LOCUS       NZ_CP109780             2690 bp    DNA     circular CON 16-APR-2024
DEFINITION  Shigella sonnei strain CIP_106347 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP109780
VERSION     NZ_CP109780.1
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 2690)
  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  JOURNAL   Unpublished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 2690)
  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
            CP109780.1.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CIP_106347"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /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(2469..2690,1..504))
                     /locus_tag="OHN14_RS25680"
                     /old_locus_tag="OHN14_25680"
     CDS             complement(join(2469..2690,1..504))
                     /locus_tag="OHN14_RS25680"
                     /old_locus_tag="OHN14_25680"
                     /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_005112197.1"
                     /translation="MKILNSNLITNISSTIRNHLLTSSKNIKTHPSPNMDVTSHRRLFQ
                     KDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFTRQKGDGWTVVPKNLRIDFYTKDNDF
                     TKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKVLANARNIPQSKLEEEMMSQAIYRKE
                     YATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKNIDIAFITDKNHKKHLSDIFKVINES
                     GVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(781..942)
                     /locus_tag="OHN14_RS25685"
                     /old_locus_tag="OHN14_25685"
     CDS             complement(781..942)
                     /locus_tag="OHN14_RS25685"
                     /old_locus_tag="OHN14_25685"
                     /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"
     gene            complement(1440..1634)
                     /locus_tag="OHN14_RS25690"
                     /old_locus_tag="OHN14_25690"
     CDS             complement(1440..1634)
                     /locus_tag="OHN14_RS25690"
                     /old_locus_tag="OHN14_25690"
                     /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            1920..2243
                     /gene="mobA"
                     /locus_tag="OHN14_RS25695"
                     /old_locus_tag="OHN14_25695"
     CDS             1920..2243
                     /gene="mobA"
                     /locus_tag="OHN14_RS25695"
                     /old_locus_tag="OHN14_25695"
                     /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"
     Typing          1673..1911
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(871..1397)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1921..2240
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 attacttgtt gcgtattctt ttctatatat ggcttgtgac atcatttctt cttctaattt
       61 tgattgaggt atattgcgcg cgttcgctag aacttttagg tcatctttgc ttatgtttag
      121 tgatggtgtt aacccttttt gagcttcagt atggcgtttg tttacctctg aaagaacgct
      181 tagtcccttt gtgaagtcgt tgtcttttgt ataaaaatca attcttaggt ttttggggac
      241 tacagtccat ccatcgcctt tttgacgcgt gaatagtgtt tgtggatggg agatctcttt
      301 ccatccacca tgcgacataa tgacaagttg tgttgctttt cctgtttggc tcaatcctat
      361 tccgtctttc tggaataaac gacgatgact tgttacgtcc atgtttggtg atgggtgtgt
      421 ttttatattt ttggatgatg ttagaaggtg atttcttatt gttgatgata tgtttgttat
      481 gagattcgaa ttgagtattt tcatttgtta acaatccatt tttgcggtgt tttttattgt
      541 tttttttctt ttgtttaagg gtgtgtcggt gtaagtgttt attttatggg ttaaagtagg
      601 ataccaagtg tgaaaaaaaa ttaaaggttc ttcttgagat cctttttttc tgcgcgtaat
      661 ctgctgcctg taaacgaaaa aaccgccctg caaggcggtt tttcgaaggt tctcagagct
      721 accaactctt tgagccgagg taactggctt ggaggagcgc agtcaccaaa acttgttctt
      781 tcagtttagc cttaacaggc gcatgacttc aagtcttact cctctaattc ggttatcagt
      841 ggctgctgcc agtggcgata attcgtgtct taccgggttg gactcaagac gatagttacc
      901 ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg
      961 aacgacctac accgggccga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc
     1021 cgaagggaga aaggcggaca ggtatccggt aaacggcagg gtcggaacag gagagcgcac
     1081 gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct
     1141 ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc
     1201 cacctgcgcg gcctttgtcc ctgccttcgg ctttttgctc acatgttctt tccggcgtta
     1261 tcccctgatt ctgtggataa ccgcattacc gcctttgagt gagctgacac cgctcgccgc
     1321 agtcgaacga ccgagcgtag cgagtcagtg agcgaggaag cggaagagcg ccttatgtga
     1381 cattttctcc ttacgcaccg gtataccgtt ctgcatcctg tctggagcag gatacactgt
     1441 tataccccgg tgccactttc cgcttcaaag cgtgtctgta tgctgttctg gagttcttcc
     1501 gcgatttcgt gcagcttctc acacatggcg gcctgttcgt cggcatcgag tgcgtccagc
     1561 ttttcgagca gcgtcaggct ctggcttttt atgaatcccg ccatgttgag tacggtttgc
     1621 tgctgcttgt tcatctttct gttttctccg ttctgtctgt catctgcgtt gtgtgattat
     1681 atcgcgtacc acttttcgac tgttttaccg ccggtattct gccgtctgac gcattgacgg
     1741 gtatttctgc ctgacaatac tgtcactgcc aaaaaaactg ccgtgccttt gtcggtaatt
     1801 cgaacttgct gacaggacag gatgtgtaat tgttataccg cgcatacatg cacgctatta
     1861 caattaccct ggtcagggct tcgccccgac accccgtgtc agatacggag ccatgtttta
     1921 tgacaaaacg aagtggaagt aatacgcgca ggcgggctat cagtcgccct gttcgtctga
     1981 cggcagaaga agaccaggaa atcagaaaaa gggctgctga atgcggcaag accgtttctg
     2041 gttttttacg ggcggcagct ctcggtaaga acgttaactc actgactgat gatcgggtgc
     2101 tgaaagaagt tatgagactg ggggcgttac agaaaaaact ctttatcgac ggcaagcgta
     2161 tcggggacag ggagtatgcg gaggtgctga tcgctattac ggagtatcac cgtgccctgt
     2221 tatccaggct tatggcagat tagcttcccg gggagaaaac tgttgaaaac agacggtatg
     2281 aacacggtaa gctcccaaag tgatctccat tcgctttcat gcatagctat gcagcgagct
     2341 gaaaacgatc ctgacgcatc cttcctgttt ttccggggta aaacatctat ttttgtggtg
     2401 tctgcgtcag aatcgcgttc agcgcgtttc agtggtgcgt acaattaagg gattatggta
     2461 aatgatgatt atttctcctc tctatttact cggcaagcgc caaagtgaat tacatcatat
     2521 tttactcctg attcatttat tactttaaat atgtcagaaa ggtgcttctt atgattttta
     2581 tcagttataa atgctatatc aatatttttg tttcctaagc catcttgatg tctttgtata
     2641 atattttggg cttgttcatg gtaatataga gcatagtttt ttatcttctc
//
