LOCUS       NZ_CP054915             3180 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_691 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP054915
VERSION     NZ_CP054915.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056406
            Assembly: GCF_013364115.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3180)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., 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  JOURNAL   Unpublished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 3180)
  AUTHORS   Fashae,K., Tallon,L., Sadzewicz,L., Vavikolanu,K., Mehta,A.,
            Aluvathingal,J., Nadendla,S., Nandy,P., Geyer,C., Yan,Y. and
            Sichtig,H.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-NOV-2019) 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                   :: canu v. 1.4
            Genome Coverage                   :: 846.51x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/28/2023 04:06:19
            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)                     :: 4,577
            CDSs (total)                      :: 4,448
            Genes (coding)                    :: 3,832
            CDSs (with protein)               :: 3,832
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 616
            CDSs (without protein)            :: 616
            Pseudo Genes (ambiguous residues) :: 0 of 616
            Pseudo Genes (frameshifted)       :: 220 of 616
            Pseudo Genes (incomplete)         :: 325 of 616
            Pseudo Genes (internal stop)      :: 147 of 616
            Pseudo Genes (multiple problems)  :: 78 of 616
            Pseudo Genes (short protein)      :: 5 of 616
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054915.1.
            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..3180
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_691"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_691"
                     /db_xref="taxon:623"
                     /plasmid="unnamed2"
                     /geo_loc_name="Nigeria: Ibadan"
                     /collected_by="University of Ibadan"
     gene            137..1246
                     /gene="wzz(fepE)"
                     /locus_tag="FOB99_RS22715"
                     /old_locus_tag="FOB99_22735"
     CDS             137..1246
                     /gene="wzz(fepE)"
                     /locus_tag="FOB99_RS22715"
                     /old_locus_tag="FOB99_22735"
                     /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_005065596.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2271..2435)
                     /locus_tag="FOB99_RS22720"
                     /old_locus_tag="FOB99_22740"
     CDS             complement(2271..2435)
                     /locus_tag="FOB99_RS22720"
                     /old_locus_tag="FOB99_22740"
                     /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_000090200.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2105..2191
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2506..2604
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2729..2986
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(1554..2080)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 cagaatcgcg ttcagcgcgt tttagcggtg cgcgcaataa aatgttatgt taaatgtctg
       61 ctgaatggtt tttaggtttt ttcctaacat atgatagaat aaaaaaacca tatgttaata
      121 tattgtgttt ttttcaatga aaatctcaaa ggtctctgac gaacattttt ctaattacaa
      181 catgttgccg aatggtaatg aagaaattga cctttttggc ttgattagcg ttttatgggc
      241 agcaaaaata aaaattgttg gggtgattct attttttgct tgtattggct ttcttgtttc
      301 ttttgttttg ccacaaaaat ggactagttc tgctgtggtt actcctgctg agtctgttca
      361 atggagtgaa ttaaataagg agctttccaa gcttcatgtt ctgggagtgg attttgatat
      421 caatcgtgat agcgcatttg ctctgtttat taagaaattt cagtccgtta attcgttgaa
      481 tgagtatatg agatcatctc cttatgttat ggagattatt aaaaagaata acattagcgc
      541 tctcgaactg catcgtgcaa ttgttgagtt gagtaaaaat atgaagtcga ttgatgataa
      601 tgccagtaag aaaaacgaca agtcatcatt gtatgtatca tggactctga gttttactgc
      661 tccaacaagt aaagaagctc acgatgtgtt gtctgggtat attaattatg tttcttccct
      721 tgttgtaagg gatttgatgg aagatataag aaataaacta gaagttaaaa ctaatgttga
      781 aaaagaaatt cttgcactgg atgagataaa aattagaaac cagctgaatg cagatattcg
      841 acgcctcaat tattcactgg aggttgctaa tgcggctgga ataaaaaaac ctgtatacag
      901 caatggtcag attatgaagg atgacccaga ttttcctgtg gctctcggtt ctgatggtat
      961 agcaactaaa ttgaacatca aaaaatcaat caaggatgtt tcggaattga gtggggagtt
     1021 gcgaaatcgt caatatgttg tgaatcaatt ggttgtggcg aaagtggggg atgttgattt
     1081 tatgccattt cagtatcaat tgagcccaac gttaccggtc agaaaggatg ggccaagtaa
     1141 tgccataatt gtaattcttt cttctgtcat tggagggatg cttgcatgtg gctatatact
     1201 tttacgtcat gccatggagg ccagaaagat gagtgtgatt gagtaaaagt tgtgctgatg
     1261 catcatttta taagcaactt ttataaaaag ttcaaaggat cttcttgaga tcattccctt
     1321 acagccgtag tcttctactc tagaaaacga aaaaaccacc tggggaggtg gtttttcgaa
     1381 ggttcagtaa gttggggaac ttctgaaccg tggtaacagt cttgtgcgag acatgtcacc
     1441 aaatctgtcc ttctagtgta gcctcagtaa ggctgccact tcaagaactc tcaatacatc
     1501 tctcgcacat cctgtttacc agtggccgct gccaatggcg ttaagtcgtg tcttaccggg
     1561 ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac ggggggttcg
     1621 tgcacacagc ccagcttgga gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg
     1681 agacgaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga
     1741 gcgcacgagg gagccaccag ggggaaacgc ctggtatctt taagtcctgt cgggtttcgc
     1801 cacctctgac ttgagcgtcg atttttgtga tgctcgtcag gggggcggag cctatggaaa
     1861 aacgccaccg gcgcggcctt ttttcggggc ctcttttttg ctcacatgtt ttttctggtg
     1921 ttatcccctg attctgtgga taaccgtata tccgtctttg cgtgagcaga caccgctcgc
     1981 cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga gcgccggaag
     2041 ctgcattttc tccttacgta tctgtgcagc atttcacacc tcatatgtcg ctgttctctc
     2101 accatctgct ctgccgcctc ataattaagc cagtatacac tccgttatcg ctacgtgact
     2161 gggtcatggc tgcgccccga cacccgctaa aaccccctga cgcgccctga cgggcttgtc
     2221 tgctgacgaa aacgcccacg ggaaagccgt gaccgcctcc gtcagcttcg ttatgttcct
     2281 gtttcacttt cggcctcaaa gcgaatctgg atgctgttct ggagttcttc tgcgagttcg
     2341 tgcagtcgtt tgcacatggc cgcctgttcg tcggcatcca gagcatccag tttttcaagc
     2401 agtgtcaggc tctggctttt gatacatcgc gccatattca gcgcagtttg ttgttatttg
     2461 ttcaccttcc gttgttctcc gtcagttccg ggtgtcgggg ggggggaccc tgagcaggtg
     2521 gtaattgtaa gacgttgcgg gcgacggtat tacaattgca catcctgtcc tgtttcttta
     2581 ggacgtatca tggcacagca tatcaactga taaataatcc ctgtgcagtg cagccgctgt
     2641 tgcataaaat ttcgctctgc gtcgagtgtt tcttaatcaa taattccgct gatactccgg
     2701 aaaaacgcga gtctgttctc atgcctgaaa tgcccacacc ccacgcaaaa acaagttttt
     2761 gctgattttt ctttataaat agagagttat gacaaattag ttcttcttgc tctctttgtg
     2821 atatttaaaa aagcggtgtc ggcgcggtgt tgtagctgcg ccaacaccgc tttttagggg
     2881 tggtactgac tattttcata aaaaaaacat tatcttatat taggggtgct gctagcggcg
     2941 cggtgtgttt ttttacagga cgcccctggg ggcgctgcta ggggtgtctg ttcagatatg
     3001 tagcaatgag tcagggattc acgaactgaa aatgtccgaa aatgtgtctc atgggcactg
     3061 tatgcgccca aaccgatcgt cattcacttt catgcatagc tatgcagtga gctgaaagcg
     3121 atcctgacgc atttttccgg tttaccccgg ggaaaacatc tctttttgcg gtgtttgcgg
//
