LOCUS       NZ_CP135223             3348 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain Escherichia coli EC16409 plasmid pEC16409-4,
            complete sequence.
ACCESSION   NZ_CP135223
VERSION     NZ_CP135223.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37528252
            Assembly: GCF_032295845.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3348)
  AUTHORS   Peirano,G. and Pitout,J.
  TITLE     Genomic sequencing of MDR E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3348)
  AUTHORS   Peirano,G. and Pitout,J.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-SEP-2023) HMH-CDI, Hackensack-Meridian Health Center
            for Discovery and Innovation, 111 ideation way, Nutley, NJ 07110,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-SEP-2023
            Assembly Method                   :: Unicycler v. v0.4.9
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MiniION and Illumina HiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 07:47:03
            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)                     :: 5,165
            CDSs (total)                      :: 5,050
            Genes (coding)                    :: 4,821
            CDSs (with protein)               :: 4,821
            Genes (RNA)                       :: 115
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 229
            CDSs (without protein)            :: 229
            Pseudo Genes (ambiguous residues) :: 0 of 229
            Pseudo Genes (frameshifted)       :: 87 of 229
            Pseudo Genes (incomplete)         :: 159 of 229
            Pseudo Genes (internal stop)      :: 37 of 229
            Pseudo Genes (multiple problems)  :: 51 of 229
            Pseudo Genes (short protein)      :: 4 of 229
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135223.1.
            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..3348
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Escherichia coli EC16409"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC16409-4"
                     /geo_loc_name="Canada"
                     /collection_date="2016"
     gene            join(3176..3348,1..28)
                     /locus_tag="RRI70_RS00015"
                     /old_locus_tag="RRI70_00015"
     CDS             join(3176..3348,1..28)
                     /locus_tag="RRI70_RS00015"
                     /old_locus_tag="RRI70_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001558245.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_061585996.1"
                     /translation="MTDDRTLQLRLTGFRKAEASLRLEGMDPSGTPLYESVKTRILSGD
                     ITFDEGRTEIRAHYQKRANSN"
                     /name="antitoxin VbhA family protein"
     gene            complement(729..1193)
                     /locus_tag="RRI70_RS00020"
                     /old_locus_tag="RRI70_00020"
     CDS             complement(729..1193)
                     /locus_tag="RRI70_RS00020"
                     /old_locus_tag="RRI70_00020"
                     /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_072796159.1"
                     /translation="MENKNNLSSEVKNHVSKWGKTNISAGWTIIPNALLENQSRLGLSC
                     IDTMVLINLIMHWWEKDNPPRPSKKRLANMLGVSLKTVQRSFIHLEQCGAIKRIPRYKE
                     GKDNARTTNHYDLNGLVDLLEGFSKELIEEREANRKSEVNRPKKRGNPKS"
                     /name="hypothetical protein"
     gene            1475..2041
                     /locus_tag="RRI70_RS00025"
                     /old_locus_tag="RRI70_00025"
     CDS             1475..2041
                     /locus_tag="RRI70_RS00025"
                     /old_locus_tag="RRI70_00025"
                     /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_061583929.1"
                     /translation="MAVFRQCEIREKYLAIYKESFDEVITYLEKAGALEPGVLRLTTID
                     DNAIRAWKSQWKGRSRKHAHGAWDWQNLVSKRARSCKRFDVAVWGEDVLCGLSVGKLTR
                     GKKTVRMDYLEACPTAHPLEKRITMIVVAVALSVAKKVGAQHVAIFNPIKDKEEKVLKH
                     YQSYGFTQRMLYGRFLKNVLYKEVV"
                     /name="hypothetical protein"
     gene            complement(2045..2215)
                     /locus_tag="RRI70_RS00030"
                     /old_locus_tag="RRI70_00030"
     CDS             complement(2045..2215)
                     /locus_tag="RRI70_RS00030"
                     /old_locus_tag="RRI70_00030"
                     /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_152924371.1"
                     /translation="MSYVSERKSELVKAQQRKMDPSSPDSAPINQGLMDFILLAMKVDD
                     GFVQRGRIHGA"
                     /name="hypothetical protein"
     gene            complement(2488..2632)
                     /locus_tag="RRI70_RS00035"
                     /old_locus_tag="RRI70_00035"
                     /pseudo=""
     CDS             complement(2488..2632)
                     /locus_tag="RRI70_RS00035"
                     /old_locus_tag="RRI70_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001717510.1"
                     /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"
     Typing          complement(2525..3125)
                     /name="rep_cluster_2324"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.05"
                     /coverage="92.0"
                     /evalue="0.0"
ORIGIN
        1 ttaccagaag cgggcgaaca gtaactgacg cggacaggaa atgtcttgtc attaccgccg
       61 ctttgcgcca gtgacaacat cagcgggaca agatgtgttt ttggagtacc gccgacactc
      121 cagaatgttt catcaggcgc cgcccgatac gctgagtttc gtgcgtacga aatttctctg
      181 ctgttgagat ctagggcagg attcgcaaag tgctggcgtt tgtacccacc ggaagctgcc
      241 gcgcctggcg gcttggccaa cgcctcacgg ccgcacagtc aactgtgcac ccgttcaccg
      301 ttaccagatc ccctgattcc ggccgggcct gcctgcactg gccaaagccc taaaactgcg
      361 caatcagcag cgcgggggca gttgataacc actttttact gtcatactta tttgccggct
      421 ctctgatcgg taccggctga ctgtttgtgc aaattttgtc ggacatcctg accctcgatg
      481 tccgtttttt ttgttcaaaa ttcgccttta gtgccagcat tcgtccgaaa ccggccgcca
      541 ttcacttccg tgcatagcca tgcaggcgcg cagaaatcat caggcgcgtt ttttcacgat
      601 atggacaggg aaaggtgccg gaaacggccc gcacgcggca gaaacgcgct gagggcctct
      661 gcggcggtgc acgcaagaga tgttatggta aattggactc tctacaggag agtgtgtttg
      721 tcagcctatt aacttttcgg attaccgcgc ttcttaggtc tattaacttc actttttcga
      781 ttcgcctctc tttcttcgat aagctctttc gaaaaacctt ccagcaggtc taccagtccg
      841 ttcagatcgt aatggtttgt tgttctggca ttgtctttcc cttctttgta tcgaggtatc
      901 cgcttgatgg caccacactg ttccaaatga ataaaacttc tttgaacggt ttttagtgaa
      961 acgcccagca tgttcgccag tctctttttc gaaggtcttg gggggttatc tttttcccac
     1021 caatgcatta tgaggtttat gagaaccatc gtatcaatac agctaagacc caacctggac
     1081 tgattttcca gtaaggcatt tgggataatc gtccatcctg cagaaatgtt tgtcttcccc
     1141 cacttgctta cgtggttctt tacttcgctc gacaggttat ttttgttttc cataaaacat
     1201 gcatcctgtg gtcatctgag gctagagggc attttatata ttgaacgttt taccgttcac
     1261 cttgcgtcat tgtcttaacg tattgtccca ctatatcttt ttctgtgtgg tcaaatcaga
     1321 ccatacccta tggtttttaa agtccacagg gtggggttta aatgtaccat aggatatggt
     1381 ctttgttgac cactaaccaa aatgttagca aatgatttaa agtggttttt ttatggcaaa
     1441 atgtttactg gtcaaggtca ggagggagac gagcgtggcg gtttttagac aatgcgaaat
     1501 tagagaaaaa tatctcgcga tttacaaaga gtcattcgat gaagttataa cttatcttga
     1561 gaaggcaggt gctttagagc ccggcgtttt aaggctcact acaatcgatg acaatgctat
     1621 tcgtgcatgg aagagccaat ggaaaggcag gtctcgtaag cacgctcatg gtgcttggga
     1681 ttggcagaac cttgtatcaa agagagctcg ttcttgtaaa agatttgatg tggctgtttg
     1741 gggagaggat gtgctttgtg ggctttcagt tggaaagcta acccgtggta aaaagacagt
     1801 tagaatggat tatctagagg cttgtccaac agctcatccg ttggagaaac gaatcacaat
     1861 gattgtggtt gctgtggctc tgtcagtagc taaaaaagta ggggcacagc acgtagccat
     1921 attcaatccg ataaaagaca aagaagaaaa agtgttaaaa cactaccagt cttacgggtt
     1981 tacacaaaga atgttgtatg gacgcttttt gaaaaacgtg ctgtacaaag aagttgtttg
     2041 atagctatgc gccgtgaata cgaccacgtt gaacaaagcc gtcatctact ttcatagcaa
     2101 gcaggatgaa gtccataaga ccctgattga ttggagctga atcaggagag gatggatcca
     2161 ttttgcgttg ctgtgccttt accagctcac ttttgcgctc agatacataa ctcatcttgt
     2221 gactctctgt cttgtatggg gatgtagaca ctataacaag tggataaaaa aataacgaga
     2281 tctctatatt ttcaaaaaga gatgactgtt gttgactcgc ctcttctgca aagcgtactc
     2341 ttttctttca aaagaaaaaa accgcctttg cggggcggtt tttttccagt tcattgagtt
     2401 tgcggctctt tgaacctagg taacagtctt gtgcgagacg tgtcaccaaa tctgtccttc
     2461 cagtgtagct gtagtcaggc tttaacttca agaactctcg atacacctct cgcactcact
     2521 gctaccaatg gctaccgcca gtggcgcttt gtcgtgtctt tcagggttgg attcaagagt
     2581 acagttacct gataaagacg tggtagtcgg gctgaacggg gagttcgtgc atacagccca
     2641 gcttggagcg aaccacctac aaggaaccca gttgcacggg taggaatgag aaaacgccac
     2701 cttacggcgg actgcaacgg gtaaacctca gggtgggaac aggagagcgc acgagggagc
     2761 gacccatcgg aaacggtggg gatctttaag tcctgtcagg tttcgccact tctgatttga
     2821 gcgccggaaa tcacctgatt tctgtgaagc ttgtcaggag ggcgaagcct atggaaaacc
     2881 ggcaatcccc agaacctcct tatggccttc tgcctgagca ggtaacgctc gccgcagtgt
     2941 catgaccgaa cgaagtgagc gaatgaccga ggaagcgtaa tgtctgtaat gctgaacagg
     3001 gatcgtgtcg ctcggtacac acgtttcctc cctgattaca cacccggctg caacagtttc
     3061 ctgtcgtttt ccacttttcc ctgcacagct atacaacggc aacatccggg caggacatgt
     3121 aaagttagct aactttacgc ctgccttatt cgcatgactg ctcaaaggaa aaaccatgac
     3181 tgatgatcgg acactgcaac tgcgcctgac agggttccgt aaagcggagg cctctctcag
     3241 gcttgaaggg atggatccat caggaacccc gctttatgaa tcggtaaaga caaggattct
     3301 ttccggtgac atcaccttcg atgaaggccg cactgagata cgggctca
//
