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
The response filed on June 1, 2026 has been entered.
Election/Restrictions
Applicant’s election of Group I with an election of species of:
Pseudomonas putida as the recombinant microorganism and comprising
functional deletion of a glucokinase gene encoding a protein comprising
an amino acid sequence of SEQ ID NO:2,
a functional deletion of a quinoprotein glucose dehydrogenase gene
encoding a protein comprising an amino acid sequence of SEQ ID NO:4,
a functional deletion of a carbohydrate transporter gene encoding a protein
comprising an amino acid sequence of SEQ ID NO:6,
a recombinant gene encoding HmfA of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:13,
a recombinant gene encoding HmfB of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:15,
a recombinant gene encoding HmfC of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:17,
a recombinant gene encoding HmfD of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:19,
a recombinant gene encoding HmfE of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:21,
a recombinant gene encoding HmfT1 of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:23,
a recombinant gene encoding HmfF of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:26,
a recombinant gene encoding HmfG of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:28,
a recombinant gene encoding HmfH' of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:30,
a recombinant gene encoding HmfH of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:32,
a recombinant gene encoding HmfS of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:34; and
a recombinant gene encoding HmfT2 of Cupriavidus basilensis encoding a
protein comprising an amino acid sequence of SEQ ID NO:36
in the reply filed on June 1, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 6-7 and 14-18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species (claims 6-7 and 14) and invention (claims 15-18), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on June 1, 2026.
Status of Claims
Claims 1-18 are pending.
Claims 6-7 and 14-18 are withdrawn.
Claims 1-5 and 8-13 are under examination.
Claim for Domestic Priority
Applicants' claim for domestic priority under 35 USC 119(e) to US provisional application 63/505,197, filed 05/31/2023, is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on February 18, 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 1 and claims 2-5 and 8-13 depending therefrom are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 1 recites the broad recitation “1 or more” and “14 or more”, which is the narrower statement of the limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. Appropriate correction is requested.
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.
Claims 1-5 and 8-13 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.
It is noted that MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' The claims have been broadly interpreted to encompass (A) any recombinant microorganism, any aerobic bacterium, or Pseudomonas comprising (B) (i) functional deletion of glucokinase gene, P. putida glk, or gene encoding the glucokinase of SEQ ID NO:2, (ii) functional deletion of quinoprotein glucose dehydrogenase gene, P. putida gcd, or gene encoding the quinoprotein glucose dehydrogenase of SEQ ID NO:4, and (iii) functional deletion of carbohydrate transporter gene, P. putida oprB-II, or gene encoding the carbohydrate transporter of SEQ ID NO:5, and (C) (i) recombinant gene encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 or any homolog thereof or (ii) recombinant gene encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 having at least 95% sequence identity to SEQ ID NO:13, 15, 17, 19, 21, 23, 26, 28, 30, 32, 34, and 36, respectively. Therefore, the claims are directed to (A) a genus of microorganism comprising (B) a genus of deletions of its glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter, and (C) a genus of genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 or any homologs thereof.
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 recitations of “glucokinase” “quinoprotein glucose dehydrogenase”, “carbohydrate transporter”, and “Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2” 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 recombinant Pseudomonas putida comprising recombinant genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2, see Koopman (WO 2011/026906 – form PTO-892. 18-19, page 27-30, pages 88-89, and Fig. 6). The prior art also discloses P. putida glucokinase (glk), P. putida quinoprotein glucose dehydrogenase (gcd), and P. putida carbohydrate transporter (oprB-II), see Q88P42 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), Q88MX4 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), and Q88MX3 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892). However, the claimed genus of any microorganism, any aerobic bacterium, or any Pseudomonas comprising a functional deletion of its glucokinase, quinoprotein glucose dehydrogenase, carbohydrate transporter, and any homologs of Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 were not known in the art.
The specification is limited to a recombinant P.putida comprising a deletion of its genes encoding glk of SEQ ID NO:2, gcd of SEQ ID NO:4, and oprB-II of SEQ ID NO:4 and comprising Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 having the amino acid sequence of SEQ ID NO:13, 15, 17, 19, 21, 23, 26, 28, 30, 32, 34, and 36, respectively, wherein the recombinant P. putida has reduced consumption of a carbohydrate and increased consumption of a substituted furan compared to the unmodified P. putida. 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.
The claimed invention requires a defined set of microorganism, glucokinase, quinoprotein glucose dehydrogenase, carbohydrate transporter, and Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2. A “laundry list” disclosure of every possible moiety does not necessarily constitute a written description of every species in a genus because it would not “reasonably lead” those skilled in the art to any particular species, see Fujikawa v. Wattanasin, 93 F.3d 1559, 1571, 39 USPQ2d 1895, 1905 (Fed. Cir. 1996) or MPEP 2163. While the exemplary microorganism, glucokinase, quinoprotein glucose dehydrogenase, carbohydrate transporter, and Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2. were known in the art, this knowledge alone would not allow one level of skill in the art to immediately envisage the claimed genus. Therefore, the level of skill and knowledge in the art is such that one of ordinary skill would not be able to identify without further testing the combination of glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter, and Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmtT2 to arrive at the claimed invention.
Also, the specification does not provide an actual reduction to practice of the genus because the specification fails to disclose the structure of genes encoding glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter from non-P. putida which must be known in order to inactivate the genes in any microorganism, any aerobic bacteria, or any Pseudomonas. The specification does not disclose the isolation or cloning of any non-P. putida genes encoding glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter. Because an P. putidai genes encoding glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter is not representative of the entire genus and the specification does not disclose structural features shared by members of the genus, the description of the above P. putidai genes encoding glucokinase, quinoprotein glucose dehydrogenase, and carbohydrate transporter would not have put the application in possession of the common structural attributes or features shared by members of the genus that structurally distinguish the members of the genus from other materials at the time of filing.
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 1-5 and 8-13.
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.
Claim(s) 1, 8-9, and 11-13 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Koopman (WO 2011/026906 – form PTO-892).
The specification of the instant application defines HmfS as a fatty acid hydroxylase and HmfT1 and HmfT2 as MFS transporters.
Regarding claims 1, 8-9, and 11-12, Koopman discloses recombinant Pseudomonas putida comprising recombinant genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2 having the amino acid sequence of SEQ ID NO:35, 37, 39, 41, 43, 45, 19, 21, 23, 25, 27, and 31, respectively (pages 18-19, page 27-30, pages 88-89, and Fig. 6).
Regarding claim 13, Koopman discloses recombinant genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, and HmfH having at least 95% sequence identity to the HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, and HmfH of SEQ ID NO:13, 15, 17, 19, 21, 23, 26, 28, 30, and 32, respectively, of the instant application (pages 18-19 and see the sequence alignments below). Koopman discloses that recombinant Pseudomonas putida comprising said genes has increased consumption of a substituted furan (pages 88-89). Koopman discloses that said recombinant Pseudomonas putida utilizes furfural as a sole carbon source (pages 88-89). Therefore, said recombinant Pseudomonas putida has reduced consumption of sugars, such as glucose, compared to the unmodified Pseudomonas putida.
Therefore, the reference of Koopman anticipates claims 1, 8-9, and 11-13.
Claim(s) 1-3 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zou (Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans. Biotechnol Biofuels. 2021 Nov 27;14(1):227 - form PTO-892).
Regarding claims 1-3, Zou discloses recombinant Pseudomonas putida comprising a functional deletion of its gcd, which encodes a quinoprotein glucose dehydrogenase (page 3, 2nd paragraph, Fig. 3, and page 5). Zou discloses deleting gcd and gtsABCD (sugar transporter) in P. putida results in efficient production of a fermentation product from lignocellulosic hydrolysate with a high content of inhibitors, present in lignocellulosic hydrolysate (page 3, 2nd paragraph and Fig 1).
Therefore, the reference of Lim anticipates claims 1-3.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 1-3, 8-9, and 11-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koopman (WO 2011/026906 – form PTO-892) and Zou (Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans. Biotechnol Biofuels. 2021 Nov 27;14(1):227 - form PTO-892).
The specification of the instant application defines HmfS as a fatty acid hydroxylase and HmfT1 and HmfT2 as MFS transporters.
Regarding claims 1, 8-9, and 11-12, Koopman discloses recombinant Pseudomonas putida comprising recombinant genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2 having the amino acid sequence of SEQ ID NO:35, 37, 39, 41, 43, 45, 19, 21, 23, 25, 27, and 31, respectively (pages 18-19, page 27-30, pages 88-89, and Fig. 6).
Regarding claim 13, Koopman discloses recombinant genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, and HmfH’, HmfH having at least 95% sequence identity to the HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, and HmfH of SEQ ID NO:13, 15, 17, 19, 21, 23, 26, 28, 30, and 32, respectively, of the instant application (pages 18-19 and see the sequence alignments below). Koopman discloses that recombinant Pseudomonas putida comprising said genes has increased consumption of a substituted furals (pages 88-89). Koopman discloses that said recombinant Pseudomonas putida utilizes furanic compounds such as furfural and HMF, as a sole carbon source (pages 88-89). Therefore, said recombinant Pseudomonas putida has reduced consumption of sugars, such as glucose, compared to the unmodified Pseudomonas putida. Further, Koopman discloses that lignocellulose-containing material evolves into fermentation inhibitors during the hydrolysis process step. Koopman discloses that furanic compounds, such as furfural, furfuryl alcohol, 5- (hydroxymethyl ) -furfural (HMF) and/or furoic acid, pose problems that are difficult to mitigate, since they inhibit the growth of microorganisms employed in the fermentation step, thereby inhibiting a suitable performance of these organisms and reducing yields (page 1).
Koopman does not disclose a functional deletion of Pseudomonas putida gcd.
Regarding claims 1-3, Zou discloses recombinant Pseudomonas putida comprising a functional deletion of its gcd, which encodes a quinoprotein glucose dehydrogenase (page 3, 2nd paragraph, Fig. 3, and page 5). Zou discloses deleting gcd and gtsABCD (sugar transporter) in P. putida results in for efficient production of a fermentation product from lignocellulosic hydrolysate with a high content of inhibitors, present in lignocellulosic hydrolysate (page 3, 2nd paragraph and Fig 1). Zou discloses that P. putida is capable of natively catabolizing glucose other than toxins and the excessive utilization of sugar during detoxification will adversely affect subsequence fermentation and reduce process efficiency (bottom of page 4 through page 5).
Therefore, in combining the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to modify the P. putida of Koopman by deleting its gcd encoding quinoprotein glucose dehydrogenase and gtsABCD. One of ordinary skill in the art would have been motivated to do so in order to improve production of a fermentation product from lignocellulosic hydrolysate with a high content of inhibitors. One of ordinary skill in the art would have had a reasonable expectation of success since Koopman discloses recombinant P. putida comprising genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2 and Zou discloses function deletion of P. putida gcd.
Therefore, the above references render claims 1-3, 8-9, and 11-13 prima facie obvious.
Claim(s) 4-5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koopman (WO 2011/026906 – form PTO-892) and Zou (Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans. Biotechnol Biofuels. 2021 Nov 27;14(1):227 - form PTO-892) as applied to claims 1-3, 8-9, and 11-13 above, and further in view of Lim (US 2023/0119263), Q88P42 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), Q88MX4 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), and Q88MX3 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892).
Koopman and Zou do not disclose the amino acid sequence of the quinoprotein glucose dehydrogenase having the amino acid sequence of SEQ ID NO:4, deleting P. putida gene encoding glucokinase having the amino acid sequence of SEQ ID NO:2, and deleting P. putida gene encoding carbohydrate transporter (oprB-II) having the amino acid sequence of SEQ ID NO:6.
Zou discloses developing a detoxified strain, P. putida, capable of removing inhibitors in hydrolysate and retaining monomeric sugars by deleting its sugar metabolism and P. putida has three glucose catabolism pathway (page 5).
Regarding claims 1-5 and 13, Zou discloses that the first route comprises transporting glucose to the cytoplasm from the periplasm by means of an ATP dependent ABC transporter, encoded by the gtsABCD operon (PP_1015-PP_1018), and is then phosphorylated by glucokinase to glucose-6-phosphate and subsequently converted by glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase to 6-phosphogluconate (page 5 and Fig. 3). Zou discloses that the second route comprises a periplasmic oxidation pathway mediated by quinoprotein glucose dehydrogenase gcd (PP_1444), wherein glucose is oxidized to gluconate by gcd in the periplasm. Gluconate is then transported to the cytoplasm and subsequently phosphorylated by gluconokinase to 6-phosphogluconate (page 5 and Fig. 3). Zou discloses gcd also oxidizes xylose to xylonate (page 5 and Fig. 3). Zou disclose that the third route comprise oxidation of gluconate to 2-ketogluconate. The resulting 2-ketogluconate is imported into the cytoplasm via the outer membrane and subsequently phosphorylated by 2-ketogluconate kinase into 2-keto-6-phosphogluconate, and later reduced to 6-phosphogluconate via 2-ketoglu conate-6-phosphate reductase (page 5 and Fig. 3). Zou discloses that the oxidation pathway and the direct phosphorylation route converge at the node of 6-phosphogluconate and therefore, gcd and gtsABCD were selectively removed (page 5 and Fig. 3).
Regarding claims 1-5 and 13, Lim discloses recombinant P. putida engineered decreased expression of quinoprotein glucose dehydrogenase (gcd PP_1444), glucokinase (glk PP_1011), carbohydrate transporter (oprB-II PP_1445) and gtsABCD operon (PP_1015-PP_1018) ([0193]). These proteins are involved in glucose catabolism (FIG. 3C). Glucose is transported into the periplasm by oprB-II, gcd converts glucose to gluconate and xylose to xylonate, and glk converts glucose to G6P (FIG. 3C).
Q88P42 discloses a P. putida glucokinase (glk PP_1011) having 100% sequence identity to the glucokinase having the amino acid sequence of SEQ ID NO:2 of the instant application (see pages 1-2 and the sequence alignment below).
Q88MX4 discloses a P. putida quinoprotein glucose dehydrogenase (gcd PP_1444) having 100% sequence identity to the quinoprotein glucose dehydrogenase having the amino acid sequence of SEQ ID NO:4 of the instant application (see pages 1-2 and the sequence alignment below).
Q88MX3 discloses a P. putida carbohydrate transporter (oprB-II PP_1445) having 100% sequence identity to the carbohydrate transporter having the amino acid sequence of SEQ ID NO:6 of the instant application (see pages 1-2 and the sequence alignment below).
Therefore, in combining the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to further modify the P. putida by deleting its glucokinase, carbohydrate transporter in addition to deleting quinoprotein glucose dehydrogenase, and gtsABCD operon. One of ordinary skill in the art would have been motivated to do so in order to further catabolize glucose to improve production of a fermentation product from lignocellulosic hydrolysate with a high content of inhibitors. One of ordinary skill in the art would have had a reasonable expectation of success since Koopman discloses recombinant P. putida comprising genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2, Zou discloses functional deletion of P. putida gcd, Lim discloses reduced expression of glk, gcd, and oprB-II and Lim disclose that glk, gcd, and oprB-II are involved in the catabolism of glucose.
Therefore, the above references render claims 1-5, 8-9, and 11-13 prima facie obvious.
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Koopman (WO 2011/026906 – form PTO-892), Zou (Efficient lactic acid production from dilute acid-pretreated lignocellulosic biomass by a synthetic consortium of engineered Pseudomonas putida and Bacillus coagulans. Biotechnol Biofuels. 2021 Nov 27;14(1):227 - form PTO-892), Lim (US 2023/0119263), Q88P42 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), Q88MX4 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892), and Q88MX3 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892) as applied to claims 1-5, 8-9, and 11-13 above, and further in view of A0A643FN29 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892) and
A0A643FNB0 (UnitProtKB/TrEMBL Database. September 29, 2021 – form PTO-892).
Koopman, Zou, and Lim do not disclose HmfS having the amino acid sequence of SEQ ID NO:34 of the instant application and HmfT2 having the amino acid sequence of SEQ ID NO: 36 of the instant application.
The specification of the instant application defines HmfS as a fatty acid hydroxylase and HmfT1 and HmfT2 as MFS transporters.
A0A643FN29 discloses a Cupriavidus basilensis fatty acid hydroxylase having 100% sequence identity to the HmfS having the amino acid sequence of SEQ ID NO:34 of the instant application (page 1 and see the sequence alignment below).
A0A643FNB0 discloses a Cupriavidus basilensis MFS sugar transporter having 100% sequence identity to the HmfT2 having the amino acid sequence of SEQ ID NO:34 of the instant application (page 1 and see the sequence alignment below).
Therefore, in combining the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to replace the HmfS and HmfT2 with the Cupriavidus basilensis fatty acid hydroxylase of A0A643FN29 and the Cupriavidus basilensis MFS sugar transporter of A0A643FNB0 because one of ordinary skill in the art would have been able to carry out such a substitution, and the results were reasonably predictable. The rationale to support a conclusion that the claims would have been obvious is that the substitution of one known element (HmfS and HmfT2) for another (fatty acid hydroxylase and MFS sugar transporter) yields predictable results to one of ordinary skill in the art. See MPEP 2143. One of ordinary skill in the art would have been motivated to do so in order to further improve production of a fermentation product from lignocellulosic hydrolysate with a high content of inhibitors. One of ordinary skill in the art would have had a reasonable expectation of success since Koopman discloses recombinant P. putida comprising genes encoding Cupriavidus basilensis HmfA, HmfB, HmfC, HmfD, HmfE, HmfT1, HmfF, HmfG, HmfH’, HmfH, HmfS, and HmfT2, Zou discloses function deletion of P. putida gcd, Lim discloses reduced expression of glk, gcd, and oprB-II and Lim disclose that glk, gcd, and oprB-II are involved in the catabolism of glucose, A0A643FN29 discloses Cupriavidus basilensis HmfS/fatty acid hydroxylase and A0A643FNB0 discloses Cupriavidus basilensis HmfT2/MFS sugar transporter.
Therefore, the above references render claims 1-5 and 8-13 prima facie obvious.
Conclusion
Claims 1-18 are pending.
Claims 6-7 and 14-18 are withdrawn.
Claims 1-5 and 8-13 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert Mondesi can be reached on 408-918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YONG D PAK/Primary Examiner, Art Unit 1652
Query: US-18-672-924-13
AZF23421
ID AZF23421 standard; protein; 1015 AA.
XX
AC AZF23421;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfA protein, SEQ ID 35.
XX
KW Furoyl-CoA dehydrogenase large subunit; biofuel; bioremediation;
KW enzyme production; ethanol; hmfA; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23422.
DR PC:NCBI; gi291619935.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 17; SEQ ID NO 35; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a furoyl-CoA dehydrogenase large subunit (hmfA)
CC protein of Cupriavidus basilensis strain HMF 14 useful in the production
CC of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 1015 AA;
Query Match 99.8%; Score 5033; Length 1015;
Best Local Similarity 99.7%;
Matches 979; Conservative 2; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MERLEDAAILTGRGRYGDDLGVKPGTLHAAIVRSPHAHAELGTIDATAALAAPGVHAVLT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 34 MERLEDAAILTGRGRYGDDLGVKPGTLHAAIVRSPHAHAELGTIDATAALAAPGVHAVLT 93
Qy 61 GADLAAWSRPFVVAVKSPMEQWALAMDRVRYVGEPVAVVMAESRALAEDALDLVRVNYRV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 94 GADLAAWSRPFVVAVKSPMEQWALAMDRVRYVGEPVAVVMAESRALAEDALDLVRVNYRV 153
Qy 121 LPPVVSIEAALADDAPILHPGVGANVVSDRHFRYGEPEAAFAAAPHRVTLTAHYPRNTCT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 154 LPPVVSIEAALADDAPILHPGVGANVVSDRHFRYGEPEAAFAAAPHRVTLTAHYPRNTCT 213
Qy 181 PIECGVVIAEFLPGDEGYDVTSNFMGPFSLHAVMAMALKVPANRLRHKAPRDSGGSFGVK 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 214 PIECGVVIAEFLPGDEGYDVTSNFMGPFSLHAVMAMALKVPANRLRHKAPRDSGGSFGVK 273
Qy 241 QAVFPYAVLMCLASRKAGAPVKWVEDRLEHLSAATSATARLSTLEAAVESDGRIKALAYD 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Db 274 QAVFPYAVLMCLASRKAGAPVKWVEDRLEHLSAATSATARLSTLEAAVESDGRIKALTYD 333
Qy 301 QIEDCGGYLRAPEPATFYRMHGCLTGAYDIPNLLVRNRVVMTNKTPTGLVRGFGGPQVYF 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 334 QIEDCGGYLRAPEPATFYRMHGCLTGAYDIPNLLVRNRVVMTNKTPTGLVRGFGGPQVYF 393
Qy 361 ALERLVHRIATQLGLDPLDVYRRNFVAADAFPYRAAAGALLDSGNYQLALARALEEGGYY 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 394 ALERLVHRIATQLGLDPLDVYRRNFVAADAFPYRAAAGALLDSGNYQLALARALEEGGYY 453
Qy 421 ELTCRREVARAEGRLYGIGFAAIVEPSVSNMGYITTAMPAEARKKAGPKNGAIA SATVSV 480
||||||:|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 454 ELTCRRDVARAEGRLYGIGFAAIVEPSVSNMGYITTAMPAEARKKAGPKNGAIA SATVSV 513
Qy 481 DLLGGVVVTIASTPAGQGHMTVCAQVVADVLGVNPADVVVNVEFDTHKDAWSVAAGNYSS 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 514 DLLGGVVVTIASTPAGQGHMTVCAQVVADVLGVNPADVVVNVEFDTHKDAWSVAAGNYSS 573
Qy 541 RFAGAVAGTVHLAAERVRDKLARIVAPQFGCTPAEVVFEDGRIARKGAPESGLPFTRVAS 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 574 RFAGAVAGTVHLAAERVRDKLARIVAPQFGCTPAEVVFEDGRIARKGAPESGLPFTRVAS 633
Qy 601 NAPHWSPQQLPAGEEPGLRETVFWSPPNLEAPDENDRINTSAAYGFAFDMCGVEIDRATG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 634 NAPHWSPQQLPAGEEPGLRETVFWSPPNLEAPDENDRINTSAAYGFAFDMCGVEIDRATG 693
Qy 661 RVRIDRYVTAHDAGTLLNPALADGQIRGAFAQGLGAALMEEFRYGADGSFQSGTLADYLM 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 694 RVRIDRYVTAHDAGTLLNPALADGQIRGAFAQGLGAALMEEFRYGADGSFQSGTLADYLM 753
Qy 721 PTTCEVPDPVIVHLETPSPFTPLGAKGLGEGNNMSTPPCIANAVADALGEQDIRLPLTPA 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 754 PTTCEVPDPVIVHLETPSPFTPLGAKGLGEGNNMSTPPCIANAVADALGEQDIRLPLTPA 813
Qy 781 KVMAMVGFDDPPPSRPELLEAMREAAVPAARKGSAKALTARGSVDLDATPEAIFAVLMDP 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 814 KVMAMVGFDDPPPSRPELLEAMREAAVPAARKGSAKALTARGSVDLDATPEAIFAVLMDP 873
Qy 841 QALAKVVPGCHALERTAENHYRADVTVGVGMIKARFEAEIALSDLDPPRRLRLAGAGMSS 900
||||:|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 874 QALARVVPGCHALERTAENHYRADVTVGVGMIKARFEAEIALSDLDPPRRLRLAGAGMSS 933
Qy 901 LGSARGAGLVELVPHGSGTRLSYDYEAEVSGKVAAVGGRMLEGAAKVVLRQLFESLGRQA 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 934 LGSARGAGLVELVPHGSGTRLSYDYEAEVSGKVAAVGGRMLEGAAKVVLRQLFESLGRQA 993
Qy 961 AGKPVRPQGWLARLLARLGVRR 982
||||||||||||||||||||||
Db 994 AGKPVRPQGWLARLLARLGVRR 1015
Query: US-18-672-924-15
AZF23423
ID AZF23423 standard; protein; 271 AA.
XX
AC AZF23423;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfB protein, SEQ ID 37.
XX
KW Furoyl-CoA dehydrogenase FAD binding subunit; biofuel; bioremediation;
KW enzyme production; ethanol; hmfB; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23424.
DR PC:NCBI; gi291619936.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 19; SEQ ID NO 37; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a furoyl-CoA dehydrogenase FAD binding subunit (hmfB)
CC protein of Cupriavidus basilensis strain HMF 14 useful in the production
CC of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 271 AA;
Query Match 99.7%; Score 1360; Length 271;
Best Local Similarity 99.6%;
Matches 270; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MKPSAFDYLRAETTQHALEALARGGEGARVLAGGQSLMAVLNMRLAQPQLLIDISRTVEL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
Db 1 MKPSAFDYLRAETTQHALEALARGGEGARVLAGGQSLMAVLNMRLAQPQLLIDISRTAEL 60
Qy 61 DTVRVEDAHLVVGAAATQGSVEWRRSLADEVPLLAMAFPHISHFQIRNRGTVCGSVAHAD 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 DTVRVEDAHLVVGAAATQGSVEWRRSLADEVPLLAMAFPHISHFQIRNRGTVCGSVAHAD 120
Qy 121 PSAELPLVLTALGGEVVLRSARRRRVLPAASFFQGMLMTAREPDELVEAVRFPLRRPGAR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PSAELPLVLTALGGEVVLRSARRRRVLPAASFFQGMLMTAREPDELVEAVRFPLRRPGAR 180
Qy 181 YGFAEFSARHGDFALVACAATVTDDAIA LAVGGVADRPVLETWPRLQGKDLEQAINDFSW 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 YGFAEFSARHGDFALVACAATVTDDAIA LAVGGVADRPVLETWPRLQGKDLEQAINDFSW 240
Qy 241 KLGAQDDAHISAQYRRHLVRQLSMRVIEEAK 271
|||||||||||||||||||||||||||||||
Db 241 KLGAQDDAHISAQYRRHLVRQLSMRVIEEAK 271
Query: US-18-672-924-17
AZF23425
ID AZF23425 standard; protein; 192 AA.
XX
AC AZF23425;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfC protein, SEQ ID 39.
XX
KW Furoyl-CoA dehydrogenase 2Fe-2S iron sulfur subunit; biofuel;
KW bioremediation; enzyme production; ethanol; hmfC; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23426.
DR PC:NCBI; gi291619937.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 21; SEQ ID NO 39; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a furoyl-CoA dehydrogenase 2Fe-2S iron sulfur subunit
CC (hmfC) protein of Cupriavidus basilensis strain HMF 14 useful in the
CC production of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 192 AA;
Query Match 98.8%; Score 995; Length 192;
Best Local Similarity 99.5%;
Matches 191; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MSKTNKGAVSGKPAEVMQRQEQRRITLTLNGRERSGHCEPRELLSDFLRHELGATGTHVG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSKTNKGAVSGKPAEVMQRQEQRRITLTLNGRERSGHCEPRELLSDFLRHELGATGTHVG 60
Qy 61 CEHGVCGACTVRVDGVAARSCLMLAVQAEHRAIDTVEGLAPAEGLGDLQEAFRRHHALQC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CEHGVCGACTVRVDGVAARSCLMLAVQAEHRAIDTVEGLAPAEGLGDLQEAFRRHHALQC 120
Qy 121 GFCTAGILMSCADYLERVPEPSEAQVRDMLSGHLCRCTGYTPIVAAVLDVAAIRARARHA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GFCTAGILMSCADYLERVPEPSEAQVRDMLSGHLCRCTGYTPIVAAVLDVAAIRARARHA 180
Qy 181 AAGVDTQEACNA 192
||||||||| ||
Db 181 AAGVDTQEARNA 192
Query: US-18-672-924-19
AZF23427
ID AZF23427 standard; protein; 532 AA.
XX
AC AZF23427;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfD protein, SEQ ID 41.
XX
KW Furoyl-CoA synthetase; biofuel; bioremediation; enzyme production;
KW ethanol; hmfD; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23428.
DR PC:NCBI; gi291619938.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 23; SEQ ID NO 41; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a furoyl-CoA synthetase (hmfD) protein of Cupriavidus
CC basilensis strain HMF 14 useful in the production of biofuels, of the
CC invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 532 AA;
Query Match 98.3%; Score 2744; Length 532;
Best Local Similarity 98.7%;
Matches 527; Conservative 3; Mismatches 2; Indels 2; Gaps 1;
Qy 1 MLDLGRTFLQSVERSPHTPAIVDGDLMLTYAQWYERIRCVASGLREIGLAPGDRLLAVLQ 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MLDLGRTFLQSVERSPHTPAIVDGDLMLTYAQWYERIRCVASGLREIGLAPGDRLLAVLQ 60
Qy 61 NRWEMATLHWACQFAGIVMVPLNWRAKPEELDYCVQDAGVKALVFEPVSADAVLGSPAAQ 120
||||||||:|||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 NRWEMATLYWACQFAGIVMVPLNWRAKPEELDYCVQDAGVKALVFEPVSADAVLGSPAAQ 120
Qy 121 AVPCIALDCAAGGSMSFASLLDSVALHGDPVAQASDVSLMLYTSGTTGKPKGVPRRHQHE 180
|||||||||||||||||||||||||||| |||:| |||||||||||||||||||||||||
Db 121 AVPCIALDCAAGGSMSFASLLDSVALHGGPVAEAGDVSLMLYTSGTTGKPKGVPRRHQHE 180
Qy 181 RAAALAHVAQNLYRHGERTLGVMPLYHTMGVRSLLAMALVDGLFVCVRRWNAGQALEEIN 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 RAAALAHVAQNLYRHGERTLGVMPLYHTMGVRSLLAMALVDGLFVCVRRWNAGQALEEIN 240
Qy 241 THRISCLYLVPTLYHDLLADPGFDACIVRSVSKLGFAGASMNDGLLRRLALAFEPELFVN 300
|||||||||||||||||||||||||||||||:||||||||||||||||||||||||||||
Db 241 THRISCLYLVPTLYHDLLADPGFDACIVRSVTKLGFAGASMNDGLLRRLALAFEPELFVN 300
Qy 301 HYGSSEVYTFSVDQRATRKPGSAGRAGINTRLRVVRLDARSPDDLAATGEEGQIIADLRG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 HYGSSEVYTFSVDQRATRKPGSAGRAGINTRLRVVRLDARSPDDLAATGEEGQIIADLRG 360
Qy 361 DEAFEGYWNRDDANAKSLRDGWYFTGDTGYFDAEGDLFVSGRVDDMIISGGENISPVDIE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 DEAFEGYWNRDDANAKSLRDGWYFTGDTGYFDAEGDLFVSGRVDDMIISGGENISPVDIE 420
Qy 421 SVLSLHPAVDEVAVAGVPDPRWGQKVVAFVKPRGNIDAQALDTYCRGSDLVNFKRPRDYV 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SVLSLHPAVDEVAVAGVPDPRWGQKVVAFVKPRGNIDAQALDTYCRGSDLVNFKRPRDYV 480
Qy 481 FVEEIPKSPVGKILRRKLSAGEYALAPHSMSPDPNTNPNPNQAADAAPVDTIKE 534
|||||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 481 FVEEIPKSPVGKILRRKLSAGEYALAPHSMSPDPNT--NPNQAADAAPVDTIKE 532
Query: US-18-672-924-21
AZF23429
ID AZF23429 standard; protein; 271 AA.
XX
AC AZF23429;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfE protein, SEQ ID 43.
XX
KW 2-oxoglutaroyl-CoA hydrolase; biofuel; bioremediation; enzyme production;
KW ethanol; hmfE; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23430.
DR PC:NCBI; gi291619939.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 25; SEQ ID NO 43; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a 2-oxoglutaroyl-CoA hydrolase (hmfE) protein of
CC Cupriavidus basilensis strain HMF 14 useful in the production of
CC biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 271 AA;
Query Match 100.0%; Score 1385; Length 271;
Best Local Similarity 100.0%;
Matches 271; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MTQATEMIHPDQQRLQQLDGFSVEIDAGRERADIILHRPPYNVIAMAARDQLRAVIEALD 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MTQATEMIHPDQQRLQQLDGFSVEIDAGRERADIILHRPPYNVIAMAARDQLRAVIEALD 60
Qy 61 ADDRVRVIVLRSQGEHFSSGGDIKGFLEASPEHVSQLAWNVAAPARCSKPVIAANRGYCF 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ADDRVRVIVLRSQGEHFSSGGDIKGFLEASPEHVSQLAWNVAAPARCSKPVIAANRGYCF 120
Qy 121 GVGFELSLACDFRIATETTQYALPEQKLGQIPGSGGSARLQKMVGIGRTKDIVMRSRRIS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GVGFELSLACDFRIATETTQYALPEQKLGQIPGSGGSARLQKMVGIGRTKDIVMRSRRIS 180
Qy 181 GKQAYEWGIAVECVADAELEAATDALVDELRGFSPLAQRTAKKLLNDTEDAPLSIAIELE 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GKQAYEWGIAVECVADAELEAATDALVDELRGFSPLAQRTAKKLLNDTEDAPLSIAIELE 240
Qy 241 GHCYSRLRSSDDFREGVEAFHGKRKPAFRGS 271
|||||||||||||||||||||||||||||||
Db 241 GHCYSRLRSSDDFREGVEAFHGKRKPAFRGS 271
Query: US-18-672-924-23
AZF23431
ID AZF23431 standard; protein; 449 AA.
XX
AC AZF23431;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 mfs2 protein, SEQ ID 45.
XX
KW Major facilitator superfamily transporter; biofuel; bioremediation;
KW enzyme production; ethanol; mfs2; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23432.
DR PC:NCBI; gi291619940.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Disclosure; SEQ ID NO 45; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a major facilitator superfamily transporter (mfs2)
CC protein of Cupriavidus basilensis strain HMF 14 useful in the production
CC of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 449 AA;
Query Match 99.5%; Score 2239; Length 449;
Best Local Similarity 99.1%;
Matches 445; Conservative 3; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MEAVAKKSAATISEALPAASNRQVFGAVAASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEAVAKKSAATISEALPAASNRQVFGAVAASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
Qy 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGSYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGSYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
Qy 121 GQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGIGALL 180
|||||||||||||||||||||||||||||||||||||||||||||||||||||||:||||
Db 121 GQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGLGALL 180
Qy 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
Qy 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKVVVKASAGEAAAILMA 300
|||||||||||||||||||||||||||||||||||||||||||||||||||||:||||||
Db 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKVVVKASAGESAAILMA 300
Qy 301 SSLGVIVASILAGHLSTMIGRKRAFLLIGALNVVLLPLLYQWMPAAPDTTTLGLYAVVLS 360
||||||||||||||||||||||||||||||||||:|||||||||||||||||||||||||
Db 301 SSLGVIVASILAGHLSTMIGRKRAFLLIGALNVVVLPLLYQWMPAAPDTTTLGLYAVVLS 360
Qy 361 MLGCSGFAPILIFLNERFPTSIRATGTGLSWNIGFAVGGMMPTFASLCASTPAELPMVLG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 MLGCSGFAPILIFLNERFPTSIRATGTGLSWNIGFAVGGMMPTFASLCASTPAELPMVLG 420
Qy 421 IFLAVVTIIYLVGAFIVPETAGRLGDNGA 449
|||||||||||||||||||| ||||||||
Db 421 IFLAVVTIIYLVGAFIVPETVGRLGDNGA 449
Query: US-18-672-924-26
AZF23405
ID AZF23405 standard; protein; 497 AA.
XX
AC AZF23405;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfF protein, SEQ ID 19.
XX
KW 5-hydroxymethyl-2-furoic acid decarboxylase 1; biofuel; bioremediation;
KW enzyme production; ethanol; hmfF; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23406.
DR PC:NCBI; gi291619943.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 9; SEQ ID NO 19; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a 5-hydroxymethyl-2-furoic acid decarboxylase 1
CC (hmfF) protein of Cupriavidus basilensis strain HMF14 useful in the
CC production of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 497 AA;
Query Match 98.4%; Score 2519; Length 497;
Best Local Similarity 98.2%;
Matches 488; Conservative 5; Mismatches 4; Indels 0; Gaps 0;
Qy 1 MSRQPAEKTNSASQAAPLPEGPLTLRSWLRHLGNTDRLAAIDEPVALEHTLAAVAKRLDG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSRQPAEKTNSASQAAPLPEGPLTLRSWLRHLGNTDRLAAIDEPVALEHTLAAVAKRLDG 60
Qy 61 ERAAFFRRPGGHAVPVVSGFMSRRAWIAEAMGVPEAGLLERVRSAAAQPLPVSEVAQGEA 120
||| ||||||||||||||||||||||||||||||||||||:||||||||||||||||||
Db 61 ERAVLFRRPGGHAVPVVSGFMSRRAWIAEAMGVPEAGLLERMRSAAAQPLPVSEVAQGEA 120
Qy 121 ACQQVIHLDKVDLRKLLPIPTHSEHDNGPYITAGLAIA RNPRTGVQNVSIHRIQVHAADR 180
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACQQVIHLDKVDLHKLLPIPTHSEHDNGPYITAGLAIA RNPRTGVQNVSIHRIQVHAADR 180
Qy 181 MAILMLPRHLDAFYRAAEECGEALPIAIVIGVDPLTMLASQAITPIDHDELEIAGALHGA 240
||||:||||||||||||||||||||||||||||||||||||||||||:||||||||||||
Db 181 MAILLLPRHLDAFYRAAEECGEALPIAIVIGVDPLTMLASQAITPIDYDELEIAGALHGA 240
Qy 241 PLEVIKCRTSDVRVPANAEIVIEGRLLPGEREMEGPFGEFPKYYSSAEPREVIQVDAVTH 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 PLEVIKCRTSDVRVPANAEIVIEGRLLPGEREMEGPFGEFPKYYSSAEPREVIQVDAVTH 300
Qy 301 RHRPIYHTIVPAEMEHLLLGAIPREATLLAHLQRSHPGVQDVHLSVGGVCRYHLYVKLDK 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 RHRPIYHTIVPAEMEHLLLGAIPREATLLAHLQRSHPGVQDVHLSVGGVCRYHLYVKLDK 360
Qy 361 KREGEAKNVILAAFGAHYDIKQVVVVDTDVDVHDPAEVEWAVATRFQADQDLVVIAGAQG 420
|||||||||||:||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 KREGEAKNVILSAFGAHYDIKQVVVVDTDVDVHDPAEVEWAVATRFQADQDLVVIAGAQG 420
Qy 421 SVLDPSTTVAANLAGIDNPEPHLQGICAKMGLDATRPVKYAAHVFTRVRIPGESTIDLQA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SVLDPSTTVAANLAGIDNPEPHLQGICAKMGLDATRPVKYAAHVFTRVRIPGESTIDLQA 480
Qy 481 LVSVDPSHWESYLGEGA 497
||||||| ||:||||||
Db 481 LVSVDPSQWEAYLGEGA 497
Query: US-18-672-924-28
AZF23407
ID AZF23407 standard; protein; 234 AA.
XX
AC AZF23407;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfG protein, SEQ ID 21.
XX
KW 5-hydroxymethyl-2-furoic acid decarboxylase 2; biofuel; bioremediation;
KW enzyme production; ethanol; hmfF; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23408.
DR PC:NCBI; gi291619944.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 11; SEQ ID NO 21; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a 5-hydroxymethyl-2-furoic acid decarboxylase 2
CC (hmfG) protein of Cupriavidus basilensis strain HMF14 useful in the
CC production of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 234 AA;
Query Match 97.6%; Score 952; Length 234;
Best Local Similarity 98.5%;
Matches 193; Conservative 0; Mismatches 3; Indels 0; Gaps 0;
Qy 1 MVSQRRIIVGISGASGAAIGVNLLKAMRNLDGVESHLIVSASGMLTATQELGIKRSELEA 60
| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
Db 38 MASQRRIIVGISGASGAAIGVNLLKAMRGLDGVESHLIVSASGMLTATQELGIKRSELEA 97
Qy 61 LADVVHNVRDIGAAVASGSFVTEGMVVAPCSMKTLASVANGFSDNLLTRAADVVLKERRR 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 98 LADVVHNVRDIGAAVASGSFVTEGMVVAPCSMKTLASVANGFSDNLLTRAADVVLKERRR 157
Qy 121 LVLVARETPLNLAHLRNMLHATEMGAIVMPPVPAFYSHPTSIEDVVNHTVGRILDLFQIE 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 158 LVLVARETPLNLAHLRNMLHATEMGAIVMPPVPAFYSHPTSIEDVVNHTVGRILDLFQIE 217
Qy 181 HDTLVSRWSGLAHDFA 196
| ||||||||||||||
Db 218 HGTLVSRWSGLAHDFA 233
Query: US-18-672-924-30
AZF23409
ID AZF23409 standard; protein; 328 AA.
XX
AC AZF23409;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 hmfH protein, SEQ ID 23.
XX
KW Extracytoplasmic solute receptor; biofuel; bioremediation;
KW enzyme production; ethanol; hmfH; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23410.
DR PC:NCBI; gi291619946.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Disclosure; SEQ ID NO 23; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is an extracytoplasmic solute receptor (hmfH) protein of
CC Cupriavidus basilensis strain HMF14 useful in the production of biofuels,
CC of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 328 AA;
Query Match 98.9%; Score 1637; Length 328;
Best Local Similarity 98.4%;
Matches 315; Conservative 4; Mismatches 1; Indels 0; Gaps 0;
Qy 1 MKTWLAHAGLALLLLTGLAHAQGYPTKPIRIVVPYPPGGFNDTLARIVGSRLTAAWGQPV 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9 MKTWLAHAGLALLLLTGLAHAQGYPTKPIRIVVPYPPGGFNDTLARIVGSRLTAAWGQPV 68
Qy 61 VVDNKPGAGTIIGTSFVAKAAPDGYTLLVVQFPFGANPWLYKSLPYDTLKDFTPVILAGE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 69 VVDNKPGAGTIIGTSFVAKAAPDGYTLLVVQFPFGANPWLYKSLPYDTLKDFTPVILAGE 128
Qy 121 SPMTLVVTNGSPIRSVDDLVKSAKGTPGKINYGSSGSGSSNHLAMALFERSAGITLAQVP 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 129 SPMTLVVTNGSPIRSVDDLVKSAKGTPGKINYGSSGSGSSNHLAMALFERSAGITLAQVP 188
Qy 181 YKGSTPMLTDLAGGQVEVAFDALPHVLPFVRSGKVRALAVADRSRFASLATVPTMAESGL 240
|||||||||||||||||||||||||||||||||||||||||||||||||:||||||||||
Db 189 YKGSTPMLTDLAGGQVEVAFDALPHVLPFVRSGKVRALAVADRSRFASLSTVPTMAESGL 248
Qy 241 PGYDASSWHGIVAPAGTPPEIVQKLNAQINDALRTADVRKLFHEQGVRPDGGSPADFSAF 300
||||||||||||||||||||||:|||||||||||||||| ||||||||||||||||||||
Db 249 PGYDASSWHGIVAPAGTPPEIVRKLNAQINDALRTADVRNLFHEQGVRPDGGSPADFSAF 308
Qy 301 IGKEMAKWKQVVHDAAIPLQ 320
||:|:|||||||||||||||
Db 309 IGRELAKWKQVVHDAAIPLQ 328
Query: US-18-672-924-32
AZF23411
ID AZF23411 standard; protein; 579 AA.
XX
AC AZF23411;
XX
DT 31-MAR-2011 (first entry)
XX
DE C. basilensis strain HMF14 HMF/furfural oxidoreductase (hmfH), SEQ 25.
XX
KW HMF; biofuel; bioremediation; enzyme production; ethanol;
KW furfural oxidoreductase; hmfH; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23412.
DR PC:NCBI; gi291619945.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Claim 13; SEQ ID NO 25; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a HMF/furfural oxidoreductase (hmfH) protein of
CC Cupriavidus basilensis strain HMF14 useful in the production of biofuels,
CC of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 579 AA;
Query Match 97.5%; Score 2907; Length 579;
Best Local Similarity 97.2%;
Matches 562; Conservative 6; Mismatches 10; Indels 0; Gaps 0;
Qy 1 MDTPRERFDYVIVGGGSAGCVLANRLSQDPAIRVALIEGGIDTPPDAVPAEILDSYPMPL 60
|||||||||||||||||||||||||||||||||||||| |:|||||||||||||||||||
Db 1 MDTPRERFDYVIVGGGSAGCVLANRLSQDPAIRVALIEAGVDTPPDAVPAEILDSYPMPL 60
Qy 61 FYGDRYIWPSLQARAVAGGRSKVYEQGRVMGGGSSINVQAANRGLPRDYDEWAALGASGW 120
|:|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Db 61 FFGDRYIWPSLQARAVAGGRSKVYEQGRVMGGGSSINVQAANRGLPRDYDEWAASGASGW 120
Qy 121 SWQDVLPYFRRLERDVDYGNSPLHGSHGPVPIRRILPQAWPPFCTEFAQAMGRSGLSELA 180
|||||||||| ||||||||||||||||||||||||||||||||||||| |||||||| ||
Db 121 SWQDVLPYFRHLERDVDYGNSPLHGSHGPVPIRRILPQAWPPFCTEFAHAMGRSGLSALA 180
Qy 181 DQNAEFGDGWFPAAFSNLDDKRVSTAIA YLDADTRRRVNLRIYAETTVRKLVVSGREARG 240
||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||
Db 181 DQNAEFGDGWFPAAFSNLDDKRVSTAIA YLDADTRRRANLRIYAETTVRKLVVSGREARG 240
Qy 241 VIAIRADGSRLALDAGEVIVSAGALQSPAILMRAGIGDAGALQALGIEVVADRPGVGRNL 300
|||:||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 VIAMRADGSRLALDAGEVIVSAGALQSPAILMRAGIGDAGALQALGIEVVADRPGVGRNL 300
Qy 301 QDHPALTFCQFLAPQYRMPLSRRRASMTAARFSSEVPGGEASDMYLSSSTRAGWHALGNR 360
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Db 301 QDHPALTFCQFLAPQYRMPLSRRRASMTAARFSSGVPGGEASDMYLSSSTRAGWHALGNR 360
Qy 361 LGLFFLWCNRPFSRGQVRLAGAQPDMPPVVELNLLDDERDLRRMVAGVRKLVQIVGASAL 420
||||||||||||||||| |||||||:||:|||||||||||||||||||||||||||||||
Db 361 LGLFFLWCNRPFSRGQVSLAGAQPDVPPMVELNLLDDERDLRRMVAGVRKLVQIVGASAL 420
Qy 421 HQHPGDFFPATFSPRVKALSRVSRGNALLTELLGAVLDVSGPLRRSLIARFVTGGANLAS 480
|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Db 421 HQHPGDFFPATFSPRVKALSRVSRGNVLLTELLGAVLDVSGPLRRSLIARFVTGGANLAS 480
Qy 481 LLADESALEGFVRQSVFGVWHASGTCRMGAHADRSAVTDAAGRVHDVGRLRVVDASLMPR 540
|| |||||||||||||||||||||||||||||||||||||||||||||||||:|||||||
Db 481 LLTDESALEGFVRQSVFGVWHASGTCRMGAHADRSAVTDAAGRVHDVGRLRVIDASLMPR 540
Qy 541 LPTANTNIPTIMLAEKIADTMQAERRAVRPASSEVAHP 578
||||||||||||||||||||||||||||||||||||||
Db 541 LPTANTNIPTIMLAEKIADTMQAERRAVRPASSEVAHP 578
Query: US-18-672-924-34
AZF23413
ID AZF23413 standard; protein; 231 AA.
XX
AC AZF23413;
XX
DT 31-MAR-2011 (first entry)
XX
DE C. basilensis strain HMF14 fatty acid hydroxylase (hyd) protein, SEQ 27.
XX
KW Fatty acid hydroxylase; biofuel; bioremediation; enzyme production;
KW ethanol; hyd; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23414.
DR PC:NCBI; gi291619947.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Disclosure; SEQ ID NO 27; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a fatty acid hydroxylase (hyd) protein of Cupriavidus
CC basilensis strain HMF14 useful in the production of biofuels, of the
CC invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 231 AA;
Query Match 84.8%; Score 1069; Length 231;
Best Local Similarity 87.1%;
Matches 203; Conservative 4; Mismatches 24; Indels 2; Gaps 1;
Qy 1 MKYDDEIRARSYRFRDEYVAATPAWYRGELHLAFTLLFTGGVIAWCAMKLQAPTLAQWLA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKYDDEIRARSYRFRDEYVAATPAWYRGELHLAFTLLFTGGVIAWCAMKLQAPTLAQWLA 60
Qy 61 IVPIFLLGNWAEWAAHRYILHRPTRLFSAIYKRHCAVHHRFFTHLTLEYKGQKHWRALLF 120
||||||||||||||||||||||||||||||||||||||||||||||| | : |
Db 61 IVPIFLLGNWAEWAAHRYILHRPTRLFSAIYKRHCAVHHRFFTHLTLSTKARSTGAPCCF 120
Qy 121 PPFAPVAFVLAAVPFALVIGLGFSKNAGYIALMTMAAYYLMYEGLHTLSHITESPLLDRM 180
| : | |||: ||||||||||||||||||||||||||||||:|||||||
Db 121 HPLR--GSLRAGAVRRAVIGVAFSKNAGYIALMTMAAYYLMYEGLHTLSHITDSPLLDRM 178
Qy 181 PFVGTVRRLHVTHHDPELMATQNFNLTFPICDTLFGTRSDVPHEVRSPMQGQG 233
|||||||||||||||||||||||||||||||||||||||||| ||||||||||
Db 179 PFVGTVRRLHVTHHDPELMATQNFNLTFPICDTLFGTRSDVPREVRSPMQGQG 231
Query: US-18-672-924-36
AZF23417
ID AZF23417 standard; protein; 441 AA.
XX
AC AZF23417;
XX
DT 31-MAR-2011 (first entry)
XX
DE Cupriavidus basilensis strain HMF14 mfs1 protein, SEQ ID 31.
XX
KW Major facilitator superfamily transporter; biofuel; bioremediation;
KW enzyme production; ethanol; mfs1; microorganism.
XX
OS Cupriavidus basilensis; Strain HMF14.
XX
CC PN WO2011026906-A2.
XX
CC PD 10-MAR-2011.
XX
CC PF 02-SEP-2010; 2010WO-EP062885.
XX
PR 02-SEP-2009; 2009EP-00169260.
PR 08-OCT-2009; 2009EP-00172567.
XX
CC PA (SHEL ) SHELL INT RES MIJ BV.
XX
CC PI Koopman FW, Ruijssenaars HJ, Wierckx NJP, De Winde JH;
XX
DR WPI; 2011-C34194/21.
DR N-PSDB; AZF23418.
DR PC:NCBI; gi291619948.
XX
CC PT New isolated microorganism which is Cupriavidus basilensis strain HMF14,
CC PT useful e.g. for in-situ detoxification of a lignocellulose hydrolysate
CC PT containing furanic compound (e.g. furfuryl alcohol), which is useful in
CC PT production of biofuels.
XX
CC PS Disclosure; SEQ ID NO 31; 112pp; English.
XX
CC The present invention relates to an isolated microorganism Cupriavidus
CC basilensis strain HMF14 having a deposit number DSM 22875 and its
CC applications. The present invention also provides: (1) a bacterial
CC culture comprising the isolated microorganism; (2) a polypeptide (see
CC AZF23401 ) having aldehyde dehydrogenase activity; (3) a polynucleotide
CC comprising nucleotide sequence (see AZF23402); (4) a polypeptide having
CC LysR family transcriptional regulator activity; 2,5-furan-dicarboxylic
CC acid decarboxylase 1or 2 activity; HMF/furfural oxidoreductase activity;
CC LysR type transcriptional regulator activity; furoyl-CoA dehydrogenase
CC (large subunit) activity; furoyl-CoA dehydrogenase (flavin adenine
CC dinucleotide (FAD) binding subunit) activity; furoyl-CoA dehydrogenase
CC (2Fe-2S iron sulfur subunit) activity; furoyl-CoA synthetase activity; 2-
CC oxoglutaroyl-CoA hydrolase activity; (5) a polynucleotide which encodes
CC any one of the polypeptide mentioned in (4); (6) a nucleic acid construct
CC comprising the polynucleotide; (7) a vector comprising the nucleic acid
CC construct; (8) a cell comprising the vector; (9) a host microorganism
CC cell transformed or transfected by the vector under conditions; (10) a
CC cell extract from the microorganism or the host cell; (11) a method for
CC the in-situ detoxification of a lignocellulose hydrolysate containing
CC furanic compounds (at least one of HMF, furfuryl alcohol, furfural and/or
CC furoic acid), with a suitable host microorganism; (12) a method for
CC producing furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl
CC -CoA hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 or HMF/furfural oxidoreductase, which
CC are at least 45\% identical to those expressed by the microorganism, or
CC the host microorganism cell; (13) a method for the conversion of 5-
CC hydroxymethylfurfural (HMF), 2,5-dihydroxymethyl furan, 5-hydroxymethyl-2
CC -furancarboxylic acid or 2,5-furandicarboxylic acid to 2-furoyl CoA,
CC comprising contacting furfuryl alcohol or furfural with furoyl-CoA
CC dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA hydrolase, and
CC 2,5- furan-dicarboxylic acid decarboxylase catalyst in the presence of at
CC least one coenzyme cofactor (s); (14) a method for the biocatalytic
CC production of biofuels (ethanol); and (15) a method for producing second-
CC generation biofuels from a lignocelluloses-containing material. The
CC microorganism of the invention is useful for in-situ detoxification of a
CC lignocellulose hydrolysate containing furanic compounds (at least one of
CC HMF, furfuryl alcohol, furfural or furoic acid), which is useful in
CC biocatalytic production of biofuels and producing second-generation
CC biofuels from a lignocelluloses-containing material; and for producing
CC furoyl-CoA dehydrogenase, furoyl-CoA synthetase, 2-oxoglutaroyl-CoA
CC hydrolase, 2,5-furan-dicarboxylic acid decarboxylase 1, 2,5-furan-
CC dicarboxylic acid decarboxylase 2 and/or HMF/furfural oxidoreductase. The
CC present sequence is a major facilitator superfamily transporter (mfs1)
CC protein of Cupriavidus basilensis strain HMF 14 useful in the production
CC of biofuels, of the invention.
CC
CC Revised record issued on 21-MAR-2011 : Enhanced with precomputed
CC information from BOND.
XX
SQ Sequence 441 AA;
Query Match 83.3%; Score 1877.5; Length 441;
Best Local Similarity 87.2%;
Matches 390; Conservative 9; Mismatches 25; Indels 23; Gaps 5;
Qy 1 MEAVAKKRTETIGEALPAASNRQVFGAVTASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
|||||||||||| ||||||:||||||||||||||||||||||||||||||||||||||||
Db 1 MEAVAKKRTETISEALPAATNRQVFGAVTASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
Qy 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGSYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
||||||||||||||||||||||||||||:|||||||||||||||||||||||||||||||
Db 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGTYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
Qy 121 SQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGIGALL 180
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGIGALL 180
Qy 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
Qy 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKIVVKAPAGASAAILMA 300
||||||||||||||||||||||||||||||||||||||||||||:|||||||||||||||
Db 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKVVVKAPAGASAAILMA 300
Qy 301 SSVGVIVASILAGHLSTLIGRKRAFLLIGALNVVLLPLIYQRMSAVPDVTTLGLYAVALA 360
||||||||||:|||||||||||||||||||||||||||||||| | |||||||:||||||
Db 301 SSVGVIVASIIAGHLSTLIGRKRAFLLIGALNVVLLPLIYQRMPAAPDVTTLGIYAVALA 360
Qy 361 MLGSTGFAPILIFLNERFPTSIRATGTGLSWNIGFAIGGMM----------PTFASLCAS 410
||||||||||||||||| | :| : | |||||||:
Db 361 MLGSTGFAPILIFLNERVSHQHPCYG---NWPV-------MEYRLCHRRHDATFASLCAA 410
Qy 411 TPADLPKVLGIFVAVVTAIYLAGAAIV 437
| ||| | | : ||||||
Db 411 PPR-LPKCWGSRRGV--KAFTAGAAIV 434
Query: US-18-672-924-2
Q88P42_PSEPK
ID Q88P42_PSEPK Unreviewed; 319 AA.
AC Q88P42;
DT 01-JUN-2003, integrated into UniProtKB/TrEMBL.
DT 01-JUN-2003, sequence version 1.
DT 28-JAN-2026, entry version 117.
DE RecName: Full=Glucokinase {ECO:0000256|HAMAP-Rule:MF_00524};
DE EC=2.7.1.2 {ECO:0000256|HAMAP-Rule:MF_00524};
DE AltName: Full=Glucose kinase {ECO:0000256|HAMAP-Rule:MF_00524};
GN Name=glk {ECO:0000256|HAMAP-Rule:MF_00524,
GN ECO:0000313|EMBL:AAN66636.1};
GN OrderedLocusNames=PP_1011 {ECO:0000313|EMBL:AAN66636.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Pseudomonadales; Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488 {ECO:0000313|EMBL:AAN66636.1, ECO:0000313|Proteomes:UP000000556};
RN [1] {ECO:0000313|EMBL:AAN66636.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L., Beanan M., DeBoy R.T., Daugherty S., Kolonay J., Madupu R.,
RA Nelson W., White O., Peterson J., Khouri H., Hance I., Chris Lee P.,
RA Holtzapple E., Scanlan D., Tran K., Moazzez A., Utterback T., Rizzo M.,
RA Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D.,
RA Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N.,
RA Dusterhoft A., Tummler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2] {ECO:0000313|EMBL:AAN66636.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=26913973; DOI=10.1111/1462-2920.13230;
RA Belda E., van Heck R.G., Lopez-Sanchez M.J., Cruveiller S., Barbe V.,
RA Fraser C., Klenk H.P., Petersen J., Morgat A., Nikel P.I., Vallenet D.,
RA Rouy Z., Sekowska A., Martins Dos Santos V.A., de Lorenzo V., Danchin A.,
RA Medigue C.;
RT "The revisited genome of Pseudomonas putida KT2440 enlightens its value as
RT a robust metabolic chassis.";
RL Environ. Microbiol. 18:3403-3424(2016).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucose + ATP = D-glucose 6-phosphate + ADP + H(+);
CC Xref=Rhea:RHEA:17825, ChEBI:CHEBI:4167, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61548, ChEBI:CHEBI:456216; EC=2.7.1.2;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00524};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00524}.
CC -!- SIMILARITY: Belongs to the bacterial glucokinase family.
CC {ECO:0000256|HAMAP-Rule:MF_00524, ECO:0000256|RuleBase:RU004046}.
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DR EMBL; AE015451; AAN66636.1; -; Genomic_DNA.
DR RefSeq; WP_010952193.1; NC_002947.4.
DR AlphaFoldDB; Q88P42; -.
DR STRING; 160488.PP_1011; -.
DR PaxDb; 160488-PP_1011; -.
DR GeneID; 83678362; -.
DR KEGG; ppu:PP_1011; -.
DR PATRIC; fig|160488.4.peg.1074; -.
DR eggNOG; COG0837; Bacteria.
DR HOGENOM; CLU_042582_1_0_6; -.
DR OrthoDB; 9800595at2; -.
DR PhylomeDB; Q88P42; -.
DR BioCyc; PPUT160488:G1G01-1084-MONOMER; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0005536; F:D-glucose binding; IEA:InterPro.
DR GO; GO:0004340; F:glucokinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006096; P:glycolytic process; IEA:UniProtKB-UniRule.
DR CDD; cd24008; ASKHA_NBD_GLK; 1.
DR Gene3D; 3.30.420.40; -; 1.
DR Gene3D; 3.40.367.20; -; 1.
DR HAMAP; MF_00524; Glucokinase; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR050201; Bacterial_glucokinase.
DR InterPro; IPR003836; Glucokinase.
DR NCBIfam; TIGR00749; glk; 1.
DR NCBIfam; NF001415; PRK00292.1-2; 1.
DR PANTHER; PTHR47690; GLUCOKINASE; 1.
DR PANTHER; PTHR47690:SF1; GLUCOKINASE; 1.
DR Pfam; PF02685; Glucokinase; 1.
DR SUPFAM; SSF53067; Actin-like ATPase domain; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00524};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00524};
KW Glycolysis {ECO:0000256|HAMAP-Rule:MF_00524};
KW Kinase {ECO:0000256|ARBA:ARBA00022777, ECO:0000256|HAMAP-Rule:MF_00524};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00524};
KW Reference proteome {ECO:0000313|Proteomes:UP000000556};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00524}.
FT BINDING 7..12
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00524"
SQ SEQUENCE 319 AA; 33905 MW; 4C10EE53E21EB601 CRC64;
Query Match 100.0%; Score 1664; Length 319;
Best Local Similarity 100.0%;
Matches 319; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKHLLVGDIGGTNARFALWRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVC 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKHLLVGDIGGTNARFALWRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVC 60
Qy 61 LAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVC 120
Qy 121 PGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAAIHQQIHS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAAIHQQIHS 180
Qy 181 QIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGEPRALAVVEQFCRF 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 QIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGEPRALAVVEQFCRF 240
Qy 241 LGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVPVWLVT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVPVWLVT 300
Qy 301 AEFSGLEGAGVALQQALDH 319
|||||||||||||||||||
Db 301 AEFSGLEGAGVALQQALDH 319
Query: US-18-672-924-4
Q88MX4_PSEPK
ID Q88MX4_PSEPK Unreviewed; 803 AA.
AC Q88MX4;
DT 01-JUN-2003, integrated into UniProtKB/TrEMBL.
DT 01-JUN-2003, sequence version 1.
DT 28-JAN-2026, entry version 118.
DE SubName: Full=Quinoprotein glucose dehydrogenase {ECO:0000313|EMBL:AAN67066.1};
DE EC=1.1.5.2 {ECO:0000313|EMBL:AAN67066.1};
GN Name=gcd {ECO:0000313|EMBL:AAN67066.1};
GN OrderedLocusNames=PP_1444 {ECO:0000313|EMBL:AAN67066.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Pseudomonadales; Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488 {ECO:0000313|EMBL:AAN67066.1, ECO:0000313|Proteomes:UP000000556};
RN [1] {ECO:0000313|EMBL:AAN67066.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L., Beanan M., DeBoy R.T., Daugherty S., Kolonay J., Madupu R.,
RA Nelson W., White O., Peterson J., Khouri H., Hance I., Chris Lee P.,
RA Holtzapple E., Scanlan D., Tran K., Moazzez A., Utterback T., Rizzo M.,
RA Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D.,
RA Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N.,
RA Dusterhoft A., Tummler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2] {ECO:0000313|EMBL:AAN67066.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=26913973; DOI=10.1111/1462-2920.13230;
RA Belda E., van Heck R.G., Lopez-Sanchez M.J., Cruveiller S., Barbe V.,
RA Fraser C., Klenk H.P., Petersen J., Morgat A., Nikel P.I., Vallenet D.,
RA Rouy Z., Sekowska A., Martins Dos Santos V.A., de Lorenzo V., Danchin A.,
RA Medigue C.;
RT "The revisited genome of Pseudomonas putida KT2440 enlightens its value as
RT a robust metabolic chassis.";
RL Environ. Microbiol. 18:3403-3424(2016).
CC -!- COFACTOR:
CC Name=pyrroloquinoline quinone; Xref=ChEBI:CHEBI:58442;
CC Evidence={ECO:0000256|ARBA:ARBA00001931};
CC -!- SIMILARITY: Belongs to the bacterial PQQ dehydrogenase family.
CC {ECO:0000256|ARBA:ARBA00008156}.
CC ---------------------------------------------------------------------------
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DR EMBL; AE015451; AAN67066.1; -; Genomic_DNA.
DR RefSeq; WP_010952544.1; NC_002947.4.
DR AlphaFoldDB; Q88MX4; -.
DR STRING; 160488.PP_1444; -.
DR PaxDb; 160488-PP_1444; -.
DR GeneID; 83682021; -.
DR KEGG; ppu:PP_1444; -.
DR PATRIC; fig|160488.4.peg.1532; -.
DR eggNOG; COG4993; Bacteria.
DR HOGENOM; CLU_018478_1_0_6; -.
DR OrthoDB; 9794322at2; -.
DR PhylomeDB; Q88MX4; -.
DR BioCyc; PPUT160488:G1G01-1536-MONOMER; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0016020; C:membrane; IEA:InterPro.
DR GO; GO:0048038; F:quinone binding; IEA:InterPro.
DR GO; GO:0008876; F:quinoprotein glucose dehydrogenase activity; IEA:UniProtKB-EC.
DR CDD; cd10280; PQQ_mGDH; 1.
DR Gene3D; 2.140.10.10; Quinoprotein alcohol dehydrogenase-like superfamily; 1.
DR InterPro; IPR018391; PQQ_b-propeller_rpt.
DR InterPro; IPR017511; PQQ_mDH.
DR InterPro; IPR002372; PQQ_rpt_dom.
DR InterPro; IPR011047; Quinoprotein_ADH-like_sf.
DR NCBIfam; TIGR03074; PQQ_membr_DH; 1.
DR PANTHER; PTHR32303; QUINOPROTEIN ALCOHOL DEHYDROGENASE (CYTOCHROME C); 1.
DR PANTHER; PTHR32303:SF4; QUINOPROTEIN GLUCOSE DEHYDROGENASE; 1.
DR Pfam; PF01011; PQQ; 1.
DR SMART; SM00564; PQQ; 5.
DR SUPFAM; SSF50998; Quinoprotein alcohol dehydrogenase-like; 1.
PE 3: Inferred from homology;
KW Membrane {ECO:0000256|SAM:Phobius};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002,
KW ECO:0000313|EMBL:AAN67066.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000000556};
KW Transmembrane {ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|SAM:Phobius}.
FT TRANSMEM 12..35
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 41..59
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 66..82
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 88..109
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 121..142
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 171..778
FT /note="Pyrrolo-quinoline quinone repeat"
FT /evidence="ECO:0000259|Pfam:PF01011"
FT REGION 532..552
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 803 AA; 86581 MW; C2CB315F4BA9E731 CRC64;
Query Match 100.0%; Score 4264; Length 803;
Best Local Similarity 100.0%;
Matches 803; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSTEGANQGSRWLPRLIGALLLLMGLALLAGGIKLSQLGGSLYYLIAGIGFALSGVLLLA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSTEGANQGSRWLPRLIGALLLLMGLALLAGGIKLSQLGGSLYYLIAGIGFALSGVLLLA 60
Qy 61 QRQIALGLYGLVLLGSTVWALFEVGLDWWQLVPRLAIWFAIGVVLLLPWARRPLIGPASK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 QRQIALGLYGLVLLGSTVWALFEVGLDWWQLVPRLAIWFAIGVVLLLPWARRPLIGPASK 120
Qy 121 ANTALLGVAVVASGACALASQFTHPGEVFGELGRDSSEMASAAPAMPDGEWQAYGRTEHG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ANTALLGVAVVASGACALASQFTHPGEVFGELGRDSSEMASAAPAMPDGEWQAYGRTEHG 180
Qy 181 DRYSPLRQITPQNAYRLEEAWRIRTGDLPTENDPVELTNQNTPLKVNGMLYACTAHSRLL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 DRYSPLRQITPQNAYRLEEAWRIRTGDLPTENDPVELTNQNTPLKVNGMLYACTAHSRLL 240
Qy 241 ALDPDTGAEIWRYDPQVKSPTGTFKGFAHMTCRGVSYYDENRYVSRDGSPAPKITDAGQA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ALDPDTGAEIWRYDPQVKSPTGTFKGFAHMTCRGVSYYDENRYVSRDGSPAPKITDAGQA 300
Qy 301 VAQACPRRLYLPTADARLIAINADNGKVCEGFANQGVIDLTTGIGPFTAGGYYSTSPAAI 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VAQACPRRLYLPTADARLIAINADNGKVCEGFANQGVIDLTTGIGPFTAGGYYSTSPAAI 360
Qy 361 TRDLVIIGGHVTDNESTNEPSGVIRAYDVHDGHLVWNWDSNNPDDTKPLAAGKMYSRNSA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 TRDLVIIGGHVTDNESTNEPSGVIRAYDVHDGHLVWNWDSNNPDDTKPLAAGKMYSRNSA 420
Qy 421 NMWSIASVDEDLGMIYLPLGNQTPDQWGADRTPGAEKYSAGVVALDLATGKARWNYQFTH 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 NMWSIASVDEDLGMIYLPLGNQTPDQWGADRTPGAEKYSAGVVALDLATGKARWNYQFTH 480
Qy 481 HDLWDMDVGSQPTLVHLKTDDGVKPAIIVPTKQGSLYVLDRRDGTPIVPIREIPTPQGAV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 HDLWDMDVGSQPTLVHLKTDDGVKPAIIVPTKQGSLYVLDRRDGTPIVPIREIPTPQGAV 540
Qy 541 EGDHTSPTQARSDLNLLGPELTEQAMWGATPFDQMLCRIQFRELRYEGQYTPPSEQGSLV 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 EGDHTSPTQARSDLNLLGPELTEQAMWGATPFDQMLCRIQFRELRYEGQYTPPSEQGSLV 600
Qy 601 YPGNVGVFNWGSVSVDPVRQLLFTSPNYMAFVSKMVPREQVAEGSKRESETSGVQPNTGA 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 YPGNVGVFNWGSVSVDPVRQLLFTSPNYMAFVSKMVPREQVAEGSKRESETSGVQPNTGA 660
Qy 661 PYAVIMHPFMSPLGVPCQAPAWGYVAAIDLFTNKVVWKHKNGTTRDSTPLPIGLPVGVPS 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 PYAVIMHPFMSPLGVPCQAPAWGYVAAIDLFTNKVVWKHKNGTTRDSTPLPIGLPVGVPS 720
Qy 721 MGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGKQYVLV 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 MGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGKQYVLV 780
Qy 781 TAGGHGSLGTKMGDYIIAYKLAE 803
|||||||||||||||||||||||
Db 781 TAGGHGSLGTKMGDYIIAYKLAE 803
Query: US-18-672-924-6
Q88MX3_PSEPK
ID Q88MX3_PSEPK Unreviewed; 444 AA.
AC Q88MX3;
DT 01-JUN-2003, integrated into UniProtKB/TrEMBL.
DT 01-JUN-2003, sequence version 1.
DT 28-JAN-2026, entry version 103.
DE SubName: Full=Carbohydrate-selective porin {ECO:0000313|EMBL:AAN67067.1};
GN Name=oprB-II {ECO:0000313|EMBL:AAN67067.1};
GN OrderedLocusNames=PP_1445 {ECO:0000313|EMBL:AAN67067.1};
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Pseudomonadales; Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488 {ECO:0000313|EMBL:AAN67067.1, ECO:0000313|Proteomes:UP000000556};
RN [1] {ECO:0000313|EMBL:AAN67067.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L., Beanan M., DeBoy R.T., Daugherty S., Kolonay J., Madupu R.,
RA Nelson W., White O., Peterson J., Khouri H., Hance I., Chris Lee P.,
RA Holtzapple E., Scanlan D., Tran K., Moazzez A., Utterback T., Rizzo M.,
RA Lee K., Kosack D., Moestl D., Wedler H., Lauber J., Stjepandic D.,
RA Hoheisel J., Straetz M., Heim S., Kiewitz C., Eisen J.A., Timmis K.N.,
RA Dusterhoft A., Tummler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
RN [2] {ECO:0000313|EMBL:AAN67067.1, ECO:0000313|Proteomes:UP000000556}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440
RC {ECO:0000313|Proteomes:UP000000556};
RX PubMed=26913973; DOI=10.1111/1462-2920.13230;
RA Belda E., van Heck R.G., Lopez-Sanchez M.J., Cruveiller S., Barbe V.,
RA Fraser C., Klenk H.P., Petersen J., Morgat A., Nikel P.I., Vallenet D.,
RA Rouy Z., Sekowska A., Martins Dos Santos V.A., de Lorenzo V., Danchin A.,
RA Medigue C.;
RT "The revisited genome of Pseudomonas putida KT2440 enlightens its value as
RT a robust metabolic chassis.";
RL Environ. Microbiol. 18:3403-3424(2016).
CC -!- SIMILARITY: Belongs to the OprB family. {ECO:0000256|ARBA:ARBA00008769,
CC ECO:0000256|RuleBase:RU363072}.
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DR EMBL; AE015451; AAN67067.1; -; Genomic_DNA.
DR RefSeq; WP_010952545.1; NC_002947.4.
DR AlphaFoldDB; Q88MX3; -.
DR SMR; Q88MX3; -.
DR STRING; 160488.PP_1445; -.
DR PaxDb; 160488-PP_1445; -.
DR GeneID; 83682020; -.
DR KEGG; ppu:PP_1445; -.
DR PATRIC; fig|160488.4.peg.1533; -.
DR eggNOG; COG3659; Bacteria.
DR HOGENOM; CLU_029684_1_0_6; -.
DR OrthoDB; 545475at2; -.
DR PhylomeDB; Q88MX3; -.
DR BioCyc; PPUT160488:G1G01-1537-MONOMER; -.
DR Proteomes; UP000000556; Chromosome.
DR GO; GO:0016020; C:membrane; IEA:InterPro.
DR GO; GO:0015288; F:porin activity; IEA:InterPro.
DR GO; GO:0008643; P:carbohydrate transport; IEA:InterPro.
DR Gene3D; 2.40.160.180; Carbohydrate-selective porin OprB; 1.
DR InterPro; IPR007049; Carb-sel_porin_OprB.
DR InterPro; IPR052932; OprB_Porin.
DR InterPro; IPR038673; OprB_sf.
DR PANTHER; PTHR37944; PORIN B; 1.
DR PANTHER; PTHR37944:SF1; PORIN B; 1.
DR Pfam; PF04966; OprB; 1.
PE 3: Inferred from homology;
KW Reference proteome {ECO:0000313|Proteomes:UP000000556};
KW Signal {ECO:0000256|RuleBase:RU363072}.
FT SIGNAL 1..23
FT /evidence="ECO:0000256|RuleBase:RU363072"
FT CHAIN 24..444
FT /evidence="ECO:0000256|RuleBase:RU363072"
FT /id="PRO_5007232436"
SQ SEQUENCE 444 AA; 49177 MW; 53AB2940667B547A CRC64;
Query Match 100.0%; Score 2395; Length 444;
Best Local Similarity 100.0%;
Matches 444; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MFQLPKTCYIGLALSALATPAGASEMFASDSPWMLGDWGGTRSELLEKGYDFTLGYTGEM 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MFQLPKTCYIGLALSALATPAGASEMFASDSPWMLGDWGGTRSELLEKGYDFTLGYTGEM 60
Qy 61 GSNLHGGYDHDRTARYSDQFTFGSHLDLEKILGWHDTEFQLTVTERHGDNISNDRINDPR 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GSNLHGGYDHDRTARYSDQFTFGSHLDLEKILGWHDTEFQLTVTERHGDNISNDRINDPR 120
Qy 121 VGGFTSAQEVWGRGETWRLTQMWIKQKYFDGALDVKFGRFGEGEDFNSFPCDFQNLAFCG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 VGGFTSAQEVWGRGETWRLTQMWIKQKYFDGALDVKFGRFGEGEDFNSFPCDFQNLAFCG 180
Qy 181 SQVGNWVGGIWYNWPVSQWALRVRYNLTPELYAQVGVFEQNPSNLESGNGFKLSGSGTQG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 SQVGNWVGGIWYNWPVSQWALRVRYNLTPELYAQVGVFEQNPSNLESGNGFKLSGSGTQG 240
Qy 241 AVMPFELVWTPRIQGLKGEYRAGYYYSNAKAQDVLKDSNGQPAALSGAAYRSSSSKHGLW 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 AVMPFELVWTPRIQGLKGEYRAGYYYSNAKAQDVLKDSNGQPAALSGAAYRSSSSKHGLW 300
Qy 301 IGAQQQVTSLASDQSRGLSVFANATVHDKKTNAIDNYVQAGLVFKGPFDARAKDDIGFAL 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 IGAQQQVTSLASDQSRGLSVFANATVHDKKTNAIDNYVQAGLVFKGPFDARAKDDIGFAL 360
Qy 361 ARVHVNPAYRKNARLVNQAAGLYDYDNPGFLPVQDTEYSAELYYGIHLADWLTVRPNLQY 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ARVHVNPAYRKNARLVNQAAGLYDYDNPGFLPVQDTEYSAELYYGIHLADWLTVRPNLQY 420
Qy 421 IRHPGGVSQVDGALIGGLKIQSSF 444
||||||||||||||||||||||||
Db 421 IRHPGGVSQVDGALIGGLKIQSSF 444
Query: US-18-672-924-34
A0A643FN29_9BURK
ID A0A643FN29_9BURK Unreviewed; 233 AA.
AC A0A643FN29;
DT 22-APR-2020, integrated into UniProtKB/TrEMBL.
DT 22-APR-2020, sequence version 1.
DT 28-JAN-2026, entry version 10.
DE SubName: Full=Sterol desaturase family protein {ECO:0000313|EMBL:QOT78123.1};
GN ORFNames=F7R26_009000 {ECO:0000313|EMBL:QOT78123.1};
OS Cupriavidus basilensis.
OC Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria;
OC Burkholderiales; Burkholderiaceae; Cupriavidus.
OX NCBI_TaxID=68895 {ECO:0000313|EMBL:QOT78123.1, ECO:0000313|Proteomes:UP000397656};
RN [1] {ECO:0000313|EMBL:QOT78123.1, ECO:0000313|Proteomes:UP000397656}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCUG 49340 {ECO:0000313|Proteomes:UP000397656};
RA Salva-Serra F., Donoso R.A., Cho K.H., Yoo J.A., Lee K., Yoon S.-H.,
RA Perez-Pantoja D., Moore E.R.B.;
RT "Complete genome sequence of Cupriavidus basilensis CCUG 49340T.";
RL Submitted (OCT-2020) to the EMBL/GenBank/DDBJ databases.
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DR EMBL; CP062803; QOT78123.1; -; Genomic_DNA.
DR RefSeq; WP_150990167.1; NZ_CP062803.1.
DR AlphaFoldDB; A0A643FN29; -.
DR GeneID; 98401038; -.
DR Proteomes; UP000397656; Chromosome 1.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR GO; GO:0008610; P:lipid biosynthetic process; IEA:InterPro.
DR InterPro; IPR006694; Fatty_acid_hydroxylase.
DR Pfam; PF04116; FA_hydroxylase; 1.
PE 4: Predicted;
SQ SEQUENCE 233 AA; 26790 MW; F55BB953165FAB75 CRC64;
Query Match 100.0%; Score 1261; Length 233;
Best Local Similarity 100.0%;
Matches 233; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKYDDEIRARSYRFRDEYVAATPAWYRGELHLAFTLLFTGGVIAWCAMKLQAPTLAQWLA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKYDDEIRARSYRFRDEYVAATPAWYRGELHLAFTLLFTGGVIAWCAMKLQAPTLAQWLA 60
Qy 61 IVPIFLLGNWAEWAAHRYILHRPTRLFSAIYKRHCAVHHRFFTHLTLEYKGQKHWRALLF 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 IVPIFLLGNWAEWAAHRYILHRPTRLFSAIYKRHCAVHHRFFTHLTLEYKGQKHWRALLF 120
Qy 121 PPFAPVAFVLAAVPFALVIGLGFSKNAGYIALMTMAAYYLMYEGLHTLSHITESPLLDRM 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PPFAPVAFVLAAVPFALVIGLGFSKNAGYIALMTMAAYYLMYEGLHTLSHITESPLLDRM 180
Qy 181 PFVGTVRRLHVTHHDPELMATQNFNLTFPICDTLFGTRSDVPHEVRSPMQGQG 233
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PFVGTVRRLHVTHHDPELMATQNFNLTFPICDTLFGTRSDVPHEVRSPMQGQG 233
Query: US-18-672-924-36
A0A643FNB0_9BURK
ID A0A643FNB0_9BURK Unreviewed; 452 AA.
AC A0A643FNB0;
DT 22-APR-2020, integrated into UniProtKB/TrEMBL.
DT 22-APR-2020, sequence version 1.
DT 28-JAN-2026, entry version 19.
DE SubName: Full=MFS transporter {ECO:0000313|EMBL:QOT78122.1};
GN ORFNames=F7R26_008995 {ECO:0000313|EMBL:QOT78122.1};
OS Cupriavidus basilensis.
OC Bacteria; Pseudomonadati; Pseudomonadota; Betaproteobacteria;
OC Burkholderiales; Burkholderiaceae; Cupriavidus.
OX NCBI_TaxID=68895 {ECO:0000313|EMBL:QOT78122.1, ECO:0000313|Proteomes:UP000397656};
RN [1] {ECO:0000313|EMBL:QOT78122.1, ECO:0000313|Proteomes:UP000397656}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CCUG 49340 {ECO:0000313|Proteomes:UP000397656};
RA Salva-Serra F., Donoso R.A., Cho K.H., Yoo J.A., Lee K., Yoon S.-H.,
RA Perez-Pantoja D., Moore E.R.B.;
RT "Complete genome sequence of Cupriavidus basilensis CCUG 49340T.";
RL Submitted (OCT-2020) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004651};
CC Multi-pass membrane protein {ECO:0000256|ARBA:ARBA00004651}.
CC -!- SIMILARITY: Belongs to the major facilitator superfamily. Metabolite:H+
CC Symporter (MHS) family (TC 2.A.1.6) family.
CC {ECO:0000256|ARBA:ARBA00008240}.
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DR EMBL; CP062803; QOT78122.1; -; Genomic_DNA.
DR RefSeq; WP_150990164.1; NZ_CP062803.1.
DR AlphaFoldDB; A0A643FNB0; -.
DR GeneID; 98401037; -.
DR Proteomes; UP000397656; Chromosome 1.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0015293; F:symporter activity; IEA:UniProtKB-KW.
DR Gene3D; 1.20.1250.20; MFS general substrate transporter like domains; 1.
DR InterPro; IPR051084; H+-coupled_symporters.
DR InterPro; IPR011701; MFS.
DR InterPro; IPR020846; MFS_dom.
DR InterPro; IPR036259; MFS_trans_sf.
DR InterPro; IPR005829; Sugar_transporter_CS.
DR PANTHER; PTHR43528; ALPHA-KETOGLUTARATE PERMEASE; 1.
DR PANTHER; PTHR43528:SF1; ALPHA-KETOGLUTARATE PERMEASE; 1.
DR Pfam; PF07690; MFS_1; 1.
DR SUPFAM; SSF103473; MFS general substrate transporter; 1.
DR PROSITE; PS50850; MFS; 1.
DR PROSITE; PS00217; SUGAR_TRANSPORT_2; 1.
PE 3: Inferred from homology;
KW Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW Membrane {ECO:0000256|ARBA:ARBA00023136};
KW Symport {ECO:0000256|ARBA:ARBA00022847};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989};
KW Transport {ECO:0000256|ARBA:ARBA00022448}.
FT DOMAIN 27..441
FT /note="Major facilitator superfamily (MFS) profile"
FT /evidence="ECO:0000259|PROSITE:PS50850"
SQ SEQUENCE 452 AA; 47017 MW; 0288716AFADDD1CE CRC64;
Query Match 100.0%; Score 2254; Length 452;
Best Local Similarity 100.0%;
Matches 452; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEAVAKKRTETIGEALPAASNRQVFGAVTASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEAVAKKRTETIGEALPAASNRQVFGAVTASCMGWALDLFDLFILLFVAPVIGRLFFPSE 60
Qy 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGSYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 HAMLSLAAVYASFAVTLLMRPLGSAIFGSYADRHGRKGAMVVAVTGVGLSTAAFGLLPTV 120
Qy 121 SQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGIGALL 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SQVGLLAPALFILLRLVQGIFVGGVVASTHTIGTESVPPSWRGAVSGLVGGGGAGIGALL 180
Qy 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ASITYMAMTALFPGEAFDAWGWRCMFFSGIISSVLGLFIFNSLEESPLWKQLQAAKGHAA 240
Qy 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKIVVKAPAGASAAILMA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 PVENPLRVIFSRQYRGVLFVNILLTVGGGSAYYLTSGYLPTFLKIVVKAPAGASAAILMA 300
Qy 301 SSVGVIVASILAGHLSTLIGRKRAFLLIGALNVVLLPLIYQRMSAVPDVTTLGLYAVALA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SSVGVIVASILAGHLSTLIGRKRAFLLIGALNVVLLPLIYQRMSAVPDVTTLGLYAVALA 360
Qy 361 MLGSTGFAPILIFLNERFPTSIRATGTGLSWNIGFAIGGMMPTFASLCASTPADLPKVLG 420
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Db 361 MLGSTGFAPILIFLNERFPTSIRATGTGLSWNIGFAIGGMMPTFASLCASTPADLPKVLG 420
Qy 421 IFVAVVTAIYLAGAAIVPETAGRLGEVSQPER 452
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Db 421 IFVAVVTAIYLAGAAIVPETAGRLGEVSQPER 452
Prosecution Insights