LOCUS       NZ_CP116083             4715 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-S586 plasmid pDETEC53, complete
            sequence.
ACCESSION   NZ_CP116083
VERSION     NZ_CP116083.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988516
            Assembly: GCF_027944615.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4715)
  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  JOURNAL   Unpublished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 4715)
  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 01:50:10
            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)                     :: 5,261
            CDSs (total)                      :: 5,142
            Genes (coding)                    :: 4,937
            CDSs (with protein)               :: 4,937
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 205
            CDSs (without protein)            :: 205
            Pseudo Genes (ambiguous residues) :: 0 of 205
            Pseudo Genes (frameshifted)       :: 65 of 205
            Pseudo Genes (incomplete)         :: 145 of 205
            Pseudo Genes (internal stop)      :: 38 of 205
            Pseudo Genes (multiple problems)  :: 43 of 205
            Pseudo Genes (short protein)      :: 5 of 205
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116083.1.
            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..4715
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-S586"
                     /isolation_source="ICU staff rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC53"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-01"
     gene            join(3867..4715,1..18)
                     /locus_tag="PIC49_RS26200"
                     /old_locus_tag="PIC49_26205"
     CDS             join(3867..4715,1..18)
                     /locus_tag="PIC49_RS26200"
                     /old_locus_tag="PIC49_26205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000409995.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nucleotidyl transferase AbiEii/AbiGii toxin
                     family protein"
                     /protein_id="WP_000409995.1"
                     /translation="MEKEINNWIEESGGKYRLMRQAVHIILKSISIEESLNEMMVMKGG
                     TLLGVKHGSDRYTKDIDFSTEKKLSEIDLGDFFNRFNDSMDVAEAELGYGIKCKVQSHK
                     IQPNAQGTFPTVQINIAFCDRSNASAMKRLESNQSPSVINIDFSFNEKTYDFDFLSLDG
                     DDDNDSVKTYSLTDLMAEKYRSVLQQKVRERNREQDIYDINYLLGKYEFSRQDKYKILE
                     SLLKKSEGKQLDNLLNVKGIRDVEIIERSSQRYQDLSSTVKSLPLFEDAYEKVACFYES
                     LPWDIFK"
                     /name="nucleotidyl transferase AbiEii/AbiGii toxin family
                     protein"
     gene            15..668
                     /locus_tag="PIC49_RS26205"
                     /old_locus_tag="PIC49_26210"
     CDS             15..668
                     /locus_tag="PIC49_RS26205"
                     /old_locus_tag="PIC49_26210"
                     /EC_number="3.1.3.16"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016249761.1"
                     /GO_function="GO:0004722 - protein serine/threonine
                     phosphatase activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="PP2C family serine/threonine-protein phosphatase"
                     /protein_id="WP_000560060.1"
                     /translation="MIAFSFSDIGNRCENLDLLSTINCQNDVFGMVIMDGYSCSEWNMK
                     ILSGRLDKCVFSGDLNKDIIEPCKSVPVKAAVCFLFKNNTHLHIYNAGDCRVYNKSGVL
                     LTEDNSVAWKRLKENGIDNKKIPHLVCYCPDRNYLTSFVDFCSDEIIFNHSVFDLNDEN
                     KEVILCTDGFWEHFNDGTVIDLMKDNPESNLAKFTKNIPGNAENHTVCYVRFPS"
                     /name="PP2C family serine/threonine-protein phosphatase"
     gene            complement(890..1003)
                     /locus_tag="PIC49_RS26335"
     CDS             complement(890..1003)
                     /locus_tag="PIC49_RS26335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427893.1"
                     /translation="MHEPPVQPDCCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="hypothetical protein"
     gene            complement(1657..1851)
                     /locus_tag="PIC49_RS26210"
                     /old_locus_tag="PIC49_26215"
     CDS             complement(1657..1851)
                     /locus_tag="PIC49_RS26210"
                     /old_locus_tag="PIC49_26215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_072665423.1"
                     /translation="MNKQQQNALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2927..3883
                     /locus_tag="PIC49_RS26215"
                     /old_locus_tag="PIC49_26220"
     CDS             2927..3883
                     /locus_tag="PIC49_RS26215"
                     /old_locus_tag="PIC49_26220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000280763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000280763.1"
                     /translation="MYLIEEALTSWLLNEYKKPVITKEEISLQIYLFYLKKEYNGERIY
                     QIRKNKAGPNEFEKNILKLLKSGVLSRVESNDKHHAYPHLIGGFYEVFFVKGNDGSPEN
                     DIVCSTYPYGYLSYLSAMDWHNITDKIPKIIHFTTCRSEQWKNKFYHDFQKDNPDIDEA
                     KQFMPRFPRNSEVNGIKIIVTQETNYVEPMKARNSPVRVSSIGKTFMDMTRRPDYCGGE
                     EHVLESFIEHGKKYAPLIIKEVDKLGRHIDKVRVGFILDRIIGVNNKKISEWKQEAGKY
                     RGSSKVLSPKSPFSPYFDEEWFISINVDMVKSYGKRN"
                     /name="hypothetical protein"
     Typing          1500..1584
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          1888..1986
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          2111..2366
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(932..1489)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.821"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgggatatat tcaaatgata gcgttcagtt ttagtgatat tggtaacaga tgtgaaaact
       61 tagacttatt atctacgata aattgtcaaa atgatgtgtt tggaatggtt attatggatg
      121 ggtattcctg ctctgagtgg aatatgaaaa ttctctctgg taggttagat aagtgcgtgt
      181 tttctggtga tctgaataaa gatattattg aaccatgcaa gtcagttcct gttaaggctg
      241 cagtatgttt cctttttaaa aataatacgc acctccatat atataacgca ggagattgcc
      301 gtgtatataa caaaagtgga gtccttctaa cagaggataa ctcggttgcc tggaaaagat
      361 taaaggaaaa tggaatcgat aataaaaaaa tacctcacct cgtttgttat tgcccagaca
      421 gaaattatct aacatcattt gttgatttct gctctgatga gataattttc aatcattcag
      481 tttttgattt aaatgatgaa aacaaagagg ttattttatg tactgatggg ttttgggagc
      541 attttaatga tggtactgtt attgacctca tgaaagataa cccagaatct aacttggcta
      601 aatttactaa aaatatcccg ggtaacgcag agaatcatac ggtttgctac gttagattcc
      661 cttcttgatt tcgtgttttt tgaagaagct attgagatct tcgtgtcata tagataatct
      721 cttttctgta aaagaaaaaa accgcctttg cggggcggtt ttctcttagg ttcaaagagt
      781 ttgcggctcg aagaaccaag gtaactggct tggaggagcg cagtcaccaa aacctgttct
      841 ttcagtttag ccttaactgg cgcatgactt caagactaac tcctctaaat cagttaccag
      901 tggctgctgc cagtggcgtt aaggcgtgtc ttaccgggtt ggactcaaga cgatagttac
      961 cggataaggc gcagcagtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc
     1021 gaacgaccta caccgaactg agataccaac agcgtgagct atgagaaagc gccacgcttc
     1081 ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca ggagagcgca
     1141 cgagggagcc accaggggga aacgtctggt atctttaagt cctgtcgggt ttcgccacct
     1201 ctgacttgag cgtcgatttc tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc
     1261 ctgcggcgcg gccttcttcc tgttcttggt cttttgctca catgttcttt ccggccttat
     1321 cccctgattc tgtggataac cgtgctgccg tttttgtgta agtcagtacc gctcgccgca
     1381 gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaaaagcgc ctggacgcgc
     1441 attttctcct tacgcatctg tgcggaattt cacacccggc atggggcact tttcatacaa
     1501 ttcgcactga tgccgcatag ttaagccagt atacactccg ctatcgctac gtgactgggt
     1561 cagggcttcg ccccgacacc cgctgacgcg ccctggcggg cttgtctgct gccgaaaacg
     1621 ctcgcggaca agccgtgagc gcctccgtca gcttcgttat gttcctgttt cactttcggt
     1681 ctcaaagcga acctggatgc tgttctggag ttcttccgcg agttcgtgca gtcgttcgca
     1741 catggccgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg tcaggctctg
     1801 gcttttgata aatcgcgcca tattcagcgc attttgttgc tgtttgttca ccttccgttg
     1861 ttctccgtca gtaccgggtg tcgggtggac cctgaccagg tggtaattgt aagacgttgc
     1921 gggcgacggt attacaattg cacatcctgt cctgtttttt taggacgtat catggcacag
     1981 catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa atttcgctct
     2041 gcgtcgagtg tttcttaatc aataattccg ctgatactcc ggaaaaacgc gagtctgttc
     2101 tcatgcctga aatgcccaca ccccacgcaa aaacaatttt ttgctgattt ttctttataa
     2161 atagagagtt atgacaaatt agttcttctt gctctctttg tgatatttaa aaaagcggtg
     2221 tcggcgcggt gttgtagctg cgccaacacc gctttttagg ggtggtactg actattttca
     2281 taaaaaacat cattttatat taggggtgct gctagcggcg cggtgtgttt ttttacagga
     2341 cgcccctggg ggcgctgcta ggggtgtctg ttcagatatg tagcaatgag tcagggattc
     2401 acgaactgaa aatgtccgaa aatgtgtctc atgggcactg tatgcgccca aaccgatcgt
     2461 cattcacttt catgcatagc tatgcagtga gctgaaagcg atcctgacgc atttttccgg
     2521 tttaccccgg ggagaacatc tctttttgcg gtgttcgcgg cagaatcgcg ttcagcgcgt
     2581 tttagcggtg cgcgtaatgc gacgttatgg taaatgacgc tgaaaaatga tcttttacgc
     2641 tcatcgttta tgagcaacag atgtcctaat catggatttg aactataacc gccgctgaat
     2701 tgatcgcatg aggtgttatg aaaacggtga tataagtaaa ctttttcttg acttcctact
     2761 tattatccta taaaataaat cctaaggatt tattttatag gatatcaaaa atataaaaat
     2821 ggcaaatgct tgtttgttat tatttttttc ttgacaatca atctctaata gaatatacgt
     2881 cctaaggacg tatattctat tagagactaa accgaaaagg ttgaatatgt atcttatcga
     2941 agaagcgcta acgtcttggt tgttgaatga atataaaaaa ccagtcataa ccaaagaaga
     3001 aatctctttg cagatttacc ttttttattt aaaaaaagaa tataatggtg agaggatata
     3061 tcaaattaga aagaacaaag caggacctaa tgaatttgaa aaaaatatat taaaattatt
     3121 aaagtcaggg gttttatcaa gagttgaaag taacgataag catcatgctt acccccattt
     3181 aattggcggt ttctatgagg tcttttttgt taaaggtaac gatggttctc cggaaaatga
     3241 tatagtgtgc tctacgtatc catatggata cttatcctat ttatccgcta tggattggca
     3301 taacatcaca gataaaatac ccaagataat ccactttacg acatgtcgtt ccgaacagtg
     3361 gaagaataag ttctatcatg attttcaaaa ggataatcct gatatagacg aagccaaaca
     3421 attcatgcct agatttccaa gaaattctga ggtcaatgga ataaaaatta tcgttacaca
     3481 agaaacaaat tatgttgagc caatgaaggc tcgtaattcc cctgtcaggg tatcatctat
     3541 cggtaagacc tttatggata tgaccaggcg gcctgattac tgtggtggtg aggagcatgt
     3601 attggaatca tttattgagc acggtaaaaa atatgcacct ctgattataa aggaagtcga
     3661 taagcttggc cgtcatattg acaaggtaag ggttggattc attttggata gaattattgg
     3721 ggttaataat aaaaaaataa gcgaatggaa acaagaggcg ggtaaataca gaggtagttc
     3781 gaaagtgcta tctccaaaga gtccattctc accttacttt gatgaagaat ggtttatttc
     3841 tattaatgtt gatatggtta agtcttatgg aaaaagaaat taataattgg atcgaagagt
     3901 ctggtgggaa gtacaggttg atgcgccagg ctgtacatat aatacttaaa tctatttcta
     3961 tagaggagag tttgaatgaa atgatggtta tgaagggagg gactcttctt ggtgttaagc
     4021 atggtagtga tagatacaca aaggatattg atttttctac cgaaaaaaaa ctttctgaaa
     4081 ttgacttggg ggattttttc aataggttta atgactcaat ggatgttgct gaggctgaat
     4141 tgggatatgg tattaaatgt aaagttcaat ctcataaaat tcaacctaat gcacaaggaa
     4201 catttccaac tgtacagata aatatagcct tttgcgatcg ttctaatgcg tctgcaatga
     4261 aaaggcttga atctaatcaa tcaccttcag tgataaatat cgattttagc tttaacgaaa
     4321 aaacgtatga ttttgacttt ttatcattag atggtgatga tgacaatgat agcgtaaaga
     4381 cctacagctt aactgatttg atggctgaaa aatatcgatc cgttttgcaa caaaaagtta
     4441 gagagagaaa tcgagagcaa gatatatatg atatcaatta tcttttaggt aaatatgagt
     4501 tttctcggca agataagtat aaaatactgg agtctctttt aaaaaagagt gaaggtaaac
     4561 aattggataa tctcttaaac gttaaaggta taagggatgt agaaattatc gagcgttcca
     4621 gtcagcgata tcaggattta tcatccaccg ttaaatcatt acctcttttt gaagatgctt
     4681 atgaaaaagt tgcctgtttc tatgaaagtc ttccg
//
