LOCUS       NZ_CP116131             4593 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P666 plasmid pDETEC28, complete
            sequence.
ACCESSION   NZ_CP116131
VERSION     NZ_CP116131.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988472
            Assembly: GCF_027944795.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4593)
  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  JOURNAL   Unpublished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 4593)
  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 02:06:33
            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)                     :: 5,170
            CDSs (total)                      :: 5,049
            Genes (coding)                    :: 4,837
            CDSs (with protein)               :: 4,837
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 83 of 212
            Pseudo Genes (incomplete)         :: 145 of 212
            Pseudo Genes (internal stop)      :: 42 of 212
            Pseudo Genes (multiple problems)  :: 52 of 212
            Pseudo Genes (short protein)      :: 3 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116131.1.
            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..4593
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="DETEC-P666"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC28"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-10"
     gene            join(4588..4593,1..318)
                     /locus_tag="PIB57_RS25715"
                     /old_locus_tag="PIB57_25720"
     CDS             join(4588..4593,1..318)
                     /locus_tag="PIB57_RS25715"
                     /old_locus_tag="PIB57_25720"
                     /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_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            527..>961
                     /locus_tag="PIB57_RS25720"
                     /old_locus_tag="PIB57_25725"
                     /pseudo=""
     CDS             527..>961
                     /locus_tag="PIB57_RS25720"
                     /old_locus_tag="PIB57_25725"
                     /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            996..1556
                     /locus_tag="PIB57_RS25725"
                     /old_locus_tag="PIB57_25730"
     CDS             996..1556
                     /locus_tag="PIB57_RS25725"
                     /old_locus_tag="PIB57_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /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_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            1563..1796
                     /locus_tag="PIB57_RS25730"
                     /old_locus_tag="PIB57_25735"
     CDS             1563..1796
                     /locus_tag="PIB57_RS25730"
                     /old_locus_tag="PIB57_25735"
                     /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_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2484..3323)
                     /locus_tag="PIB57_RS25735"
                     /old_locus_tag="PIB57_25740"
     CDS             complement(2484..3323)
                     /locus_tag="PIB57_RS25735"
                     /old_locus_tag="PIB57_25740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(3515..3664)
                     /locus_tag="PIB57_RS25900"
     CDS             complement(3515..3664)
                     /locus_tag="PIB57_RS25900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     gene            complement(4334..4525)
                     /locus_tag="PIB57_RS25740"
                     /old_locus_tag="PIB57_25745"
     CDS             complement(4334..4525)
                     /locus_tag="PIB57_RS25740"
                     /old_locus_tag="PIB57_25745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_001677262.1"
                     /translation="MTKQEKTAINMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          4162..4246
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(3593..4151)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          309..1894
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acaatacggg ttagcgatga ggagcacgcc cggttactgg aacgctgcga gggtaaacga
       61 ctggcagaat ggatgcggcg ggtctgtctg ggggagccgg ttgcgcgcac aggaaaactg
      121 ccgacactat cgccgccatt gctgcggcat ctggctgcca tcgggaacaa tctgaaccag
      181 acagcccgga aggtgaacag cggccactgg tcttcgattg accgggttca tgtggtggcc
      241 gctctgatgg ccatcgaggg tgaattgcgc cagttgcggc aggctgtcag ggaacagggg
      301 ggacgggatg atagttaaat ttcatgccag ggggaaaggc ggtggaagtg gcccggtcga
      361 ttacctgctg gggcgggagc gtaaccgcga aggcgcaacg gtgctccggg gtaacccgga
      421 agaaatccgg gaactcattg atgccacgcc attttcgaag aaatacacgt caggcgttct
      481 gtcgttcgcg gagaaggagt taccgccggg tgaacgcgaa agagtgatga cgagctttga
      541 gcgtgttctt atgcccggtc tcgaaaaaga ccagtacagc attctctggg tggaacacca
      601 ggataagggg cggctcgaac tgaattttgt cattccgaac atggaactac agagcggtaa
      661 gcgcctccag ccgtactacg accgtgcgga caggccgagg ataaatgcct ggcagacgct
      721 ggttaatcat cattacgggc tgcgtgaccc gaacgcaccg gagaacagac ggacgcttgt
      781 cacaccgaat aatctgccaa aagcgaaaca ggaggccgca gaagcgatta cacggggtct
      841 tgaggcgctt taccgtgccg gagcaataaa aacgcgtcag gatgtcactg aggcgctcac
      901 agcggcaggt tttgaggtgg tgaggacaac cagaagcagt atcagtattg ccgacccgga
      961 gggggggcgg aatctcaggc taaagggggc gctgtatgag caatctttta caaatgggaa
     1021 cggacttcga gaagaaactg aaagagcgag ccgcttctac cgagaacatg ctgaacagcg
     1081 agttcaggaa gctagaagag tctgtagaca aggcactgag cttaaacagg cagaaaatca
     1141 gagacgctat cagcgaacat acaacatccg tgaaacagca actggatacg ctgagcacca
     1201 ccgtgagcac gcagctcagc accacagagg ccgaactgtc ccggcagcag aaaaacctgc
     1261 tctggcaggt gatcaaaggg cgggtactgt ttccggcgct gaccgcgctc agcgtcacgg
     1321 gcggcatttt cctggggtgc tgggggctga ttcagtggca ggaaagcagg attgcgaaaa
     1381 atatcttgac catcagagag caggaaaaca cgctggcgaa actcgaggca aaaacctggg
     1441 gggtgacgtt cgtcaatggc gagaacggga aatttctggt gctgccggac ggggtgaaag
     1501 gggaaaacac ctggacggtg ggcgacaaga acgccgtgag gctggtcagg gagtaaacga
     1561 gtatgacgga actggaaggg catttgctga acgccttaga gcatttgcaa caggactata
     1621 tgcggcggct gaacgagtgg gagagcgcct tcgcagaatt gcagaagatg cacgcggtta
     1681 cgcaacagaa caacgcgata ctgaacgagc gtgtcgtgaa cttgagtcag caggtgcagc
     1741 tattagccgg acaagtcgac cgcttgagtc ggttatttat cacgaacaac agataaggga
     1801 tgaacaggag cgtcaggcgc aggagcttgc ccggcgctgg catgaagagc aggaacccga
     1861 agcgcggatc tggcgtggcc cgtcaatggg gatgtgaccg gggtaccccc tgaaatcgag
     1921 ccagtttgtg gcacgcccta cccggatggc gccaatgtta atgtacgtac attagcatta
     1981 acaatatcca aacctcccca ttttgccccg ttcgacggct ggaacgtgcg aaactgatcg
     2041 tcattcagtt tcgcgcataa ctatgcatga ggttaaaatt taccaggcgc gatcgcggca
     2101 gtttttcggg tggtttgttg ctgtttttac ctgtctgctg ccgtgatcgc gctgaacgcg
     2161 tttaagcggt acgcgcaatg cgacgttatg gtaaatacgg agtattttaa ttgcgggcct
     2221 ttgttgtata tctctgtcgt ttgtccccgg ggggaagcat tactgctaac aagtcccgtg
     2281 agaaaactgc gcaatcgtat tgcgcaccat gaacctattc tcaaccgcaa tctggaggat
     2341 gattttgcta cgataaagag aattatcgcg tatcggtgtc agcattcatt ggagtggatg
     2401 ctgaaaaacc aggtgttact ccctctactt acacttaaac ctctctaaaa atataagtaa
     2461 gtactatcga gggctatcat gaactatggt gccctctgag catagctacc cattacttct
     2521 tctatgtcat tgaataattc atttcttaac tctaagtatt ctagtaactc catttctaat
     2581 gactctgtcg tgaacttaaa tctagaagga tctttgattg agtttactag tcttgataac
     2641 gctctatatg ttttgagtga aggttgcatt atagatggaa agtatttgaa aacctcttca
     2701 tctctgttga aattaactaa aaacttgtag tcatcattta taaatctcaa gcatacagcg
     2761 tcaagcttat cgccttttct tattattatt tctttatagg aaagatattt ttcagaagat
     2821 aagtcccaca tcaagcgaaa atctctcttt gcgaacgagt tcgcgtcatc attgaaaaga
     2881 gatgatgtga tggctttgga tagaccttct gtgtttatct ctttgttgga tgggtagtaa
     2941 attttattaa ttgctttcat tctctcaaat gatgaatata ggtcattatg ccaccttgtt
     3001 gaaatcactc ctttagttat attctccttg ctaaaattaa gccctgtatc aaaaataaat
     3061 gcagccatca gtgaatatga tatgtttttt attaactcag acttaaatgg ttccgctatg
     3121 gagtagtaca gtgataaaat aactaaaaat aaaaggtatt gtcttacctt tcccgatgag
     3181 tatatgtaaa ggcgatattt atttattgat agttttattt tgtatggaat gatctcattt
     3241 ctgtcatatc ctcttcgtgg tggagcaaaa caaaagaaac atgcagctat taataaaaca
     3301 aaaaagatga acagtgtaag caagttcggc tcctgtgtat gctcactatg catgattgtc
     3361 ttgagatcta acgatcctga aggtagtctt gtccgtaaac gaaaaaaccg cccagcaagg
     3421 cggcttttcg aaggttctca gagcagcaac tctttgaacc aaggtaactg gcttggagga
     3481 gcacagccac caaatctgtc ctttcagttt agccttaacc ggcgcataac ttcaagacta
     3541 actcctctaa acggttacca atggctgctg ccagtggcgt ttttacgtgt ctttccgggt
     3601 tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt
     3661 gcacacagcc cagcttggag cgaacgacct acaccgggcc gagataccaa cagcgtgagc
     3721 tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca
     3781 gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata
     3841 gtcctgtcgg gtttcgccac ctctgacttg agcatctgtt tttgtgatgc tcgtcagggg
     3901 ggcggagcct atggaaaaac gccagcggcg cggccttctt cctgttcctg gccttttgct
     3961 cacatgtttc ttttggcgtt atcccctgat tctgtggata accgcatcac cgtctttgag
     4021 tgagctgata ccgctcgccg cagccgaacg accgagcgta gcgagtcagt gagcgaggaa
     4081 gcggaagagc gcctgatgcg gcattttctc cttacgcatc tgtgcggtat ttcacaccgc
     4141 atatggtgca cttttcttat aatccgcact gatgccacat agttaagcca gtatacactc
     4201 cgctatcgct acgtgactgg gtcagggctg cgccccgaca cccgctaaaa cccgctgacg
     4261 cgccctgacg ggcttgtctg ctcccggcat ccgctcacag gcaagctgtg aacgtctccg
     4321 ggagctgcat gtttcagttg ctttcaccgt catcgccgaa gcgtgcgagg caactacggt
     4381 agagttcgtc ggcgtggtcg tgaagtgatt cgcagatgtc tgcctgttcg tccgcgtcca
     4441 gctcgttgag tttttccagc agggtcagcg tctggcttct gataaagcgg gccatgttaa
     4501 tggctgtttt ttcctgtttg gtcatggtct taaggctcct taatagggga ttttttaggg
     4561 ggaatgatac cgatgaaacg cgagaagatg ctc
//
