LOCUS       NZ_CP116186             4087 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-E480 plasmid pDETEC58, complete
            sequence.
ACCESSION   NZ_CP116186
VERSION     NZ_CP116186.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988416
            Assembly: GCF_027944955.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4087)
  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  JOURNAL   Unpublished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 4087)
  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 01:54:50
            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)                     :: 5,153
            CDSs (total)                      :: 5,044
            Genes (coding)                    :: 4,810
            CDSs (with protein)               :: 4,810
            Genes (RNA)                       :: 109
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 82
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 234
            CDSs (without protein)            :: 234
            Pseudo Genes (ambiguous residues) :: 0 of 234
            Pseudo Genes (frameshifted)       :: 77 of 234
            Pseudo Genes (incomplete)         :: 176 of 234
            Pseudo Genes (internal stop)      :: 34 of 234
            Pseudo Genes (multiple problems)  :: 47 of 234
            Pseudo Genes (short protein)      :: 3 of 234
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116186.1.
            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..4087
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-E480"
                     /isolation_source="button"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC58"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-19"
     gene            complement(join(4070..4087,1..2142))
                     /gene="mobQ"
                     /locus_tag="PIB86_RS25725"
                     /old_locus_tag="PIB86_25725"
     CDS             complement(join(4070..4087,1..2142))
                     /gene="mobQ"
                     /locus_tag="PIB86_RS25725"
                     /old_locus_tag="PIB86_25725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_023142279.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTEYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLATL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            2321..2575
                     /gene="mobC"
                     /locus_tag="PIB86_RS25730"
                     /old_locus_tag="PIB86_25730"
     CDS             2321..2575
                     /gene="mobC"
                     /locus_tag="PIB86_RS25730"
                     /old_locus_tag="PIB86_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            3107..3814
                     /locus_tag="PIB86_RS25735"
                     /old_locus_tag="PIB86_25735"
     CDS             3107..3814
                     /locus_tag="PIB86_RS25735"
                     /old_locus_tag="PIB86_25735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1785..2143)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2144..2320
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          3108..3814
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2..2229)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.596"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atcatgtctc ctctcggtgg cgtgtgttcg tgcatcttcc tcgcgccgcc attcgtccca
       61 ggtacgatta aaacccagcg agcggaacag atgatccggc tgtttttctg gtgtgttgac
      121 ggcagcaaaa agcggtgcct cacgggtttt cagatgaaac tccataagtt ccggcgcagg
      181 tgatatgtgg ctgtctgcat cgtgatttac ggcaacacca taccctgcat accgtaaccc
      241 cttatcggtc agtgcactga tgaccagctg gctgttatcg gctgagggaa cggcaaacgc
      301 gggatacagc gtaccattaa gccggacaac accgcccaga gagtcatcca cgcccatgac
      361 cagcaaaagc tgaagctggc gggtttcccg gtcgacagaa ctcattaccg gcatcagcgt
      421 cgctagcaga cgtccctgcg taaaatccac cttccttgct gccagtgatg gcatggctgg
      481 ctggcggtct tctccaagac agaaagactc cggccatgtc ttcggctggc ggagattgcg
      541 ggtatattgc ggccatgtct ggcaaacctg cgtcagaagt tgctcaaagg tcgcagagga
      601 ataaacacgt tgcagtggtg gatgttgacc gatttcgctt cggtcacaga tataaccact
      661 cctgtcacgc attaaatcaa cacgctcaaa gattctggtg cggtatttct ccagctcgtt
      721 cccccagagc gtgtattctc cgttccggtt gtgaagcaga aggtaacagg tcatttcccc
      781 gttaccaggc atgggggcct cgccatactc cgtaacgact gcgctcagta cccctgaatc
      841 cataacggca ttgtcatttt tcctgagctg ttccgctcgt cgctccgcgc gactacgttc
      901 tgtatcctcc tgctccttcc ggcgcaattc ctcttcacgt ttaagcaact ggactctgag
      961 agctgcaagg ccggatgccc cccactgctg ccactgtttt tcaaatgccg tctgactcgc
     1021 gggaatgtcc tgtttctcca ccttccggta atgctgtcgc aatttttcca tttgctggct
     1081 cagcgactgg atttttccct gttcgctacg gtattccggt gccgcccatt gcatcagggg
     1141 aatacgggaa aaaccggacg aaaacggcga tgattttttc aggctggcag catggctcat
     1201 cgcttccttt cgttcggtgt tcagctcttc ccagcgtctg cgcgtcgcct gcatatctgc
     1261 catcatcgac atggcattac tggtgagttt ccatgccgca ttactgtcct tcggcaacgc
     1321 ttcgatgatg tcacgtagtg tgtacgaagt tgcgttgtca ggaagcacga tattcagaag
     1381 gtcagccaca cggcgggcag gctctgtcag cccgctgttt ctgagttcgg tacgggaaat
     1441 ctgtatttcc aggttaagtc tgttaatcag acgattctgt tcgccgcgtt ctgtttcgat
     1501 accgcgtgtt tccatcgcac aggcagactt tccgaggtga ataccaggcg ttttctcaag
     1561 cccctgtcgc tcgtatgaac gatggtctat ctcttcctga taaccggcgt tcgccagtgc
     1621 cctgttcgca tggtcagccc atgatgcacg ccacgtctcg gcatgtgtcc ggtcgttcca
     1681 gtccctgacc tttccaccga atccagcagg tccgacagct ctcgtggtca gcatgatgtg
     1741 cgcatgggga tttgttttat ccatgtgatg gaacgccaca tcagcaatca tgccctgact
     1801 gacaaagttt tctctgacaa aggcgagaac ggtttcccgt gcggcatcct gcggtagttc
     1861 gcgggggatg gcgagttcaa tttcccgcgc aagttgtgag ttcttccggc gttcggcctt
     1921 ctcaacggca ttccagagtt cggcacggtt cgtacaccag gcaggggctg tcgcgggagt
     1981 cagaatcaca gcttcagcca caccgctttt gcgggtgtag tcgtgagtca gtccggtacg
     2041 ctcatcaagc atcagtgaac cggaacgata ggcagcagaa gcaacggcgc tgtagccgct
     2101 gtttctggag atgattttca tgctgagatg ataaatcgcc atttctgccg taatgccttt
     2161 ttgtggtttt ctttcagccc cgcagggcgc acacaatcga aacggagtgg agattgtata
     2221 agtgcgcact tcgtgatttt ccgtgcatta tgccagctca gtttttaaac taccagtgac
     2281 gcgctaaaat gcgatttttc atcgcgcacg gagttacatc atgagcagaa cactcgaaca
     2341 gaagattgct gatgctgagg ccagattaca gcgcctgaag gcgaagagca ggagtctgga
     2401 cacagcgcag aaggtcattg tgggtgcagc attgctggca aaggtcagaa agccggagga
     2461 ggtgcagttg cgtgcctggt tactccagtt cctgaaggca gaggtgacac gacaggctga
     2521 tgtgacgcgc atactgccgc tgattaacga gctggaagcg ctgccaggac agtgattgta
     2581 tcgtccgctc gccgcagtcc cagcgaccga gcgttagcga gcgagtgggc gaggaagcgg
     2641 aagtgaatcc gtcgcctgat tgagcacata cgcacggttt ttcgggaggt gatatgcgct
     2701 gaacccgcat gaatactgga tttccacagg gttggagggg gtgtattcgg aacttgcaat
     2761 tctgcttttt tgcaacgcat tgtttttatt ggttttttgt tttcagcact ccaagttatc
     2821 cacaggctcg tcgttaagtt tttagatctt gtttttaaga tcttgttttt aatacttgtt
     2881 ttagcgccaa aattccttat agaaaacaaa atgttacaac gctataggtg atatgattta
     2941 aggtaaaggt gatataattt aaggtgcttg ggtgaggtaa tttaaggtaa aggtgaggag
     3001 atttaaggta atattcacag gaaaatgggg ggtgaaaata taattgctca ccaatgctaa
     3061 aggtgatagg tttttatttc acctcatttt tggcctggtg gttaaaatga catcaaaccc
     3121 tctgatagcc tataagtcca atgcgctggt tgaggccagt tacaagctaa ctttacaaga
     3181 acagcgtttc ttattgctct gcataagccg acttaactcc ggtactgacg tagcttcacc
     3241 tgaattgcaa aagacaatga ccattacagc tgcggaatat tttgattcat tccctgatat
     3301 ggggcggaaa aatgccgagg ttcagctaca ggaagcgatc gatcgtttgt gggacaggtc
     3361 gatcattctc aaggacgacg agaagcgcga ggagttccgc tggattcagt atcgggcaca
     3421 gtacgcgagg ggagagggga aagcacaaat cactttttct gacgcggtaa tgccttatct
     3481 gacacagttg aaggggcaat tcaccagagt cgtcattaaa aatatttcta atttatcaag
     3541 aagttacagc ataagaatat acgaaattct ccagcaattc cgcagtactg gggaacgtat
     3601 tatcgccctc gatgatttta aatcatcact gatgcttgat ggtaaatata aagatttcaa
     3661 aacgttaaac agggatctaa taaaaccctg tgttgacgaa ctgaacaaaa aaagcgacct
     3721 ggctgtaacg gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt
     3781 caaggaagac aaacagatca agatgacgat ctagaatcga ttttaaggca cctaaaacgc
     3841 tccctgctgc gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg
     3901 tcaaaagcgc tctaatgcag cgaaaaaaga acccccattt ttcgggggcg gaaaaacaaa
     3961 actatgcttg cattatgtgt gtgcttcttg cattcatccc tgtcgatgaa catcgaagaa
     4021 catcgacgaa cataacacga tgttaaacaa aacaaaatat tgttcacatt cactgtgacc
     4081 aaccgcg
//
