LOCUS       NZ_CP110403             2089 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD06357 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP110403
VERSION     NZ_CP110403.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28885482
            Assembly: GCF_026016165.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2089)
  AUTHORS   Berbers,B., Vanneste,K., Roosens,N.H.C.J., Marchal,K.,
            Ceyssens,P.-J. and De Keersmaecker,S.C.J.
  TITLE     Using a combination of short and long read sequencing to investigate
            the diversity in plasmid- and chromosomally encoded
            extended-spectrum-beta-lactamases (ESBL) in clinical Shigella and
            Salmonella isolates in Belgium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2089)
  AUTHORS   Berbers,B., Vanneste,K., Roosens,N.H.C.J., Marchal,K.,
            Ceyssens,P.-J. and De Keersmaecker,S.C.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (31-OCT-2022) Transversal Activities in Applied Genomics,
            Sciensano, Juliette Wytsmanstraat 14, Brussels 1050, Belgium
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Partial
            Expected Final Version            :: Yes
            Genome Coverage                   :: 60x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 17:11:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,952
            CDSs (total)                      :: 4,823
            Genes (coding)                    :: 4,205
            CDSs (with protein)               :: 4,205
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 618
            CDSs (without protein)            :: 618
            Pseudo Genes (ambiguous residues) :: 0 of 618
            Pseudo Genes (frameshifted)       :: 161 of 618
            Pseudo Genes (incomplete)         :: 433 of 618
            Pseudo Genes (internal stop)      :: 108 of 618
            Pseudo Genes (multiple problems)  :: 82 of 618
            Pseudo Genes (short protein)      :: 3 of 618
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110403.1.
            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..2089
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="S17BD06357"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed5"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-09-14"
     gene            join(1169..2089,1..45)
                     /locus_tag="OKF40_RS24680"
     CDS             join(1169..2089,1..45)
                     /locus_tag="OKF40_RS24680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_012421200.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQIAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            49..315
                     /locus_tag="OKF40_RS24685"
     CDS             49..315
                     /locus_tag="OKF40_RS24685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          1563..1794
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 aaacggcgtt acaaacgcgc ccctgagaag gataaatcgg attaacgtat gaatattaat
       61 attgaatacc tgaatggaaa taagactatt ggtttatttt ttttaagaag tgaagcggtg
      121 attcctgaca ggtttaaaaa ccttattttg cttattgatg gattaagttt tggcacattt
      181 ggttttcatc cgcacgaagg ttttgaggat gaattaattt tatatattca gaaaacaaac
      241 gagagggtaa aaactctttt tgtgaaaata gatttaaacg gtatcaagtt tggattttta
      301 agaacgcatt cttagttctg gaaaagagcc agcggcaggc tgaggtgata ggtacgagat
      361 tgcatgcaat ctctagtgct ctgtctatcc tgcattatcc tcagcattat cctcagcctt
      421 gccaactcga caccaatgca ggatagacaa tccgatgtca aatgttaaca ctctgcgagt
      481 ggtacatttt ccccggatta tcgtcctgag cctgccgctg gctctctttc taccgcctcg
      541 ctttgctcgt tgctcaacgc ctcacagaca cggattaaaa tccgcatccg ttcaccgttt
      601 tttaaagtcc gttaaaagca tgatgccatc tccgagagtt aatctcgtca aatgctaaat
      661 cgtgggggtc ccctttgggg ttccgattta gtgattgacg acaccaccga ttaaaaaact
      721 tatgcggggt ggatggtttc acgaagtgag gccatccacc tgtaagacag ggttttgttt
      781 ttattccctg ttttggtgat cgggtgtgtg gaaaaggttg ggctcagccg ttcgggagtg
      841 cttgttttgg ggggttaaaa ttgtggttat tttttgcgca agtctcgcgc gtgatccttg
      901 tatttatact taagggataa atggcggata tgaaatagtg gtttagccca gtaatgacga
      961 ggctttgagt gggttttgac aggtcaaaga aaatggagca gaattgaggc gtttttaatc
     1021 ggcgttgggg agtgcgtcaa cactccccaa catttcgaat gtgtcacctc agcggcaaac
     1081 tctggtgaca tgtactggct cgcaatgcac aggtacgtga tgaatatacc acatcaaatc
     1141 acagcctgcc cagatcggag caggcttaat gtcagaagat aaattccttt cggactacag
     1201 cccccgtgat gcagtttggg atacccagcg cacgcttacc gattctgtcg ggggtatcta
     1261 ccagattgct gctgaattcg agcgctatgc actccgtatg gcctcctgta gcggtttgtt
     1321 acgttttggt tggtctacca tcatggaaac cggagaaacg cgcctacggc ttcgtagtgc
     1381 gcaattttgc cgtgtccgtc attgccctgt ctgccagtgg agaagaaccc tcatgtggca
     1441 agcccgtttt tatcaggctc taccgaaaat cgttgtggat tacccgtctt cccgatggtt
     1501 gtttctgacg ttaactgtca ggaactgcga gataggtgaa cttggaacag tccttacagc
     1561 aatgaatgcg gcgtttaagc gaatggaaaa gcgaaaggag ctatcacctg ttcaggggtg
     1621 gatcagggct acggaggtga cgcgaggtaa ggatggcagc gcacatccgc attttcactg
     1681 tctgctgatg gtgcaacctt cttggtttaa agggaagaac tacgttaagc acgaacgttg
     1741 ggtagaactc tggcgcgatt gcttgcgggt gaactatgag ccgaatatcg atattcgggc
     1801 agtaaaaact aagacaggtg aggttgtggc caacgttgcc gagcaactgc aaagcgcggt
     1861 tgctgaaacg ctgaaatact ccgttaaacc ggaagatatg gcaaacgatc ctgagtggtt
     1921 tcttgagctg acgcggcagc ttcacaagcg ccgttttatc tcgaccggtg gggcgctaaa
     1981 aaacgtcctc cagttggatc gagaaaccaa tgaggatctt gtcattgccg acgatgtagg
     2041 ggatggcact gatgacggga agcggacggc gtttgtctgg gattcaggt
//
