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
Applicant’s response filed on 07/24/2025 is duly acknowledged.
Claims 8, 14 and 19 were previously canceled by applicants.
Claims 1-7, 9-13, 15-18 and 20-23, as currently amended/presented, are pending in this application.
Election/Restrictions
Applicant’s election of Group I (claims 1-7, 9-13 and 15; directed to “A recombinant nucleic acid encoding a heterodimeric protein...”, “An expression vector or cassette comprising the recombinant nucleic acid as defined in claim 1”, “A recombinant host cell comprising the expression vector or cassette of claim 7”, and “A pharmaceutical composition comprising the recombinant host cell of claim 11...”) in the reply filed on 07/24/2025 (see REM, page 1) is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, and did not specifically state if the election was made with or without traverse, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 16-18 and 20-23 (non-elected Groups II-IV) have been withdrawn from further considerations.
Claims 1-7, 9-13 and 15 (elected Group I; directed to “A recombinant nucleic acid encoding a heterodimeric protein...”, expression vector, host cell, and pharmaceutical composition), as currently presented, have been examined on their merits in this action hereinafter.
Priority
This application is a 371 of PCT/EP2021/051535 (filed on 01/22/2021), which claims foreign priority from a European application EP 20305055.4 filed on 01/23/2020.
Claim Terms
It is noted that applicants have broadly defined the terms recited in instant claims (see pages 6 and 9, for instance) as reproduced below:
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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.
1. Claim 12 (as recited) is 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.
Regarding claim 12, the phrase “e.g.” in line 4 (taken as "for example") renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). Claim 12 recites the limitations “e.g., Bacillus coagulans, Bacillus subtilis, Bacteroides fragilis… and Saccharomyces boulardii”, wherein it is unclear if the limitations presented after the term “e.g.” are in fact required by the claimed product, or they are recited just as examples. The metes and bounds of the claim is therefore not properly defined. Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
1. Claims 1-7, 9-13 and 15 (as presented) are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claim(s) recite judicial exceptions in the form of nature-based products (i.e. product of nature, “nucleic acid” encoding polypeptides, an expression vector/cassette, and a host cell with said nucleic acid, and a composition having said host cell), all derived from naturally existing bacterial genome sequence; see discussion below) as depicted below:
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See also dependent claims 7, 9 and 15 as presented, in particular.
The aforementioned judicial exceptions are not integrated into any meaningful practical application(s), and the instant claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception itself (see instant claims 7, 9 and 15). The analysis under 35 UCS 101 guide lines (USPTO October, 2019) is as follows:
Step 1. Does the claim fall within any of the statutory categories ?
Under BRI in light of the disclosure of record (see instant specification, disclosure on pages 2-3, and page 39, section 2.1 and 2.2, for instance), instant claims are directed to a composition of matter- in the form of “a nucleic acid” that encodes polypeptides having amino acid sequences of SEQ ID NO: 1 and 2 (or homologous sequences thereof), and therefore do fall under the statutory category of composition of matter.
Step 2A. (Prong one)- Does the claim recite a judicial exception ?
Claim 1 as recited pertains to a nucleic acid (represented in dependent claims as having SEQ ID NOs: 3, 4, 5 and 8; see dependent claims 3-5) that encodes two polypeptides using the same open reading frame (consecutively, SEQ ID NOs 1 and 2) and is naturally present in Firmicutes bacteria (see Nielsen et al., 2013; GenBank Acc. No: CBGU010000081; cited as ref. [U] on PTO 892 form; discloses the respective genes/orf as putative ABC transporter-like polypeptides linked in the same open reading frame, one after the other in a 14 kb contig from Firmicutes bacterium CAG:94, with protein IDs CDD28188.1 and CDD28190.1, which are 95.3% and 97% identical to claimed polypeptides SEQ ID NOs: 1 and 2, respectively; see below), and that has been also disclosed by the applicants as the source of said nucleic acid (see instant specification, page 7, 2nd paragraph; and page 39, entire section “2. Results”, for instance) that was derived from “F4 clone” identified using metagenomic screening of a library made from a healthy donor, wherein F4 clone was found to encode “a contig of about 41 kb coming from a Firmicutes Gram-positive bacterium” (see instant specification, section 2.1, for instance), from which the nucleic acid was later cloned into an expression vector for functional characterization. Thus, the claimed product and compositions comprising the same are all based on a judicial exception of a nature-based nucleic acid product (as also evidenced by applicant’s own disclosure).
Claim 1 recites “recombinant” nucleic acid, but does not provide any structural features that distinguish it from the nucleic acid sequence found in the naturally occurring contig from Firmicutes bacteria. The recitation of limitations of “homologous sequence thereof having the same biological function” for the two polypeptides in the same open reading frame of the claimed nucleic acid, does not structurally change the fact that said nucleic acid is a nature-based product. It is to be noted that cloning and/or recombinantly expressing a gene to obtain a protein product in a host does not in itself constitute imparting markedly different characteristics on the gene or protein product. Since, claim 1, and claims dependent therefrom, as currently presented are directed solely to nature-based products (that do not recite any markedly different structural features and/or characteristics than the product existing in nature), they are deemed to recite a judicial exception.
Step 2A. (Prong two)- Does the claim as a whole integrates the recited judicial exception into a practical application of the exception ?
As currently presented, none of the claims 1, 7, 9 and 15, as presented, recite structural and/or functional features or any additional limitations (in addition to nucleotide and polypeptide sequences in the form of SEQ ID NOs. 1-5 and 8) that would provide and/or integrate the recited judicial exception into a meaningful practical application of the nucleic acid, as claimed. No practical application of the nature-based products have been recited in the claims, and therefore, the claims as a whole do not integrate the judicial exception to any practical application of the exception, and therefore are taken as being directed to a nature-based judicial exception.
Step 2B. Does the claim as a whole amounts to significantly more than the recited exception ?
The dependent claims (see claims 2-6, 10, 11-13 and 15) additionally recited the limitations of “homologous sequences thereof”, or “homologous thereof having at least 80% sequence identity” with SEQ ID NOs” 1-4, 5 and 8, or “operably linked to regulatory sequences” for expression (which is also naturally occurring arrangement of genes and their regulatory elements) do not practically integrate the nature-based product into a practical application such that it is considered significantly more that the recited exception itself. For example, claim 11 recites “genetically engineered prokaryotic bacterium” as a host cell without providing structural features as to what constitutes such genetic engineering per se. Probiotic bacterial hosts are known in the art as non-pathogenic bacterial that can be transformed with such nucleic acids for expression purposes. Therefore, when considered as a whole, instant claims, as presented, do not recite any other structural and/or functional features, or provide other limitation(s) that amount to “significantly more” than the recited nature-based judicial exceptions itself. Thus, claims are deemed to be patent ineligible for reciting nature-based products as judicial exception, as discussed above. Appropriate correction is required.
Claim Rejections - 35 USC § 112- WD Rejection
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.
1. Claims 1-7, 9-13 and 15 (as presented) are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the entire scope of the claimed invention.
Claim 1 is directed to “A recombinant nucleic acid encoding a heterodimeric protein comprising a first polypeptide whose amino acid sequence is SEQ ID NO: 1 or a homologous sequence thereof having the same biological function, and a second polypeptide whose amino acid sequence is SEQ ID NO: 2 or a homologous sequence thereof having the same biological function.”
It is noted that the term “homologous sequence” has been broadly intended to refer any modification of claimed nucleic acid including “such as in particular a deletion, a truncation, an extension, a chimeric fusion and/or a mutation, in particular a point mutation…can show at least 80%, preferably 90% or 95%, identity…” (see instant specification, page 9, 2nd paragraph).
It is also noted that the claims 1-7, 9-13 and 15 as currently presented do not recite any specific “biological function” per se. The only function disclosed on record for the claimed “nucleic acid encoding a heterodimeric protein” of claim 1 pertains to biological function of a transporter that helps secrete muropeptide precursors from transformed prokaryotic host cells (see instant disclosure, page 5, 2nd paragraph; and page 11, lines 13-23, for instance). No other specific “biological function” has been disclosed on record for said nucleic acid as recited in the claims, as presented.
More importantly, although the disclosure of record provided generic statements about “variants” for the claimed nucleic acid (SEQ ID NO: 3 and 4; see page 12, lines 4-26, for instance) and that “polynucleotide encoding the heterodimeric protein of the invention or the fragment or sequence variant thereof, may be codon-optimized…”, the only disclosure of such nucleic acid that encodes the heterodimeric protein of the invention pertains to the nucleic acid encoding the polypeptides in the same open reading frame whose amino acid sequence are SEQ ID NO: 1 and 2, respectively and have the corresponding polynucleotide sequences of SEQ ID NOs: 3 and 4 as recited in instant claims and cloned in a prokaryotic expression vector for expression in a non-pathogenic E. coli strain (see also instant disclosure, page 24, 2nd paragraph; and section “2. Results” on page 39). No other variants, such as having deletions, truncations, substitutions, or mutations have been disclosed on record of the nucleic acid that encodes the heterodimeric protein of the invention having SEQ ID NOs: 1 and 2, as recited in instant claims. It is noted that the polypeptides 1 and 2 have 588 and 589 amino acids respectively, and the polynucleotides of SEQ ID NOs 3 and 4 have 1767bp and 1770bp, and the fact that at least 80% identity (see instant claims 2, 4-5, for instance) would mean changes (insertions, deletions, mutations, etc.) in at least 20% of the amino acids (i.e. alterations in more than 117 amino acids in each protein). However, there appears to be no real disclosure for any such variants, deletions, truncations, and/or mutations that are still having the “same biological function” such as acting as a transporter of muropeptides, as intended in the disclosure of record. It is known in the art that unless the core structure of the protein has been shown to be functional and has been retained in a polypeptide with the same three dimensional folds, the biological function does not necessarily follow with such alterations in a given protein, and at least that has not been reasonably disclosed to be the case (with pertinent number of species and structure-function relationships, thereof) in the instant specification of record. No such guidance has been provided on record that would show the required nexus between the structural alterations (to the extent claimed, i.e. up to 20% sequence alterations/variations for the polypeptides, in particular) and biological function intended as per the current disclosure of record.
Thus, considering the entire disclosure of record as currently presented, it appears that applicants do not seem to be in possession of the entire scope of the claimed invention. Appropriate correction and/or explanation is required.
Homology – Sequence Alignments
SEQ ID NO: 1 (UNIPROT DATABASE SEARCH)
RESULT 2
R6XWR4_9FIRM
ID R6XWR4_9FIRM Unreviewed; 588 AA.
AC R6XWR4;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 18-JUN-2025, entry version 41.
DE SubName: Full=ABC transporter ATP-binding protein {ECO:0000313|EMBL:CDD28188.1};
GN ORFNames=BN815_00777 {ECO:0000313|EMBL:CDD28188.1};
OS Firmicutes bacterium CAG:94.
OC Bacteria; Bacillati; Bacillota.
OX NCBI_TaxID=1262989 {ECO:0000313|EMBL:CDD28188.1, ECO:0000313|Proteomes:UP000018237};
RN [1] {ECO:0000313|EMBL:CDD28188.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) 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 -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:CDD28188.1}.
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DR EMBL; CBGU010000081; CDD28188.1; -; Genomic_DNA.
DR AlphaFoldDB; R6XWR4; -.
DR Proteomes; UP000018237; Unassembled WGS sequence.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0015421; F:ABC-type oligopeptide transporter activity; IEA:TreeGrafter.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR CDD; cd18542; ABC_6TM_YknU_like; 1.
DR FunFam; 3.40.50.300:FF:000221; Multidrug ABC transporter ATP-binding protein; 1.
DR Gene3D; 1.20.1560.10; ABC transporter type 1, transmembrane domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011527; ABC1_TM_dom.
DR InterPro; IPR036640; ABC1_TM_sf.
DR InterPro; IPR003439; ABC_transporter-like_ATP-bd.
DR InterPro; IPR017871; ABC_transporter-like_CS.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR039421; Type_1_exporter.
DR PANTHER; PTHR43394:SF1; ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL; 1.
DR PANTHER; PTHR43394; ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL; 1.
DR Pfam; PF00664; ABC_membrane; 1.
DR Pfam; PF00005; ABC_tran; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF90123; ABC transporter transmembrane region; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS50929; ABC_TM1F; 1.
DR PROSITE; PS00211; ABC_TRANSPORTER_1; 1.
DR PROSITE; PS50893; ABC_TRANSPORTER_2; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000313|EMBL:CDD28188.1};
KW Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}; Transport {ECO:0000256|ARBA:ARBA00022448}.
FT TRANSMEM 60..77
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 137..159
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 165..185
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 264..287
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 19..310
FT /note="ABC transmembrane type-1"
FT /evidence="ECO:0000259|PROSITE:PS50929"
FT DOMAIN 345..577
FT /note="ABC transporter"
FT /evidence="ECO:0000259|PROSITE:PS50893"
SQ SEQUENCE 588 AA; 66119 MW; 91D31515DD6945C6 CRC64;
Query Match 95.3%; Score 2836; Length 588;
Best Local Similarity 94.7%;
Matches 557; Conservative 14; Mismatches 17; Indels 0; Gaps 0;
Qy 1 MFQLKWVWKQMEGFRKRYIFALFSTALLAMLTLGNSVITASIMDTVFQPLTESGVVTQQV 60
|||||||||||||||||||||| |||||||| |||| ||| |||||| || ||||||:||
Db 1 MFQLKWVWKQMEGFRKRYIFALCSTALLAMLALGNSTITAMIMDTVFSPLQESGVVTEQV 60
Qy 61 VHHLAVLVAVLIGFTLFRTSFQYLSIMTYEGCSQKLIFKLRRDLYKNMQEQDQDFFSKTR 120
|| |||:||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 FQHLIFLVALLIGFTLFRTSFQYLSIMTYEGCSQKLIFKLRRDLYKNMQEQDQDFFSKTR 120
Qy 121 TGDLMTRLTGDLDMVRFAVAWVVRQLIHCTVLFVTTSIVFLVTDWLFALSMLAVTPIIFA 180
||||||||||||||||||||||:||||||||||||||||||||||||||||||||||||
Db 121 TGDLMTRLTGDLDMVRFAVAWVLRQLIHCTVLFVTTSIVFLVTDWLFALSMLAVTPIIFG 180
Qy 181 LTLAFSKRVHPLYVDLRERLSLLNTQAQENISGNRVVKAFAREDYEIDRFDEKNADYKKA 240
|||||||||||||||||||||||||||||||||||||||||||||||:||||||||||||
Db 181 LTLAFSKRVHPLYVDLRERLSLLNTQAQENISGNRVVKAFAREDYEIERFDEKNADYKKA 240
Qy 241 NTRASLLWLQYSPYIEGLSQSLSIAVLLVGGVFLITGRISIGTFTLFNGLTWTLTDPMRM 300
||:|||||||||||||||||||||||||||| |||:||||||||||||||||||||||||
Db 241 NTKASLLWLQYSPYIEGLSQSLSIAVLLVGGAFLISGRISIGTFTLFNGLTWTLTDPMRM 300
Qy 301 LGMHLNDLQRFFASSNKIIELYYAKSTITSRPDAKKVDTRLKGEIDFSGVDLNLHGQPVL 360
||||||||||||||:|||||||||||||||||||||: |:|||||||||||||||||||
Db 301 LGMHLNDLQRFFASANKIIELYYAKSTITSRPDAKKLQGRMKGEIDFSGVDLNLHGQPVL 360
Qy 361 RHIDLHINPGETVAIMGPTGSGKTSLVNLIPRFTDVSGGTLTIDGTPVGRYDLQGLRHAI 420
|||||||:|||||||||||||||||||||||||:||||||||||||||||||| |||:|
Db 361 RHIDLHIDPGETVAIMGPTGSGKTSLVNLIPRFSDVSGGTLTIDGTPVGRYDLHDLRHSI 420
Qy 421 GIATQDVFLFSDTVDGNIAYGDSSLSEDDVKRYAKMADVDFVEKLPDGFDTLIGERGTGL 480
|||||||||||||||||||||||||||:||||||||||||||||||||||||||||||||
Db 421 GIATQDVFLFSDTVDGNIAYGDSSLSEEDVKRYAKMADVDFVEKLPDGFDTLIGERGTGL 480
Qy 481 SGGQKQRIALARALAVRPSILILDDTTSAVDLETEKYIQEQLASLDFPCTKIIVAQRIST 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 SGGQKQRIALARALAVRPSILILDDTTSAVDLETEKYIQEQLASLDFPCTKIIVAQRIST 540
Qy 541 TKRADKIVILDKGRVVDIGTHEELSQRPGYYREVFLLQNGMEEEKEVV 588
||||||||||||| |||||||:||||||||||||||||||||||||||
Db 541 TKRADKIVILDKGEVVDIGTHQELSQRPGYYREVFLLQNGMEEEKEVV 588
SEQ ID NO: 2 (UNIPROT DATABASE SEARCH)
RESULT 2
R6Y2Y5_9FIRM
ID R6Y2Y5_9FIRM Unreviewed; 599 AA.
AC R6Y2Y5;
DT 24-JUL-2013, integrated into UniProtKB/TrEMBL.
DT 24-JUL-2013, sequence version 1.
DT 05-FEB-2025, entry version 38.
DE SubName: Full=ABC transporter related {ECO:0000313|EMBL:CDD28190.1};
GN ORFNames=BN815_00778 {ECO:0000313|EMBL:CDD28190.1};
OS Firmicutes bacterium CAG:94.
OC Bacteria; Bacillati; Bacillota.
OX NCBI_TaxID=1262989 {ECO:0000313|EMBL:CDD28190.1, ECO:0000313|Proteomes:UP000018237};
RN [1] {ECO:0000313|EMBL:CDD28190.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Nielsen H.B., Almeida M., Juncker A.S., Rasmussen S., Li J., Sunagawa S.,
RA Plichta D., Gautier L., Le Chatelier E., Peletier E., Bonde I., Nielsen T.,
RA Manichanh C., Arumugam M., Batto J., Santos M.B.Q.D., Blom N., Borruel N.,
RA Burgdorf K.S., Boumezbeur F., Casellas F., Dore J., Guarner F., Hansen T.,
RA Hildebrand F., Kaas R.S., Kennedy S., Kristiansen K., Kultima J.R.,
RA Leonard P., Levenez F., Lund O., Moumen B., Le Paslier D., Pons N.,
RA Pedersen O., Prifti E., Qin J., Raes J., Tap J., Tims S., Ussery D.W.,
RA Yamada T., MetaHit consortium, Renault P., Sicheritz-Ponten T., Bork P.,
RA Wang J., Brunak S., Ehrlich S.D.;
RT "Dependencies among metagenomic species, viruses, plasmids and units of
RT genetic variation.";
RL Submitted (NOV-2012) 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 -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:CDD28190.1}.
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DR EMBL; CBGU010000081; CDD28190.1; -; Genomic_DNA.
DR AlphaFoldDB; R6Y2Y5; -.
DR Proteomes; UP000018237; Unassembled WGS sequence.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005840; C:ribosome; IEA:InterPro.
DR GO; GO:0015421; F:ABC-type oligopeptide transporter activity; IEA:TreeGrafter.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0003735; F:structural constituent of ribosome; IEA:InterPro.
DR GO; GO:0006412; P:translation; IEA:InterPro.
DR CDD; cd18545; ABC_6TM_YknV_like; 1.
DR FunFam; 3.40.50.300:FF:000218; Multidrug ABC transporter ATP-binding protein; 1.
DR Gene3D; 1.20.1560.10; ABC transporter type 1, transmembrane domain; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011527; ABC1_TM_dom.
DR InterPro; IPR036640; ABC1_TM_sf.
DR InterPro; IPR003439; ABC_transporter-like_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR018130; Ribosomal_uS2_CS.
DR InterPro; IPR039421; Type_1_exporter.
DR PANTHER; PTHR43394:SF1; ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL; 1.
DR PANTHER; PTHR43394; ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL; 1.
DR Pfam; PF00664; ABC_membrane; 1.
DR Pfam; PF00005; ABC_tran; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF90123; ABC transporter transmembrane region; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS50929; ABC_TM1F; 1.
DR PROSITE; PS50893; ABC_TRANSPORTER_2; 1.
DR PROSITE; PS00962; RIBOSOMAL_S2_1; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT TRANSMEM 36..60
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 72..90
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 151..169
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 175..193
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 258..278
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 36..317
FT /note="ABC transmembrane type-1"
FT /evidence="ECO:0000259|PROSITE:PS50929"
FT DOMAIN 351..595
FT /note="ABC transporter"
FT /evidence="ECO:0000259|PROSITE:PS50893"
SQ SEQUENCE 599 AA; 67669 MW; 15F0E6D0DA26CF32 CRC64;
Query Match 97.0%; Score 2897.5; Length 599;
Best Local Similarity 96.0%;
Matches 575; Conservative 5; Mismatches 8; Indels 11; Gaps 2;
Qy 1 ARNKFDVDETLETPFNIKHLLRAGVYIGRHKKKMILSLLFSAISAACSLLGPMLIQRAID 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2 ARNKFDVDETLETPFNIKHLLRAGVYIGRHKKKMILSLLFSAISAACSLLGPMLIQRAID 61
Qy 61 VSVPQKDYTELMVVLAVIMLVSIVASVLFARARSKYMIVVGQEIIYDIRKDLFEHLQKLP 120
|||| |||||| ||||:|||||||||||||||||||||||||||||||||||||||||||
Db 62 VSVPNKDYTEL-VVLAIIMLVSIVASVLFARARSKYMIVVGQEIIYDIRKDLFEHLQKLP 120
Qy 121 FQFYDDRPHGKILTRVINYVNSVSDALSNGIINFVLEIFNLILIAVFMFLCDVRLSLIVM 180
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Db 121 FQFYDDRPHGKILTRVINYVNSVSDALSNGIINFVLEIFNLILIAVFMFLCDVRLSFIVM 180
Qy 181 AGIPLFLVIVLLIKPAQRRAWQDVSNKSSNINAYLHESLDGMKITQAFTREEENRGIYEK 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 AGIPLFLVIVLLIKPAQRRAWQDVSNKSSNINAYLHESLDGMKITQAFTREEENRGIYEK 240
Qy 241 LNKKCYQTWMKAQYTSNLVWYSVDNISTWVVGAMYLIGLWMLGPAMQIGTLIAISSYAWR 300
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LNKKCYNTWMKAQYTSNLVWYSVDNISTWVVGAMYLIGLWMLGPAMQIGTLIAISSYAWR 300
Qy 301 FWQPILNLSNLYNTFINAVAYLERIFEMIDEPVTVDDAPGATELPPITGRVTFDDVTFSY 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 FWQPILNLSNLYNTFINAVAYLERIFEMIDEPVTVDDAPGATELPPITGRVTFDDVTFSY 360
Qy 361 DGQINILEHFNLDVKPGESIALVGPTGAGKTTVVNLISRFYNIDRGRLLLDGHDIAQVTL 420
||:||||||||||||||||||||||||||||||||||||||||: ||||||||||| |||
Db 361 DGKINILEHFNLDVKPGESIALVGPTGAGKTTVVNLISRFYNINSGRLLLDGHDIAGVTL 420
Qy 421 RSLRSQMGIMLQDSFIFSGTIMDNIRYGRLDATDEEVIAAAKTVRADEFIREMEDGYYTQ 480
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 HSLRSQMGIMLQDSFIFSGTIMDNIRYGRLDATDEEVIAAAKTVRADEFIREMEDGYYTQ 480
Qy 481 VNERGSRLSQGQRQL----------VAFARTLLSDPKILVLDEATSSIDAKTERLVQEGL 530
||||||||||||||| :||||||||||||||||||||||||||||||||||
Db 481 VNERGSRLSQGQRQLGAFARTLLSDLAFARTLLSDPKILVLDEATSSIDAKTERLVQEGL 540
Qy 531 NALLKGRTSFIIAHRLSTIKNCDRILYISNKGIAEMGTHQQLLEKKGYYYHLYTAQLES 589
||||||||||||||||||||||||||||||||||||| |||||:| |||||||||||||
Db 541 NALLKGRTSFIIAHRLSTIKNCDRILYISNKGIAEMGNHQQLLDKHGYYYHLYTAQLES 599
Prior Art
Claims 1-7, 9-13 and 15 appear to be free of prior art issues.
Conclusion
NO claims are currently allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SATYENDRA K. SINGH whose telephone number is (571)272-8790. The examiner can normally be reached M-F 8:00- 5:00.
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SATYENDRA K. SINGH
Primary Examiner
Art Unit 1657
/SATYENDRA K SINGH/Primary Examiner, Art Unit 1657