LOCUS       NZ_CP116140             4593 bp    DNA     circular CON 25-FEB-2024
DEFINITION  Escherichia coli strain DETEC-P649 plasmid pDETEC28, complete
            sequence.
ACCESSION   NZ_CP116140
VERSION     NZ_CP116140.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31988469
            Assembly: GCF_027944815.1
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  JOURNAL   Unpublished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 01:50:27
            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)                     :: 4,984
            CDSs (total)                      :: 4,864
            Genes (coding)                    :: 4,648
            CDSs (with protein)               :: 4,648
            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)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 82 of 216
            Pseudo Genes (incomplete)         :: 150 of 216
            Pseudo Genes (internal stop)      :: 41 of 216
            Pseudo Genes (multiple problems)  :: 52 of 216
            Pseudo Genes (short protein)      :: 3 of 216
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP116140.1.
            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-P649"
                     /isolation_source="ICU patient oral swab"
                     /db_xref="taxon:562"
                     /plasmid="pDETEC28"
                     /geo_loc_name="China: Guangzhou"
                     /collection_date="2019-09-05"
     gene            join(4068..4593,1..35)
                     /locus_tag="PIB66_RS24785"
                     /old_locus_tag="PIB66_24785"
     CDS             join(4068..4593,1..35)
                     /locus_tag="PIB66_RS24785"
                     /old_locus_tag="PIB66_24785"
                     /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            42..275
                     /locus_tag="PIB66_RS24790"
                     /old_locus_tag="PIB66_24790"
     CDS             42..275
                     /locus_tag="PIB66_RS24790"
                     /old_locus_tag="PIB66_24790"
                     /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(963..1802)
                     /locus_tag="PIB66_RS24795"
                     /old_locus_tag="PIB66_24795"
     CDS             complement(963..1802)
                     /locus_tag="PIB66_RS24795"
                     /old_locus_tag="PIB66_24795"
                     /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(1994..2143)
                     /locus_tag="PIB66_RS24970"
     CDS             complement(1994..2143)
                     /locus_tag="PIB66_RS24970"
                     /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(2813..3004)
                     /locus_tag="PIB66_RS24800"
                     /old_locus_tag="PIB66_24800"
     CDS             complement(2813..3004)
                     /locus_tag="PIB66_RS24800"
                     /old_locus_tag="PIB66_24800"
                     /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"
     gene            3067..3390
                     /locus_tag="PIB66_RS24805"
                     /old_locus_tag="PIB66_24805"
     CDS             3067..3390
                     /locus_tag="PIB66_RS24805"
                     /old_locus_tag="PIB66_24805"
                     /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            3599..>4033
                     /locus_tag="PIB66_RS24810"
                     /old_locus_tag="PIB66_24810"
                     /pseudo=""
     CDS             3599..>4033
                     /locus_tag="PIB66_RS24810"
                     /old_locus_tag="PIB66_24810"
                     /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"
     Typing          2641..2725
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          complement(2072..2630)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.761"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3381..4588
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gcgacaagaa cgccgtgagg ctggtcaggg agtaaacgag tatgacggaa ctggaagggc
       61 atttgctgaa cgccttagag catttgcaac aggactatat gcggcggctg aacgagtggg
      121 agagcgcctt cgcagaattg cagaagatgc acgcggttac gcaacagaac aacgcgatac
      181 tgaacgagcg tgtcgtgaac ttgagtcagc aggtgcagct attagccgga caagtcgacc
      241 gcttgagtcg gttatttatc acgaacaaca gataagggat gaacaggagc gtcaggcgca
      301 ggagcttgcc cggcgctggc atgaagagca ggaacccgaa gcgcggatct ggcgtggccc
      361 gtcaatgggg atgtgaccgg ggtaccccct gaaatcgagc cagtttgtgg cacgccctac
      421 ccggatggcg ccaatgttaa tgtacgtaca ttagcattaa caatatccaa acctccccat
      481 tttgccccgt tcgacggctg gaacgtgcga aactgatcgt cattcagttt cgcgcataac
      541 tatgcatgag gttaaaattt accaggcgcg atcgcggcag tttttcgggt ggtttgttgc
      601 tgtttttacc tgtctgctgc cgtgatcgcg ctgaacgcgt ttaagcggta cgcgcaatgc
      661 gacgttatgg taaatacgga gtattttaat tgcgggcctt tgttgtatat ctctgtcgtt
      721 tgtccccggg gggaagcatt actgctaaca agtcccgtga gaaaactgcg caatcgtatt
      781 gcgcaccatg aacctattct caaccgcaat ctggaggatg attttgctac gataaagaga
      841 attatcgcgt atcggtgtca gcattcattg gagtggatgc tgaaaaacca ggtgttactc
      901 cctctactta cacttaaacc tctctaaaaa tataagtaag tactatcgag ggctatcatg
      961 aactatggtg ccctctgagc atagctaccc attacttctt ctatgtcatt gaataattca
     1021 tttcttaact ctaagtattc tagtaactcc atttctaatg actctgtcgt gaacttaaat
     1081 ctagaaggat ctttgattga gtttactagt cttgataacg ctctatatgt tttgagtgaa
     1141 ggttgcatta tagatggaaa gtatttgaaa acctcttcat ctctgttgaa attaactaaa
     1201 aacttgtagt catcatttat aaatctcaag catacagcgt caagcttatc gccttttctt
     1261 attattattt ctttatagga aagatatttt tcagaagata agtcccacat caagcgaaaa
     1321 tctctctttg cgaacgagtt cgcgtcatca ttgaaaagag atgatgtgat ggctttggat
     1381 agaccttctg tgtttatctc tttgttggat gggtagtaaa ttttattaat tgctttcatt
     1441 ctctcaaatg atgaatatag gtcattatgc caccttgttg aaatcactcc tttagttata
     1501 ttctccttgc taaaattaag ccctgtatca aaaataaatg cagccatcag tgaatatgat
     1561 atgtttttta ttaactcaga cttaaatggt tccgctatgg agtagtacag tgataaaata
     1621 actaaaaata aaaggtattg tcttaccttt cccgatgagt atatgtaaag gcgatattta
     1681 tttattgata gttttatttt gtatggaatg atctcatttc tgtcatatcc tcttcgtggt
     1741 ggagcaaaac aaaagaaaca tgcagctatt aataaaacaa aaaagatgaa cagtgtaagc
     1801 aagttcggct cctgtgtatg ctcactatgc atgattgtct tgagatctaa cgatcctgaa
     1861 ggtagtcttg tccgtaaacg aaaaaaccgc ccagcaaggc ggcttttcga aggttctcag
     1921 agcagcaact ctttgaacca aggtaactgg cttggaggag cacagccacc aaatctgtcc
     1981 tttcagttta gccttaaccg gcgcataact tcaagactaa ctcctctaaa cggttaccaa
     2041 tggctgctgc cagtggcgtt tttacgtgtc tttccgggtt ggactcaaga cgatagttac
     2101 cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc
     2161 gaacgaccta caccgggccg agataccaac agcgtgagct atgagaaagc gccacgcttc
     2221 ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca ggagagcgca
     2281 cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc
     2341 tctgacttga gcatctgttt ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg
     2401 ccagcggcgc ggccttcttc ctgttcctgg ccttttgctc acatgtttct tttggcgtta
     2461 tcccctgatt ctgtggataa ccgcatcacc gtctttgagt gagctgatac cgctcgccgc
     2521 agccgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg cctgatgcgg
     2581 cattttctcc ttacgcatct gtgcggtatt tcacaccgca tatggtgcac ttttcttata
     2641 atccgcactg atgccacata gttaagccag tatacactcc gctatcgcta cgtgactggg
     2701 tcagggctgc gccccgacac ccgctaaaac ccgctgacgc gccctgacgg gcttgtctgc
     2761 tcccggcatc cgctcacagg caagctgtga acgtctccgg gagctgcatg tttcagttgc
     2821 tttcaccgtc atcgccgaag cgtgcgaggc aactacggta gagttcgtcg gcgtggtcgt
     2881 gaagtgattc gcagatgtct gcctgttcgt ccgcgtccag ctcgttgagt ttttccagca
     2941 gggtcagcgt ctggcttctg ataaagcggg ccatgttaat ggctgttttt tcctgtttgg
     3001 tcatggtctt aaggctcctt aataggggat tttttagggg gaatgatacc gatgaaacgc
     3061 gagaagatgc tcacaatacg ggttagcgat gaggagcacg cccggttact ggaacgctgc
     3121 gagggtaaac gactggcaga atggatgcgg cgggtctgtc tgggggagcc ggttgcgcgc
     3181 acaggaaaac tgccgacact atcgccgcca ttgctgcggc atctggctgc catcgggaac
     3241 aatctgaacc agacagcccg gaaggtgaac agcggccact ggtcttcgat tgaccgggtt
     3301 catgtggtgg ccgctctgat ggccatcgag ggtgaattgc gccagttgcg gcaggctgtc
     3361 agggaacagg ggggacggga tgatagttaa atttcatgcc agggggaaag gcggtggaag
     3421 tggcccggtc gattacctgc tggggcggga gcgtaaccgc gaaggcgcaa cggtgctccg
     3481 gggtaacccg gaagaaatcc gggaactcat tgatgccacg ccattttcga agaaatacac
     3541 gtcaggcgtt ctgtcgttcg cggagaagga gttaccgccg ggtgaacgcg aaagagtgat
     3601 gacgagcttt gagcgtgttc ttatgcccgg tctcgaaaaa gaccagtaca gcattctctg
     3661 ggtggaacac caggataagg ggcggctcga actgaatttt gtcattccga acatggaact
     3721 acagagcggt aagcgcctcc agccgtacta cgaccgtgcg gacaggccga ggataaatgc
     3781 ctggcagacg ctggttaatc atcattacgg gctgcgtgac ccgaacgcac cggagaacag
     3841 acggacgctt gtcacaccga ataatctgcc aaaagcgaaa caggaggccg cagaagcgat
     3901 tacacggggt cttgaggcgc tttaccgtgc cggagcaata aaaacgcgtc aggatgtcac
     3961 tgaggcgctc acagcggcag gttttgaggt ggtgaggaca accagaagca gtatcagtat
     4021 tgccgacccg gagggggggc ggaatctcag gctaaagggg gcgctgtatg agcaatcttt
     4081 tacaaatggg aacggacttc gagaagaaac tgaaagagcg agccgcttct accgagaaca
     4141 tgctgaacag cgagttcagg aagctagaag agtctgtaga caaggcactg agcttaaaca
     4201 ggcagaaaat cagagacgct atcagcgaac atacaacatc cgtgaaacag caactggata
     4261 cgctgagcac caccgtgagc acgcagctca gcaccacaga ggccgaactg tcccggcagc
     4321 agaaaaacct gctctggcag gtgatcaaag ggcgggtact gtttccggcg ctgaccgcgc
     4381 tcagcgtcac gggcggcatt ttcctggggt gctgggggct gattcagtgg caggaaagca
     4441 ggattgcgaa aaatatcttg accatcagag agcaggaaaa cacgctggcg aaactcgagg
     4501 caaaaacctg gggggtgacg ttcgtcaatg gcgagaacgg gaaatttctg gtgctgccgg
     4561 acggggtgaa aggggaaaac acctggacgg tgg
//
