LOCUS       NZ_CP135708             1558 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain TUM1880 plasmid pMTY1880_Col, complete
            sequence.
ACCESSION   NZ_CP135708
VERSION     NZ_CP135708.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35768949
            Assembly: GCF_032384295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1558)
  AUTHORS   Komori,K., Aoki,K., Ishii,Y. and Tateda,K.
  TITLE     Analysis of the Plasmid-Driven Acquisition of blaCTX-M-14 in
            Escherichia coli ST131 Subclone H30
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1558)
  AUTHORS   Komori,K., Aoki,K., Ishii,Y. and Tateda,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-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                     :: 13-SEP-2021
            Assembly Method                   :: SPAdes v. v3.15.5
            Assembly Name                     :: Toho-u_TUM1880_Comp_v1.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: missing
            Genome Coverage                   :: 191x
            Sequencing Technology             :: Complete Genomics
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 14:54:06
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,476
            CDSs (total)                      :: 5,352
            Genes (coding)                    :: 5,077
            CDSs (with protein)               :: 5,077
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 113 of 275
            Pseudo Genes (incomplete)         :: 186 of 275
            Pseudo Genes (internal stop)      :: 55 of 275
            Pseudo Genes (multiple problems)  :: 71 of 275
            Pseudo Genes (short protein)      :: 2 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135708.1.
            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..1558
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="TUM1880"
                     /db_xref="taxon:562"
                     /plasmid="pMTY1880_Col"
                     /geo_loc_name="Japan"
                     /collection_date="2003"
                     /collected_by="Toho University School of Medicine"
     gene            1..477
                     /locus_tag="RS160_RS27375"
                     /old_locus_tag="RS160_27375"
     CDS             1..477
                     /locus_tag="RS160_RS27375"
                     /old_locus_tag="RS160_27375"
                     /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"
     gene            complement(929..1150)
                     /locus_tag="RS160_RS27380"
                     /old_locus_tag="RS160_27380"
     CDS             complement(929..1150)
                     /locus_tag="RS160_RS27380"
                     /old_locus_tag="RS160_27380"
                     /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_152921959.1"
                     /translation="MCKCNTVTRDDIPFAIWSGLRPDTPHQCVRAQCGFRFSSASSPTR
                     SLRSVAGAAASGITSRMLSVIPVLFFWG"
                     /name="hypothetical protein"
     Typing          1078..1169
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.398"
                     /coverage="100.0"
                     /evalue="3.4000000000000004e-27"
     Typing          complement(1372..1480)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.182"
                     /coverage="100.0"
                     /evalue="4.23e-47"
     Typing          complement(716..976)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.985"
                     /coverage="100.0"
                     /evalue="1.85e-99"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgtgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagct
      481 agcggcaggc ggacaatcag ggctacgtgt taacgttctg accatgattg tctatcctgc
      541 attgctccat tgctcttttg ccgcctcaaa atcctttgcg tgtttttgct ccccgttctc
      601 cagaaaaaac cgagccgcca cggttccggc agcgccttga gcgctaccgg aaaccgtctg
      661 gggagaaccc cagaccccca tcgctgcaac accgacggtc tacgaccacc taccaaccgc
      721 atggctgcct gttccgtgca aatgggcttt gcagggggct ggcgcggttc ctggcgacct
      781 gaaagcccct ggttaggggt atcggcgcgc ttgacctcct gagagcctct gtaagcgttt
      841 ttcgcgcctt ccatgccctg gcgggcatct aaaacccgtt tcgtgcgtct gagagctttt
      901 gagcgcgttt gaggggctat ctggcgactc atccccaaaa gaacaacacc gggatcaccg
      961 acaacatgcg agaggtgatc ccgctcgccg cagccccagc gaccgaacgt agtgagcgag
     1021 tgggcgagga agcggaagag aaccggaaac cacattgagc acgtacgcac tgatgcgggg
     1081 tgtcggggcg aagccctgac cagatggcaa acggaatatc gtcgcgggtg acggtattac
     1141 atttgcacat cctgtcccga tttttggggc gttttagcgg tgaacggaag gcaaaaacat
     1201 gatcgagctg ttgaacgtgg agagcgcgaa atcgtgcaaa atcacggctg acgaggcttg
     1261 cagaggagta agccagtata cactccgcta tcgctacgtg actgggtcag ggcttcgccc
     1321 cgacaccccc aaagggcgtt gcgttgcacg caacaccctt gcctagaata gatcttttac
     1381 gccgatttgt aagtgcttgt ttttttagtg tgttttttat ttacctgtcg catccaggat
     1441 gacacaacgt tgtcgcatcc tggatgcgac aacacgcaac aaggtgttgc acagatgtgt
     1501 catgatggct tagatttgaa ccaacgttag tgcatgggat tttcagaggg aaaaaatc
//
