LOCUS       NZ_CP142952             2101 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain EC190329 plasmid pEC190329_3, complete
            sequence.
ACCESSION   NZ_CP142952
VERSION     NZ_CP142952.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39501223
            Assembly: GCF_036287705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2101)
  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  JOURNAL   Unpublished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 2101)
  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                   :: 126.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/30/2024 20:14:13
            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)                     :: 5,279
            CDSs (total)                      :: 5,152
            Genes (coding)                    :: 4,932
            CDSs (with protein)               :: 4,932
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 14
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 78 of 220
            Pseudo Genes (incomplete)         :: 146 of 220
            Pseudo Genes (internal stop)      :: 46 of 220
            Pseudo Genes (multiple problems)  :: 47 of 220
            Pseudo Genes (short protein)      :: 4 of 220
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP142952.1.
            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..2101
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC190329"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC190329_3"
                     /geo_loc_name="Ireland"
                     /collection_date="2019"
     gene            complement(415..681)
                     /locus_tag="VYI52_RS26390"
                     /old_locus_tag="VYI52_26390"
     CDS             complement(415..681)
                     /locus_tag="VYI52_RS26390"
                     /old_locus_tag="VYI52_26390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     gene            complement(685..1650)
                     /locus_tag="VYI52_RS26395"
                     /old_locus_tag="VYI52_26395"
     CDS             complement(685..1650)
                     /locus_tag="VYI52_RS26395"
                     /old_locus_tag="VYI52_26395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     Typing          complement(1026..1257)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 tttttaatcg gtggtgtcgt caatcactaa atcggaaccc caaaggggac ccccacgatt
       61 tagcatttga cgagattaac tctcggagat ggcatcatgc ttttaacgga ctttaaaaaa
      121 cggtgaacgg atgcggattt taatccgtgt ctgtgaggcg ttgagcaacg agcaaagcga
      181 ggcggtagaa agagagccag cggcaggctc aggacgataa tccggggaaa atgtaccact
      241 cgcagagtgt taacatttga catcggattg tctatcctgc attggtgtcg agttggcaag
      301 gctgaggata atgctgagga taatgctgag gataatgcag gatagacaga gcactagaga
      361 ttgcatgcaa tctcgtacct atcacctcag cctgccgctg gctcttttcc agaactaaga
      421 atgcgttctt aaaaatccaa acttgatacc gtttaaatct attttcacaa aaagagtttt
      481 taccctctcg tttgttttct gaatatataa aattaattca tcctcaaaac cttcgtgcgg
      541 atgaaaacca aatgtgccaa aacttaatcc atcaataagc aaaataaggt ttttaaacct
      601 gtcaggaatc accgcttcac ttcttaaaaa aaataaacca atagtcttat ttccattcag
      661 gtattcaata ttaatattca tacgttaatc cgatttatcc ttctcagggg cgcgtttgta
      721 acgccgttta cctgaatccc agacaaacgc cgtccgcttc ccgtcatcag tgccatcccc
      781 tacatcgtcg gcaatgacaa gatcctcatt ggtttctcga tccaactgga ggacgttttt
      841 tagcgcccca ccggtcgaga taaaacggcg cttgtgaagc tgccgcgtca gctcaagaaa
      901 ccactcagga tcgtttgcca tatcttccgg tttaacggag tatttcagcg tttcagcaac
      961 cgcgctttgc agttgctcgg caacgttggc cacaacctca cctgtcttag tttttactgc
     1021 ccgaatatcg atattcggct catagttcac ccgcaagcaa tcgcgccaga gttctaccca
     1081 acgttcgtgc ttaacgtagt tcttcccttt aaaccaagaa ggttgcacca tcagcagaca
     1141 gtgaaaatgc ggatgtgcgc tgccatcctt acctcgcgtc acctccgtag ccctgatcca
     1201 cccctgaaca ggtgatagct cctttcgctt ttccattcgc ttaaacgccg cattcattgc
     1261 tgtaaggact gttccaagtt cacctatctc gcagttcctg acagttaacg tcagaaacaa
     1321 ccatcgggaa gacgggtaat ccacaacgat tttcggtaga gcctgataaa aacgggcttg
     1381 ccacatgagg gttcttctcc actggcagac agggcaatga cggacacggc aaaattgcgc
     1441 actacgaagc cgtaggcgcg tttctccggt ttccatgatg gtagaccaac caaaacgtaa
     1501 caaaccgcta caggaggcca tacggagtgc atagcgctcg aattcagcag cagtctggta
     1561 gatacccccg acagaatcgg taagcgtgcg ctgggtatcc caaactgcat cacgggggct
     1621 gtagtccgaa aggaatttat cttctgacat taagcctgct ccgatctggg caggctgtga
     1681 tttgatgtgg tatattcatc acgtacctgt gcattgcgag ccagtacatg tcaccagagt
     1741 ttgccgctga ggtgacacat tcgaaatgtt ggggagtgtt gacgcactcc ccaacgccga
     1801 ttaaaaacgc ctcaattctg ctccattttc tttgacctgt caaaacccac tcaaagcctc
     1861 gtcattactg ggctaaacca ctatttcata tccgccattt atcccttaag tataaataca
     1921 aggatcacgc gcgagaattg cgcaaaaaat aaccacaatt ttaacacccc aaaacaagca
     1981 cccccgaacg gcttacccca accttttcca cacacccgat caccaaaaca gggaataaaa
     2041 acaaaaccct gtcttacagg tggatggcct cacttcgtga aaccatccac cccgcataag
     2101 t
//
