LOCUS       NZ_CP075679             1448 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-n.
ACCESSION   NZ_CP075679
VERSION     NZ_CP075679.1
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 1448)
  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  JOURNAL   Unpublished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 1448)
  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 1448)
  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
            CP075679.1.
            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..1448
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-n"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            83..227
                     /locus_tag="JFY30_RS28975"
                     /pseudo=""
     CDS             83..227
                     /locus_tag="JFY30_RS28975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318239.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            818..1117
                     /locus_tag="JFY30_RS28590"
                     /old_locus_tag="JFY30_28590"
     CDS             818..1117
                     /locus_tag="JFY30_RS28590"
                     /old_locus_tag="JFY30_28590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529699.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042969137.1"
                     /translation="MREISQRDLYQVLGAGNTDPNTQLLKDLANNMAWGAALGAKGGLG
                     TAAVGAGGAAVQTVVQGLINHGPVSVPVPVLIGPSWNGSGSGYNSATSSANGGS"
                     /name="hypothetical protein"
     Typing          complement(3..187)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.774"
                     /coverage="98.0"
                     /evalue="2.18e-82"
ORIGIN
        1 gcgggacacg tggcgctttc tcatagctca cgtcttctgg tatctcgggg cgacttaggc
       61 agttcgctcc gggccgggct gtatgcagga accccccgtt cagcccgact gctgcgcctt
      121 ctccggtaac tgttctctta ggtccaaccc ggaaaagaca cgacttaacg ccactggcag
      181 cagccattgg taaccgggtt agcagagcga gatttataag ttggtaacag agttcttgaa
      241 gtatcagtct gattttgact acactagaag gaccatttag gtacctgtgc tccactaaag
      301 ccagttacca ccgccgatta gaagaggtcg aagacttctg atcggacgga agaacccgcc
      361 acaaggcggg ttttttcgtt tacaggcagc agattacgca tagaaaaaaa ggatctcaag
      421 agctcctttg atctttttcc aaatagcccc gtcctccccc tcctaaaaaa gcgatagata
      481 agaacaaaaa ttcggttaat aatcatacta atgcatctgt tttggatatt aaggataata
      541 cgcatgacat tactttcatt tgcattttcc cctgttttct tgtcagtcat ggcgttctgt
      601 attattttgc gcagccgctc atatccccaa aaaacacaca acagagttat cgtgttgata
      661 ttaatgtctt ttttcatttg ttttttatat ccattaacaa aggtgtactt aactggaagt
      721 tacaatatat ttgacaattt ctacctcttt tgttttttgt cttcattagt agcaattgca
      781 ataaacatag gaatacttac agttatagga gtaaagaatg agagagatta gtcaaagaga
      841 cttatatcag gttcttggcg caggcaacac cgacccaaat actcaactgc taaaagatct
      901 tgctaataac atggcatggg gtgcagcttt aggtgcaaaa ggagggcttg gcacggcagc
      961 tgtgggtgct ggtggagcag cggtacaaac agtagtacaa ggactaatta accatggacc
     1021 tgtaagtgtc cctgtccccg tactcattgg accaagctgg aatggtagtg gtagtggtta
     1081 taacagcgca acatctagcg ccaatggtgg cagttaatct tatttggagc tccaaaccgt
     1141 aatgcctttg acaacaaaaa gttggcgctc agcggtctgg tacgtaagag cgctgttaac
     1201 ctaacagcaa agaaattgca gcttaaaacc ggaagaaggg acggaaccct gggaagggat
     1261 ttaccataat cccttattgt acgcaccgct gaaatgcgtt cagcgcgatc acggctgctg
     1321 acaggtaaaa atggcaacaa accacccgaa aagctgccgc gatcgcacct gataaatttt
     1381 aaccgtatgc atagctattc agccatgtga ataacgctgg ttttgtctgc gtaaacctca
     1441 tgacactg
//
