LOCUS       NZ_CP119453             5153 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Shigella dysenteriae strain NCDC 599-52 plasmid p2, complete
            sequence.
ACCESSION   NZ_CP119453
VERSION     NZ_CP119453.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33336696
            Assembly: GCF_032363495.1
KEYWORDS    RefSeq.
SOURCE      Shigella dysenteriae
  ORGANISM  Shigella dysenteriae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5153)
  AUTHORS   Parsot,C.
  TITLE     Comparative analysis of the pINV from Shigella and EIEC strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5153)
  AUTHORS   Parsot,C.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-MAR-2023) Bacteries Pathogenes Enteriques, Institut
            Pasteur, 25, Rue du Dr ROUX, PARIS 75015, France
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2022
            Assembly Method                   :: Unicycler/0.4.8 v. JAN-2022
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 250.0x
            Sequencing Technology             :: Illumina; PacBio Sequel
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 13:57:59
            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)                     :: 5,152
            CDSs (total)                      :: 5,034
            Genes (coding)                    :: 4,401
            CDSs (with protein)               :: 4,401
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 633
            CDSs (without protein)            :: 633
            Pseudo Genes (ambiguous residues) :: 0 of 633
            Pseudo Genes (frameshifted)       :: 168 of 633
            Pseudo Genes (incomplete)         :: 451 of 633
            Pseudo Genes (internal stop)      :: 105 of 633
            Pseudo Genes (multiple problems)  :: 85 of 633
            Pseudo Genes (short protein)      :: 4 of 633
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP119453.1.
            Bacteria and source DNA available from Bacteries Pathogenes
            Enteriques, Institut Pasteur, France.
            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 dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="NCDC 599-52"
                     /serotype="8"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="p2"
                     /geo_loc_name="USA"
                     /collection_date="1952"
                     /collected_by="NCDC"
     gene            955..1182
                     /locus_tag="PWE30_RS25705"
                     /old_locus_tag="PWE30_25650"
     CDS             955..1182
                     /locus_tag="PWE30_RS25705"
                     /old_locus_tag="PWE30_25650"
                     /inference="COORDINATES: protein motif:HMM:NF015489.3"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 immunity protein"
                     /protein_id="WP_015056439.1"
                     /translation="MLYAIVISTILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAK
                     LNLFMLYNLLCLVLAIPFGLLGLFISIKNN"
                     /name="colicin E1 immunity protein"
     gene            complement(1179..2744)
                     /locus_tag="PWE30_RS25710"
                     /old_locus_tag="PWE30_25655"
     CDS             complement(1179..2744)
                     /locus_tag="PWE30_RS25710"
                     /old_locus_tag="PWE30_25655"
                     /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_000447003.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            3004..3441
                     /locus_tag="PWE30_RS25715"
                     /old_locus_tag="PWE30_25660"
     CDS             3004..3441
                     /locus_tag="PWE30_RS25715"
                     /old_locus_tag="PWE30_25660"
                     /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            3522..3941
                     /locus_tag="PWE30_RS25720"
                     /old_locus_tag="PWE30_25665"
     CDS             3522..3941
                     /locus_tag="PWE30_RS25720"
                     /old_locus_tag="PWE30_25665"
                     /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"
     gene            complement(4166..4489)
                     /gene="mobA"
                     /locus_tag="PWE30_RS25725"
                     /old_locus_tag="PWE30_25670"
     CDS             complement(4166..4489)
                     /gene="mobA"
                     /locus_tag="PWE30_RS25725"
                     /old_locus_tag="PWE30_25670"
                     /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            4773..4967
                     /locus_tag="PWE30_RS25730"
                     /old_locus_tag="PWE30_25675"
     CDS             4773..4967
                     /locus_tag="PWE30_RS25730"
                     /old_locus_tag="PWE30_25675"
                     /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"
     Typing          complement(4499..4738)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          3..410
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.634"
                     /coverage="95.0"
                     /evalue="2.8700000000000013e-179"
     Typing          complement(4170..4489)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.11e-62"
ORIGIN
        1 tgtgagcaaa aagcaaagca ccggaagaag ccagagccgc aggcgttttt ccataggctc
       61 cgcccccctg acgagcatca caaaaatcga cgctcaagcc agaggtggcg aaacccgaca
      121 ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg
      181 accctgccgc ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct
      241 catagctcac gctgttggta tctcggctcg gtgtaggtcg ttcgctccaa gctgggctgt
      301 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag
      361 tccaacccgg taagacacga cttagcgcca ctggcagcag ccgttggtaa cttggttagc
      421 agagcgatga tggcgcaaat ggtgcaacag agttcttgaa gtagtggccc gactacggct
      481 acactggaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc tcggttaagc
      541 agttccccaa ctgacttaac cttcgatcaa accgcctccc caggcggttt tttcgtttac
      601 aggcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctact
      661 gaacagagat ccccgtcaat ttagaagaag atgatggagc cacagtccct ccctgaacat
      721 cacgtatata gttagcctga catccaacaa ggaggtttat agcgaatatt cccacaaaaa
      781 atcttttcct cataactcga tccttataaa atgaaaagaa tatataacga ggtttaattt
      841 atgagtttaa gatactacat aaaaaatatt ttgtttggcc tatactgcgc acttatatat
      901 atatacctta taacaaaaaa caacgaaggg tattatttcc tagcgtcaga taagatgcta
      961 tacgcaatag tgataagcac tattctatgc ccatattcaa aatatgctat tgaacacata
     1021 ttttttaagt tcataaagaa agattttttc agaaaaagaa aaaacctaaa taatgccccc
     1081 gtggcaaaat taaacctatt tatgctatac aatctacttt gtttggtcct agcaatccca
     1141 tttggattgc taggactgtt tatatcaata aagaataatt aaatacccaa cacctcattt
     1201 atagtattaa gtttattctt atcaataaag gcacatagaa tgcctgtaac aatagcaatc
     1261 ccccagatac ctaatgtagt tccagcaagc acactaaaaa gtaaaacaac aacataacta
     1321 actccagcat ctacagcttt cttctctaat gtaagaaata gcggcttcca gtcacctgta
     1381 tccttaattt ttaggatatc agataccaca tcatatccaa aagaaacatg tcccgtaatc
     1441 ttcaagtact tggcaaactg atctaaatgc ttagcccagt cttcatactt aaccgcctcc
     1501 agtgcattga aaattgcatc acggtctgct ttgctgaatt tcttatttaa tacatccttg
     1561 tatttctcaa aagcagctag agcttcattc acattgctga ttttcttacc tttagattta
     1621 tcagcaagtt cctgtgccat ttttgaatat ttttcaccat atttttcaga tagcgtttga
     1681 taaaagctaa ctgttgcatc cacagcatcc ttaatctgcg agttcaggag attagtctgt
     1741 gctgttttca aattatcttc agcatcatga atacgtgaaa ctgctgtact tcgcttatta
     1801 ttagcctgag aaatagcctc ttggattcca tttatctcag agctaatctg gttaagacgc
     1861 gtttctgatg ctgttacctg cttttgtttt tcctccatct catcaccagc tctcgcccgt
     1921 agtctggtgg cctcaaaaaa aggacgactc tgaagcggat cattcgccct aggagataaa
     1981 agtttaaccc tttcatccag ttctttatat ttagcagatg cctgatccaa ctcatttcgt
     2041 tttccggaca gcgtattcgt ttctgcatca cgggcatgaa tactggagct taaacgggta
     2101 ttgagcgtat taatctcttc atccactttc gccagctcag attgtgcagc agcaagattt
     2161 ttttgtgcca cctccacagc ccgggcctct tcactcaatg ctgccaggcg tttctcttca
     2221 tcctcagcca gtttcaattg gcgttctgtt tcagcctgct ccttctctat ctctttacgt
     2281 cgttgttctg cttcctgaaa agccttttcc gcagcttccg cttctttacg ggctttttct
     2341 tctgcttttg caaggcgcaa ccgctctgct tctgcctgca tcgctgcatt attggcatga
     2401 gccaggtcaa taacctccgg atgagtggaa ttatggcgaa gcgcctcatt cacaatatcc
     2461 ttcagatgtt gagtcagcgc atcccggttt gcttttgctt tagcctgtgc ttctgcggca
     2521 gcttttgctc gggcagcctg ttctgcctgc gttttcttca attgagcagt agaccattta
     2581 gctgtggcat gaatggctgc agaactttca cttttgctac ctccagttcc accaccaccg
     2641 ccagagccac tcccgtctgg attaccattc aaaagagtaa tgattacctg ccccttatca
     2701 tcataaggaa caccatcttt atagtacgct acagctgttt ccattataaa atcctctttg
     2761 acattaaaaa caaatagtta aaagcaatat actgtatata taatcactgg ttttatatac
     2821 agtttaaaat tacgccgctg cattttccct gtcaaccctg tggattttca tttttgtgaa
     2881 aacgatcaaa aaaacagcca cccacaccac gtgctatttc cacccgatgc cacaaaaacc
     2941 agcacaaaca ttaccgttct cagacctcat tatgttttac tgaaaccatg agatgagaca
     3001 cctatgggac actgtaactt tatggcatgg cacacactcc gggacgcact gaaaatgact
     3061 ggaagatcgc gttcacagtt ttaccgtgat atgcgctcag gtcttgtcag ttaccgtacc
     3121 agccaggacg gacgacggga gtttgaaacc agtgaactga tccgggcata cggcgaatta
     3181 aagcggaatg agacaccaga aaggcacact caaggacact cagaaaaacc tcatgatcag
     3241 cagacagaac gcattctccg ggaactgaat gagctgaaac aatgcctgac gctgatgctt
     3301 gaggataaac aagcccagga tacggagcgc cggcgccagg aagcagaacg gaaacagcta
     3361 cagaatgaga tagcccagct caggcaggct ctggagcagg aaaagaaacg gggattctgg
     3421 tccaggctgt tcggtcactg aacgcgctca gaaactgatg ataagataat cttcggataa
     3481 taactcaccg agaataaata ctttaaggta gggagacact catgagacgt accggaaaca
     3541 aactttgtct tatcgccatg ataacagcaa cagtagctct cacagcctgt accccaaagg
     3601 gcagcgtgga acaacatacc cggcattacg tatatgcttc tgatgacggt tttgatccca
     3661 acttttccac ccaaaaagcc gacacaacac gaatgatggt gccttttttt cggcagttct
     3721 gggatatggg agctaaagat aaagcgacag gaaaatcacg gagtgatgtg caacaacgca
     3781 ttcaacagtt tcacagccag gaatttttaa actcactccg gggcacaact caatttgcgg
     3841 gtactgatta ccgcagcaaa gaccttaccc cgaaaaaatc caggctgctg gctgacacga
     3901 tttctgcggt ttatctcgat ggctacgagg gcagacagta agtggattta ccataatccc
     3961 ttaattgtac gcaccactga aacgcgctga acgcgattct gacgcagaca ccgcaaaaag
     4021 agatgtttta ccccggaaaa acaggaagga tgcgtcagga tcgttttcag ctctctgcat
     4081 agctatgcat gaaagcgaat ggtgatcact ttgggagctt acggtgttca taccgtcagt
     4141 tttcgacagt tttctctccg ggaagctaat ctgccataag cctggataac agggcacggt
     4201 gatactccgt aatagcgatc agcacctccg catactccct gtccccgaca cgcttgccgt
     4261 cgataaagag ttttttctgt aacgccccca gtctcataac ttctttcagt acccgatcat
     4321 cagtcagtga gttaactttc ttaccgagag ctgccgcccg taaaaaaccg gaaacggtct
     4381 tgccgcattc agcagccctt tttctgattt cctggtcttc ttctgccgtc agacgaacag
     4441 ggcgactgat agcccgcctg cgcgtattac ttccacttcg ttttgtcata aaacatggct
     4501 ccgtatctga catgggtgtc ggggcaaagc cctgaccagg gtaattgtaa tagcgtgcat
     4561 gtatgcgcgg tataacaatt acacatcctg tcctgtcagc aagttcgaat taccgacaaa
     4621 ggcacggcag ttttttggca gtgacagtat tgtcaggcag aaatacccgt caaagcgtca
     4681 gacggcagaa taccggcggt aaaacagtcg aaaagtggta cgcgatataa tcacacaacg
     4741 cagatgacag acagaacgga gaaaacgaaa agatgaacaa gcagcagcaa gccgtactca
     4801 acatggcagg attcataaaa agccaaagcc tgacgctgct cgaaaagctg gacgcactcg
     4861 atgctgacga acaggctacc atgtgtgaga agctgcacga actcgcagaa gaactccaga
     4921 acagcatcca gacacgcttt gaagtagaaa atagcacaga gagataacgc tcaggacagg
     4981 atgccgaacg gcacaacaga gcgtaaggag aaaatgtcac ataaggcgct cttccgcttc
     5041 ctcgctcact gactcgctac gctcggacgt tcgactgcgg cgagcggtgt cagctcactc
     5101 aaaagcggta atacggttat ccacagaatc aggggataaa gccggaaaga aca
//
