LOCUS       NZ_CP075677             1560 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-l.
ACCESSION   NZ_CP075677
VERSION     NZ_CP075677.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993384
            Assembly: GCF_016403675.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1560)
  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  JOURNAL   Unpublished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 1560)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (15-MAY-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
REFERENCE   3  (bases 1 to 1560)
  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
            Assembly Name                     :: STEC2018-553
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Illumina MiniSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:09:25
            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)                     :: 5,752
            CDSs (total)                      :: 5,624
            Genes (coding)                    :: 5,342
            CDSs (with protein)               :: 5,342
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 98
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 118 of 282
            Pseudo Genes (incomplete)         :: 157 of 282
            Pseudo Genes (internal stop)      :: 61 of 282
            Pseudo Genes (multiple problems)  :: 52 of 282
            Pseudo Genes (short protein)      :: 4 of 282
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075677.1.
            Bacteria and source DNA available from Institute Food Hygiene and
            Safety, University Zurich.
            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..1560
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-l"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            complement(682..1161)
                     /locus_tag="JFY30_RS28570"
                     /old_locus_tag="JFY30_28570"
     CDS             complement(682..1161)
                     /locus_tag="JFY30_RS28570"
                     /old_locus_tag="JFY30_28570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001620079.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000275450.1"
                     /translation="MYIGTEEQRKKRLKELEKLNKESESDPKNNGPFTQVYQKGWERIR
                     ELSKDKQGVVAIPLYSFLAEHIDPSCGAVVADQQFLADKLGVSRSTIKRWLNYLESKNA
                     LVRIPVAGKVCAYALDPHEVWKGYNTSKNYAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          177..437
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.275"
                     /coverage="100.0"
                     /evalue="1.83e-109"
ORIGIN
        1 atgtgcaaat gtaataccgt cacccgcgac gatattccgt ttgccatctg gtcagggctt
       61 cgccccgaca ccccgcatca gtgcgtacgt gctcaatgtg gtttccggtt ctcttccgct
      121 tcctcgccca ctcgctcact aacgttcggt cgctggggct gcggcgagcg gtgccacctc
      181 tcgcatgttg tcggtgattc cgctgttgtt ctttcgggga taagtcgtca gatagccctt
      241 caaacgcgct cagaagctct cagacgcacg aaacggggtt taaatgcccg tcagggcatg
      301 gaaggcgcga aaaacgctta cagagcgttt caggaggtca ggcgcgccga tacccctagc
      361 caggggcttt caggtcgcca ggaaccgcgc cagccccctg caaagcccat ttgcacggta
      421 caggcagcca ctcggttggt aggtggtcgt agaccgtcgg tgttacagcg atgggggtct
      481 ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc tgccggaacc gtggcggctc
      541 gatcgttctg gagatcgggg agcaaaaaca cgcaagggat tgcggcaaaa gagcaatgca
      601 ggatagacaa cccgatgtca aatgttaaca tttgaatcag attgtccaaa aacggggttt
      661 ttgcctgtgc ctgccgctgg ctcaatttga aaacatggcc atgattcggc gctgaatatc
      721 accgtctttg ttgaccagtg ttttagtgac aaacgccgcg tagtttttag atgtgttgta
      781 tcccttccag acttcatgtg gatcgagtgc atacgcacaa accttaccag caacaggaat
      841 tctgactaac gcgttttttg attctaagta gttgagccag cgcttaattg tgcttcggct
      901 aacacccaat ttatctgcta aaaactgctg atcggcaaca acagcaccgc atgagggatc
      961 tatgtgctca gctaaaaacg agtaaagcgg tattgctaca actccctgct tgtccttcga
     1021 cagttctcgg atcctttccc agcccttctg ataaacctgg gtgaatgggc cgttattttt
     1081 cggatctgat tccgattctt tgtttaattt ttccagttct tttagacgct tttttcgctg
     1141 ctcttcagtc ccgatataca tggtaaatct ccacggtcta atgatggctc aaatataagc
     1201 catcatagct caaacgtaaa ccatgatagg tcgacctagc tcacacatgc gtgagctaac
     1261 cttagaccac acatgcgtga gctaacccat aatgcaagta gctaaaaaat caataactta
     1321 caaaatcgcc cttaaatatc ttttctgctg aaagtgttgc gcaaagcgga acactttttt
     1381 ggggtgtcgg ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt
     1441 actcctctgc aagccttacc agctgtgatt tttgccagat ttcacgctct caacgttcaa
     1501 cagctccatc atggttttgc cgtccgttca ccgctaaaac gcctcagaaa tcgggacagg
//
