LOCUS       NZ_CP034065             2551 bp    DNA     linear   CON 09-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_535 plasmid unnamed6.
ACCESSION   NZ_CP034065
VERSION     NZ_CP034065.1
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 2551)
  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  JOURNAL   Unpublished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 2551)
  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                   :: 15.85x
            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
            CP034065.1.
            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..2551
                     /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="unnamed6"
                     /collection_date="2016-04-01"
                     /collected_by="Children's National Hospital"
     gene            complement(362..556)
                     /locus_tag="EGX88_RS25400"
                     /old_locus_tag="EGX88_25425"
     CDS             complement(362..556)
                     /locus_tag="EGX88_RS25400"
                     /old_locus_tag="EGX88_25425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            842..1165
                     /gene="mobA"
                     /locus_tag="EGX88_RS25405"
                     /old_locus_tag="EGX88_25430"
     CDS             842..1165
                     /gene="mobA"
                     /locus_tag="EGX88_RS25405"
                     /old_locus_tag="EGX88_25430"
                     /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            complement(1391..2014)
                     /locus_tag="EGX88_RS25415"
                     /old_locus_tag="EGX88_25435"
     CDS             complement(1391..2014)
                     /locus_tag="EGX88_RS25415"
                     /old_locus_tag="EGX88_25435"
                     /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_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(2393..>2551)
                     /locus_tag="EGX88_RS26460"
     CDS             complement(2393..>2551)
                     /locus_tag="EGX88_RS26460"
                     /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_249974391.1"
                     /translation="HEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLEV
                     MRLLRLN"
                     /name="replication initiation protein"
     Typing          595..833
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          843..1162
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="5.28e-62"
ORIGIN
        1 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
       61 ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
      121 gccacctgcg cggcctttgc ccctgccttc ggctttttgc tcacatgttc tttccggcgt
      181 tatcccctga ttctgtggat aaccgcatta ccgcctttga gtgagctgac accgctcgcc
      241 gcagtcgaac gaccgagcgt agcgagtcag tgagcgagga agcggaagag cgccttatgt
      301 gacattttct ccttacgcac cggtataccg ttctgcatcc tgtctggagc aggatacact
      361 gttatacccc ggtgccactt tccgcttcaa agcgtgtctg tatgctgttc tggagttctt
      421 ccgcgatttc gtgcagcttc tcacacatgg cggcctgttc gtcggcatcg agtgcgtcca
      481 gcttttcgag cagcgtcagg ctctggcttt ttatgaatcc cgccatgttg agtacggttt
      541 gctgctgctt gttcatcttt ctgttttctc cgttctgtct gtcatctgcg ttgtgtgatt
      601 atatcgcgta ccacttttcg actgttttac cgccggtatt ctgccgtctg acgcattgac
      661 gggtatttct gcctgacaat actgtcactg ccaaaaaaac tgccgtgcct ttgtcggtaa
      721 ttcgaacttg ctgacaggac aggatgtgta attgttatac cgcgcataca tgcacgctat
      781 tacaattacc ctggtcaggg cttcgccccg acaccccgtg tcagatacgg agccatgttt
      841 tatgacaaaa cgaagtggaa gtaatacgcg caggcgggct atcagtcgcc ctgttcgtct
      901 gacggcagaa gaagaccagg aaatcagaaa aagggctgct gaatgcggca agaccgtttc
      961 tggtttttta cgggcggcag ctctcggtaa gaacgttaac tcactgactg atgatcgggt
     1021 gctgaaagaa gttatgagac tgggggcgtt acagaaaaaa ctctttatcg acggcaagcg
     1081 tatcggggac agggagtatg cggaggtgct gatcgctatt acggagtatc accgtgccct
     1141 gttatccagg cttatggcag attagcttcc cggggagaaa actgttgaaa acagacggta
     1201 tgaacacggt aagctcccaa agtgatctcc attcgctttc atgcatagct atgcagcgag
     1261 ctgaaaacga tcctgacgca tccttcctgt ttttccgggg taaaacatct atttttgtgg
     1321 tgtctgcgtc agaatcgcgt tcagcgcgtt tcagtggtgc gtacaattaa gggattatgg
     1381 taaatgatga ttatttctcc tctctattta ctcggcaagc gccaaagtga attacatcat
     1441 attttactcc tgattcattt attactttaa atatgtcaga aaggtgcttc ttatgatttt
     1501 tatcagttat aaatgctata tcaatatttt tgtttcctaa gccatcttga tgtctttgta
     1561 taatattttg ggcttgttca tggtaatata gagcatagtt ttttatcttc tcattacttg
     1621 ttgcgtattc ttttctatat atggcttgtg acatcatttc ttcttctaat tttgattgag
     1681 gtatattgcg cgcgttcgct agaactttta ggtcatcttt gcttatgttt agtgatggtg
     1741 ttaacccttt ttgagcttca gtatggcgtt tgtttacctc tgaaagaacg cttagtccct
     1801 ttgtgaagtc gttgtctttt gtataaaaat caattcttag gtttttgggg actacagtcc
     1861 atccatcgcc tttttgacgc gtgaatagtg tttgtggatg ggagatctct ttccatccac
     1921 catgcgacat aatgacaagt tgtgttgctt ttcctgtttg gctcaatcct attccgtctt
     1981 tctggaataa acgacgatga cttgttacgt ccatgtttgg tgatgggtgt gtttttatat
     2041 ttttggatga tgttagaagg tgatttctta ttgttgatga tatgtttgtt atgagattcg
     2101 aattgagtat tttcatttgt taacaatcca tttttgcggt gttttttatt gttttttttc
     2161 ttttgtttaa gggtgtgtcg gtgtaagtgt ttattttatg ggttaaagta ggataccaag
     2221 tgtgaaaaaa aattaaaggt tcttcttgag atcctttttt tctgcgcgta atctgctgcc
     2281 tgtaaacgaa aaaaccgccc tgcaaggcgg tttttcgaag gttctcagag ctatcaactc
     2341 tttgagccga ggtaactggc ttggaggagc gcagtcacca aaacttgttc tttcagttta
     2401 gccttaacag gcgcatgact tcaagtctta ctcctctaat tcggttatca gtggctgctg
     2461 ccagtggcga taattcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     2521 cgcagcggtc gggctgaacg gggggttcgt g
//
