DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The Information Disclosure Statements filed on 1/3/2025 have been entered and considered. Initialed copies of the form PTO-1449 are enclosed with this action.
Restriction/Election/Status of claims
On 6/15/2026, applicant elected SEQ ID NO: 52 as the first polypeptide (from SEQ ID NOs: 1-495), and elected SEQ ID NO: 53 as the second polypeptide (also from SEQ ID NOs: 1-495, see claim 4), without traverse.
In view of the specification, and upon further consideration, SEQ ID NO: 53 is also analyzed as a first peptide as SEQ ID NO: 52 is; SEQ ID NO: 52 is also analyzed as a first peptide as SEQ ID NO: 53 is.
In summary, claims 1-24 are pending and examined in the office action. Non-elected species are withdrawn.
Priority
Instant application 18898088 filed 09/26/2024 is a Divisional of 17973124, filed 10/25/2022, now U.S. Patent # 12116588.
17973124 is a Continuation of 16980087, filed 09/11/2020, now U.S. Patent # 11525144.
16980087 is a National Stage entry of PCT/US2019/021775, International Filing Date: 03/12/2019.
PCT/US2019/021775 Claims Priority from Provisional Application 62642642, filed 03/14/2018.
62642642 disclosed the claimed subject matter including the elected SEQ ID NOs: 52-53 and subject matter thereof. The priority of 03/14/2018 is recognized for the rest of claims.
Claim Objections
Claims 4 and 12 are objected to because of the following informalities:
Claim 4, at the end, after SEQ ID NO: 495, the “whrein” should be a typographic error, and should be changed to --- wherein ---.
Claim 12, line 1, a comma ---,--- should be inserted between “….claim 7” and “wherein….”
See the requirement of 37 CFR 1.71(a) for “full, clear, and exact terms”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Lacking written description
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.
Claims 1-24 are rejected under 35 U.S.C. 112(a), 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
To claim a genus under the written description requirement, the applicant is required to describe a representative number of species to reflect the variation within the genus or structures sufficient to define the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combinations thereof.
By court’s statement in Regents of the Univ. of Cal. v. Eli Lilly, 119 F.3d 1559, 1566, 43 USPQ2d 1398, 1404 (Fed. Cir. 1997), a written description of an invention “requires a precise definition, such as a structure, formula, or chemical name, of the claimed subject matter sufficient to distinguish it from other materials”; further, a written description of a claimed genus requires a description of a representative number of species of the claimed genus, and one of skill in the art should be able to “visualize or recognize the identity of the members of the genus”.
Claim 1 is broadly drawn to a genus of amino acid sequences having at least 80% sequence identities to SEQ ID NO: 52 or 53 (elected species), and a genus of fragments of SEQ ID NO: 52 or 53, fusion proteins and compositions comprising such fragments, polynucleotides and DNA constructs encoding such fragments, and methods of using the fragments.
The claimed function is insecticidal activity (all claims), particularly against Lepidopteran pest (claim 2), and corn earworm (CEW), European corn borer (ECB), fall armyworm (FAW), soybean looper (SBL), and velvet bean caterpillar (VBC) (claim 23).
Claim 7 is broadly drawn to a genus of encoding the polynucleotides of claim 1.
The specification provides a sequence listing for SEQ ID NO: 52 (533AA) and SEQ ID NO: 53 (401AA).
The specification identified SEQ ID NO: 52 as IPD113Fl protein, and SEQ ID NO: 53 as IPD113Ga protein (Example 4, Table 3 in page 193). The specification provides example of transient expression of SEQ ID NO: 52 and SEQ ID NO: 53 in plant (bean plant), and demonstrated that SEQ ID NO: 52 and SEQ ID NO: 53 confer insecticidal activity against SBL, FAW, CEW, ECB, and VBC (Example 5, Table 6 in page 199).
However, the specification does not describe any structure feature of any peptide having 80% sequence identity to SEQ ID NO: 52 or 53, or any “fragment” of SEQ ID NO: 52 or 53, not to mention common structure feature of the genus of sequences and fragment, and not to mention
any association of such sequences or fragments to the functions of controlling insect, Lepidopteran pest, CEW, ECB, FAW, SBL and VBC.
According to specification (page 46, last para), “Fragments” or “biologically active portions” include polypeptide fragments comprising amino acid sequences sufficiently identical to an IPD113 polypeptide and that exhibit insecticidal activity.
Moreover, SEQ ID NO: 315, is 92.8% (at least 80% and at least 90%) identical to SEQ ID NO: 52. See “Sequence Matches at the end of office action). However, SEQ ID NO: 315 is not in the Table 6 above having demonstrated insecticidal activity. by the examiner’s search, no any other sequences are within at least 80% sequence identity to SEQ ID NO: 52.
The specification attempts to analyze the conserved domains of IPD113 polypeptides by using bioinformatics tools (page 60, 2nd para). However, the specification only states that the residues that are conserved and that MAY BE essential for protein activity (page 60, 2nd para). The specification does not describe that the common residues among sequences are sufficiently related to the claimed function.
According to the specification, protein identities are performed by using bioinformatics tool BLAST (page 189, 2nd para).
However, in the art, Friedberg (Automated protein function prediction--the genomic challenge. Brief. Bioinformatics. 7:225-242, 2006) teaches that homology-based transfer is not reliable for functional annotation even with high- alignment percentages (page 227, second column). Friedberg also teaches that identification of functionally significant sub-regions is critical to functional annotation, and that often addition, deletion, or re-shuffling of domains can lead to errors in annotation (page 227, second column; page 228, 1st paragraph). Friedberg teaches that sequence-based tools are just not sensitive enough to identify functional protein similarity as databases get larger, and diversity of sequences gets larger (page 228, first full paragraph).
Wang et al (From Protein Sequence to Protein Function via Multi-Label Linear Discriminant Analysis. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 14, NO. 3, 503-513, 2017) teach that FASTA and Basic Local Alignment Search Tool (BLAST) are useful but have limitations. Because a duplicate of a gene could adopt a new function in response to selective pressure during evolution, function transfer by homology on such gene and its product could produce erroneous results (p503, left col, 2nd para). There is no literature addressing the issue which criterion and which algorithm is optimal for protein function prediction. Moreover, genes evolve at different rates due to both uneven selection pressure on their functions and the inherent mutation rate of different species, which means that it is difficult to establish a similarity measure that is reliable in all cases (p504, left col, 1st para). Computational approaches to predict protein function is to assist biologist to discover new functional roles of proteins for experimental verification (p508, right col, last para).
Thus, the sequences and percentage identical thereof obtained by algorithms of bioinformatics tools are not consistent or reliable. Experimental data is the most reliable, specifically for new proteins and new functions.
In this case, SEQ ID NO: 52 or 53 is a newly disclosed and characterized protein. There is no published sequence similar to SEQ ID NO: 52 or 53, not to mention description of a common structural feature associated to any function of the sequence.
Regarding representative number of species, SEQ ID NO: 52 is a polypeptide sequence of 533 amino acids. For at least 80% identity, up to 106 AA can be substituted, deleted or inserted, in any positions. In addition, the sequences can be 427-649 AA long. Since the fragments are not structurally and functionally described, they can be as short as 2 amino acids long. The genus of fragments of SEQ ID NO: 52 are 532, 531, 530, ……..4, 3, 2 amino acid long, and can be at any positions of SEQ ID NO: 52.
The genus of polynucleotide encoding such sequences and fragments has even more species.
Thus, applicant is claiming an extremely large number of species including small fragments that are heterologous in structure.
In addition, SEQ ID NO: 52 or 53 is a newly disclosed sequence, neither its structure nor function is taught in prior art. Prior art does not describe any fragment SEQ ID NO: 52 or 53, not to mention the use of any fragments for conferring insect resistance.
Thus, the lone examples of SEQ ID NO: 52 or 53 does not demonstrate any common structure feature of the heterologous genus of fragments, and is not sufficient to represent the heterologous genus of fragments regarding the insecticidal function.
Therefore, the application has not met either of the two elements of the written description requirement as set forth in the court’s decision in Eli Lilly, and has not shown her/his possession of the claimed genus at the time of the application.
Dependent claims do not cure the deficiency, thus, are included.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the claims at issue are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the reference application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO internet Web site contains terminal disclaimer forms which may be used. Please visit http://www.uspto.gov/forms/. The filing date of the application will determine what form should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to http://www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1-24 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of US Patent 12116588.
The instant application and the USP share multiple inventors, and the same applicant.
The USP claims:
Claim 1. A recombinant polypeptide comprising an insecticidal amino acid sequence having at least 94% sequence identity to SEQ ID NO: 40, and a heterologous signal sequence, a histidine tag, or heterologous transit sequence operably linked to said insecticidal amino acid sequence.
Claim 4. A chimeric insecticidal protein comprising:
i) a first peptide comprising the insecticidal amino acid sequence of claim 1;
ii) a second peptide comprising an amino acid sequence from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 416, SEQ ID NO: 419, SEQ ID NO: 420, SEQ ID NO: 422, SEQ ID NO: 423, SEQ ID NO: 424, SEQ ID NO: 425, SEQ ID NO: 426, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, SEQ ID NO: 430, SEQ ID NO: 431, SEQ ID NO: 432, SEQ ID NO: 433, SEQ ID NO: 434, SEQ ID NO: 435, SEQ ID NO: 436, SEQ ID NO: 438, SEQ ID NO: 439, SEQ ID NO: 440, SEQ ID NO: 441, SEQ ID NO: 443, SEQ ID NO: 445, SEQ ID NO: 447, SEQ ID NO: 448, SEQ ID NO: 450, SEQ ID NO: 451, SEQ ID NO: 452, SEQ ID NO: 453, SEQ ID NO: 458, SEQ ID NO: 460, SEQ ID NO: 461, SEQ ID NO: 463, SEQ ID NO: 466, SEQ ID NO: 469, SEQ ID NO: 470, SEQ ID NO: 472, SEQ ID NO: 473, SEQ ID NO: 474, SEQ ID NO: 475, SEQ ID NO: 477, SEQ ID NO: 478, SEQ ID NO: 479, SEQ ID NO: 480, SEQ ID NO: 481, SEQ ID NO: 482, SEQ ID NO: 483, SEQ ID NO: 484, SEQ ID NO: 485, SEQ ID NO: 486, SEQ ID NO: 487, SEQ ID NO: 488, SEQ ID NO: 489, SEQ ID NO: 490, SEQ ID NO: 491, SEQ ID NO: 492, SEQ ID NO: 494, and SEQ ID NO: 495, wherein said first and second peptides are linked to one another via a covalent bond; and
iii) a heterologous signal sequence, a histidine tag, or heterologous transit sequence operably linked to said first or second peptide.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
By sequence alignment and search, SEQ ID NOs: 52 and 53 are identical in instant application and the USP.
Claims 1 and 4 of the USP claims a combination of insecticidal polypeptides of SEQ ID NO: 52 or SEQ ID NO: 53 with SEQ ID NO: 40. Thus, the reference claims are more specific than instant claim 1 is. Thus, the reference US patent recites a species of the genus recited in the instant application. Claims directed to a genus are prima facie obvious over claims directed to species of that genus.
Regarding dependent claims, reference claims 2-3, 6-25 have essentially the same subject matter, and essentially the same claim language.
Therefore, the claims are obvious over each other.
Remarks
SEQ ID NO: 52 or 53, and sequences having at least 90% identity thereof, and encoding polynucleotide sequences, had not been disclosed, not to mention characterized by any prior art.
Sequence Matches
Against instant SEQ ID NO: 52
Against Polypeptides
SEQ ID NO: 315 against SEQ ID NO: 52
ALIGNMENT:
Query Match 92.8%; Score 2577; Length 533;
Best Local Similarity 91.4%;
Matches 487; Conservative 25; Mismatches 21; Indels 0; Gaps 0;
Qy 1 MAAPGVKAEDVTASPAEPEENVHEVKLATTTDMEEGGGPLHGEKAGGVSSSHQHHEAGSL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAAPGVKAEDVTASPAEPEENVHEVKLATTTDMEEGGGPLHGEKAGGVSSSHQHHEAGSL 60
Qy 61 DDAIVEEFARNSQMEAHDWHNRTRDVVLALISIIPTVGAIA SVVLGIFWPANKVDIWVAL 120
|||||||||||||||||||||| | :| ||| :| ||| | ::|:|||:|||||| ||
Db 61 DDAIVEEFARNSQMEAHDWHNRIRGAILGLISAVPKVGAAISRLIGLFWPSNKVDIWEAL 120
Qy 121 SLEEYVRNIVKQEIFEFEMRQHQSSIEALESTIRRYNTAALPEKGNFLSIWISQADALCI 180
: |||:||||:||:|||||: |: |:|||:|: ||:|||| |||||||||||||||| |
Db 121 NAEEYIRNIVQQELFEFEMQLLQNDIQALETTVGRYDTAALTEKGNFLSIWISQADALYI 180
Qy 181 RLRNSTNDIHLLLHIVTVSVLHMAAMHERLTFGEELYGTDNTANWTRDLVEVFQMYTSDL 240
|:|||||:||||||:|||| ||:||:|||||||||||||:| ||||:|||: |: |||||
Db 181 RMRNSTNNIHLLLHMVTVSTLHLAALHERLTFGEELYGTNNAANWTQDLVDKFERYTSDL 240
Qy 241 IPSLFRKWKQWREGLIEIRSWVVPGRWGNLVQLPDVSHATVEDKLTGAIVRFSVARRNST 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 IPSLFRKWKQWREGLIEIRSWVVPGRWGNLVQLPDVSHATVEDKLTGAIVRFSVARRNST 300
Qy 301 TIFLDVCQDHKSRMANEAVADMASCMSSTFAFRSLLPDRIQGQYPAYDRELFGQVFRGPY 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 TIFLDVCQDHKSRMANEAVADMASCMSSTFAFRSLLPDRIQGQYPAYDRELFGQVFRGPY 360
Qy 361 SQDHCRLVVTEFRTFRTRPTHFDQTAIDRVSELIVMTAIHFGTMQFVYFDNNSRIPGLVA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 SQDHCRLVVTEFRTFRTRPTHFDQTAIDRVSELIVMTAIHFGTMQFVYFDNNSRIPGLVA 420
Qy 421 GNASGGGRWQRHVIDVLDKPIRDLRLEFNNEALASLQLSFEDGSSTPRLGNFSGSAEEKV 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GNASGGGRWQRHVIDVLDKPIRDLRLEFNNEALASLQLSFEDGSSTPRLGNFSGSAEEKV 480
Qy 481 TCTVPRGYRLSSWAFRADPAISVLRFQFTPEELRPSSRVRPQYTTPALHPIIN 533
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 TCTVPRGYRLSSWAFRADPAISVLRFQFTPEELRPSSRVRPQYTTPALHPIIN 533
DUPLICATES:
US-18-898-088-315
Filing date in PALM: 2024-09-26
Sequence 315, US/18898088
Publication No. US20250011808A1
GENERAL INFORMATION
APPLICANT: Pioneer Hi-Bred International, Inc (en)
TITLE OF INVENTION: Insecticidal Proteins From Plants And Methods For Their Use (en)
FILE REFERENCE: 76751-373463
CURRENT APPLICATION NUMBER: US/18/898,088
CURRENT FILING DATE: 2024-09-26
NUMBER OF SEQ ID NOS: 496
SEQ ID NO 315
LENGTH: 533
TYPE: PRT
FEATURE:
NAME/KEY: REGION
LOCATION: 1..533
QUALIFIERS: note = IPD113 chimeric protein
FEATURE:
NAME/KEY: source
LOCATION: 1..533
QUALIFIERS: mol_type = protein
organism = synthetic construct
RESULT 11
A0A0K9YUD2_9BACL
ID A0A0K9YUD2_9BACL Unreviewed; 429 AA.
AC A0A0K9YUD2;
DT 11-NOV-2015, integrated into UniProtKB/TrEMBL.
DT 11-NOV-2015, sequence version 1.
DT 08-OCT-2025, entry version 27.
DE RecName: Full=Pesticidal crystal protein domain-containing protein {ECO:0000259|Pfam:PF03945};
GN ORFNames=ADS79_10350 {ECO:0000313|EMBL:KNB72291.1}, BRE01_65700
GN {ECO:0000313|EMBL:GED72868.1};
OS Brevibacillus reuszeri.
OC Bacteria; Bacillati; Bacillota; Bacilli; Bacillales; Paenibacillaceae;
OC Brevibacillus.
OX NCBI_TaxID=54915 {ECO:0000313|EMBL:KNB72291.1, ECO:0000313|Proteomes:UP000036834};
RN [1] {ECO:0000313|Proteomes:UP000036834}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 9887 {ECO:0000313|Proteomes:UP000036834};
RA Liu B., Wang J., Zhu Y., Liu G., Chen Q., Chen Z., Lan J., Che J., Ge C.,
RA Shi H., Pan Z., Liu X.;
RT "Genome sequencing project for genomic taxonomy and phylogenomics of
RT Bacillus-like bacteria.";
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KNB72291.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=DSM 9887 {ECO:0000313|EMBL:KNB72291.1};
RA Tran T., Druce J.;
RT "MeaNS - Measles Nucleotide Surveillance Program.";
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:GED72868.1, ECO:0000313|Proteomes:UP000319578}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 15719 {ECO:0000313|EMBL:GED72868.1,
RC ECO:0000313|Proteomes:UP000319578};
RA Hosoyama A., Uohara A., Ohji S., Ichikawa N.;
RT "Whole genome shotgun sequence of Brevibacillus reuszeri NBRC 15719.";
RL Submitted (JUN-2019) to the EMBL/GenBank/DDBJ databases.
CC -!- SIMILARITY: Belongs to the delta endotoxin family.
CC {ECO:0000256|ARBA:ARBA00007819}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KNB72291.1}.
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; BJON01000036; GED72868.1; -; Genomic_DNA.
DR EMBL; LGIQ01000007; KNB72291.1; -; Genomic_DNA.
DR RefSeq; WP_049738340.1; NZ_BJON01000036.1.
DR AlphaFoldDB; A0A0K9YUD2; -.
DR PATRIC; fig|54915.3.peg.1007; -.
DR Proteomes; UP000036834; Unassembled WGS sequence.
DR Proteomes; UP000319578; Unassembled WGS sequence.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR GO; GO:0001907; P:symbiont-mediated killing of host cell; IEA:InterPro.
DR Gene3D; 1.20.190.10; Pesticidal crystal protein, N-terminal domain; 1.
DR InterPro; IPR005639; Pest_crys_dom_I.
DR InterPro; IPR036716; Pest_crys_N_sf.
DR Pfam; PF03945; Endotoxin_N; 1.
DR SUPFAM; SSF56849; delta-Endotoxin (insectocide), N-terminal domain; 1.
PE 3: Inferred from homology;
KW Reference proteome {ECO:0000313|Proteomes:UP000319578};
KW Sporulation {ECO:0000256|ARBA:ARBA00022969};
KW Toxin {ECO:0000256|ARBA:ARBA00022656};
KW Virulence {ECO:0000256|ARBA:ARBA00023026}.
FT DOMAIN 21..172
FT /note="Pesticidal crystal protein"
FT /evidence="ECO:0000259|Pfam:PF03945"
SQ SEQUENCE 429 AA; 48599 MW; BED8786155C46677 CRC64;
Query Match 17.7%; Score 491.5; Length 429;
Best Local Similarity 28.9%;
Matches 131; Conservative 80; Mismatches 195; Indels 47; Gaps 12;
Qy 74 MEAHDWHNRTRDVVLALISIIPTVGAIA SVVLGIFWPANKVDIWVALSLEEYVRNIVKQE 133
: | |:|| | : | || |||| | :| || :| ||: ::: |: :| |
Db 2 IHADTWNNRIRSISEAAAKKIPYVGAIVSFAIGQLWPTDKADIFSL--IKDQVKGLVDQA 59
Qy 134 IFEFEMRQHQSSIEALESTIRRYNTAALPEKGNFLSIWISQADALCIRLRNSTNDIHLLL 193
| : || : : || | |: :| | ||| |:: ::| : : :| ||| |||:
Db 60 ILDKEMEERKHEIEGLNDTMNQYVDAGNHEKGGFMTSMLTQLNIMHHKLTESTNSIHLIP 119
Qy 194 HIVTVSVLHMAAMHERLTFGEELYGTDNTANWTRDLVEVFQMYTSDLIPSLFRKWKQWRE 253
:|:: :|: : |||: |:|:| ||| | :|| : :| | : :: ||| |||
Db 120 LTITIANIHLTLLRERLSHGKEIYTEDNTTVWQKDLTKRYQDYHKFFL-EIYPKWKTWRE 178
Qy 254 GLIEIRSWVVPGRWGNLVQLPD----VSHATVEDKLTGAIVRFSVARRNSTTIFLDVCQD 309
|||: | | :| :| | : : | : | | ||:
Db 179 SKIEIK-WYTD---KNPTTVPPFFYWAAHGYANDTFVERKIHYRVDFNSIETTFQGVCEA 234
Qy 310 HKSRMANEAVADMASCMSSTFAFRSLLPDRIQGQYPAYDRELFGQVFRGPY--------S 361
| |:|:| :|: :::|| || | || :: ||| |
Db 235 IKESWMNDAIA KIAASIATTFTLHHYLPGR--EDEPAIVDPNLETIWMGPYSLSIFGNDS 292
Qy 362 QDHCRLVVTEFRTFRTRPTHFDQTAIDRVSELIVMTAIHFGTMQFVYFDNNSRIPGLVAG 421
: : ||: :| | | : : || :| |:: | |
Db 293 KVSYAVNVTD------QPGELKQVYIREYNSI--------DGMQLIYTDHS----GNFIG 334
Qy 422 NASGGGRWQRHVIDVLDKPIRDLRLEFNNEALASLQLSFEDGSSTPRLGNFSGSAEEKVT 481
| || | || : ::: |:: : |::: | ||||: ||| : |
Db 335 NPKGGEPHYLHATQ--DKYVAGMKMRFSSGIICSVEVIFSDGSSSGMLGNRKNWSGTDVD 392
Qy 482 CTVPRGYRLSSWAFR------ADPAISVLRFQF 508
| |:| |:: ||||: |
Db 393 AVVESNYKLVCGAYKTGSGPSGTTGISVLKLGF 425
RESULT 2
US-16-980-087-315
(NOTE: this sequence has 1 duplicate in the database searched.
See complete list at the end of this report)
Sequence 315, US/16980087
Patent No. 11525144
GENERAL INFORMATION
APPLICANT: PIONEER HI-BRED INTERNATIONAL, INC.
APPLICANT: Hexima Limited
APPLICANT: Liu, Lu
APPLICANT: Lum, Amy
APPLICANT: Ong, Azalea
APPLICANT: Schepers, Eric
APPLICANT: Urdanszky, Ingid
APPLICANT: Zhong, Xiaohong
TITLE OF INVENTION: INSECTICIDAL PROTEINS FROM PLANTS AND METHODS FOR THEIR USE
FILE REFERENCE: RTS21844-WO-PCT
CURRENT APPLICATION NUMBER: US/16/980,087
CURRENT FILING DATE: 2020-09-11
PRIOR APPLICATION NUMBER: US 62/642,642
PRIOR FILING DATE: 2018-03-14
NUMBER OF SEQ ID NOS: 496
SEQ ID NO 315
LENGTH: 533
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: IPD113 chimeric protein
Query Match 92.8%; Score 2577; Length 533;
Best Local Similarity 91.4%;
Matches 487; Conservative 25; Mismatches 21; Indels 0; Gaps 0;
Qy 1 MAAPGVKAEDVTASPAEPEENVHEVKLATTTDMEEGGGPLHGEKAGGVSSSHQHHEAGSL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAAPGVKAEDVTASPAEPEENVHEVKLATTTDMEEGGGPLHGEKAGGVSSSHQHHEAGSL 60
Qy 61 DDAIVEEFARNSQMEAHDWHNRTRDVVLALISIIPTVGAIA SVVLGIFWPANKVDIWVAL 120
|||||||||||||||||||||| | :| ||| :| ||| | ::|:|||:|||||| ||
Db 61 DDAIVEEFARNSQMEAHDWHNRIRGAILGLISAVPKVGAAISRLIGLFWPSNKVDIWEAL 120
Qy 121 SLEEYVRNIVKQEIFEFEMRQHQSSIEALESTIRRYNTAALPEKGNFLSIWISQADALCI 180
: |||:||||:||:|||||: |: |:|||:|: ||:|||| |||||||||||||||| |
Db 121 NAEEYIRNIVQQELFEFEMQLLQNDIQALETTVGRYDTAALTEKGNFLSIWISQADALYI 180
Qy 181 RLRNSTNDIHLLLHIVTVSVLHMAAMHERLTFGEELYGTDNTANWTRDLVEVFQMYTSDL 240
|:|||||:||||||:|||| ||:||:|||||||||||||:| ||||:|||: |: |||||
Db 181 RMRNSTNNIHLLLHMVTVSTLHLAALHERLTFGEELYGTNNAANWTQDLVDKFERYTSDL 240
Qy 241 IPSLFRKWKQWREGLIEIRSWVVPGRWGNLVQLPDVSHATVEDKLTGAIVRFSVARRNST 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 IPSLFRKWKQWREGLIEIRSWVVPGRWGNLVQLPDVSHATVEDKLTGAIVRFSVARRNST 300
Qy 301 TIFLDVCQDHKSRMANEAVADMASCMSSTFAFRSLLPDRIQGQYPAYDRELFGQVFRGPY 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 TIFLDVCQDHKSRMANEAVADMASCMSSTFAFRSLLPDRIQGQYPAYDRELFGQVFRGPY 360
Qy 361 SQDHCRLVVTEFRTFRTRPTHFDQTAIDRVSELIVMTAIHFGTMQFVYFDNNSRIPGLVA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 SQDHCRLVVTEFRTFRTRPTHFDQTAIDRVSELIVMTAIHFGTMQFVYFDNNSRIPGLVA 420
Qy 421 GNASGGGRWQRHVIDVLDKPIRDLRLEFNNEALASLQLSFEDGSSTPRLGNFSGSAEEKV 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GNASGGGRWQRHVIDVLDKPIRDLRLEFNNEALASLQLSFEDGSSTPRLGNFSGSAEEKV 480
Qy 481 TCTVPRGYRLSSWAFRADPAISVLRFQFTPEELRPSSRVRPQYTTPALHPIIN 533
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 TCTVPRGYRLSSWAFRADPAISVLRFQFTPEELRPSSRVRPQYTTPALHPIIN 533
Against Polynucleotides
RESULT 1
EL774105
LOCUS EL774105 656 bp mRNA linear EST 30-JUN-2009
DEFINITION CF_WO0_43e08_SP6 Copepod Whole Organism, Normalized Calanus
finmarchicus cDNA clone CF_WO0_43e08 5', mRNA sequence.
ACCESSION EL774105
VERSION EL774105.1
DBLINK BioSample: SAMN00152581
KEYWORDS EST.
SOURCE Calanus finmarchicus
ORGANISM Calanus finmarchicus
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea;
Multicrustacea; Hexanauplia; Copepoda; Calanoida; Calanidae;
Calanus.
REFERENCE 1 (bases 1 to 656)
AUTHORS Towle,D.W. and Smith,C.M.
TITLE Expressed sequence tags in a normalized cDNA library prepared from
whole organism C5 juvenile and adult copepod, Calanus finmarchicus
JOURNAL Unpublished
COMMENT Contact: Christine M. Smith
Marine DNA Sequencing and Analysis Facility
Mount Desert Island Biological Laboratory
Old Bar Harbor Road, Salsbury Cove, ME 04672, USA
Tel: 207-288-9880 x130
Fax: 207-288-2130
Email: cmsmith\@mdibl.org
Plate: 43 row: e column: 08
Seq primer: SP6
High quality sequence stop: 655.
FEATURES Location/Qualifiers
source 1..656
/organism="Calanus finmarchicus"
/mol_type="mRNA"
/db_xref="taxon:6837"
/clone="CF_WO0_43e08"
/clone_lib="SAMN00152581 Copepod Whole Organism,
Normalized"
/dev_stage="C5 juveniles and adults"
/note="Vector: pCMV Sport 6.1; Total RNA was extracted
from whole organisms, checked for quality, then prepared
for construction and normalization of the cDNA library by
Invitrogen. Plasmids were isolated and inserts
end-sequenced by the Marine DNA Sequencing and Analysis
Facility at the Center for Marine Functional Genomic
Studies, Mount Desert Island Biological Laboratory (J.N.
Forrest, Jr., Director). Traces were processed for
submission to dbEST by trace2dbest software (Parkinson,
Anthony and Blaxter, unpublished software). The project
was supported by NIH Grant Number P20-RR-16463 from the
INBRE Program of the National Center for Research
Resources (P.H. Hand, PI)."
ORIGIN
Alignment Scores:
Length: 656
Score: 244.00 Matches: 52
Percent Similarity: 52.9% Conservative: 47
Best Local Similarity: 27.8% Mismatches: 82
Query Match: 8.8% Indels: 6
Gaps: 4
US-18-898-088-52 (1-533) x EL774105 (1-656)
Qy 73 GlnMetGluAlaHisAspTrpHisAsnArgThrArgAspValValLeuAlaLeuIleSer 92
|||::: ::: ||| ::: ::: |||
Db 88 CAAATATCCAGTGCACAATGGAAGATGATAATCAATGCAGCAATAACCGAGATCTTCTCT 147
Qy 93 IleIle------ProThrValGlyAlaIleAlaSerValValLeuGlyIlePheTrpPro 110
::: ||| |||||| :::::::::::: |||||||||
Db 148 GCTGTCGGGGAGCCAGTTGTGGGCAAATGGGTGAATATGTTGATGAATTTCTTTTGGCCA 207
Qy 111 Ala---AsnLysValAspIleTrpValAlaLeuSerLeuGluGluTyrValArgAsnIle 129
::: ||| |||:::::: ::: ::: ::: :::
Db 208 TCTCCAGGCAAGCCAGATGTTTTTGAGACCATCAGGGCCCAG------ATTGAAGAATTA 261
Qy 130 ValLysGlnGluIlePheGluPheGluMetArgGlnHisGlnSerSerIleGluAlaLeu 149
||| :::|||||||||||||||:::::: ||| ||| |||
Db 262 GTGGACACTAAGATATTTGAATTTGAGCTTAAGTTGTTGCAAGGTGACATCAATGGACTT 321
Qy 150 GluSerThrIleArgArgTyrAsnThrAlaAlaLeuProGluLysGlyAsnPheLeuSer 169
::: ::::::::: ||| ||| ||| ||||||||| |||
Db 322 CAGCAATCAATGCAAATGTACAAAGATGCGAAATTGCATGAAAAAGGAGTTCTGCTTGGG 381
Qy 170 IleTrpIleSerGlnAlaAspAlaLeuCysIleArgLeuArgAsnSerThrAsnAspIle 189
::::::|||:::::: ::: ::::::||| ||| :::
Db 382 GCTGTTCTGACACAATCCAATGGTGTTTTTTCCAAGATAAGGATAAGTGACCACAGACGT 441
Qy 190 HisLeuLeuLeuHisIleValThrValSerValLeuHisMetAlaAlaMetHisGluArg 209
||||||::: :::||||||::: :::::: ::: ::: ||||||
Db 442 CACCTGGTTCCAGTTATGGTAACTTTGGGAATGATTCAACTGACCATGCTGAAGGAGAGA 501
Qy 210 LeuThrPheGlyGluGluLeuTyrGlyThrAspAsnThrAlaAsnTrpThrArgAspLeu 229
|||||||||::::::|||||| |||||| ||| ::::::|||
Db 502 TCGACATTTGGAAAAGACCTCTATGATGAAGATAACCAGAAACAATGGGACAAAGAGTTG 561
Qy 230 ValGluValPheGlnMetTyrThrSerAspLeuIleProSerLeuPheArgLysTrpLys 249
::::::||| ||| :::::: :::||||||
Db 562 AAAAGAGAAGTTGAACTCTATGAAAGAACCTTG---AAGCAGATGTACCTTGAGTGGAAA 618
Qy 250 GlnTrpArgGluGlyLeuIle 256
|||||| |||
Db 619 GTCTGGAGAAACGACAAGATA 639
Against instant SEQ ID NO: 53
Against Polypeptides
RESULT 11
A0A0K9YUD2_9BACL
ID A0A0K9YUD2_9BACL Unreviewed; 429 AA.
AC A0A0K9YUD2;
DT 11-NOV-2015, integrated into UniProtKB/TrEMBL.
DT 11-NOV-2015, sequence version 1.
DT 08-OCT-2025, entry version 27.
DE RecName: Full=Pesticidal crystal protein domain-containing protein {ECO:0000259|Pfam:PF03945};
GN ORFNames=ADS79_10350 {ECO:0000313|EMBL:KNB72291.1}, BRE01_65700
GN {ECO:0000313|EMBL:GED72868.1};
OS Brevibacillus reuszeri.
OC Bacteria; Bacillati; Bacillota; Bacilli; Bacillales; Paenibacillaceae;
OC Brevibacillus.
OX NCBI_TaxID=54915 {ECO:0000313|EMBL:KNB72291.1, ECO:0000313|Proteomes:UP000036834};
RN [1] {ECO:0000313|Proteomes:UP000036834}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 9887 {ECO:0000313|Proteomes:UP000036834};
RA Liu B., Wang J., Zhu Y., Liu G., Chen Q., Chen Z., Lan J., Che J., Ge C.,
RA Shi H., Pan Z., Liu X.;
RT "Genome sequencing project for genomic taxonomy and phylogenomics of
RT Bacillus-like bacteria.";
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KNB72291.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=DSM 9887 {ECO:0000313|EMBL:KNB72291.1};
RA Tran T., Druce J.;
RT "MeaNS - Measles Nucleotide Surveillance Program.";
RL Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:GED72868.1, ECO:0000313|Proteomes:UP000319578}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NBRC 15719 {ECO:0000313|EMBL:GED72868.1,
RC ECO:0000313|Proteomes:UP000319578};
RA Hosoyama A., Uohara A., Ohji S., Ichikawa N.;
RT "Whole genome shotgun sequence of Brevibacillus reuszeri NBRC 15719.";
RL Submitted (JUN-2019) to the EMBL/GenBank/DDBJ databases.
CC -!- SIMILARITY: Belongs to the delta endotoxin family.
CC {ECO:0000256|ARBA:ARBA00007819}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KNB72291.1}.
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; BJON01000036; GED72868.1; -; Genomic_DNA.
DR EMBL; LGIQ01000007; KNB72291.1; -; Genomic_DNA.
DR RefSeq; WP_049738340.1; NZ_BJON01000036.1.
DR AlphaFoldDB; A0A0K9YUD2; -.
DR PATRIC; fig|54915.3.peg.1007; -.
DR Proteomes; UP000036834; Unassembled WGS sequence.
DR Proteomes; UP000319578; Unassembled WGS sequence.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR GO; GO:0001907; P:symbiont-mediated killing of host cell; IEA:InterPro.
DR Gene3D; 1.20.190.10; Pesticidal crystal protein, N-terminal domain; 1.
DR InterPro; IPR005639; Pest_crys_dom_I.
DR InterPro; IPR036716; Pest_crys_N_sf.
DR Pfam; PF03945; Endotoxin_N; 1.
DR SUPFAM; SSF56849; delta-Endotoxin (insectocide), N-terminal domain; 1.
PE 3: Inferred from homology;
KW Reference proteome {ECO:0000313|Proteomes:UP000319578};
KW Sporulation {ECO:0000256|ARBA:ARBA00022969};
KW Toxin {ECO:0000256|ARBA:ARBA00022656};
KW Virulence {ECO:0000256|ARBA:ARBA00023026}.
FT DOMAIN 21..172
FT /note="Pesticidal crystal protein"
FT /evidence="ECO:0000259|Pfam:PF03945"
SQ SEQUENCE 429 AA; 48599 MW; BED8786155C46677 CRC64;
Query Match 16.9%; Score 353; Length 429;
Best Local Similarity 23.3%;
Matches 101; Conservative 66; Mismatches 137; Indels 130; Gaps 9;
Qy 78 VDAHDWHNRLRGAVLGLLSDLPLGGAI-STLVGLFWPATRVNIWEALGMEAYVTNIVRKE 136
: | |:||:| :| ||| | :| || : :|: : : | :| :
Db 2 IHADTWNNRIRSISEAAAKKIPYVGAIVSFAIGQLWPTDKADIFSLI--KDQVKGLVDQA 59
Qy 137 IFEFEMRQHESDIEALERSILRYERGLLTEKATALGIWIAQADALSIRLGNSTNRIHLLL 196
| : || : : :|| | :: :| || : : | : : :| ||| |||:
Db 60 ILDKEMEERKHEIEGLNDTMNQYVDAGNHEKGGFMTSMLTQLNIMHHKLTESTNSIHLIP 119
Qy 197 HIVTVAVLHMAALHERLTFGEEIYGANNTANWTKELEETFQRY----------------- 239
:|:| :|: | |||: |:||| :|| | |:| : :| |
Db 120 LTITIANIHLTLLRERLSHGKEIYTEDNTTVWQKDLTKRYQDYHKFFLEIYPKWKTWRES 179
Qy 240 ------TSDRIPV----------------------------------------------- 246
:|: |
Db 180 KIEIKWYTDKNPTTVPPFFYWAAHGYANDTFVERKIHYRVDFNSIETTFQGVCEAIKESW 239
Qy 247 -----------ILKTFRMH---PTRSD-----------IMLGTRVL-------------- 267
| || :| | | | | :| |
Db 240 MNDAIA KIAASIATTFTLHHYLPGREDEPAIVDPNLETIWMGPYSLSIFGNDSKVSYAVN 299
Qy 268 ---------QVNVRAGTLLESIQFVYYHPSSPNGIPNWGNIAGNPRGGE-SFVVDVRTRH 317
|| :| :: :| :| | || |||:||| :: : ::
Db 300 VTDQPGELKQVYIREYNSIDGMQLIYTDHS--------GNFIGNPKGGEPHYLHATQDKY 351
Qy 318 IQDLRLEFSRDVLVSLQIRFEDGTSTQKFGNATGWATSAVTCTAPSGYTLNSWDFREDPG 377
: ::: || :: |::: | ||:|: || |: : | | | | :: |
Db 352 VAGMKMRFSSGIICSVEVIFSDGSSSGMLGNRKNWSGTDVDAVVESNYKLVCGAYKTGSG 411
Qy 378 PNGTTAISVAGYGF 391
|:||| ||| ||
Db 412 PSGTTGISVLKLGF 425
RESULT 2
US-16-980-087-31
(NOTE: this sequence has 1 duplicate in the database searched.
See complete list at the end of this report)
Sequence 31, US/16980087
Patent No. 11525144
GENERAL INFORMATION
APPLICANT: PIONEER HI-BRED INTERNATIONAL, INC.
APPLICANT: Hexima Limited
APPLICANT: Liu, Lu
APPLICANT: Lum, Amy
APPLICANT: Ong, Azalea
APPLICANT: Schepers, Eric
APPLICANT: Urdanszky, Ingid
APPLICANT: Zhong, Xiaohong
TITLE OF INVENTION: INSECTICIDAL PROTEINS FROM PLANTS AND METHODS FOR THEIR USE
FILE REFERENCE: RTS21844-WO-PCT
CURRENT APPLICATION NUMBER: US/16/980,087
CURRENT FILING DATE: 2020-09-11
PRIOR APPLICATION NUMBER: US 62/642,642
PRIOR FILING DATE: 2018-03-14
NUMBER OF SEQ ID NOS: 496
SEQ ID NO 31
LENGTH: 527
TYPE: PRT
ORGANISM: Blechnum medium
Query Match 96.5%; Score 2012; Length 527;
Best Local Similarity 76.1%;
Matches 401; Conservative 0; Mismatches 0; Indels 126; Gaps 1;
Qy 1 MAALDHTKDSEIIAGRAVATDHDPATVVSEEDSETKIAEVACDPATAGDPAGEVHELDKL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MAALDHTKDSEIIAGRAVATDHDPATVVSEEDSETKIAEVACDPATAGDPAGEVHELDKL 60
Qy 61 ALECGSDGIDLLAKRMQVDAHDWHNRLRGAVLGLLSDLPLGGAISTLVGLFWPATRVNIW 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ALECGSDGIDLLAKRMQVDAHDWHNRLRGAVLGLLSDLPLGGAISTLVGLFWPATRVNIW 120
Qy 121 EALGMEAYVTNIVRKEIFEFEMRQHESDIEALERSILRYERGLLTEKATALGIWIAQADA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 EALGMEAYVTNIVRKEIFEFEMRQHESDIEALERSILRYERGLLTEKATALGIWIAQADA 180
Qy 181 LSIRLGNSTNRIHLLLHIVTVAVLHMAALHERLTFGEEIYGANNTANWTKELEETFQRYT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LSIRLGNSTNRIHLLLHIVTVAVLHMAALHERLTFGEEIYGANNTANWTKELEETFQRYT 240
Qy 241 SDRIPVI----------------------------------------------------- 247
|||||||
Db 241 SDRIPVIFKEWRPWRESQIEIRAWRRRASGMVIFNPDASFATVEDKISGAIFNFSVNYHY 300
Qy 248 ------------------------------------------------------------ 247
Db 301 SMSIFSDICEAHKARMMNEANADMASCMSPTFAFHKLLPGDSQSKFSPYDRQLFGQVFRG 360
Qy 248 -------------LKTFRMHPTRSDIMLGTRVLQVNVRAGTLLESIQFVYYHPSSPNGIP 294
|||||||||||||||||||||||||||||||||||||||||||||||
Db 361 PFSQDLLQPRFTSLKTFRMHPTRSDIMLGTRVLQVNVRAGTLLESIQFVYYHPSSPNGIP 420
Qy 295 NWGNIAGNPRGGESFVVDVRTRHIQDLRLEFSRDVLVSLQIRFEDGTSTQKFGNATGWAT 354
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 NWGNIAGNPRGGESFVVDVRTRHIQDLRLEFSRDVLVSLQIRFEDGTSTQKFGNATGWAT 480
Qy 355 SAVTCTAPSGYTLNSWDFREDPGPNGTTAISVAGYGFTPDDIRLPPA 401
|||||||||||||||||||||||||||||||||||||||||||||||
Db 481 SAVTCTAPSGYTLNSWDFREDPGPNGTTAISVAGYGFTPDDIRLPPA 527
Against Polynucleotides
RESULT 1
EL774105
LOCUS EL774105 656 bp mRNA linear EST 30-JUN-2009
DEFINITION CF_WO0_43e08_SP6 Copepod Whole Organism, Normalized Calanus
finmarchicus cDNA clone CF_WO0_43e08 5', mRNA sequence.
ACCESSION EL774105
VERSION EL774105.1
DBLINK BioSample: SAMN00152581
KEYWORDS EST.
SOURCE Calanus finmarchicus
ORGANISM Calanus finmarchicus
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Crustacea;
Multicrustacea; Hexanauplia; Copepoda; Calanoida; Calanidae;
Calanus.
REFERENCE 1 (bases 1 to 656)
AUTHORS Towle,D.W. and Smith,C.M.
TITLE Expressed sequence tags in a normalized cDNA library prepared from
whole organism C5 juvenile and adult copepod, Calanus finmarchicus
JOURNAL Unpublished
COMMENT Contact: Christine M. Smith
Marine DNA Sequencing and Analysis Facility
Mount Desert Island Biological Laboratory
Old Bar Harbor Road, Salsbury Cove, ME 04672, USA
Tel: 207-288-9880 x130
Fax: 207-288-2130
Email: cmsmith\@mdibl.org
Plate: 43 row: e column: 08
Seq primer: SP6
High quality sequence stop: 655.
FEATURES Location/Qualifiers
source 1..656
/organism="Calanus finmarchicus"
/mol_type="mRNA"
/db_xref="taxon:6837"
/clone="CF_WO0_43e08"
/clone_lib="SAMN00152581 Copepod Whole Organism,
Normalized"
/dev_stage="C5 juveniles and adults"
/note="Vector: pCMV Sport 6.1; Total RNA was extracted
from whole organisms, checked for quality, then prepared
for construction and normalization of the cDNA library by
Invitrogen. Plasmids were isolated and inserts
end-sequenced by the Marine DNA Sequencing and Analysis
Facility at the Center for Marine Functional Genomic
Studies, Mount Desert Island Biological Laboratory (J.N.
Forrest, Jr., Director). Traces were processed for
submission to dbEST by trace2dbest software (Parkinson,
Anthony and Blaxter, unpublished software). The project
was supported by NIH Grant Number P20-RR-16463 from the
INBRE Program of the National Center for Research
Resources (P.H. Hand, PI)."
ORIGIN
Alignment Scores:
Length: 656
Score: 216.00 Matches: 47
Percent Similarity: 55.1% Conservative: 45
Best Local Similarity: 28.1% Mismatches: 69
Query Match: 10.4% Indels: 6
Gaps: 3
US-18-898-088-53 (1-401) x EL774105 (1-656)
Qy 77 GlnValAspAlaHisAspTrpHisAsnArgLeuArgGlyAlaValLeuGlyLeuLeuSer 96
|||::: ::: ||| ::: |||::: ::: |||
Db 88 CAAATATCCAGTGCACAATGGAAGATGATAATCAATGCAGCAATAACCGAGATCTTCTCT 147
Qy 97 ---------AspLeuProLeuGlyGlyAlaIleSerThrLeuValGlyLeuPheTrpPro 113
::: :::||| :::::: |||::: |||||||||
Db 148 GCTGTCGGGGAGCCAGTTGTGGGCAAATGGGTGAATATGTTGATGAATTTCTTTTGGCCA 207
Qy 114 AlaThr---ArgValAsnIleTrpGluAlaLeuGlyMetGluAlaTyrValThrAsnIle 132
::: ::: :::::::::||| ::: ||| ::: :::
Db 208 TCTCCAGGCAAGCCAGATGTTTTTGAGACCATC------AGGGCCCAGATTGAAGAATTA 261
Qy 133 ValArgLysGluIlePheGluPheGluMetArgGlnHisGluSerAspIleGluAlaLeu 152
||| :::|||||||||||||||:::::: ::: |||||| |||
Db 262 GTGGACACTAAGATATTTGAATTTGAGCTTAAGTTGTTGCAAGGTGACATCAATGGACTT 321
Qy 153 GluArgSerIleLeuArgTyrGluArgGlyLeuLeuThrGluLysAlaThrAlaLeuGly 172
::::::|||::: |||::: ||| |||||| ||||||
Db 322 CAGCAATCAATGCAAATGTACAAAGATGCGAAATTGCATGAAAAAGGAGTTCTGCTTGGG 381
Qy 173 IleTrpIleAlaGlnAlaAspAlaLeuSerIleArgLeuGlyAsnSerThrAsnArgIle 192
::: |||:::::: ::: :::::: ||| :::|||
Db 382 GCTGTTCTGACACAATCCAATGGTGTTTTTTCCAAGATAAGGATAAGTGACCACAGACGT 441
Qy 193 HisLeuLeuLeuHisIleValThrValAlaValLeuHisMetAlaAlaLeuHisGluArg 212
||||||::: :::||||||::: :::::: ::: ||| ||||||
Db 442 CACCTGGTTCCAGTTATGGTAACTTTGGGAATGATTCAACTGACCATGCTGAAGGAGAGA 501
Qy 213 LeuThrPheGlyGluGluIleTyrGlyAlaAsnAsnThrAlaAsnTrpThrLysGluLeu 232
|||||||||:::::::::||| :::||| ||| |||||||||
Db 502 TCGACATTTGGAAAAGACCTCTATGATGAAGATAACCAGAAACAATGGGACAAAGAGTTG 561
Qy 233 GluGluThrPheGlnArgTyr 239
::: ::: |||
Db 562 AAAAGAGAAGTTGAACTCTAT 582
Conclusion
No claim is allowed.
Contact information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to WAYNE ZHONG whose telephone number is (571)270-0311. The examiner can normally be reached 8:30am to 5:00pm EST.
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.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic, can be reached on 571-270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Wayne Zhong/
Primary Examiner, Art Unit 1662
Prosecution Insights