LOCUS       NZ_CP075709             3904 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain STEC2018-607 plasmid pSTEC2018_607-l.
ACCESSION   NZ_CP075709
VERSION     NZ_CP075709.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993387
            Assembly: GCF_016403625.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3904)
  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  JOURNAL   Unpublished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 3904)
  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 3904)
  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                     :: STEC2018-607
            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 06:12:10
            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)                     :: 5,666
            CDSs (total)                      :: 5,550
            Genes (coding)                    :: 5,293
            CDSs (with protein)               :: 5,293
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 257
            CDSs (without protein)            :: 257
            Pseudo Genes (ambiguous residues) :: 0 of 257
            Pseudo Genes (frameshifted)       :: 100 of 257
            Pseudo Genes (incomplete)         :: 139 of 257
            Pseudo Genes (internal stop)      :: 55 of 257
            Pseudo Genes (multiple problems)  :: 37 of 257
            Pseudo Genes (short protein)      :: 4 of 257
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075709.1.
            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..3904
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="STEC2018-607"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_607-l"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            <1..1002
                     /locus_tag="JFX52_RS27985"
                     /old_locus_tag="JFX52_27985"
     CDS             <1..1002
                     /locus_tag="JFX52_RS27985"
                     /old_locus_tag="JFX52_27985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271372.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_215771241.1"
                     /translation="YFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQPHAQFWL
                     VFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKALKYAAA
                     VERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASERRSIDK
                     HYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSPAECRAI
                     GRSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKSAAVRWT
                     ANDDKRRRALDMYILGASTEDIAEAVGVSRWTVRRWMDSSVEWLLSKQIIKI"
                     /name="replication initiation protein"
     gene            complement(1263..1709)
                     /locus_tag="JFX52_RS27990"
                     /old_locus_tag="JFX52_27990"
     CDS             complement(1263..1709)
                     /locus_tag="JFX52_RS27990"
                     /old_locus_tag="JFX52_27990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_000184723.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWERRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            1881..3431
                     /locus_tag="JFX52_RS27995"
                     /old_locus_tag="JFX52_27995"
     CDS             1881..3431
                     /locus_tag="JFX52_RS27995"
                     /old_locus_tag="JFX52_27995"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_147659182.1"
                     /translation="MASYHCTVKTGAKGSALKHADYISRTGEYENYKSREDLEFSSSGN
                     MPSWAKKNPSELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKLPERGGAKKARF
                     GETQQERKSALVELRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRSAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNERDQDMER"
                     /name="MobA/MobL family protein"
     Typing          2..758
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.098"
                     /coverage="81.0"
                     /evalue="0.0"
     Typing          1882..3428
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.541"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tacttcgaag aaaatttacc ccaccgcccc tatcacacgg atgatctcgc tttcggcctt
       61 cgcatctccg gcaaagggcg tgcgcttctt gcgcggtaca tccagcagaa ccagcctcat
      121 gcgcagttct ggctggtttt tgacgttgac cgcgaggggg ctgcgattga ctggagcgac
      181 cggaacgccc ccgcgccgaa catcaccgtt aaaaatcctg tgaacggaca cgctcacctg
      241 ctctacgcac tcaacatcgc cgtgagaacc gcgcctgatg cctcggttaa ggcgctgaaa
      301 tatgccgcag cggttgaacg ttcgctgtgt gagaaacttt gtgctgatgt gaactacagc
      361 ggcctgattt gcaaaaatcc gttccacctg gaatggcagg tgatggagtg gcgcgaggac
      421 gcctataccc tcgatgaact ggcagattat ctcgatttga gcgcctcaga gcgtcgtagc
      481 atcgataaac attacgggat ggggcgaaac tgccacctgt tcgaaatgac gcgcaaatgg
      541 gcttacaggg cgattcgtca gggctggcct gcattctcac aatggcttga tgccgtgatc
      601 cagcgtgtcg aaatgtacaa cgcatcactt cccgttccgc tttctccggc tgaatgtcgg
      661 gctattggca ggagcattgc gaaatacacg cacaggaact tcacgccgga aactttcgca
      721 cagtatgtgg ctgatacgca cacgccagaa attcaggcag cacgcggtcg caagggcggg
      781 aaggccaatt cgtcagaaaa tcagtcggac aaagggaaaa aaagcgccgc tgttcggtgg
      841 actgctaacg atgacaagcg tcgtagggcg cttgatatgt acatcttggg agcctcaaca
      901 gaagatattg cagaggcggt tggtgttagc cgttggactg ttcgacgctg gatggatagc
      961 tctgtagaat ggctactgag taaacaaata attaaaattt aattaacaag aatggcacat
     1021 acccccccct attttgttaa aattctgtta attttgggtg catgaacaag cctatatcag
     1081 ataacagcgc ctttcggcgt ctttttgagc agcgggcttt ccggcggttt tctcctttca
     1141 gcccagcaat ggtgcggctt accgcatgat tgaggtggtt gtgctcgccg cagtctcatg
     1201 accgagcgta gcgagcgaat gagcgaggaa gcaccaggga accggaacgt gaacggaggc
     1261 tcttacgcac tgtctttggt tagtagctcc ttcccgcgtc tttcccattc ctgccatttt
     1321 ggatggttgc gtggtagctc tgctattcct gcgagtgcgc ctaccagttc ggcagcacta
     1381 aactttggtt ttccggtttt gctgtccacc agtcctgcca caatcatgag gcctgcggcc
     1441 ttgtagagtt catgatcccg cgcctttcgt tctgcccttg cggctgcctt ccgttctgcc
     1501 gctatgattg ccgttaccct ggcttttgct gcggctgctt tctctgcggt tttttctgcc
     1561 cgtatcagtg cggacaacgt tttttcatcc gtcgttgttc ggtttttttt ctctgccagt
     1621 aacacaagta atctctgctg ctctgacggt gatttcagtc cgttgatgta ggcaattttt
     1681 gcacttaacc actcttcacg atttgtcatt cttacctctg aacttttgcc gttaatgtga
     1741 gttgttattg tgcataatat caccttgtct gcctgcgtgt gagaccgtaa aatcatccct
     1801 gattaattca gggatgcgca cttagacgtt tctctccttc gtcgagaaac tgtgcgctcc
     1861 tgcggagggc taaaaggcag atggctagtt accattgcac cgttaaaact ggtgcaaaag
     1921 gcagtgcctt aaaacatgct gattacattt ccagaaccgg cgaatacgag aactataaat
     1981 cgcgggagga tctggagttt tcgtcatccg gtaacatgcc atcatgggcg aagaaaaatc
     2041 cctccgagct atggaaagcc gcagatgaat ttgaacgaaa aaacgggacg gcataccgtg
     2101 aaattgagat cgcgttaccg cgtgaactga cacgcgaaca acggatagaa cttgttgaag
     2161 attttgtgca aaaggaactt ggcgatcgcc atgcctacca gtacgcgatc cacaatccgc
     2221 caggtgcaat tgacggaaag gaacaaccac acgcgcatat catgttttgc gagcggatta
     2281 atgatggtat tgaacgcgat ccgcagcagt tttttaaacg tgctaacagc aaattaccgg
     2341 agagaggagg cgcaaaaaag gcacgctttg gtgaaacaca acaagagcga aaatctgccc
     2401 ttgttgaatt acgttcccgc tgggcggatg tgcagaatga gcaccttgcg cgtcacggtc
     2461 acgagtcgcg cgtagatcat cgttcgctga aagaacaggg tatcaatcgc acgccggaag
     2521 ttcatcttgg ccccgttcag gccgccagtc tgaatggtga gcagattgtt gcaatccagg
     2581 aacggaggag tgctgagcgg gaactcaaga ccgccagaga tgccgcaaat gccattcagc
     2641 aggaacagga gcaaaagcaa aaaatcaagg cagttgagcc tgttcgttca gcccgttcac
     2701 cggagttatt gcttcagtac cgcaaggtta tgaaaacggt cattcaggga gaagcaaggc
     2761 ttgctcgttt aggggatgcc aatcccaatg cgctcaaaga acataagctg cttcagaatg
     2821 cgaaagcaaa aaaagactct ctttccgaat ggagcaggcg aatatatgaa ggagcacggt
     2881 atttagacaa actggggcgt aatgtcgttt ccgcacaaag ggagctgcgg gagctacagg
     2941 aacaacgcaa tgctttgaat gggattcgtg gcctgtttcg gggggctgac aaaagggaga
     3001 ttgatgcgcg tattctggag caaaaaagtg tgctggaaac cgctgaacat gaaaggaatg
     3061 aattcaggaa caagctacag caagctgaat ccgagtggga caaagaaaac gctgctttta
     3121 agcgtaccga gggatataag tacgttgggg atctggacag gtacagagaa cgtgagattc
     3181 tggccgcggc atctttagag aataccaggc aaaaggttgc tgaagaagta tccgttgccc
     3241 gtagccagat gttatctctg gagcctgaac tcagtatatc tggagatgaa aaagctcaaa
     3301 tgcgacatga gttactggca gaaatggcgc aggaacggca gcaacaggag gaaaaggcac
     3361 tgcgtataca gcgatcctgg gccagggagg catcacgtag taacgaacgt gatcaagata
     3421 tggagcgttg aaaatgtagc aatatcggga ctgcgccccg aaccccgcca acgtttcacg
     3481 gaacgcgaaa aaattccgcg tcccgttcac cgttttctga tgagaaagtt tgctgttttg
     3541 acccgttcgc ccttctgaac gctcgaaaca gatcgcgcat tgctttcgtg aatagttatg
     3601 cagcctccta aaaacaattc tgacgcgttt ttctggttcc tcctggtgtt tccttgtgtt
     3661 tttgcgtttt ttgcgtcaga aagcgtctga gagcgtttta aggggtgcac acaacgggag
     3721 ttatggtaaa tggatcggtt ttgcgggaag gctcgacagg ttttgttgtt gggggtagtg
     3781 taagcgactg aaaaacaaac gcccctgaaa ttcgtgtctc tccgccaaga ttgtcacgag
     3841 aatacagggg cgaggtcggt cgataacctg gaaggaatcg taacacatga gcgccgcgct
     3901 tcaa
//
