LOCUS       NZ_CP110407             5114 bp    DNA     circular CON 28-NOV-2023
DEFINITION  Shigella sonnei strain S17BD05200 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP110407
VERSION     NZ_CP110407.1
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 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  JOURNAL   Unpublished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                   :: 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
            CP110407.1.
            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="S17BD05200"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="Belgium"
                     /collection_date="2017-08-15"
     gene            complement(join(4301..5114,1..737))
                     /locus_tag="OKF41_RS24510"
     CDS             complement(join(4301..5114,1..737))
                     /locus_tag="OKF41_RS24510"
                     /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            909..1355
                     /locus_tag="OKF41_RS24515"
     CDS             909..1355
                     /locus_tag="OKF41_RS24515"
                     /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            complement(1549..2484)
                     /locus_tag="OKF41_RS24520"
     CDS             complement(1549..2484)
                     /locus_tag="OKF41_RS24520"
                     /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            3005..4105
                     /locus_tag="OKF41_RS24525"
     CDS             3005..4105
                     /locus_tag="OKF41_RS24525"
                     /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          complement(1550..2484)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..737)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.776"
                     /coverage="99.0"
                     /evalue="1.3500000000000002e-161"
     Typing          complement(4305..5038)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.061"
                     /coverage="92.0"
                     /evalue="1.62e-128"
ORIGIN
        1 ctggcggtct tgagttcccg ctcggcattc ctccgttcct ggattgcaac aatctgctcc
       61 ccattcagac tggcggcctg aacggggcca agatgaactt ccggcgtgcg attgataccc
      121 tgttctttca gagaacgatg atctacgcgc gactcgtgac cgtgtcgcgc aaggtgctca
      181 ttctgcacat ctgcccagcg ggaacgcagc gcaacaaggg cggcttttcg ctctccggct
      241 gtctggggaa tactcgcttt ttttgcgcct ccccgctctg gtgatttgct gttggcacgt
      301 ttaaaaaatt gctgtggatc gcgttcaata ccatcattaa tccgctcgca aaacatgata
      361 tgcgcgtgtg gctgttcctt tccgtcgatt gcacctggcg gattgtggat cgcgtactgg
      421 taggcatggc gatcgccaag ttccttttgc acgaaatctt caacaagttc tatccgttgt
      481 tcgcgtgtca gttcacgcgg taacgcgatc tcaatttcac ggtatgcagt cccgtttttt
      541 cgttcaaatt catctgcggc tttccatagc tctgcgggat ttttcttcgc ccatgatggc
      601 atgttaccgg atgacgaaaa ttccagatcc tcccgcgatt tgtaactctt atattcgccg
      661 gatctggaaa tgtaatcagc atgttttaag gcactgcctt ttgctccagc tttgacagtg
      721 caatggtagc ttgccatctg ccttttagcc ctccgcagga gcgcacagtt tctcgacgaa
      781 ggagagaaac tactaagtgc gcatccctga attaatcatg gatgatttta cggtctcaca
      841 cgcaggcaaa caaggtgata ttatgcataa taacaactca cattaacggc aaaagtgcag
      901 aggtaagaat gacaaatcgt gaagagtggt taagtgcaaa aattgcctac atcaacggac
      961 tgaaatcacc atcagagcag cagagattac ttgtgttact ggcagagaaa aaaaaccgaa
     1021 caacgacgga tgaaaaaacg ttgtccgcac tgatacgggc agaaaaaacc gcagagaaag
     1081 cagccgcagc aaaagccaga gtaacggcaa tcatagcggc agaacggaag gcagccgcaa
     1141 gggcggaacg aaaggcgcgg gatcatgaac tctacaaggc cgcaggcctc atgattgtgg
     1201 caggactggt ggacagcaaa accggaaagc caaagtttag tgctgccgaa ctggtaggcg
     1261 cactcgcagg aatcgcagag ctaccgcaca accatccaaa atggcaggaa tgggaaaaac
     1321 gcgggaaaga gctactcacc aaagacagtg cgtaagagcc tccgttcacg ttccagttcc
     1381 ctggtgcttc ctcgctcatt cgctcgctac gctcggtcat gagactgcgg cgagcacgac
     1441 cacctcaatc atacggtaag ccgcaccatt gctgggctga aaggagaaaa ccgccggaaa
     1501 gcccgctgct caaaaagacg ccgaaaaggc gctgttatct gatataggct atttgtgcat
     1561 tgcccaatta cggatcgtat tacgatgtac attcagcatc gccgcaatag ctttctgaga
     1621 atatccattc tccagcatac atagcgccat gaaacgcttg tcatcgtagg cttcgccttt
     1681 agcgatgcca cctttccggc ctctcttggc ctgtatttct ggtgtgtgcg tatcagccac
     1741 atactgtgcg aaactttccg gcgtgaagtt cctgtgcgtg tatttcgcaa tgctcttgcc
     1801 aatagcccga cattcaggcg gagaaagcgg aacgggaagc gatgcgttgt acatttcgac
     1861 acgctgaatc acagcatcaa gccactgtga gaatgctggc cagccctgcc gaatcgccct
     1921 gtaagcccat ttgcgcgtca tttcgaacag atggcagttt cgccccagcc cgtaatgttt
     1981 atcgacgcta cgacgctctg aggctctcaa atcgagataa tcagccagtt catcgagggc
     2041 gtaggcttcc tcgcgccact ccatcacctg ccattccagg tggaacggat ttttgcaaat
     2101 cagtccgctg tagttcacat ctgcgtcaag tttctcacac agcgcacgtt caattgcagc
     2161 ggcgtatttc agcgccttaa ccgacgcatc aggcgcggtt ctcacggcaa gattgagcgc
     2221 gtagagcagg tgagcgtgcc cgttctcggg attttttacg gtgatgttcg gcgcgggggc
     2281 gttccggtcg ctccagtcaa tcgcagctcc tacgcggtca acgtcaaaaa ccagccagaa
     2341 ctgcgcatga ggctgatttt gctggatgta gcgagcaagc agcgcacgcc ctttgccgga
     2401 gatacgaaga ccgaaagcga gctcatccgt gtgataggga cggtgaggta aattttcttc
     2461 gaagtattga agcgcggcgc tcatgtgtta cgattccttc caggttatcg accgacatcg
     2521 cccctgtatc ttcgtgaaag tcttgccgga tagacacgaa tttcaggggc gtttgttttt
     2581 cagtcgctta cactaccccc aacgacaaaa cctgtcgagt cttcccgcaa acccgatcca
     2641 tttaccataa ctcccgttgt gcgcccccct taaaacgccc tcagtcgctt tctgtcgcaa
     2701 aaaacgcaaa aagacaggga aacaacaggc cagaccaaaa aaacgcgcca gaattgtttt
     2761 cagggggctg cataactatg cacgaaagcg attcatgtcc ggtttcactc gttttgaaca
     2821 gcgaacaggt caaaacagca aactttctca tccagaaaaa ggtgaactgg tgcgaaatct
     2881 tttcgaactg cgtaagacgt tgagcacaaa catagtaagt cggtttatcg gtatgtatgg
     2941 attccattaa catatcgcct gtattaatat ttcctcgtta ttgttagaaa taaaaatggg
     3001 aaaaatgaat attaacttta aacatatcct tcctttattg tcgtcatttt ttatttcagg
     3061 atgcgactct gatggaataa gcaaggtaaa gtctttcgta tattacgaca ttgacgactc
     3121 aatgactgtt ggtaaagcct tcgatacaag gagtgattgc atcaatggca catggagtga
     3181 aaaagaggat gatcgaggaa gaaccatcgt cacatatacc tgtgatatta gtgaaagtgg
     3241 cctaaaaata ataaattcag ccattatgca agaacctgaa gataaggctg aatattctat
     3301 agcacaaaat aacaacagca taaaatcaac caatgaatca ctagaggaat acaaacagaa
     3361 aacgcctctg gtggaaaaaa caaaagaggt cataatagat catataagaa agctaaacag
     3421 tgcttttaat gaagatccaa tgatatatag caaactcaca attagccctt atttagacag
     3481 aatgctatat ctaaaggacc ataatgacaa tgcgctaaat gaaatttgtg gtgggtacga
     3541 atacattcaa tctgccgata gttacagttg gcgtgatgta agtgaagagt atgcaaaaga
     3601 atcatgcgaa aagcatatat ataaagtata tcaatcgttt aagaaaaatg catcaccatt
     3661 aataactaaa aacttccccg gtttctacga acgtgtcccc ccctgtgaga acgcagatga
     3721 atgcataaaa aaaacaaata tatactttga tgataacttt ctaaatatct acaaaagaag
     3781 ccaagataga gcacctcaaa taatttctga tttaaaaaaa cacaatatag aaataggtga
     3841 aaagttaaat gattgtagga aaaaactaaa tatctcagat gtcaaattaa cctattactg
     3901 gtttgtaaca gataccggag gagttgatta tttagatggg gtgttgacat ataattttca
     3961 gggaaagaat agagctgaaa actttcataa acaactattg caatatgcat acattaacta
     4021 cagcaaaaat caaatacctc gggactttgt aacatcaata aaaaatagta tttattataa
     4081 aatagaagat tgcactaagt tttagtcctt cccttacagg tggttacaca tataaccacc
     4141 tgcaaatatt taacacctgt taacttcatt aatctgaact gtgagtaaat caaaacgaca
     4201 atttttctca ttcagaaaac gtttcacggg acgcggaatt ttttcgcgtt ccgtgaaacg
     4261 ttggcggggt tcggggcgca gtcccgatat tgctacattt tcaacgctcc atatcttgat
     4321 cacgttcgtt actacgtgat acccccctgg cccaggatcg ctgtatacac agtgcttttt
     4381 cctcctgttg ctgccgttcc tgcgccattt ctgccagtaa ctcatgtcgc atttgagctt
     4441 tttcatctcc agatatactg agttcaggct ccagagataa catctggcta cgggcaacgg
     4501 atacctcttc agcaaccttt tgcctggtgt tctctaaaga tgccgccgcc agaatctcgc
     4561 gttctctgta cctgtccagc tccccaacgt acttatatcc ctcggtacgc ttaaaagcag
     4621 cgttttcttt gtcccactcg gattcggctt gctgtagctt gttcctgaat tcattccttt
     4681 catgttcagc ggtttccagc acactttttt gctccagaat acgcgcatca atctcccttt
     4741 tgtcagcccc ccgaaacagg ccacgaatcc cattcaaagc attgcgttgt tcctgtagct
     4801 cccgcagctc cctttgtgcg gaaacaacat tacgccccag tttgtctaaa taccgtgccc
     4861 cttcatatat tcgtctactc cattcggaaa gagagtcttt tttagctttc gcattctgaa
     4921 gcagcttatg ttctttgagc gcattgggat tggcatcccc taaacgagca agccttgcct
     4981 ctccctgaat gaccgttttc ataaccttgc ggtactgaag caataactcc ggtgaacggg
     5041 ctgaacgaac aggctcaact gccttgattt tttgcttttg ctcctgttcc tgctgaatgg
     5101 catttgcggc atct
//
