LOCUS       NZ_CP075648             3064 bp    DNA     circular CON 27-JUN-2023
DEFINITION  Escherichia coli strain S19-141 plasmid pS19_141-h, complete
            sequence.
ACCESSION   NZ_CP075648
VERSION     NZ_CP075648.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993351
            Assembly: GCF_016404325.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3064)
  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  JOURNAL   Unpublished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 3064)
  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 3064)
  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                     :: S19-141_NP
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 80.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiniSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/27/2023 06:11:28
            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)                     :: 5,151
            CDSs (total)                      :: 5,035
            Genes (coding)                    :: 4,825
            CDSs (with protein)               :: 4,825
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 210
            CDSs (without protein)            :: 210
            Pseudo Genes (ambiguous residues) :: 0 of 210
            Pseudo Genes (frameshifted)       :: 90 of 210
            Pseudo Genes (incomplete)         :: 109 of 210
            Pseudo Genes (internal stop)      :: 63 of 210
            Pseudo Genes (multiple problems)  :: 49 of 210
            Pseudo Genes (short protein)      :: 5 of 210
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075648.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3064
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S19-141"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS19_141-h"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2019"
                     /collected_by="ILS/NENT"
     gene            complement(947..1066)
                     /locus_tag="JFX59_RS25965"
     CDS             complement(947..1066)
                     /locus_tag="JFX59_RS25965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005104653.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001529707.1"
                     /translation="MPTDARQGMEGAKNAYRAFQEVRRADTPNQGLSGRQELR"
                     /name="hypothetical protein"
     gene            1112..1291
                     /locus_tag="JFX59_RS25625"
                     /old_locus_tag="JFX59_025625"
     CDS             1112..1291
                     /locus_tag="JFX59_RS25625"
                     /old_locus_tag="JFX59_025625"
                     /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_086219049.1"
                     /translation="MGYHYRHQKIAFWCSVGLVKRIFEQNHNGLADNMREDVPLAAAPA
                     TERSERVGEEAEES"
                     /name="hypothetical protein"
     gene            1491..2069
                     /locus_tag="JFX59_RS25630"
                     /old_locus_tag="JFX59_025630"
     CDS             1491..2069
                     /locus_tag="JFX59_RS25630"
                     /old_locus_tag="JFX59_025630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001279566.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /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_001279566.1"
                     /translation="MSDGRYKTNPFIPDMIIPIKDKQVRLSVLGREQNVLVNQATGEIH
                     GTHVTTYKRVDGEQFVKLFTANIALTFDLSAQGIKAFNVLMWAMQNKSLAKDEVYLDTH
                     TREDFLAAHNDTDKPIKLSQPTFARGLAELTKAQIIAKTVRQGVYWINPNFAFNGDRIA
                     FTTLIERKRKNENETNAIQDGANAANETY"
                     /name="replication/maintenance protein RepL"
     gene            complement(2182..2634)
                     /locus_tag="JFX59_RS25635"
                     /old_locus_tag="JFX59_025635"
     CDS             complement(2182..2634)
                     /locus_tag="JFX59_RS25635"
                     /old_locus_tag="JFX59_025635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000640392.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000640392.1"
                     /translation="MIYRLATPEDYEYIPEINLWELSFDKRPVRGVRCEDPVIGSQIYN
                     ETRQKFISHKQTEKRRKQKFFRLKNISWDGIFDWCLSKGTPEECDLIIQLYYAKDKDEH
                     YSILNKLKKHEGFFHESDLYLWICIFFISGNKIASCDKLNLVKTRH"
                     /name="hypothetical protein"
ORIGIN
        1 cacgttagct gatcttgtcg ggataacccg ccactggctc agacaaacta ctaggctacg
       61 ccttaccatt tctggctttc agggggccga gattccaaag cacctccctt actcataatt
      121 tgccttcagc accatagcca gacacttaag tcatggctgg ttatcactta cccgaatgcg
      181 acctcttcgg acgcaattac aggcttgagc tttacagcga tctgcaaagg ttgcccctca
      241 cagtaccgac gtttccaggt ttcccctcaa cgtcctgaca cctcacgatg ccctcagcag
      301 cccacctgtc gggaatatgt tgtaccctct caagcacccc atattcggga ttttcacccg
      361 ttcaagatca acagggatca cgtagtcacc tacgttcccg tttccgtgtc gcccagcctc
      421 acgcttctgc gcggattggg tcggacgggg gagtttcacc cccgaacgcc cgtcgtagcc
      481 gtaccagccc aattacaggc atacggcttc ggcagtcgct gttaacgaag ttggcagttt
      541 cgttaactcc cccttactgg caataagggg tttcagtttc agctatagac tcaaacaaaa
      601 cacctcacag attggcagtc tgcaaagtac gttctgtcat gttacaggtg caaatgcctg
      661 gagccttaag gccgcaccaa ccaggcaaaa gcgagcataa aacaaccact caaggcctta
      721 caaccccgaa aaatggaatc tctttttaac gtgcccccat ttagagcatc tgcttataca
      781 gcggttacta catcatcgga tgccgccacg gttccggctg cgccttgagc gcaaccggaa
      841 accgtctggg gagaacccca gacccccatc gctgcaatat cgacggtcta cgaccaccta
      901 ccagtcatgt ggctgcctgt tccgtgcaaa tgagctttgc agggggctag cgcagttcct
      961 ggcgacctga aagcccctgg ttaggggtat cggcgcgcct gacctcctga aacgctctgt
     1021 aagcgttttt cgcgccttcc atgccctgac gggcatctgt tggcatttta gcgcctcaga
     1081 gagcctctga gcgcgcttta agggctaagg cgtgggatac cattaccggc accagaaaat
     1141 cgcgttctgg tgctctgtag gcctcgtaaa acgcattttc gaacagaatc acaacggact
     1201 tgccgacaac atgcgagagg atgtaccgct cgccgcagcc ccagcgaccg aacgtagtga
     1261 gcgagtgggc gaggaagcgg aagagagcta atgcgaaaat gagcacttac gcaccaccgt
     1321 ataagaacta agaagggaat ttctcgtaac ccgcatgaaa tggggatcca attttcagat
     1381 cgtgttagac ggtctatcag acgtccgcag acggtctatc aaaatttcag ttgattttga
     1441 tagaccgggt atctaagatt gaaagaggtc tatcaaaatg agtgcttttt atgagcgacg
     1501 gtcgatacaa aacgaaccca tttataccag acatgatcat tccgataaaa gataaacaag
     1561 ttcggttgtc tgttttagga agagagcaaa atgtactggt caatcaggct actggtgaga
     1621 tccacggaac gcacgtaaca acatataaac gggttgatgg tgagcagttt gtaaaactat
     1681 tcacggcaaa tatagcatta acctttgatt tatcagcaca aggtataaag gcgtttaatg
     1741 ttttgatgtg ggcaatgcaa aataaatctt tggcaaagga tgaagtttat ttagacactc
     1801 acacgagaga agattttcta gccgctcaca acgatacaga taaaccaatt aagttaagtc
     1861 aaccgacatt tgcgagagga ttagctgaac ttacgaaggc tcaaattatc gctaaaaccg
     1921 tacgacaagg tgtgtattgg ataaatccta actttgcttt caatggtgac agaatagcat
     1981 ttacaactct cattgaacga aagagaaaaa atgagaacga aaccaatgcg atacaggatg
     2041 gagcaaacgc cgcaaatgaa acctattagt aagatataaa aatagaatca aaaaactcac
     2101 gagagtgaac atctcagtca tcatttttgg acatattgat accctcggcg ttctttagat
     2161 ggtggagggt gtcaatatat gttaatgtct tgtttttact aggtttaatt tatcgcagga
     2221 tgcgatttta ttcccactta taaagaaaat acatatccat aaatataagt ctgactcatg
     2281 gaaaaaacct tcgtgttttt tcaacttatt taagattgag taatgttcgt ctttatcttt
     2341 tgcgtaatat aactgaatta tcaaatcaca ttcttctggt gttccttttg ataaacacca
     2401 gtcgaagatg ccatcccatg atatattttt taacctgaaa aatttctgtt ttcttctttt
     2461 ttctgtttgt ttatgagaaa tgaatttttg tctggtctcg ttgtatattt gtgagccaat
     2521 cacaggatct tcacagcgta cccctctaac aggtctttta tcaaaagaaa gctcccataa
     2581 attaatttca ggtatatatt cataatcttc tggagttgcc agtcggtata tcacttttca
     2641 tcccctcata ggaaacagct ctcattcgag agctgtttat cattggtaat gccagtacca
     2701 tatttatgat cacgacaaac gtgatgagta ttcatatctg gtaaatacca gagagtgcgt
     2761 tttttgtgaa tatgtacttt cacatcaatt agttatggta acaatcaaga tagtgtctac
     2821 gttctttgtt tgagtcctct gtctggtatc agcagacaga atacgctgaa caggctaaaa
     2881 aattgcctac cttgctgact gctgtgaact ttcagctact tatctgtacc ggatgccgcc
     2941 agtatgctca gattcaccca cagacttcgg ctatatcgtc tgtagatttt tgcgcctact
     3001 cgtccactct cccacactca ggaatgtaat ttcggtgcca cccgaaattt tccagagtgc
     3061 ttcc
//
