LOCUS       NZ_CP128938             3988 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM9757 plasmid pMTY9757_Col440I, complete
            sequence.
ACCESSION   NZ_CP128938
VERSION     NZ_CP128938.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35769033
            Assembly: GCF_030389715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3988)
  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  JOURNAL   Unpublished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 3988)
  AUTHORS   Ikegaya,K., Aoki,K., Komori,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-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                     :: 18-NOV-2021
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM9757_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 413x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 08:03:42
            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)                     :: 5,507
            CDSs (total)                      :: 5,387
            Genes (coding)                    :: 5,109
            CDSs (with protein)               :: 5,109
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 278
            CDSs (without protein)            :: 278
            Pseudo Genes (ambiguous residues) :: 0 of 278
            Pseudo Genes (frameshifted)       :: 101 of 278
            Pseudo Genes (incomplete)         :: 168 of 278
            Pseudo Genes (internal stop)      :: 51 of 278
            Pseudo Genes (multiple problems)  :: 39 of 278
            Pseudo Genes (short protein)      :: 3 of 278
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128938.1.
            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..3988
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM9757"
                     /db_xref="taxon:562"
                     /plasmid="pMTY9757_Col440I"
                     /geo_loc_name="Japan"
                     /collection_date="2010"
                     /collected_by="Toho University School of Medicine"
     gene            complement(join(3918..3988,1..97))
                     /locus_tag="QVM97_RS27505"
                     /old_locus_tag="QVM97_27505"
     CDS             complement(join(3918..3988,1..97))
                     /locus_tag="QVM97_RS27505"
                     /old_locus_tag="QVM97_27505"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_159427097.1"
                     /translation="MSYVADTKARNEEAKLVREETSSNSRKPSNKGLLAFIVASAAVDD
                     FEQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(400..513)
                     /locus_tag="QVM97_RS27510"
                     /old_locus_tag="QVM97_27510"
     CDS             complement(400..513)
                     /locus_tag="QVM97_RS27510"
                     /old_locus_tag="QVM97_27510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_077897077.1"
                     /translation="MHEPPVQSDCYALSGNYQLESKPERHDKAPLAAATGN"
                     /name="replication initiation protein"
     gene            929..1120
                     /locus_tag="QVM97_RS27515"
                     /old_locus_tag="QVM97_27515"
     CDS             929..1120
                     /locus_tag="QVM97_RS27515"
                     /old_locus_tag="QVM97_27515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_000166327.1"
                     /translation="MTKQQKTALNMAKFIQGQTLLLLEKLNELDLDVEADLCEKLHEDA
                     EQLCRTLTIRLDGHQGDL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1120..1551
                     /locus_tag="QVM97_RS27520"
                     /old_locus_tag="QVM97_27520"
     CDS             1120..1551
                     /locus_tag="QVM97_RS27520"
                     /old_locus_tag="QVM97_27520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_073545078.1"
                     /translation="MARVSISEAARLASVSRPTIYKLLKSGELSYTSVVKHGKSVKAID
                     TTELIRVFGSLSFDSERDNAVVKFDEHSTGVNSNFLQDLQHQVALLQAENAGLKDAVNA
                     RNEHINSLRQAMQLLEHKQDTADPQHVPAKSWWQFWKSR"
                     /name="helix-turn-helix domain-containing protein"
     gene            2059..2280
                     /locus_tag="QVM97_RS27525"
                     /old_locus_tag="QVM97_27525"
     CDS             2059..2280
                     /locus_tag="QVM97_RS27525"
                     /old_locus_tag="QVM97_27525"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_073545079.1"
                     /translation="MKKWLATLIDDLKFLGAEFKREFSDLGITPVMAEQHQQRIAEMRR
                     STVAGKLSRGVLQIRDGVLTFYGMKTKW"
                     /name="hypothetical protein"
     gene            2846..3364
                     /locus_tag="QVM97_RS27530"
                     /old_locus_tag="QVM97_27530"
     CDS             2846..3364
                     /locus_tag="QVM97_RS27530"
                     /old_locus_tag="QVM97_27530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032436807.1"
                     /translation="MSERAKRSGRRSLSKRREELLEELWGEELDDLNIWNRAEHKGFTT
                     VPRTLNYINRIIDHLAGTGSPVSQTYLSLWCRVFDEGFVEIRDKDSIAYESGFNGQRAV
                     TTWMSRMKKLRELGLIKTKAGTSGEFHYVLMLNPLSIIKSHYESNGMSKDERYNALFSR
                     MQEVGAKWE"
                     /name="hypothetical protein"
     gene            3361..3921
                     /locus_tag="QVM97_RS27535"
                     /old_locus_tag="QVM97_27535"
     CDS             3361..3921
                     /locus_tag="QVM97_RS27535"
                     /old_locus_tag="QVM97_27535"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_073545080.1"
                     /translation="MSTFCGVRERYLKIYQEAFDEVVATYVEAGVLAGIELRLSPIDKT
                     ALSAWSSEWMGKSAKQKHGEWQWDRMVAKRIKRCKKFDLAIWGDGILCGLSLGLVTRGK
                     KTVRMNYLQACPVKHPLEKQIAAIAVAVAIAVGQRVGADHVAIFNPVNEKVENHYRKLG
                     FEKRTVYSRFVKNAMYMDIPSRD"
                     /name="hypothetical protein"
     Typing          complement(397..750)
                     /name="rep_cluster_2373"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.493"
                     /coverage="82.0"
                     /evalue="2.95e-159"
ORIGIN
        1 ggcctttgtt ggaaggtttg cggctgtttg atgatgtttc ttcgcgaacc aatttagcct
       61 cttcatttct ggctttggtg tctgctacgt aactcatatt tatagcctct gcttaacgtg
      121 tagtatcact atacaacatc tttgttttaa aaataactat aagtagccag ataagcaacc
      181 acaacaagct gtgagtattg ttgactcctg gctgttcatc agcgtaatct tttgctctgt
      241 aaacgaaaaa aaccacccgg caaggtggtt ttttcgaagg ttcattaacc ggcaagtttc
      301 tgaaccgagg taactggcta atgaggagcg cagtaaccaa aacttgttct ttcagtttag
      361 ccttaacagg cgcataactt caagactaac tcctctaaat cagttaccag tggctgctgc
      421 cagtggcgct ttgtcgtgtc tttccggctt ggactcaagt tgatagttac cggataaggc
      481 gtagcagtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc gaactgcctt
      541 cccggaactg agtgtcaggc gtggaatgag ataaacgcgg ccataacagc ggaatgacac
      601 cggtaaaccg aaaggcagga acaggagagc gcacgaggga gccgccaggg ggaaacgcct
      661 ggtatcttta tagtcctgtc gggtttcgcc accactgatt tgagcgtcag attctgtgat
      721 gcttatcagg ggggcgaagc ctatggaaaa acgcccgtgg ggcgtggcct tgtcgttctc
      781 tttctggttt ttcgttacgc tttccgtcta cgttatttgt ctcttcgaaa gatccgtccg
      841 ctcgccgcag acaagtgacc gagcgtagcg agcgaacggt cgaggaagcg gaaaagaacc
      901 ggatatcact tggagcactg acgctgtgat gacgaaacaa cagaaaactg cgcttaatat
      961 ggcgaagttt atccaggggc agaccctgct tttgttggaa aagcttaatg aactcgatct
     1021 cgatgttgag gcggatcttt gtgaaaagct ccatgaggat gcggaacaac tctgtcgtac
     1081 tctgactatt cgtctggatg gtcatcaggg ggatttataa tggccagggt atctattagc
     1141 gaagcggcac gccttgccag tgtcagtcgt ccgactattt acaagttact caaatctggt
     1201 gagttaagtt acacctctgt tgtaaagcat ggaaaatctg taaaagcaat tgatactaca
     1261 gagcttattc gtgttttcgg ctctcttagt tttgacagtg aacgtgacaa tgccgttgta
     1321 aaatttgacg aacactctac aggtgttaac agtaattttt tacaggattt acagcatcag
     1381 gtggcacttt tgcaggcaga aaacgccggg ctgaaagatg cagtgaatgc ccggaatgaa
     1441 catatcaact cacttcgcca ggctatgcag ctgctggagc ataaacagga cactgctgat
     1501 ccgcagcatg tccctgcaaa gtcctggtgg cagttctgga aatcccgctg agtcattacc
     1561 acgcattccg gccatagcgt tcgtcctgcc actcagtttc tgccggatat ggatttttgt
     1621 actcttttgt cctgctgatt ttcctgcatg tttgactcct gatggctgag aaaggccata
     1681 aaatcgtgtc acaccccacg cattatgcaa tgcaaagccc aaagccgtgc tgagactggc
     1741 tttggggggg catgacaccc aatgtgcaaa tgtcatgcat ttttttatga aattggactg
     1801 aaagcccaga gttacaggcg ttcgcggcgt catgcccccc ctgcatgatg tttctctcat
     1861 tttattcata taatgtgttg attttaatta ttatttttac ctgttcgacg tgcatgactt
     1921 ttcccgttgc taaatttgct agacgatcct gccagcgcct cacgaccccg caataaattg
     1981 cgtgcccgtt caccgctttc tttctccagt ctgtgccaga ctgttatctg aataacttaa
     2041 atgatgtgag gcagaacggt gaaaaaatgg cttgcgaccc ttatcgatga cctgaagttt
     2101 ctgggggctg agtttaagag agagttttcg gatctgggta tcacccctgt gatggccgag
     2161 caacatcagc agagaatagc tgaaatgcgc cgttccaccg tagccgggaa gttatcccgg
     2221 ggtgttttgc aaatcaggga cggggtactg accttttatg gcatgaaaac gaaatggtag
     2281 gcttccgccc ggaaatccgg gcaggaaaac cgggaaaaat cgcggtttca ccagcttttt
     2341 tgtgccaggc ctgagctcat tcactgcgct gcataatcat tcacaggccg taaacgcgct
     2401 cagatcgatt ctggcgcgtt tttgccggat aagctgtggt tttcatcgtc ttcgcgccga
     2461 aatcgcactc agcgcgtttt agcggtgcgc gtaatgagac gttatggtaa atgcactcaa
     2521 gtagctttac taacttagtt ttatgcccat ccatactatc tgcccccctt tgcatacccc
     2581 cttggagtac cgcgagcaca atgagaacaa tatgagaaca atcagaacag cgagtacaaa
     2641 atgtgttgta acttactgtt ttataaaacg cttactgtaa tatatattac atctcaatta
     2701 ttgttttgta atttatttaa tatcttgtag tgtgtgctgt attgaccttt gactctttgt
     2761 ttttgaatgt tctcgtataa ctcattgaaa taaaatgaat ttttatagag aatgagagtg
     2821 ttgactggct gtaaggatga ttgatatgtc agaacgagca aaaagatctg gacggcgctc
     2881 tttgtcaaag cgaagagaag agcttcttga agaactatgg ggtgaggaac ttgatgattt
     2941 aaatatatgg aatagggctg agcataaagg ttttacgacc gttccaagaa cattaaatta
     3001 catcaaccgt atcattgatc acttagctgg taccggctcc ccagtgtctc aaacgtactt
     3061 gagcttatgg tgccgggtgt ttgatgaagg ttttgttgaa atcagagaca aagactccat
     3121 cgcttatgag tcagggttta atgggcagag agctgtgact acatggatga gtcggatgaa
     3181 gaaactgcgt gagttagggc tcatcaagac aaaggccggc acgtctggtg agtttcacta
     3241 tgtattaatg ctgaatccac taagtattat aaaaagtcat tatgaatcaa atggtatgag
     3301 taaagatgag cggtataacg ctctattttc tcgaatgcaa gaagtggggg ctaagtggga
     3361 atgagtacat tttgtggggt tcgtgagcga taccttaaaa tttatcaaga agcatttgat
     3421 gaggtcgttg ctacatacgt tgaagctggt gttttagctg ggattgaact gcgtttatct
     3481 ccaatcgata aaacggcttt atctgcatgg tcttcggagt ggatggggaa atcagctaag
     3541 caaaaacatg gagaatggca gtgggataga atggtcgcca agcggattaa acgatgtaag
     3601 aagtttgatc tggcaatttg gggtgatggg attctatgtg gactctctct tggcctggtc
     3661 acccgaggaa agaaaactgt ccgaatgaat tatttgcaag cgtgtcctgt aaagcaccct
     3721 ttggaaaagc aaatagccgc tattgcggtt gcggttgcga ttgctgtagg acagcgggtt
     3781 ggcgctgacc atgtagcaat tttcaaccct gtaaatgaga aggtcgaaaa ccactacagg
     3841 aagttaggat ttgaaaaaag gacggtatac agccggtttg tgaagaatgc tatgtatatg
     3901 gacattccaa gccgagatta agcgccgtgt atacggcctc tctgctcgaa atcatcgaca
     3961 gctgcggaag caacaataaa ggcaagca
//
