LOCUS       NZ_CP110409             2089 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD05200 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP110409
VERSION     NZ_CP110409.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28885477
            Assembly: GCF_026016185.1
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  JOURNAL   Unpublished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                   :: 30x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/28/2023 18:09:23
            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)                     :: 4,926
            CDSs (total)                      :: 4,801
            Genes (coding)                    :: 4,173
            CDSs (with protein)               :: 4,173
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 628
            CDSs (without protein)            :: 628
            Pseudo Genes (ambiguous residues) :: 0 of 628
            Pseudo Genes (frameshifted)       :: 169 of 628
            Pseudo Genes (incomplete)         :: 438 of 628
            Pseudo Genes (internal stop)      :: 108 of 628
            Pseudo Genes (multiple problems)  :: 85 of 628
            Pseudo Genes (short protein)      :: 3 of 628
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110409.1.
            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="S17BD05200"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed5"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-08-15"
     gene            join(1942..2089,1..818)
                     /locus_tag="OKF41_RS24550"
     CDS             join(1942..2089,1..818)
                     /locus_tag="OKF41_RS24550"
                     /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            822..1088
                     /locus_tag="OKF41_RS24555"
     CDS             822..1088
                     /locus_tag="OKF41_RS24555"
                     /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          247..478
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 tgttacgttt tggttggtct accatcatgg aaaccggaga aacgcgccta cggcttcgta
       61 gtgcgcaatt ttgccgtgtc cgtcattgcc ctgtctgcca gtggagaaga accctcatgt
      121 ggcaagcccg tttttatcag gctctaccga aaatcgttgt ggattacccg tcttcccgat
      181 ggttgtttct gacgttaact gtcaggaact gcgagatagg tgaacttgga acagtcctta
      241 cagcaatgaa tgcggcgttt aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg
      301 ggtggatcag ggctacggag gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc
      361 actgtctgct gatggtgcaa ccttcttggt ttaaagggaa gaactacgtt aagcacgaac
      421 gttgggtaga actctggcgc gattgcttgc gggtgaacta tgagccgaat atcgatattc
      481 gggcagtaaa aactaagaca ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg
      541 cggttgctga aacgctgaaa tactccgtta aaccggaaga tatggcaaac gatcctgagt
      601 ggtttcttga gctgacgcgg cagcttcaca agcgccgttt tatctcgacc ggtggggcgc
      661 taaaaaacgt cctccagttg gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg
      721 taggggatgg cactgatgac gggaagcgga cggcgtttgt ctgggattca ggtaaacggc
      781 gttacaaacg cgcccctgag aaggataaat cggattaacg tatgaatatt aatattgaat
      841 acctgaatgg aaataagact attggtttat tttttttaag aagtgaagcg gtgattcctg
      901 acaggtttaa aaaccttatt ttgcttattg atggattaag ttttggcaca tttggttttc
      961 atccgcacga aggttttgag gatgaattaa ttttatatat tcagaaaaca aacgagaggg
     1021 taaaaactct ttttgtgaaa atagatttaa acggtatcaa gtttggattt ttaagaacgc
     1081 attcttagtt ctggaaaaga gccagcggca ggctgaggtg ataggtacga gattgcatgc
     1141 aatctctagt gctctgtcta tcctgcatta tcctcagcat tatcctcagc cttgccaact
     1201 cgacaccaat gcaggataga caatccgatg tcaaatgtta acactctgcg agtggtacat
     1261 tttccccgga ttatcgtcct gagcctgccg ctggctctct ttctaccgcc tcgctttgct
     1321 cgttgctcaa cgcctcacag acacggatta aaatccgcat ccgttcaccg ttttttaaag
     1381 tccgttaaaa gcatgatgcc atctccgaga gttaatctcg tcaaatgcta aatcgtgggg
     1441 gtcccctttg gggttccgat ttagtgattg acgacaccac cgattaaaaa acttatgcgg
     1501 ggtggatggt ttcacgaagt gaggccatcc acctgtaaga cagggttttg tttttattcc
     1561 ctgttttggt gatcgggtgt gtggaaaagg ttgggctcag ccgttcggga gtgcttgttt
     1621 tggggggtta aaattgtggt tattttttgc gcaagtctcg cgcgtgatcc ttgtatttat
     1681 acttaaggga taaatggcgg atatgaaata gtggtttagc ccagtaatga cgaggctttg
     1741 agtgggtttt gacaggtcaa agaaaatgga gcagaattga ggcgttttta atcggcgttg
     1801 gggagtgcgt caacactccc caacatttcg aatgtgtcac ctcagcggca aactctggtg
     1861 acatgtactg gctcgcaatg cacaggtacg tgatgaatat accacatcaa atcacagcct
     1921 gcccagatcg gagcaggctt aatgtcagaa gataaattcc tttcggacta cagcccccgt
     1981 gatgcagttt gggataccca gcgcacgctt accgattctg tcgggggtat ctaccagatt
     2041 gctgctgaat tcgagcgcta tgcactccgt atggcctcct gtagcggtt
//
