LOCUS       NZ_CP023648             2136 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CFSAN030807 plasmid pCFSAN030807_3, complete
            sequence.
ACCESSION   NZ_CP023648
VERSION     NZ_CP023648.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03612247
            Assembly: GCF_002442535.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2136)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Whole genome sequencing of cultured foodborne pathogen
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2136)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 700.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002442535.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 03:16:54
            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)                     :: 5,167
            CDSs (total)                      :: 5,037
            Genes (coding)                    :: 4,336
            CDSs (with protein)               :: 4,336
            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)              :: 701
            CDSs (without protein)            :: 701
            Pseudo Genes (ambiguous residues) :: 0 of 701
            Pseudo Genes (frameshifted)       :: 197 of 701
            Pseudo Genes (incomplete)         :: 506 of 701
            Pseudo Genes (internal stop)      :: 123 of 701
            Pseudo Genes (multiple problems)  :: 117 of 701
            Pseudo Genes (short protein)      :: 3 of 701
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023648.1.
            Bacteria and source DNA available from Dwayne Roberson, US FDA.
            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..2136
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CFSAN030807"
                     /serovar="Serotype group D"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCFSAN030807_3"
                     /geo_loc_name="Somalia"
     gene            join(1188..2136,1..59)
                     /locus_tag="AT852_RS27905"
                     /old_locus_tag="AT852_27905"
     CDS             join(1188..2136,1..59)
                     /locus_tag="AT852_RS27905"
                     /old_locus_tag="AT852_27905"
                     /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="protein rep"
                     /protein_id="WP_252981439.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPGIQVNGVTNAPLRRINRINV"
                     /name="protein rep"
     gene            56..322
                     /locus_tag="AT852_RS27895"
                     /old_locus_tag="AT852_27895"
     CDS             56..322
                     /locus_tag="AT852_RS27895"
                     /old_locus_tag="AT852_27895"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          1582..1813
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ttcaggtaaa cggcgttaca aacgcgcccc tgagaaggat aaatcggatt aacgtatgaa
       61 tattaatatt gaatacctga atggaaataa gactattggt ttattttttt taagaagtga
      121 agcggtgatt cctgacaggt ttaaaaacct tattttgctt attgatggat taagttttgg
      181 cacatttggt tttcatccgc acgaaggttt tgaggatgaa ttaattttat atattcagaa
      241 aacaaacgag agggtaaaaa ctctttttgt gaaaatagat ttaaacggta tcaagtttgg
      301 atttttaaga acgcattctt agttctggaa aagagccagc ggcaggctga ggtgataggt
      361 acgagattgc atgcaatctc tagtgctctg tctatcctgc attatcctca gcattatcct
      421 cagcattatc ctcagccttg ccaactcgac accaatgcag gatagacaat ccgatgtcaa
      481 atgttaacac tctgcgagtg gtatattttc cccggattat cgtcctgagc ctgccgctgg
      541 ctctctttct accgcctcgc tttgctcgtt gctcaacgcc tcacagacac ggattaaaat
      601 ccgcatccgt tcaccgtttt ttaaagtccg ttaaaagcat gatgccatct ccgagagtta
      661 atctcgtcaa atgctaaatc gtgggggtcc cctttggggt tccgatttag tgattgacga
      721 caccaccgat taaaaaactt atgcggggtg gatggtttca cgaagtgagg ccatccacct
      781 gtaagacagg gttttgtttt tattccctgt tttggtgatc gggtgtgtgg aaaaggttgg
      841 ggtaagccgt tcgggggtgc ttgttttggg gggttaaaat tgtggttatt ttttgcgcaa
      901 ttctcgcgcg tgatccttgt atttatactt aagggataaa tggcggatat gaaatagtgg
      961 tttagcccag taatgacgag gctttgagtg ggttttgaca ggtcaaagaa aatggagcag
     1021 aattgaggcg tttttaatcg gcgttgggga gtgcgtcaac actccccaac atttcgaatg
     1081 tgtcacctca gcggcaaact ctggtgacat gtactggctc gcaatgcaca ggtacgtgat
     1141 gaatatacca catcaaatca cagcctgccc agatcggagc aggcttaatg tcagaagata
     1201 aattcctttc ggactacagc ccccgtgatg cagtttggga tacccagcgc acgcttaccg
     1261 attctgtcgg gggtatctac cagactgctg ctgaattcga gcgctatgca ctccgtatgg
     1321 cctcctgtag cggtttgtta cgttttggtt ggtctaccat catggaaacc ggagaaacgc
     1381 gcctacggct tcgtagtgcg caattttgcc gtgtccgtca ttgccctgtc tgccagtgga
     1441 gaagaaccct catgtggcaa gcccgttttt atcaggctct accgaaaatc gttgtggatt
     1501 acccgtcttc ccgatggttg tttctgacgt taactgtcag gaactgcgag ataggtgaac
     1561 ttggaacagt ccttacagca atgaatgcgg cgtttaagcg aatggaaaag cgaaaggagc
     1621 tatcacctgt tcaggggtgg atcagggcta cggaggtgac gcgaggtaag gatggcagcg
     1681 cacatccgca ttttcactgt ctgctgatgg tgcaaccttc ttggtttaaa gggaagaact
     1741 acgttaagca cgaacgttgg gtagaactct ggcgcgattg cttgcgggtg aactatgagc
     1801 cgaatatcga tattcgggca gtaaaaacta agacaggtga ggttgtggcc aacgttgccg
     1861 agcaactgca aagcgcggtt gctgaaacgc tgaaatactc cgttaaaccg gaagatatgg
     1921 caaacgatcc tgagtggttt cttgagctga cgcggcagct tcacaagcgc cgttttatct
     1981 cgaccggtgg ggcgctaaaa aacgtcctcc agttggatcg agaaaccaat gaggatcttg
     2041 tcattgccga cgatgtaggg gatggcactg atgacgggaa gcggacggcg tttgtctggg
     2101 attcaggtaa acggcgttac aaacgcgccc ctggga
//
