LOCUS       NZ_CP075638             1548 bp    DNA     linear   CON 27-JUN-2023
DEFINITION  Escherichia coli strain 2018-166 plasmid pSTEC2018_166-g.
ACCESSION   NZ_CP075638
VERSION     NZ_CP075638.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993346
            Assembly: GCF_016404485.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1548)
  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  JOURNAL   Unpublished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 1548)
  AUTHORS   Nusch-Inderbinnen,M., Stevens,M.J.A., Cernela,N., Muller,A.,
            Biggel,M. and Stephan,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAY-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich, Zurich 8057,
            Switzerland
REFERENCE   3  (bases 1 to 1548)
  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; SPAdes v. 3.15.2
            Assembly Name                     :: 2018-166_NP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:22:39
            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)                     :: 5,465
            CDSs (total)                      :: 5,343
            Genes (coding)                    :: 5,049
            CDSs (with protein)               :: 5,049
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 294
            CDSs (without protein)            :: 294
            Pseudo Genes (ambiguous residues) :: 0 of 294
            Pseudo Genes (frameshifted)       :: 133 of 294
            Pseudo Genes (incomplete)         :: 162 of 294
            Pseudo Genes (internal stop)      :: 52 of 294
            Pseudo Genes (multiple problems)  :: 50 of 294
            Pseudo Genes (short protein)      :: 4 of 294
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075638.1.
            Bacteria and source DNA available from ILS.
            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..1548
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="2018-166"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSTEC2018_166-g"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2018"
                     /collected_by="ILS/NENT"
     gene            <1..477
                     /locus_tag="JFX80_RS27055"
                     /old_locus_tag="JFX80_27075"
     CDS             <1..477
                     /locus_tag="JFX80_RS27055"
                     /old_locus_tag="JFX80_27075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /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_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            525..815
                     /locus_tag="JFX80_RS27060"
                     /old_locus_tag="JFX80_27080"
     CDS             525..815
                     /locus_tag="JFX80_RS27060"
                     /old_locus_tag="JFX80_27080"
                     /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_157911427.1"
                     /translation="MIVYPALLFCRLKILCVFLLPVLQKKPSRHGSGSALSATGNRLGR
                     TPDPHRCNTDGLRQPTNRMAACSVQMGFAGGWRGSWRPESPWLGVSARLTS"
                     /name="hypothetical protein"
     gene            892..1050
                     /locus_tag="JFX80_RS27065"
                     /old_locus_tag="JFX80_27085"
     CDS             892..1050
                     /locus_tag="JFX80_RS27065"
                     /old_locus_tag="JFX80_27085"
                     /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_158003786.1"
                     /translation="MSAFEGLSGDSSPKEQQRDHRQHARGDPARRKSMTERSERIDEEA
                     EENRKPH"
                     /name="hypothetical protein"
     Typing          1069..1167
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(1363..1471)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          complement(709..969)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.13"
                     /coverage="100.0"
                     /evalue="1.84e-104"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaaaaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcgtt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagct
      481 agcggcaggc ggacaatcag gggctacgtg ctaacgttct gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccttt gcgtgttttt gctccccgtt ctccagaaaa
      601 aaccgagccg ccacggttcc ggcagcgcct tgagcgctac cggaaaccgt ctggggagaa
      661 ccccagaccc ccatcgctgc aacaccgacg gtctacgaca acctaccaac cgcatggctg
      721 cctgttccgt gcaaatgggc tttgcagggg gctggcgcgg ttcctggcga cctgaaagcc
      781 cctggttagg ggtatcggcg cgcctgacct cctgagagcc tctgtaagcg tttttcgcgc
      841 cttccatgcc ctggcgggca tctaaaaccc gtttcgtgcg tctgagagct tgtgagcgcg
      901 tttgaggggc tatctggcga ctcatccccg aaagaacaac aacgggatca ccgacaacat
      961 gcgagaggtg atcccgctcg ccgcaagtcg atgaccgagc gtagcgagcg aatcgacgag
     1021 gaagcggaag agaaccggaa gccacattga gcacttacgc actgatgcgg ggtgtcgggg
     1081 tgaagccctg accaggtggt aatcgtatcg gcgtgcgtgc gcggttatac gattacacat
     1141 cctgtcccga tttctgaggc gttttaacgg tgaacggacg gcaaaaacac gatggagctg
     1201 ttgaacgtga aaaccacgaa atctggcaaa aatcacggct ggcgaggctt gcagaggagt
     1261 aagccagtat acactccgct atcgctaggt gactgggtca gggcttcgcc ccgacacccc
     1321 caaagggcgt tgcgttgcac gcaacaccct tgcctagaat agatctttta cgccgatttg
     1381 taagttgttg tttttttagt gtgtttttta tttacctgtc gcatccaggg tgacacaacg
     1441 ttgtcgcatc ctggatgcga caacacgcaa caaggtgttg cacagatgtg tcatgatggc
     1501 ttagatttga accaacgtta gtgcatggga ttttcagagg gaaaaatc
//
