LOCUS       NZ_CP116093             1565 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-S565 plasmid pDETEC76, complete
            sequence.
ACCESSION   NZ_CP116093
VERSION     NZ_CP116093.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988496
            Assembly: GCF_027944655.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1565)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Extended-spectrum beta-lactamase genes traverse the Escherichia coli
            populations of ICU patients, staff and environment
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1565)
  AUTHORS   Moran,R.A., Baomo,L., Doughty,E.L., Guo,Y., Ba,X., van Schaik,W.,
            Zhuo,C. and McNally,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JAN-2023) Institute of Microbiology and Infection,
            University of Birmingham, Institute of Microbiology and Infection,
            Birmingham B15 2TT, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 10x
            Sequencing Technology             :: Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/25/2024 02:39:27
            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)                     :: 5,104
            CDSs (total)                      :: 4,983
            Genes (coding)                    :: 4,803
            CDSs (with protein)               :: 4,803
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 180
            CDSs (without protein)            :: 180
            Pseudo Genes (ambiguous residues) :: 0 of 180
            Pseudo Genes (frameshifted)       :: 74 of 180
            Pseudo Genes (incomplete)         :: 111 of 180
            Pseudo Genes (internal stop)      :: 34 of 180
            Pseudo Genes (multiple problems)  :: 36 of 180
            Pseudo Genes (short protein)      :: 2 of 180
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116093.1.
            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..1565
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-S565"
                     /isolation_source="ICU staff rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC76"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-01"
     gene            complement(687..1166)
                     /locus_tag="PIC22_RS25445"
                     /old_locus_tag="PIC22_25440"
     CDS             complement(687..1166)
                     /locus_tag="PIC22_RS25445"
                     /old_locus_tag="PIC22_25440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001620079.1"
                     /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_000275450.1"
                     /translation="MYIGTEEQRKKRLKELEKLNKESESDPKNNGPFTQVYQKGWERIR
                     ELSKDKQGVVAIPLYSFLAEHIDPSCGAVVADQQFLADKLGVSRSTIKRWLNYLESKNA
                     LVRIPVAGKVCAYALDPHEVWKGYNTSKNYAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          177..437
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="1.83e-109"
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 cgctgttgtt ctttcgggga taagtcgtca gatagccctt
      241 caaacgcgct cagaagctct cagacgcacg aaacggggtt taaatgcccg tcagggcatg
      301 gaaggcgcga aaaacgctta cagagcgttt caggaggtca ggcgcgccga tacccctagc
      361 caggggcttt caggtcgcca ggaaccgcgc cagccccctg caaagcccat ttgcacggta
      421 caggcagcca ctcggttggt aggtggtcgt agaccgtcgg tgttacagcg atgggggtct
      481 ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc tgccggaacc gtggcggctc
      541 ggtcgttctg gagatcgggg agcaaaaaca cgcaagggat tttgaggcgg caaaagagca
      601 atgcaggata gacaacccga tgtcaaatgt taacatttga atcagattgt ccaaaaacgg
      661 ggtttttgcc tgtgtctgcc gctggctcaa tttgaaaaca tggccatgat tcggcgctga
      721 atatcaccgt ctttgttgac cagtgtttta gtgacaaacg ccgcgtagtt tttagatgtg
      781 ttgtatccct tccagacttc atgtggatcg agtgcatacg cacaaacctt accagcaaca
      841 ggaattctga ctaacgcgtt ttttgattct aagtagttga gccagcgctt aattgtgctt
      901 cggctaacac ccaatttatc tgctaaaaac tgctgatcgg caacaacagc accgcatgag
      961 ggatctatgt gctcagctaa aaacgagtaa agcggtattg ctacaactcc ctgcttgtcc
     1021 ttcgacagtt ctcggatcct ttcccagccc ttctgataaa cctgggtgaa tgggccgtta
     1081 tttttcggat ctgattccga ttctttgttt aatttttcca gttcttttag acgctttttt
     1141 cgctgctctt cagtcccgat atacatggta aatctccacg gtctaatgat ggctcaaata
     1201 taagccatca tagctcaaac gtaaaccatg ataggtcgac ctagctcaca catgcgtgag
     1261 ctaaccttag accacacatg cgtgagctaa cccataatgc aagtagctaa aaaatcaata
     1321 acttacaaaa tcgcccttaa atatcttttc tgctgaaagt gttgcgcaaa gcggaacact
     1381 tttttggggt gtcggggcga agccctgaca cagtcacgta gcgatagcgg agtgtatact
     1441 ggcttactcc tctgcaagcc ttaccagctg tgatttttgc cagatttcac gctctcaacg
     1501 ttcaacagct ccatcatggt tttgccgtcc gttcaccgct aaaacgcctc agaaatcggg
     1561 acagg
//
