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 .
DETAILED ACTION
This application is a 371 of PCT/IB2022/058118.
The amendment filed on April 6, 2026 has been entered.
Election/Restrictions
Applicant's election with traverse of Group I with a species election of the T7 RNA polymerase mutant consisting of the amino acid sequence of SEQ ID NO:26 (mutant having the amino acid sequence of SEQ ID NO:1 except having N15A, I20N, Q655N, D659E, and K779A substitutions according to page 78 of the specification) in the reply filed on April 6, 2026 is acknowledged. The traversal is on the ground(s) that the amended claims have unity of invention because the technical feature is not taught by US 2019/0002850. US 2019/0002850 no longer discloses the technical feature of the amended claims. However, A0A2P1CL25 (UniProtKB/TrEMBL Database. January 16, 2019 - form PTO-892) discloses a T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 or 2 of the instant application having an Val residue at the position corresponding to I20 of SEQ ID NO:1 of the instant application and Rabideau (WO 2019/036682 - form PTO-1449) discloses a T7 RNA polymerase mutant having at least 90% sequence identity to SEQ ID NO:1 or 2 of the instant application and having A264L and A268L amino acid substitutions, the rejections under 35 USC 102 below. Therefore, the technical feature linking the inventions of Groups I-III and species does not constitute a special technical feature as defined by PCT Rule 13.2, as it does not define a contribution over the prior art.
Claims 12-13, 16-17, 19-21, and 25-26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species (claims 12-13 and 16-17) and invention (claims 19-21 and 25-26), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on April 6, 2026.
Applicant’s request for rejoinder has been noted.
The elected species, T7 RNA polymerase mutant consisting of the amino acid sequence of SEQ ID NO:26 is free of the prior art. Therefore, search and examination has been extended to a subsequent species, a T7 RNA polymerase mutant having at least 90% sequence identity to SEQ ID NO:1 and having an I20X, A264X and/or A268X amino acid substitutions, see the rejections under 35 USC 102 below. Therefore, search and examination has not been extended to other subsequent species.
Status of Claims
Claims 1-4, 6, 8-9, 11-13, 15-17, 19-22, and 25-26 are pending.
Claims 12-13, 16-17, 19-21, and 25-26 are withdrawn.
Claims 1-4, 6, 8-9, 11, 15, and 22 are under examination.
Claim for Domestic Priority
Applicants' claim for domestic priority under 35 USC 119(e) to US provisional application 63/395,070 filed 08/04/2022 and 63/239,458 filed 09/01/2021 is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on February 20, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 and 15 and claims 2-4, 6, 8-9, 11, and 22 depending therefrom are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1 and 15 recite the limitation T7 RNA polymerase “comprising at least 90% identity to SEQ ID NO:1”. The metes and bounds of the limitation in the context of the above claims are not clear. It is unclear what property of SEQ ID NO:1 the claimed T7 RNA polymerase has at least 90% identity to. Clarification is requested.
This rejection maybe overcome by amending the claims to recite “T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:”, for example.
Claims 8 and claims 9 and 11 depending therefrom are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 8 recites the limitation “D660 in SEQ ID NO:1, optionally… D659..”. The metes and bounds of the limitation in the context of the above claims are not clear. The amino acid sequence of SEQ ID NO:1 does not have an Asp residue at position 660. Therefore, it is unclear if the claimed T7 RNA polymerase has an amino acid substitution at T660 or D659. Clarification is requested.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 15 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 15 recites “T7 RNA polymerase of claim 1, comprising at least 90% identity to SEQ ID NO:1”. However, claim 1 stipulates that the T7 RNA polymerase has at least 90% identity to SEQ ID NO:1. Therefore, claim 15 fails to further limit claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-4, 15, and 22 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Rabideau (WO 2019/036682 - form PTO-1449).
Rabideau discloses a T7 RNA polymerase having the amino acid sequence of SEQ ID NO:1 (Table 1 at page 74). The T7 RNA polymerase of Rabideau has 100% sequence identity to amino acids 8-889 of the T7 RNA polymerase of SEQ ID NO:1 (amino acids 1-7 consists of M + HisTag) of the instant application (see the sequence alignment below).
Regarding claims 1 and 15, Rabideau discloses a T7 RNA polymerase mutant of SEQ ID NO:1, wherein the mutant has A258 and/or A262 amino acid substitutions, corresponding to A264 and A268 of SEQ ID NO:1 of the instant application (1st full paragraph at page 5, claims 9-10, and see the sequence alignment below). The T7 RNA polymerase mutant of Rabideua has at least 90% sequence identity to SEQ ID NO:1 of the instant application.
Regarding claim 2, the T7 RNA polymerase mutant of Rabideau has A258 L and/or A262L amino acid substitutions, corresponding to A264L and A268L of SEQ ID NO:1 of the instant application (1st full paragraph at page 5, claims 9-10, and see the sequence alignment below).
Regarding claims 3-4, even though the amino acid substitutions A258F/V and A262C (corresponding to A264F/V and A268C of SEQ ID NO:1 of the instant application) are not explicitly named in Rabideau, anticipation is found since substitution with 19 other amino acid at a given amino acid position is sufficiently limited or well delineated. Ex parte A, 17 USPQ2d 1716 (Bd. Pat. App. & Inter. 1990). Since one of ordinary skill in the art is able to “at once envisage” the specific A258F/V and A262C substitutions within the generic chemical formula of A258X and A262X, the T7 RNA polymerase mutant of the instant application is anticipated.
Regarding claim 22, Rabideau discloses a composition comprising T7 RNA polymerase mutants (page 64).
Therefore, the reference of Rabideau anticipates claims 1-4, 15, and 22
Claim(s) 1-2 and 15 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by A0A2P1CL25 (UniProtKB/TrEMBL Database. January 16, 2019 - form PTO-892).
MPEP 2113 states that “The patentability of a product does not depend on its method of production.”. In the instant case, the structure of the claimed T7 RNA polymerase mutant implied is the same whether the T7 RNA polymerase is obtained from recombinant engineering or is obtained from any source (including wild type proteins), as long as the resulting product has the structural limitations recited in the claims (T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 and not having an Ile residue at the position corresponding to I20 of SEQ ID NO:1).
Regarding clams 1-2 and 15, A0A2P1CL25 discloses an Escherichia phage Ebrios T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 of the instant application and having a Val residue at the position corresponding to I20 of SEQ ID NO:1 of the instant application (see pages 1-2 and see the sequence alignment below).
Therefore, the reference of A0A2P1CL25 anticipates claims 1-2 and 15.
Claim Rejections - 35 USC § 103
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.
Claims 1-2, 15, and 22 are rejected under 35 U.S.C. 103 as being unpatentable over A0A2P1CL25 (UniProtKB/TrEMBL Database. January 16, 2019 - form PTO-892) and Rabideau (WO 2019/036682 - form PTO-1449).
MPEP 2113 states that “The patentability of a product does not depend on its method of production.”. In the instant case, the structure of the claimed T7 RNA polymerase mutant implied is the same whether the T7 RNA polymerase is obtained from recombinant engineering or is obtained from any source (including wild type proteins), as long as the resulting product has the structural limitations recited in the claims (T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 and not having an Ile residue at the position corresponding to 20 of SEQ ID NO:1).
Regarding clams 1-2 and 15, A0A2P1CL25 discloses an Escherichia phage Ebrios T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 of the instant application and having a Val residue at the position corresponding to I20 of SEQ ID NO:1 of the instant application (see pages 1-2 and see the sequence alignment below).
A0A2P1CL25 does not disclose a composition comprising the T7 RNA polymerase.
Regarding claim 22, Rabideau discloses a composition comprising T7 RNA polymerase mutants for use in in vitro transcription (page 64).
Therefore, combining the teachings of A0A2P1CL25 and Rabideau, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to make a composition comprising the T7 RNA polymerase of A0A2P1CL25. One of ordinary skill in the art would have been motivated to do so in order to use the T7 RNA polymerase of A0A2P1CL25 in in vitro transcription. One of ordinary skill in the art would have had a reasonable expectation of success since A0A2P1CL25 discloses a T7 RNA polymerase. and Rabideau teaches a composition comprising T7 RNA polymerase.
Therefore, the above references render claims 1-2, 15, and 22 prima facie obvious.
Claim Rejections - 35 USC § 101
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.
Claims 1-2, 15, and 22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim interpretation
MPEP 2113 states that “The patentability of a product does not depend on its method of production.”. In the instant case, the structure of the claimed T7 RNA polymerase mutant implied is the same whether the T7 RNA polymerase is obtained from recombinant engineering or is obtained from any source (including wild type proteins), as long as the resulting product has the structural limitations recited in the claims (T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 and not having an Ile residue at the position corresponding to I20 of SEQ ID NO:1).
Regarding clams 1-2 and 15, A0A2P1CL25 (UniProtKB/TrEMBL Database. January 16, 2019 - form PTO-892) discloses an Escherichia phage Ebrios T7 RNA polymerase having at least 90% sequence identity to SEQ ID NO:1 of the instant application and having a Val residue at the position corresponding to I20 of SEQ ID NO:1 of the instant application (see pages 1-2 and see the sequence alignment below).
Therefore, claims 1-2 and 15 are directed to a product of nature and claim 22 is directed to a generic composition comprising said product of nature.
Step 1: This part of the eligibility analysis evaluates whether the claim falls within any statutory category (see MPEP 2106.03). Since the claims are directed to a T7 RNA polymerase mutants, the claims are directed to a composition of matter, which is one of the statutory categories of invention. (Step 1: YES)
Step 2A Prong 1: This part of the eligibility analysis evaluates whether the claim recites a judicial exception (see MPEP 2106.04). The claimed T7 RNA polymerase mutant and the composition comprising the T7 RNA polymerase mutant are not considered to have markedly different characteristics from what occurs in nature, Escherichia phage Ebrios T7 RNA polymerase, as discussed above, and is considered to be a law of nature exception. Regarding claim 22, there is no indication in the specification that placing the T7 RNA polymerase mutant in a generic composition results in the T7 RNA polymerase mutant having any characteristics (structural, functional, or otherwise) that are different from the naturally occurring Escherichia phage Ebrios T7 RNA polymerase. Because there is no difference in characteristics (structural, functional, or otherwise) between the claimed T7 RNA polymerase mutant and the naturally occurring Escherichia phage Ebrios T7 RNA polymerase, the claimed T7 RNA polymerase mutant and a composition comprising said T7 RNA polymerase mutant are directed to a judicial exception.
Step 2A Prong 2: This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application (see MPEP 2106.04(d)). This evaluation is performed by (a) identifying whether there are any additional recited elements in the claim beyond the judicial exception and (b) evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. Regarding claims 1-2 and 15, there are no additional elements recited in the claim beyond the judicial exception. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claimed T7 RNA polymerase mutant is found naturally occurring in nature (Escherichia phage Ebrios T7 RNA polymerase). Regarding claim 22, the claim recites a generic composition comprising the naturally occurring T7 RNA polymerase but does not recite any components of the composition other than the T7 RNA polymerase (Step2 A: YES)
Step 2B: This part of the eligibility analysis evaluates whether the claim as a whole amounts to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim (see MPEP § 2106.05). The claims only recite the laws of nature and do not include any additional elements that could add significantly more to the judicial exceptions. (Step 2B: NO)
As such, the claims do not qualify as eligible subject matter.
Other Relevant Art
Miller (US 2019/036682 - form PTO-1449) discloses a T7 RNA polymerase comprising the amino acid sequence of SEQ ID NO:4, which has at least 90% sequence identity to SEQ ID NO:1 of the instant application ([0007] and see the sequence alignment below). Miller discloses a T7 RNA polymerase mutant of SEQ ID NO:4 having several amino acid substitutions, including Q656W amino acid substitution (Table 5.3). Q656 of the T7 RNA polymerase of Miller corresponds to Q655 of SEQ ID NO:1 of the instant application. However, Miller does not teach or suggest T7 RNA polymerase mutants having at least 90% sequence identity to SEQ ID NO:1 of the instant application and comprising one or more amino acid substitutions recited in claim 1.
Duplicate Claims, Warning
Applicant is advised that should claim 1 be found allowable, claim 15 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Conclusion
Claims 1-4, 6, 8-9, 11-13, 15-17, 19-22, and 25-26 are pending.
Claims 12-13, 16-17, 19-21, and 25-26 are withdrawn.
Claims 1-4, 6, 8-9, 11, 15, and 22 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
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, Robert Mondesi can be reached on 408-918-7584. 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.
/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment between the T7 RNA polymerase of SEQ ID NO:1 of the instant application (“Qy”) and the T7 RNA polymerase of SEQ ID NO:1 of Rabideau (“Db”)
BGC20033
ID BGC20033 standard; protein; 883 AA.
XX
AC BGC20033;
XX
DT 04-APR-2019 (first entry)
XX
DE Enterobacteria phage T7 RNA polymerase, SEQ:1.
XX
KW RNA polymerase; enzyme engineering; transcription.
XX
OS Enterobacteria phage T7.
XX
CC PN WO2019036682-A1.
XX
CC PD 21-FEB-2019.
XX
CC PF 17-AUG-2018; 2018WO-US046989.
XX
PR 18-AUG-2017; 2017US-0547677P.
PR 09-FEB-2018; 2018US-0628484P.
PR 05-MAR-2018; 2018US-0638684P.
PR 29-MAY-2018; 2018US-0677527P.
XX
CC PA (MODE-) MODERNATX INC.
XX
CC PI Rabideau AE, Dousis A, Ravichandran K, Hobert E;
XX
DR WPI; 2019-179436/19.
XX
CC PT Ribonucleic acid polymerase variant comprises amino acid substitution,
CC PT relative to wild-type RNA polymerase that causes loop structure of RNA
CC PT polymerase variant to undergo conformational change to helix structure.
XX
CC PS Claim 9; SEQ ID NO 1; 252pp; English.
XX
CC The present invention relates to a T7 ribonucleic acid polymerase variant
CC useful for increasing the transcription efficiency during an in vitro
CC transcription reaction. The invention further discloses: (1) a method for
CC producing a ribonucleic acid (RNA); (2) a method for performing an in
CC vitro transcription (IVT) reaction; (3) a nucleic acid encoding the RNA
CC polymerase variant; (4) a vector comprising the nucleic acid; (5) a host
CC cell comprising the nucleic acid or the vector; (6) a composition or a
CC kit comprising the RNA polymerase variant; (7) a co-transcriptional
CC capping method for ribonucleic acid (RNA) synthesis; and (8) a
CC composition comprising an in vitro-transcribed (IVT) RNA. The present
CC sequence is an Enterobacteria phage T7 RNA polymerase, a mutant of which
CC is useful in the method of the invention for increasing the transcription
CC efficiency during an in vitro transcription reaction.
XX
SQ Sequence 883 AA;
Query Match 98.9%; Score 4616; Length 883;
Best Local Similarity 100.0%;
Matches 882; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 8 NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKA 67
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2 NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKA 61
Qy 68 GEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT 127
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 62 GEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT 121
Qy 128 TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKA 187
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 122 TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKA 181
Qy 188 FMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDS 247
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 182 FMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDS 241
Qy 248 ETIELAPEYAEAIA TRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS 307
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 ETIELAPEYAEAIA TRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS 301
Qy 308 KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP 367
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP 361
Qy 368 MKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMD 427
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 362 MKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMD 421
Qy 428 WRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF 487
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 422 WRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF 481
Qy 488 IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCS 547
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 482 IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCS 541
Qy 548 GIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN 607
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 542 GIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN 601
Qy 608 TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDS 667
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 602 TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDS 661
Qy 668 GKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK 727
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 662 GKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK 721
Qy 728 RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPN 787
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 722 RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPN 781
Qy 788 FVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV 847
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 782 FVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV 841
Qy 848 LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 889
||||||||||||||||||||||||||||||||||||||||||
Db 842 LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 883
Sequence alignment between the T7 RNA polymerase of SEQ ID NO:1 of the instant application (“Qy”) and the T7 RNA polymerase of A0A2P1CL25 (“Db”)
A0A2P1CL25_9CAUD
ID A0A2P1CL25_9CAUD Unreviewed; 883 AA.
AC A0A2P1CL25;
DT 23-MAY-2018, integrated into UniProtKB/TrEMBL.
DT 23-MAY-2018, sequence version 1.
DT 08-OCT-2025, entry version 30.
DE RecName: Full=DNA-directed RNA polymerase {ECO:0000256|ARBA:ARBA00012418, ECO:0000256|RuleBase:RU003805};
DE EC=2.7.7.6 {ECO:0000256|ARBA:ARBA00012418, ECO:0000256|RuleBase:RU003805};
GN ORFNames=ebrios_5 {ECO:0000313|EMBL:AVJ51888.1};
OS Escherichia phage Ebrios.
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Autographiviridae; Studiervirinae; Teseptimavirus; Teseptimavirus ebrios.
OX NCBI_TaxID=2099356 {ECO:0000313|EMBL:AVJ51888.1, ECO:0000313|Proteomes:UP000240985};
RN [1] {ECO:0000313|EMBL:AVJ51888.1, ECO:0000313|Proteomes:UP000240985}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Ngazoa-Kakou S., Philippe C., Tremblay D.M., Loignon S., Koudou A.,
RA Abole A., Coulibaly D.N., Kan Kouassi S., Kouame-Sina M., Aoussi S.,
RA Dosso M., Moineau S.;
RT "Complete Genome Sequence of Ebrios, a novel T7-like phage isolated from
RT the Lagoon Ebrie in Abidjan.";
RL Submitted (FEB-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC {ECO:0000256|RuleBase:RU003805}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) +
CC diphosphate; Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6; Evidence={ECO:0000256|ARBA:ARBA00048552,
CC ECO:0000256|RuleBase:RU003805};
CC -!- SIMILARITY: Belongs to the phage and mitochondrial RNA polymerase
CC family. {ECO:0000256|ARBA:ARBA00009493, ECO:0000256|RuleBase:RU003805}.
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DR EMBL; MG966531; AVJ51888.1; -; Genomic_DNA.
DR Proteomes; UP000240985; Genome.
DR GO; GO:0000428; C:DNA-directed RNA polymerase complex; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed RNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro.
DR GO; GO:0019083; P:viral transcription; IEA:UniProtKB-KW.
DR Gene3D; 1.10.287.260; -; 1.
DR Gene3D; 1.10.287.280; -; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 1.
DR Gene3D; 1.10.1320.10; DNA-directed RNA polymerase, N-terminal domain; 1.
DR InterPro; IPR024075; DNA-dir_RNA_pol_helix_hairp_sf.
DR InterPro; IPR046950; DNA-dir_Rpol_C_phage-type.
DR InterPro; IPR002092; DNA-dir_Rpol_phage-type.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR037159; RNA_POL_N_sf.
DR InterPro; IPR029262; RPOL_N.
DR PANTHER; PTHR10102; DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL; 1.
DR PANTHER; PTHR10102:SF0; DNA-DIRECTED RNA POLYMERASE, MITOCHONDRIAL; 1.
DR Pfam; PF00940; RNA_pol; 1.
DR Pfam; PF14700; RPOL_N; 1.
DR SMART; SM01311; RPOL_N; 1.
DR SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR PROSITE; PS00900; RNA_POL_PHAGE_1; 1.
DR PROSITE; PS00489; RNA_POL_PHAGE_2; 1.
PE 3: Inferred from homology;
KW DNA-directed RNA polymerase {ECO:0000256|ARBA:ARBA00022478,
KW ECO:0000256|RuleBase:RU003805};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695,
KW ECO:0000256|RuleBase:RU003805};
KW Reference proteome {ECO:0000313|Proteomes:UP000240985};
KW Transcription {ECO:0000256|ARBA:ARBA00023163,
KW ECO:0000256|RuleBase:RU003805};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|RuleBase:RU003805};
KW Viral transcription {ECO:0000256|ARBA:ARBA00023314}.
FT DOMAIN 34..325
FT /note="DNA-directed RNA polymerase N-terminal"
FT /evidence="ECO:0000259|SMART:SM01311"
SQ SEQUENCE 883 AA; 98754 MW; 0004EABB2FEA37EA CRC64;
Query Match 90.7%; Score 4233; Length 883;
Best Local Similarity 90.6%;
Matches 797; Conservative 42; Mismatches 41; Indels 0; Gaps 0;
Qy 10 INIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGE 69
| | ||||||:||| ||||||||||||:|||||||||||:||||||||||:|||||||||
Db 4 IAIEKNDFSDVELAVIPFNTLADHYGEKLAREQLALEHEAYEMGEARFRKIFERQLKAGE 63
Qy 70 VADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTL 129
||||||||||: ||||||| ||| ||||| ||||||||||:||||:||||:||||||| |
Db 64 VADNAAAKPLVATLLPKMIERINIWFEEVSAKRGKRPTAFKFLQEVKPEAIA YITIKTVL 123
Qy 130 ACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFM 189
||||: ||||| |||:||||||||||||||||||||||||||||||||||:||||||:
Db 124 GALTSAEQTTVQAAASAVGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGNVYKKAFL 183
Qy 190 QVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSET 249
||||||||||||:|||||||||||||||||||||||||||||:| | |||||||| |:||
Db 184 QVVEADMLSKGLMGGEAWSSWHKEDSIHVGVRCIEMLIESTGLVVLERQNAGVVGADAET 243
Qy 250 IELAPEYAEAIA TRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKK 309
: || |||:|||||||||||||||:||||||||||| :||||||||||||||||||| ||
Db 244 LSLASEYADAIA TRAGALAGISPMYQPCVVPPKPWTTVTGGGYWANGRRPLALVRTHGKK 303
Qy 310 ALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMK 369
||||||||||||||||:|:|| |||||||||||||| |||||||||||||||||||||:|
Db 304 ALMRYEDVYMPEVYKAVNLAQATAWKINKKVLAVANEITKWKHCPVEDIPAIEREELPVK 363
Qy 370 PEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWR 429
|:||| |||||| |||||||||||||||||||:|||||||||||||||||||||||||||
Db 364 PDDIDENPEALTNWKRAAAAVYRKDKARKSRRLSLEFMLEQANKFANHKAIWFPYNMDWR 423
Qy 430 GRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIE 489
||||||||||||||||||||||||||| |||||:||||||||||||||||||||||||||
Db 424 GRVYAVSMFNPQGNDMTKGLLTLAKGKAIGKEGFYWLKIHGANCAGVDKVPFPERIKFIE 483
Qy 490 ENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGI 549
:|||:||| ||:||| |||||||||||||||||||||| |||||||||||||||||||||
Db 484 DNHEHIMASAKNPLEYTWWAEQDSPFCFLAFCFEYAGVMHHGLSYNCSLPLAFDGSCSGI 543
Qy 550 QHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTG 609
|||||||||||||||||||||||||||||||||||||||| | |:|||:|:|| ||: ||
Db 544 QHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQRDVISGTDDELVTETDKTTG 603
Qy 610 EISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGK 669
||:|| |||: |||||||||| |||||||||||||||||||||||||||||:|||||||
Db 604 EITEKTVLGTRTLAGQWLAYGVNRSVTKRSVMTLAYGSKEFGFRQQVLEDTIRPAIDSGK 663
Qy 670 GLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRC 729
||||| |||||||||||||:||||||||||||| ||:|||||||||||||||||:|| ||
Db 664 GLMFTIPNQAAGYMAKLIWDSVSVTVVAAVEAMKWLQSAAKLLAAEVKDKKTGEVLRNRC 723
Qy 730 AVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFV 789
||||||||||||||||:||:|||||||||||||||||||||||| |||||||||||||||
Db 724 AVHWVTPDGFPVWQEYRKPLQTRLNLMFLGQFRLQPTINTNKDSGIDAHKQESGIAPNFV 783
Qy 790 HSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLA 849
|||||||||||||||||||||||||||||||||||||| |||||||||||||||:|||||
Db 784 HSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAGNLFKAVRETMVDTYENCDVLA 843
Qy 850 DFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 889
|||:|||||||||||||||||| |||||||||||||||||
Db 844 DFYEQFADQLHESQLDKMPALPKKGNLNLRDILESDFAFA 883
Sequence alignment between the T7 RNA polymerase of SEQ ID NO:1 of the instant application (“Qy”) and the T7 RNA polymerase of SEQ ID NO:4 of Miller (“Db”)
US-16-012-462-4
Sequence 4, US/16012462
Publication No. US20190002850A1
GENERAL INFORMATION
APPLICANT: CODEXIS, INC.
APPLICANT: ALEXION PHARMACEUTICALS, INC.
TITLE OF INVENTION: T7 RNA POLYMERASE VARIANTS
FILE REFERENCE: CX8-168USP1
CURRENT APPLICATION NUMBER: US/16/012,462
CURRENT FILING DATE: 2018-06-19
NUMBER OF SEQ ID NOS: 40
SEQ ID NO 4
LENGTH: 890
TYPE: PRT
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: 6His-T7RNAP
Query Match 99.8%; Score 4658.5; Length 890;
Best Local Similarity 99.9%;
Matches 889; Conservative 0; Mismatches 0; Indels 1; Gaps 1;
Qy 1 MHHHHHH-NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRK 59
||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MHHHHHHMNTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRK 60
Qy 60 MFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEA 119
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEA 120
Qy 120 VAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKR 179
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 VAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKR 180
Qy 180 VGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN 239
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN 240
Qy 240 AGVVGQDSETIELAPEYAEAIA TRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRP 299
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AGVVGQDSETIELAPEYAEAIA TRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRP 300
Qy 300 LALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIP 359
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIP 360
Qy 360 AIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKA 419
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 AIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKA 420
Qy 420 IWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKV 479
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 IWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKV 480
Qy 480 PFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLP 539
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 PFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLP 540
Qy 540 LAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNE 599
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 LAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNE 600
Qy 600 VVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLED 659
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 VVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLED 660
Qy 660 TIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDK 719
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 TIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDK 720
Qy 720 KTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHK 779
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 KTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHK 780
Qy 780 QESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMV 839
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 QESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMV 840
Qy 840 DTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 889
||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 DTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA 890
Prosecution Insights