LOCUS       NZ_CP075675             2225 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-553 plasmid pSTEC2018_553-j.
ACCESSION   NZ_CP075675
VERSION     NZ_CP075675.1
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 2225)
  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  JOURNAL   Unpublished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 2225)
  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 2225)
  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
            CP075675.1.
            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..2225
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-553"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_553-j"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            <1..630
                     /locus_tag="JFY30_RS28540"
                     /old_locus_tag="JFY30_28540"
     CDS             <1..630
                     /locus_tag="JFY30_RS28540"
                     /old_locus_tag="JFY30_28540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001672436.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_252354521.1"
                     /translation="IDALGETLTSMNAGFKRLKERKEFRHVLGWVRTTEVTRGKDGSVH
                     PHFHTLLMVPPSMLSGREYVKHARWVELWRDCLRVAYDPNVDIRVVKSRKPKDDESLPC
                     VVAEQLRGAVVETLKYSTKPADMLADPEWFLELTRQVHKRRFVATGGALKNVLQLERET
                     NEDLIMADGMAEGTDDGSRLAFSWVPIVKKYQRDRAKDKRQLSGED"
                     /name="protein rep"
     gene            1857..>2225
                     /locus_tag="JFY30_RS28545"
                     /old_locus_tag="JFY30_28545"
     CDS             1857..>2225
                     /locus_tag="JFY30_RS28545"
                     /old_locus_tag="JFY30_28545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001362017.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_215744943.1"
                     /translation="MKNPELKNLTDYSPADKPWDEHRSFSDDVGGIYLRAAGFEHYGER
                     VGACSGILRFGWSTNTETGETRLRLRDARFCRVRHCPICQWRRSMMWQARFYQSLPKIV
                     TEHPGARWLFLTLTVRNCS"
                     /name="protein rep"
     Typing          869..961
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.684"
                     /coverage="98.0"
                     /evalue="1.29e-31"
     Typing          1207..1285
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.25"
                     /coverage="80.0"
                     /evalue="8.21e-29"
     Typing          complement(348..539)
                     /name="Col(MP18)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.83e-96"
ORIGIN
        1 attgacgcgc ttggtgagac gcttacctcg atgaatgcgg ggtttaagcg gttgaaagag
       61 cgtaaggaat ttcgccatgt gttgggatgg gttcgtacca cggaagtaac gcgcggcaag
      121 gatggtagcg tacatcccca ttttcacact ctgctgatgg ttcccccttc gatgttgtcc
      181 ggccgtgagt atgtgaaaca tgcccgttgg gtggaactgt ggcgtgattg tctgcgggtg
      241 gcgtatgacc cgaatgtgga tatcagagtg gtgaagtcac ggaaaccaaa agacgatgaa
      301 tctttacctt gtgttgttgc ggaacagctg cgcggcgcgg tggttgaaac tctgaaatat
      361 tccacaaagc ctgctgatat gctggctgat cctgaatggt tcctcgaatt aacacggcag
      421 gtacacaagc gtcgttttgt tgctacgggg ggagcgctta agaacgttct gcaactggag
      481 cgggaaacga acgaggattt aatcatggcg gatggcatgg cagagggtac agatgacggt
      541 tcccgtctgg cgttttcgtg ggtgccgatt gtcaaaaaat accagcgcga tcgggcgaaa
      601 gataaacgtc agctaagtgg cgaggattga gcgcgtttca ggcgcgaact attcatgcac
      661 tgggagaata ttcagaaacg cgctcagaag cgttctaacg tgattttcag aaacgggcaa
      721 ggttttgccc gttttttttg tttctctgcg ctcagaagcg ttttaagcgc gtttccgggt
      781 ctctgctacg gcaatccacg gctgacagct tttcgctcac cagaaacgcg cagatgtcgt
      841 tttaacgtgt cccgggcagg ttgtcgaggg tgtcggggtg cagccctgac caggaggtaa
      901 tcgtatcggc gtgcgtgcgc ggttatacga ttacacatcc tgtcccgatt tctgcgggtt
      961 tgtgtcaccg gaacactggc gcaatgtcgg cagtttttgc gccgcgccgc cctccacgta
     1021 agcgcgcagt tctggcaacc ggacagcaaa tcattctgcc gttttcgtgc cacagctgtt
     1081 ccgcgcgatc gacaaactgg cagtcgggga atctcacgaa gtgcgcactc atacaaacta
     1141 cacttcgttt cgtttgtcgt gcggtctgcg acgctcaaaa aaccgagaaa cggcgggaat
     1201 tttcgggaca ggatgtggga atgtcggacc gcgcacgcgc actcagacat tccccacctg
     1261 gtcagggctg caccccgaca ccccgccaac gcctcacggc acgcgaaaaa attccgcgtc
     1321 ccgctcaccg ttcacgaact cgtcaaacag aaaatcgcgg gggcccctcc ggggttccga
     1381 ttttgtgatt gacgacggca cgggaaaaac actggggatg gtggttggtg tcacggagtg
     1441 agaccaacca cctgcaagac ggtttttgct gttcacaaaa tcggtggaaa agcctgtgtg
     1501 tgttttgtcg ggaaaacgct ttcgcggttg ttgtttttgc cctcggggaa tcgaacaaaa
     1561 aacaggcgat tttgctgcta tcttcgcgcg cgtttccttg tatttatact taagggataa
     1621 atgcgatttt ttggatcgcc tctatccctt gccatatctg gcctgagcgc ggatttgcgt
     1681 gtaaataggt ttgagagtat tttgtcggga gtggttataa attagcccct gcgagtcttc
     1741 caccactcca ggggcgcgac cacctagaac atgaactgat ttgacgacaa ttggtacagg
     1801 tgatacagga atgataacac gcaatttcgt ctgtcgctcg caaggggacg gcagacatga
     1861 aaaatcctga acttaagaat ctgacggatt actctccagc agataaaccg tgggatgaac
     1921 accgaagctt ttccgatgat gtgggcggta tttatctgcg tgctgccgga tttgagcact
     1981 acggcgaacg cgtcggggct tgtagtggta ttttgcggtt tgggtggtca acaaacacag
     2041 agaccggaga aacgcgcctg cggttgcgtg atgcacggtt ctgtcgcgtc cggcactgtc
     2101 cgatctgtca gtggaggcgt tccatgatgt ggcaagcccg tttctatcag tccctgccaa
     2161 agattgtgac ggaacatccc ggcgcgcgct ggttgtttct cacactgaca gtgcgcaact
     2221 gttcc
//
