LOCUS       NZ_CP128884             5631 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM14759 plasmid pMTY14759_untypable2,
            complete sequence.
ACCESSION   NZ_CP128884
VERSION     NZ_CP128884.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35654571
            Assembly: GCF_030389215.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Analysis of the stepwise acquisition of blaCTX-M-2 and subsequent
            acquisition of either blaIMP-1 or blaIMP-6 in highly conserved
            IncN-pST5 plasmids
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5631)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUN-2023) Department of Microbiology and Infectious
            Diseases, Toho University, 5-21-16, Omori-Nishi, Ota-Ku, Tokyo
            143-8540, Japan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-JUN-2023
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM14759_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 61x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 07:44:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,236
            CDSs (total)                      :: 5,117
            Genes (coding)                    :: 4,856
            CDSs (with protein)               :: 4,856
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 261
            CDSs (without protein)            :: 261
            Pseudo Genes (ambiguous residues) :: 0 of 261
            Pseudo Genes (frameshifted)       :: 146 of 261
            Pseudo Genes (incomplete)         :: 132 of 261
            Pseudo Genes (internal stop)      :: 34 of 261
            Pseudo Genes (multiple problems)  :: 45 of 261
            Pseudo Genes (short protein)      :: 4 of 261
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128884.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM14759"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pMTY14759_untypable2"
                     /geo_loc_name="Japan"
                     /collection_date="2014"
                     /collected_by="Toho University School of Medicine"
     gene            382..1434
                     /locus_tag="QVN09_RS26110"
                     /old_locus_tag="QVN09_26110"
     CDS             382..1434
                     /locus_tag="QVN09_RS26110"
                     /old_locus_tag="QVN09_26110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1436..2302
                     /locus_tag="QVN09_RS26115"
                     /old_locus_tag="QVN09_26115"
     CDS             1436..2302
                     /locus_tag="QVN09_RS26115"
                     /old_locus_tag="QVN09_26115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3505..3696)
                     /locus_tag="QVN09_RS26120"
                     /old_locus_tag="QVN09_26120"
     CDS             complement(3505..3696)
                     /locus_tag="QVN09_RS26120"
                     /old_locus_tag="QVN09_26120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3761..4084
                     /locus_tag="QVN09_RS26125"
                     /old_locus_tag="QVN09_26125"
     CDS             3761..4084
                     /locus_tag="QVN09_RS26125"
                     /old_locus_tag="QVN09_26125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4293..>4724
                     /locus_tag="QVN09_RS26130"
                     /old_locus_tag="QVN09_26130"
                     /pseudo=""
     CDS             4293..>4724
                     /locus_tag="QVN09_RS26130"
                     /old_locus_tag="QVN09_26130"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4762..5292
                     /locus_tag="QVN09_RS26135"
                     /old_locus_tag="QVN09_26135"
     CDS             4762..5292
                     /locus_tag="QVN09_RS26135"
                     /old_locus_tag="QVN09_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            5299..5532
                     /locus_tag="QVN09_RS26140"
                     /old_locus_tag="QVN09_26140"
     CDS             5299..5532
                     /locus_tag="QVN09_RS26140"
                     /old_locus_tag="QVN09_26140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3330..3411
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2686..2873
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          4075..5630
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gatggtgaaa ccatgaaaaa tgacgtgttc agtggattaa ggcgggctaa tgtggcctgt
       61 agcatctggt tgcataggta ttcatgcggt taaaatttat caggtgcgat cgcggcagtt
      121 tttcgggtgg tttgttgcca tttttacctg tctgctgccg tgatcgcacc gaacgcgttt
      181 tggcggtgcg tacaatgcga cgttatggta aatggagcgg attttcagga aggagtgata
      241 ctaacaactc gaacactgtg caaataatga tttttttaaa atatcggtaa cgataataaa
      301 ttatttcgtt ttacgccggt aataaatata atgtagtttc agtatataaa aaaatatatg
      361 aggtgtcttg tgggagcttt catgaatctt caacaacgta taaataaact accacaatta
      421 tcatccagtt tttcatttgg aaaagatatt gataatattc attcatttat ctttaacgaa
      481 acttctaaag ataaaattga agatttacta agaaaatggg tgtcaggcaa tcagccctgt
      541 gtatttggta aattggcaag caagaaaatt aaagggcttg atttccattt atctattgta
      601 aatagccccc aactatataa tgatgatggt catttgtttg attttttgcg taatgaaaga
      661 gttcgtttta aagaacgcgc aagaagagga gaggtcagtg cgcatctcat ttattttatt
      721 catccacaac ttgcctttgc tcgtccatca gaagagttag tggacataca aaaatatatt
      781 tgttcgctgc atatgccaga gtgctatcca ataaaagagg atgttattta tactgaaagc
      841 gtaccatttc aggataaaga tgggctaaaa atatataagg ctggtgttaa tgttttttac
      901 tcttctgctc atagaacaag aaatcatgat agaagaatac cagggggaat acttatttct
      961 gtaaatgccc cggggcattt tatgaggctg gcgatagaaa aaggtttcta taaagatcaa
     1021 gaacaagcgt tagcggatat tcgtaacatg actattcagt ctgttggtaa gggtgggtat
     1081 tcacatccgg aagggatttc tacaacatgg cattcagaat ctaatttgga tcgttttgga
     1141 tgcccagtgc acaccggtaa tagttcttat tacagcggtt tttatcatac tgatgtatta
     1201 attccaggag aattaactaa ggatgaaaga ttgctccatg aaatagaaaa tagtgatcca
     1261 atgatcttca actggaatgt attgttttat gtttcattag aagagtttcc tatagatgat
     1321 ccttattatg gagagtttat tggtattcct gtagatgatg catctatgtt ttttaactcc
     1381 tttcaaccaa ggaaatttga aaacaaaccc ctttatgaga aagaggatga ttaatatgat
     1441 taaaggaatg ctttttgctt ttttagcagc gttctcatgg ggggcagcta tcgtaatgag
     1501 caaaaaagga gttgaagaac tagatgccgg aggggtgttt ttctggcaga tttgtagtgc
     1561 agtaatacta tcttggatag ttctttttat aaaaagaaaa aaactcccat taaactcaaa
     1621 agcgatactt gcttatgcga caggcgtttt tgaaccattc ttagcgtata cttttacact
     1681 ctacggactt tattttattt cagcaggaag cgcatcaatt attttttcac ttgaatcagt
     1741 gtttatattg gtgttgtctg ttcttatttg ctcagttaaa attaattccc cgcaatattt
     1801 tatattgttc cttataggtg caattgttgg cagtattttg gtagccttgc cagacatcag
     1861 taatggatcg aataatattg ttggatattg tcttgttgtt gccggtgtgt tatcggcagc
     1921 attttatgtt gttatatcgt ctcgccttat taaatcgttt gagcctatca cattattgag
     1981 cggacagttg acattctccc ttatactgtc atcgctcttt atttttatat ctaaatcatc
     2041 aatttatctt ccgttggaat ccgtgattat tgttttttca tctggaatat tacaatattt
     2101 tttagctttt tgtttttact tgaactcctt gcgttggctc ccagttcatt tggcagggat
     2161 aatgttgtac tttattccgc tagttgcatt atttttgtca tggttgtttt tggatgaaca
     2221 attcacattc ttacaggggg taggatttat tgtaactgtg ctaagtgtat attttcttaa
     2281 cagaaaatac tcagaggagt aacattctgt tcaggattgc cccccggcct ccatcgatac
     2341 cgtgccaaat gcacgtaaaa aacgggagcg tttctggtgt cggaatgtaa ccaagggggt
     2401 cagaggcgcg ctaaaacgct ctcaggggag tcaaatagag acgtttgtaa caaaaagatc
     2461 aaaggatcct cttgagatcc tttttttctg cgcgtaatct gctgcctgta aacgaaaaaa
     2521 ccgccttgca gggcggtttg atcgaaggtt aagtcagctt gcagactgct taaccaggta
     2581 actgtcttat gcgagacgag tcaccaaaat tgttcttcta gtgtagccgc actccggcag
     2641 ccacttcaag tactctctaa atatctcgca catgactttt accaatggct gctgccagtg
     2701 gcgctttgtg gtgtcttttc cgggttggac ccaagagaac agttaccgga gaaggcgcag
     2761 cagtcgggct gaacgggggg ttcctgcata cagcccagcc cggagcgaac tgcctaagtc
     2821 gccccgagat accagaagac gtgagctatg agaaagcgcc acgtgtcccg taagggagaa
     2881 aggcggaaaa ggtatccggt aatcgatatg gcgggaacgt gggggcgcag gagggagcga
     2941 ttcaccggaa acggtgatga tctttaagcc acgtcgggtt tcgccaccgc tggcggattt
     3001 catggttgag ccgcaaggct cccacagatg caccgaaaaa gtgtctgttt tgtgaagtcc
     3061 gtcagggggg cggagcctat ggaaaaagcg cctccggcgc ggcctttccc ggggtttcgt
     3121 tttttgcgca catgttcttt cctggtttat ccccgggttc tgtggataac agggttagcg
     3181 tttttgagaa aggagagtcc gctcgccgca gccgaacgac cgagcgtagc gagtcagtga
     3241 gcgaggaagc ggaagagcgc ctgaactggc attttctcct tacgcatctg tgcggcattt
     3301 cacaccggac atggcgcact tttcatacaa tccgcactga tgccgaatgg ttaagccagt
     3361 atacactccg ctatcgctac gtgactgggt cagggcttcg ccccgacacc ccaaaggtca
     3421 acggcctgac gcgccctggc gggcttgtct gctcccggca tccgctcaca gacaagctgt
     3481 gaccgtctcc gggagctgca tgtgtcagcg gttttcaccg tcatccccga agcgtgcgag
     3541 gcaactgcgg taaagctcat cggcgtggtc gtgaagcgat tcacagatgt ctgcctgttc
     3601 atccgcgtcc agttcgttga gcttctccag cagcgttaat gtctggcctc tgatgaagcg
     3661 ggccatgtta agggcggttt tttcctgttt ggtcactgat gcctccgtgt aagggggggt
     3721 tctgttcatg ggggtaatga taccgatgaa acgcgagagg atgctcacga tacgggttac
     3781 tgatgatgaa catgcccggt tactggaacg ctgtgagggt aaacaactgg cggtatggat
     3841 gcggcgggtc tgcctgggtg agccggttgc ccgttccggg aagctgccga cactggcacc
     3901 gccgttactg cgtcagctgg ccgccatcgg gaataacctt aaccagacag cgaggaaggt
     3961 gaacagcggg cagtggtctt ccggtgaccg ggttcaggtg gtggccgcac tgatggccat
     4021 cggggatgag ctgcgccggc tgcgtctggc ggtcagggaa cagggggcgc gggatgatag
     4081 ttaagtttca tgccagggga aaaggtggtg gcagtggtcc ggttgattac ctgctgggaa
     4141 gggagcgtaa ccgggaaggg gcaacggtgc ttcaggggaa tccggaagag gtccgggaac
     4201 tcatcgatgc cacgccattt gcgaagaaat acacgtcagg tgttctgtcg ttcgcggaga
     4261 aggagctgcc gcctggaggg cgtgaaaaag tgatggcgag ctttgagcgt gtactgatgc
     4321 ccggtctcga gaaaaatcag tacagcatcc tgtgggtgga gcaccaggac aagggacggc
     4381 ttgagctgaa ttttgtcatt ccgaacatgg agctacagac cggaaaacgc ctccagccgt
     4441 actacgaccg ggcagacagg ccgagaattg atgcctggca gacgctggtg aatcaccatt
     4501 acggtctgca tgaccccaac gccccggaga accgccggac gctgaccctt cctgataacc
     4561 tgccggaaac gaaacaggcg cttgctgagg gcgtcacacg cgggatagac gcgctttacc
     4621 atgccggaga gataaaaggc cgtcaggatg tgattcaggc gctcacagag gcggggcttg
     4681 aagtggtcag ggtgacgcga agcagtatca gcattgcaga cccgaacggc gggaggaata
     4741 tcagactgaa aggagcgttt tatgagcaat cttttacaga cgggcgcgga gttcgagaaa
     4801 aagctgaaag agagagccga atctacagag aaaatgctga acgacgagtt caggaagctc
     4861 gaagaatctg taaacaggga actgacctca aacgaatctt taatcaggaa cgctatcaac
     4921 gaccatacaa cagccctgaa agaactgctg gagaggtatc agaaaacgac cgtcgatacg
     4981 atggacgcgc actggaaaac cgtactgaaa atgagcgtga aacgctggct gtggctgatt
     5041 atcgtctcag tactgatgtt tgccacgacc gggagtctgc tgtggtacca gggcatgaag
     5101 ataaacgcga atatgaatat tctccgcgag cagaaagaga gtctggagaa gctgaacgcg
     5161 aagacatggg gcgtgcgtta tcacgaggac agcaacggac gttttctggt gttgccgaag
     5221 gggatgaaag ccgaaacgaa ctggacgaag gacaacggca aactgaacgc agtgagactg
     5281 gtgcaggagt gacagagcat gacggagctg gaaagacatt tgctgaacgc attagagcaa
     5341 ctgcaacagg actatatgca gcggctgaac gaatgggaga acgccttcgt ggaattgcag
     5401 aaaatgtttt cgcttacgca acgggacaac gcgatgctga acgggcgagt catgcagttg
     5461 agtcagcagg tgcagcactt gagcgagcgg acagaacgct tgagccagtt atacagcgag
     5521 aacaggagat aagggatgaa cggctgatgc aggaacgcga acatgagtta tctctggagc
     5581 gggagcgtca gccggaaatc caggagcgga cactggatgg cccttcgctg g
//
