LOCUS       NZ_CP034064             3057 bp    DNA     linear   CON 09-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_535 plasmid unnamed5.
ACCESSION   NZ_CP034064
VERSION     NZ_CP034064.1
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 3057)
  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  JOURNAL   Unpublished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 3057)
  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
            CP034064.1.
            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..3057
                     /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="unnamed5"
                     /collection_date="2016-04-01"
                     /collected_by="Children's National Hospital"
     gene            complement(527..697)
                     /locus_tag="EGX88_RS25390"
                     /old_locus_tag="EGX88_25415"
     CDS             complement(527..697)
                     /locus_tag="EGX88_RS25390"
                     /old_locus_tag="EGX88_25415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_255625548.1"
                     /translation="MNMARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQ
                     IRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1572..2681
                     /gene="wzz(fepE)"
                     /locus_tag="EGX88_RS25395"
                     /old_locus_tag="EGX88_25420"
     CDS             1572..2681
                     /gene="wzz(fepE)"
                     /locus_tag="EGX88_RS25395"
                     /old_locus_tag="EGX88_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_025760792.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVGFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2926..>3057)
                     /locus_tag="EGX88_RS26455"
     CDS             complement(2926..>3057)
                     /locus_tag="EGX88_RS26455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_252967032.1"
                     /translation="HEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     Typing          361..447
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          761..859
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          984..1241
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.402"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(2914..3057)
                     /name="rep_cluster_2406"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.354"
                     /coverage="92.0"
                     /evalue="2.46e-31"
ORIGIN
        1 acgagggagc caccaggggg aaacgcctgg tatctttaag tcctgtcggg tttcgccacc
       61 tctgacttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg
      121 ccaccggcgc ggcctttttt cggggcctct cttttgctca catgtttttt ctggtgttat
      181 cccctgattc tgtggataac cgtatatccg tctttgcgtg agcagacacc gctcgccgca
      241 gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc ggaagagcgc cggaagctgc
      301 attttctcct tacgtatctg tgcagcattt cacacctcat atgtcgctgt tctctcacca
      361 tctgctctgc cgcctcataa ttaagccagt atacactccg ttatcgctac gtgactgggt
      421 catggctgcg ccccgacacc cgctaaaacc ccctgacgcg ccctgacggg cttgtctgct
      481 gacgaaaacg cccacgggaa agccgtgacc gcctccgtca gcttcgttat gttcctgttt
      541 cactttcggc ctcaaagcga atctggatgc tgttctggag ttcttctgcg agttcgtgca
      601 gtcgtttgca catggccgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg
      661 tcaggctctg gcttttgata catcgcgcca tattcagcgc agtttgttgt tatttgttca
      721 ccttccgttg ttctccgtca gttccgggtg tcgggggggg gaccctgagc aggtggtaat
      781 tgtaagacgt tgcgggcgat ggtattacaa ttgcacatcc tgtcctgttt ctttaggacg
      841 tatcatggca cagcatatca actgataaat aattcctgtg cagtgcagcc gctgttgcat
      901 aaaatttcgc tctgcgtcga gtgtttctta atcaataatt ccgctgatac tccggaaaaa
      961 cgcgagtctg ttctcatgcc tgaaatgccc acaccccacg caaaaacaag tttttgctga
     1021 tttttcttta taaatagaga gttatgacaa attagttctt cttgctctct ttgtgatatt
     1081 taaaaaagcg gtgtcggcgc ggtgttgtag ctgcgccaac accgcttttt aggggtggta
     1141 ctgactattt tcataaaaaa aaacatcatc ttatattagg ggtgctgcta gcggcgcggt
     1201 gtgttttttt acaggacgcc ctgggggcgc tgctaggggt gtctgttcag atatgtagca
     1261 atgagtcagg gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg cactgtatgc
     1321 gcccaaaccg atcgtcattc actttcatgc atagctatgc agtgagctga aagcgatcct
     1381 gacgcatttt tccggtttac cccggggaaa acatctcttt ttgcggtgtt tgcggcagaa
     1441 tcgcgttcag cgcgttttag cggtgcgcgc aataaaatgt tatgttaaat gtctgctgaa
     1501 tggtttttag gttttttcct aacatatgat agaataaaaa aaccatatgt taatatattg
     1561 tgtttttttc aatgaaaatc tcaaaggtct ctgacgaaca tttttctaat tacaacatgt
     1621 tgccgaatgg taatgaagaa attgaccttt ttggcttgat tagcgtttta tgggcagcaa
     1681 aaataaaaat tgttggggtg attctatttt ttgcttgtat tggctttctt gtttcttttg
     1741 ttttgccaca aaaatggact agttctgctg tggttactcc tgctgagtct gttcaatgga
     1801 gtgaattaaa taaggagctt tccaagcttc atgttctggg agtgggtttt gatatcaatc
     1861 gtgatagcgc atttgctctg tttattaaga aatttcagtc cgttaattcg ttgaatgagt
     1921 atatgagatc atctccttat gttatggaga ttattaaaaa gaataacatt agtgctctcg
     1981 aactgcatcg tgcaattgtt gagttgagta aaaatatgaa gtcgattgat gataatgcca
     2041 gtaagaaaaa cgacaagtca tcattgtatg tatcatggac tctgagtttt actgctccaa
     2101 caagtaaaga agctcacgat gtgttgtctg ggtatattaa ttatgtttct tcccttgttg
     2161 taagggattt gatggaagat ataagaaata aactagaagt taaaactaat gttgaaaaag
     2221 aaattcttgc actggatgag ataaaaatta gaaaccagct gaatgcagat attcgacgcc
     2281 tcaattattc actggaggtt gctaatgcgg ctggaataaa aaaacctgta tacagcaatg
     2341 gtcagattat gaaggatgac ccagattttc ctgtggctct cggttctgat ggtatagcaa
     2401 ctaaattgaa catcaaaaaa tcaatcaagg atgtttcgga attgagtggg gagttgcgaa
     2461 atcgtcaata tgttgtgaat caattggttg tggcgaaagt gggggatgtt gattttatgc
     2521 catttcagta tcaattgagc ccaacgttac cggtcagaaa ggatgggcca agtaatgcca
     2581 taattgtaat tctttcttct gtcattggag ggatgcttgc atgtggctat atacttttac
     2641 gtcatgccat ggaggccaga aagatgagtg tgattgagta aaagttgtgc tgatgcatca
     2701 ttttataagc aacttttata aaaagttcaa aggatcttct tgagatcatt cccttacagc
     2761 cgtagtcttc tactctagaa aacgaaaaaa ccacctgggg aggtggtttt tcgaaggttc
     2821 agtaagttgg ggaacttctg aaccgtggta acagtcttgt gcgagacatg tcaccaaatc
     2881 tgtccttcta gtgtagcctc agtaaggctg ccacttcaag aactctcaat acatctctcg
     2941 cacatcctgt ttaccagtgg ccgctgccaa tggcgttaag tcgtgtctta ccgggttgga
     3001 ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtg
//
