LOCUS       NZ_CP116190             6200 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-E223 plasmid pDETEC12, complete
            sequence.
ACCESSION   NZ_CP116190
VERSION     NZ_CP116190.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988404
            Assembly: GCF_027944995.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  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  JOURNAL   Unpublished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 6200)
  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 01:55:01
            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)                     :: 4,969
            CDSs (total)                      :: 4,849
            Genes (coding)                    :: 4,574
            CDSs (with protein)               :: 4,574
            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)              :: 275
            CDSs (without protein)            :: 275
            Pseudo Genes (ambiguous residues) :: 0 of 275
            Pseudo Genes (frameshifted)       :: 91 of 275
            Pseudo Genes (incomplete)         :: 188 of 275
            Pseudo Genes (internal stop)      :: 55 of 275
            Pseudo Genes (multiple problems)  :: 54 of 275
            Pseudo Genes (short protein)      :: 4 of 275
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116190.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-E223"
                     /isolation_source="bed curtain"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC12"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-06"
     gene            97..912
                     /gene="sul2"
                     /locus_tag="PIC88_RS24805"
                     /old_locus_tag="PIC88_24800"
     ARG             98..909
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            973..1776
                     /gene="aph(3'')-Ib"
                     /locus_tag="PIC88_RS24810"
                     /old_locus_tag="PIC88_24805"
     ARG             974..1773
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1776..2612
                     /locus_tag="PIC88_RS24815"
                     /old_locus_tag="PIC88_24810"
     CDS             1776..2612
                     /locus_tag="PIC88_RS24815"
                     /old_locus_tag="PIC88_24810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<2719..3123)
                     /locus_tag="PIC88_RS24820"
                     /old_locus_tag="PIC88_24815"
                     /pseudo=""
     CDS             complement(<2719..3123)
                     /locus_tag="PIC88_RS24820"
                     /old_locus_tag="PIC88_24815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3167..3556)
                     /locus_tag="PIC88_RS24825"
                     /old_locus_tag="PIC88_24820"
     CDS             complement(3167..3556)
                     /locus_tag="PIC88_RS24825"
                     /old_locus_tag="PIC88_24820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            3774..4214
                     /locus_tag="PIC88_RS24830"
                     /old_locus_tag="PIC88_24825"
     CDS             3774..4214
                     /locus_tag="PIC88_RS24830"
                     /old_locus_tag="PIC88_24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(4959..5108)
                     /locus_tag="PIC88_RS24835"
                     /old_locus_tag="PIC88_24830"
     CDS             complement(4959..5108)
                     /locus_tag="PIC88_RS24835"
                     /old_locus_tag="PIC88_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            5679..5837
                     /locus_tag="PIC88_RS24900"
     CDS             5679..5837
                     /locus_tag="PIC88_RS24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     ARG             1777..2609
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5144..5317)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5241..5846
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ggatcaccgc aaacaggtta ctcgcctggg gattcccttt cgacccgagc atccgtatga
       61 gactcatgct cgattattat tattatagaa gcccccatga ataaatcgct catcattttc
      121 ggcatcgtca acataacctc ggacagtttc tccgatggag gccggtatct ggcgccagac
      181 gcagccattg cgcaggcgcg taagctgatg gccgaggggg cagatgtgat cgacctcggt
      241 ccggcatcca gcaatcccga cgccgcgcct gtttcgtccg acacagaaat cgcgcgtatc
      301 gcgccggtgc tggacgcgct caaggcagat ggcattcccg tctcgctcga cagttatcaa
      361 cccgcgacgc aagcctatgc cttgtcgcgt ggtgtggcct atctcaatga tattcgcggt
      421 tttccagacg ctgcgttcta tccgcaattg gcgaaatcat ctgccaaact cgtcgttatg
      481 cattcggtgc aagacgggca ggcagatcgg cgcgaggcac ccgctggcga catcatggat
      541 cacattgcgg cgttctttga cgcgcgcatc gcggcgctga cgggtgccgg tatcaaacgc
      601 aaccgccttg tccttgatcc cggcatgggg ttttttctgg gggctgctcc cgaaacctcg
      661 ctctcggtgc tggcgcggtt cgatgaattg cggctgcgct tcgatttgcc ggtgcttctg
      721 tctgtttcgc gcaaatcctt tctgcgcgcg ctcacaggcc gtggtccggg ggatgtcggg
      781 gccgcgacac tcgctgcaga gcttgccgcc gccgcaggtg gagctgactt catccgcaca
      841 cacgagccgc gccccttgcg cgacgggctg gcggtattgg cggcgctgaa agaaaccgca
      901 agaattcgtt aactgcacat tcgggatatt tctctatatt cgcgcttcat cagaaaactg
      961 aaggaacctc cattgaatcg aactaatatt ttttttggtg aatcgcattc tgactggttg
     1021 cctgtcagag gcggagaatc tggtgatttt gtttttcgac gtggtgacgg gcatgccttc
     1081 gcgaaaatcg cacctgcttc ccgccgcggt gagctcgctg gagagcgtga ccgcctcatt
     1141 tggctcaaag gtcgaggtgt ggcttgcccc gaggtcatca actggcagga ggaacaggag
     1201 ggtgcatgct tggtgataac ggcaattccg ggagtaccgg cggctgatct gtctggagcg
     1261 gatttgctca aagcgtggcc gtcaatgggg cagcaacttg gcgctgttca cagcctatcg
     1321 gttgatcaat gtccgtttga gcgcaggctg tcgcgaatgt tcggacgcgc cgttgatgtg
     1381 gtgtcccgca atgccgtcaa tcccgacttc ttaccggacg aggacaagag tacgccgcag
     1441 ctcgatcttt tggctcgtgt cgaacgagag ctaccggtgc ggctcgacca agagcgcacc
     1501 gatatggttg tttgccatgg tgatccctgc atgccgaact tcatggtgga ccctaaaact
     1561 cttcaatgca cgggtctgat cgaccttggg cggctcggaa cagcagatcg ctatgccgat
     1621 ttggcactca tgattgctaa cgccgaagag aactgggcag cgccagatga agcagagcgc
     1681 gccttcgctg tcctattcaa tgtattgggg atcgaagccc ccgaccgcga acgccttgcc
     1741 ttctatctgc gattggaccc tctgacttgg ggttgatgtt catgccgcct gtttttcctg
     1801 ctcattggca cgtttcgcaa cctgttctca ttgcggacac cttttccagc ctcgtttgga
     1861 aagtttcatt gccagacggg actcctgcaa tcgtcaaggg attgaaacct atagaagaca
     1921 ttgctgatga actgcgcggg gccgactatc tggtatggcg caatgggagg ggagcagtcc
     1981 ggttgctcgg tcgtgagaac aatctgatgt tgctcgaata tgccggggag cgaatgctct
     2041 ctcacatcgt tgccgagcac ggcgactacc aggcgaccga aattgcagcg gaactaatgg
     2101 cgaagctgta tgccgcatct gaggaacccc tgccttctgc ccttctcccg atccgggatc
     2161 gctttgcagc tttgtttcag cgggcgcgcg atgatcaaaa cgcaggttgt caaactgact
     2221 acgtccacgc ggcgattata gccgatcaaa tgatgagcaa tgcctcggaa ctgcgtgggc
     2281 tacatggcga tctgcatcat gaaaacatca tgttctccag tcgcggctgg ctggtgatag
     2341 atcccgtcgg tctggtcggt gaagtgggct ttggcgccgc caatatgttc tacgatccgg
     2401 ctgacagaga cgacctttgt ctcgatccta gacgcattgc acagatggcg gacgcattct
     2461 ctcgtgcgct ggacgtcgat ccgcgtcgcc tgctcgacca ggcgtacgct tatgggtgcc
     2521 tttccgcagc ttggaacgcg gatggagaag aggagcaacg cgatctagct atcgcggccg
     2581 cgatcaagca ggtgcgacag acgtcatact agatatcaag cgacttctcc tatcccctgg
     2641 gaacacatca atctcaccgg agaatatcgc tggccaaagc cttagcgtag gattccgccc
     2701 cttcccgcaa acgaccccaa acaggaaacg cagctgaaac gggaagctca acacccactg
     2761 acgcatgggt tgttcaggca gtacttcatc aaccagcaag gcggcacttt cggccatccg
     2821 ccgcgcccca cagctcgggc agaaaccgcg acgcttacag ctgaaagcga ccaggtgctc
     2881 ggcgtggcaa gactcgcagc gaacccgtag aaagccatgc tccagccgcc cgcattggag
     2941 aaattcttca aattcccgtt gcacatagcc cggcaattcc tttccctgct ctgccataag
     3001 cgcagcgaat gccgggtaat actcgtcaac gatctgatag agaagggttt gctcgggtcg
     3061 gtggctctgg taacgaccag tatcccgatc ccggctggcc gtcctggccg ccacatgagg
     3121 catgttccgc gtccttgcaa tactgtgttt acatacagtc tatcgcttag cggaaagttc
     3181 ttttaccctc agccgaaatg cctgccgttg ctagacattg ccagccagtg cccgtcactc
     3241 ccactcttac attgttcgca gtatctaggt acatgttatt gcgtgcacct tcatgatgta
     3301 taatgttatt aatgacagca gaaagatcga cagaattaat attcttcgta cctgggacag
     3361 ttatcgggtg tcggccagtg atgagaccaa aggatgcagt ataagatgaa ccactactat
     3421 tatcatggcc accattacca ccaccgttaa aactacctcc cgaacttcca gagccgctat
     3481 gaccatcatt gtaggggtca tttggtccca tgtgaccaaa accaccgaca gtaccgctat
     3541 ttaactctgt actcataaaa ttatcctctt tgacttttaa aaacagcaaa aactgtattt
     3601 ataacaatgt gtttatatac agtattcgaa atactacgcc cgtcaaaacc acaccgtcaa
     3661 caggtttttt gtgtattttt cacgcctcac gggcagcctc agaccttttg tgttaaaaca
     3721 gtaatatgtt ctgctgttac aatacggtac acacaggaga cactgtcact tttatggcat
     3781 ggcacacagt tcaagagaca ctgaaattaa caggaaagtc gcgctcgcaa ttatatcgtg
     3841 acatggctaa aggccttgtc agctatcgca caggaaaaaa tgatcgccgg gagttcgaga
     3901 ccagtgaact gattcgggcc tatggcgagc tgcgcacttc tgagacacca aaaaggcaca
     3961 aggagggaca ctccaaatct gtcgttagcc aggcggaaaa tgctcagcta gacgtcattc
     4021 agcagaaact ggacgctctg cagcagactg ttaccctaat gcttgaagac aagatggcgc
     4081 gggaagcaga aaaccgcctg cgaaatgagg agagggaaca actacaggcc gaaattagcc
     4141 gtctggctga cgcgctggca caggaaaaaa agcggggatt ctggtcgcgg ctgtttcgct
     4201 ccggttcaga gtaacagtgc aggtgactct gatttaccat aacatctgtt atcagcaccg
     4261 cctgagaggc cctcagggcg tttctgacgg gaaaccggta aaacaggcaa caaaccaccc
     4321 gaaaacccgc cagaaacgcg caggctctgt ttttacggca tgcatgagta tgcgcacaag
     4381 tgcatagcgc ggaaattcac accattcagc cggggtaagt cctgtttccg gcgttcttcc
     4441 catccgaaaa cggtgaacgg ggacgcaatt tattgcgtgg ccgtgaagcg ttgccggcgc
     4501 agccggaaaa cccgctgtca gcacgttcag gaagggggtg atgtacaaat ggcacagagg
     4561 atgaaagtga cgtatgagct gaaggaatga tgtaaaagtg atgtataagt gatgtaaaag
     4621 tgatgtatga actgaaggag cgatgtaatt ctgtagtcag gaagaataac ccgttcatgc
     4681 aggcatgaac gatacagtga ggaacgcttt ttttgtcacg atctcccctt aacctgcgta
     4741 aatcacccgc catggttgat tatttttcaa cctcaaaatg gtcatacacc taacgcagcc
     4801 gcgattttca tcgcaactgc atgaattaaa agaaaaaaaa ggaatatttc gttttcacga
     4861 gtaatacccg ggtattaaaa atccactgta attacatgaa aataaagaaa taaaaggtaa
     4921 taccggagta ttaccacgta cgcgggcaag cgaaaaagct ataacgcttc ccggccgaca
     4981 ggcgacccaa aatccacagg ggcatgcagg ttctcttcag taacctgcgc cattaaatca
     5041 aaaaggtcat attcgccggg aagctgcgta tcagtcgaat ccagttgttc atcatattca
     5101 gatggcatgg ggtgatatcc agtagctgag aggttgttag cgggtttcgg ggcgcagccc
     5161 tgaaccagtc atgtagcgct agcggagtgt atactggctt actatgttgc cacgattgcg
     5221 aaaatcagtg aagtgcttca tgtggcagga gaaaaaaggc agcaccggcg cgtcagcaga
     5281 atatgcgata caggagatat tccgcttcct cgctcactga ctcgctacgc tcggtcgttc
     5341 ggctgcggcg agcggtaccg gcttacggac ggggacggaa atttcctgga agataccagg
     5401 aagacactta gcaaagaaga gataaggcca cggcgaagcc gtttttccat aggctccgcc
     5461 cccctgacaa gcatcgcaaa atctgacgct caaatcagtg gtggcgaaac ccgacaggac
     5521 tataaagatc ccaggcgttt ccccctggta gctccctcgt gcgctctcct gttcctgcct
     5581 ttcggtttac cggtgtcatt ccgctgttat ggccgcggtt tctcattcca cgcctgacac
     5641 tcagttccgt gaaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt
     5701 ccgaccgctg cgccttgtcc ggtaactatc aacttgagtc caacccggaa agacacgaca
     5761 aaacgccact ggcagcagcc attagtaaca ggagtgcacg agaagataga ttaagaggtc
     5821 ttgaagtaga ggcctgactg cggctacact gaaagaacag ttttggtaat ggcggtctcg
     5881 tgaaccctgt taccgggtta agcagttccc caactgactt aaccttcgaa caaaccgcct
     5941 ccccaggcgg ttttttcgtt tacagagcaa gagattacga ttcattgaaa aggatctcaa
     6001 gaagatcctt tgtagattac tatcaattaa tcttccgaac atgacaccag tcactgttga
     6061 ttacggttaa accgctccgt aacaggtttc cctcgtattg gtgacttgca gcaccaaaga
     6121 agcaaaaaag ataaatatat ctacttattg agagatgata tatttatttc caaaatgcta
     6181 cagatacatc atcatgaaac
//
