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/JP2021/031386.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on March 12, 2026 has been entered.
Status of Claims
Claims 13-20 are pending.
Claims 13-20 are under examination.
Response to Amendments/Arguments
Claim Objections
Due to the amendment of the claims 13 and 15-16, claims 13-16 are no longer directed to improper multiple dependent claims. Therefore, the objection of claims 13-16 has been withdrawn.
Claim Rejections - 35 USC § 112(b)
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.
Claim 13 and claims 14 and 17-18 depending therefrom are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are: step (II). Claim 13 recites “step (I)” but does not recite any subsequent steps.
Claim Rejections - 35 USC § 112(a)
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.
Applicant’s arguments, see page 9 of the Remarks, filed March 12, 2026, with respect to claims 6-7 and 9-12 have been fully considered and are persuasive. Claims 6-7 and 9-12 have been cancelled. Therefore, all previous rejections of claims 6-7 and 9-12 under 35 U.S.C. 112(a) have been withdrawn.
Claims 13-20 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' Regarding the limitation “an amino acid of SEQ ID NO..” has been broadly interpreted as a polypeptide comprising as little as two contiguous amino acids of SEQ ID NOs:1-9 and comprising any number of amino acid substitutions, deletions, insertions, or additions. Claims 13-20 have been broadly interpreted as a method of dehydroxylating a hydroxyl group at a 9-position of any urolithins, ellagic acid, urolithin M5, urolithin M6, urolithin C, or isourolithin A to produce any urolithin, urolithin C, urolithin E, urolithin M7, urolithin A, and urolithin B, respectively, using any polypeptide or any microorganism comprising said polypeptide, wherein (1) the polypeptide comprises as little as two contiguous amino acids of SEQ ID NOs:1-9 or (2) the polypeptide comprises as little as two contiguous amino acids of SEQ ID NOs:1-9 and also comprises 1 to 78 number of amino acid substitutions, deletions, insertions, or additions, and wherein the polypeptide of (1) and (2) has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins.
MPEP 2163 I. states that to “satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention.
MPEP 2163. II.A.3.(a) sates that “Possession may be shown in many ways. For example, possession may be shown by describing an actual reduction to practice of the claimed invention. Possession may also be shown by a clear depiction of the invention in detailed drawings or in structural chemical formulas which permit a person skilled in the art to clearly recognize that inventor had possession of the claimed invention. An adequate written description of the invention may be shown by any description of sufficient, relevant, identifying characteristics so long as a person skilled in the art would recognize that the inventor had possession of the claimed invention.
According to MPEP 2163.II.A.3.(a).ii), “Satisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’"
The recitation of “retains dehydroxylation activity of the hydroxyl group at a 9-position of urolithins” fail to provide a sufficient description of the genus of the enzymes used in the claimed method as it merely describes the functional features of the genus without providing any definition of the structural features of the species within the genus. The specification does not specifically define any of the species that fall within the genus. The specification does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus.
The prior art discloses polypeptides having 100% sequence identity to SEQ ID NOs:1-9 (see the 102 rejections below). However, enzymes having unknown structure but having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins were not known in the prior art.
The specification is limited to a method of converting urolithin C to urolithin A using C. bolteae JCM 12443 enzyme having the amino acid sequence of SEQ ID NO:1 (CbUroC1), SEQ ID NO:2 (CbUroC3), and SEQ ID NO:3 (CbUroC3), wherein the enzyme has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithin C. While MPEP 2163 acknowledges that in certain situations “one species adequately supports a genus,” it also acknowledges that “[f]or inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus.” In view of the widely variant species encompassed by the genus, the example described above is not enough and does not constitute a representative number of species to describe the whole genus. Therefore, the specification fails to describe a representative species of the claimed genus.
Regarding claims 13 and 15-20, one of skill in the art could identify variants of SEQ ID NO:1-9. However, there is no teaching regarding which amino acids of SEQ ID NO:1-9 can vary and result in a polypeptide having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – cited previously on form PTO-892) reviews protein engineering techniques, such as random mutagenesis and recombination, directed evolution and iterative or combinatory saturation “hotspots”. Fransceus states that “a recurring problem, however, is choosing which amino acid positions should be targeted. Answering this question is not an easy feat and requires substantial insight in the relationship between an enzyme’s sequence or structure and its properties.” Sanavia (Computational and Structural Biotechnology Journal, Volume 18, 2020, Pages 1968-1979. – cited previously on form PTO-892) discloses challenges in the prediction of protein stability in the occurrence of multiple mutations. “Multiple-point mutations are common variations of the protein sequence that may be needed in protein engineering when a single-point mutation is not enough to yield the desired stability change. Dealing with multiple-site variations adds another level of complexity beyond the prediction of the effect of a single variant on protein stability, since it requires the learning of many types of combinatorial effects”.
An important consideration is that structure is not necessarily a reliable indicator of function. In the instant case, there is no disclosure relating similarity of structure to conservation of function. Conservation of structure is not necessarily a surrogate for conservation of function.
While general knowledge in the art may have allowed one of skill in the art to identify other polypeptides expected to have the same or similar tertiary structure, there was no general knowledge in the art in the ability of polypeptides having the function dehydroxylation activity of the hydroxyl group at a 9-position of urolithins.
Given this lack of description of the representative species encompassed by the genus of the claims, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the inventions of claims 13-20.
Claims 13-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of converting urolithin C to urolithin A using C. bolteae JCM 12443 enzyme having the amino acid sequence of SEQ ID NO:1 (CbUroC1), SEQ ID NO:2 (CbUroC3), and SEQ ID NO:3 (CbUroC3), wherein the enzyme has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithin C, does not reasonably provide enablement for a method of dehydroxylating any urolithin using polypeptides or a microorganism comprising said polypeptides, wherein the polypeptides have unknown structure but has the function dehydroxylation activity of the hydroxyl group at a 9-position of urolithins. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988). They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.
The breadth of the claims.
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' Regarding the limitation “an amino acid of SEQ ID NO..” has been broadly interpreted as a polypeptide comprising as little as two contiguous amino acids of SEQ ID NOs:1-9 and comprising any number of amino acid substitutions, deletions, insertions, or additions. Claims 13-20 have been broadly interpreted as a method of dehydroxylating a hydroxyl group at a 9-position of any urolithins, ellagic acid, urolithin M5, urolithin M6, urolithin C, or isourolithin A to produce any urolithin, urolithin C, urolithin E, urolithin M7, urolithin A, and urolithin B, respectively, using any polypeptide or any microorganism comprising said polypeptide, wherein (1) the polypeptide comprises as little as two contiguous amino acids of SEQ ID NOs:1-9 or (2) the polypeptide comprises as little as two contiguous amino acids of SEQ ID NOs:1-9 and also comprises 1 to 78 number of amino acid substitutions, deletions, insertions, or additions, and wherein the polypeptide of (1) and (2) has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins.
The claims are not commensurate with the enablement provided by the disclosure with regard to the extremely large number of polypeptides used in the claimed method. The specification is limited to a method of converting urolithin C to urolithin A using C. bolteae JCM 12443 enzyme having the amino acid sequence of SEQ ID NO:1 (CbUroC1), SEQ ID NO:2 (CbUroC3), and SEQ ID NO:3 (CbUroC3), wherein the enzyme has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithin C.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification.
While enzyme isolation techniques, recombinant and mutagenesis techniques were known in the art at the time of the invention, e.g. mutagenesis, and it is routine in the art to screen for variants comprising multiple substitutions or multiple modifications as encompassed by the instant claims, the specific amino acid positions within the protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
In the absence of: (a) rational and predictable scheme for producing any urolithin, urolithin E, urolithin M7, urolithin A, urolithin B, or urolithin C using polypeptides or a microorganism comprising said polypeptides, wherein the polypeptides having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins, and (b) a correlation between structure and the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins, the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful. One of skill in the art would have to test these infinite possible polypeptides/microorganisms to determine which polypeptides have the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins. While enablement is not precluded by the necessity for routine screening, if a large amount of screening is required, as is the case herein, the specification must provide a reasonable amount of guidance which respect to the direction in which the experimentation should proceed so that a reasonable number of species can be selected for testing. In view of the fact that such guidance has not been provided in the instant specification, it would require undue experimentation to enable the full scope of the claims.
The state of prior art, the relative skill of those in the art, and predictability or unpredictability of the art.
The prior art discloses polypeptides having 100% sequence identity to SEQ ID NOs:1-9 (see the 102 rejections below). However, any enzyme having unknown structure but having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins were not known in the prior art.
Since the amino acid sequence of the polypeptide determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence, if any, are tolerant of modification and which are conserved (i.e. expectedly intolerant to modification), and detailed knowledge of the ways in which the proteins' structure relates to its function. In the instant case, neither the specification or the art provide a correlation between structure and activity such that one of skill in the art can envision the structure of any polypeptide having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins. In addition, the art does not provide any teaching or guidance as to (1) which amino acids within the polypeptide of SEQ ID NO:1-9 that can be modified and which ones are conserved such that one of skill in the art can make and use a polypeptide having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins, (2) which segments of the polypeptide of SEQ ID NO:1-9 that are essential for having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins, and (3) the general tolerance of any polypeptide, the polypeptide of SEQ ID NO:1-9 to structural modifications and the extent of such tolerance. The art clearly teaches that changes in a protein's amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are required for that activity is highly unpredictable. At the time of the invention there was a high level of unpredictability associated with altering a polypeptide sequence with an expectation that the polypeptide will maintain the desired activity. For example, Studer (Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem. J. (2013) 449, 581–594. – cited previously on form PTO-892) teach that (1) protein engineers are frequently surprised by the range of effects caused by single mutations that they hoped would change only one specific and simple property in enzymes, (2) the often surprising results obtained by experiments where single mutations are made reveal how little is known about the rules of protein stability, and (3) the difficulties in designing de novo stable proteins with specific functions.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – cited previously form PTO-892) reviews protein engineering techniques, such as random mutagenesis and recombination, directed evolution and iterative or combinatory saturation “hotspots”. Fransceus states that “a recurring problem, however, is choosing which amino acid positions should be targeted. Answering this question is not an easy feat and requires substantial insight in the relationship between an enzyme’s sequence or structure and its properties.” Sanavia (Computational and Structural Biotechnology Journal, Volume 18, 2020, Pages 1968-1979. – cited previously on form PTO-892) discloses challenges in the prediction of protein stability in the occurrence of multiple mutations. “Multiple-point mutations are common variations of the protein sequence that may be needed in protein engineering when a single-point mutation is not enough to yield the desired stability change. Dealing with multiple-site variations adds another level of complexity beyond the prediction of the effect of a single variant on protein stability, since it requires the learning of many types of combinatorial effects”.
The amount of direction or guidance presented and the existence of working examples.
The specification is limited to a method of converting urolithin C to urolithin A using C. bolteae JCM 12443 enzyme having the amino acid sequence of SEQ ID NO:1 (CbUroC1), SEQ ID NO:2 (CbUroC3), and SEQ ID NO:3 (CbUroC3), wherein the enzyme has the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithin C. However, the speciation fails to provide any information as to the structural elements required in a polypeptide having the function of dehydroxylation activity of the hydroxyl group at a 9-position of urolithins.
Thus, in view of the overly broad scope of the claims, the lack of guidance and working examples provided in the specification, the high level of unpredictability of the prior art in regard to structural changes and their effect on function and the lack of knowledge about a correlation between structure and function, an undue experimentation would be necessary one having ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of polypeptides having the desired biological characteristics recited in the claims are unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
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 (i.e., changing from AIA to pre-AIA ) 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 13-20 is/are rejected under 35 U.S.C. 102(a)(1) or 102(a)(2) as being anticipated by Kudoh (102(a)(1): WO 2018/124135 – form PTO-1449. 102(a)(2): US Patent No. 12,006,524 – form PTO-892. US Patent No. 12,006,524 is used for specific portions of Kudoh).
Regarding claims 13-20, Kudoh discloses a method for dehydroxylating a hydroxyl group at a 9-position of urolithin M5, urolithin M6, urolithin C, isourolithin A by (I) bringing a Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain into contact with said urolithins or urolithin C having a hydroxyl group at a 9-position to dehydroxylate the hydroxyl group at the 9-postion and (II) producing urolithin E, urolithin M7, urolithin A, and urolithin B, respectively (abstract, Column 2, line 37 through Column 3, line 31, Column 4, line 40 through Column 7, line 47, and claims 1-18). Regarding claims 15 and 17, Kudoh discloses allowing the strains to produce urolithin C from ellagic acid (Column 10, lines 60-67, Column 13, lines 43-49, Column 13, lines 58-63, and claim 14). Regarding claims 16-20, Kudoh discloses allowing the strains to produce urolithin C from ellagic acid and produce urolithin A from urolithin C (Column 10, lines 60-67, Column 13, lines 43-49, Column 13, lines 58-63, and claim 14).
The Clostridium bolteae DSM 15670 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:1, 2, and 3, as evidenced by ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ABCC02000040 discloses the genome sequence of Clostridium bolteae ATCC BAA-613, also known as Clostridium bolteae DSM 15670, as evidenced by Taxonomy – Enterocloster bolteae (UniProt Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). ABCC02000040 discloses enzymes EDP14314.1 (A8RZR5), EDP14313.1 (A8RZR3), and EDP14312.1 (A8RZR2), and having 100% sequence identity to SEQ ID NO:1, 2, and 3, respectively (see pages 3-12 and see the sequence alignment below) and evidenced by A8RZR5
The Clostridium asparagiforme DSM 15981 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:3, 4, and 5, as evidenced by QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892). QSBM01000001 discloses the genome sequence of Clostridium asparagiforme Taxonomy 333367, also known as Clostridium asparagiforme DSM 15981, as evidenced by Taxonomy – Enterocloster asparagiformis (NCBI Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). QSBM01000001 discloses Clostridium asparagiforme DSM 15981 polypeptides RGX32804.1, RGX32805.1, and RGX32806.1 having 100% sequence identity to SEQ ID NO:4, 5, and 6, respectively (see pages 3-10 and see the sequence alignments below).
The Clostridium citroniae DSM 19261 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:7, 8, and 9, as evidenced by ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ADLJ01000009 discloses the genome sequence of Clostridium citroniae WL-17108, also known as Clostridium citroniae DSM 19261, as evidenced by Taxonomy – Enterocloster citroniae (UniProt Database. Retrieved on April 20, 2026 – form PTO-892). ADLJ01000009 discloses Clostridium citroniae DSM 19261 polypeptides EHE99819.1, EHE99818.1, and EHE99817.1 having 100% sequence identity to SEQ ID NO:7, 8, and 9, respectively (see pages 3-9 and see the sequence alignments below).
Therefore, the reference of Kudoh anticipates claims 13-20.
The applied reference (US Patent No. 12,006,524) has a common assignee and inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Claim(s) 13-20 is/are rejected under 35 U.S.C. 102(a)(1) or 102(a)(2) as being anticipated by Nakajima (102(a)(1): WO 2019/130681 – form PTO-1449. 102(a)(2): US Patent No. 11,667,937– form PTO-892. US Patent No. 11,667,937 is used for specific portions of Nakajima).
Regarding claims 13-20, Nakajima discloses a method for dehydroxylating a hydroxyl group at a 9-position of urolithin M5, urolithin M6, urolithin C, isourolithin A by (I) bringing a Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain into contact with said urolithins or urolithin C having a hydroxyl group at a 9-position to dehydroxylate the hydroxyl group at the 9-postion and (II) producing urolithin E, urolithin M7, urolithin A, and urolithin B, respectively (Column 17, line 15 through Column 18, line 3, Column 20, lines 1-22, Examples 3-5, and claims 12-13). Regarding claims 15 and 17, Nakajima discloses allowing the strains to produce urolithin C from ellagic acid (Column 17, line 15 through Column 18, line 3, Examples 3-5 and claims 12-13). Regarding claims 16-20, Kudoh discloses allowing the strains to produce urolithin C from ellagic acid and produce urolithin A from urolithin C (Column 17, line 15 through Column 18, line 3, Column 20, lines 1-22, and Examples 3-5).
The Clostridium bolteae DSM 15670 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:1, 2, and 3, as evidenced by ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ABCC02000040 discloses the genome sequence of Clostridium bolteae ATCC BAA-613, also known as Clostridium bolteae DSM 15670, as evidenced by Taxonomy – Enterocloster bolteae (UniProt Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). ABCC02000040 discloses enzymes EDP14314.1 (A8RZR5), EDP14313.1 (A8RZR3), and EDP14312.1 (A8RZR2), and having 100% sequence identity to SEQ ID NO:1, 2, and 3, respectively (see pages 3-12 and see the sequence alignment below) and evidenced by A8RZR5
The Clostridium asparagiforme DSM 15981 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:3, 4, and 5, as evidenced by QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892). QSBM01000001 discloses the genome sequence of Clostridium asparagiforme Taxonomy 333367, also known as Clostridium asparagiforme DSM 15981, as evidenced by Taxonomy – Enterocloster asparagiformis (NCBI Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). QSBM01000001 discloses Clostridium asparagiforme DSM 15981 polypeptides RGX32804.1, RGX32805.1, and RGX32806.1 having 100% sequence identity to SEQ ID NO:4, 5, and 6, respectively (see pages 3-10 and see the sequence alignments below).
The Clostridium citroniae DSM 19261 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:7, 8, and 9, as evidenced by ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ADLJ01000009 discloses the genome sequence of Clostridium citroniae WL-17108, also known as Clostridium citroniae DSM 19261, as evidenced by Taxonomy – Enterocloster citroniae (UniProt Database. Retrieved on April 20, 2026 – form PTO-892). ADLJ01000009 discloses Clostridium citroniae DSM 19261 polypeptides EHE99819.1, EHE99818.1, and EHE99817.1 having 100% sequence identity to SEQ ID NO:7, 8, and 9, respectively (see pages 3-9 and see the sequence alignments below).
Therefore, the reference of Kudoh anticipates claims 13-20.
The applied reference (US Patent No. 11,667,937) has a common assignee and inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Claim Rejections - 35 USC § 103
Applicant’s arguments, see page 9 of the Remarks, filed March 12, 2026, with respect to claims 6-7 and 9-12 have been fully considered and are persuasive. Claims 6-7 and 9-12 have been cancelled. Therefore, all previous rejections of claims 6-7 and 9-12 under 35 U.S.C. 103 have been withdrawn.
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 conflicting claims 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) 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 www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 13-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 12,006,524 (reference patent) in view of (1) ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), (2) QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and (3) ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the instant application and the claims of the reference patent are directed to a method of dehydroxylating a hydroxyl group at a 9-position of urolithins and producing urolithins.
Regarding claims 13-20 of the instant application, claims 1-4 of the reference patent recite a method for dehydroxylating a hydroxyl group at a 9-position of urolithin M5, urolithin M6, urolithin C, isourolithin A by (I) bringing a Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain into contact with said urolithins or urolithin C having a hydroxyl group at a 9-position to dehydroxylate the hydroxyl group at the 9-postion and (II) producing urolithin E, urolithin M7, urolithin A, and urolithin B, respectively.
Regarding claims 16-20, claim 14 of the reference patent discloses allowing the strains to produce urolithin C from ellagic acid.
The Clostridium bolteae DSM 15670 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:1, 2, and 3, as evidenced by ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ABCC02000040 discloses the genome sequence of Clostridium bolteae ATCC BAA-613, also known as Clostridium bolteae DSM 15670, as evidenced by Taxonomy – Enterocloster bolteae (UniProt Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). ABCC02000040 discloses enzymes EDP14314.1 (A8RZR5), EDP14313.1 (A8RZR3), and EDP14312.1 (A8RZR2), and having 100% sequence identity to SEQ ID NO:1, 2, and 3, respectively (see pages 3-12 and see the sequence alignment below) and evidenced by A8RZR5
The Clostridium asparagiforme DSM 15981 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:3, 4, and 5, as evidenced by QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892). QSBM01000001 discloses the genome sequence of Clostridium asparagiforme Taxonomy 333367, also known as Clostridium asparagiforme DSM 15981, as evidenced by Taxonomy – Enterocloster asparagiformis (NCBI Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). QSBM01000001 discloses Clostridium asparagiforme DSM 15981 polypeptides RGX32804.1, RGX32805.1, and RGX32806.1 having 100% sequence identity to SEQ ID NO:4, 5, and 6, respectively (see pages 3-10 and see the sequence alignments below).
The Clostridium citroniae DSM 19261 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:7, 8, and 9, as evidenced by ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ADLJ01000009 discloses the genome sequence of Clostridium citroniae WL-17108, also known as Clostridium citroniae DSM 19261, as evidenced by Taxonomy – Enterocloster citroniae (UniProt Database. Retrieved on April 20, 2026 – form PTO-892). ADLJ01000009 discloses Clostridium citroniae DSM 19261 polypeptides EHE99819.1, EHE99818.1, and EHE99817.1 having 100% sequence identity to SEQ ID NO:7, 8, and 9, respectively (see pages 3-9 and see the sequence alignments below).
Therefore, the claims 13-20 of the instant application are anticipated by claims 1-4 and 14 of the reference patent.
Therefore, the conflicting claims are not patentably distinct from each other.
Claims 13-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 11,667,937 (reference patent) in view of (1) Kudoh (WO 2018/124135 – form PTO-1449. US Patent No. 12,006,524 is used for specific portions of Kudoh), (2) ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), (3) QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and (4) ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892).
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the instant application and the claims of the reference patent are directed to a method of producing urolithins.
Regarding claims 13-20 of the instant application, claims 12-13 of the reference patent recite a method for dehydroxylating a hydroxyl group at a 9-position of urolithins by converting ellagic acid → urolithin C and converting isourolithin A →urolithin B by bringing a Clostridium strain into contact with said ellagic acid and isourolithin A.
The claims of the reference do not recite using Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain, converting urolithin C→ urolithin A and producing urolithin E, urolithin M7 and urolithin A.
Regarding claims 13-20, Kudoh discloses a method for dehydroxylating a hydroxyl group at a 9-position of urolithin M5, urolithin M6, urolithin C, isourolithin A by (I) bringing a Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain into contact with said urolithins or urolithin C having a hydroxyl group at a 9-position to dehydroxylate the hydroxyl group at the 9-postion and (II) producing urolithin E, urolithin M7, urolithin A, and urolithin B, respectively (abstract, Column 2, line 37 through Column 3, line 31, Column 4, line 40 through Column 7, line 47, and claims 1-18). Regarding claims 15 and 17, Kudoh discloses allowing the strains to produce urolithin C from ellagic acid (Column 10, lines 60-67, Column 13, lines 43-49, Column 13, lines 58-63, and claim 14). Regarding claims 16-20, Kudoh discloses allowing the strains to produce urolithin C from ellagic acid and produce urolithin A from urolithin C (Column 10, lines 60-67, Column 13, lines 43-49, Column 13, lines 58-63, and claim 14). Kudoh discloses that urolithins are useful as materials for drugs, cosmetic, and food and drinks (Column 1, lines 30-32).
The Clostridium bolteae DSM 15670 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:1, 2, and 3, as evidenced by ABCC02000040 (GenBank Database. Pages 1-12. January 14, 2008 – cited previously on form PTO-892), A8RZR5 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), A8RZR3 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and A8RZR2 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ABCC02000040 discloses the genome sequence of Clostridium bolteae ATCC BAA-613, also known as Clostridium bolteae DSM 15670, as evidenced by Taxonomy – Enterocloster bolteae (UniProt Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). ABCC02000040 discloses enzymes EDP14314.1 (A8RZR5), EDP14313.1 (A8RZR3), and EDP14312.1 (A8RZR2), and having 100% sequence identity to SEQ ID NO:1, 2, and 3, respectively (see pages 3-12 and see the sequence alignment below) and evidenced by A8RZR5
The Clostridium asparagiforme DSM 15981 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:3, 4, and 5, as evidenced by QSBM01000001 (GenBank Database. Pages 1-10. September 6, 2018 – cited previously on form PTO-892), RGX32804.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), RGX32805.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892), and RGX32806;.1 (UniProtKB/TrEMBL Database. July 3, 2019 - cited previously on form PTO-892). QSBM01000001 discloses the genome sequence of Clostridium asparagiforme Taxonomy 333367, also known as Clostridium asparagiforme DSM 15981, as evidenced by Taxonomy – Enterocloster asparagiformis (NCBI Database. Retrieved on May 29, 2025 – cited previously on form PTO-892). QSBM01000001 discloses Clostridium asparagiforme DSM 15981 polypeptides RGX32804.1, RGX32805.1, and RGX32806.1 having 100% sequence identity to SEQ ID NO:4, 5, and 6, respectively (see pages 3-10 and see the sequence alignments below).
The Clostridium citroniae DSM 19261 strain comprises enzymes having 100% sequence identity to the amino sequence of SEQ ID NO:7, 8, and 9, as evidenced by ADLJ01000009 (GenBank Database. Pages 1-9. October 31, 2011 – cited previously on form PTO-892), EHE99819.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), EHE99818.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892), and EHE99817.1 (UniProtKB/TrEMBL Database. July 31, 2019 - cited previously on form PTO-892). ADLJ01000009 discloses the genome sequence of Clostridium citroniae WL-17108, also known as Clostridium citroniae DSM 19261, as evidenced by Taxonomy – Enterocloster citroniae (UniProt Database. Retrieved on April 20, 2026 – form PTO-892). ADLJ01000009 discloses Clostridium citroniae DSM 19261 polypeptides EHE99819.1, EHE99818.1, and EHE99817.1 having 100% sequence identity to SEQ ID NO:7, 8, and 9, respectively (see pages 3-9 and see the sequence alignments below).
Therefore, it would have been obvious to one having ordinary skill in the art to modify the claims of the reference patent by brining into contact Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain with ellagic acid, urolithin M5, urolithin M6, urolithin C, or isourolithin A to produce urolithin C, urolithin E, urolithin M7, urolithin A, and urolithin B, respectively. One having ordinary skill in the art would have been motivated to do so in order to make various urolithins, which are useful as materials for drugs, cosmetic, and food and drinks. One having ordinary skill in the art would have had a reasonable expectation of success since the claims of the reference patent recites a method of producing urolithin C and urolithin B using a Clostridium strain and Kudoh discloses a method of producing urolithin C, urolithin E, urolithin M7, urolithin A, and urolithin B, respectively, using Clostridium bolteae DSM 15670 strain, Clostridium asparagiforme DSM 15981 strain, or Clostridium citroniae DSM 19261 strain.
Therefore, the conflicting claims are not patentably distinct from each other.
Conclusion
Claims 13-20 are pending.
Claims 13-20 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.
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/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment of SEQ ID NO:1 of the instant application (“Qy”) and the polypeptide of A8RZR5 (EDP14314.1) (“Db”)
ID A8RZR5_ENTBW Unreviewed; 289 AA.
AC A8RZR5;
DT 15-JAN-2008, integrated into UniProtKB/TrEMBL.
DT 15-JAN-2008, sequence version 1.
DT 05-FEB-2025, entry version 66.
DE RecName: Full=FAD-binding PCMH-type domain-containing protein {ECO:0000259|PROSITE:PS51387};
GN ORFNames=CLOBOL_05482 {ECO:0000313|EMBL:EDP14314.1};
OS Enterocloster bolteae (strain ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM
OS 12243 / WAL 16351) (Clostridium bolteae).
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=411902 {ECO:0000313|EMBL:EDP14314.1, ECO:0000313|Proteomes:UP000005396};
RN [1] {ECO:0000313|EMBL:EDP14314.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Fulton L., Clifton S., Fulton B., Xu J., Minx P., Pepin K.H., Johnson M.,
RA Thiruvilangam P., Bhonagiri V., Nash W.E., Mardis E.R., Wilson R.K.;
RL Submitted (AUG-2007) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:EDP14314.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Sudarsanam P., Ley R., Guruge J., Turnbaugh P.J., Mahowald M., Liep D.,
RA Gordon J.;
RT "Draft genome sequence of Clostridium bolteae (ATCC BAA-613).";
RL Submitted (SEP-2007) to the EMBL/GenBank/DDBJ databases.
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:EDP14314.1}.
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DR EMBL; ABCC02000040; EDP14314.1; -; Genomic_DNA.
DR RefSeq; WP_002569575.1; NZ_DS480695.1.
DR AlphaFoldDB; A8RZR5; -.
DR PaxDb; 411902-CLOBOL_05482; -.
DR eggNOG; COG1319; Bacteria.
DR HOGENOM; CLU_058050_0_1_9; -.
DR Proteomes; UP000005396; Unassembled WGS sequence.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.30.465.10; -; 1.
DR Gene3D; 3.30.390.50; CO dehydrogenase flavoprotein, C-terminal domain; 1.
DR Gene3D; 3.30.43.10; Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2; 1.
DR InterPro; IPR005107; CO_DH_flav_C.
DR InterPro; IPR036683; CO_DH_flav_C_dom_sf.
DR InterPro; IPR051312; Diverse_Substr_Oxidored.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR002346; Mopterin_DH_FAD-bd.
DR PANTHER; PTHR42659; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR PANTHER; PTHR42659:SF2; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR Pfam; PF03450; CO_deh_flav_C; 1.
DR Pfam; PF00941; FAD_binding_5; 1.
DR SMART; SM01092; CO_deh_flav_C; 1.
DR SUPFAM; SSF55447; CO dehydrogenase flavoprotein C-terminal domain-like; 1.
DR SUPFAM; SSF56176; FAD-binding/transporter-associated domain-like; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 4: Predicted;
KW FAD {ECO:0000256|ARBA:ARBA00022827};
KW Flavoprotein {ECO:0000256|ARBA:ARBA00022630}.
FT DOMAIN 1..178
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000259|PROSITE:PS51387"
SQ SEQUENCE 289 AA; 31140 MW; AF79E2DA84F8F4C3 CRC64;
Query Match 100.0%; Score 1453; Length 289;
Best Local Similarity 100.0%;
Matches 289; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MVLPQFEYLAPKTIGEACNLFLELGSTARVMAGATDLIPPMKDKVISPEYIIDLKKIPGL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MVLPQFEYLAPKTIGEACNLFLELGSTARVMAGATDLIPPMKDKVISPEYIIDLKKIPGL 60
Qy 61 DYLEYDDREGLKIGALTTLRTIETSPLVKEKNPAVAHAAKVVASTQIRTKGTMAGNICNA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 DYLEYDDREGLKIGALTTLRTIETSPLVKEKNPAVAHAAKVVASTQIRTKGTMAGNICNA 120
Qy 121 SPSCDTAPNLLAQGAKILVQGPNKDRVIQIEDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SPSCDTAPNLLAQGAKILVQGPNKDRVIQIEDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
Qy 181 RAAYIKHAVRKAMDLAIIGVAVKIKVEDGVCTDARIALGAVAATPVRAPGAEEALIGKEL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 RAAYIKHAVRKAMDLAIIGVAVKIKVEDGVCTDARIALGAVAATPVRAPGAEEALIGKEL 240
Qy 241 TDEVIVKASEEAMNSCHPISDIRASAEYRKDMIRVFTKRAIKQAMECYN 289
|||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TDEVIVKASEEAMNSCHPISDIRASAEYRKDMIRVFTKRAIKQAMECYN 289
Sequence alignment of SEQ ID NO:2 of the instant application (“Qy”) and the polypeptide of A8RZR3 (EDP14313.1) (“Db”)
ID A8RZR3_ENTBW Unreviewed; 163 AA.
AC A8RZR3;
DT 15-JAN-2008, integrated into UniProtKB/TrEMBL.
DT 15-JAN-2008, sequence version 1.
DT 05-FEB-2025, entry version 72.
DE RecName: Full=2Fe-2S ferredoxin-type domain-containing protein {ECO:0000259|PROSITE:PS51085};
GN ORFNames=CLOBOL_05481 {ECO:0000313|EMBL:EDP14313.1};
OS Enterocloster bolteae (strain ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM
OS 12243 / WAL 16351) (Clostridium bolteae).
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=411902 {ECO:0000313|EMBL:EDP14313.1, ECO:0000313|Proteomes:UP000005396};
RN [1] {ECO:0000313|EMBL:EDP14313.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Fulton L., Clifton S., Fulton B., Xu J., Minx P., Pepin K.H., Johnson M.,
RA Thiruvilangam P., Bhonagiri V., Nash W.E., Mardis E.R., Wilson R.K.;
RL Submitted (AUG-2007) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:EDP14313.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Sudarsanam P., Ley R., Guruge J., Turnbaugh P.J., Mahowald M., Liep D.,
RA Gordon J.;
RT "Draft genome sequence of Clostridium bolteae (ATCC BAA-613).";
RL Submitted (SEP-2007) to the EMBL/GenBank/DDBJ databases.
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:EDP14313.1}.
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; ABCC02000040; EDP14313.1; -; Genomic_DNA.
DR RefSeq; WP_002569574.1; NZ_DS480695.1.
DR AlphaFoldDB; A8RZR3; -.
DR PaxDb; 411902-CLOBOL_05481; -.
DR GeneID; 23113308; -.
DR eggNOG; COG2080; Bacteria.
DR HOGENOM; CLU_052511_3_1_9; -.
DR Proteomes; UP000005396; Unassembled WGS sequence.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR CDD; cd00207; fer2; 1.
DR FunFam; 1.10.150.120:FF:000003; Carbon monoxide dehydrogenase, small subunit; 1.
DR FunFam; 3.10.20.30:FF:000020; Xanthine dehydrogenase iron-sulfur subunit; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 1.10.150.120; [2Fe-2S]-binding domain; 1.
DR InterPro; IPR002888; 2Fe-2S-bd.
DR InterPro; IPR036884; 2Fe-2S-bd_dom_sf.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR051452; Diverse_Oxidoreductases.
DR PANTHER; PTHR44379; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR PANTHER; PTHR44379:SF5; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF01799; Fer2_2; 1.
DR SUPFAM; SSF54292; 2Fe-2S ferredoxin-like; 1.
DR SUPFAM; SSF47741; CO dehydrogenase ISP C-domain like; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
PE 4: Predicted;
KW 2Fe-2S {ECO:0000256|ARBA:ARBA00022714};
KW Iron {ECO:0000256|ARBA:ARBA00023004};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022714};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002}.
FT DOMAIN 3..79
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000259|PROSITE:PS51085"
SQ SEQUENCE 163 AA; 17830 MW; D9D238192E29434C CRC64;
Query Match 100.0%; Score 868; Length 163;
Best Local Similarity 100.0%;
Matches 163; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKHSISLIINGDPVDAIVKDNLTLLDFLRDQLFLTGTKKGCEEGECGACTVMLDGKPVNS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKHSISLIINGDPVDAIVKDNLTLLDFLRDQLFLTGTKKGCEEGECGACTVMLDGKPVNS 60
Qy 61 CCTLAVECDGHEIITVEGIAREGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNKH 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCTLAVECDGHEIITVEGIAREGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNKH 120
Qy 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAAAQMNWEEEAKNA 163
|||||||||||||||||||||||||||||||||||||||||||
Db 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAAAQMNWEEEAKNA 163
Sequence alignment of SEQ ID NO:3 of the instant application (“Qy”) and the polypeptide of A8RZR2 (EDP14312.1) (“Db”)
ID A8RZR2_ENTBW Unreviewed; 787 AA.
AC A8RZR2;
DT 15-JAN-2008, integrated into UniProtKB/TrEMBL.
DT 15-JAN-2008, sequence version 1.
DT 05-FEB-2025, entry version 60.
DE RecName: Full=Aldehyde oxidase/xanthine dehydrogenase a/b hammerhead domain-containing protein {ECO:0000259|SMART:SM01008};
GN ORFNames=CLOBOL_05480 {ECO:0000313|EMBL:EDP14312.1};
OS Enterocloster bolteae (strain ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM
OS 12243 / WAL 16351) (Clostridium bolteae).
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=411902 {ECO:0000313|EMBL:EDP14312.1, ECO:0000313|Proteomes:UP000005396};
RN [1] {ECO:0000313|EMBL:EDP14312.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Fulton L., Clifton S., Fulton B., Xu J., Minx P., Pepin K.H., Johnson M.,
RA Thiruvilangam P., Bhonagiri V., Nash W.E., Mardis E.R., Wilson R.K.;
RL Submitted (AUG-2007) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:EDP14312.1, ECO:0000313|Proteomes:UP000005396}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-613 / DSM 15670 / CCUG 46953 / JCM 12243 / WAL 16351
RC {ECO:0000313|Proteomes:UP000005396};
RA Sudarsanam P., Ley R., Guruge J., Turnbaugh P.J., Mahowald M., Liep D.,
RA Gordon J.;
RT "Draft genome sequence of Clostridium bolteae (ATCC BAA-613).";
RL Submitted (SEP-2007) to the EMBL/GenBank/DDBJ databases.
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:EDP14312.1}.
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; ABCC02000040; EDP14312.1; -; Genomic_DNA.
DR RefSeq; WP_002569573.1; NZ_DS480695.1.
DR AlphaFoldDB; A8RZR2; -.
DR PaxDb; 411902-CLOBOL_05480; -.
DR eggNOG; COG1529; Bacteria.
DR HOGENOM; CLU_001681_2_1_9; -.
DR Proteomes; UP000005396; Unassembled WGS sequence.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.90.1170.50; Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead; 1.
DR Gene3D; 3.30.365.10; Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain; 4.
DR InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR InterPro; IPR016208; Ald_Oxase/xanthine_DH-like.
DR InterPro; IPR008274; AldOxase/xan_DH_MoCoBD1.
DR InterPro; IPR046867; AldOxase/xan_DH_MoCoBD2.
DR InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR PANTHER; PTHR11908; XANTHINE DEHYDROGENASE; 1.
DR PANTHER; PTHR11908:SF157; XANTHINE DEHYDROGENASE SUBUNIT D-RELATED; 1.
DR Pfam; PF01315; Ald_Xan_dh_C; 1.
DR Pfam; PF02738; MoCoBD_1; 1.
DR Pfam; PF20256; MoCoBD_2; 1.
DR SMART; SM01008; Ald_Xan_dh_C; 1.
DR SUPFAM; SSF54665; CO dehydrogenase molybdoprotein N-domain-like; 1.
DR SUPFAM; SSF56003; Molybdenum cofactor-binding domain; 1.
PE 4: Predicted;
FT DOMAIN 34..145
FT /note="Aldehyde oxidase/xanthine dehydrogenase a/b
FT hammerhead"
FT /evidence="ECO:0000259|SMART:SM01008"
SQ SEQUENCE 787 AA; 86556 MW; 998DA8EDA72DF33F CRC64;
Query Match 100.0%; Score 4169; Length 787;
Best Local Similarity 100.0%;
Matches 787; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MHKDCDKHYFKKPEFYRLTGENNYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MHKDCDKHYFKKPEFYRLTGENNYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
Qy 61 AKILSIDTSEAEKLPGVKCILTARDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDVA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 AKILSIDTSEAEKLPGVKCILTARDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDVA 120
Qy 121 AVAAVDEETAQRAADLIKVEYQVLPGVFDPFEAMEENAPEVNWEGKGIHNIGMQSVMKAG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 AVAAVDEETAQRAADLIKVEYQVLPGVFDPFEAMEENAPEVNWEGKGIHNIGMQSVMKAG 180
Qy 181 TDIDEEFDRASYVQHRDYKTHRMVHAAMEPHGAVATYRNGTYTIWMSTQMSFVDQFWYAR 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TDIDEEFDRASYVQHRDYKTHRMVHAAMEPHGAVATYRNGTYTIWMSTQMSFVDQFWYAR 240
Qy 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMAEMTGRPVRMILSREEVFQTTRNR 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMAEMTGRPVRMILSREEVFQTTRNR 300
Qy 301 HPIYMHIDTAFGTDGKLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 HPIYMHIDTAFGTDGKLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
Qy 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQMGIDPVEFRKISAADPGYVAPAGLAI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQMGIDPVEFRKISAADPGYVAPAGLAI 420
Qy 421 TSCAYKETLDTAAKEIGWYEKKDKLKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TSCAYKETLDTAAKEIGWYEKKDKLKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
Qy 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMDMVKTFMSDTFLTPWDSGSYGSRV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMDMVKTFMSDTFLTPWDSGSYGSRV 540
Qy 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISKEKAEYQMSIGDAMFKY 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISKEKAEYQMSIGDAMFKY 600
Qy 601 MTVKGGDELIGVGSYYHRTDNSQYNGNNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 MTVKGGDELIGVGSYYHRTDNSQYNGNNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
Qy 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTREGKILNPNFRDYRLPTALDMPKM 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTREGKILNPNFRDYRLPTALDMPKM 720
Qy 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGM 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGM 780
Qy 781 KDDRNSK 787
|||||||
Db 781 KDDRNSK 787
Sequence alignment of SEQ ID NO:4 of the instant application (“Qy”) and the polypeptide of RGX32804.1 (“Db”)
A0A413FKP9_9FIRM
ID A0A413FKP9_9FIRM Unreviewed; 288 AA.
AC A0A413FKP9;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 05-FEB-2025, entry version 15.
DE SubName: Full=Xanthine dehydrogenase family protein subunit M {ECO:0000313|EMBL:RGX32804.1};
GN ORFNames=DWV29_00885 {ECO:0000313|EMBL:RGX32804.1};
OS Enterocloster asparagiformis.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=333367 {ECO:0000313|EMBL:RGX32804.1, ECO:0000313|Proteomes:UP000283880};
RN [1] {ECO:0000313|EMBL:RGX32804.1, ECO:0000313|Proteomes:UP000283880}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF04-15 {ECO:0000313|EMBL:RGX32804.1,
RC ECO:0000313|Proteomes:UP000283880};
RA Zou Y., Xue W., Luo G.;
RT "A genome reference for cultivated species of the human gut microbiota.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
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:RGX32804.1}.
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; QSBM01000001; RGX32804.1; -; Genomic_DNA.
DR RefSeq; WP_024734846.1; NZ_QSBM01000001.1.
DR AlphaFoldDB; A0A413FKP9; -.
DR OrthoDB; 9789842at2; -.
DR Proteomes; UP000283880; Unassembled WGS sequence.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.30.465.10; -; 1.
DR Gene3D; 3.30.390.50; CO dehydrogenase flavoprotein, C-terminal domain; 1.
DR Gene3D; 3.30.43.10; Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2; 1.
DR InterPro; IPR005107; CO_DH_flav_C.
DR InterPro; IPR036683; CO_DH_flav_C_dom_sf.
DR InterPro; IPR051312; Diverse_Substr_Oxidored.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR002346; Mopterin_DH_FAD-bd.
DR PANTHER; PTHR42659; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR PANTHER; PTHR42659:SF2; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR Pfam; PF03450; CO_deh_flav_C; 1.
DR Pfam; PF00941; FAD_binding_5; 1.
DR SMART; SM01092; CO_deh_flav_C; 1.
DR SUPFAM; SSF55447; CO dehydrogenase flavoprotein C-terminal domain-like; 1.
DR SUPFAM; SSF56176; FAD-binding/transporter-associated domain-like; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 4: Predicted;
KW FAD {ECO:0000256|ARBA:ARBA00022827};
KW Flavoprotein {ECO:0000256|ARBA:ARBA00022630}.
FT DOMAIN 1..178
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000259|PROSITE:PS51387"
SQ SEQUENCE 288 AA; 30841 MW; 7BC5DFF4EBAF9C6E CRC64;
Query Match 100.0%; Score 1430; Length 288;
Best Local Similarity 100.0%;
Matches 288; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MVLPQFEYLAPKTIGEACNLLLELGSTAKVMAGATDLIPPMKDKVIAPEYIIDLKKIPGL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MVLPQFEYLAPKTIGEACNLLLELGSTAKVMAGATDLIPPMKDKVIAPEYIIDLKKIPGL 60
Qy 61 DDLEYDEKEGLKIGALTTLRAIETSPLVKEKNPAIA HAAKVVASTQIRAKGTMAGNICNA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 DDLEYDEKEGLKIGALTTLRAIETSPLVKEKNPAIA HAAKVVASTQIRAKGTMAGNICNA 120
Qy 121 SPSCDTAPNLLAQGAKILVQGPNKDRVIKIDDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SPSCDTAPNLLAQGAKILVQGPNKDRVIKIDDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
Qy 181 RAAYIKHAVRKAMDLAIIGVAVKIRVEVGICTDAKIALGAVAATPIRAPRAEEALIGKAL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 RAAYIKHAVRKAMDLAIIGVAVKIRVEVGICTDAKIALGAVAATPIRAPRAEEALIGKAL 240
Qy 241 TDEVIVRASEEAMNSCHPISDIRASAEYRKDMIRVFTKRAIKQAMESL 288
||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TDEVIVRASEEAMNSCHPISDIRASAEYRKDMIRVFTKRAIKQAMESL 288
Sequence alignment of SEQ ID NO:5 of the instant application (“Qy”) and the polypeptide of RGX32805.1 (“Db”)
ID A0A413FKG8_9FIRM Unreviewed; 163 AA.
AC A0A413FKG8;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 05-FEB-2025, entry version 15.
DE SubName: Full=(2Fe-2S)-binding protein {ECO:0000313|EMBL:RGX32805.1};
GN ORFNames=DWV29_00890 {ECO:0000313|EMBL:RGX32805.1};
OS Enterocloster asparagiformis.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=333367 {ECO:0000313|EMBL:RGX32805.1, ECO:0000313|Proteomes:UP000283880};
RN [1] {ECO:0000313|EMBL:RGX32805.1, ECO:0000313|Proteomes:UP000283880}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF04-15 {ECO:0000313|EMBL:RGX32805.1,
RC ECO:0000313|Proteomes:UP000283880};
RA Zou Y., Xue W., Luo G.;
RT "A genome reference for cultivated species of the human gut microbiota.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
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:RGX32805.1}.
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; QSBM01000001; RGX32805.1; -; Genomic_DNA.
DR RefSeq; WP_007711967.1; NZ_QSBM01000001.1.
DR AlphaFoldDB; A0A413FKG8; -.
DR OrthoDB; 9796880at2; -.
DR Proteomes; UP000283880; Unassembled WGS sequence.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR CDD; cd00207; fer2; 1.
DR FunFam; 1.10.150.120:FF:000003; Carbon monoxide dehydrogenase, small subunit; 1.
DR FunFam; 3.10.20.30:FF:000020; Xanthine dehydrogenase iron-sulfur subunit; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 1.10.150.120; [2Fe-2S]-binding domain; 1.
DR InterPro; IPR002888; 2Fe-2S-bd.
DR InterPro; IPR036884; 2Fe-2S-bd_dom_sf.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR051452; Diverse_Oxidoreductases.
DR PANTHER; PTHR44379; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR PANTHER; PTHR44379:SF5; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF01799; Fer2_2; 1.
DR SUPFAM; SSF54292; 2Fe-2S ferredoxin-like; 1.
DR SUPFAM; SSF47741; CO dehydrogenase ISP C-domain like; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
PE 4: Predicted;
KW 2Fe-2S {ECO:0000256|ARBA:ARBA00022714};
KW Iron {ECO:0000256|ARBA:ARBA00023004};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022714};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002}.
FT DOMAIN 3..79
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000259|PROSITE:PS51085"
SQ SEQUENCE 163 AA; 17896 MW; 0FC8CCC1F52AD375 CRC64;
Query Match 100.0%; Score 871; Length 163;
Best Local Similarity 100.0%;
Matches 163; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKHSISLIINGDPVDAIVKDNLTLLDFLRDQMFLTGTKKGCEEGECGACTVMLDGKPVNS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKHSISLIINGDPVDAIVKDNLTLLDFLRDQMFLTGTKKGCEEGECGACTVMLDGKPVNS 60
Qy 61 CCTLAVECDGHEILTVEGVAKEGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNRH 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCTLAVECDGHEILTVEGVAKEGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNRH 120
Qy 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAADEMNWEEESENA 163
|||||||||||||||||||||||||||||||||||||||||||
Db 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAADEMNWEEESENA 163
Sequence alignment of SEQ ID NO:6 of the instant application (“Qy”) and the polypeptide of RGX32806.1 (“Db”)
ID A0A413FKI6_9FIRM Unreviewed; 787 AA.
AC A0A413FKI6;
DT 08-MAY-2019, integrated into UniProtKB/TrEMBL.
DT 08-MAY-2019, sequence version 1.
DT 05-FEB-2025, entry version 14.
DE SubName: Full=4-hydroxybenzoyl-CoA reductase {ECO:0000313|EMBL:RGX32806.1};
GN ORFNames=DWV29_00895 {ECO:0000313|EMBL:RGX32806.1};
OS Enterocloster asparagiformis.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=333367 {ECO:0000313|EMBL:RGX32806.1, ECO:0000313|Proteomes:UP000283880};
RN [1] {ECO:0000313|EMBL:RGX32806.1, ECO:0000313|Proteomes:UP000283880}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF04-15 {ECO:0000313|EMBL:RGX32806.1,
RC ECO:0000313|Proteomes:UP000283880};
RA Zou Y., Xue W., Luo G.;
RT "A genome reference for cultivated species of the human gut microbiota.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
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:RGX32806.1}.
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; QSBM01000001; RGX32806.1; -; Genomic_DNA.
DR RefSeq; WP_007711966.1; NZ_QSBM01000001.1.
DR AlphaFoldDB; A0A413FKI6; -.
DR OrthoDB; 9759099at2; -.
DR Proteomes; UP000283880; Unassembled WGS sequence.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.90.1170.50; Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead; 1.
DR Gene3D; 3.30.365.10; Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain; 4.
DR InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR InterPro; IPR016208; Ald_Oxase/xanthine_DH-like.
DR InterPro; IPR008274; AldOxase/xan_DH_MoCoBD1.
DR InterPro; IPR046867; AldOxase/xan_DH_MoCoBD2.
DR InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR PANTHER; PTHR11908; XANTHINE DEHYDROGENASE; 1.
DR PANTHER; PTHR11908:SF157; XANTHINE DEHYDROGENASE SUBUNIT D-RELATED; 1.
DR Pfam; PF01315; Ald_Xan_dh_C; 1.
DR Pfam; PF02738; MoCoBD_1; 1.
DR Pfam; PF20256; MoCoBD_2; 1.
DR SMART; SM01008; Ald_Xan_dh_C; 1.
DR SUPFAM; SSF54665; CO dehydrogenase molybdoprotein N-domain-like; 1.
DR SUPFAM; SSF56003; Molybdenum cofactor-binding domain; 1.
PE 4: Predicted;
FT DOMAIN 34..145
FT /note="Aldehyde oxidase/xanthine dehydrogenase a/b
FT hammerhead"
FT /evidence="ECO:0000259|SMART:SM01008"
SQ SEQUENCE 787 AA; 86310 MW; 6727620E7CA20090 CRC64;
Query Match 100.0%; Score 4167; Length 787;
Best Local Similarity 100.0%;
Matches 787; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MHKDCDKHYFKKPEFYRLTGGNNYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MHKDCDKHYFKKPEFYRLTGGNNYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
Qy 61 ARIISIDTSAAEKLPGVKCILTAKDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDIA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ARIISIDTSAAEKLPGVKCILTAKDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDIA 120
Qy 121 AVAAVDEETAQRAVDLIKVEYEVLPGVFDPFEAMEDDAPEVNWEGKGIHNIGMQSVMKAG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 AVAAVDEETAQRAVDLIKVEYEVLPGVFDPFEAMEDDAPEVNWEGKGIHNIGMQSVMKAG 180
Qy 181 TDIDQEFDSASYVQHRDYKTHRMVHAAMEPHGAVATYRNGTYTIWMSTQMSFVDQFWYAR 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TDIDQEFDSASYVQHRDYKTHRMVHAAMEPHGAVATYRNGTYTIWMSTQMSFVDQFWYAR 240
Qy 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMSEITGRPVRMILSREEVFQTTRNR 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMSEITGRPVRMILSREEVFQTTRNR 300
Qy 301 HPIYMHIDTAFGADGRLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 HPIYMHIDTAFGADGRLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
Qy 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQLGMDPVEFRKISAADPGYVAPAGLAI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQLGMDPVEFRKISAADPGYVAPAGLAI 420
Qy 421 TSCAYKETLDTAAREIGWNEKKDKMKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TSCAYKETLDTAAREIGWNEKKDKMKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
Qy 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMNMVKTFMSDTFLTPWDSGSYGSRV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMNMVKTFMSDTFLTPWDSGSYGSRV 540
Qy 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISRENAQLQMPIGDAMFKY 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISRENAQLQMPIGDAMFKY 600
Qy 601 MTVKGGDELIGVGSYYHRTDNSQYNGTNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 MTVKGGDELIGVGSYYHRTDNSQYNGTNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
Qy 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTKEGKILNPNFRDYRLPTALDMPKM 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTKEGKILNPNFRDYRLPTALDMPKM 720
Qy 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGM 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGM 780
Qy 781 KDDRNSK 787
|||||||
Db 781 KDDRNSK 787
Sequence alignment of SEQ ID NO:7 of the instant application (“Qy”) and the polypeptide of EHE99819.1 (“Db”)
G5HFF4_9FIRM
ID G5HFF4_9FIRM Unreviewed; 288 AA.
AC G5HFF4;
DT 25-JAN-2012, integrated into UniProtKB/TrEMBL.
DT 25-JAN-2012, sequence version 1.
DT 05-FEB-2025, entry version 43.
DE RecName: Full=FAD-binding PCMH-type domain-containing protein {ECO:0000259|PROSITE:PS51387};
GN ORFNames=HMPREF9469_01316 {ECO:0000313|EMBL:EHE99819.1};
OS [Clostridium] citroniae WAL-17108.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=742733 {ECO:0000313|EMBL:EHE99819.1, ECO:0000313|Proteomes:UP000003763};
RN [1] {ECO:0000313|EMBL:EHE99819.1, ECO:0000313|Proteomes:UP000003763}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=WAL-17108 {ECO:0000313|EMBL:EHE99819.1,
RC ECO:0000313|Proteomes:UP000003763};
RG The Broad Institute Genome Sequencing Platform;
RA Earl A., Ward D., Feldgarden M., Gevers D., Finegold S.M., Summanen P.H.,
RA Molitoris D.R., Vaisanen M.L., Daigneault M., Allen-Vercoe E., Young S.K.,
RA Zeng Q., Gargeya S., Fitzgerald M., Haas B., Abouelleil A., Alvarado L.,
RA Arachchi H.M., Berlin A., Brown A., Chapman S.B., Chen Z., Dunbar C.,
RA Freedman E., Gearin G., Gellesch M., Goldberg J., Griggs A., Gujja S.,
RA Heiman D., Howarth C., Larson L., Lui A., MacDonald P.J.P., Montmayeur A.,
RA Murphy C., Neiman D., Pearson M., Priest M., Roberts A., Saif S., Shea T.,
RA Shenoy N., Sisk P., Stolte C., Sykes S., Wortman J., Nusbaum C., Birren B.;
RT "The Genome Sequence of Clostridium citroniae WAL-17108.";
RL Submitted (AUG-2011) to the EMBL/GenBank/DDBJ databases.
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:EHE99819.1}.
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; ADLJ01000009; EHE99819.1; -; Genomic_DNA.
DR RefSeq; WP_007860287.1; NZ_JH376420.1.
DR AlphaFoldDB; G5HFF4; -.
DR PATRIC; fig|742733.3.peg.1352; -.
DR eggNOG; COG1319; Bacteria.
DR HOGENOM; CLU_058050_0_1_9; -.
DR Proteomes; UP000003763; Unassembled WGS sequence.
DR GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.30.465.10; -; 1.
DR Gene3D; 3.30.390.50; CO dehydrogenase flavoprotein, C-terminal domain; 1.
DR Gene3D; 3.30.43.10; Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2; 1.
DR InterPro; IPR005107; CO_DH_flav_C.
DR InterPro; IPR036683; CO_DH_flav_C_dom_sf.
DR InterPro; IPR051312; Diverse_Substr_Oxidored.
DR InterPro; IPR016166; FAD-bd_PCMH.
DR InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR InterPro; IPR002346; Mopterin_DH_FAD-bd.
DR PANTHER; PTHR42659; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR PANTHER; PTHR42659:SF2; XANTHINE DEHYDROGENASE SUBUNIT C-RELATED; 1.
DR Pfam; PF03450; CO_deh_flav_C; 1.
DR Pfam; PF00941; FAD_binding_5; 1.
DR SMART; SM01092; CO_deh_flav_C; 1.
DR SUPFAM; SSF55447; CO dehydrogenase flavoprotein C-terminal domain-like; 1.
DR SUPFAM; SSF56176; FAD-binding/transporter-associated domain-like; 1.
DR PROSITE; PS51387; FAD_PCMH; 1.
PE 4: Predicted;
KW FAD {ECO:0000256|ARBA:ARBA00022827};
KW Flavoprotein {ECO:0000256|ARBA:ARBA00022630}.
FT DOMAIN 1..178
FT /note="FAD-binding PCMH-type"
FT /evidence="ECO:0000259|PROSITE:PS51387"
SQ SEQUENCE 288 AA; 30933 MW; 49352867714ACAC1 CRC64;
Query Match 100.0%; Score 1443; Length 288;
Best Local Similarity 100.0%;
Matches 288; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MVLPQFEYLAPKTIGEACNLLLELGSPAKVMAGATDLIPPMKDKAISPEYLIDLKKIPDL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MVLPQFEYLAPKTIGEACNLLLELGSPAKVMAGATDLIPPMKDKAISPEYLIDLKKIPDL 60
Qy 61 DYLEYDEKEGLKIGALTTLRTIETSPLVKEKNPAVAHAAKVVASTQIRAKGTMAGNICNA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 DYLEYDEKEGLKIGALTTLRTIETSPLVKEKNPAVAHAAKVVASTQIRAKGTMAGNICNA 120
Qy 121 SPSCDTAPNLLAQGAKILVQGPNKDRIIQAEDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SPSCDTAPNLLAQGAKILVQGPNKDRIIQAEDFFLGVKKTSLEPGEIVTGIVIPPLAENE 180
Qy 181 RAAYIKHAVRKAMDLAIIGVAVKIKVEDGICTDVHIALGAVAATPIRAPKAEEALIGKAL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 RAAYIKHAVRKAMDLAIIGVAVKIKVEDGICTDVHIALGAVAATPIRAPKAEEALIGKAL 240
Qy 241 TDEVIVKASEEAMDSCHPISDIRASAEYRKDMIRVFTKRAVRQAMECL 288
||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TDEVIVKASEEAMDSCHPISDIRASAEYRKDMIRVFTKRAVRQAMECL 288
Sequence alignment of SEQ ID NO:8 of the instant application (“Qy”) and the polypeptide of EHE99818.1 (“Db”)
ID G5HFF3_9FIRM Unreviewed; 163 AA.
AC G5HFF3;
DT 25-JAN-2012, integrated into UniProtKB/TrEMBL.
DT 25-JAN-2012, sequence version 1.
DT 05-FEB-2025, entry version 44.
DE RecName: Full=2Fe-2S ferredoxin-type domain-containing protein {ECO:0000259|PROSITE:PS51085};
GN ORFNames=HMPREF9469_01315 {ECO:0000313|EMBL:EHE99818.1};
OS [Clostridium] citroniae WAL-17108.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=742733 {ECO:0000313|EMBL:EHE99818.1, ECO:0000313|Proteomes:UP000003763};
RN [1] {ECO:0000313|EMBL:EHE99818.1, ECO:0000313|Proteomes:UP000003763}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=WAL-17108 {ECO:0000313|EMBL:EHE99818.1,
RC ECO:0000313|Proteomes:UP000003763};
RG The Broad Institute Genome Sequencing Platform;
RA Earl A., Ward D., Feldgarden M., Gevers D., Finegold S.M., Summanen P.H.,
RA Molitoris D.R., Vaisanen M.L., Daigneault M., Allen-Vercoe E., Young S.K.,
RA Zeng Q., Gargeya S., Fitzgerald M., Haas B., Abouelleil A., Alvarado L.,
RA Arachchi H.M., Berlin A., Brown A., Chapman S.B., Chen Z., Dunbar C.,
RA Freedman E., Gearin G., Gellesch M., Goldberg J., Griggs A., Gujja S.,
RA Heiman D., Howarth C., Larson L., Lui A., MacDonald P.J.P., Montmayeur A.,
RA Murphy C., Neiman D., Pearson M., Priest M., Roberts A., Saif S., Shea T.,
RA Shenoy N., Sisk P., Stolte C., Sykes S., Wortman J., Nusbaum C., Birren B.;
RT "The Genome Sequence of Clostridium citroniae WAL-17108.";
RL Submitted (AUG-2011) to the EMBL/GenBank/DDBJ databases.
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:EHE99818.1}.
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; ADLJ01000009; EHE99818.1; -; Genomic_DNA.
DR RefSeq; WP_007860286.1; NZ_JH376420.1.
DR AlphaFoldDB; G5HFF3; -.
DR GeneID; 77448557; -.
DR PATRIC; fig|742733.3.peg.1351; -.
DR eggNOG; COG2080; Bacteria.
DR HOGENOM; CLU_052511_3_1_9; -.
DR Proteomes; UP000003763; Unassembled WGS sequence.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR CDD; cd00207; fer2; 1.
DR FunFam; 1.10.150.120:FF:000003; Carbon monoxide dehydrogenase, small subunit; 1.
DR FunFam; 3.10.20.30:FF:000020; Xanthine dehydrogenase iron-sulfur subunit; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 1.10.150.120; [2Fe-2S]-binding domain; 1.
DR InterPro; IPR002888; 2Fe-2S-bd.
DR InterPro; IPR036884; 2Fe-2S-bd_dom_sf.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR051452; Diverse_Oxidoreductases.
DR PANTHER; PTHR44379; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR PANTHER; PTHR44379:SF5; OXIDOREDUCTASE WITH IRON-SULFUR SUBUNIT; 1.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF01799; Fer2_2; 1.
DR SUPFAM; SSF54292; 2Fe-2S ferredoxin-like; 1.
DR SUPFAM; SSF47741; CO dehydrogenase ISP C-domain like; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
PE 4: Predicted;
KW 2Fe-2S {ECO:0000256|ARBA:ARBA00022714};
KW Iron {ECO:0000256|ARBA:ARBA00023004};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022714};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002}.
FT DOMAIN 3..79
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000259|PROSITE:PS51085"
SQ SEQUENCE 163 AA; 17784 MW; 47CC3E6F84F65661 CRC64;
Query Match 100.0%; Score 873; Length 163;
Best Local Similarity 100.0%;
Matches 163; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKHSISLTVNGDCVDAVVKDNLTLLDFLRDQLFLTGTKKGCEEGECGACTVMLDGKPVNS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKHSISLTVNGDCVDAVVKDNLTLLDFLRDQLFLTGTKKGCEEGECGACTVMLDGKPVNS 60
Qy 61 CCTLAVECDGHDIITVEGIAENGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNRH 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCTLAVECDGHDIITVEGIAENGMLHPIQKQFIEKWAMQCGYCTPGMIMSAKALLDVNRH 120
Qy 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAAAQMNWEEESENA 163
|||||||||||||||||||||||||||||||||||||||||||
Db 121 PTELEIREAIEGNLCRCTGYAKIVEAIQAAAAQMNWEEESENA 163
Sequence alignment of SEQ ID NO:9 of the instant application (“Qy”) and the polypeptide of EHE99817.1 (“Db”)
ID G5HFF2_9FIRM Unreviewed; 787 AA.
AC G5HFF2;
DT 25-JAN-2012, integrated into UniProtKB/TrEMBL.
DT 25-JAN-2012, sequence version 1.
DT 05-FEB-2025, entry version 40.
DE RecName: Full=Aldehyde oxidase/xanthine dehydrogenase a/b hammerhead domain-containing protein {ECO:0000259|SMART:SM01008};
GN ORFNames=HMPREF9469_01314 {ECO:0000313|EMBL:EHE99817.1};
OS [Clostridium] citroniae WAL-17108.
OC Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales;
OC Lachnospiraceae; Enterocloster.
OX NCBI_TaxID=742733 {ECO:0000313|EMBL:EHE99817.1, ECO:0000313|Proteomes:UP000003763};
RN [1] {ECO:0000313|EMBL:EHE99817.1, ECO:0000313|Proteomes:UP000003763}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=WAL-17108 {ECO:0000313|EMBL:EHE99817.1,
RC ECO:0000313|Proteomes:UP000003763};
RG The Broad Institute Genome Sequencing Platform;
RA Earl A., Ward D., Feldgarden M., Gevers D., Finegold S.M., Summanen P.H.,
RA Molitoris D.R., Vaisanen M.L., Daigneault M., Allen-Vercoe E., Young S.K.,
RA Zeng Q., Gargeya S., Fitzgerald M., Haas B., Abouelleil A., Alvarado L.,
RA Arachchi H.M., Berlin A., Brown A., Chapman S.B., Chen Z., Dunbar C.,
RA Freedman E., Gearin G., Gellesch M., Goldberg J., Griggs A., Gujja S.,
RA Heiman D., Howarth C., Larson L., Lui A., MacDonald P.J.P., Montmayeur A.,
RA Murphy C., Neiman D., Pearson M., Priest M., Roberts A., Saif S., Shea T.,
RA Shenoy N., Sisk P., Stolte C., Sykes S., Wortman J., Nusbaum C., Birren B.;
RT "The Genome Sequence of Clostridium citroniae WAL-17108.";
RL Submitted (AUG-2011) to the EMBL/GenBank/DDBJ databases.
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:EHE99817.1}.
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DR EMBL; ADLJ01000009; EHE99817.1; -; Genomic_DNA.
DR RefSeq; WP_007860285.1; NZ_JH376420.1.
DR AlphaFoldDB; G5HFF2; -.
DR GeneID; 77448556; -.
DR PATRIC; fig|742733.3.peg.1350; -.
DR eggNOG; COG1529; Bacteria.
DR HOGENOM; CLU_001681_2_1_9; -.
DR Proteomes; UP000003763; Unassembled WGS sequence.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR Gene3D; 3.90.1170.50; Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead; 1.
DR Gene3D; 3.30.365.10; Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain; 4.
DR InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR InterPro; IPR016208; Ald_Oxase/xanthine_DH-like.
DR InterPro; IPR008274; AldOxase/xan_DH_MoCoBD1.
DR InterPro; IPR046867; AldOxase/xan_DH_MoCoBD2.
DR InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR PANTHER; PTHR11908; XANTHINE DEHYDROGENASE; 1.
DR PANTHER; PTHR11908:SF157; XANTHINE DEHYDROGENASE SUBUNIT D-RELATED; 1.
DR Pfam; PF01315; Ald_Xan_dh_C; 1.
DR Pfam; PF02738; MoCoBD_1; 1.
DR Pfam; PF20256; MoCoBD_2; 1.
DR SMART; SM01008; Ald_Xan_dh_C; 1.
DR SUPFAM; SSF54665; CO dehydrogenase molybdoprotein N-domain-like; 1.
DR SUPFAM; SSF56003; Molybdenum cofactor-binding domain; 1.
PE 4: Predicted;
FT DOMAIN 34..145
FT /note="Aldehyde oxidase/xanthine dehydrogenase a/b
FT hammerhead"
FT /evidence="ECO:0000259|SMART:SM01008"
SQ SEQUENCE 787 AA; 86383 MW; F3C7F7C641979752 CRC64;
Query Match 100.0%; Score 4174; Length 787;
Best Local Similarity 100.0%;
Matches 787; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MHKDCDKHYFKKPEFYRLTGENHYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MHKDCDKHYFKKPEFYRLTGENHYVRIDAEDKVTGHGQYVGDIMFPDMLTGKMVRSPYAS 60
Qy 61 ARILSIDTSEAEKLPGVKCILTAKDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDVA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ARILSIDTSEAEKLPGVKCILTAKDFEWKSLVGNGEFAAEFADKEVLCSEKVRQVGDDVA 120
Qy 121 AVAAVDEETAQRAVDLIKVEYEVLPGVFDPFEAMEEGAPEVNWEGKGLHNIGMQSVMKAG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 AVAAVDEETAQRAVDLIKVEYEVLPGVFDPFEAMEEGAPEVNWEGKGLHNIGMQSVMKAG 180
Qy 181 TDIDQEFDNAGYVQHRDYKTHRMVHAAMEPHGAVATFRNGTYTIWMSTQMSYVDQFWYAR 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TDIDQEFDNAGYVQHRDYKTHRMVHAAMEPHGAVATFRNGTYTIWMSTQMSYVDQFWYAR 240
Qy 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMSELTGRPVRMILSREEVFQTTRNR 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CLGVGENQVRVIKPLVGGGFGGKLDSYSFGLCAAKMSELTGRPVRMILSREEVFQTTRNR 300
Qy 301 HPIYMHIDTAFGADGKLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 HPIYMHIDTAFGADGKLLAKKCYHVLDGGPYGGSGVAACAQSTLWANFPYKMNSVDFLAR 360
Qy 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQMGIDPVEFRKMSAADPGYVAPAGLAI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 RVYTNNPSAGAMRGYTACQVHFAHDLNMQFAADQMGIDPVEFRKMSAADPGYVAPAGLAI 420
Qy 421 TSCAYKETLDTAAREIGWYDKKDQMKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 TSCAYKETLDTAAREIGWYDKKDQMKKGEGIGFAGTGFVSGTGFAVLEAPNQSSACVTLR 480
Qy 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMDMVKTFMSDTFLTPWDSGSYGSRV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 MNKRGMATLYIGSHDIGQGSDTVMTAIVAEELGLPMDMVKTFMSDTFLTPWDSGSYGSRV 540
Qy 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISKENAELQMPIGDAMFKY 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TFLAGNAARRAAVDAKRQLFEVIAPMWGVMPETLECLDGKVISKENAELQMPIGDAMFKY 600
Qy 601 MTVKGGDELVGIGSYYHRTDNSQYNGTNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 MTVKGGDELVGIGSYYHRTDNSQYNGTNTTNYAPAYSFSTGAAHLTVDEETGVLDIDEFV 660
Qy 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTKEGKILNPNFRDYRLPTALDMPKM 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 FAHDCGRALNKRAVEGQLEGSIGMGLGYAVYEHNVTKEGKILNPNFRDYRLPTALDMPKM 720
Qy 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGL 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 RTFYDFTPDEEGPLGAKEAGEGSAAPVAPAIA NAVNMATGVYFTELPLDPEHIWRALHGL 780
Qy 781 KDDRNSK 787
|||||||
Db 781 KDDRNSK 787
Prosecution Insights