LOCUS       NZ_CP034063             3920 bp    DNA     linear   CON 09-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_535 plasmid unnamed4.
ACCESSION   NZ_CP034063
VERSION     NZ_CP034063.1
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 3920)
  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  JOURNAL   Unpublished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 3920)
  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
            CP034063.1.
            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..3920
                     /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="unnamed4"
                     /collection_date="2016-04-01"
                     /collected_by="Children's National Hospital"
     gene            388..855
                     /locus_tag="EGX88_RS25345"
                     /old_locus_tag="EGX88_25365"
     CDS             388..855
                     /locus_tag="EGX88_RS25345"
                     /old_locus_tag="EGX88_25365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014526575.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_075332508.1"
                     /translation="MRIDISHQTRHTPPNMLPREQNCVAMALSACFRQQLNPVVNSLLK
                     ERIIHSPKELEHDNAVIRVLQKLQIQEVCNNTLWETAKQQLLQKSDGRYFAINSKHLSF
                     PGPGESHAFCCIKYKNAIGINGNNAETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(1401..1634)
                     /locus_tag="EGX88_RS25350"
                     /old_locus_tag="EGX88_25370"
     CDS             complement(1401..1634)
                     /locus_tag="EGX88_RS25350"
                     /old_locus_tag="EGX88_25370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1641..1760)
                     /locus_tag="EGX88_RS26445"
     CDS             complement(1641..1760)
                     /locus_tag="EGX88_RS26445"
                     /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="hypothetical protein"
                     /protein_id="WP_005065476.1"
                     /translation="MRYHEDSNGRFLVLPEGMKAETNWTMENGKQNAVRLVQE"
                     /name="hypothetical protein"
     gene            complement(1800..2171)
                     /locus_tag="EGX88_RS25355"
                     /old_locus_tag="EGX88_25375"
     CDS             complement(1800..2171)
                     /locus_tag="EGX88_RS25355"
                     /old_locus_tag="EGX88_25375"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067494.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTSALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILRE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2212..2526)
                     /locus_tag="EGX88_RS25360"
                     /old_locus_tag="EGX88_25380"
                     /pseudo=""
     CDS             complement(<2212..2526)
                     /locus_tag="EGX88_RS25360"
                     /old_locus_tag="EGX88_25380"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2549..2860)
                     /locus_tag="EGX88_RS25365"
                     /old_locus_tag="EGX88_25385"
     CDS             complement(2549..2860)
                     /locus_tag="EGX88_RS25365"
                     /old_locus_tag="EGX88_25385"
                     /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="hypothetical protein"
                     /protein_id="WP_005065488.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEKNQYSILWVDAPGQGTA"
                     /name="hypothetical protein"
     gene            complement(2850..3173)
                     /locus_tag="EGX88_RS25370"
                     /old_locus_tag="EGX88_25390"
     CDS             complement(2850..3173)
                     /locus_tag="EGX88_RS25370"
                     /old_locus_tag="EGX88_25390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955991.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLCQLAAIGNNLNQTARKVNSGQWSSGNRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3237..3428
                     /locus_tag="EGX88_RS25375"
                     /old_locus_tag="EGX88_25395"
     CDS             3237..3428
                     /locus_tag="EGX88_RS25375"
                     /old_locus_tag="EGX88_25395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165981.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESFHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3695..>3920)
                     /locus_tag="EGX88_RS26450"
                     /old_locus_tag="EGX88_25405"
     CDS             complement(3695..>3920)
                     /locus_tag="EGX88_RS26450"
                     /old_locus_tag="EGX88_25405"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=2
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_215254033.1"
                     /translation="RGSFQGETPGIFIVLSGFATSDLSVGFCDARQGGGAYGKTPSARP
                     SSCPWSFAHMFFPALSPDSVDNSISFLSE"
                     /name="hypothetical protein"
     Typing          complement(3474..3559)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(1298..2586)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.575"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2854..3200)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.552"
                     /coverage="98.0"
                     /evalue="7.529999999999999e-67"
ORIGIN
        1 ccgttcagcc cgaccgctgc gccttatccg gtaactatcg tcttgagtcc aacccggtaa
       61 gacacgactt aacgccactg gcagcagcca ttggtaactg gacaaggtgg attgagatat
      121 taagagttct tgaagtggtg gcctaactgc ggctacacta gaaggacagc atttggtatc
      181 tgtgctccac caagccagtt accttcggaa gaaagagttg gtagctctag attccggcaa
      241 acaaaccacc gttggtagcg gtggtttttt tgtttgcagg cagcagatta cgcgccgcaa
      301 aaaaggatct caagaagatc ttgaatcact ctatgaaaat tttgttttat agccgtattt
      361 gttgatgcta taagccagag accttctatg agaatagaca tatcacatca aacacggcat
      421 accccgccaa acatgcttcc tcgggaacaa aattgtgtag caatggcatt atctgcgtgc
      481 tttagacaac aactaaaccc tgtggtaaac agcttattaa aagagagaat aatacactcc
      541 cctaaagaat tggaacatga taacgcagta ataagagtcc tgcaaaaact acaaattcaa
      601 gaagtttgta acaacaccct ttgggagaca gccaaacaac aactacttca aaaatcggat
      661 ggaagatatt ttgccatcaa ttctaaacac ttatcctttc caggcccagg agaatctcac
      721 gccttctgtt gcatcaaata caaaaatgca attggcatta acggaaacaa tgccgaaacc
      781 caatcgaccc actaccaacc ctatccctat gataaagtca gtatatgggg accattccct
      841 cacaatttaa cgtaatatct taattgtacg caccgctgaa acgcgttcgg cgcgatcacg
      901 gcagcagaca ggtaaaaatg gcaacaaacc acccgaaaaa ctgccgcgat cgcacccggt
      961 aaattttaac cacatgcata gctatgcagc catgtgaatc acgcaggaat tgccagccag
     1021 agacagctga aacggatttt tttcatgctt tcggaagcga agaagacggg gacctgagcg
     1081 ggaaaaaaga agttcagggg aatgagcgcg atctggcaat agaggcaaaa cacagcaaca
     1141 aaagacacac cagaatcgcg cccgtatgcg ttttaacgcg ttcctatgtt ttcagcaagg
     1201 tctgactgaa gcgcgttccc ggtgcccccg aaccaaccat tatcccaaaa aatgcaccgg
     1261 aaacgcgctg acaacatttt agcctgtctc tgattaccat cccagcgaag ggccatccag
     1321 tgtccgttcc tgtatttcca gctggtgctc acgctccagg gataacgcat gttcgcattc
     1381 ctgtatcagc cgttcgtccc ttatctcctg ttctcgctgt ataactggct caagcgttct
     1441 gtctgctcgc tcaagtgctg cacctgctga ctcaactgca tgacccgctc gttcagcatc
     1501 gcgttgtccc gttgcgtaag cgaaaacatt ttctgcaatt ccacgaaggc gctctcccat
     1561 tcgttcagcc gctgcatata gtcctgttgc agttgttcta atgcgttcag caaatgtctt
     1621 tccagctccg tcatgctctg ttactcctgt accagcctta cggcattctg tttcccgttt
     1681 tccatcgtcc agttcgtttc ggctttcatc ccctcgggca acaccagaaa acgtccgttg
     1741 ctgtcctcgt gataacgcac gccccatgtc ttcgcgttca gcttctccag actctctttc
     1801 tactcgcgga gaatattcat gttcgcgttt atcttcatgc cctggtacca cagcaggctc
     1861 ccggtcgtgg caaacatcag tactgagacg ataatcagcc acagccagcg tttcacgctc
     1921 attttcagta cggttttcca gtgtgcgtcc atcgtatcga cggtcgtttt ctgatacctc
     1981 tccagaagtt ctttcagggc tgatgtatgg tcgttgatag cgttcctgat taaagattcg
     2041 tttgaggtca gttccctgtt tacagattct tcgagcttcc tgaactcgtc gttcagcatt
     2101 ttctctgtag attcggctct ctctttcagc tttttctcga actccgcacc cgtctgtaaa
     2161 agattgctca taaaacgctc ctttcagtct gatattcttc ccgccgttcg ggtctgcaat
     2221 gctgatactg cttcgcgtca ccctaaccac gtcaatccct gcctctgtga gagcctgaat
     2281 cacatcctga cggcctttta tctctccggc atggtaaagc gcgtctatcc cgcgtgtaac
     2341 gccctcagca atcgcctgtt tcgtttccgg cagattatca gggagtgtca gcgtcctgcg
     2401 gttctccggg gcgttcgggt catgcagccc gtaatagtga ttaaccagcg tctgccaggc
     2461 atcaattcta ggcctgtctg cgcggtcgta gtacggctgg aggcgttttc cggtctgtag
     2521 ctccatgttc ggaatgacaa aattcagctc aagccgtccc ttgtcctggt gcatccaccc
     2581 acaggatgct gtactgattt ttttcgagac cgggcatcag tacacgctca aagctcgcca
     2641 tcactttttc acgtcctccc ggcggcagct ccttctccgc gaacgacaga acaccggacg
     2701 tgtatttctt cgcaaatggc gtggcatcga tgagttcccg gacttcttcc ggattaccct
     2761 gaagcaccgt tgccccttcc cggttacgct cccttcccag caggtaatca accggaccac
     2821 tgccaccacc ttttccccgg gcatgaaact taactatcat cccgcgtccc ctgttccctg
     2881 acggccagac gcagccggcg cagctcgtcc ccgatggcca tcagtgcggc caccacctga
     2941 acccggttac cggaagacca ctgcccgctg ttcaccttcc tcgctgtctg attcaggtta
     3001 ttcccgatgg cagccagctg acacagtaac ggcggtgcca gtgtcggcag tttcccggaa
     3061 cgggcaaccg gctcccccag gcagacccgc cgcatccata ccgccagctg tttaccctca
     3121 cagcgttcca gtaaccgggc atgttcatca tcagtaaccc gtatcgtgag catcctctcg
     3181 cgtttcatcg gtatcattac ctcctgaaca gaaatccccc ttacacggag gcatcagtga
     3241 ctaaacagga aaaaaccgcc cttaacatgg cccgctttat cagaagccag acattaacgc
     3301 tgctggagaa gctcaacgaa ctggacgcgg atgaacaggc tgatatctgt gaatcgtttc
     3361 acgaccacgc cgatgagctt taccgcagct gcctcgcacg tttcggggat gacggtgaaa
     3421 acctctgaca tatgccggga gcagacaagc ccgtcagggc gcatcagcag gttttagcgg
     3481 gtgtcggggc gcagccatga cccagtcacg tagcgatagc ggagtgtata ctggcttaac
     3541 catgcggcat cagtgcagat tgtatgaaaa gtgcgccata ccgggtatga aataccgcac
     3601 agatgcgtaa ggagaaaatg cacgtccagg cgcttttccg cttcctcgct cactgactcg
     3661 ctacgctcgg tcgttcgact gcggcgagcg gtatctactc actcaaaaac gaaatgctgt
     3721 tatccacaga atcaggggat aacgccggaa agaacatgtg agcaaaagac cagggacagg
     3781 aagaaggccg cgccgatggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
     3841 aaccgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
     3901 ccccctggaa gctccctcgt
//
