LOCUS       NZ_CP110408             2690 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD05200 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP110408
VERSION     NZ_CP110408.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP110408.1.
            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="S17BD05200"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-08-15"
     gene            join(2677..2690,1..610)
                     /locus_tag="OKF41_RS24530"
     CDS             join(2677..2690,1..610)
                     /locus_tag="OKF41_RS24530"
                     /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(836..1159)
                     /gene="mobA"
                     /locus_tag="OKF41_RS24535"
     CDS             complement(836..1159)
                     /gene="mobA"
                     /locus_tag="OKF41_RS24535"
                     /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            1445..1639
                     /locus_tag="OKF41_RS24540"
     CDS             1445..1639
                     /locus_tag="OKF41_RS24540"
                     /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            2137..2298
                     /locus_tag="OKF41_RS24545"
     CDS             2137..2298
                     /locus_tag="OKF41_RS24545"
                     /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          complement(1169..1407)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          1683..2209
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(840..1159)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 tcatcgtcgt ttattccaga aagacggaat aggattgagc caaacaggaa aagcaacaca
       61 acttgtcatt atgtcgcatg gtggatggaa agagatctcc catccacaaa cactattcac
      121 gcgtcaaaaa ggcgatggat ggactgtagt ccccaaaaac ctaagaattg atttttatac
      181 aaaagacaac gacttcacaa agggactaag cgttctttca gaggtaaaca aacgccatac
      241 tgaagctcaa aaagggttaa caccatcact aaacataagc aaagatgacc taaaagttct
      301 agcgaacgcg cgcaatatac ctcaatcaaa attagaagaa gaaatgatgt cacaagccat
      361 atatagaaaa gaatacgcaa caagtaatga gaagataaaa aactatgctc tatattacca
      421 tgaacaagcc caaaatatta tacaaagaca tcaagatggc ttaggaaaca aaaatattga
      481 tatagcattt ataactgata aaaatcataa gaagcacctt tctgacatat ttaaagtaat
      541 aaatgaatca ggagtaaaat atgatgtaat tcactttggc gcttgccgag taaatagaga
      601 ggagaaataa tcatcattta ccataatccc ttaattgtac gcaccactga aacgcgctga
      661 acgcgattct gacgcagaca ccacaaaaat agatgtttta ccccggaaaa acaggaagga
      721 tgcgtcagga tcgttttcag ctcgctgcat agctatgcat gaaagcgaat ggagatcact
      781 ttgggagctt accgtgttca taccgtctgt tttcaacagt tttctccccg ggaagctaat
      841 ctgccataag cctggataac agggcacggt gatactccgt aatagcgatc agcacctccg
      901 catactccct gtccccgata cgcttgccgt cgataaagag ttttttctgt aacgccccca
      961 gtctcataac ttctttcagc acccgatcat cagtcagtga gttaacgttc ttaccgagag
     1021 ctgccgcccg taaaaaacca gaaacggtct tgccgcattc agcagccctt tttctgattt
     1081 cctggtcttc ttctgccgtc agacgaacag ggcgactgat agcccgcctg cgcgtattac
     1141 ttccacttcg ttttgtcata aaacatggct ccgtatctga cacggggtgt cggggcgaag
     1201 ccctgaccag ggtaattgta atagcgtgca tgtatgcgcg gtataacaat tacacatcct
     1261 gtcctgtcag caagttcgaa ttaccgacaa aggcacggca gtttttttgg cagtgacagt
     1321 attgtcaggc agaaataccc gtcaatgcgt cagacggcag aataccggcg gtaaaacagt
     1381 cgaaaagtgg tacgcgatat aatcacacaa cgcagatgac agacagaacg gagaaaacag
     1441 aaagatgaac aagcagcagc aaaccgtact caacatggcg ggattcataa aaagccagag
     1501 cctgacgctg ctcgaaaagc tggacgcact cgatgccgac gaacaggccg ccatgtgtga
     1561 gaagctgcac gaaatcgcgg aagaactcca gaacagcata cagacacgct ttgaagcgga
     1621 aagtggcacc ggggtataac agtgtatcct gctccagaca ggatgcagaa cggtataccg
     1681 gtgcgtaagg agaaaatgtc acataaggcg ctcttccgct tcctcgctca ctgactcgct
     1741 acgctcggtc gttcgactgc ggcgagcggt gtcagctcac tcaaaggcgg taatgcggtt
     1801 atccacagaa tcaggggata acgccggaaa gaacatgtga gcaaaaagcc gaaggcaggg
     1861 acaaaggccg cgcaggtggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
     1921 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     1981 ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgtttac cggatacctg
     2041 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg ttggtatctc
     2101 ggcccggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
     2161 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgaatta
     2221 tcgccactgg cagcagccac tgataaccga attagaggag taagacttga agtcatgcgc
     2281 ctgttaaggc taaactgaaa gaacaagttt tggtgactgc gctcctccaa gccagttacc
     2341 tcggctcaaa gagttggtag ctctgagaac cttcgaaaaa ccgccttgca gggcggtttt
     2401 ttcgtttaca ggcagcagat tacgcgcaga aaaaaaggat ctcaagaaga acctttaatt
     2461 ttttttcaca cttggtatcc tactttaacc cataaaataa acacttacac cgacacaccc
     2521 ttaaacaaaa gaaaaaaaac aataaaaaac accgcaaaaa tggattgtta acaaatgaaa
     2581 atactcaatt cgaatctcat aacaaacata tcatcaacaa taagaaatca ccttctaaca
     2641 tcatccaaaa atataaaaac acacccatca ccaaacatgg acgtaacaag
//
