LOCUS       NZ_CP034070             2504 bp    DNA     linear   CON 16-APR-2024
DEFINITION  Shigella sonnei strain FDAARGOS_524 plasmid unnamed4.
ACCESSION   NZ_CP034070
VERSION     NZ_CP034070.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10163218
            Assembly: GCF_003855115.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2504)
  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  JOURNAL   Unpublished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 2504)
  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                   :: 1000.9613794x
            Sequencing Technology             :: PacBio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_003855115.1-RS_2024_04_16
            Annotation Date                   :: 04/16/2024 11:34:55
            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)                     :: 5,040
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,266
            CDSs (with protein)               :: 4,266
            Genes (RNA)                       :: 133
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 641
            CDSs (without protein)            :: 641
            Pseudo Genes (ambiguous residues) :: 0 of 641
            Pseudo Genes (frameshifted)       :: 184 of 641
            Pseudo Genes (incomplete)         :: 434 of 641
            Pseudo Genes (internal stop)      :: 110 of 641
            Pseudo Genes (multiple problems)  :: 84 of 641
            Pseudo Genes (short protein)      :: 3 of 641
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP034070.1.
            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..2504
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_524"
                     /isolation_source="Stool"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_524"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /collection_date="2015-12-29"
                     /collected_by="Children's National Hospital"
     gene            <1..159
                     /locus_tag="EGX92_RS26115"
     CDS             <1..159
                     /locus_tag="EGX92_RS26115"
                     /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"
     gene            538..1161
                     /locus_tag="EGX92_RS25420"
                     /old_locus_tag="EGX92_25460"
     CDS             538..1161
                     /locus_tag="EGX92_RS25420"
                     /old_locus_tag="EGX92_25460"
                     /inference="COORDINATES: protein motif:HMM:NF045398.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(1387..1710)
                     /gene="mobA"
                     /locus_tag="EGX92_RS25430"
                     /old_locus_tag="EGX92_25465"
     CDS             complement(1387..1710)
                     /gene="mobA"
                     /locus_tag="EGX92_RS25430"
                     /old_locus_tag="EGX92_25465"
                     /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            1996..2190
                     /locus_tag="EGX92_RS25435"
                     /old_locus_tag="EGX92_25470"
     CDS             1996..2190
                     /locus_tag="EGX92_RS25435"
                     /old_locus_tag="EGX92_25470"
                     /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"
     Typing          complement(1720..1958)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(1391..1710)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="4.58e-62"
ORIGIN
        1 cacgaacccc ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc
       61 aacccggtaa gacacgaatt atcgccactg gcagcagcca ctgataaccg aattagagga
      121 gtaagacttg aagtcatgcg cctgttaagg ctaaactgaa agaacaagtt ttggtgactg
      181 cgctcctcca agccagttac ctcggctcaa agagttggta gctctgagaa ccttcgaaaa
      241 accgccttgc agggcggttt tttcgtttac aggcagcaga ttacgcgcag aaaaaaagga
      301 tctcaagaag aacctttaat tttttttcac acttggtatc ctactttaac ccataaaata
      361 aacacttaca ccgacacacc cttaaacaaa agaaaaaaaa caataaaaaa caccgcaaaa
      421 atggattgtt aacaaatgaa aatactcaat tcgaatctca taacaaacat atcatcaaca
      481 ataagaaatc accttctaac atcatccaaa aatataaaaa cacacccatc accaaacatg
      541 gacgtaacaa gtcatcgtcg tttattccag aaagacggaa taggattgag ccaaacagga
      601 aaagcaacac aacttgtcat tatgtcgcat ggtggatgga aagagatctc ccatccacaa
      661 acactattca cgcgtcaaaa aggcgatgga tggactgtag tccccaaaaa cctaagaatt
      721 gatttttata caaaagacaa cgacttcaca aagggactaa gcgttctttc agaggtaaac
      781 aaacgccata ctgaagctca aaaagggtta acaccatcac taaacataag caaagatgac
      841 ctaaaagttc tagcgaacgc gcgcaatata cctcaatcaa aattagaaga agaaatgatg
      901 tcacaagcca tatatagaaa agaatacgca acaagtaatg agaagataaa aaactatgct
      961 ctatattacc atgaacaagc ccaaaatatt atacaaagac atcaagatgg cttaggaaac
     1021 aaaaatattg atatagcatt tataactgat aaaaatcata agaagcacct ttctgacata
     1081 tttaaagtaa taaatgaatc aggagtaaaa tatgatgtaa ttcactttgg cgcttgccga
     1141 gtaaatagag aggagaaata atcatcattt accataatcc cttaattgta cgcaccactg
     1201 aaacgcgctg aacgcgattc tgacgcagac accacaaaaa tagatgtttt accccggaaa
     1261 aacaggaagg atgcgtcagg atcgttttca gctcgctgca tagctatgca tgaaagcgaa
     1321 tggagatcac tttgggagct taccgtgttc ataccgtctg ttttcaacag ttttctcccc
     1381 gggaagctaa tctgccataa gcctggataa cagggcacgg tgatactccg taatagcgat
     1441 cagcacctcc gcatactccc tgtccccgat acgcttgccg tcgataaaga gttttttctg
     1501 taacgccccc agtctcataa cttctttcag cacccgatca tcagtcagtg agttaacgtt
     1561 cttaccgaga gctgccgccc gtaaaaaacc agaaacggtc ttgccgcatt cagcagccct
     1621 ttttctgatt tcctggtctt cttctgccgt cagacgaaca gggcgactga tagcccgcct
     1681 gcgcgtatta cttccacttc gttttgtcat aaaacatggc tccgtatctg acacggggtg
     1741 tcggggcgaa gccctgacca gggtaattgt aatagcgtgc atgtatgcgc ggtataacaa
     1801 ttacacatcc tgtcctgtca gcaagttcga attaccgaca aaggcacggc agtttttttg
     1861 gcagtgacag tattgtcagg cagaaatacc cgtcaatgcg tcagacggca gaataccggc
     1921 ggtaaaacag tcgaaaagtg gtacgcgata taatcacaca acgcagatga cagacagaac
     1981 ggagaaaaca gaaagatgaa caagcagcag caaaccgtac tcaacatggc gggattcata
     2041 aaaagccaga gcctgacgct gctcgaaaag ctggacgcac tcgatgccga cgaacaggcc
     2101 gccatgtgtg agaagctgca cgaaatcgcg gaagaactcc agaacagcat acagacacgc
     2161 tttgaagcgg aaagtggcac cggggtataa cagtgtatcc tgctccagac aggatgcaga
     2221 acggtatacc ggtgcgtaag gagaaaatgt cacataaggc gctcttccgc ttcctcgctc
     2281 actgactcgc tacgctcggt cgttcgactg cggcgagcgg tgtcagctca ctcaaaggcg
     2341 gtaatgcggt tatccacaga atcaggggat aacgccggaa agaacatgtg agcaaaaagc
     2401 cgaaggcagg gacaaaggcc gcgcaggtgg cgtttttcca taggctccgc ccccctgacg
     2461 agcatcacaa aaatcgacgc tcaagtcaga ggtggcgaaa cccg
//
