NO:14; and wherein the condition to be treated or prevented comprises a condition caused by a pathogen, a cancer, or an allergic disease.
Claim 3. The method as claimed in claim 1, wherein the condition to be treated or prevented is caused by a pathogen, wherein the pathogen is a bacterium, a virus, a fungus or a parasite.
Castado et al. teach a method for treating or preventing Bordetella infection comprising administering an immunogenic composition comprising lipoproteins (see abstract and claims.
Castado et al. teach a method for enhancing a Th1 response in a subject in need thereof by proteins of Bordetella pertussis (see paragraph 0271-0277). Castado et al. teach an immunogenic composition comprising at least or exactly two, three, four, five, six, seven, eight, nine or ten different Bordetella, preferably B. pertussis, antigens wherein the antigens are selected from at least two, three, four or five groups of proteins (see claim 11). Castado et al., teach the immunogenic composition comprising lipoproteins. Castado et al. teach also teach vaccine, adjuvants, and a method for treating or preventing Bordetella infection comprising administering the vaccine (see claims 65-66 and 69). A method for treating or preventing Bordetella infection comprising administering the immunogenic composition. Castado et al. teach also teach limitations of claims pathogen, infectious agent, bacterium, Bordetella pertussis and antigen from the pathogen (see abstract and claims).
Castado et al. teach the provision of the Bordetella pertussis BASB232 polypeptide encoded by Orf48, Orf45 and Orf46 (see abstract, para 0001, 0008, 0018-0023 and 0035-0037) Orf48 comprises also SEQ ID NO: 14 of the present application (see sequence alignment VB60452 below). Castado et al. discloses corresponding immunogenic compositions. Also described is a vaccine comprising the above immunogenic composition. The vaccine formulation of the invention may also include adjuvant systems for enhancing the immunogenicity of the formulation. Preferably the adjuvant system raises preferentially a TH1 type of response. The immunogenic composition is useful in the preparation of a medicament for use in the treatment or prevention of Bordetella disease such as whooping cough. The immunogenic composition and vaccine are useful for treating or preventing Bordetella infections such as B. pertussis, B. parapertussis or B. bronchiseptica infections, by administering the vaccine to a host. Orf45 is disclosed as a peptidoglycan-associated lipoprotein, Orf46 as an outer membrane lipoprotein (OmIA) (see claim 27), and orf48 as an outer membrane and transmembrane lipoprotein Orf48, Orf45 and Orf46, (see para 0019,). Castado et al. teach N-terminal (para 0230, exp.9) and signal peptides (see para 0096. 0114, 0117, 118, 0258).The limitations lipoprotein having an N terminal signal peptide of less than 40 amino acids in length wherein the N terminal signal peptide comprises a lipobox comprising an amino acid sequence X1, X2, X3, X4, wherein X1 can be selected from Leucine, Valine and Isoleucine; X2 can be selected from Alanine, Serine, Threonine, Valine and Isoleucine; X3 can be selected from Glycine, Alanine, and Serine; and X4 is Cysteine, wherein X4 is capable of being acylated would be inherent in the lipoproteins of Castado et al. Castado et al., teach a wherein the lipoprotein is a lipopeptide comprising the amino acid sequence of SEQ ID NO: 14 ( see sequence alignment below). However, Castado et al., do not teach SEQ ID NOs:1 and 13.
Castado et al. teach limitations of clams 3, 4 (pathogens, bacteria, virus) see claim 64, para 0050, 0095, 0098, 0113, 0236, 0263, 0254, 0247, 0248, 0265, exp 9). Castado et al. teach limitations of claim 6 (antigen from pathogen) see claims 33, 34, 35, 56, 59 and para 0218, 0219, 0230, 0263, 0271. 0273, 0277, 0281 and exp 3. Castado et al. teach limitations of claim 5 (induction of immunity against pathogen) see para 0238, 0247, 0263. Castado et al., do not teach SEQ ID NOs:1 and 13.
Parkhill et al. teach lipoproteins from Bordetella pertussis having 100% identity to SEQ ID NOs: 1, and 13 (see below the sequence alignments). The limitations lipoprotein having an N terminal signal peptide of less than 40 amino acids in length wherein the N terminal signal peptide comprises a lipobox comprising an amino acid sequence XI, X2, X3, X4, wherein XI can be selected from Leucine, Valine and Isoleucine; X2 can be selected from Alanine, Serine, Threonine, Valine and Isoleucine; X3 can be selected from Glycine, Alanine, and Serine; and X4 is Cysteine, wherein X4 is capable of being acylated would be inherent in the lipoproteins of Parkhill et al.
It would have been obvious to one of ordinary skill in the art at the time of the invention to combine the teachings of the cited references to obtain the instant invention. Parkhill et al. teach lipoproteins from Bordetella pertussis and sequences 100% identical to SEQ IDs 1, and 13. Castado et al. teach a method for treating or preventing Bordetella infection comprising administering an immunogenic composition comprising lipoprotein. Castado et al. also teach a method for enhancing a Th1 response in a subject in need thereof by proteins of Bordetella pertussis using lipoproteins. It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the teaching of Castado et al., to include the Bordetella pertussis lipoproteins taught by Parkhill et al. in their immunogenic composition.
The motivation for including other sequences or protein comes from teaching of Castado et al. that recite “an immunogenic composition comprising at least or exactly two, three, four, five, six, seven, eight, nine or ten different Bordetella, preferably B. pertussis, antigens wherein the antigens are selected from at least two, three, four or five groups of proteins”.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses combining prior art elements according to known methods to yield predictable results, thus the combination is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses "The combination of familiar element according to known methods is likely to be obvious when it does no more than yield predictable results". It is well known to include or exclude an immunogenic composition or a system thus the combination would have yielded a reasonable expectation of success along with predictable results to one of ordinary skill in the art at the time of the invention. Thus, it would have been obvious to a person of ordinary skill in the art to combine prior art elements according to known methods that is ready for improvement to yield predictable results. The claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Result for SEQ ID NO:13
RESULT 4
Q7VXZ9_BORPE
ID Q7VXZ9_BORPE Unreviewed; 375 AA.
AC Q7VXZ9;
DT 01-OCT-2003, integrated into UniProtKB/TrEMBL.
DT 01-OCT-2003, sequence version 1.
DT 02-APR-2025, entry version 82.
DE SubName: Full=Lipoprotein {ECO:0000313|EMBL:CAE41858.1};
GN OrderedLocusNames=BP1569 {ECO:0000313|EMBL:CAE41858.1};
OS Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251).
OC Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria;
OC Burkholderiales; Alcaligenaceae; Bordetella.
OX NCBI_TaxID=257313 {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676};
RN [1] {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tohama I / ATCC BAA-589 / NCTC 13251
RC {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676};
RX PubMed=12910271; DOI=10.1038/ng1227;
RA Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R.,
RA Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L.,
RA Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A.,
RA Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I.,
RA Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T.,
RA Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S.,
RA Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E.,
RA Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M.,
RA Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S.,
RA Barrell B.G., Maskell D.J.;
RT "Comparative analysis of the genome sequences of Bordetella pertussis,
RT Bordetella parapertussis and Bordetella bronchiseptica.";
RL Nat. Genet. 35:32-40(2003).
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DR EMBL; BX640415; CAE41858.1; -; Genomic_DNA.
DR RefSeq; NP_880303.1; NC_002929.2.
DR AlphaFoldDB; Q7VXZ9; -.
DR STRING; 257313.BP1569; -.
DR PaxDb; 257313-BP1569; -.
DR KEGG; bpe:BP1569; -.
DR PATRIC; fig|257313.5.peg.1684; -.
DR eggNOG; COG3317; Bacteria.
DR HOGENOM; CLU_056157_0_0_4; -.
DR Proteomes; UP000002676; Chromosome.
DR Gene3D; 3.30.310.170; Outer membrane protein assembly factor BamC; 1.
DR InterPro; IPR042268; BamC_C.
DR InterPro; IPR010653; NlpB/DapX.
DR Pfam; PF06804; Lipoprotein_18; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 4: Predicted;
KW Lipoprotein {ECO:0000313|EMBL:CAE41858.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000002676};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..22
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 23..375
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5004293147"
FT REGION 36..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 375 AA; 41495 MW; F8654E77C5403E1E CRC64;
Query Match 100.0%; Score 78; Length 375;
Best Local Similarity 100.0%;
Matches 15; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CSDVNQLLGNEESVD 15
Db 22 CSDVNQLLGNEESVD 36
Result for SEQ ID NO: 1
Q7VXZ9_BORPE
ID Q7VXZ9_BORPE Unreviewed; 375 AA.
AC Q7VXZ9;
DT 01-OCT-2003, integrated into UniProtKB/TrEMBL.
DT 01-OCT-2003, sequence version 1.
DT 02-APR-2025, entry version 82.
DE SubName: Full=Lipoprotein {ECO:0000313|EMBL:CAE41858.1};
GN OrderedLocusNames=BP1569 {ECO:0000313|EMBL:CAE41858.1};
OS Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251).
OC Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria;
OC Burkholderiales; Alcaligenaceae; Bordetella.
OX NCBI_TaxID=257313 {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676};
RN [1] {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tohama I / ATCC BAA-589 / NCTC 13251
RC {ECO:0000313|EMBL:CAE41858.1, ECO:0000313|Proteomes:UP000002676};
RX PubMed=12910271; DOI=10.1038/ng1227;
RA Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R.,
RA Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L.,
RA Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A.,
RA Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I.,
RA Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T.,
RA Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S.,
RA Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E.,
RA Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M.,
RA Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S.,
RA Barrell B.G., Maskell D.J.;
RT "Comparative analysis of the genome sequences of Bordetella pertussis,
RT Bordetella parapertussis and Bordetella bronchiseptica.";
RL Nat. Genet. 35:32-40(2003).
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BX640415; CAE41858.1; -; Genomic_DNA.
DR RefSeq; NP_880303.1; NC_002929.2.
DR AlphaFoldDB; Q7VXZ9; -.
DR STRING; 257313.BP1569; -.
DR PaxDb; 257313-BP1569; -.
DR KEGG; bpe:BP1569; -.
DR PATRIC; fig|257313.5.peg.1684; -.
DR eggNOG; COG3317; Bacteria.
DR HOGENOM; CLU_056157_0_0_4; -.
DR Proteomes; UP000002676; Chromosome.
DR Gene3D; 3.30.310.170; Outer membrane protein assembly factor BamC; 1.
DR InterPro; IPR042268; BamC_C.
DR InterPro; IPR010653; NlpB/DapX.
DR Pfam; PF06804; Lipoprotein_18; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 4: Predicted;
KW Lipoprotein {ECO:0000313|EMBL:CAE41858.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000002676};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..22
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 23..375
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5004293147"
FT REGION 36..67
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 375 AA; 41495 MW; F8654E77C5403E1E CRC64;
Query Match 100.0%; Score 1930; Length 375;
Best Local Similarity 100.0%;
Matches 375; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MRMNKRHAGASALMALALLAGCSDVNQLLGNEESVDYKSTRRGDPLSIPPDLTQANNDPR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MRMNKRHAGASALMALALLAGCSDVNQLLGNEESVDYKSTRRGDPLSIPPDLTQANNDPR 60
Qy 61 YKAPASGTATYSQFQQQGLQQQASAGQNTNVLPERADMRVERDGDLRWLVIERPPEQLFS 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 YKAPASGTATYSQFQQQGLQQQASAGQNTNVLPERADMRVERDGDLRWLVIERPPEQLFS 120
Qy 121 KVVDFWTDTGFTVSVNNPQAGIIETDWAENRAKIPESWLRQVLGSVLETAWDSGEREKFR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KVVDFWTDTGFTVSVNNPQAGIIETDWAENRAKIPESWLRQVLGSVLETAWDSGEREKFR 180
Qy 181 TRVERVNGHTEIYITHNQMLEKRVGSDGGQVQWTHGKEDPGLNAAMLARLMVYLGTDVDA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TRVERVNGHTEIYITHNQMLEKRVGSDGGQVQWTHGKEDPGLNAAMLARLMVYLGTDVDA 240
Qy 241 ARKLVAQAEAAPQAPKVQSVRAEGAMLVVDESFDRAWRRVGVALDSGGFAVDDRDRSAGE 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ARKLVAQAEAAPQAPKVQSVRAEGAMLVVDESFDRAWRRVGVALDSGGFAVDDRDRSAGE 300
Qy 301 YFVRYVDTDTGAQNEQPGFFSRLFSSDKKAQAPQYRIRLTGSGTQTQVTVLDANGQRDSS 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 YFVRYVDTDTGAQNEQPGFFSRLFSSDKKAQAPQYRIRLTGSGTQTQVTVLDANGQRDSS 360
Qy 361 ATAQRMLSVLKDKMV 375
|||||||||||||||
Db 361 ATAQRMLSVLKDKMV 375
Result for SEQ ID NO: 14
US-10-574-297-96
Sequence 96, US/10574297
Publication No. US20070116711A1
GENERAL INFORMATION
APPLICANT: CASTADO, Cindy
APPLICANT: DENOEL, Philippe
APPLICANT: GODFROID, Fabrice
APPLICANT: POOLMAN, Jan
TITLE OF INVENTION: PERTUSSIS ANTIGENS AND USE THEREOF IN
TITLE OF INVENTION: VACCINATION
FILE REFERENCE: VB60452
CURRENT APPLICATION NUMBER: US/10/574,297
CURRENT FILING DATE: 2006-03-31
PRIOR APPLICATION NUMBER: PCT/EP2004/011082
PRIOR FILING DATE: 2004-10-01
PRIOR APPLICATION NUMBER: GB 0323113.1
PRIOR FILING DATE: 2003-10-02
PRIOR APPLICATION NUMBER: GB 0323112.3
PRIOR FILING DATE: 2003-10-02
NUMBER OF SEQ ID NOS: 110
SEQ ID NO 96
LENGTH: 167
TYPE: PRT
ORGANISM: Bordetella pertussis
Query Match 100.0%; Score 82; Length 167;
Best Local Similarity 100.0%;
Matches 15; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CANPSASSGVYTYGQ 15
|||||||||||||||
Db 33 CANPSASSGVYTYGQ 47
Conclusion
13. No claims are allowed.
14. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KHATOL S SHAHNAN SHAH whose telephone number is (571)272-0863. The examiner can normally be reached Mon-Tues, Thurs-Fri 12pm-8pm. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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KHATOL SHAHNAN -SHAH/
Examiner, Art Unit 1645
November 20, 2025
/JANA A HINES/Primary Examiner, Art Unit 1645