LOCUS       NZ_CP075637             1603 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain 2018-166 plasmid pSTEC2018_166-f.
ACCESSION   NZ_CP075637
VERSION     NZ_CP075637.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993346
            Assembly: GCF_016404485.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1603)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Distribution of virulence factors, antimicrobial resistance genes
            and phylogenetic relatedness among Shiga toxin-producing Escherichia
            coli serogroup O91 from human infections
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1603)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAY-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
REFERENCE   3  (bases 1 to 1603)
  AUTHORS   Stevens,M.J.A., Stephan,R. and Nusch-Inderbinnen,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-DEC-2020) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAY-2021
            Assembly Method :: unicycler v. 0.4.9b; SPAdes v. 3.15.2
            Assembly Name                     :: 2018-166_NP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:22:39
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,465
            CDSs (total)                      :: 5,343
            Genes (coding)                    :: 5,049
            CDSs (with protein)               :: 5,049
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 133 of 294
            Pseudo Genes (incomplete)         :: 162 of 294
            Pseudo Genes (internal stop)      :: 52 of 294
            Pseudo Genes (multiple problems)  :: 50 of 294
            Pseudo Genes (short protein)      :: 4 of 294
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075637.1.
            Bacteria and source DNA available from ILS.
            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/
FEATURES             Location/Qualifiers
     source          1..1603
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2018-166"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_166-f"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            405..911
                     /locus_tag="JFX80_RS27045"
                     /old_locus_tag="JFX80_27065"
     CDS             405..911
                     /locus_tag="JFX80_RS27045"
                     /old_locus_tag="JFX80_27065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001194694.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RepA plasmid replication protein"
                     /protein_id="WP_033806469.1"
                     /translation="MAAQEVITDAQIRQRLLDLEEQNKKLRQELLDERRNTNFTQTYPK
                     GWERIRNLIQANPGAARLYSVLSEHIDGNCGAVVADQQFLADQLSVTTRTIRNWVNFLE
                     ENKCLVRIPIAGKLCAYALNPTEVWKGYNTSKPYAAFLTKTLVNSEGVIKRRLQACFGT
                     SEPNE"
                     /name="RepA plasmid replication protein"
     gene            1356..1508
                     /locus_tag="JFX80_RS27050"
                     /old_locus_tag="JFX80_27070"
     CDS             1356..1508
                     /locus_tag="JFX80_RS27050"
                     /old_locus_tag="JFX80_27070"
                     /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_157794697.1"
                     /translation="MFEGLSDDSSPKEQQRDHRQHARGDTARRKSMTERSERIDEEAEE
                     NRKPH"
                     /name="hypothetical protein"
     Typing          complement(1167..1427)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.802"
                     /coverage="100.0"
                     /evalue="3.9e-116"
ORIGIN
        1 cccgatttct gaggcgtttt aacggtgaac ggacggcaaa aacatgatcg agctgttgaa
       61 cgtggagagc gcgaaatcgg gcaaaatcac ggctgacgag gcttgcagag gagtaaacca
      121 gtatacactc cgctatcgct acgtgactgg gtcagggctg cgccccgaca ccccctaacg
      181 cgccctgaag ggcttgtttt tttagataag aggagaaaag ttctatatgg ttgattttat
      241 gggggttttc gaaaagtaac cggaaacgat cgttccggtt aaccggaaac aagctctttc
      301 cggttaattc ccataatagg aaatgaatag attgacgttg gaaataaaac aacataaatt
      361 tgcaatcatt cttccgctta tgaggaaatt aattgggagg tattatggct gctcaagaag
      421 taatcactga tgctcaaatt agacaacgac ttctggatct cgaagagcaa aataaaaaat
      481 tgcgacaaga gcttctggat gagcgcagaa acaccaattt cactcaaacc taccctaagg
      541 gatgggagcg aattagaaac ctcatacaag ctaaccctgg agcagcaaga ttgtattcgg
      601 tcctgtcaga acacattgac ggtaattgcg gtgcagtcgt tgcagaccaa caatttttag
      661 cagaccagtt atctgtgaca acaagaacga tacgtaattg ggttaatttc ttagaggaaa
      721 acaaatgctt ggttaggatt cctatcgcgg gaaaattatg cgcctatgct ttgaatccta
      781 ctgaggtttg gaagggctat aacacatcca aaccttacgc tgcgttttta acaaaaacac
      841 ttgttaacag cgagggggtt ataaagcgtc gacttcaagc atgttttggc acatcagaac
      901 cgaatgaata acagagcctg cggcaggcac aggcaaaaac cccgtttttg gacaatctga
      961 ttcaaatgtt aacatttgac atcgggttgt ctatcctgca ttgctctttt gccgcctcaa
     1021 aatcccttgc gtgtttttgc tccccgatct ccagaacgac cgagccgcca cggtttcggc
     1081 tgcgccttga gcgcaaccgg aaaccgtctg gggagaaccc cagaccccct atcgctgtga
     1141 taccgacggt ctacgaccac ctaccaaccg aatagctgcc tgtaccgtgc aaatgggctt
     1201 tgcagggggc tgacgctgtt cctgacgacc tgaaagcccc tggttagggg tatcggcgcg
     1261 cctgacctcc tgaaaccctc tgtaagcgtt tttcgcgcct tccatgccct ggcgggcatc
     1321 taaaacccgt ttcgtgcgtc tgagagcttc tgagcgtgtt tgaagggcta tctgacgact
     1381 catccccgaa agaacaacaa cgggatcacc gacaacatgc gagaggtgac accgctcgcc
     1441 gcaagtcgat gaccgagcgt agcgagcgaa tcgacgagga agcggaagag aaccggaagc
     1501 cacattgagc acttacgcac ggatgcgggg tgtcggggtg aagccctgac caggtgggga
     1561 atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc tgt
//
