LOCUS       NZ_CP116201             3537 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-C31 plasmid pDETEC90, complete
            sequence.
ACCESSION   NZ_CP116201
VERSION     NZ_CP116201.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988385
            Assembly: GCF_027945055.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3537)
  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  JOURNAL   Unpublished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 3537)
  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 01:50:24
            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)                     :: 5,033
            CDSs (total)                      :: 4,913
            Genes (coding)                    :: 4,747
            CDSs (with protein)               :: 4,747
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 60 of 166
            Pseudo Genes (incomplete)         :: 109 of 166
            Pseudo Genes (internal stop)      :: 31 of 166
            Pseudo Genes (multiple problems)  :: 31 of 166
            Pseudo Genes (short protein)      :: 2 of 166
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116201.1.
            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..3537
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-C31"
                     /isolation_source="human clinical specimen"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC90"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2020"
     gene            complement(join(2530..3537,1..216))
                     /locus_tag="PIB97_RS25120"
                     /old_locus_tag="PIB97_25110"
     CDS             complement(join(2530..3537,1..216))
                     /locus_tag="PIB97_RS25120"
                     /old_locus_tag="PIB97_25110"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="oligosaccharide flippase family protein"
                     /protein_id="WP_250908633.1"
                     /translation="MMAEKLVSIIGLVFVNSYMAKYIGPTDFGKITFATTIFTFVQAMA
                     WFGGQNILFKRMSEKRKSGIALALHTQKQRRVIFALSSLIALFYLFFFTDTLTFVFGVA
                     NCIATYYIVMDIFAVYNNTQLISRINALTNGAGLCIAYIFRFLISYLELPVYTFSIPII
                     LIPAIPYVIRCIYFYNTVEDTSVLKSKTKKYNKYLISAGGSLLLSTLSIVVYTQVSNIF
                     LAKVTSYSNLGIYNVALTLGSAYSFISVALITSFFSKIYQEKDFEKMSRLLTSINRIVI
                     VITIFILFGFYFLGPYIISMLYGSAYKMAVELVPIIILATMFSSLGAICYRFIIKYSGY
                     KYLSYKMMLTGLLSIPFSYVMINRYDVFGAAYCFLVVEVLSCTLLNYFFRSGMILRIHL
                     NVIGLMRR"
                     /name="oligosaccharide flippase family protein"
     gene            complement(1740..2437)
                     /locus_tag="PIB97_RS25130"
                     /old_locus_tag="PIB97_25120"
     CDS             complement(join(1740..2188,2188..2437))
                     /locus_tag="PIB97_RS25130"
                     /old_locus_tag="PIB97_25120"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558267.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_250908635.1"
                     /translation="MASVSISCPSCSATEGVVRNGKSTAGHQRYLCSHCRKTWQLQFTY
                     TASQPGTHQKIIDMAMNGVGCRASARIMGVGLNTILRHFKKLRPQSVNSRIQPGSNVIV
                     CAEMDEQWGYVGAKSRQRWLFYAYDRIRRTVVVHVFGERTMATLERLPGLLSAFEVVVW
                     MRDGWPLYEPRLKGELHVISKRYTQRIERHNLNLRQHLSRLGRKSLSFSKSVELHDKVI
                     GHYLNIKHDL"
                     /name="IS1 family transposase"
     Typing          862..1346
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.634"
                     /coverage="93.0"
                     /evalue="4.5400000000000006e-173"
ORIGIN
        1 ttgagtatgt aatgcaagag caatacctga ttttcttttc tcactcatcc ttttaaaaag
       61 gatgttttgc ccaccaaacc aagccatggc ctgtacaaac gtaaatattg tcgtagcaaa
      121 agtaatctta ccaaaatcag taggtcctat atattttgcc atataggagt ttacaaacac
      181 aagaccgatg atgctgacta atttttcagc catcatccaa aaggcattag aatacattac
      241 tcactcgcaa aaaattaatc ccatagaaat tttggtaata ctgtcaacct gttgatgact
      301 attttaatct gtagtcattc aatccttgta acatcaggat aatcctggtg tcagtgaaaa
      361 cacgaaatca acaatttggt atcattacca gcgtcggcat ggttccagcg atcagatgtc
      421 accgacagaa tatgaaaacc agtattatca acgtctcgga agtgtctaga ttatccgtgg
      481 cgattcaaaa gctgattttt gtcgtggtct aactactgta aagaatccac ctaaaagctc
      541 tcttttgaca tatctactgc atcttatgaa ttgaataaaa acccataaaa acaacaactt
      601 agccacgcta ccgccctggg ctcttcagct acctatccac tgcactaacg ctaacgacta
      661 tctttaacat ttgggttgag gtcaaatcat taagtaactt aacaataaac acgataactt
      721 caggaaggac cgatttcacc cttgcttatg atggcgtaac gttttcttaa tattttaaac
      781 cgaagtggtg atttgccaaa gtgcttcatg tggcaggagt gaaatgaggc tttccggcgt
      841 caggagaaga tgctggttca ggtgatattc cgcttcctcg ctcactgact cgctgcgctc
      901 ggtcgttcgg ctgcggcgag cggacgaagc tcacggataa gagcataaag ctatgacaca
      961 ggaataaaga ggtctcagaa aggatgcggc gttgccgttt ttccataggc tccgcccccc
     1021 tgacaagcat cacgaaatct gacgctcaaa tcagtggtgg cgaaacccga caggactata
     1081 aagataccag gcgtttcccc ctgatggctc cctcgtgcgc tctcctgttc ctgcctttcg
     1141 gtttaccggt gtcattccgc tgttatggcc gcgtttatct cattccacgc ctgacactca
     1201 gttccgggta ggcagttcgc tccaagctgg actgtatgca cgaacccccc gttcagtccg
     1261 accgctgcgc cttatccggt aactatcgtc ttgagtccaa cccggagagg cacgacaaaa
     1321 cgccactggc agcagccact ggtaacagga tttacggagc agagtagtag agtgcttcta
     1381 cagagttctt gaagtggtgg cctgactgcg gctacactgg aaggactgtt ttggtatctg
     1441 cgctccgtga aagccagtta ccttcggaaa aaagagttgg tagctcttga ttccggcaaa
     1501 cgaaccaccg ttggtagcgg tggttttttt gtttgcagga catgagatta cgacgcaaca
     1561 gaaaggatct caagaagttc cttgctgtat tgctactatc ctagagatct gaccgattag
     1621 gggcattatc agattacggc cttgtaatcc acgataaaaa cccagaaacc agaagagttg
     1681 gcccagcgac atatgttaca taaacgccca catatgaaac tgtaggtaat gactccaact
     1741 tacagatcgt gttttatgtt cagataatgc ccgatgactt tgtcatgcag ctccaccgat
     1801 tttgagaacg acagtgactt cctgcccagc cttgacagat gctgcctcag attcaggtta
     1861 tgccgctcaa tacgctgcgt atatcgcttg ctgataacgt gcagttctcc cttcaggcgt
     1921 ggttcataaa gcggccagcc atccctcatc cataccacga cctcaaaggc cgacagcagg
     1981 cccggaagac gctccagcgt ggccatcgtg cgttcaccga atacgtgcac cacaactgtc
     2041 ctccgtatcc tgtcatacgc gtaaaacaac cagcgctggc gtgatttagc gccgacgtaa
     2101 ccccactgtt cgtccatttc cgcgcaaaca atgacgttac tgcccggttg tatgcgtgag
     2161 tttaccgact gcggcctgag ttttttaagt gtcgtaaaat cgtgttgagg ccaacgccca
     2221 taatgcgtgc actggcgcga catccgacgc cattcatggc catatcaata attttctggt
     2281 gtgtaccggg ctgagaggcg gtgtaagtga actgtagctg ccatgtttta cggcagtgag
     2341 agcagagata gcgctgatgt ccggcagtac ttttaccgtt acgcaccacg ccttcagtag
     2401 ctgaacagga gggacaactg atagaaacag aagccactgg agcacctcaa aaacaccatc
     2461 atacactaaa tcagtaagtt ggcaccatta ccaacacaac ctataaataa acctgccccc
     2521 cccccaccat caacgcctca tcaacccaat aacatttaaa tgaatcctta gaatcattcc
     2581 actcctaaag aaataattta ataatgtgca tgacagaacc tcgaccacaa gaaaacaata
     2641 cgcagcaccg aaaacatcat aacggttaat cataacatat gagaatggga tgctgagcaa
     2701 gccagttaac atcattttat atgaaaggta tttgtagcca gagtatttta ttataaatct
     2761 ataacaaata gctcccaagg atgaaaacat tgtcgcgaga ataatgattg gcaccaactc
     2821 aacagccatt ttataggccg aaccatagag catactgata atgtacggcc caagaaaata
     2881 aaaaccaaat aagataaaaa ttgttatcac gatcacaatt ctatttattg aggttagaag
     2941 tctagacatt ttttcaaaat ctttctcttg atagatttta gaaaagaaac tagtaattaa
     3001 cgcaactgaa ataaatgaat acgcactgcc aagagtcagc gccacattat aaatacccaa
     3061 attagaatat gaggttactt tagccaaaaa aatatttgat acctgtgtgt aaaccacaat
     3121 ggacagggtt gatagtaaca acgaccctcc cgctgaaatt aaatacttat tatatttctt
     3181 cgttttcgat tttaataccg aagtgtcttc aacggtattg taaaaatata tacacctaat
     3241 aacataaggt attgctggaa ttaatataat aggaatgcta aatgtatata ctggcaactc
     3301 caagtatgaa attaaaaagc ggaatatata agcaatacac aaccctgcgc catttgttaa
     3361 tgcattaatt ctagatatta actgcgtatt attatataca gcgaaaatat ccatcactat
     3421 ataataagtg gcaatgcagt tagccacccc aaaaacaaat gtcagggtgt ctgtaaaaaa
     3481 aaacaaatag aacaaggcaa tcaatgaaga gagtgcaaaa ataaccctgc gctgctt
//
