LOCUS       NZ_CP142964             1718 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain EC200461 plasmid pEC200461_8, complete
            sequence.
ACCESSION   NZ_CP142964
VERSION     NZ_CP142964.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39501436
            Assembly: GCF_036287745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1718)
  AUTHORS   Maguire,M.
  TITLE     Spatiotemporal and genomic analysis of carbapenem resistance
            elements in Enterobacterales from hospital inpatients and natural
            water ecosystems of an Irish city
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1718)
  AUTHORS   Maguire,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-JAN-2024) Bacteriology, University of Galway,
            University Road, Galway, Galway 000000, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 84.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 20:05:42
            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)                     :: 4,998
            CDSs (total)                      :: 4,885
            Genes (coding)                    :: 4,693
            CDSs (with protein)               :: 4,693
            Genes (RNA)                       :: 113
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 79 of 192
            Pseudo Genes (incomplete)         :: 124 of 192
            Pseudo Genes (internal stop)      :: 43 of 192
            Pseudo Genes (multiple problems)  :: 49 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142964.1.
            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..1718
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC200461"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC200461_8"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     gene            join(1678..1718,1..364)
                     /locus_tag="VYI50_RS24985"
                     /old_locus_tag="VYI50_24985"
     CDS             join(1678..1718,1..364)
                     /locus_tag="VYI50_RS24985"
                     /old_locus_tag="VYI50_24985"
                     /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_061604172.1"
                     /translation="MKILAAMEIADCDFEHMDMDVLVGALLKLKLWDSHHHNLNMQGKR
                     SFLDDLRADGIEAIKKYEAEIESENESFAEERLILRIYQNELGLWLGRLFCGEAEIGQC
                     GVYGSADEVRTAARQSGILCDSIEIFQKDA"
                     /name="hypothetical protein"
     gene            1228..1464
                     /locus_tag="VYI50_RS24990"
                     /old_locus_tag="VYI50_24990"
     CDS             1228..1464
                     /locus_tag="VYI50_RS24990"
                     /old_locus_tag="VYI50_24990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016230891.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016230891.1"
                     /translation="MTRLTNLTPAEKKFIDDAIAAAERAAGKKLNQPNRHIVLNRARAQ
                     IESQRYADRQRALREDERQQSDFAWSRPRAPRR"
                     /name="hypothetical protein"
     Typing          987..1071
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="100.0"
                     /evalue="3.06e-32"
ORIGIN
        1 tgaacatatg gatatggatg tcttagtagg ggctttactg aaattaaaat tgtgggatag
       61 ccaccatcac aacttgaaca tgcaaggtaa gaggagcttt ctcgatgatt taagagcgga
      121 tggtattgag gctattaaga aatacgaggc tgaaattgaa tctgagaatg agtcctttgc
      181 ggaggagcga ttaatactga ggatctatca gaacgagctt ggcttatggt tagggaggct
      241 cttttgtggt gaggctgaga tcggtcagtg tggtgtttat ggatcggctg atgaggttcg
      301 aacagctgcg cgtcaaagcg gtattttgtg cgatagcatc gaaatttttc aaaaggatgc
      361 ctaatgcccc cgtggtgggt acaccagaaa acggggagcg gagcgaccag cgtcaggtcg
      421 ttctatgttg ttctgattgt gtgggtgttg tgccagactg ggcaatcgca tttcaccgca
      481 actcctgcct tgaatctcac tttatcaggt gcctgttatc gtacagcgag acggggtaga
      541 gcttaactct ttcgcggcta agttacgttt ccaccgtttg cctgtttatc ctgccggagt
      601 ccggggcgta gacctgagtt tcaagggtgc agatatgatt ttaatgtcgt tgaatggtat
      661 taagctggta gtgacaaggc tagccagccc tgctaggata ggattgctac gtctgatcct
      721 ggcaggtatc tgcgaagaat tagagtaccg aagccctgtg attctgtcac ggggcttttg
      781 tacatctgta gcctgatttt tcaacaagat ccccgtcaca cctcacttca tgtatgtgaa
      841 aaaagttgta gtgcccgccg cagtctcacg tccggagcgt agcgaccgag tgagcgagga
      901 ggcatcattt cactattcgg gcatggtatt gcggacgctt ctgagccaca tatcacacct
      961 gccacatgac gcactttcct gataaccgca cctatgccaa catattaagc cagtatacac
     1021 tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacccgctaa atccactgac
     1081 gcgcctgcgg cttgtccaac gcctcacggc accggattaa aatccgctcc cgttcaccgt
     1141 ttctgactgc ctttcaccgt cgcttacgct tcatcgttcc tactgtgtct ggcagactgc
     1201 aggggctatt ctcatacgga gataaacatg acgagactga caaacctgac ccccgctgag
     1261 aaaaagttta tcgacgacgc tatagccgct gccgaacgtg cggccgggaa gaagctcaat
     1321 cagcctaacc ggcacatcgt cctgaacaga gcgcgtgcgc agattgagtc gcagcgttac
     1381 gccgaccgcc agcgtgcatt acgtgaggat gagcggcagc agtccgattt tgcctggtca
     1441 cgtccgcgcg cgccgcgccg ctgattgcgg attttggcgg tttagtggtg ctgatgctgc
     1501 gaaatcacct gcggttcacc cgcgtgcata gctatgcagt cgcgcagaaa tcatcagggg
     1561 cgtttttccg ggatgtgggt gaggaaatgt gccggaaacg gctctgatgc gtcagaattg
     1621 cgctgagggc ctgtcagggg gtgctgataa cggatgttat ggtaaatcgg agggtgtatg
     1681 aagattttgg ctgcaatgga aatagctgat tgtgattt
//
