LOCUS       NZ_CP075674             2396 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-i.
ACCESSION   NZ_CP075674
VERSION     NZ_CP075674.1
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 2396)
  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  JOURNAL   Unpublished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 2396)
  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 2396)
  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
            CP075674.1.
            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..2396
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-i"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            complement(484..714)
                     /locus_tag="JFY30_RS28525"
                     /old_locus_tag="JFY30_28525"
     CDS             complement(484..714)
                     /locus_tag="JFY30_RS28525"
                     /old_locus_tag="JFY30_28525"
                     /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_198789145.1"
                     /translation="MRIKYESRWRLEELKLEICSSIDELINKYDIEYATGINLYMNCED
                     KEFNPVDVINEDGNKIMFVVGNNEKIQKPKK"
                     /name="hypothetical protein"
     gene            complement(721..1260)
                     /locus_tag="JFY30_RS28530"
                     /old_locus_tag="JFY30_28530"
     CDS             complement(721..1260)
                     /locus_tag="JFY30_RS28530"
                     /old_locus_tag="JFY30_28530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000893324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000893325.1"
                     /translation="MLEQQFEDFEQQKRRDHQVQDQSKNAKQKRDRLNPPDWSQVTKAG
                     WNMLDAISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNNTKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFESSLKYSNHDSEQG"
                     /name="replication/maintenance protein RepL"
     gene            1669..1932
                     /locus_tag="JFY30_RS28535"
                     /old_locus_tag="JFY30_28535"
     CDS             1669..1932
                     /locus_tag="JFY30_RS28535"
                     /old_locus_tag="JFY30_28535"
                     /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_158004283.1"
                     /translation="MSDRARALRHSPPGQGFTPTPRISAYVLNVTSGSLPLPRPLAHSR
                     SVAGAAASGTTSRMLSAILLLFCSKMRSVSHPEHQNAIFWCR"
                     /name="hypothetical protein"
     Typing          complement(1637..1718)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
ORIGIN
        1 ttctatcgca tcgcagaaac ggtgtcgaga tgaaattatg cccggatgat gtttgtctgg
       61 ttgtgtcgcg tggtcacaaa catccagggt tgttttgtgc gactttttcc ggcaaattca
      121 agcttgttat gtgttctctc cagcacgtaa caggtcaatg atgttcgaag ttagtcctat
      181 gataattatc tcgctattcc tcttgcgtcc cctgaaatac atcaggggat ttttttgcgc
      241 cttctgcatc gaaagaaaaa caggaatctc attatgacgc tccctccatt cagggatttt
      301 ttatgtagcg tttactacat gcagctcgtt gatgagtcgt tcaaaaccaa tgcgatgcag
      361 gatagacaat ccactagaaa ttgcatgcaa tgttctgtgg attgtccacc tgccgctggc
      421 tcaatggtca tttttttcga tatttatcta gctcaattac aggtgctgga gtttttttct
      481 ttgctatttt tttggctttt gtattttttc attgttgcca acgacaaaca ttattttatt
      541 tccatcttca ttgataacat caacaggatt aaattcttta tcttcgcaat tcatataaag
      601 atttattcct gttgcatatt caatatcata tttattaatt aactcatcta ttgaactgca
      661 tatttctaat tttagttctt ctaatctcca acgtgattca tatttaattc tcatagtgca
      721 tcacccctgc tctgagtcat gattagagta ctttaaggaa ctttcaaact cttcacgtct
      781 agaaagcata agccgcaatt tacgatctat aaccccatct ttttgagtta atgtttttgc
      841 gttaaatgct gcatattttt tagtattgtt atatccacgc catacctgat aaggatctaa
      901 tgcataggca taatatatac ctactggtat tttaactatt gcgccaatac tttctaaatc
      961 tccaatccaa tattggatcg ttcttaaact aacaccgaaa taatcagcta agaatttttg
     1021 atcacataca acagccccac atgatttatc tatattctgg gcaaaaaaag aatataaccg
     1081 aaatgctcta ggaacttttt ctgatatagc gtccaacata ttccaaccag ccttagtaac
     1141 ctgcgaccag tctggaggat tcaaccgatc tcgtttttgc ttagcgttct tggattgatc
     1201 ttgtacctga tgatctcgcc gtttttgctg ttcaaagtct tcaaattgct gttccaacat
     1261 acttgcatcc ttacctgcaa tgatatttcg taccttacga aatttatatc gtacagtacg
     1321 aaacaacaca tgcaaacatg tttgcgtata cacatgcaaa taacgtttcg tatgatggtg
     1381 tcttaagcta atgattttta tagaaatgtc gatttttgct ctaaagatct atcaaagcgt
     1441 ttttttactg ctcatgattt aacactacct aactgctttt ggggtgtcgg ggcgaagccc
     1501 tgacccagtc acgtagcgat agcggagtgt atactggctt actcctctgc aagcctcgtc
     1561 aaccgtgatt tttgtccgat ttcgtgctct ccacgttcaa cagctccatc atgtttttgc
     1621 cgtccgttca ccgttaaaac gcctcagaaa tcgggacagg atgtgggaat gtcggaccgc
     1681 gcacgcgcac tcagacattc cccacctggt cagggcttca ccccgacacc ccgcatcagt
     1741 gcgtacgtgc tcaatgtaac ttccggttct cttccgcttc ctcgcccact cgctcactcg
     1801 cgttcggtcg ctggggctgc ggcgagcggt accacctctc gcatgttgtc ggcgattctg
     1861 ttgctgttct gttcgaaaat gcgttctgta agccatccag agcaccagaa cgcgattttc
     1921 tggtgtcggt aatgattggg tgcgtatcgg cccttaaaac gcgctcagaa gctctcagac
     1981 gcacgaaacg ggttttaaat gcccgtcagg gcatggaagg cgcgaaaaac gcttacagag
     2041 cgtttcagga ggtcaggcgc gccgataccc ctaaccaggg gctttcaggt cgccaggaac
     2101 cgcgtcagcc ccctgcaaag cccaatttgc acggcatagg cagctattcg gttggttggt
     2161 ggtcgtagac cgtcggtgtt acagcgatgg gggtctgggg ttctccccag acggtttccg
     2221 gttgcgctca aggcgctgcc ggaaccgtga aggaataggg gaaattgtag attgttcgac
     2281 acggggattt ttttaatgtg cggagtaaaa ctcagcgaat cgcgcgcatt tccggcgctt
     2341 gctgctaacg caaaccatcc ccacggtcag ttggttgccg gaaatgcgcc ttgatg
//
