LOCUS       NZ_CP110400             6015 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD06357 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP110400
VERSION     NZ_CP110400.1
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 6015)
  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  JOURNAL   Unpublished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 6015)
  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
            CP110400.1.
            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..6015
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="S17BD06357"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-09-14"
     gene            10..153
                     /locus_tag="OKF40_RS24605"
     CDS             10..153
                     /locus_tag="OKF40_RS24605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001419703.1"
                     /translation="MKKITGIILLLLAAIILAACQANYIRDVQGGTVSPSSSAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     gene            651..1586
                     /locus_tag="OKF40_RS24610"
     CDS             651..1586
                     /locus_tag="OKF40_RS24610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_001271369.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDLNAPAPNITIKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSTSA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTAETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(1780..2178)
                     /locus_tag="OKF40_RS24615"
     CDS             complement(1780..2178)
                     /locus_tag="OKF40_RS24615"
                     /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="hypothetical protein"
                     /protein_id="WP_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            2354..3280
                     /locus_tag="OKF40_RS24620"
     CDS             2354..3280
                     /locus_tag="OKF40_RS24620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_001314449.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            3283..3816
                     /locus_tag="OKF40_RS24625"
     CDS             3283..3816
                     /locus_tag="OKF40_RS24625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021546188.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQRLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFSVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            4037..5674
                     /locus_tag="OKF40_RS24630"
     CDS             4037..5674
                     /locus_tag="OKF40_RS24630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WP_039063724.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRLQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     gene            5684..5941
                     /locus_tag="OKF40_RS24635"
     CDS             5684..5941
                     /locus_tag="OKF40_RS24635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891189.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cloacin immunity family protein"
                     /protein_id="WP_001419702.1"
                     /translation="MGLKLHIHWFDKKNEEFKGGEYSKDFGDDGSVIERLGMPLKDNIN
                     NGWFDVEKRWVPILQPYFKNVIDISKFDYFVSFDYRDGDW"
                     /name="cloacin immunity family protein"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          652..1586
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2355..3277
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gggaatcgta tgaagaaaat aacagggatt attttgttgc ttcttgcagc cattattctt
       61 gctgcatgtc aggcaaacta tatccgtgat gttcagggcg ggactgtatc accgtcatcc
      121 tctgctgaac tgaccggagt ggaaacgcag taacctgcaa tcctcatttg acaaggacaa
      181 agcgtgtcag gctgattctg acgcgctttt tttgttgaag tgccacaaaa attccatgtg
      241 ggagatggga tctaaaatct ccgtgcagaa ccttccatcc ggagggagaa aacttttcgt
      301 tttgagccgt tcggtgttca gaacgcacga aaccgatcgc acatcgcttt cgtgcatagt
      361 tatgcaacgc cctgaaaacg attctgacgc gtttttctgg tttgtcctgg tgttttcttg
      421 tctttttgcg ttttttgcgc cagaaagcga ttgagggcgt tttaaggggt acgtacaacg
      481 ggagttatgg taaatggatc gggttttcgg gaaggatcga caggatttgc cgttgggtgt
      541 agtgtaagcg actgaaaaac aaacgcccct gaaattcgtg tctctccgcc aagattgtca
      601 cgagaataca ggggcgaggt cggtcgataa cctggaagga atcgtaacac atgagcgccg
      661 cgcttcaata cttcgaagaa aatttacccc tccgccccta tcacacggat gatctcgctt
      721 tcggccttcg tatctccggt aaagggcgcg cgcttcttgc acggtatatc cagcagaacc
      781 aacctcatgc gcagttctgg ctggtttttg acgttgaccg cgagggggct gcgattgact
      841 ggagcgacct gaacgccccc gcaccgaaca tcaccataaa aaatcccgtg aacggtcacg
      901 cccacctgct ctacgcactc aatatcgccg tgagaaccgc gcctgatgct tcggttaagg
      961 cgctgaaata cgccgccgcg attgaacgtg cgttgtgtga aaaactgggc gcagatgtaa
     1021 actacagcgg actgatttgc aaaaatccgt tccatctgga atggcaggtg atggagtggc
     1081 gtgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc acttcagcgc
     1141 gccgtagcat cgataaacat tacggaatgg ggagaaactg ccatctgttc gaaatgacgc
     1201 gcaaatgggc ttacagggcg attcgtcagg gctggccagc attctcacag tggcttgatg
     1261 ccgtgattca gcgtgtcgaa atgtacaacg catcgcttcc cgttccgctt tcacctcctg
     1321 aatgtcgggc tattggcaag agtattgcga aatacacgca caggaacttc acggcggaaa
     1381 ctttcgcaca gtatgtggct gatacgcaca cgccagaaat acaggccaag agaggcagga
     1441 aaggtggcat cgctaaaggc gaagcctacg atgacaagcg tttcatggcg ctatgtatgc
     1501 tggagaatgg atattctcag aaagctattg cggcgatgtt ggaggtttct actcgaacca
     1561 ttcgaaactg gaaaagcgga aaatagccta tatcagataa cagcgccttt ctggcgtttt
     1621 tttgagcctt aggtcttttg ccgtttttcc ccgttcagcc ctgcaatggt gctgttttcc
     1681 gcatgattgt gctggtagtg ctcgccgcag tctcatgacc gagcgtagcg agcgaatgag
     1741 cgaggaagca ccagggaaca ggaacacgga tggaggcact tacgcgtctg ggtttgggga
     1801 tgtctccaga tcgtacttaa tttccttaag tgcctgtaat atcctgtctt ttttatagca
     1861 tagctcgcct gtttttgtgt ctaccagtcc tgcttcgatc agtagcccag ccgcgagaaa
     1921 gagtcggtga ttgcgttctc gtcgttgttt ttttccctcg attcgttttt ggaccgcctg
     1981 ttttcgttcg ctctcctgtg cctgtaagtc gtttttttcc gctgttgcca gtacgtggag
     2041 gagtttgcgt tcctgttctg tgagtcctgc ttcgttgtcg agcaggtcaa taatctgtct
     2101 ctgtcgtgcg gtctgttctc cgagcttcct gatgaatccg atccgtttct tcagccattc
     2161 gatgttgctg atgcgcatgt tcgtggtgct ccctggtgtt ttttgctgtg tgttgtggtc
     2221 gtgcagtata tcgcttgcgg tcggtgggtg cagggggtat cttccgtgct aattcgtaaa
     2281 attagaagga agcgcactta tatgtttctc tccttcgtcg agaaacagtg cgctcctgcg
     2341 gagggctgaa accgtggcaa cctatcacct cagcgttaaa tttggtggca aggggcaggc
     2401 tgcaaaccac gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aggatttgga
     2461 atattccgca cacggaaaca tgccggaatg ggcgcgagat aatccctcac atttctggca
     2521 ggcggctgac cagtttgaac gtgcgaacgg ttcgacctat cgggaacttg aaattgcatt
     2581 accccgtgaa ctgacagcgg aacagcgcct tgaactggtg caggattttg tacgtcagga
     2641 agctggcgaa cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg
     2701 cggcgaacag cctcatgcgc atatcatgat gagccagcgt gtgaatgatg gcattgaacg
     2761 tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa
     2821 aaaggattcc ggaagcctga ctctcactca gcaaaaagag cagttgcggg aattgcgaaa
     2881 acgctgggag gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat
     2941 tgactgccgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt
     3001 tgaagctgcc ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga
     3061 accggactat tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcagggaatg
     3121 gctggacact ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg
     3181 ggagcatggc tttgacatga gagacagagt gagcagacag aaccgaactg aacctgaacg
     3241 ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa
     3301 aaattactca cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag
     3361 aaagctgttg ctgattctct ggctgtggca agggaaacac ttcgcggata tcgggatatt
     3421 tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa acgaagtgca gaggctggat
     3481 gttgcagggc tgataggtga gcgcatcagt caggattttc agcggctgga agagtcagtc
     3541 gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat
     3601 atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca
     3661 gtggcctttc tggttatgtt cagtgtgctc ggatggggga tgaaaacaat tctcgacagg
     3721 aactacaacg ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggtg
     3781 gagaaacctg tcacgggtaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc
     3841 acgacccgcg aaaggatttc gcgttccgtt caccgttttc atgagtgatt cctccgaact
     3901 gccaaaaaat atccccccct gacttgacag aaaaaataat ggcgagtact ttttggtctg
     3961 tacataaaac cagtggtttt atgtacagta tcaactatat aatcaattgt tttaacgctt
     4021 aaaagaggga atttttatga gcggtggaga tggacgcgac cacaacagtg gcgcacataa
     4081 cacaggtggt aacattaatg gcggccctac ggggcttggt ggaaatggtg gggcttctga
     4141 cggttcagga tggagttcgg aaaataaccc atggggtggc ggttccggta gtggtgttca
     4201 ctggggaggt ggctccggca atggtaatgg cggggggaat ggtaattccg gtggtggcag
     4261 caattcatcc gtagcagcag tggcatttgg ttttcctgct ttggcaactc ctggtgccgg
     4321 aacgctgggt atcgccgtct ctggtgaggc tttatctgcg gcaatagcgg atatctttgc
     4381 agccctgaaa ggcccgttta aattcagcgc atggggtatt gcgctttacg gcattctgcc
     4441 atctgaaata gcaaaagatg acccgaatat gatgtcaaag attgtgacgt cattaccggc
     4501 agaaacagtg acgaatgttc aggtcagtac acttccgctg gaccaggcaa ctgtcagcgt
     4561 gacgaaacgt gtgacagatg ttgtgaagga cacacgacag catattgccg tagttgcagg
     4621 tgtgcctatg agtgtgcctg ttgtgaatgc caaaccaaca cgtactccag gtgtatttca
     4681 cgcatcattt cctggtgtcc cttctctgac agtcagcact gtcaaaggcc ttccggtgtc
     4741 aacaaccctt ccccgtggta ttacggagga taaaggccgg actgccgttc ctgcgggatt
     4801 tacctttggt ggtggttcac atgaagcggt gattcgcttt ccgaaagaaa gtgggcagaa
     4861 gccggtttat gtatcagtga cagatgttct taccccagca caggtaaaac aacgtcagga
     4921 tgaggaaaaa cgcctccagc aggaatggaa tgacgcacat ccggtggaag tggctgaacg
     4981 caattatgaa caggcccgcg cagaactgaa tcaggctaat aaagatgttg ccagaaacca
     5041 ggaacgacag gctaaagctg ttcaggttta taattctcgt aaaagtgaac ttgatgcagc
     5101 gaataaaact cttgctgatg caaaggctga aataaaacaa ttcgagcgat ttgcccgaga
     5161 accaatggct gctggtcaca gaatgtggca aatggcaggg cttaaggccc agcgggcaca
     5221 gacggatgta aataataaga aggctgcatt tgatgctgcc gcaaaagaga agtcagcagc
     5281 agatgctgca ttgagttctg cgatggaaag caggaagaag aaagaagata agaaaaggag
     5341 tgctgaaaat aaattaaacg aagagaaaaa taaacgccga aaaggcacta aagattatgg
     5401 ccatgattat catccagctc ctaaaactga ggatattaaa ggtttggggg aattaaaaga
     5461 ggggaggcca aaaactccaa agcaaggtgg tggaggtaag cgtgccagat ggtatggaga
     5521 taaggggcgt aaaatttatg agtgggactc tcagcatggt gagcttgagg gctatcgagc
     5581 cagtgatggt cagcatcttg gttcatttga ccctaaaacc ggtaagcagt tgaaaggtcc
     5641 agatccgaaa cgaagtatta aaaagtatct ttaaggtgat gttatgggac ttaaattaca
     5701 cattcattgg tttgataaga agaatgagga atttaaaggt ggtgagtatt caaaggattt
     5761 cggtgatgat ggttcggtta ttgaacgtct tggaatgcct ttaaaggata atattaataa
     5821 cggttggttt gatgttgaaa agagatgggt gccaatatta cagccatact ttaaaaatgt
     5881 tattgatatt agtaagttcg attactttgt ttctttcgat tatcgtgatg gtgactggta
     5941 attaaactat cagggacgag taataaagtg tttgattcag gtgttcaagg atgaattcct
     6001 gaatccatat ataca
//
