LOCUS       NZ_CP135230             5073 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain Escherichia coli EC16611 plasmid pEC16611-3,
            complete sequence.
ACCESSION   NZ_CP135230
VERSION     NZ_CP135230.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN37528253
            Assembly: GCF_032295145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5073)
  AUTHORS   Peirano,G. and Pitout,J.
  TITLE     Genomic sequencing of MDR E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5073)
  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 07:08:40
            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)                     :: 5,115
            CDSs (total)                      :: 5,007
            Genes (coding)                    :: 4,787
            CDSs (with protein)               :: 4,787
            Genes (RNA)                       :: 108
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 81
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 220
            CDSs (without protein)            :: 220
            Pseudo Genes (ambiguous residues) :: 0 of 220
            Pseudo Genes (frameshifted)       :: 80 of 220
            Pseudo Genes (incomplete)         :: 154 of 220
            Pseudo Genes (internal stop)      :: 40 of 220
            Pseudo Genes (multiple problems)  :: 48 of 220
            Pseudo Genes (short protein)      :: 3 of 220
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP135230.1.
            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..5073
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Escherichia coli EC16611"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEC16611-3"
                     /geo_loc_name="Canada"
                     /collection_date="2016"
     gene            complement(join(4860..5073,1..98))
                     /locus_tag="RRI67_RS00020"
                     /old_locus_tag="RRI67_00020"
     CDS             complement(join(4860..5073,1..98))
                     /locus_tag="RRI67_RS00020"
                     /old_locus_tag="RRI67_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_315429447.1"
                     /translation="MNKTKGCLIANFATVPYKAQQLTNLSNSGYNTVSKTIYTSSKNTV
                     VIPYEVLEKMVSAKNCRLRIHTTEGNQDIDFSAASIPGGKATAIVSIKEFMTKVAKVK"
                     /name="hypothetical protein"
     gene            complement(104..808)
                     /locus_tag="RRI67_RS00025"
                     /old_locus_tag="RRI67_00025"
     CDS             complement(104..808)
                     /locus_tag="RRI67_RS00025"
                     /old_locus_tag="RRI67_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221000.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS6-like element IS26 family transposase"
                     /protein_id="WP_001067855.1"
                     /translation="MNPFKGRHFQRDIILWAVRWYCKYGISYRELQEMLAERGVNVDHS
                     TIYRWVQRYAPEMEKRLRWYWRNPSDLCPWHMDETYVKVNGRWAYLYRAVDSRGRTVDF
                     YLSSRRNSKAAYRFLGKILNNVKKWQIPRFINTDKAPAYGRALALLKREGRCPSDVEHR
                     QIKYRNNVIECDHGKLKRIIGATLGFKSMKTAYATIKGIEVMRALRKGQASAFYYGDPL
                     GEMRLVSRVFEM"
                     /name="IS6-like element IS26 family transposase"
     gene            complement(1517..1630)
                     /locus_tag="RRI67_RS00030"
                     /old_locus_tag="RRI67_00030"
     CDS             complement(1517..1630)
                     /locus_tag="RRI67_RS00030"
                     /old_locus_tag="RRI67_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_071590655.1"
                     /translation="MHEPPVQSDRCALSGNYHLESNPERHAKAPLAAATDN"
                     /name="replication initiation protein"
     gene            <1946..2128
                     /locus_tag="RRI67_RS00035"
                     /old_locus_tag="RRI67_00035"
                     /pseudo=""
     CDS             <1946..2128
                     /locus_tag="RRI67_RS00035"
                     /old_locus_tag="RRI67_00035"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001441803.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            2278..2601
                     /locus_tag="RRI67_RS00040"
                     /old_locus_tag="RRI67_00040"
     CDS             2278..2601
                     /locus_tag="RRI67_RS00040"
                     /old_locus_tag="RRI67_00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_001347450.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2810..>3244
                     /locus_tag="RRI67_RS00045"
                     /old_locus_tag="RRI67_00045"
                     /pseudo=""
     CDS             2810..>3244
                     /locus_tag="RRI67_RS00045"
                     /old_locus_tag="RRI67_00045"
                     /inference="COORDINATES: protein motif:HMM:NF015397.3"
                     /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"
     gene            3279..3764
                     /locus_tag="RRI67_RS00050"
                     /old_locus_tag="RRI67_00050"
     CDS             3279..3764
                     /locus_tag="RRI67_RS00050"
                     /old_locus_tag="RRI67_00050"
                     /inference="COORDINATES: protein motif:HMM:NF016710.3"
                     /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_023139312.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3768..3983
                     /locus_tag="RRI67_RS00055"
                     /old_locus_tag="RRI67_00055"
     CDS             3768..3983
                     /locus_tag="RRI67_RS00055"
                     /old_locus_tag="RRI67_00055"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /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_058671277.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            4112..4630
                     /locus_tag="RRI67_RS00060"
                     /old_locus_tag="RRI67_00060"
     CDS             4112..4630
                     /locus_tag="RRI67_RS00060"
                     /old_locus_tag="RRI67_00060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011017199.1"
                     /translation="MKCFWACSVSVVLVMSFTVASAENITHTKPLARSDLYLTCKGYQV
                     KGASVINVEKPSYLEGTGEQVEFAIISLGDASDGLKVFFDSWGFSPFGLIESHVMHEHW
                     SLVHVGGRVSVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCINSDKRPSWVEKIYTRT
                     GVFRGGIED"
                     /name="hypothetical protein"
     Typing          1992..2164
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="94.828"
                     /coverage="100.0"
                     /evalue="9.34e-71"
     Typing          complement(1522..2067)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.078"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          2592..4075
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.313"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acagtattgt atccactgtt acttagatta gttagttgct gtgctttata gggcactgtt
       61 gcaaagttag cgatgaggca gccttttgtc ttattcaaag gccttacatt tcaaaaactc
      121 tgcttaccag gcgcatttcg cccaggggat caccataata aaatgctgag gcctggcctt
      181 tgcgtagtgc acgcatcacc tcaatacctt tgatggtggc gtaagccgtc ttcatggatt
      241 taaatcccag cgtggcgccg attatccgtt tcagtttgcc atgatcgcat tcaatcacgt
      301 tgttccggta cttaatctgt cggtgttcaa cgtcagacgg gcaccggcct tcgcgtttga
      361 gcagagcaag cgcgcgacca taggcgggcg ctttatccgt gttgatgaat cgcgggatct
      421 gccacttctt cacgttgttg aggattttac ccagaaaccg gtatgcagct ttgctgttac
      481 gacgggagga gagataaaaa tcgacagtgc ggccccggct gtcgacggcc cggtacagat
      541 acgcccagcg gccattgacc ttcacgtagg tttcatccat gtgccacggg caaagatcgg
      601 aagggttacg ccagtaccag cgcagccgtt tttccatttc aggcgcataa cgctgaaccc
      661 agcggtaaat cgtggagtga tcgacattca ctccgcgttc agccagcatc tcctgcagct
      721 cacggtaact gatgccgtat ttgcagtacc agcgtacggc ccacagaatg atgtcacgct
      781 gaaaatgccg gcctttgaat gggttcatgt gcagctccat cagcaaaaag ggatgataag
      841 tttatcacca ccgactattt gcaacagtgc cctttatagc tagatatctt gccatcaata
      901 tttatatcta ttcctatgaa acctaagtat gcggaacttc cattagatac atttgaattg
      961 taggaaagga tcagccctac ttgatctggt tgggagctgg accatattgc tcctaactga
     1021 agttgtgttc cccaagtgct gttcgggtcg tatagcgaat ttggagagac atctatgaca
     1081 gttgagttgt caaaagtgga tgtttgttga gaaaccacac ccattcccgc cagtttatcc
     1141 attgctgtac agccagagat ggctactacg atcgcagaag caaaaaaaat attccttatc
     1201 atttcgttat cctatttttt tcttgttacc agagagtgaa aaaagcatcg tattaccgaa
     1261 actattttgc acgcgatttt ctttttaaga aggattttga aaggatacgg gcagatcttc
     1321 ttgagatcct taagcgagcg tcgtaatctc ttgaccacga aacgaaaaaa ccgccttgca
     1381 gggcggtttt tcgaaggttc tcagagctac caactctttg aaccgaggta actggcttgg
     1441 aggagcgcag tcaccaaaac ttgtcctttc agtttagcct taaccggcgc ataacttcaa
     1501 gactaactcc tctaaatcag ttatcagtgg ctgctgccag tggcgctttt gcatgtcttt
     1561 ccgggttgga ctcaagatga tagttaccgg acaaggcgca gcggtcggac tgaacggggg
     1621 gttcgtgcat acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg
     1681 gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca
     1741 ggagagcgca cgagggagcc accaggggga aacgcctggt atctttaagt cctgtcgggt
     1801 ttcgccacca ctgatttgag cgtcagattt cgtgatgctt gtcagggggg cggagcctat
     1861 ggaaaaacgg cttcgccgcg gccttctcat ttccctgtta agttccttct tggcatttac
     1921 caggaaactt ccgccctatt cgtaagcccg caccgctcgc cgcagccgaa cgaccgagcg
     1981 cagcgagtca gtgagcgagg aagcggaata tatcctgtct catatattct gcttacgctc
     2041 cgctgctgca tttttctcct gccacatgaa gcgcttcact gattcccgca cccgtgccaa
     2101 catagtaagc cagtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga
     2161 aacccgctaa aaccactgac gcgcctgcgg cttgtccaac accgcgccga ccgggaaaag
     2221 atttcccgcc cgtcccggcg ttatcaggag gccggattgg cagacaaacg cagcaaaatg
     2281 ctcacgatgt gggtgaccga agatgagcac cgccgtctgc tggagcgctg cgacggtaaa
     2341 cagcttgcag cctggatgcg ccagacgtgc ctggacgaga aacccgcccg cgccggcaag
     2401 cttccctcgc tctcgccggc gctgcttcgt cagcttgccg gcatggggaa caacctcaac
     2461 cagattgccc ggcaggttaa cgccggtggt ggcagcgggc acgaccgcgt gcaggtcgtc
     2521 gccgcgctga tggccatcga tgccggactc gagcggctgc ggcatgccgt gctggaaaag
     2581 ggtgcagacg atgatcgtta agtttcaccc gcgagggcgc ggcggtggcg ccggtccggt
     2641 ggattatctg ctggggaaag accgacagcg cgacggcgcc accgttctgc aggggaagcc
     2701 ggaagaagtc agggagctta tcgacgcctc gccctacgca aaaaagtaca catccggcgt
     2761 cctgtccttt gccgaaaagg atttaccgcc cgggcagcgc gaaaagctga tggcgagctt
     2821 tgaacgggtt ctgatgcccg gactcgataa agaccagtac agcgtgttgt gggttgagca
     2881 ccaggataag gggcggctgg agctgaactt cctgatcccg aacacggagc tgctgaccgg
     2941 caggcgtctc cagccgtatt acgaccgcgc cgaccgtccg cgcattgatg cctggcagac
     3001 catcgtgaac ggcaggctgg ggctgcatga cccgaacgcg cctgaaaacc ggcgggcgct
     3061 ggtcacgccg tccgcgctgc cggaaacgaa gcaggaagcc gctcaggcaa ttacacgggg
     3121 tttactggcc ttagcctcgt ccggggagct gaaaacccgc caggacgtca ctgaggcgct
     3181 ggaaagcgca ggttttgagg tggtacgcac cacaaaaagc agcatcagca ttgccgaccc
     3241 ggacgggggg cgaaacatcc gactgaaggg agccatctat gaacagtctt ttaacgctgg
     3301 caaaggactt agagcagaaa tcgaaagcgc agcagcagag taccggcgag atgctgaaag
     3361 ccgcattcag cgagcacgag aagtctgtca gagcggaact gagcgaaagc gagaagagaa
     3421 tcagcgccgc catcctcgac cacgaccgga agctgtcctc agccatgagc cagcgcacga
     3481 aaggcatggt gcgtatggtc agccagacgt ggctgaccat cgtcctggtg tctgcactgc
     3541 tgacagcatc gggcgcaagc attctgtggt ggcaggggca gcagatactc gacaattaca
     3601 cgactatccg ggagcagaag cgcacgcagg ccatgctgtc cgagaggaac agcggcgtgc
     3661 agctctcgac ctgcggagag cagagacgcc gctgcgtgag ggtgaacccg gaagcgggac
     3721 ggttcggaga ggattcgagc tggatgatac tggcggggaa atagcacatg acggagctgg
     3781 aaaaacagtt gctgagcgca ttagagcagc tacagcagga ctactcgaaa aggctggacg
     3841 agtgggagaa cgccttcgcg gaatggcgga cgatgtctgg tcttatgcaa cgggagaacg
     3901 cggcgctgag cgagcgcgtc acgggcttga gcaggcaggt gcagagtttg agcgatcagc
     3961 tgcgccggtt gtcgaaaggc tgaactcgat tgaagcacac aggcagcagg agcgggcggc
     4021 gcagcatcag aaaacgctgg agctggaacg atcgcagcgg cagaaaggtt ttgagcttgg
     4081 aatgtagtta atcaatgaaa agggatgcgt tatgaagtgt ttctgggctt gctcagtctc
     4141 agtagttttg gttatgtcat ttacagtcgc ttctgcggag aacattacac acacaaaacc
     4201 gttagccagg agcgacttat atcttacctg taaaggttat caggtgaagg gggcgtctgt
     4261 aattaacgtc gagaaacctt cttaccttga aggtacaggt gagcaggttg agtttgcaat
     4321 catttctctc ggtgatgcat ctgatggact caaggttttt tttgattcat ggggtttttc
     4381 tccttttgga ttgattgaaa gtcatgtaat gcatgagcac tggtctttag ttcatgttgg
     4441 ggggcgtgtt tcagtcaagg gtgaaaagat tgattattca tttgtagata accagccaca
     4501 ggagggtggg agctataaac ccaaaacagg tgtgttcctg tatggctgca ttaactctga
     4561 taaaaggcca tcttgggtcg aaaaaatcta cacaagaaca ggcgtgtttc gagggggcat
     4621 agaagactaa aatactgcgt acagcatgaa aattcattga acagagtgtt agttcatttt
     4681 cgtgcatggc tatgcataca cgcaaaactt atcagcgcga ttccgggcgg ttttcggtga
     4741 gaagacgggc tcttttgtgg ctcaggacgg aaaaacgccc tgagcgcgtc tgagcggtgc
     4801 gcccaaggga tgttatggta aatagtgtga agtgccgcct gtaatggcgg cttagttacc
     4861 tatttaactt ttgccacttt agtcatgaat tctttaatgg aaacaatcgc agtagctttc
     4921 cccccaggga tacttgcagc tgagaaatcg atgtcttgat taccttcagt tgtatgtatg
     4981 cgaaggcggc agtttttagc cgacaccatc ttttctagca cttcatatgg gataacaacg
     5041 gtatttttgc tggatgtgta gatcgttttg gat
//
