LOCUS       NZ_CP116134             2089 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P666 plasmid pDETEC4, complete
            sequence.
ACCESSION   NZ_CP116134
VERSION     NZ_CP116134.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988472
            Assembly: GCF_027944795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2089)
  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  JOURNAL   Unpublished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 2089)
  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 02:06:33
            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)                     :: 5,170
            CDSs (total)                      :: 5,049
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 83 of 212
            Pseudo Genes (incomplete)         :: 145 of 212
            Pseudo Genes (internal stop)      :: 42 of 212
            Pseudo Genes (multiple problems)  :: 52 of 212
            Pseudo Genes (short protein)      :: 3 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116134.1.
            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..2089
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P666"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC4"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-10"
     gene            84..1049
                     /locus_tag="PIB57_RS25785"
                     /old_locus_tag="PIB57_25790"
     CDS             84..1049
                     /locus_tag="PIB57_RS25785"
                     /old_locus_tag="PIB57_25790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            1053..1319
                     /locus_tag="PIB57_RS25790"
                     /old_locus_tag="PIB57_25795"
     CDS             1053..1319
                     /locus_tag="PIB57_RS25790"
                     /old_locus_tag="PIB57_25795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          478..709
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 tgacatgtac tggctcgcaa tgcacaggta cgtgatgaat ataccacatc aaatcacagc
       61 ctgcccagat cggagcaggc ttaatgtcag aagataaatt cctttcggac tacagccccc
      121 gtgatgcagt ttgggatacc cagcgcacgc ttaccgattc tgtcgggggt atctaccaga
      181 ctgctgctga attcgagcgc tatgcactcc gtatggcctc ctgtagcggt ttgttacgtt
      241 ttggttggtc taccatcatg gaaaccggag aaacgcgcct acggcttcgt agtgcgcaat
      301 tttgccgtgt ccgtcattgc cctgtctgcc agtggagaag aaccctcatg tggcaagccc
      361 gtttttatca ggctctaccg aaaatcgttg tggattaccc gtcttcccga tggttgtttc
      421 tgacgttaac tgtcaggaac tgcgagatag gtgaacttgg aacagtcctt acagcaatga
      481 atgcggcgtt taagcgaatg gaaaagcgaa aggagctatc acctgttcag gggtggatca
      541 gggctacgga ggtgacgcga ggtaaggatg gcagcgcaca tccgcatttt cactgtctgc
      601 tgatggtgca accttcttgg tttaaaggga agaactacgt taagcacgaa cgttgggtag
      661 aactctggcg cgattgcttg cgggtgaact atgagccgaa tatcgatatt cgggcagtaa
      721 aaactaagac aggtgaggtt gtggccaacg ttgccgagca actgcaaagc gcggttgctg
      781 aaacgctgaa atactccgtt aaaccggaag atatggcaaa cgatcctgag tggtttcttg
      841 agctgacgcg gcagcttcac aagcgccgtt ttatctcgac cggtggggcg ctaaaaaacg
      901 tcctccagtt ggatcgagaa accaatgagg atcttgtcat tgccgacgat gtaggggatg
      961 gcactgatga cgggaagcgg acggcgtttg tctgggattc aggtaaacgg cgttacaaac
     1021 gcgcccctga gaaggataaa tcggattaac gtatgaatat taatattgaa tacctgaatg
     1081 gaaataagac tattggttta ttttttttaa gaagtgaagc ggtgattcct gacaggttta
     1141 aaaaccttat tttgcttatt gatggattaa gttttggcac atttggtttt catccgcacg
     1201 aaggttttga ggatgaatta attttatata ttcagaaaac aaacgagagg gtaaaaactc
     1261 tttttgtgaa aatagattta aacggtatca agtttggatt tttaagaacg cattcttagt
     1321 tctggaaaag agccagcggc aggctgaggt gataggtacg agattgcatg caatctctag
     1381 tgctctgtct atcctgcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa
     1441 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg
     1501 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca
     1561 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa
     1621 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt
     1681 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg
     1741 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttag
     1801 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt
     1861 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg
     1921 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt
     1981 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg
     2041 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctgg
//
