LOCUS       NZ_CP116164             3684 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P351 plasmid pDETEC9, complete
            sequence.
ACCESSION   NZ_CP116164
VERSION     NZ_CP116164.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988454
            Assembly: GCF_027944875.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3684)
  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  JOURNAL   Unpublished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 3684)
  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 01:52:08
            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)                     :: 4,895
            CDSs (total)                      :: 4,775
            Genes (coding)                    :: 4,533
            CDSs (with protein)               :: 4,533
            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)              :: 242
            CDSs (without protein)            :: 242
            Pseudo Genes (ambiguous residues) :: 0 of 242
            Pseudo Genes (frameshifted)       :: 84 of 242
            Pseudo Genes (incomplete)         :: 155 of 242
            Pseudo Genes (internal stop)      :: 54 of 242
            Pseudo Genes (multiple problems)  :: 50 of 242
            Pseudo Genes (short protein)      :: 4 of 242
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116164.1.
            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..3684
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P351"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC9"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-13"
     gene            273..419
                     /locus_tag="PIC26_RS24390"
                     /old_locus_tag="PIC26_24385"
     CDS             273..419
                     /locus_tag="PIC26_RS24390"
                     /old_locus_tag="PIC26_24385"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_073545459.1"
                     /translation="MHEPPVQSDCCTLSGNYHLESNPVRHAQAPLAAATGKKVYKRLLI
                     QSS"
                     /name="replication initiation protein"
     gene            complement(877..1158)
                     /locus_tag="PIC26_RS24395"
                     /old_locus_tag="PIC26_24390"
     CDS             complement(877..1158)
                     /locus_tag="PIC26_RS24395"
                     /old_locus_tag="PIC26_24390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000594459.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_032440460.1"
                     /translation="MIKNIKHKGLRSFAEEGSTAGIQPSMAKRLRMILTTLSTATCIQD
                     VVDVRALGCHPLKGERKGEYSVEVNGNWRVVFKVEEPNVLDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1495..1788
                     /locus_tag="PIC26_RS24400"
                     /old_locus_tag="PIC26_24395"
     CDS             1495..1788
                     /locus_tag="PIC26_RS24400"
                     /old_locus_tag="PIC26_24395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609279.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_023317864.1"
                     /translation="MINLYDPVHPGEFIREMFMEPFEIPAAELADKLDVSQSTLSRLLN
                     GKTDLSYEMALRLSKVVGRSAESWVNMQTQFSLSKSRKSLAAELEHLHPMFP"
                     /name="HigA family addiction module antitoxin"
     gene            1852..2154
                     /locus_tag="PIC26_RS24405"
                     /old_locus_tag="PIC26_24400"
     CDS             1852..2154
                     /locus_tag="PIC26_RS24405"
                     /old_locus_tag="PIC26_24400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006326557.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3892 domain-containing protein"
                     /protein_id="WP_039023182.1"
                     /translation="MVDFYISAIKMDSAGQHIEFVKVHKINRDGSWNTAGSISSRKFIS
                     ELISMGKASFMTVVKNSSTGKWNLGAKVEAMDDGYITTDPNKTKLDNLGNLPKFV"
                     /name="DUF3892 domain-containing protein"
     gene            complement(2939..3361)
                     /locus_tag="PIC26_RS24410"
                     /old_locus_tag="PIC26_24405"
     CDS             complement(2939..3361)
                     /locus_tag="PIC26_RS24410"
                     /old_locus_tag="PIC26_24405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_039023181.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVLKHGKTIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAGSTGVNSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPDSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3361..3552)
                     /locus_tag="PIC26_RS24415"
                     /old_locus_tag="PIC26_24410"
     CDS             complement(3361..3552)
                     /locus_tag="PIC26_RS24415"
                     /old_locus_tag="PIC26_24410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_039023180.1"
                     /translation="MSKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          10..382
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.467"
                     /coverage="91.0"
                     /evalue="1.28e-167"
ORIGIN
        1 cagcacggag agggagaagg ccgcacaccg gccgtttttc cataggctcc gcccccctga
       61 caagcatcac gaaatctgac gctcaaatca gtggtggcga accccgacag gactataaag
      121 ataccaggcg tttccccctg atggctccct cgtgcgctct cctgttcctg cctttcggtt
      181 taccggtgtc attccgctgt tatggccgcg tttatctcat tccacgccag acactcagtt
      241 ccgggtaggc agttcgctcc aagctggact gtatgcacga accccccgtt cagtccgact
      301 gctgcacctt atccggtaac tatcatcttg agtccaaccc ggtaagacac gcacaagcgc
      361 cactggcagc agccactggt aagaaggtgt acaagagatt actgatacag agttcttgaa
      421 gtctcagccc aactacggct aaactgaaag gacagaattt ggtttcagcg gtcttgtaca
      481 ccctgttacc acggttcaga agttccccaa cttactgaac cctcgaaaaa accgcctccc
      541 caggcggttt tttcgtctcg gcgagtaaga tacgctttat cattcaaagc agtcaaggaa
      601 gaaccaagac agctcactca ccagcaggct cctttttatt ggtagacaca tgcttctgga
      661 cagtatcagc ccctgcacaa agtacagcag ctaacaagaa ccatccccag ccatcaatac
      721 cacgaaaagc taggactcca gcaatagtta cgctaatcaa cgggaacaat aaaaccataa
      781 aggatctcat actttctcca gaggttactt ttttaataaa gtccctaatc catccgtact
      841 ttcacttgga tggattagca acttacttat tgataactaa tgataatctt caagatcaac
      901 gtctaagacg tttggttcct caaccttgaa aactacccgc cagttcccat taacttcaac
      961 ggaatactcg cctttacgct ccccctttag ggggtggcac cctaacgccc taacgtcaac
     1021 aacgtcttga atgcaagttg ctgtgcttag cgtagtcaaa atcatgcgaa gtcttttcgc
     1081 catactgggc tgaataccgg cggtgctacc ttcttcagca aagctcctaa gtcctttatg
     1141 ttttatgttt tttatcatct acaatcccca tatttttttc gtctatacct gtatctatat
     1201 tttaaaatca ttttaattag ttccattttg cccccttgct ttattaaaac aattgacgta
     1261 agtttgttct tgaggtcaat cacctcattt gacttcaacg aatcctaagg gtaaaatact
     1321 gcgccttgaa aaggccataa aagcccatac atacgcagta gctttgactc caacgagtat
     1381 cctaaagctg actgcttttt ttgtcaatat catgaacttg cacattgtgc aatgcgcata
     1441 ctgaaaggca gtaatttttt tgtataatca aatacaaaac aaacagagga aggcatgata
     1501 aatctttacg atcctgttca tcctggtgag tttatcagag aaatgttcat ggaaccgttc
     1561 gaaatacctg ccgcagagtt agccgataaa cttgatgtat cccagtctac cttaagtaga
     1621 ctgttaaatg ggaaaacaga cttaagctat gaaatggcac ttagattgtc gaaggtcgta
     1681 ggccgctctg cagagtcgtg ggtaaacatg cagacccaat tcagcctgtc aaaaagtcgc
     1741 aaatctttag cggcagagct ggaacacttg catccaatgt ttccatgaaa aaagcccgca
     1801 gaacgcgggc ttttgttacg taaaacaccc agcagccatc aggaggcaac catggtagat
     1861 ttctatatct cagcaatcaa aatggacagt gctggtcagc acatcgaatt cgtaaaagtt
     1921 cataaaataa accgagatgg ctcatggaac actgccggct caatcagctc tcgcaaattc
     1981 atcagcgagc tgatcagcat gggaaaagcc agctttatga cagttgtaaa gaacagctct
     2041 actggtaagt ggaacctagg agccaaagtg gaagcgatgg acgatggcta cataaccaca
     2101 gatccaaaca aaactaaact cgataacttg ggaaatctgc cgaaatttgt ctgatatgca
     2161 ataacatcca ctaagttcca gcagaatccc ctccctaatg atttaacata aagtcataat
     2221 tgtacgcacc gccagaacgg cctcagggcg tttctgacag gaaaccggta aaacaggcaa
     2281 caaaccaccc gaaaacccgt cagaaacgcg caggctctgt ttttacggca tgcatgagta
     2341 tgcacgcaag tgcatagcgc gaaaattcac gccattcagc cagggtaagt cctgtttccg
     2401 gcgttcttcc catccgaaaa cggtgaacgg ggacgcaatt tattgcgtgg ccgtgaagcg
     2461 ttgccggcgc agccggaaaa ccggttttca gcacgttcag gaatcgtgtt cgtcgacggc
     2521 cggcaatcac gtcatggcaa gtcgccggac gactcaccac acgattcacc ggcgactctt
     2581 cactagagtc gtacccagag tcgccgagtc taaaaaacaa ccaaacgggg agtcgggtct
     2641 agagtcgggt cgttattaac tcattgtttt tatagctctg agtcgttacc gactctatga
     2701 cgactcgccg gggactctat gacgagtcgt catagagtcg gatctatgta aataaaattt
     2761 aaaaaccgaa acttcaggaa agtaagctac tgatattaaa tacaaatctg caaaatttta
     2821 attttgcgta gtgtgtgggt atttttagtc gtgaggagcg ttcagagatc tggcgatttt
     2881 tgggaaggtt caggaactcc ccgggatggc cggagaggaa aacggaagca tgacggagtc
     2941 aggatttttt ccagaatttc caccacgggg aatcgggtgg tgaagaaggt tcgtgcttgt
     3001 gctccagaag ctgcatagcc tgacgaaggg aatcaatatg ctcatctcga gccttaacag
     3061 cccctttaag accatcgttt tcagcttcta gtaaagcaat tctatgttgt aaatcatgta
     3121 aaccaacgct gttaacacct gtagatcctg cgtcactttt tacatcatat tttacagtat
     3181 cgatgacacc atcaagagaa ccaaaaactc taataagctc tgaagtatca ataactttaa
     3241 tggtcttccc gtgctttaaa acagaggtgt aacttaactt cccactgtta atcatcttgt
     3301 aaattgtggg gcgactaacc ttaacaagcc gtgccgcttc actaatagac actctggcca
     3361 tcagttacca tcctgtaatt catccagtct cgaggacagt gtacggaaaa gatgctccgc
     3421 atcatcgtgg agtttctcac aaaggtcggc ctctgcatca agatcaagct cgttaagctt
     3481 ctccagcagg agcagagact gattctggat gaatttagcc atgttcagcg ctgttttctg
     3541 ttgtttcgac ataagaggcc tcagagcgtc agtgctcagt gtaggtatgt tctcttttcc
     3601 gcttcctcgc tcactcagtc gctacgctcc tgccgttcgg ctgcggcgag cggtcgcaat
     3661 acacacataa cgacatagga caga
//
