LOCUS       NZ_CP119454             2679 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Shigella dysenteriae strain NCDC 599-52 plasmid p3, complete
            sequence.
ACCESSION   NZ_CP119454
VERSION     NZ_CP119454.1
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 2679)
  AUTHORS   Parsot,C.
  TITLE     Comparative analysis of the pINV from Shigella and EIEC strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2679)
  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
            CP119454.1.
            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..2679
                     /organism="Shigella dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="NCDC 599-52"
                     /serotype="8"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="p3"
                     /geo_loc_name="USA"
                     /collection_date="1952"
                     /collected_by="NCDC"
     gene            174..335
                     /locus_tag="PWE30_RS25735"
                     /old_locus_tag="PWE30_25680"
     CDS             174..335
                     /locus_tag="PWE30_RS25735"
                     /old_locus_tag="PWE30_25680"
                     /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            613..1338
                     /locus_tag="PWE30_RS25740"
                     /old_locus_tag="PWE30_25685"
     CDS             613..1338
                     /locus_tag="PWE30_RS25740"
                     /old_locus_tag="PWE30_25685"
                     /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(1564..1887)
                     /gene="mobA"
                     /locus_tag="PWE30_RS25745"
                     /old_locus_tag="PWE30_25690"
     CDS             complement(1564..1887)
                     /gene="mobA"
                     /locus_tag="PWE30_RS25745"
                     /old_locus_tag="PWE30_25690"
                     /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"
     gene            2171..2365
                     /locus_tag="PWE30_RS25750"
                     /old_locus_tag="PWE30_25695"
     CDS             2171..2365
                     /locus_tag="PWE30_RS25750"
                     /old_locus_tag="PWE30_25695"
                     /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(1897..2136)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          2..324
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.753"
                     /coverage="100.0"
                     /evalue="2.45e-140"
     Typing          2395..2679
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.388"
                     /coverage="97.0"
                     /evalue="8.82e-111"
     Typing          complement(1568..1887)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="6.59e-62"
ORIGIN
        1 aaagatacca ggcgtttccc cctggaagct ccctcgtgcg ctctcctgtt ccgaccctgc
       61 cgcttaccgg atacctgtcc gcctttctcc cttcgggaag cgtggcgctt tctcatagct
      121 cacgctgttg gtatctcagt tcggtgtagg tcgttcgctc caagctgggc tgtgtgcacg
      181 aaccccccgt tcagcccgac cgctgcgcct tatccggtaa ctatcgtctt gagtccaacc
      241 cggtaagaca cgaattatcg ccactggcag cagccactga taaccgaatt agaggagtaa
      301 gacttgaagt catgcgcctg ttaaggctaa actgaaagaa caagttttgg tgactgcgct
      361 cctccaagcc agttacctcg gctcaaagag tttgtatctc tgagaacctt cgaaaaaccg
      421 ccttgcaggg cggttttttc gtttacaggc agtagattac gcgcagaaaa aaaggatctc
      481 aagaagaacc tttaattttt tttcacactt ggtatcctac tttaacccat aaaataaaca
      541 cttacaccga cacgccctta aacaaaagaa aaaaaaacaa taaaaaacac cgcaaaaatg
      601 gattgttaac aaatgaaaat actcaattcg aatctcataa caaacatatc atcaacaata
      661 agaaatcacc ttctaacatc atccaaaaat ataaaaacac acccatcacc aaacatggac
      721 gtaacaagtc atcgtcgttt attccagaaa gacggaatag gattgagcca aacaggaaaa
      781 gcaacacaac ttgtcattat gtcgcatggt ggatggaaag agatctccca tccacaaaca
      841 ctattcacgc gtcaaaaagg cgatggatgg actgtagtcc ccaaaaacct aagaattgat
      901 ttttatacaa aagacaacga cttcacaaag ggactaagcg ttctttcaga ggtaaacaaa
      961 cgccatactg aagctcaaaa agggttaaca ccatcactaa acataagcaa agatgaccta
     1021 aaagttctag cgaacgcgcg caatatacct caatcaaaat tagaagaaga aatgatgtca
     1081 caagccatat atagaaaaga atacgcaaca agtaatgaga agataaaaaa ctatgctcta
     1141 tattaccatg aacaagccca aaatattata caaagacatc aagatggctt aggaaacaaa
     1201 aatattgata tagcatttat aactgataaa aatcataaga agcacctttc tgacatattt
     1261 aaagtaataa atgaatcagg agtaaaatat gatgtaattc actttggcgc ttgccgagta
     1321 aatagagagg agaaataatc atcatttacc ataatccctt aattgtacgc accactgaaa
     1381 cgcgctgaac gcgattctga cgcagacacc acaaaaatag atgttttacc ccggaaaaac
     1441 aggaaggatg cgtcaggatc gttttcagct cgctgcatag ctatgcatga aagcgaatgg
     1501 agatcacttt gggagcttac cgtgttcata ccgtctgttt tcaacagttt tctccccggg
     1561 aagctaatct gccataagcc tggataacag ggcacggtga tactccgtaa tagcgatcag
     1621 cacctccgca tactccctgt ccccgatacg cttgccgtcg ataaagagtt ttttctgtaa
     1681 cgcccccagt ctcataactt ctttcagtac ccgatcatca gtcagtgagt taacgttctt
     1741 accgagagct gccgcccgta aaaaaccgga aacggtcttg ccgcattcag cagccctttt
     1801 tctgatttcc tggtcttctt ctgccgtcag acgaacaggg cgactgatag cccgcctgcg
     1861 cgtattactt ccacttcgtt ttgtcataaa acatggctcc gtatctgaca tgggtgtcgg
     1921 ggcaaagccc tgaccagggc aattgtaata gcgtgcatgt atgcgcggta taacaattgc
     1981 acatcctgtc ctgtcagcaa gctcgaatta ccgacaaagg cacggcagtt ttttggcagt
     2041 tacagtgttg tctgacagaa atgcccgtca aaaagccagg cggcagaata gcggcagcaa
     2101 aacagtcgaa aagtggtacg cgatataatc acataacgca gatgacagac agaacggaga
     2161 aaacgaaaag atgaacaagc agcagcaagc cgtactcaac atggcgggat tcataaaaag
     2221 ccagagcctg acgctgctcg aaaaactgga cgcactcgat gctgacgagc aggccaccat
     2281 gtgtgagaaa ctacacgaac tcgcagaaga actccagaac agcatacaga cacgctttga
     2341 agtagaaaat agcacagaga gataacgctc aggacaggat gtcgaacggc acaacagagc
     2401 gtaaggagaa aatgtcacat aaggcgctct tccgcttcct cgctcactga ctcgctacgc
     2461 tcggtcgttc gactgcggcg agcggtatca gctcactcaa agacggtaat gcggttatcc
     2521 acagaatcag gggataacgc cggaaagaac atgtgagcaa aaagccgaag gcagggacaa
     2581 aggccgcgca ggtggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc
     2641 gacgctcaag tcagaggtgg cgaaacccga caggactat
//
