LOCUS       NZ_CP110401             5114 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD06357 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP110401
VERSION     NZ_CP110401.1
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 5114)
  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  JOURNAL   Unpublished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 5114)
  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
            CP110401.1.
            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..5114
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="S17BD06357"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-09-14"
     gene            233..1168
                     /locus_tag="OKF40_RS24640"
     CDS             233..1168
                     /locus_tag="OKF40_RS24640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_024235833.1"
                     /translation="MSAALQYFEENLPHRPYHTDELAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNAPAPNITVKNPENGHAHLLYALNLAVRTAPDASVKA
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYALDELADYLDLRASE
                     RRSVDKHYGLGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPESFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(1362..1808)
                     /locus_tag="OKF40_RS24645"
     CDS             complement(1362..1808)
                     /locus_tag="OKF40_RS24645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_024235834.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     gene            1980..3530
                     /locus_tag="OKF40_RS24650"
     CDS             1980..3530
                     /locus_tag="OKF40_RS24650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_039063720.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGELDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALCIQRSWARGVSRSNERDQDMER"
                     /name="MobA/MobL family protein"
     gene            complement(3726..4826)
                     /locus_tag="OKF40_RS24655"
     CDS             complement(3726..4826)
                     /locus_tag="OKF40_RS24655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001569522.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024235836.1"
                     /translation="MNINFKHILPLLSSFFISGCDSDGISKVKSFVYYDIDDSMTVGKA
                     FDTRSDCINGTWSEKEDDRGRTIVTYTCDISESGLKIINSAIMQEPEDKAEYSIAQNNN
                     SIKSTNESLEEYKQKTPLVEKTKEVIIDHIRKLNSAFNEDPMIYSKLTISPYLDRMLYL
                     KDHNDNALNEICGGYEYIQSADSYSWRDVSEEYAKESCEKHIYKVYQSFKKNASPLITK
                     NFPGFYERVPPCENADECIKKTNIYFDDNFLNIYKRSQDRAPQIISDLKKHNIEIGEKL
                     NDCRKKLNISDVKLTYYWFVTDTGGVDYLDGVLTYNFQGKNRAENFHKQLLQYAYINYS
                     KNQIPRDFVTSIKNSIYYKIEDCTKF"
                     /name="hypothetical protein"
     Typing          234..1168
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1981..3527
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtctttttg cgttttttgc gacagaaagc gactgagggc gttttaaggg gggcgcacaa
       61 cgggagttat ggtaaatgga tcgggtttgc gggaagactc gacaggtttt gtcgttgggg
      121 gtagtgtaag cgactgaaaa acaaacgccc ctgaaattcg tgtctatccg gcaagacttt
      181 cacgaagata caggggcgat gtcggtcgat aacctggaag gaatcgtaac acatgagcgc
      241 cgcgcttcaa tacttcgaag aaaatttacc tcaccgtccc tatcacacgg atgagctcgc
      301 tttcggtctt cgtatctccg gcaaagggcg tgcgctgctt gctcgctaca tccagcaaaa
      361 tcagcctcat gcgcagttct ggctggtttt tgacgttgac cgcgtaggag ctgcgattga
      421 ctggagcgac cggaacgccc ccgcgccgaa catcaccgta aaaaatcccg agaacgggca
      481 cgctcacctg ctctacgcgc tcaatcttgc cgtgagaacc gcgcctgatg cgtcggttaa
      541 ggcgctgaaa tacgccgctg caattgaacg tgcgctgtgt gagaaacttg acgcagatgt
      601 gaactacagc ggactgattt gcaaaaatcc gttccacctg gaatggcagg tgatggagtg
      661 gcgcgaggaa gcctacgccc tcgatgaact ggctgattat ctcgatttga gagcctcaga
      721 gcgtcgtagc gtcgataaac attacgggct ggggcgaaac tgccatctgt tcgaaatgac
      781 gcgcaaatgg gcttacaggg cgattcggca gggctggcca gcattctcac agtggcttga
      841 tgctgtgatt cagcgtgtcg aaatgtacaa cgcatcgctt cccgttccgc tttctccgcc
      901 tgaatgtcgg gctattggca agagcattgc gaaatacacg cacaggaact tcacgccgga
      961 aagtttcgca cagtatgtgg ctgatacgca cacaccagaa atacaggcca agagaggccg
     1021 gaaaggtggc atcgctaaag gcgaagccta cgatgacaag cgtttcatgg cgctatgtat
     1081 gctggagaat ggatattctc agaaagctat tgcggcgatg ctgaatgtac atcgtaatac
     1141 gatccgtaat tgggcaatgc acaaatagcc tatatcagat aacagcgcct tttcggcgtc
     1201 tttttgagca gcgggctttc cggcggtttt ctcctttcag cccagcaatg gtgcggctta
     1261 ccgtatgatt gaggtggtcg tgctcgccgc agtctcatga ccgagcgtag cgagcgaatg
     1321 agcgaggaag caccagggaa ctggaacgtg aacggaggct cttacgcact gtctttggtg
     1381 agtagctctt tcccgcgttt ttcccattcc tgccattttg gatggttgtg cggtagctct
     1441 gcgattcctg cgagtgcgcc taccagttcg gcagcactaa actttggctt tccggttttg
     1501 ctgtccacca gtcctgccac aatcatgagg cctgcggcct tgtagagttc atgatcccgc
     1561 gcctttcgtt ccgcccttgc ggctgccttc cgttctgccg ctatgattgc cgttactctg
     1621 gcttttgctg cggctgcttt ctctgcggtt ttttctgccc gtatcagtgc ggacaacgtt
     1681 ttttcatccg tcgttgttcg gttttttttc tctgccagta acacaagtaa tctctgctgc
     1741 tctgatggtg atttcagtcc gttgatgtag gcaatttttg cacttaacca ctcttcacga
     1801 tttgtcattc ttacctctgc acttttgccg ttaatgtgag ttgttattat gcataatatc
     1861 accttgtttg cctgcgtgtg agaccgtaaa atcatccatg attaattcag ggatgcgcac
     1921 ttagtagttt ctctccttcg tcgagaaact gtgcgctcct gcggagggct aaaaggcaga
     1981 tggcaagcta ccattgcact gtcaaagctg gagcaaaagg cagtgcctta aaacatgctg
     2041 attacatttc cagatccggc gaatataaga gttacaaatc gcgggaggat ctggaatttt
     2101 cgtcatccgg taacatgcca tcatgggcga agaaaaatcc cgcagagcta tggaaagccg
     2161 cagatgaatt tgaacgaaaa aacgggactg cataccgtga aattgagatc gcgttaccgc
     2221 gtgaactgac acgcgaacaa cggatagaac ttgttgaaga tttcgtgcaa aaggaacttg
     2281 gcgatcgcca tgcctaccag tacgcgatcc acaatccgcc aggtgcaatc gacggaaagg
     2341 aacagccaca cgcgcatatc atgttttgcg agcggattaa tgatggtatt gaacgcgatc
     2401 cacagcaatt ttttaaacgt gccaacagca aatcaccaga gcggggaggc gcaaaaaaag
     2461 cgagtattcc ccagacagcc ggagagcgaa aagccgccct tgttgcgctg cgttcccgct
     2521 gggcagatgt gcagaatgag caccttgcgc gacacggtca cgagtcgcgc gtagatcatc
     2581 gttctctgaa agaacagggt atcaatcgca cgccggaagt tcatcttggc cccgttcagg
     2641 ccgccagtct gaatggggag cagattgttg caatccagga acggaggaat gccgagcggg
     2701 aactcaagac cgccagagat gccgcaaatg ccattcagca ggaacaggag caaaagcaaa
     2761 aaatcaaggc agttgagcct gttcgttcag cccgttcacc ggagttattg cttcagtacc
     2821 gcaaggttat gaaaacggtc attcagggag aggcaaggct tgctcgttta ggggatgcca
     2881 atcccaatgc gctcaaagaa cataagctgc ttcagaatgc gaaagctaaa aaagactctc
     2941 tttccgaatg gagtagacga atatatgaag gggcacggta tttagacaaa ctggggcgta
     3001 atgttgtttc cgcacaaagg gagctgcggg agctacagga acaacgcaat gctttgaatg
     3061 ggattcgtgg cctgtttcgg ggggctgaca aaagggagat tgatgcgcgt attctggagc
     3121 aaaaaagtgt gctggaaacc gctgaacatg aaaggaatga attcaggaac aagctacagc
     3181 aagccgaatc cgagtgggac aaagaaaacg ctgcttttaa gcgtaccgag ggatataagt
     3241 acgttgggga gctggacagg tacagagaac gcgagattct ggcggcggca tctttagaga
     3301 acaccaggca aaaggttgct gaagaggtat ccgttgcccg tagccagatg ttatctctgg
     3361 agcctgaact cagtatatct ggagatgaaa aagctcaaat gcgacatgag ttactggcag
     3421 aaatggcgca ggaacggcag caacaggagg aaaaagcact gtgtatacag cgatcctggg
     3481 ccaggggggt atcacgtagt aacgaacgtg atcaagatat ggagcgttga aaatgtagca
     3541 atatcgggac tgcgccccga accccgccaa cgtttcacgg aacgcgaaaa aattccgcgt
     3601 cccgtgaaac gttttctgaa tgagaaaaat tgtcgttttg atttactcac agttcagatt
     3661 aatgaagtta acaggtgtta aatatttgca ggtggttata tgtgtaacca cctgtaaggg
     3721 aaggactaaa acttagtgca atcttctatt ttataataaa tactattttt tattgatgtt
     3781 acaaagtccc gaggtatttg atttttgctg tagttaatgt atgcatattg caatagttgt
     3841 ttatgaaagt tttcagctct attctttccc tgaaaattat atgtcaacac cccatctaaa
     3901 taatcaactc ctccggtatc tgttacaaac cagtaatagg ttaatttgac atctgagata
     3961 tttagttttt tcctacaatc atttaacttt tcacctattt ctatattgtg tttttttaaa
     4021 tcagaaatta tttgaggtgc tctatcttgg cttcttttgt agatatttag aaagttatca
     4081 tcaaagtata tatttgtttt ttttatgcat tcatctgcgt tctcacaggg ggggacacgt
     4141 tcgtagaaac cggggaagtt tttagttatt aatggtgatg catttttctt aaacgattga
     4201 tatactttat atatatgctt ttcgcatgat tcttttgcat actcttcact tacatcacgc
     4261 caactgtaac tatcggcaga ttgaatgtat tcgtacccac cacaaatttc atttagcgca
     4321 ttgtcattat ggtcctttag atatagcatt ctgtctaaat aagggctaat tgtgagtttg
     4381 ctatatatca ttggatcttc attaaaagca ctgtttagct ttcttatatg atctattatg
     4441 acctcttttg ttttttccac cagaggcgtt ttctgtttgt attcctctag tgattcattg
     4501 gttgatttta tgctgttgtt attttgtgct atagaatatt cagccttatc ttcaggttct
     4561 tgcataatgg ctgaatttat tatttttagg ccactttcac taatatcaca ggtatatgtg
     4621 acgatggttc ttcctcgatc atcctctttt tcactccatg tgccattgat gcaatcactc
     4681 cttgtatcga aggctttacc aacagtcatt gagtcgtcaa tgtcgtaata tacgaaagac
     4741 tttaccttgc ttattccatc agagtcgcat cctgaaataa aaaatgacga caataaagga
     4801 aggatatgtt taaagttaat attcattttt cccattttta tttctaacaa taacgaggaa
     4861 atattaatac aggcgatatg ttaatggaat ccatacatac cgataaaccg acttactatg
     4921 tttgtgctca acgtcttacg cagttcgaaa agatttcgca ccagttcacc tttttctgga
     4981 tgagaaagtt tgctgttttg acctgttcgc tgttcaaaac gagtgaaacc ggacatgaat
     5041 cgctttcgtg catagttatg cagccccctg aaaacaattc tggcgcgttt ttttggtctg
     5101 gcctgttgtt tccc
//
