LOCUS       NZ_CP075862             2255 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Escherichia coli strain S19-651 plasmid pS19_651-j, complete
            sequence.
ACCESSION   NZ_CP075862
VERSION     NZ_CP075862.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16993361
            Assembly: GCF_016404165.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2255)
  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  JOURNAL   Unpublished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 2255)
  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 2255)
  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
            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                   :: 07/21/2023 04:43:18
            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)                     :: 5,346
            CDSs (total)                      :: 5,228
            Genes (coding)                    :: 4,987
            CDSs (with protein)               :: 4,987
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 241
            CDSs (without protein)            :: 241
            Pseudo Genes (ambiguous residues) :: 0 of 241
            Pseudo Genes (frameshifted)       :: 99 of 241
            Pseudo Genes (incomplete)         :: 130 of 241
            Pseudo Genes (internal stop)      :: 53 of 241
            Pseudo Genes (multiple problems)  :: 41 of 241
            Pseudo Genes (short protein)      :: 4 of 241
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP075862.1.
            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..2255
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="S19-651"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pS19_651-j"
                     /geo_loc_name="Switzerland: Zurich"
                     /lat_lon="47.40 N 8.55 E"
                     /collection_date="2019"
                     /collected_by="ILS/NENT"
     gene            join(1895..2255,1..143)
                     /gene="ddp1"
                     /locus_tag="JFY28_RS26540"
                     /old_locus_tag="JFY28_026540"
     CDS             join(1895..2255,1..143)
                     /gene="ddp1"
                     /locus_tag="JFY28_RS26540"
                     /old_locus_tag="JFY28_026540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_000809479.1"
                     /translation="MKQIKFRLTDEEYNVAHINAISNGVNSVNAFAKRKVLDISATPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAALHGMSVSREIAIRLRKSVLKSEVCLYPEEVQ
                     VLRKLSTTINRIGRNIHFIISGDRFCTVNDPDFRNEIRELTALCETVDKTIEQLVFSVN
                     NRFG"
                     /name="ddp1"
     gene            918..1433
                     /locus_tag="JFY28_RS26545"
                     /old_locus_tag="JFY28_026545"
     CDS             918..1433
                     /locus_tag="JFY28_RS26545"
                     /old_locus_tag="JFY28_026545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000097059.1"
                     /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_000097059.1"
                     /translation="MSSLSLQRYETNPFLELMTIPMKGKRIQVSRLGRDDNVLVNQNTG
                     EKFGTHVTTFKRVDSEQFVKLFTANIGLTFDLSSAGIKAFNVLLWAVQKQAFAKDQVLL
                     DSRALDDFLKSYDSLKLSYATLKRGINELEKAQIIAKTMRKGFYFINPNFVFNGDRIAF
                     TTLIERDC"
                     /name="replication/maintenance protein RepL"
     gene            1508..1792
                     /locus_tag="JFY28_RS26550"
                     /old_locus_tag="JFY28_026550"
     CDS             1508..1792
                     /locus_tag="JFY28_RS26550"
                     /old_locus_tag="JFY28_026550"
                     /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_000160398.1"
                     /translation="MTKHDAIRISQLHQIFYDDEGLIDSEKNVTILYSIGFTIDEIAYF
                     GNTTPGTVQGQLFNARAKLSCASASSLRPMILLRLLSLIIFEQDRLNRL"
                     /name="hypothetical protein"
     Typing          complement(389..649)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.893"
                     /coverage="100.0"
                     /evalue="8.5e-108"
ORIGIN
        1 attttataat tagtggcgat cgtttttgca cagttaacga tcctgatttc agaaatgaga
       61 taagggaact tacagcatta tgcgaaacag tcgataaaac aatagagcaa ttagttttta
      121 gtgttaataa tcgttttggg taaaaacgta ttatcaagaa ccgactgtag gtcatgggca
      181 aacgttgcag aattgcgtca gagacgtcat tttgcggcgt ttgccctatc ctgcatcggg
      241 gttaaaccac gaagattttt attccccgtt cttcggaacg accgaagccg ccacggttcc
      301 gattgcgcct tgagcgcaac cggaaaccga ctggggagaa ccccagaccc ccatcgcggc
      361 aacaccgacg gtctacggcc acctaccaac cgcgtggctg cctgttccgt gcaaatgggc
      421 tttgcagggg gctgacgcgg ttcctggcga cctgaaagcc cctggttagg ggtatcggcg
      481 cgcctgacct cctgaaaccc tctgtaagcg tttttcgcgc cttccatgcc ctgacgggca
      541 tttaaacccc gtctcgtgcg tctgagagct tctgagcgcg tttcaggggc tatctgacga
      601 ctcatccccg aaagaataac aacgggatca ccgacaacat gcgagaggtg acaccgctcg
      661 ccgcagcccc agcgaccgaa cgtagtgagc gagtgggcga ggaagcggaa gagaaccaga
      721 agccatattg agcacttacg ctcgtagtta agaactaaga agggaatttc ttgaaacccg
      781 catgaatcct agaaagtggt gatcaggatc tgtaccttgt aagctcagat ccggtacctt
      841 gcaggctcaa aaaatcattg attttgagct tatgaggatt tattgtgaat ctccaaagcc
      901 caaaaaagga tgcaataatg agctcactaa gcttgcagag atacgaaacg aacccatttt
      961 tagagcttat gacaatcccg atgaagggga aacggataca agtatctcgt cttggacgtg
     1021 atgacaacgt tttggttaat caaaacacgg gagaaaagtt tgggacgcat gtaaccactt
     1081 ttaagcgtgt ggatagtgag caatttgtta aattgtttac tgcgaatatt gggctaacat
     1141 ttgatttatc atcggcagga attaaagctt ttaatgtcct gttatgggct gttcaaaaac
     1201 aggcttttgc aaaagatcag gttcttttag attccagagc tcttgatgac tttttgaaaa
     1261 gctatgatag cttaaaacta agttacgcta cgttaaagcg agggatcaat gagttagaaa
     1321 aagctcagat tatagcaaag acaatgcgaa aaggatttta tttcataaat cctaactttg
     1381 tatttaatgg cgatagaata gcgtttacaa ctctgatcga gagggattgt taatataatc
     1441 gtcgcagtcg aacaaaactc cacttttgtt cgactgctaa tcacaacaac ctattaggga
     1501 ggttattatg actaagcatg atgctatacg catttctcaa cttcatcaaa tcttttacga
     1561 tgacgaggga ttaattgatt cagaaaagaa cgtgaccatt ttatacagca taggatttac
     1621 tattgatgaa atagcttatt ttgggaatac aacaccggga acagttcagg gacagttatt
     1681 taatgcaaga gctaaattaa gttgtgcttc agcttcatct ttaagaccga tgattttgtt
     1741 gagattgctt tcactcataa tctttgagca agaccgctta aataggctgt aatcaatgca
     1801 ggatagacaa tcatggtcaa atgggtacca ttttccatga ttgtccaaaa acggggtttt
     1861 tgcctgtgcc tgccgcaggc tcttaggagg ttctatgaag caaattaaat tcagattgac
     1921 cgacgaggaa tacaacgttg ctcatattaa tgctatttca aatggcgtta atagtgtaaa
     1981 tgcttttgca aagaggaagg ttttagatat tagcgcaaca ccttcaaagg ttatcgtatc
     2041 gaatgaacca tctgtaccag taaaaacatg tttataccca catgaactgg agttaataaa
     2101 gcgtaatgct gcattacacg ggatgagtgt tagccgagaa atagcaatac gcttacgtaa
     2161 atcagtgttg aaaagcgaag tttgtcttta tcccgaagaa gtgcaggtgc tcagaaagct
     2221 ttcaacaacg attaatagaa ttggtcgaaa tattc
//
