LOCUS       NZ_CP110406             6015 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD05200 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP110406
VERSION     NZ_CP110406.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP110406.1.
            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="S17BD05200"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-08-15"
     gene            join(4762..6015,1..384)
                     /locus_tag="OKF41_RS24475"
     CDS             join(4762..6015,1..384)
                     /locus_tag="OKF41_RS24475"
                     /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            394..651
                     /locus_tag="OKF41_RS24480"
     CDS             394..651
                     /locus_tag="OKF41_RS24480"
                     /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"
     gene            735..878
                     /locus_tag="OKF41_RS24485"
     CDS             735..878
                     /locus_tag="OKF41_RS24485"
                     /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            1376..2311
                     /locus_tag="OKF41_RS24490"
     CDS             1376..2311
                     /locus_tag="OKF41_RS24490"
                     /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(2505..2903)
                     /locus_tag="OKF41_RS24495"
     CDS             complement(2505..2903)
                     /locus_tag="OKF41_RS24495"
                     /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            3079..4005
                     /locus_tag="OKF41_RS24500"
     CDS             3079..4005
                     /locus_tag="OKF41_RS24500"
                     /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            4008..4541
                     /locus_tag="OKF41_RS24505"
     CDS             4008..4541
                     /locus_tag="OKF41_RS24505"
                     /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"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          1377..2311
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          3080..4002
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgagttctg cgatggaaag caggaagaag aaagaagata agaaaaggag tgctgaaaat
       61 aaattaaacg aagagaaaaa taaacgccga aaaggcacta aagattatgg ccatgattat
      121 catccagctc ctaaaactga ggatattaaa ggtttggggg aattaaaaga ggggaggcca
      181 aaaactccaa agcaaggtgg tggaggtaag cgtgccagat ggtatggaga taaggggcgt
      241 aaaatttatg agtgggactc tcagcatggt gagcttgagg gctatcgagc cagtgatggt
      301 cagcatcttg gttcatttga ccctaaaacc ggtaagcagt tgaaaggtcc agatccgaaa
      361 cgaagtatta aaaagtatct ttaaggtgat gttatgggac ttaaattaca cattcattgg
      421 tttgataaga agaatgagga atttaaaggt ggtgagtatt caaaggattt cggtgatgat
      481 ggttcggtta ttgaacgtct tggaatgcct ttaaaggata atattaataa cggttggttt
      541 gatgttgaaa agagatgggt gccaatatta cagccatact ttaaaaatgt tattgatatt
      601 agtaagttcg attactttgt ttctttcgat tatcgtgatg gtgactggta attaaactat
      661 cagggacgag taataaagtg tttgattcag gtgttcaagg atgaattcct gaatccatat
      721 atacagggaa tcgtatgaag aaaataacag ggattatttt gttgcttctt gcagccatta
      781 ttcttgctgc atgtcaggca aactatatcc gtgatgttca gggcgggact gtatcaccgt
      841 catcctctgc tgaactgacc ggagtggaaa cgcagtaacc tgcaatcctc atttgacaag
      901 gacaaagcgt gtcaggctga ttctgacgcg ctttttttgt tgaagtgcca caaaaattcc
      961 atgtgggaga tgggatctaa aatctccgtg cagaaccttc catccggagg gagaaaactt
     1021 ttcgttttga gccgttcggt gttcagaacg cacgaaaccg atcgcacatc gctttcgtgc
     1081 atagttatgc aacgccctga aaacgattct gacgcgtttt tctggtttgt cctggtgttt
     1141 tcttgtcttt ttgcgttttt tgcgccagaa agcgattgag ggcgttttaa ggggtacgta
     1201 caacgggagt tatggtaaat ggatcgggtt ttcgggaagg atcgacagga tttgccgttg
     1261 ggtgtagtgt aagcgactga aaaacaaacg cccctgaaat tcgtgtctct ccgccaagat
     1321 tgtcacgaga atacaggggc gaggtcggtc gataacctgg aaggaatcgt aacacatgag
     1381 cgccgcgctt caatacttcg aagaaaattt acccctccgc ccctatcaca cggatgatct
     1441 cgctttcggc cttcgtatct ccggtaaagg gcgcgcgctt cttgcacggt atatccagca
     1501 gaaccaacct catgcgcagt tctggctggt ttttgacgtt gaccgcgagg gggctgcgat
     1561 tgactggagc gacctgaacg cccccgcacc gaacatcacc ataaaaaatc ccgtgaacgg
     1621 tcacgcccac ctgctctacg cactcaatat cgccgtgaga accgcgcctg atgcttcggt
     1681 taaggcgctg aaatacgccg ccgcgattga acgtgcgttg tgtgaaaaac tgggcgcaga
     1741 tgtaaactac agcggactga tttgcaaaaa tccgttccat ctggaatggc aggtgatgga
     1801 gtggcgtgag gaagcctata ccctcgatga actggctgat tatctcgatt tgagcacttc
     1861 agcgcgccgt agcatcgata aacattacgg aatggggaga aactgccatc tgttcgaaat
     1921 gacgcgcaaa tgggcttaca gggcgattcg tcagggctgg ccagcattct cacagtggct
     1981 tgatgccgtg attcagcgtg tcgaaatgta caacgcatcg cttcccgttc cgctttcacc
     2041 tcctgaatgt cgggctattg gcaagagtat tgcgaaatac acgcacagga acttcacggc
     2101 ggaaactttc gcacagtatg tggctgatac gcacacgcca gaaatacagg ccaagagagg
     2161 caggaaaggt ggcatcgcta aaggcgaagc ctacgatgac aagcgtttca tggcgctatg
     2221 tatgctggag aatggatatt ctcagaaagc tattgcggcg atgttggagg tttctactcg
     2281 aaccattcga aactggaaaa gcggaaaata gcctatatca gataacagcg cctttctggc
     2341 gtttttttga gccttaggtc ttttgccgtt tttccccgtt cagccctgca atggtgctgt
     2401 tttccgcatg attgtgctgg tagtgctcgc cgcagtctca tgaccgagcg tagcgagcga
     2461 atgagcgagg aagcaccagg gaacaggaac acggatggag gcacttacgc gtctgggttt
     2521 ggggatgtct ccagatcgta cttaatttcc ttaagtgcct gtaatatcct gtctttttta
     2581 tagcatagct cgcctgtttt tgtgtctacc agtcctgctt cgatcagtag cccagccgcg
     2641 agaaagagtc ggtgattgcg ttctcgtcgt tgtttttttc cctcgattcg tttttggacc
     2701 gcctgttttc gttcgctctc ctgtgcctgt aagtcgtttt tttccgctgt tgccagtacg
     2761 tggaggagtt tgcgttcctg ttctgtgagt cctgcttcgt tgtcgagcag gtcaataatc
     2821 tgtctctgtc gtgcggtctg ttctccgagc ttcctgatga atccgatccg tttcttcagc
     2881 cattcgatgt tgctgatgcg catgttcgtg gtgctccctg gtgttttttg ctgtgtgttg
     2941 tggtcgtgca gtatatcgct tgcggtcggt gggtgcaggg ggtatcttcc gtgctaattc
     3001 gtaaaattag aaggaagcgc acttatatgt ttctctcctt cgtcgagaaa cagtgcgctc
     3061 ctgcggaggg ctgaaaccgt ggcaacctat cacctcagcg ttaaatttgg tggcaagggg
     3121 caggctgcaa accacgccga ttacatcgag cgcaaagaga aataccgcga ccgtcaggat
     3181 ttggaatatt ccgcacacgg aaacatgccg gaatgggcgc gagataatcc ctcacatttc
     3241 tggcaggcgg ctgaccagtt tgaacgtgcg aacggttcga cctatcggga acttgaaatt
     3301 gcattacccc gtgaactgac agcggaacag cgccttgaac tggtgcagga ttttgtacgt
     3361 caggaagctg gcgaacggca cgcctggagt tttgccattc acaatccgaa agcgagcatt
     3421 gacggcggcg aacagcctca tgcgcatatc atgatgagcc agcgtgtgaa tgatggcatt
     3481 gaacgtacac cggaacagta tttccggcgc tataacgcca ggtatcccga gcggggaggt
     3541 gcgaaaaagg attccggaag cctgactctc actcagcaaa aagagcagtt gcgggaattg
     3601 cgaaaacgct gggaggtgaa gcacaacgaa catatgagaa agcatggctt tgaaaggggc
     3661 ttcattgact gccggacgct gaaagaacag ggcattgaac gacgtcccga agtgcatctg
     3721 ggttttgaag ctgccggacg gcttgatgat gcccagcgtc atgacatcat gcaaaaacgg
     3781 tctgaaccgg actattcccg ccatcttgaa caggcgcgaa cggtcgggca tgacatcagg
     3841 gaatggctgg acactccggt taagcaacat gaactggtca gaaggctgca acatgatgtt
     3901 gcgcgggagc atggctttga catgagagac agagtgagca gacagaaccg aactgaacct
     3961 gaacgggtta aatcaccgtc acgtggattt tctatgggat tctgaacatg gccagcacag
     4021 aagaaaaatt actcacgctc ctgttatcgg tggagcatct gcaacatacc gcaatggagc
     4081 aacagaaagc tgttgctgat tctctggctg tggcaaggga aacacttcgc ggatatcggg
     4141 atatttctga cggtgtggca aaacaggtca gggatgaagt cagaaacgaa gtgcagaggc
     4201 tggatgttgc agggctgata ggtgagcgca tcagtcagga ttttcagcgg ctggaagagt
     4261 cagtcgcaaa catgaaggca aacgcggatg ccctgaacag ggatattgcg acaattcaca
     4321 gcaatatcgt gcaggaatac aacaccctta aagggtatag ctggaaatgg ctgggtgggg
     4381 tgtcagtggc ctttctggtt atgttcagtg tgctcggatg ggggatgaaa acaattctcg
     4441 acaggaacta caacgccaca gcggcggtgt atcagaaagt tgtgacactg gaagataaac
     4501 tggtggagaa acctgtcacg ggtaagagcc ggaaaaactg acgcgcttcg cttgtccaac
     4561 gcctcacgac ccgcgaaagg atttcgcgtt ccgttcaccg ttttcatgag tgattcctcc
     4621 gaactgccaa aaaatatccc cccctgactt gacagaaaaa ataatggcga gtactttttg
     4681 gtctgtacat aaaaccagtg gttttatgta cagtatcaac tatataatca attgttttaa
     4741 cgcttaaaag agggaatttt tatgagcggt ggagatggac gcgaccacaa cagtggcgca
     4801 cataacacag gtggtaacat taatggcggc cctacggggc ttggtggaaa tggtggggct
     4861 tctgacggtt caggatggag ttcggaaaat aacccatggg gtggcggttc cggtagtggt
     4921 gttcactggg gaggtggctc cggcaatggt aatggcgggg ggaatggtaa ttccggtggt
     4981 ggcagcaatt catccgtagc agcagtggca tttggttttc ctgctttggc aactcctggt
     5041 gccggaacgc tgggtatcgc cgtctctggt gaggctttat ctgcggcaat agcggatatc
     5101 tttgcagccc tgaaaggccc gtttaaattc agcgcatggg gtattgcgct ttacggcatt
     5161 ctgccatctg aaatagcaaa agatgacccg aatatgatgt caaagattgt gacgtcatta
     5221 ccggcagaaa cagtgacgaa tgttcaggtc agtacacttc cgctggacca ggcaactgtc
     5281 agcgtgacga aacgtgtgac agatgttgtg aaggacacac gacagcatat tgccgtagtt
     5341 gcaggtgtgc ctatgagtgt gcctgttgtg aatgccaaac caacacgtac tccaggtgta
     5401 tttcacgcat catttcctgg tgtcccttct ctgacagtca gcactgtcaa aggccttccg
     5461 gtgtcaacaa cccttccccg tggtattacg gaggataaag gccggactgc cgttcctgcg
     5521 ggatttacct ttggtggtgg ttcacatgaa gcggtgattc gctttccgaa agaaagtggg
     5581 cagaagccgg tttatgtatc agtgacagat gttcttaccc cagcacaggt aaaacaacgt
     5641 caggatgagg aaaaacgcct ccagcaggaa tggaatgacg cacatccggt ggaagtggct
     5701 gaacgcaatt atgaacaggc ccgcgcagaa ctgaatcagg ctaataaaga tgttgccaga
     5761 aaccaggaac gacaggctaa agctgttcag gtttataatt ctcgtaaaag tgaacttgat
     5821 gcagcgaata aaactcttgc tgatgcaaag gctgaaataa aacaattcga gcgatttgcc
     5881 cgagaaccaa tggctgctgg tcacagaatg tggcaaatgg cagggcttaa ggcccagcgg
     5941 gcacagacgg atgtaaataa taagaaggct gcatttgatg ctgccgcaaa agagaagtca
     6001 gcagcagatg ctgca
//
