LOCUS       NZ_CP046288             2089 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Shigella sonnei strain FDAARGOS_715 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP046288
VERSION     NZ_CP046288.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056430
            Assembly: GCF_009729995.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2089)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y. and
            Sichtig,H.
  TITLE     FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS):
            Supporting development and validation of Infectious Disease Dx tests
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2089)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y. and
            Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-NOV-2019) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SMRT v. 2.3.0, HGAP v. 3
            Genome Coverage                   :: 521.02x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 03:33:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,196
            CDSs (total)                      :: 5,069
            Genes (coding)                    :: 4,349
            CDSs (with protein)               :: 4,349
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 720
            CDSs (without protein)            :: 720
            Pseudo Genes (ambiguous residues) :: 0 of 720
            Pseudo Genes (frameshifted)       :: 217 of 720
            Pseudo Genes (incomplete)         :: 505 of 720
            Pseudo Genes (internal stop)      :: 128 of 720
            Pseudo Genes (multiple problems)  :: 123 of 720
            Pseudo Genes (short protein)      :: 3 of 720
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP046288.1.
            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..2089
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_715"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_715"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="Nigeria: Ibadan"
                     /collected_by="University of Ibadan"
     gene            complement(822..1088)
                     /locus_tag="FOC23_RS25490"
                     /old_locus_tag="FOC23_25455"
     CDS             complement(822..1088)
                     /locus_tag="FOC23_RS25490"
                     /old_locus_tag="FOC23_25455"
                     /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"
     gene            complement(1092..2057)
                     /locus_tag="FOC23_RS25495"
                     /old_locus_tag="FOC23_25460"
     CDS             complement(1092..2057)
                     /locus_tag="FOC23_RS25495"
                     /old_locus_tag="FOC23_25460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     Typing          complement(1433..1664)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 tgatgtggta tattcatcac gtacctgtgc attgcgagcc agtacatgtc accagagttt
       61 gccgctgagg tgacacattc gaaatgttgg ggagtgttga cgcactcccc aacgccgatt
      121 aaaaacgcct caattctgct ccattttctt tgacctgtca aaacccactc aaagcctcgt
      181 cattactggg ctaaaccact atttcatatc cgccatttat cccttaagta taaatacaag
      241 gatcacgcgc gagaattgcg caaaaaataa ccgcaatttt aaccccccaa aacaagcacc
      301 cccgaacggc tgagcccaac cttttccaca cacccgatca ccaaaacagg gaataaaaac
      361 aaaaccctgt cttacaggtg gatggcctca cttcgtgaaa ccatccaccc cgcataagtt
      421 ttttaatcgg tggtgtcgtc aatcactaaa tcggaacccc aaaggggacc cccacgattt
      481 atcatttgac gagattaact ctcggagatg gcatcatgct tttaacggac tttaaaaaac
      541 ggtgaacgga tgcggatttt aatccgtgtc tgtgaggcgt tgagcaacga gcaaagcgag
      601 gcggtagaaa gagagccagc ggcaggctca ggacgataat ccggggaaaa tgtaccactc
      661 gcagagtgtt aacatttgac atcggattgt ctatcctgca ttggtgtcga gttggcaagg
      721 ctgaggataa tgctgaggat aatgcaggat agacagagca ctagagattg catgcaatct
      781 cgtacctatc acctcagcct gccgctggct cttttccaga actaagaatg cgttcttaaa
      841 aatccaaact tgataccgtt taaatctatt ttcacaaaaa gagtttttac cctctcgttt
      901 gttttctgaa tatataaaat taattcatcc tcaaaacctt cgtgcggatg aaaaccaaat
      961 gtgccaaaac ttaatccatc aataagcaaa ataaggtttt taaacctgtc aggaatcacc
     1021 gcttcacttc ttaaaaaaaa taaaccaata gtcttatttc cattcaggta ttcaatatta
     1081 atattcatac gttaatccga tttatccttc tcaggggcgc gtttgtaacg ccgtttacct
     1141 gaatcccaga caaacgccgt ccgcttcccg tcatcagtgc catcccctac atcgtcggca
     1201 atgacaagat cctcattggt ttctcgatcc aactggagga cgttttttag cgccccaccg
     1261 gtcgagataa aacggcgctt gtgaagctgc cgcgtcaact caagaaacca ctcaggatcg
     1321 tttgccatat cttccggttt aacggagtat ttcagcgttt cagcaaccgc gctttgcagt
     1381 tgctcggcaa cgttggccac aacctcacct gtcttagttt ttactgcccg aatatcgata
     1441 ttcggctcat agttcacccg caagcaatcg cgccagagtt ctacccaacg ttcgtgctta
     1501 acgtagttct tccctttaaa ccaagaaggt tgcaccatca gcagacagtg aaaatgcgga
     1561 tgtgcgctgc catccttacc tcgcgtcacc tccgtagccc tgatccaccc ctgaacaggt
     1621 gatagctcct ttcgcttttc cattcgctta aacgccgcat tcattgctgt aaggactgtt
     1681 ccaagttcac ctatctcgca gttcctgaca gttaacgtca gaaacaacca tcgggaagac
     1741 gggtaatcca caacgatttt cggtagagcc tgataaaaac gggcttgcca catgagggtt
     1801 cttctccact ggcagacagg gcaatgacgg acacggcaaa attgcgcact acgaagccgt
     1861 aggcgcgttt ctccggtttc catgatggta gaccaaccaa aacgtaacaa accgctacag
     1921 gaggccatac ggagtgcata gcgctcgaat tcagcagcag tctggtagat acccccgaca
     1981 gaatcggtaa gcgtgcgctg ggtatcccaa actgcatcac gggggctgta gtccgaaagg
     2041 aatttatctt ctgacattaa gcctgctccg atctgggcag gctgtgatt
//
