LOCUS       NZ_CP109778             5153 bp    DNA     circular CON 16-APR-2024
DEFINITION  Shigella sonnei strain CIP_106347 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP109778
VERSION     NZ_CP109778.1
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 5153)
  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  JOURNAL   Unpublished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 5153)
  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
            CP109778.1.
            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..5153
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CIP_106347"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed2"
                     /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(4837..5153,1..121))
                     /locus_tag="OHN14_RS25625"
                     /old_locus_tag="OHN14_25625"
     CDS             complement(join(4837..5153,1..121))
                     /locus_tag="OHN14_RS25625"
                     /old_locus_tag="OHN14_25625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001318234.1"
                     /translation="MGHCNFMAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRR
                     EFETSELIRAYGELKRNETPERHTQGHSEKPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDTERRRQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="hypothetical protein"
     gene            381..1946
                     /locus_tag="OHN14_RS25630"
                     /old_locus_tag="OHN14_25630"
     CDS             381..1946
                     /locus_tag="OHN14_RS25630"
                     /old_locus_tag="OHN14_25630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_000447004.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTVQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(1943..2284)
                     /locus_tag="OHN14_RS25635"
                     /old_locus_tag="OHN14_25635"
     CDS             complement(1943..2284)
                     /locus_tag="OHN14_RS25635"
                     /old_locus_tag="OHN14_25635"
                     /inference="COORDINATES: protein motif:HMM:NF015489.4"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            2332..2469
                     /locus_tag="OHN14_RS25640"
                     /old_locus_tag="OHN14_25640"
     CDS             2332..2469
                     /locus_tag="OHN14_RS25640"
                     /old_locus_tag="OHN14_25640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /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_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(3311..3505)
                     /locus_tag="OHN14_RS25645"
                     /old_locus_tag="OHN14_25645"
     CDS             complement(3311..3505)
                     /locus_tag="OHN14_RS25645"
                     /old_locus_tag="OHN14_25645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3789..4112
                     /gene="mobA"
                     /locus_tag="OHN14_RS25650"
                     /old_locus_tag="OHN14_25650"
     CDS             3789..4112
                     /gene="mobA"
                     /locus_tag="OHN14_RS25650"
                     /old_locus_tag="OHN14_25650"
                     /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_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(4337..4756)
                     /locus_tag="OHN14_RS25655"
                     /old_locus_tag="OHN14_25655"
     CDS             complement(4337..4756)
                     /locus_tag="OHN14_RS25655"
                     /old_locus_tag="OHN14_25655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     Typing          3541..3780
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(2753..3282)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.59"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          3790..4109
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 ggctggtacg gtaactgaca agacctgagc gcatatcacg gtaaaactgt gaacgcgatc
       61 ttccagtcat tttcagtgcg tcccggagtg tgtgccatgc cataaagtta cagtgtccca
      121 taggtgtctc atctcatggt ttcagtaaaa cataatgagg tctgagaacg gtaatgtttg
      181 tgctggtttt tgtggcatcg ggtggaaata gcacgtggtg tgggtggctg tttttttgat
      241 cgttttcaca aaaatgaaaa tccacagggt tgacagggaa aatgcagcgg cgtaatttta
      301 aactgtatat aaaaccagtg attatatata cagtatgttg cttttaacta tttgttttta
      361 atgtcaaaga ggattttata atggaaacag ctgtagcgta ctataaagat ggtgttcctt
      421 atgatgataa ggggcaggta atcattactc ttttgaatgg taatccagac gggagtggct
      481 ctggcggtgg tggtggaact ggaggtagca aaagtgaaag ttctgcagcc attcatgcca
      541 cagctaaatg gtctactgct caattgaaga aaacgcaggc agaacaggct gcccgagcaa
      601 aagctgccgc agaagcacag gctaaagcaa aagcaaaccg ggatgcgctg actcaacatc
      661 tgaaggatat tgtgaatgag gcgcttcgcc ataattccac tcatccggag gttattgacc
      721 tggctcatgc caataatgca gcgatgcagg cagaagcaga gcggttgcgc cttgcaaaag
      781 cagaagaaaa agcccgtaaa gaagcggaag ctgcggaaaa ggcttttcag gaagcagaac
      841 aacgacgtaa agagatagag aaggagcagg ctgaaacaga acgccaattg aaactggctg
      901 aggatgaaga gaaacgcctg gcagcattga gtgaagaggc ccgggctgtg gaggtggcac
      961 aaaaaaatct tgctgctgca caatctgagc tggcgaaagt ggatgaagag attaatacgc
     1021 tcaatacccg tttaagctcc agtattcatg cccgtgatgc agaaacgaat acgctgtccg
     1081 gaaaacgaaa tgagttggat caggcatctg ctaaatataa agaactggat gaaagggtta
     1141 aacttttatc tcctagggcg aatgatccgc ttcagagtcg tccttttttt gaggccacca
     1201 gactacgggc gagagctggt gatgagatgg aggaaaaaca aaagcaggta acagcatcag
     1261 aaacgcgtct taaccagatt agctctgaga taaatggaat ccaagaggct atttctcagg
     1321 ctaataataa gcgaagtaca gcagtttcac gtattcatga tgctgaagat aatttgaaaa
     1381 cagtacagac taatctcctg aactcgcaga ttaaggatgc tgtggatgca acagttagct
     1441 tttatcaaac gctatctgaa aaatatggtg aaaaatattc aaaaatggca caggaacttg
     1501 ctgataaatc taaaggtaag aaaatcagca atgtgaatga agctctagct gcttttgaga
     1561 aatacaagga tgtattaaat aagaaattca gcaaagcaga ccgtgatgca attttcaatg
     1621 cactggaggc ggttaagtat gaagactggg ctaagcattt agatcagttt gccaagtact
     1681 tgaagattac gggacatgtt tcttttggat atgatgtggt atctgatatc ctaaaaatta
     1741 aggatacagg tgactggaag ccgctatttc ttacattaga gaagaaagct gtagatgctg
     1801 gagttagtta tgttgttgtt ttacttttta gtgtgcttgc tggaactaca ttaggtatct
     1861 gggggattgc tattgttaca ggcattctat gtgcctttat tgataagaat aaacttaata
     1921 ctataaatga ggtgttgggt atttaattat tctttattga tataaacagt cctagcaatc
     1981 caaatgggat tgctaggacc aaacaaagta gattgtatag cataaatagg tttaattttg
     2041 ccacgggggc attatttagg ttttttcttt ttctgaaaaa atctttcttt atgaacttaa
     2101 aaaatatgtg ttcaatagca tattttgaat atgggcatag aatagtgctt atcactattg
     2161 cgtatagcat cttatctgac gctaggaaat aatacccttc gttgtttttt gttataaggt
     2221 atatatatat aagtgcgcag tataggccaa acaaaatatt ttttatgtag tatcttaaac
     2281 tcataaatta aacctcgtta tatattcttt tcattttata aggatcgagt tatgaggaaa
     2341 agattttttg tgggaatatt cgctataaac ctccttgttg gatgtcaggc taactatata
     2401 cgtgatgttc agggagggac tgtggctcca tcatcttctt ctaaattgac ggggatctct
     2461 gttcagtaga aaagatcaaa ggatcttctt gagatccttt ttttctgcgc gtaatctgct
     2521 gcctgtaaac gaaaaaaccg cctggggagg cggtttgatc gaaggttaag tcagttgggg
     2581 aactgcttaa ccgaggtaac tggcttcagc agagcgcaga taccaaatac tgtccttcca
     2641 gtgtagccgt agtcgggcca ctacttcaag aactctgttg caccatttgc gccatcatcg
     2701 ctctgctaac caagttacca acggctgctg ccagtggcgc taagtcgtgt cttaccgggt
     2761 tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt
     2821 gcacacagcc cagcttggag cgaacgacct acaccgagcc gagataccaa cagcgtgagc
     2881 tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca
     2941 gggtcggaac aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata
     3001 gtcctgtcgg gtttcgccac ctctggcttg agcgtcgatt tttgtgatgc tcgtcagggg
     3061 ggcggagcct atggaaaaac gcctgcggcg ctggcttctt ccggtgcttt gctttttgct
     3121 cacatgttct ttccggcttt atcccctgat tctgtggata accgtattac cgcttttgag
     3181 tgagctgaca ccgctcgccg cagtcgaacg tccgagcgta gcgagtcagt gagcgaggaa
     3241 gcggaagagc gccttatgtg acattttctc cttacgctct gttgtgccgt tcggcatcct
     3301 gtcctgagcg ttatctctct gtgctatttt ctacttcaaa gcgtgtctgg atgctgttct
     3361 ggagttcttc tgcgagttcg tgcagcttct cacacatggt agcctgttcg tcagcatcga
     3421 gtgcgtccag cttttcgagc agcgtcaggc tttggctttt tatgaatcct gccatgttga
     3481 gtacggcttg ctgctgcttg ttcatctttt cgttttctcc gttctgtctg tcatctgcgt
     3541 tgtgtgatta tatcgcgtac cacttttcaa ctgttttacc gccggtattc tgccgtctga
     3601 cgctttgacg ggtatttctg cctgacaata ctgtcactgc caaaaaactg ccgtgccttt
     3661 gtcggtaatt cgaacttgct gacaggacag gatgtgtaat tgttataccg cgcatacatg
     3721 cacgctatta caattaccct ggtcagggct ttgccccgac acccatgtca gatacggagc
     3781 catgttttat gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg
     3841 ttcgtctgac ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga
     3901 ccgtttccgg ttttttacgg gcggcagctc tcggtaagaa agttaactca ctgactgatg
     3961 atcgggtact gaaagaagtt atgagactgg gggcgttaca gaaaaaactc tttatcgacg
     4021 gcaagcgtgt cggggacagg gagtatgcgg aggtgctgat cgctattacg gagtatcacc
     4081 gtgccctgtt atccaggctt atggcagatt agcttcccgg agagaaaact gtcgaaaact
     4141 gacggtatga acaccgtaag ctcccaaagt gatcaccatt cgctttcatg catagctatg
     4201 cagagagctg aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa aacatctctt
     4261 tttgcggtgt ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta caattaaggg
     4321 attatggtaa atccacttac tgtctgccct cgtagccatc gagataaacc gcagaaatcg
     4381 tgtcagccag cagcctggat tttttcgggg taaggtcttt gctgcggtaa tcagtacccg
     4441 caaattgagt tgtgccccgg agtgagttta aaaattcctg gctgtgaaac tgttgaatgc
     4501 gttgttgcac atcactccgt gattttcctg tcgctttatc tttagctccc atatcccaga
     4561 actgccgaaa aaaaggcacc atcattcgtg ttgtgtcggc tttttgggtg gaaaagttgg
     4621 gatcaaaacc gtcatcagaa gcatatacgt aatgccgggt atgttgttcc acgctgccct
     4681 ttggggtaca ggctgtgaga gctactgttg ctgttatcat ggcgataaga caaagtttgt
     4741 ttccggtacg tctcatgagt gtctccctac cttaaagtat ttattctcgg tgagttatta
     4801 tccgaagatt atcttatcat cagtttctga gcgcgttcag tgaccgaaca gcctggacca
     4861 gaatccccgt ttcttttcct gctccagagc ctgcctgagc tgggctatct cattctgtag
     4921 ctgtttccgt tctgcttcct ggcgccggcg ctccgtatcc tgggcttgtt tatcctcaag
     4981 catcagcgtc aggcattgtt tcagctcatt cagttcccgg agaatgcgtt ctgtctgctg
     5041 atcatgaggt ttttctgagt gtccttgagt gtgcctttct ggtgtctcat tccgctttaa
     5101 ttcgccgtat gcccggatca gttcactggt ttcaaactcc cgtcgtccgt cct
//
