LOCUS       NZ_CP142963             3257 bp    DNA     circular CON 31-JAN-2024
DEFINITION  Escherichia coli strain EC200461 plasmid pEC200461_7, complete
            sequence.
ACCESSION   NZ_CP142963
VERSION     NZ_CP142963.1
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 3257)
  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  JOURNAL   Unpublished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 3257)
  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
            CP142963.1.
            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..3257
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EC200461"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC200461_7"
                     /geo_loc_name="Ireland"
                     /collection_date="2020"
     gene            5..286
                     /locus_tag="VYI50_RS24965"
                     /old_locus_tag="VYI50_24965"
     CDS             5..286
                     /locus_tag="VYI50_RS24965"
                     /old_locus_tag="VYI50_24965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            1430..1624
                     /locus_tag="VYI50_RS24970"
                     /old_locus_tag="VYI50_24970"
     CDS             1430..1624
                     /locus_tag="VYI50_RS24970"
                     /old_locus_tag="VYI50_24970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2278..2390
                     /locus_tag="VYI50_RS24975"
                     /old_locus_tag="VYI50_24975"
                     /pseudo=""
     CDS             2278..2390
                     /locus_tag="VYI50_RS24975"
                     /old_locus_tag="VYI50_24975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(2621..2917)
                     /locus_tag="VYI50_RS24980"
                     /old_locus_tag="VYI50_24980"
     CDS             complement(2621..2917)
                     /locus_tag="VYI50_RS24980"
                     /old_locus_tag="VYI50_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     Typing          complement(916..1171)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.512"
                     /coverage="89.0"
                     /evalue="1.21e-116"
     Typing          complement(1296..1394)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(1698..1780)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1793..2347
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 attaatgatc ataaatatca agcataaagg tttgcgtaag tttgccgaaa caggtaacaa
       61 cgcaggaatt ccgcaacagt ttactcaacg tctgaagctg atcctaacag ccttaagcac
      121 agcgacgaac ttgcaggata tgatggattt aaaggcattg cgctgccatc cattgaaggg
      181 agaccgtcaa ggagagtatt cgttagaggt caatggaaac tggcgcgtag tgtttaagct
      241 cgaagaacct aacgtctttg acgtggatct cgaggattat cactaagaag gtccttaaag
      301 catcaaagtg acagtatcga tgctttaggg tctcataaaa aagcaaaacc tcggggtaag
      361 ttatatgaag tattttctgt accagatagt ccctatagca gccatcatta gcgcagcaat
      421 tctagcgcta aaaggtatca atggctgggg gtggttctta actgttgggt tcctgcttgc
      481 aggggcagat acagtaaagg ctcagttatc taagtagtaa taaacactat caatagtggt
      541 tggataattg ccaaaaaagc ctctatctgt tctgaaacag acaacaagga aaaatcggtg
      601 taagccacct ccataggagg tggtattgat atcaacatag ataaaaccat cccgtaaatc
      661 acagcattta ccataacgtc gcattacgcg caccgctaaa acgcgctgaa cgcgattctg
      721 ccgcgaacac cgcaaaaaga gatgttttac caagcgaaaa ccggaaaaat gcgtcaggat
      781 cgctttcagc tcactgcata gctatgcatg aaagtgaatg gcgatcggtt tgggcgcata
      841 cggtgcccat gagacacatt ttcggacatt ttcagttcgt gaatccctga ctcattgcta
      901 catatctgaa cagacacccc tagcagcgcc cccaggggcg tcctgtaaaa aaacacaccg
      961 cgccgctagc agcaccccta atataaaatg atgtttttta tgaaaatagt cagtaccacc
     1021 cctaaaaagc ggtgttggcg cagctacaac accgcgccga caccgctttt ttaaatatca
     1081 caaagagagc aagaagaact aatttgtcat aactctctat ttataaagaa aaatcagcaa
     1141 aaaattgttt ttgcgtgggg tgtgggcatt tcaggcatga gaacagactc gcgtttttcc
     1201 ggagtatcag cggaattatt gattaagaaa cactcgacgc agagcgaaat tttatgcaac
     1261 agcggctgca ctgcacaggg attatttatc agttgatatg ctgtgccatg atacgtccta
     1321 aaaaaacagg acaggatgtg caattgtaat accgtcgccc gcaacgtctt acaattacca
     1381 cctggtcagg gtccacccga cacccggtac tgacggagaa caacggaagg tgaacaaaca
     1441 gcaacaaact gcgctgaata tggcgcgatt tatcaaaagc cagagcctga cactgcttga
     1501 aaaactggat gctctggatg ccgacgaaca ggcggccatg tgcgaacgac tgcacgaact
     1561 cgcggaagaa ctccagaaca gcatccaggt tcgctttgag accgaaagtg aaacaggaac
     1621 ataacgaagc tgacggaggc gctcacggct tgtccgcgag cgttttcggc agcagacaag
     1681 cccgccaggg cgcgtcagcg ggtgtcgggg cgaagccctg acccagtcac gtagcgatag
     1741 cggagtgtat actggcttaa ctatgcggca tcagtgcaga ttgtatgaaa agtgccccat
     1801 gccgggtgtg aaattccgca cagatgcgta aggagaaaat gcgcgtccag gcgcttttcc
     1861 gcttcctcgc tcactgactc gctacgctcg gtcgttcggc tgcggcgagc ggtactgact
     1921 tacacaaaaa cggcagcacg gttatctaca gaatcagggg ataaggccgg aaagaacatg
     1981 tgagcaaaag accaagaaca ggaagaaggc cgcgccgcag gcgtttttcc ataggctccg
     2041 cccccctgac gagcatcaca gaaatcgacg ctcaagtcag aggtggcgaa acccgacagg
     2101 acttaaagat accagacgtt tccccctggt ggctccctcg tgcgctctcc tgttccgacc
     2161 ctgccgctta ccggatacct gtccgccttt ctcccttcgg gaagcgtggc gctttctcat
     2221 agctcacgct gtaggtatct cggttcagtg taggtcgttc gctccaagct gggctgtgtg
     2281 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatca tcttgagtcc
     2341 aacccggaaa gacatgcaaa acaccattgg cagcagccac tggtaactga tttagaggag
     2401 ttagtcttga agttatgcgc cagttaaggc taaactgaaa gaacaagttt tggtgactgc
     2461 gctcctccaa gccagttacc ctggttcaga aacttgccgg ttactgaacc ttcgaaaaaa
     2521 ccaccttgcc gggtggtttt ttcgtttacg agaaacgata cgatccagtt gcctgagagt
     2581 caagacagaa aaaggccgca tatagcggcc ttttcttttc tcaaaatata ggaaccaatt
     2641 catctaattc cttaatgaca ttaggtgact tcctgctcgc gttaagactg tattgagtct
     2701 gcatgtttat ccacgactcg gcactgcgac caagaactcg agaaagcctt aatgccatct
     2761 caacacttaa atcagctttt ccattcagca ctctacttag agtggaaggt gatacatgca
     2821 gtttttcaga caggtccgcg gctgatattt caaacggttc cataaacatc tcacggataa
     2881 aaacccctgg atgtactgga tcgacaagat taatcatacc ttcctctgaa gcctatatta
     2941 gttttaaaaa gataggccta ttgcgttttc agattgcgca ttgcgcataa cgcaactcat
     3001 tgttgactaa aaaaaagaat gacattatga tgcacattgg tgcgtctaat cattccttat
     3061 gatgtgggta cttgatgtga aattcaaggc cccggcattg tacagcgcat caaaccaatg
     3121 tcaacagatt aaaatgcgac ttggttaagt aaaacctacg tcatttattc aaatagagca
     3181 aggggtttgc aatggaaata cggatgaacc ggaaaaataa actgcgatgt ttctatctaa
     3241 acaaatatgg gatggtg
//
