LOCUS       NZ_CP116120             5631 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P793 plasmid pDETEC17, complete
            sequence.
ACCESSION   NZ_CP116120
VERSION     NZ_CP116120.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988477
            Assembly: GCF_027944775.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  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  JOURNAL   Unpublished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 5631)
  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 01:55:41
            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)                     :: 5,351
            CDSs (total)                      :: 5,234
            Genes (coding)                    :: 4,997
            CDSs (with protein)               :: 4,997
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 237
            CDSs (without protein)            :: 237
            Pseudo Genes (ambiguous residues) :: 0 of 237
            Pseudo Genes (frameshifted)       :: 84 of 237
            Pseudo Genes (incomplete)         :: 166 of 237
            Pseudo Genes (internal stop)      :: 38 of 237
            Pseudo Genes (multiple problems)  :: 48 of 237
            Pseudo Genes (short protein)      :: 4 of 237
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116120.1.
            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..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P793"
                     /isolation_source="ICU patient rectal swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC17"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-12"
     gene            complement(1057..1923)
                     /locus_tag="PIC92_RS26630"
                     /old_locus_tag="PIC92_26635"
     CDS             complement(1057..1923)
                     /locus_tag="PIC92_RS26630"
                     /old_locus_tag="PIC92_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(1925..2977)
                     /locus_tag="PIC92_RS26635"
                     /old_locus_tag="PIC92_26640"
     CDS             complement(1925..2977)
                     /locus_tag="PIC92_RS26635"
                     /old_locus_tag="PIC92_26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(3458..3691)
                     /locus_tag="PIC92_RS26640"
                     /old_locus_tag="PIC92_26645"
     CDS             complement(3458..3691)
                     /locus_tag="PIC92_RS26640"
                     /old_locus_tag="PIC92_26645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3698..4228)
                     /locus_tag="PIC92_RS26645"
                     /old_locus_tag="PIC92_26650"
     CDS             complement(3698..4228)
                     /locus_tag="PIC92_RS26645"
                     /old_locus_tag="PIC92_26650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4266..4964)
                     /locus_tag="PIC92_RS26795"
                     /pseudo=""
     CDS             complement(<4266..4964)
                     /locus_tag="PIC92_RS26795"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(4906..5229)
                     /locus_tag="PIC92_RS26655"
                     /old_locus_tag="PIC92_26660"
     CDS             complement(4906..5229)
                     /locus_tag="PIC92_RS26655"
                     /old_locus_tag="PIC92_26660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024192446.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     AQPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            5294..5485
                     /locus_tag="PIC92_RS26660"
                     /old_locus_tag="PIC92_26665"
     CDS             5294..5485
                     /locus_tag="PIC92_RS26660"
                     /old_locus_tag="PIC92_26665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(487..674)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(3355..4916)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggcttaacc attcggcatc agtgcggatt gtatgaaaag tgcgccatgt ccggtgtgaa
       61 atgccgcaca gatgcgtaag gagaaaatgc cagttcaggc gctcttccgc ttcctcgctc
      121 actgactcgc tacgctcggt cgttcggctg cggcgagcgg actctccttt ctcaaaaacg
      181 ctaaccctgt tatccacaga acccggggat aaaccaggaa agaacatgtg cgcaaaaaac
      241 gaaaccccgg gaaaggccgc gccggaggcg ctttttccat aggctccgcc cccctgacgg
      301 acttcacaaa acagacactt tttcggtgca tctgtgggag ccttgcggct caaccatgaa
      361 atccgccagc ggtggcgaaa cccgacgtgg cttaaagatc atcaccgttt ccggtgaatc
      421 gctccctcct gcgcccccac gttcccgcca tatcgattac cggatacctt ttccgccttt
      481 ctcccttacg ggacacgtgg cgctttctca tagctcacgt cttctggtat ctcggggcga
      541 cttaggcagt tcgctccggg ctgggctgta tgcaggaacc ccccgttcag cccgactgct
      601 gcgccttctc cggtaactgt tctcttgggt ccaacccgga aaagacacca caaagcgcca
      661 ctggcagcag ccattggtaa aagtcatgtg cgagatattt agagagtact tgaagtggct
      721 gccggagtgc ggctacacta gaagaacaat tttggtgact cgtctcgcat aagacagtta
      781 cctggttaag cagtctgcaa gctgacttaa ccttcgatca aaccgccctg caaggcggtt
      841 ttttcgttta caggcagcag attacgcgca gaaaaaaagg atctcaagag gatcctttga
      901 tctttttgtt acaaacgtct ctatttgact cccctgagag cgttttagcg cgcctctgac
      961 ccccttggtt acattccgac accagaaacg ctcccgtttt ttacgtgcat ttggcacggt
     1021 atcgatggag gccggggggc aatcctgaac agaatgttac tcctctgagt attttctgtt
     1081 aagaaaatat acacttagca cagttacaat aaatcctacc ccctgtaaga atgtgaattg
     1141 ttcatccaaa aacaaccatg acaaaaataa tgcaactagc ggaataaagt acaacattat
     1201 ccctgccaaa tgaactggga gccaacgcaa ggagttcaag taaaaacaaa aagctaaaaa
     1261 atattgtaat attccagatg aaaaaacaat aatcacggat tccaacggaa gataaattga
     1321 tgatttagat ataaaaataa agagcgatga cagtataagg gagaatgtca actgtccgct
     1381 caataatgtg ataggctcaa acgatttaat aaggcgagac gatataacaa cataaaatgc
     1441 tgccgataac acaccggcaa caacaagaca atatccaaca atattattcg atccattact
     1501 gatgtctggc aaggctacca aaatactgcc aacaattgca cctataagga acaatataaa
     1561 atattgcggg gaattaattt taactgagca aataagaaca gacaacacca atataaacac
     1621 tgattcaagt gaaaaaataa ttgatgcgct tcctgctgaa ataaaataaa gtccgtagag
     1681 tgtaaaagta tacgctaaga atggttcaaa aacgcctgtc gcataagcaa gtatcgcttt
     1741 tgagtttaat gggagttttt ttctttttat aaaaagaact atccaagata gtattactgc
     1801 actacaaatc tgccagaaaa acacccctcc ggcatctagt tcttcaactc cttttttgct
     1861 cattacgata gctgcccccc atgagaacgc tgctaaaaaa gcaaaaagca ttcctttaat
     1921 catattaatc atcctctttc tcataaaggg gtttgttttc aaatttcctt ggttgaaagg
     1981 agttaaaaaa catagatgca tcatctacag gaataccaat aaactctcca taataaggat
     2041 catctatagg aaactcttct aatgaaacat aaaacaatac attccagttg aagatcattg
     2101 gatcactatt ttctatttca tggagcaatc tttcatcctt agttaattct cctggaatta
     2161 atacatcagt atgataaaaa ccgctgtaat aagaactatt accggtgtgc actgggcatc
     2221 caaaacgatc caaattagat tctgaatgcc atgttgtaga aatcccttcc ggatgtgaat
     2281 acccaccctt accaacagac tgaatagtca tgttacgaat atccgctaac gcttgttctt
     2341 gatctttata gaaacctttt tctatcgcca gcctcataaa atgccccggg gcatttacag
     2401 aaataagtat tccccctggt attcttctat catgatttct tgttctatga gcagaagagt
     2461 aaaaaacatt aacaccagcc ttatatattt ttagcccatc tttatcctga aatggtacgc
     2521 tttcagtata aataacatcc tcttttattg gatagcactc tggcatatgc agcgaacaaa
     2581 tatatttttg tatgtccact aactcttctg atggacgagc aaaggcaagt tgtggatgaa
     2641 taaaataaat gagatgcgca ctgacctctc ctcttcttgc gcgttcttta aaacgaactc
     2701 tttcattacg caaaaaatca aacaaatgac catcatcatt atatagttgg gggctattta
     2761 caatagataa atggaaatca agccctttaa ttttcttgct tgccaattta ccaaatacac
     2821 agggctgatt gcctgacacc cattttctta gtaaatcttc aattttatct ttagaagttt
     2881 cgttaaagat aaatgaatga atattatcaa tatcttttcc aaatgaaaaa ctggatgata
     2941 attgtggtag tttatttata cgttgttgaa gattcatgaa agctcccaca agacacctca
     3001 tatatttttt tatatactga aactacatta tatttattac cggcgtaaaa cgaaataatt
     3061 tattatcgtt accgatattt taaaaaaatc attatttgca cagtgttcga gttgttagta
     3121 tcactccttc ctgaaaatcc gctccattta ccataacgtc gcattgtacg caccgccaaa
     3181 acgcgttcgg tgcgatcacg gcagcagaca ggtaaaaatg gcaacaaacc acccgaaaaa
     3241 ctgccgcgat cgcacctgat aaattttaac cgcatgaata cctatgcaac cagatgctac
     3301 aggccacatt agcccgcctt aatccactga acacgtcatt tttcatggtt tcaccatccc
     3361 agcgaagggc catccagtgt ccgctcctgg atttccggct gacgctcccg ctccagagat
     3421 aactcatgtt cgcgttcctg catcagccgt tcatccctta tctcctgttc tcgctgtata
     3481 actggctcaa gcgttctgtc cgctcgctca agtgctgcac ctgctgactc aactgcatga
     3541 ctcgcccgtt cagcatcgcg ttgtcccgtt gcgtaagcga aaacattttc tgcaattcca
     3601 cgaaggcgtt ctcccattcg ttcagccgct gcatatagtc ctgttgcagt tgctctaatg
     3661 cgttcagcaa atgtctttcc agctccgtca tgctctgtca ctcctgcacc agtctcactg
     3721 cgttcagttt gccgttgtcc ttcgtccagt tcgtttcggc tttcatcccc ttcggcaaca
     3781 ccagaaaacg tccgttgctg tcctcgtgat aacgcacgcc ccatgtcttc gcgttcagct
     3841 tctccagact ctctttctgc tcgcggagaa tattcatatt cgcgtttatc ttcatgccct
     3901 ggtaccacag cagactcccg gtcgtggcaa acatcagtac tgagacgata atcagccaca
     3961 gccagcgttt cacgctcatt ttcagtacgg ttttccagtg cgcgtccatc gtatcgacgg
     4021 tcgttttctg atacctctcc agcagttctt tcagggctgt tgtatggtcg ttgatagcgt
     4081 tcctgattaa agattcgttt gaggtcagtt ccctgtttac agattcttcg agcttcctga
     4141 actcgtcgtt cagcattttc tctgtagatt cggctctctc tttcagcttt ttctcgaact
     4201 ccgcgcccgt ctgtaaaaga ttgctcataa aacgctcctt tcagtctgat attcctcccg
     4261 ccgttcgggt ctgcaatgct gatactgctt cgcgtcaccc tgaccacttc aagccccgcc
     4321 tctgtgagcg cctgaatcac atcctgacgg ccttttatct ctccggcatg gtaaagcgcg
     4381 tctatcccgc gtgtgacgcc ctcagcaagc gcctgtttcg tttccggcag gttatcagga
     4441 agggtcagcg tccggcggtt ctccggggcg ttggggtcat gcagaccgta atggtgattc
     4501 accagcgtct gccaggcatc aattctcggc ctgtctgccc ggtcgtagta cggctggagg
     4561 cgttttccgg tctgtagctc catgttcgga atgacaaaat tcagctcaag ccgtcccttg
     4621 tcctggtgct ccacccacag gatgctgtac tgatttttct cgagaccggg catcagtaca
     4681 cgctcaaagc tcgccatcac tttttcacgc cctccaggcg gcagctcctt ctccgcgaac
     4741 gacagaacac ctgacgtgta tttcttcgca aatggcgtgg catcgatgag ttcccggacc
     4801 tcttccggat tcccctgaag caccgttgcc ccttcccggt tacgctccct tcccagcagg
     4861 taatcaaccg gaccactgcc accacctttt cccctggcat gaaacttaac tatcatcccg
     4921 cgccccctgt tccctgaccg ccagacgcag ccggcgcagc tcatccccga tggccatcag
     4981 tgcggccacc acctgaaccc ggtcaccgga agaccactgc ccgctgttca ccttcctcgc
     5041 tgtctggtta aggttattcc cgatggcggc cagctgacgc agtaacggct gtgccagtgt
     5101 cggcagcttc ccggaacggg caaccggctc acccaggcag acccgccgca tccataccgc
     5161 cagttgttta ccctcacagc gttccagtaa ccgggcatgt tcatcatcag taacccgtat
     5221 cgtgagcatc ctctcgcgtt tcatcggtat cattaccccc atgaacagaa ccccccctta
     5281 cacggaggca tcagtgacca aacaggaaaa aaccgccctt aacatggccc gcttcatcag
     5341 aggccagaca ttaacgctgc tggagaagct caacgaactg gacgcggatg aacaggcaga
     5401 catctgtgaa tcgcttcacg accacgccga tgagctttac cgcagttgcc tcgcacgctt
     5461 cggggatgac ggtgaaaacc gctgacacat gcagctcccg gagacggtca cagcttgtct
     5521 gtgagcggat gccgggagca gacaagcccg ccagggcgcg tcaggccgtt gacctttggg
     5581 gtgtcggggc gaagccctga cccagtcacg tagcgatagc ggagtgtata c
//
