LOCUS       NZ_CP086478             4773 bp    DNA     circular CON 28-MAY-2024
DEFINITION  Escherichia coli strain Ec-050-T20-ESBL plasmid pEc-050-T20-ESBL_8,
            complete sequence.
ACCESSION   NZ_CP086478
VERSION     NZ_CP086478.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN22108725
            Assembly: GCF_022759785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4773)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Genome plasticity in E. coli and K. pneumoniae: SNV accumulation
            over time
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4773)
  AUTHORS   Moser,A.I., Endimiani,A., Campos-Madueno,E.I. and Vallone,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2021) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 390x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022759785.1-RS_2024_05_28
            Annotation Date                   :: 05/28/2024 04:58:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,279
            CDSs (total)                      :: 5,157
            Genes (coding)                    :: 4,884
            CDSs (with protein)               :: 4,884
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 273
            CDSs (without protein)            :: 273
            Pseudo Genes (ambiguous residues) :: 0 of 273
            Pseudo Genes (frameshifted)       :: 109 of 273
            Pseudo Genes (incomplete)         :: 176 of 273
            Pseudo Genes (internal stop)      :: 53 of 273
            Pseudo Genes (multiple problems)  :: 57 of 273
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP086478.1.
            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..4773
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-050-T20-ESBL"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEc-050-T20-ESBL_8"
                     /geo_loc_name="Switzerland"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            263..478
                     /locus_tag="LNN47_RS26170"
                     /old_locus_tag="LNN47_26175"
     CDS             263..478
                     /locus_tag="LNN47_RS26170"
                     /old_locus_tag="LNN47_26175"
                     /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_000137420.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(677..1228)
                     /locus_tag="LNN47_RS26175"
                     /old_locus_tag="LNN47_26180"
     CDS             complement(677..1228)
                     /locus_tag="LNN47_RS26175"
                     /old_locus_tag="LNN47_26180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000654246.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654246.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            1764..2231
                     /locus_tag="LNN47_RS26180"
                     /old_locus_tag="LNN47_26185"
     CDS             1764..2231
                     /locus_tag="LNN47_RS26180"
                     /old_locus_tag="LNN47_26185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011899450.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_157186121.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYTTVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     gene            complement(2825..2908)
                     /locus_tag="LNN47_RS26490"
     CDS             complement(2825..2908)
                     /locus_tag="LNN47_RS26490"
                     /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="hypothetical protein"
                     /protein_id="WP_058652899.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="hypothetical protein"
     gene            3546..3869
                     /locus_tag="LNN47_RS26185"
                     /old_locus_tag="LNN47_26190"
     CDS             3546..3869
                     /locus_tag="LNN47_RS26185"
                     /old_locus_tag="LNN47_26190"
                     /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_000957080.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3859..>4560
                     /locus_tag="LNN47_RS26390"
                     /old_locus_tag="LNN47_26195"
                     /pseudo=""
     CDS             3859..>4560
                     /locus_tag="LNN47_RS26390"
                     /old_locus_tag="LNN47_26195"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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"
     Typing          3258..3442
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.17"
                     /coverage="86.0"
                     /evalue="5.83e-49"
     Typing          complement(2800..3312)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2..582
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="89.175"
                     /coverage="100.0"
                     /evalue="8.800000000000001e-100"
     Typing          3860..4773
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.066"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gacgtggctg accatcgtcc tggtgtctac actgctgaca gcatcgggcg caagcattct
       61 atggtggcag gggcagcaga tactcgacaa ttacacgatc atccgggagc agaagagcac
      121 gcaggccatg ctgtccgaga ggaacagcgg cgtgcagctc tcgacctgcg gagagcagag
      181 acggcgctgc gtgagggtga acccggaagc gggacggttc ggagaggatt cgagctggat
      241 gatactggcg gggaaatagc acatgacgga gctggaaaaa cagttgctga gcgcattaga
      301 gcagctacag caggactact cgaaaaggct ggacgagtgg gagaacgcct tcgcggaatg
      361 gcggacgatg tttggtctta tgcaacggga gaacgcggcg ctgagcgagc gcgtcacggg
      421 cttgagcagg caggtgcaga gtttgagcga gcagctgcgc cggttgtcac aaggctgaac
      481 gtgatagagg cacatcgtga gcaggaacgg gcggcgcagc atcagaaagc gctggagctg
      541 gaacgatctc agcgacagcg aacgtacaac ggtccgtcac tttgaatctg tgcgccggaa
      601 aagcatgggc ttgctgtttc tggcgcacag gttcagttct agaacatgag gctgctatct
      661 tgttgttcac gcttcatcag atcttgatgc ttattgttat ggctgagcta tcaatccctg
      721 ttgcgttgct aatatccttt ttggctcttt caattgcctc gttaagggag agtttttctg
      781 ttttctcttc agccagacca ggaatcactg tattaggaac cgatggggat gaaggatgga
      841 atttcttcca ttccagttgt tccggtgtta ccccaatacg taaaaaagct tcctgtgcgc
      901 tcaggtaagc aaccggatag cgctgaccat cggttagcat tttccatgct tttggagtgt
      961 gaatttctgc gtattcatca aaggttatga cgttcctgtc gtcgtaatca gggcttttaa
     1021 aacacccggt aattttggcg atcaggaatg ctgtgccgtg ttccaggtct tttactgccc
     1081 acgtttccct tctgtttctt actgctatga ggtaatcggc atcgttgagc ctgtctgttc
     1141 tggcatgcca gtagcctgac cccccctcgg ttctcattat gttcaaatcc ttcccggtaa
     1201 aaaccacaac agctttcata tctttcatat agaaaccctt aataggtgag tcaatttcat
     1261 ttttttatga aatctatacg atagaattcg tgttgtaaat gttttttatg cgataaaatg
     1321 cagcccccta cctcttttat tgttagtgat aaggcttcct gtttgttttt ttgataaacc
     1381 ggttaaaaca ggggcttgga cgaggatata cattgaaagc atgagccatt cacgtggctg
     1441 catggctatg cagccgcgtg aaatttatca ggcgcagaat gcgcggttta gcggggagtt
     1501 tactgccggt tttaccgggc taacgccgct ttcacgctga acccgtccgg agcggtgcgg
     1561 gcaagggatg ttatggtaaa tctagctgct agggcgattc gcacgtcaca ttttcaggtg
     1621 tgatatcctt atgcgccaag gatgaaagga caaaaaaata atccataagg attcttttta
     1681 tcgtctctgc ttttttcttg ggctccttcc gcttgtttcc tctctggtac catatgcgga
     1741 ctctactcaa taaggatcgt tttgtgcctg ctccaaacaa ttacggtgta gctggttcac
     1801 ctaacagcgc tatagctcac cctgatgggc ttgattgcta tggccgtgtc cctgaaatta
     1861 attctaaagg tgatgttatt cctgctggcg acatcttctt gcgtgttggt aggcatactg
     1921 gccctaaccg gggctttggt gttcgccata tctgggctga gcacgagcag gaactggtta
     1981 agctgggata tacgaccgtt aatgatgtgg ctcgttttgt ccgggatatt attcgtcgtg
     2041 gcgtaccaat atattgcgag ttcaacagta caagcggtaa acatcggcct gcagtgctaa
     2101 agtcgtcggt aggcatcgta attcttgagc ccagagaagc gcctgaaact gagtcaggtt
     2161 ggatctatgt cgttgtgact gcgtacacac gaaggacggc gcacggtact ttggttggtc
     2221 atattgaata aaaaaatagg gcgctaaaaa gcgcccttta tgaattcgtt ggtagtcgca
     2281 gcatttcctt agcacatagg gttcagaaac cgacgcttgt cgtaactacc cggcagatga
     2341 ccagccatct gactgcccgg cacagaaggc ctattactgg ttgatgcccc ctgcgaatgc
     2401 tcttgcagta caataatcat aaacatcgtg atgtagattt gcaaccaaca ttttggttgc
     2461 aacctatata ctaatttttt tcgataaccc tggaatccat tgctgtgtct ggatttcttg
     2521 aagctcctgg ctatagatac cctatatcct aacagttatt ctgctgtgaa tatcagaaat
     2581 gaacacttga gatcatcagt ggctcgtcgt agtctcttgc tcagaaacga aaaaaccacc
     2641 ctggcaggtg gttttttcga aggttagtta atcctggcag attctctaac cgtggtaaca
     2701 gtcttgtgcg agacatgtca ccaaatactg tcctttcagt gtagcctcag ttaggccgcc
     2761 acttcaagaa ctctcgttac atctctcgca catcctgctt accagtggcc gttgccaatg
     2821 gcgattagtc gtgtctatcc gggttggact caagacgata gttaccggac aaggcgcagc
     2881 ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
     2941 aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggaat gacaccggta
     3001 aaccgaaagg caggaacagg agagcgcacg agggagccac cagggggaaa cgcctggtat
     3061 ctttaagtcc tgtcgggttt cgccaccact gatttgagcg tcagatttcg tgatgcttgt
     3121 caggggggcg gagcctatgg aaaaacggca gcgccgcatc cttttcctgt cctgcttgcc
     3181 atgccgtatg cctttgctct tatccgtttg caggtaacgc ccgccgcagc cgaacgtcag
     3241 gagcggaagc gaccgagtga gcgaggaggc gtcatatcac cgtaacctcc attttctcct
     3301 gtacgccctg cagctgcatt tttcccctgc cacatgaagc actttcatta cgtgttactc
     3361 cgccgtaaca tattgagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     3421 cgccccgaaa cctgctaaaa ccactgacgc gcctgcggct tgtccaacac cgcgccgacc
     3481 gggaaaagat ttcccgcccg tcccggcgtt atcaggagat cggtttgtca gagaaacgga
     3541 acaagatgct caccatgtgg gtgaccgaag atgagcaccg ccgtctgctg gaacgctgcg
     3601 acggtaaaca gcttgcagcc tggatgcgcc agacgtgcct ggccgagaaa cccgcccgcg
     3661 ccggcaagct tccctcaatc tcgccggcgc tgcttcgtca gcttgccggc atggggaata
     3721 acctcaacca gattgcccgg caggttaacg ccggtggcgg cagcgggcac gaccgcgtgc
     3781 aggtcgtcgc cgcgctgatg gccatagatg ccggactcga gcggctgcgg catgccgtgc
     3841 tggaaaaggg tgcagacgat gatcgttaag tttcacccgc gagggcgcgg cggtggcgcc
     3901 ggtccggtgg attatctgct ggggaaagac cgacagcgcg acggcgccac cgttctgcag
     3961 gggaagccgg aagaagtcag ggagcttatc gacgcctcgc cctacgcaaa aaagtacaca
     4021 tccggcgtcc tgtcctttgc cgaaaaggat ttaccgcccg ggcagcgcga aaagctgatg
     4081 gcgagctttg aacgggttct gatgcccgga ctcgataaag accagtacag cgtgctatgg
     4141 gttgagcacc aggataaggg gcggctggag ctgaacttcc tgatcccgaa catggagctg
     4201 ctgacaggca ggcgtctcca gccgtattac gaccgcgccg accgtccgcg cattgatgcc
     4261 tggcagacca tcgtgaacgg caggctgggg ctgcatgacc cgaacgcgcc tgaaaaccgg
     4321 cgggcgctgg tcacgccgtc cgcgctgccg aaaacgaagc aggaagccgc tcaggcaatt
     4381 acacggggtt tactggcctt agcctcgtcc ggggagctga aaacccgcca ggacgtcact
     4441 gaggcgctag aaagcgcagg ttttgaggtg gtgcgcacca caaaaagcag catcagcatt
     4501 gccgacccgg acggggggcg aaacatccga ctgaagggag ccatctatga acagtctttt
     4561 aacgctggcg aaggacttag agcagaaatc gaaagcgcag cagcagagta ccggcgagat
     4621 gctgaaagtc gcattcagcg agcacgagaa gtttgtcaga gcggaactga gcgaaagcga
     4681 gaagagaatc agcgccgcca tcctcgacca cgaccggaag ctgtcctcag ccatgagcca
     4741 gcgcacgaaa ggcatggtgc gtatggtcag cca
//
