LOCUS       NZ_CP116143             2089 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P649 plasmid pDETEC4, complete
            sequence.
ACCESSION   NZ_CP116143
VERSION     NZ_CP116143.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988469
            Assembly: GCF_027944815.1
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  JOURNAL   Unpublished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 01:50:27
            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)                     :: 4,984
            CDSs (total)                      :: 4,864
            Genes (coding)                    :: 4,648
            CDSs (with protein)               :: 4,648
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 82 of 216
            Pseudo Genes (incomplete)         :: 150 of 216
            Pseudo Genes (internal stop)      :: 41 of 216
            Pseudo Genes (multiple problems)  :: 52 of 216
            Pseudo Genes (short protein)      :: 3 of 216
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116143.1.
            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-P649"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC4"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-05"
     gene            join(1554..2089,1..430)
                     /locus_tag="PIB66_RS24855"
                     /old_locus_tag="PIB66_24855"
     CDS             join(1554..2089,1..430)
                     /locus_tag="PIB66_RS24855"
                     /old_locus_tag="PIB66_24855"
                     /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            434..700
                     /locus_tag="PIB66_RS24860"
                     /old_locus_tag="PIB66_24860"
     CDS             434..700
                     /locus_tag="PIB66_RS24860"
                     /old_locus_tag="PIB66_24860"
                     /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          2..90
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.38e-39"
ORIGIN
        1 gtttaaaggg aagaactacg ttaagcacga acgttgggta gaactctggc gcgattgctt
       61 gcgggtgaac tatgagccga atatcgatat tcgggcagta aaaactaaga caggtgaggt
      121 tgtggccaac gttgccgagc aactgcaaag cgcggttgct gaaacgctga aatactccgt
      181 taaaccggaa gatatggcaa acgatcctga gtggtttctt gagctgacgc ggcagcttca
      241 caagcgccgt tttatctcga ccggtggggc gctaaaaaac gtcctccagt tggatcgaga
      301 aaccaatgag gatcttgtca ttgccgacga tgtaggggat ggcactgatg acgggaagcg
      361 gacggcgttt gtctgggatt caggtaaacg gcgttacaaa cgcgcccctg agaaggataa
      421 atcggattaa cgtatgaata ttaatattga atacctgaat ggaaataaga ctattggttt
      481 atttttttta agaagtgaag cggtgattcc tgacaggttt aaaaacctta ttttgcttat
      541 tgatggatta agttttggca catttggttt tcatccgcac gaaggttttg aggatgaatt
      601 aattttatat attcagaaaa caaacgagag ggtaaaaact ctttttgtga aaatagattt
      661 aaacggtatc aagtttggat ttttaagaac gcattcttag ttctggaaaa gagccagcgg
      721 caggctgagg tgataggtac gagattgcat gcaatctcta gtgctctgtc tatcctgcat
      781 tatcctcagc attatcctca gccttgccaa ctcgacacca atgcaggata gacaatccga
      841 tgtcaaatgt taacactctg cgagtggtac attttccccg gattatcgtc ctgagcctgc
      901 cgctggctct ctttctaccg cctcgctttg ctcgttgctc aacgcctcac agacacggat
      961 taaaatccgc atccgttcac cgttttttaa agtccgttaa aagcatgatg ccatctccga
     1021 gagttaatct cgtcaaatgc taaatcgtgg gggtcccctt tggggttccg atttagtgat
     1081 tgacgacacc accgattaaa aaacttatgc ggggtggatg gtttcacgaa gtgaggccat
     1141 ccacctgtaa gacagggttt tgtttttatt ccctgtttta gtgatcgggt gtgtggaaaa
     1201 ggttggggta agccgttcgg gggtgcttgt tttggggggt taaaattgtg gttatttttt
     1261 gcgcaattct cgcgcgtgat ccttgtattt atacttaagg gataaatggc ggatatgaaa
     1321 tagtggttta gcccagtaat gacgaggctt tgagtgggtt ttgacaggtc aaagaaaatg
     1381 gagcagaatt gaggcgtttt taatcggcgt tggggagtgc gtcaacactc cccaacattt
     1441 cgaatgtgtc acctcagcgg caaactctgg tgacatgtac tggctcgcaa tgcacaggta
     1501 cgtgatgaat ataccacatc aaatcacagc ctgcccagat cggagcaggc ttaatgtcag
     1561 aagataaatt cctttcggac tacagccccc gtgatgcagt ttgggatacc cagcgcacgc
     1621 ttaccgattc tgtcgggggt atctaccaga ctgctgctga attcgagcgc tatgcactcc
     1681 gtatggcctc ctgtagcggt ttgttacgtt ttggttggtc taccatcatg gaaaccggag
     1741 aaacgcgcct acggcttcgt agtgcgcaat tttgccgtgt ccgtcattgc cctgtctgcc
     1801 agtggagaag aaccctcatg tggcaagccc gtttttatca ggctctaccg aaaatcgttg
     1861 tggattaccc gtcttcccga tggttgtttc tgacgttaac tgtcaggaac tgcgagatag
     1921 gtgaacttgg aacagtcctt acagcaatga atgcggcgtt taagcgaatg gaaaagcgaa
     1981 aggagctatc acctgttcag gggtggatca gggctacgga ggtgacgcga ggtaaggatg
     2041 gcagcgcaca tccgcatttt cactgtctgc tgatggtgca accttcttg
//
