LOCUS       NZ_CP116122             2113 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P793 plasmid pDETEC4, complete
            sequence.
ACCESSION   NZ_CP116122
VERSION     NZ_CP116122.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988477
            Assembly: GCF_027944775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2113)
  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  JOURNAL   Unpublished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 2113)
  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 01:55:41
            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)                     :: 5,351
            CDSs (total)                      :: 5,234
            Genes (coding)                    :: 4,997
            CDSs (with protein)               :: 4,997
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 84 of 237
            Pseudo Genes (incomplete)         :: 166 of 237
            Pseudo Genes (internal stop)      :: 38 of 237
            Pseudo Genes (multiple problems)  :: 48 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116122.1.
            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..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P793"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC4"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-12"
     gene            84..1049
                     /locus_tag="PIC92_RS26680"
                     /old_locus_tag="PIC92_26685"
     CDS             84..1049
                     /locus_tag="PIC92_RS26680"
                     /old_locus_tag="PIC92_26685"
                     /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="PIC92_RS26685"
                     /old_locus_tag="PIC92_26690"
     CDS             1053..1319
                     /locus_tag="PIC92_RS26685"
                     /old_locus_tag="PIC92_26690"
                     /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 cattatcctc agcattatcc
     1441 tcagccttgc caactcgaca ccaatgcagg atagacaatc cgatgtcaaa tgttaacact
     1501 ctgcgagtgg tacattttcc ccggattatc gtcctgagcc tgccgctggc tctctttcta
     1561 ccgcctcgct ttgctcgttg ctcaacgcct cacagacacg gattaaaatc cgcatccgtt
     1621 caccgttttt taaagtccgt taaaagcatg atgccatctc cgagagttaa tctcgtcaaa
     1681 tgctaaatcg tgggggtccc ctttggggtt ccgatttagt gattgacgac accaccgatt
     1741 aaaaaactta tgcggggtgg atggtttcac gaagtgaggc catccacctg taagacaggg
     1801 ttttgttttt attccctgtt ttggtgatcg ggtgtgtgga aaaggttggg gtaagccgtt
     1861 cgggggtgct tgttttgggg ggttaaaatt gtggttattt tttgcgcaat tctcgcgcgt
     1921 gatccttgta tttatactta agggataaat ggcggatatg aaatagtggt ttagcccagt
     1981 aatgacgagg ctttgagtgg gttttgacag gtcaaagaaa atggagcaga attgaggcgt
     2041 ttttaatcgg cgttggggag tgcgtcaaca ctccccaaca tttcgaatgt gtcacctcag
     2101 cggcaaactc tgg
//
