LOCUS       NZ_CP116162             6074 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P351 plasmid pDETEC7, complete
            sequence.
ACCESSION   NZ_CP116162
VERSION     NZ_CP116162.1
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 6074)
  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  JOURNAL   Unpublished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 6074)
  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
            CP116162.1.
            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..6074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P351"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC7"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-08-13"
     gene            99..1013
                     /locus_tag="PIC26_RS24340"
                     /old_locus_tag="PIC26_24335"
     CDS             99..1013
                     /locus_tag="PIC26_RS24340"
                     /old_locus_tag="PIC26_24335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /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_032333168.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDSSVKA
                     LKYAAAIERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPEFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGRSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="replication initiation protein"
     gene            complement(1217..1615)
                     /locus_tag="PIC26_RS24345"
                     /old_locus_tag="PIC26_24340"
     CDS             complement(1217..1615)
                     /locus_tag="PIC26_RS24345"
                     /old_locus_tag="PIC26_24340"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042969092.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQTQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQELKELKYDLDTSPTPDA"
                     /name="hypothetical protein"
     gene            1791..2717
                     /locus_tag="PIC26_RS24350"
                     /old_locus_tag="PIC26_24345"
     CDS             1791..2717
                     /locus_tag="PIC26_RS24350"
                     /old_locus_tag="PIC26_24345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_042969091.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKGEYAKRKDLEYTEHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FSIHNPKASIDGGEQPHAHIMMSQRVNDGIDRTPEQYFRRYNARYPDRGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDGVSRQERTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2720..3253
                     /locus_tag="PIC26_RS24355"
                     /old_locus_tag="PIC26_24350"
     CDS             2720..3253
                     /locus_tag="PIC26_RS24355"
                     /old_locus_tag="PIC26_24350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168772.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            3474..5204
                     /locus_tag="PIC26_RS24360"
                     /old_locus_tag="PIC26_24355"
     CDS             3474..5204
                     /locus_tag="PIC26_RS24360"
                     /old_locus_tag="PIC26_24355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012961.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WP_044108843.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGHGNGGGNSNSGGGSNSSVAAPMAFGFPALAAPGAGTLGISVSG
                     EALSAAIADIFAALKGPFKFSAWGIALYGILPAEIAKDDPNMMSKIVTSLPAETVTDAQ
                     VSSLPLDQATVSVTKRVTDVVKDERQHIAVVSGIPMSVPVVDAKPTNTPGVFSTSFPGV
                     PSLTVSTVNDAPVSTSLPVGVTEDKDRTAFPAGFTFGGGSHEAIIRFPADSGQKPVYVS
                     VTDVLTPEQIKQRQDEENRRQQEWDDTHPVEVAERNYEQARAELNQANEDVARNQERQA
                     QAEQVYNSRKSELDAANKTFADAIAEIKQFERFAHDPMAGGHRMWQMAGLKAQRAQTDV
                     NNKQAAFDAAAKDKSDADAALGAALERRNQKENKEKDAKDKLDKESKRNKPGKATGKGK
                     PVGDKWLDDAGKDSGVPIPDRIADKLRDKEFKSFDDFRKKFWEEVSKDPELSKNLSPSN
                     KSGVSKGYSPFTPKGQQVGGRKVYELHHDNPISQGGEVYDMDNIRVTTPKRHIDIHRGQ
                     "
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            5207..5467
                     /locus_tag="PIC26_RS24365"
                     /old_locus_tag="PIC26_24360"
     CDS             5207..5467
                     /locus_tag="PIC26_RS24365"
                     /old_locus_tag="PIC26_24360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000412701.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin immunity protein"
                     /protein_id="WP_042969089.1"
                     /translation="MEIKNSISDYTEAEFLQLVTVIYNADTASEEEQVKLVSEFERLTE
                     HPDGSDLIYYPRDDREDSPEGIVKEIKEWRSANGKSGFKQG"
                     /name="bacteriocin immunity protein"
     gene            5529..5672
                     /locus_tag="PIC26_RS24370"
                     /old_locus_tag="PIC26_24365"
     CDS             5529..5672
                     /locus_tag="PIC26_RS24370"
                     /old_locus_tag="PIC26_24365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_021553018.1"
                     /translation="MKKITGIILLLLAVIILAACQANYIRDVQGGTVSPSSTAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     BGC             1..6074
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          100..874
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.396"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          1792..2714
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaaacaaac gcccctgaaa tcatgtccag atccggcaag attcaacatg aaatacagag
       61 ggcgtgtagg tcgcataacc cggagagaat cgtaacacat gagcgccgcg cttcaatact
      121 tcgacgaaaa tttaccccac cgtccctatc acacggatga tctcgctttt ggtcttcgca
      181 tctccggcaa agggcgtgcg cttcttgcgc ggtacataca gcagaaccag cctcatgcgc
      241 agttctggct ggtttttgac gttgaccgcg agggggcagc gattgactgg agcgaccgga
      301 acgctcccgc gccgaacatc accgtaaaaa atcctgtgaa cggtcatgct cacctgctct
      361 acgcgctcaa tatcgccgtg agaaccgcgc cggacagctc ggttaaggcg ctgaaatacg
      421 ccgctgcgat tgaacgttcg ctgtgtgaga aactttgtgc tgatgtgaac tacagcggac
      481 tgatttgtaa aaatccgttc cacctggaat ggcaggtgat ggagtggcga gaggaagcct
      541 ataccctcga tgaactggct gattatctcg atttgagcgc ctcagcgcgc cgtagcatcg
      601 ataaacatta cgggatgggg cgaaactgcc acctgttcga aatgacgcgc aaatgggctt
      661 acagggcgat tcgtcagggc tggcctgaat tctcacagtg gcttgatgcc gtgattcagc
      721 gtgtcgaaat gtacaacgca tcgcttcccg ttccgctttc accgcctgaa tgtcgggcta
      781 ttggcaggag cattgcgaaa tacacgcaca ggaacttcac gccggaaact ttcgcacagt
      841 atgtggctga tacgcacaca ccagaaattc aggctgcacg cggtcgcaag ggcggttcta
      901 agtctaagcg cagcacagtg gctacatctg cacgcacgct gaaaccgtgg gaggcattag
      961 ggatcagtcg cgcctggtat taccaactga aaaaacgagg tctcgtagag tagaccaaat
     1021 aagcctatat cagataacag cgcctttttg gcgtcttttt gagcagcagg ttttttgccg
     1081 ttttcccccg ctcagccctg caatggtgct gttttccgca tgattgcgct ggtagtgctc
     1141 gccgcagtct catgaccgag cgtagcgagc gaatgagcga ggaagcacca gggaatcgga
     1201 acacggatgg aggcacttac gcgtctgggg ttggggatgt atccagatcg tacttaagtt
     1261 ccttaagttc ctgtaatatc ctgtcttttt tatagcatag ctcgcctgtt tttgtgtcta
     1321 ccagtcctgc ttctatcagt agcccagccg cgagaaagag ccggtgattg cgttctcgtc
     1381 gttgtttttt tccctcgatt cgtttttgga ccgcctgttt tcgttcgctc tcctgtgtct
     1441 gtaagtcgtt tttttccgct gttgccagta cgtggaggag tttgcgttcc tgttctgtga
     1501 gtcctgcttc gttgtcgagc aggtcaataa tctgtctctg tcgtgcggtc tgttctccga
     1561 gcttcctgat gaatccgatc cgtttcttca gccattcgat gttgctgatg cgcatgttcg
     1621 ttgtgctccc tggtgttttt tgcggtgtgt tgtggtcgtg cagtatatcg cttgcggtcg
     1681 gtgggtgcag ggggtatctt ccgtgctaat tcgtaaaatt agaaggaagc gcacttatat
     1741 gtttctctcc ttcgtcaaga aacagtgcgc tcctgcggag ggctgaaacc gtggcaacct
     1801 atcacctcag cgtcaaattt ggaggcaagg gacaggctgc aaaccacgcc gattacatcg
     1861 agcgcaaagg ggagtatgcg aaacggaaag acctggagta cacggagcac gggaacatgc
     1921 cggaatgggc gcgagataat ccctcccatt tctggcaggc ggctgaccag tttgaacgtg
     1981 cgaacggttc gacttatcgg gaattggaaa tcgcgctgcc ccgtgaactg acaccggaac
     2041 agcgccttga actggtgcag gattttgtac gtcaggaagc cggcgaacgg cacgcctgga
     2101 gtttttccat tcacaatccg aaagcgagta ttgacggtgg cgaacagcct catgcgcata
     2161 tcatgatgag ccagcgtgtg aatgatggta ttgaccgtac accggaacag tatttccggc
     2221 gctataacgc caggtatccc gaccggggtg gtgcgaaaaa ggattccgga agcttgactc
     2281 tcactcagca aaaagagcag ttgcgggaat tgcgaaaacg ctgggaggtg aagcacaacg
     2341 aacatatgag aaagcatggc tttgaaaggg gcttcattga ctgccggacg ctgaaagaac
     2401 agggcattga acgacgtccc gaagtacatc tgggttttga agctgccgga cggcttgatg
     2461 atgcccagcg tcatgacatc atgcaaaaac ggtctgaacc ggactattcc cgccatcttg
     2521 aacaggcgcg aacggtcggg catgacatca gggaatggct ggacactccg gttaagcaac
     2581 atgaactggt cagaaggctg caacatgatg ttgcgcggga gcatggcttt gacatgagag
     2641 acggagtgag cagacaggag cgaactgaac ctgaacgggt taaatcaccg tcacgtggat
     2701 tttctatggg attctgaaca tggccagcac agaagaaaaa ttactcacgc tcctgttatc
     2761 ggtggagcat ctgcaacata ccgcaatgga gcaacagaaa gctgttgctg attctctggc
     2821 tgtggcaagg gaaacacttc gcggatatcg ggatatttct gacggtgtgg caaaacaggt
     2881 cagggatgaa gtcagaaacg aggtgcagaa gctggacgta gcagggctga taggtgagcg
     2941 catcagccag gattttcagc ggctggaaga gtcagttgca aacatgaagg caaacgcgga
     3001 cgccctgaac agggatattg cgacaattca cagcaatatc gtgcaggaat acaacaccct
     3061 taaagggtat agctggaaat ggctgggagg ggtgtcagtg gcttttctgg ttatgttctg
     3121 tgtgctcgga tggggaatga aaacaatgct cgacaggaac tacaacgcca cagcggcggt
     3181 gtatcagaaa gttgtgacac tggaagataa actggcggag aaacctgtca cgggtaagag
     3241 ccggaaaaac tgacgcgctt tgcttgtcca acgcctcacg acccgcgaaa ggatttcgcg
     3301 ttccgttcac cgttttcatg agtgactcct ccgaactgcc aaaaaatatc cctccctgac
     3361 ttgacagaaa aaataatggc gagtactttt tgatctgtac ataaaaccag tggttttatg
     3421 tacagtatta actatgtaat taattgtttt aacgcttaaa agagggaatt tttatgagcg
     3481 gtggagatgg acgcgaccac aacagtggcg cacataacac aggtggtaac attaatggcg
     3541 gccctacggg gcttggtgga aatggtgggg cttctgacgg ctccggatgg agttcggaaa
     3601 ataacccatg gggtggcggt tccggtagtg gtgttcactg gggtggtggc tccggccatg
     3661 gcaatggtgg ggggaatagt aattccggtg gtggcagcaa ttcatccgta gcagcaccta
     3721 tggcatttgg ttttcctgct ttggctgctc ctggtgccgg aactcttggt atttccgtat
     3781 ctggtgaggc tttatctgcg gcaatagcgg atatctttgc agccctgaaa ggcccgttta
     3841 aattcagtgc ctggggtatt gcgctttacg gcattcttcc tgctgaaata gcaaaagatg
     3901 acccgaacat gatgtcaaaa atcgtgacgt cattaccggc agaaacggtg acagatgcac
     3961 aggtcagttc tctgccactg gatcaggcaa ctgtcagcgt gacgaaacgt gtgacagatg
     4021 ttgtgaagga cgaacgacag catattgccg ttgtttcagg tataccaatg agtgtacctg
     4081 ttgtggatgc aaaaccgaca aacactccgg gtgtatttag cacatcattt ccaggtgttc
     4141 cttccctgac tgtcagtact gtcaacgatg cgcctgtatc aacctcgctt cccgtcggag
     4201 ttacggagga taaagaccgg acagcttttc cggcaggctt taccttcggt ggtggctctc
     4261 atgaggcgat aatccgcttc ccggcagaca gtggtcagaa accggtgtat gtgtcggtaa
     4321 cggacgttct gacacctgag cagataaaac agcgtcagga tgaagaaaat cgtcgtcagc
     4381 aggaatggga tgatacgcat ccggttgaag tagctgaacg aaattatgaa caggctcgcg
     4441 ccgaactgaa tcaggcaaat gaagatgttg ccagaaatca ggaacgacag gctcaggctg
     4501 agcaggtcta taattctcgt aaaagtgaac ttgatgcggc aaataaaacc tttgctgatg
     4561 caatagctga aataaaacaa tttgagcgat ttgcccatga tccaatggct ggcggccaca
     4621 gaatgtggca aatggctggg cttaaagctc agcgggcaca gacggatgta aataataagc
     4681 aagctgcatt tgatgctgct gcaaaagaca agtctgatgc tgatgctgcg ttaggtgctg
     4741 cgctggaacg ccgtaatcag aaggaaaata aagaaaagga cgctaaggat aaattagata
     4801 aggagagtaa acggaataag ccagggaagg cgacaggtaa aggtaaacca gttggtgata
     4861 aatggctgga tgatgcgggt aaagattcag gtgtaccgat tccagatcgt attgctgata
     4921 agttacgcga taaagagttc aaaagctttg atgattttcg gaagaaattc tgggaagaag
     4981 tctcaaaaga tcctgaactt agtaaaaatc taagtccgag taataaatct ggtgtttcaa
     5041 agggttactc tccatttact ccaaaggggc agcaggttgg agggagaaag gtatatgaac
     5101 ttcatcacga caatcctatt agtcagggag gtgaggtcta tgatatggat aatatcagag
     5161 tgacaacgcc taaacgtcat attgatattc acaggggaca gtaaagatgg aaataaaaaa
     5221 tagtatcagt gattatacag aggccgagtt tttacagttg gttactgtaa tttataatgc
     5281 agataccgct agtgaagaag aacaagtgaa attggtgagt gagtttgaac gattaactga
     5341 gcacccagat ggttcagacc tgatttatta tcctcgagat gacagggaag atagtcctga
     5401 agggattgtt aaagagatta aagaatggcg atccgctaac ggtaagtcag gatttaaaca
     5461 gggctgaaat atgaatgccg gttgtttaag gatgaatgac tggcattctt tcacaacaag
     5521 gagtcgttat gaaaaaaata acagggatta ttttattgct tcttgcagtc attattcttg
     5581 ctgcatgtca ggcaaattat atccgggatg ttcagggcgg gactgtatca ccgtcatcaa
     5641 ctgctgaact gaccggagtg gaaacgcagt aaccagcaat cctcatttga caagaacaaa
     5701 gcgtgtcagg ctgatcctga cgcgcttttt tttgaagtat cacaaaaatt ctgagctgga
     5761 gaagggcgct aaaatcatca ccgggttgaa ctccatattc cagacgagaa aacttgtcat
     5821 tttgacttgt tcgcccttcg gaacagccga aatcgatcgc gcatcgcttt cgtgcatagt
     5881 tatgcaacgc gctaaaaacg attctgacgc atttttctgg tttagcctgg tgtttccttg
     5941 tctttttgcg ttttttgcgc cagagagcga ctgagggcgt tttaaggggg gcgtacaacg
     6001 ggagttatgg taaatggatc ggggtttcgg gaaggttcga caggatttgc cgttgggtgt
     6061 agtgtaagcg actg
//
