LOCUS       NZ_CP128978             1552 bp    DNA     circular CON 07-JUL-2023
DEFINITION  Escherichia coli strain TUM1886 plasmid pMTY1886_Col, complete
            sequence.
ACCESSION   NZ_CP128978
VERSION     NZ_CP128978.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35768952
            Assembly: GCF_030389925.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1552)
  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  JOURNAL   Unpublished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 1552)
  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_TUM1886_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 238x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/05/2023 07:48:43
            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)                     :: 5,941
            CDSs (total)                      :: 5,819
            Genes (coding)                    :: 5,506
            CDSs (with protein)               :: 5,506
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 313
            CDSs (without protein)            :: 313
            Pseudo Genes (ambiguous residues) :: 1 of 313
            Pseudo Genes (frameshifted)       :: 142 of 313
            Pseudo Genes (incomplete)         :: 201 of 313
            Pseudo Genes (internal stop)      :: 78 of 313
            Pseudo Genes (multiple problems)  :: 89 of 313
            Pseudo Genes (short protein)      :: 3 of 313
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP128978.1.
            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..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM1886"
                     /db_xref="taxon:562"
                     /plasmid="pMTY1886_Col"
                     /geo_loc_name="Japan"
                     /collection_date="2003"
                     /collected_by="Toho University School of Medicine"
     gene            complement(668..1144)
                     /locus_tag="QVM91_RS29705"
                     /old_locus_tag="QVM91_29705"
     CDS             complement(668..1144)
                     /locus_tag="QVM91_RS29705"
                     /old_locus_tag="QVM91_29705"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          177..428
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.885"
                     /coverage="97.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtgcaaat gtaataccgt cacccgcgac gatattccgt ttgccatctg gtcagggctt
       61 cgccccgaca ccccgcatca gtgcgtacgt gctcaatgtg gtttccggtt ctcttccgct
      121 tcctcgccca ctcgctcact aacgttcggt cgctggggct gcggcgagcg gtgccacctc
      181 tcgcatgttg tcggtgattc tgctgttgcc ctttcgggga tgagtcgcca gatagcccct
      241 caaacgcgct cagaagccct cagacgcacg aaacgggttt taaatgcccg tcagggcatg
      301 gaaggcgcga aaaacgctta cagagggttt taggaggtca ggcgcgccga tacccctaac
      361 caggggcttt caggtcgcca ggaaccgcgt cagccccctg caaagcccat ttgcacggaa
      421 taggcagcca cgcggttggt aggtggtcgt agaccgtcga tgttacagcg atgggggtct
      481 ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc tgccggaacc gtggcagcgc
      541 ggtcgttctg gagatcggga aacaaaaaca cgcgaggggt tttgaggtcg gcaaaagagc
      601 aatgcaggat agacaatcca ctagaaattg catgcaatgt tctgtggatt gtccgcctgc
      661 cgctggctca atttgaaaac atggccatga ttcggcgctg aatatcaccg tctttgttaa
      721 ccagtgtttt agtgacaaac gctgcatggt ttttcgtggt gttgtatccc ttccagactt
      781 catgtggatc gagggcatac gcacatacct taccagcaac agggattcta actaatgcgt
      841 tttttgattc taagtaattg agccaacgaa taattgtgct tctgctaact ccaagttttt
      901 cagctaagaa ttgctgatcc gcaacgacag cgccacatgt cggatcgata tgctccgcta
      961 aaaatgagta cagcttcagt gctgatatgc cttggctatc cttcagcagc tctcgaacgc
     1021 gctcccaacc ttttggagat acctgtgtaa accttgaatt tttctttgct tcttcgagat
     1081 cctcggtgtt tttctttgcc tcatctgaaa gttgtttcag tcgtttttct gaatcaataa
     1141 acatgatttt tccctctgaa aatcccatgc actaacgttg gctcaaatct aaaccatcat
     1201 gacacatcca tgcaacacct tgttgcacgt tgtcgcatcc tgtatgcgac aacgttgtgt
     1261 caccctgtat gcgacaggta aataaaaaac actctaaaaa aacaatggct tacaaatcga
     1321 cgcaaaagat ctattctagg caagggtgtt gcgggccacg caacaccctt taggggtgtc
     1381 ggggcgaagc cctgacccag tcacgtagcg atagcggagt gtatactggc ttactcctct
     1441 gcaagcctta ccagctgtga tttttgccag atttcacgct ctcaacgttc aacagctcca
     1501 tcatggtttt gccgtccgtt caccgctaaa acgcctcaga aatcgggaca gg
//
