LOCUS       NZ_CP014097             1587 bp    DNA     linear   CON 05-MAR-2024
DEFINITION  Shigella sonnei strain FDAARGOS_90 plasmid unnamed2.
ACCESSION   NZ_CP014097
VERSION     NZ_CP014097.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03996263
            Assembly: GCF_001558295.2
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1587)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Sengamalay,N.,
            Ott,S., Godinez,A., Nagaraj,S., Vavikolanu,K., Aluvathingal,J.,
            Nadendla,S., Nandy,P., Hobson,J. 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  JOURNAL   Unpublished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 1587)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Sengamalay,N.,
            Ott,S., Godinez,A., Nagaraj,S., Vavikolanu,K., Aluvathingal,J.,
            Nadendla,S., Nandy,P., Hobson,J. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-DEC-2017) Center for Devices and Radiological Health,
            US Food and Drug Administration, 10903 New Hampshire Avenue, Silver
            Spring, MD 20993-0002, USA
  REMARK    Sequence update by submitter
REFERENCE   3  (bases 1 to 1587)
  AUTHORS   Goldberg,B., Campos,J., Tallon,L., Sadzewicz,L., Sengamalay,N.,
            Ott,S., Godinez,A., Nagaraj,S., Nadendla,S. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-DEC-2015) Institute for Genome Sciences, University of
            Maryland, 801 W.Baltimore Street, Baltimore, MD 21201, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP3 v. Oct 2014
            Genome Coverage                   :: 255.63x
            Sequencing Technology             :: Pacbio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 03/05/2024 04:09:28
            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)                     :: 5,070
            CDSs (total)                      :: 4,940
            Genes (coding)                    :: 4,303
            CDSs (with protein)               :: 4,303
            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)              :: 637
            CDSs (without protein)            :: 637
            Pseudo Genes (ambiguous residues) :: 0 of 637
            Pseudo Genes (frameshifted)       :: 174 of 637
            Pseudo Genes (incomplete)         :: 439 of 637
            Pseudo Genes (internal stop)      :: 110 of 637
            Pseudo Genes (multiple problems)  :: 83 of 637
            Pseudo Genes (short protein)      :: 3 of 637
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP014097.2.
            On Apr 2, 2019 this sequence version replaced NZ_CP014097.1.
            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/
FEATURES             Location/Qualifiers
     source          1..1587
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_90"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_90"
                     /db_xref="taxon:624"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: DC"
                     /collection_date="2013-09-08"
                     /collected_by="Children's National Hospital"
     gene            3..275
                     /locus_tag="AL477_RS00585"
                     /old_locus_tag="AL477_26295"
     CDS             3..275
                     /locus_tag="AL477_RS00585"
                     /old_locus_tag="AL477_26295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_145811.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_011310366.1"
                     /translation="MSHNLEHQKVHTRMVKEVLKAVARANNHPYQSVFADFITGHPSCT
                     VCFWETFHKMYPDSPYEYVTFCHTCRRFDLYETEAEMKADDPKWW"
                     /name="hypothetical protein"
     gene            256..1464
                     /locus_tag="AL477_RS00590"
                     /old_locus_tag="AL477_00485"
     CDS             256..1464
                     /locus_tag="AL477_RS00590"
                     /old_locus_tag="AL477_00485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000198547.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="WP_000198534.1"
                     /translation="MTRSGGDFQPRPLKRLFTANQCWTSFLDAGGLRDIEVEAVTKMLA
                     CGTRILGVKEYNCDKPECPHVRYVTNSCGSRACPSCGKKATDLWIATQLNRLPDCDWVH
                     LVFTLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGQEPGIFCAIHTYGRRLNWHP
                     HVHVSVTCGCLNKHGQWKKLSFLKDAMRSRWMWNMRQRLLKAWSEGLAMPESLSHITTE
                     SQWRSLVLKAGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGASLSFR
                     YLDHKTGETATETLTQRELVARLKQHIPEKFFKMVRYFGFLANRVCGEKLPQVYRALGM
                     DKPEPVAKVCYAQMVKQFLSRDPFECVLCGGRMVYRRAIAGLNVEGLKKNARDISLLRY
                     MPA"
                     /name="IS91 family transposase"
ORIGIN
        1 ccatgtcaca caacctggag caccagaaag tccacaccag aatggtgaaa gaggttctga
       61 aagccgtcgc cagagccaat aatcaccctt atcagtccgt atttgcagac tttatcaccg
      121 gtcatccctc ctgcacggtc tgtttctggg aaaccttcca caaaatgtac ccggattcac
      181 cgtacgaata cgtcacgttc tgccatacct gccgtcgttt tgatttatac gaaacagaag
      241 cggagatgaa ggcggatgac ccgaagtggt ggtgattttc agccccgacc gctgaaacgc
      301 ctgttcacag ccaaccagtg ctggacgtcc ttcctggatg cgggcggtct gcgcgatatc
      361 gaggttgagg ctgtcacaaa aatgctggcc tgcggcacgc ggatactggg agtgaaggaa
      421 tacaactgcg ataaacctga gtgcccccac gtcagatacg tcactaactc atgcggcagc
      481 cgtgcctgcc cgtcctgcgg aaaaaaggcc acagacctgt ggatagcgac acagctgaat
      541 cgtcttcctg actgcgactg ggtacatctg gtcttcaccc tgccggacac gctgtggccg
      601 gtgttcgaaa gcaaccggtg gctgctgaat gacgtgtgcc gtctggcggt ggagaatctg
      661 ctgtatgccg cccggaaacg ggggcaggaa cccggtatct tctgcgccat ccacacgtat
      721 ggccgtcgtc tcaactggca tccgcatgta catgtgtctg taacctgtgg atgtctgaat
      781 aagcatggtc agtggaaaaa gctgagcttc ctgaaagacg cgatgcgttc gcggtggatg
      841 tggaatatgc ggcaacggct tctgaaagcg tggtcagagg ggctggcgat gccggagtcg
      901 ttgtcacata tcacgacgga atcacagtgg agaagcctgg tgctgaaagc cggaggaaaa
      961 tactggcatg tgtacatgtc gaaaaaaacg gccggcggga ggaatacggc gcgctacctg
     1021 ggtcgttatc tgaagaagcc gccgatagcg gcctcccggc tggcacatta caacggaggg
     1081 gcgagcctga gcttccgtta cctggaccac aaaacgggag aaacggcgac ggaaacgctg
     1141 acacagcgtg agctggtcgc gaggctgaaa cagcacatcc cggagaagtt ttttaagatg
     1201 gtgaggtact tcgggttcct tgccaaccgg gtgtgtggag agaagctgcc gcaggtgtac
     1261 cgtgctctgg ggatggataa accggaacca gtggcgaaag tgtgctatgc acaaatggtg
     1321 aaacagttcc tgagtcgtga cccgttcgaa tgcgtgctgt gtggcggccg gatggtatac
     1381 cgccgggcca ttgcggggct gaatgtggag gggctgaaga aaaacgcgcg ggatatcagt
     1441 ctgctgaggt atatgccggc ctgacacagg ctaagtgtgc ccgggaatcg gtgcaagtat
     1501 aaaaaacagc ctgttgcggt ataagaatcg accatgcaga gagagaaaac accggagtgg
     1561 tggggaaaaa cagaaaggct cacgtgg
//
