LOCUS       NZ_CP034062             1538 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_535 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP034062
VERSION     NZ_CP034062.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163230
            Assembly: GCF_003855135.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1538)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., 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  JOURNAL   Unpublished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 1538)
  AUTHORS   Campos,J., Goldberg,B., Tallon,L., Sadzewicz,L., Zhao,X.,
            Vavikolanu,K., Mehta,A., Aluvathingal,J., Nadendla,S., Geyer,C.,
            Nandy,P., Yan,Y. and Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-NOV-2018) 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. 3.0, SPAdes v. 3.6.0
            Genome Coverage                   :: 1311.02438897959x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 03:05:06
            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)                     :: 4,990
            CDSs (total)                      :: 4,859
            Genes (coding)                    :: 4,112
            CDSs (with protein)               :: 4,112
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 747
            CDSs (without protein)            :: 747
            Pseudo Genes (ambiguous residues) :: 0 of 747
            Pseudo Genes (frameshifted)       :: 273 of 747
            Pseudo Genes (incomplete)         :: 419 of 747
            Pseudo Genes (internal stop)      :: 175 of 747
            Pseudo Genes (multiple problems)  :: 117 of 747
            Pseudo Genes (short protein)      :: 5 of 747
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034062.1.
            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..1538
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_535"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_535"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /collection_date="2016-04-01"
                     /collected_by="Children's National Hospital"
     gene            join(1199..1538,1..137)
                     /locus_tag="EGX88_RS25325"
                     /old_locus_tag="EGX88_25345"
     CDS             join(1199..1538,1..137)
                     /locus_tag="EGX88_RS25325"
                     /old_locus_tag="EGX88_25345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          742..823
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          complement(1012..1120)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.091"
                     /coverage="100.0"
                     /evalue="9.09e-49"
     Typing          complement(370..627)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="99.0"
                     /evalue="3.9e-116"
ORIGIN
        1 gtgcgtatgc cctcgatcca catgaagtct ggaagggata caacactacg aaaaaccatg
       61 cagcgtttgt cactaaaaca ctggtcaaca aagacggtga tattcagcgc cgaatcatgg
      121 ccatgttttc aaattgagcc agcggcaggc ggacaatcag gggctacgtg ttaacgtttt
      181 gaccatgatt gtctatcctg cattgctctt ttgccgcctc aaaatccctt gcgtgttttt
      241 gctccccgat ccccagaacg accgcgccgc cacggttccg gctgcgcctt gagcgcaacc
      301 ggaaaccgtc tggggagaac cccagacccc catcgctgta acaccgacgg tctacgacca
      361 ccaaccagcc gaatagctgc ctgtgccgtg caaataggct ttgcagggag ctgacgcggt
      421 tcctggcgac ctgaaagccc ctggttaggg gtatcggcgc gcctgacctc ctgagagcct
      481 ctgtaagcgt ttttcgcgcc ttccatgccc tgacgggcat ttaaacccgt ttcgtgcgtc
      541 tgagagcttc tgagcgtgtt tgaagggcta tctgacgact catccccgaa agaacaacaa
      601 cgggatcacc gacaacatgc gagaggtgat cccgctcgcc gcaagtcgat gaccgagcgt
      661 agcgagcgaa tcgacgagga agcggaagag aaccggaagt tacattgagc acttacgcac
      721 ggatgcgggg tgtcggggtg aagccctgac caagtgggga atgtctgagt gcgcgtgcgc
      781 ggtccgacat tcccacatcc tgtcccgatt tctgaggcgt tttaacggtg aacggacggc
      841 aaaaacatga tcgagcgtgg agagcgcgaa atcgggcaaa atcacggctg acgaggcttg
      901 cagaggagta agccagtata cactccgcta tcgctacgtg actgggtcag ggcttcgccc
      961 cgacacccca aaagggcgtt gcgttgcgcg caacgccctt gcctagaata gatcttttac
     1021 gtcgatttgt aagttgttgt ttttttagtg tgttttttgt ttacctgtcg catccagggt
     1081 gacacaacgt tgtcgcatcc tggatgcgac aacacgcaac aaggtgttgc acagatgtgt
     1141 catgatggct tagatttgaa ccaacattag tgcatgggat tttcagaggg aaaaaatcat
     1201 gtttattgat tcagaaaaac gactgaaaca actttcagat gaggcaaaga aaaacaccga
     1261 agatctcgaa gaagcaaaga agaattcaag gtttacacag gtatccccaa aaggttggga
     1321 acgcgttcga gagctgctga aggatagcca aggcatatca gcactgaagc tgtactcatt
     1381 tttagcagag catatcgatc ctacgtgtgg cgctgtcgtt gcggatcagc aattcctagc
     1441 tgaaaaactt ggagttagca gaagcacaat tattcggtgg ctcaattact tagaatcaaa
     1501 aaatgcatta gttagaatcc ccgttgctgg taaggttt
//
