LOCUS       NZ_CP109779             5114 bp    DNA     circular CON 16-APR-2024
DEFINITION  Shigella sonnei strain CIP_106347 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP109779
VERSION     NZ_CP109779.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31285702
            Assembly: GCF_025908455.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5114)
  AUTHORS   De Silva,P.M., Bennett,R.J., Kuhn,L., Ngondo,P., Debande,L.,
            Njamkepo,E., Ho,B., Weill,F.-X., Marteyn,B.S., Jenkins,C. and
            Baker,K.S.
  TITLE     Escherichia coli killing by epidemiologically successful sublineages
            of Shigella sonnei is mediated by colicins
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5114)
  AUTHORS   De Silva,P.M., Bennett,R.J., Kuhn,L., Ngondo,P., Debande,L.,
            Njamkepo,E., Ho,B., Weill,F.-X., Marteyn,B.S., Jenkins,C. and
            Baker,K.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-OCT-2022) Department of Clinical Infection,
            Microbiology and Immunology, University of Liverpool, Crown Street,
            Liverpool L69 7ZB, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: UniCycler v. 0.4.8
            Assembly Name                     :: CIP_106347
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology             :: Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_025908455.1-RS_2024_04_16
            Annotation Date                   :: 04/16/2024 08:58:56
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,153
            CDSs (total)                      :: 5,023
            Genes (coding)                    :: 4,319
            CDSs (with protein)               :: 4,319
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 704
            CDSs (without protein)            :: 704
            Pseudo Genes (ambiguous residues) :: 0 of 704
            Pseudo Genes (frameshifted)       :: 193 of 704
            Pseudo Genes (incomplete)         :: 510 of 704
            Pseudo Genes (internal stop)      :: 123 of 704
            Pseudo Genes (multiple problems)  :: 114 of 704
            Pseudo Genes (short protein)      :: 3 of 704
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP109779.1.
            Bacteria and source DNA available from CNRSS 99-9901, Institut
            Pasteur.
            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="CIP_106347"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="France"
                     /lat_lon="48.8566 N 2.3522 E"
                     /collection_date="1999"
                     /collected_by="Institut Pasteur"
                     /genotype="3.7"
     gene            complement(join(4505..5114,1..941))
                     /locus_tag="OHN14_RS25660"
                     /old_locus_tag="OHN14_25660"
     CDS             complement(join(4505..5114,1..941))
                     /locus_tag="OHN14_RS25660"
                     /old_locus_tag="OHN14_25660"
                     /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            1113..1559
                     /locus_tag="OHN14_RS25665"
                     /old_locus_tag="OHN14_25665"
     CDS             1113..1559
                     /locus_tag="OHN14_RS25665"
                     /old_locus_tag="OHN14_25665"
                     /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(1753..2688)
                     /locus_tag="OHN14_RS25670"
                     /old_locus_tag="OHN14_25670"
     CDS             complement(1753..2688)
                     /locus_tag="OHN14_RS25670"
                     /old_locus_tag="OHN14_25670"
                     /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            3209..4309
                     /locus_tag="OHN14_RS25675"
                     /old_locus_tag="OHN14_25675"
     CDS             3209..4309
                     /locus_tag="OHN14_RS25675"
                     /old_locus_tag="OHN14_25675"
                     /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(1754..2688)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..941)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.403"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(4509..5113)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.069"
                     /coverage="99.0"
                     /evalue="4.52e-100"
ORIGIN
        1 gcattctgaa gcagcttatg ttctttgagc gcattgggat tggcatcccc taaacgagca
       61 agccttgcct ctccctgaat gaccgttttc ataaccttgc ggtactgaag caataactcc
      121 ggtgaacggg ctgaacgaac aggctcaact gccttgattt tttgcttttg ctcctgttcc
      181 tgctgaatgg catttgcggc atctctggcg gtcttgagtt cccgctcggc attcctccgt
      241 tcctggattg caacaatctg ctccccattc agactggcgg cctgaacggg gccaagatga
      301 acttccggcg tgcgattgat accctgttct ttcagagaac gatgatctac gcgcgactcg
      361 tgaccgtgtc gcgcaaggtg ctcattctgc acatctgccc agcgggaacg cagcgcaaca
      421 agggcggctt ttcgctctcc ggctgtctgg ggaatactcg ctttttttgc gcctccccgc
      481 tctggtgatt tgctgttggc acgtttaaaa aattgctgtg gatcgcgttc aataccatca
      541 ttaatccgct cgcaaaacat gatatgcgcg tgtggctgtt cctttccgtc gattgcacct
      601 ggcggattgt ggatcgcgta ctggtaggca tggcgatcgc caagttcctt ttgcacgaaa
      661 tcttcaacaa gttctatccg ttgttcgcgt gtcagttcac gcggtaacgc gatctcaatt
      721 tcacggtatg cagtcccgtt ttttcgttca aattcatctg cggctttcca tagctctgcg
      781 ggatttttct tcgcccatga tggcatgtta ccggatgacg aaaattccag atcctcccgc
      841 gatttgtaac tcttatattc gccggatctg gaaatgtaat cagcatgttt taaggcactg
      901 ccttttgctc cagctttgac agtgcaatgg tagcttgcca tctgcctttt agccctccgc
      961 aggagcgcac agtttctcga cgaaggagag aaactactaa gtgcgcatcc ctgaattaat
     1021 catggatgat tttacggtct cacacgcagg caaacaaggt gatattatgc ataataacaa
     1081 ctcacattaa cggcaaaagt gcagaggtaa gaatgacaaa tcgtgaagag tggttaagtg
     1141 caaaaattgc ctacatcaac ggactgaaat caccatcaga gcagcagaga ttacttgtgt
     1201 tactggcaga gaaaaaaaac cgaacaacga cggatgaaaa aacgttgtcc gcactgatac
     1261 gggcagaaaa aaccgcagag aaagcagccg cagcaaaagc cagagtaacg gcaatcatag
     1321 cggcagaacg gaaggcagcc gcaagggcgg aacgaaaggc gcgggatcat gaactctaca
     1381 aggccgcagg cctcatgatt gtggcaggac tggtggacag caaaaccgga aagccaaagt
     1441 ttagtgctgc cgaactggta ggcgcactcg caggaatcgc agagctaccg cacaaccatc
     1501 caaaatggca ggaatgggaa aaacgcggga aagagctact caccaaagac agtgcgtaag
     1561 agcctccgtt cacgttccag ttccctggtg cttcctcgct cattcgctcg ctacgctcgg
     1621 tcatgagact gcggcgagca cgaccacctc aatcatacgg taagccgcac cattgctggg
     1681 ctgaaaggag aaaaccgccg gaaagcccgc tgctcaaaaa gacgccgaaa aggcgctgtt
     1741 atctgatata ggctatttgt gcattgccca attacggatc gtattacgat gtacattcag
     1801 catcgccgca atagctttct gagaatatcc attctccagc atacatagcg ccatgaaacg
     1861 cttgtcatcg taggcttcgc ctttagcgat gccacctttc cggcctctct tggcctgtat
     1921 ttctggtgtg tgcgtatcag ccacatactg tgcgaaactt tccggcgtga agttcctgtg
     1981 cgtgtatttc gcaatgctct tgccaatagc ccgacattca ggcggagaaa gcggaacggg
     2041 aagcgatgcg ttgtacattt cgacacgctg aatcacagca tcaagccact gtgagaatgc
     2101 tggccagccc tgccgaatcg ccctgtaagc ccatttgcgc gtcatttcga acagatggca
     2161 gtttcgcccc agcccgtaat gtttatcgac gctacgacgc tctgaggctc tcaaatcgag
     2221 ataatcagcc agttcatcga gggcgtaggc ttcctcgcgc cactccatca cctgccattc
     2281 caggtggaac ggatttttgc aaatcagtcc gctgtagttc acatctgcgt caagtttctc
     2341 acacagcgca cgttcaattg cagcggcgta tttcagcgcc ttaaccgacg catcaggcgc
     2401 ggttctcacg gcaagattga gcgcgtagag caggtgagcg tgcccgttct cgggattttt
     2461 tacggtgatg ttcggcgcgg gggcgttccg gtcgctccag tcaatcgcag ctcctacgcg
     2521 gtcaacgtca aaaaccagcc agaactgcgc atgaggctga ttttgctgga tgtagcgagc
     2581 aagcagcgca cgccctttgc cggagatacg aagaccgaaa gcgagctcat ccgtgtgata
     2641 gggacggtga ggtaaatttt cttcgaagta ttgaagcgcg gcgctcatgt gttacgattc
     2701 cttccaggtt atcgaccgac atcgcccctg tatcttcgtg aaagtcttgc cggatagaca
     2761 cgaatttcag gggcgtttgt ttttcagtcg cttacactac ccccaacgac aaaacctgtc
     2821 gagtcttccc gcaaacccga tccatttacc ataactcccg ttgtgcgccc cccttaaaac
     2881 gccctcagtc gctttctgtc gcaaaaaacg caaaaagaca gggaaacaac aggccagacc
     2941 aaaaaaacgc gccagaattg ttttcagggg gctgcataac tatgcacgaa agcgattcat
     3001 gtccggtttc actcgttttg aacagcgaac aggtcaaaac agcaaacttt ctcatccaga
     3061 aaaaggtgaa ctggtgcgaa atcttttcga actgcgtaag acgttgagca caaacatagt
     3121 aagtcggttt atcggtatgt atggattcca ttaacatatc gcctgtatta atatttcctc
     3181 gttattgtta gaaataaaaa tgggaaaaat gaatattaac tttaaacata tccttccttt
     3241 attgtcgtca ttttttattt caggatgcga ctctgatgga ataagcaagg taaagtcttt
     3301 cgtatattac gacattgacg actcaatgac tgttggtaaa gccttcgata caaggagtga
     3361 ttgcatcaat ggcacatgga gtgaaaaaga ggatgatcga ggaagaacca tcgtcacata
     3421 tacctgtgat attagtgaaa gtggcctaaa aataataaat tcagccatta tgcaagaacc
     3481 tgaagataag gctgaatatt ctatagcaca aaataacaac agcataaaat caaccaatga
     3541 atcactagag gaatacaaac agaaaacgcc tctggtggaa aaaacaaaag aggtcataat
     3601 agatcatata agaaagctaa acagtgcttt taatgaagat ccaatgatat atagcaaact
     3661 cacaattagc ccttatttag acagaatgct atatctaaag gaccataatg acaatgcgct
     3721 aaatgaaatt tgtggtgggt acgaatacat tcaatctgcc gatagttaca gttggcgtga
     3781 tgtaagtgaa gagtatgcaa aagaatcatg cgaaaagcat atatataaag tatatcaatc
     3841 gtttaagaaa aatgcatcac cattaataac taaaaacttc cccggtttct acgaacgtgt
     3901 ccccccctgt gagaacgcag atgaatgcat aaaaaaaaca aatatatact ttgatgataa
     3961 ctttctaaat atctacaaaa gaagccaaga tagagcacct caaataattt ctgatttaaa
     4021 aaaacacaat atagaaatag gtgaaaagtt aaatgattgt aggaaaaaac taaatatctc
     4081 agatgtcaaa ttaacctatt actggtttgt aacagatacc ggaggagttg attatttaga
     4141 tggggtgttg acatataatt ttcagggaaa gaatagagct gaaaactttc ataaacaact
     4201 attgcaatat gcatacatta actacagcaa aaatcaaata cctcgggact ttgtaacatc
     4261 aataaaaaat agtatttatt ataaaataga agattgcact aagttttagt ccttccctta
     4321 caggtggtta cacatataac cacctgcaaa tatttaacac ctgttaactt cattaatctg
     4381 aactgtgagt aaatcaaaac gacaattttt ctcattcaga aaacgtttca cgggacgcgg
     4441 aattttttcg cgttccgtga aacgttggcg gggttcgggg cgcagtcccg atattgctac
     4501 attttcaacg ctccatatct tgatcacgtt cgttactacg tgataccccc ctggcccagg
     4561 atcgctgtat acacagtgct ttttcctcct gttgctgccg ttcctgcgcc atttctgcca
     4621 gtaactcatg tcgcatttga gctttttcat ctccagatat actgagttca ggctccagag
     4681 ataacatctg gctacgggca acggatacct cttcagcaac cttttgcctg gtgttctcta
     4741 aagatgccgc cgccagaatc tcgcgttctc tgtacctgtc cagctcccca acgtacttat
     4801 atccctcggt acgcttaaaa gcagcgtttt ctttgtccca ctcggattcg gcttgctgta
     4861 gcttgttcct gaattcattc ctttcatgtt cagcggtttc cagcacactt ttttgctcca
     4921 gaatacgcgc atcaatctcc cttttgtcag ccccccgaaa caggccacga atcccattca
     4981 aagcattgcg ttgttcctgt agctcccgca gctccctttg tgcggaaaca acattacgcc
     5041 ccagtttgtc taaataccgt gccccttcat atattcgtct actccattcg gaaagagagt
     5101 cttttttagc tttc
//
