LOCUS       NZ_CP110402             2690 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD06357 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP110402
VERSION     NZ_CP110402.1
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 2690)
  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  JOURNAL   Unpublished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 2690)
  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
            CP110402.1.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="S17BD06357"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-09-14"
     gene            complement(93..287)
                     /locus_tag="OKF40_RS24660"
     CDS             complement(93..287)
                     /locus_tag="OKF40_RS24660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            573..896
                     /gene="mobA"
                     /locus_tag="OKF40_RS24665"
     CDS             573..896
                     /gene="mobA"
                     /locus_tag="OKF40_RS24665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1122..1745)
                     /locus_tag="OKF40_RS24670"
     CDS             complement(1122..1745)
                     /locus_tag="OKF40_RS24670"
                     /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="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(2124..2285)
                     /locus_tag="OKF40_RS24675"
     CDS             complement(2124..2285)
                     /locus_tag="OKF40_RS24675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     Typing          326..564
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(2214..2690)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.417"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          574..893
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 gtgagcgagg aagcggaaga gcgccttatg tgacattttc tccttacgca ccggtatacc
       61 gttctgcatc ctgtctggag caggatacac tgttataccc cggtgccact ttccgcttca
      121 aagcgtgtct gtatgctgtt ctggagttct tccgcgattt cgtgcagctt ctcacacatg
      181 gcggcctgtt cgtcggcatc gagtgcgtcc agcttttcga gcagcgtcag gctctggctt
      241 tttatgaatc ccgccatgtt gagtacggtt tgctgctgct tgttcatctt tctgttttct
      301 ccgttctgtc tgtcatctgc gttgtgtgat tatatcgcgt accacttttc gactgtttta
      361 ccgccggtat tctgccgtct gacgcattga cgggtatttc tgcctgacaa tactgtcact
      421 gccaaaaaaa ctgccgtgcc tttgtcggta attcgaactt gctgacagga caggatgtgt
      481 aattgttata ccgcgcatac atgcacgcta ttacaattac cctggtcagg gcttcgcccc
      541 gacaccccgt gtcagatacg gagccatgtt ttatgacaaa acgaagtgga agtaatacgc
      601 gcaggcgggc tatcagtcgc cctgttcgtc tgacggcaga agaagaccag gaaatcagaa
      661 aaagggctgc tgaatgcggc aagaccgttt ctggtttttt acgggcggca gctctcggta
      721 agaacgttaa ctcactgact gatgatcggg tgctgaaaga agttatgaga ctgggggcgt
      781 tacagaaaaa actctttatc gacggcaagc gtatcgggga cagggagtat gcggaggtgc
      841 tgatcgctat tacggagtat caccgtgccc tgttatccag gcttatggca gattagcttc
      901 ccggggagaa aactgttgaa aacagacggt atgaacacgg taagctccca aagtgatctc
      961 cattcgcttt catgcatagc tatgcagcga gctgaaaacg atcctgacgc atccttcctg
     1021 tttttccggg gtaaaacatc tatttttgtg gtgtctgcgt cagaatcgcg ttcagcgcgt
     1081 ttcagtggtg cgtacaatta agggattatg gtaaatgatg attatttctc ctctctattt
     1141 actcggcaag cgccaaagtg aattacatca tattttactc ctgattcatt tattacttta
     1201 aatatgtcag aaaggtgctt cttatgattt ttatcagtta taaatgctat atcaatattt
     1261 ttgtttccta agccatcttg atgtctttgt ataatatttt gggcttgttc atggtaatat
     1321 agagcatagt tttttatctt ctcattactt gttgcgtatt cttttctata tatggcttgt
     1381 gacatcattt cttcttctaa ttttgattga ggtatattgc gcgcgttcgc tagaactttt
     1441 aggtcatctt tgcttatgtt tagtgatggt gttaaccctt tttgagcttc agtatggcgt
     1501 ttgtttacct ctgaaagaac gcttagtccc tttgtgaagt cgttgtcttt tgtataaaaa
     1561 tcaattctta ggtttttggg gactacagtc catccatcgc ctttttgacg cgtgaatagt
     1621 gtttgtggat gggagatctc tttccatcca ccatgcgaca taatgacaag ttgtgttgct
     1681 tttcctgttt ggctcaatcc tattccgtct ttctggaata aacgacgatg acttgttacg
     1741 tccatgtttg gtgatgggtg tgtttttata tttttggatg atgttagaag gtgatttctt
     1801 attgttgatg atatgtttgt tatgagattc gaattgagta ttttcatttg ttaacaatcc
     1861 atttttgcgg tgttttttat tgtttttttt cttttgttta agggtgtgtc ggtgtaagtg
     1921 tttattttat gggttaaagt aggataccaa gtgtgaaaaa aaattaaagg ttcttcttga
     1981 gatccttttt ttctgcgcgt aatctgctgc ctgtaaacga aaaaaccgcc ctgcaaggcg
     2041 gtttttcgaa ggttctcaga gctaccaact ctttgagccg aggtaactgg cttggaggag
     2101 cgcagtcacc aaaacttgtt ctttcagttt agccttaaca ggcgcatgac ttcaagtctt
     2161 actcctctaa ttcggttatc agtggctgct gccagtggcg ataattcgtg tcttaccggg
     2221 ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     2281 tgcacacagc ccagcttgga gcgaacgacc tacaccgggc cgagatacca acagcgtgag
     2341 ctatgagaaa gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaaacggc
     2401 agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg gtatctttat
     2461 agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg
     2521 gggcggagcc tatggaaaaa cgccacctgc gcggcctttg tccctgcctt cggctttttg
     2581 ctcacatgtt ctttccggcg ttatcccctg attctgtgga taaccgcatt accgcctttg
     2641 agtgagctga caccgctcgc cgcagtcgaa cgaccgagcg tagcgagtca
//
