LOCUS       NZ_CP054914             4042 bp    DNA     circular CON 29-JUL-2023
DEFINITION  Shigella flexneri strain FDAARGOS_691 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP054914
VERSION     NZ_CP054914.1
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 4042)
  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  JOURNAL   Unpublished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 4042)
  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
            CP054914.1.
            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..4042
                     /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="unnamed1"
                     /geo_loc_name="Nigeria: Ibadan"
                     /collected_by="University of Ibadan"
     gene            join(3915..4042,1..403)
                     /locus_tag="FOB99_RS22690"
                     /old_locus_tag="FOB99_22710"
     CDS             join(3915..4042,1..403)
                     /locus_tag="FOB99_RS22690"
                     /old_locus_tag="FOB99_22710"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_000067502.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLSDEFRKLEESVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNESLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            410..643
                     /locus_tag="FOB99_RS22695"
                     /old_locus_tag="FOB99_22715"
     CDS             410..643
                     /locus_tag="FOB99_RS22695"
                     /old_locus_tag="FOB99_22715"
                     /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_000137443.1"
                     /translation="MTELESHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVLHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1189..1581)
                     /locus_tag="FOB99_RS22700"
                     /old_locus_tag="FOB99_22720"
     CDS             complement(1189..1581)
                     /locus_tag="FOB99_RS22700"
                     /old_locus_tag="FOB99_22720"
                     /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_128567429.1"
                     /translation="MALSACFRQQLNPVVNSLLKERIIHSPKELEHDNAVIRVLQKLQI
                     QEVCNSTLWETAKQQLLQKSDGRYFAINSKHLAFPGPGESHAFCCIKYKNAIGINGNNA
                     ETQSTHYQPYPYDKVSIWGPFPHNLT"
                     /name="hypothetical protein"
     gene            complement(2658..2849)
                     /locus_tag="FOB99_RS22705"
                     /old_locus_tag="FOB99_22725"
     CDS             complement(2658..2849)
                     /locus_tag="FOB99_RS22705"
                     /old_locus_tag="FOB99_22725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_111779737.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLYDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2899..3237
                     /locus_tag="FOB99_RS22710"
                     /old_locus_tag="FOB99_22730"
     CDS             2899..3237
                     /locus_tag="FOB99_RS22710"
                     /old_locus_tag="FOB99_22730"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_254880330.1"
                     /translation="MKRERMLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSG
                     RLPTLAPPLLRQLAAIGNNLNQAARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVR
                     EQGTRDDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          2553..2639
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(1985..2542)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.032"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..747
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.189"
                     /coverage="100.0"
                     /evalue="9.82e-125"
     Typing          3228..4042
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.426"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaacgagacg aaaatcaaag acgctatagc cctgttcaca gcttcgacag aggaatcact
       61 gaaaaaacat cgggaagggg tgaaagaggc gatgatgcag cacaggaagg acgtgttaaa
      121 gctggcaggg aatacgggca tgatgttact ggggatggtc attttcctgt ttaccgtgag
      181 tggcgggacg ctctggtatc ttggcgggat gatacaggcg aacctggaag aaatcaggaa
      241 gcagaacgag agtctggaga agctgaacgc gaagacatgg ggcgtgcgtt atcacgaggg
      301 gagcaacgga cgttttctgg tgttgcccga ggggatgaaa gccgaaacga actggacgat
      361 ggaaaacggg aaacagaatg ccgtaaggct ggtacaggag tgacagagca tgacggagct
      421 ggaaagccat ttgctgaacg cattagagca gctgcaacag gactatatgc agcggctgaa
      481 cgaatgggag agcgccttcg tggaattgca gaaaatgttt tcgcttacgc aacgggacaa
      541 cgcgatgctg aacgagcggg tcatgcagtt gagtcagcag gtgctgcact tgagcgagca
      601 gacagaacgc ttgagccagt tatacagcga gaactggaga taagagagga acggttgata
      661 caggagcgcg aacatgcgtt attcctggaa cgggaacgcc agccggaaat acaggaacgg
      721 acactggatg gcccttcgct gggatggtaa tcagagacag gctaaaatgt tgtcagcgcg
      781 tttccggtgc attttttggg ataatggttg gttcgggggc accgggaacg cgcttcagtc
      841 agaccttgct gaaaacacag gaacgagtta aaacgcatac gggcgcgatt ctggtgtgtc
      901 ttttgtcgct gtgttttgcc tctattgcca gatcgcgctc attcccctga acttctgttt
      961 tcccgctcag gtccccgtct tcttcgcttc cgaaagcatg aataaaatcc gtttcagctg
     1021 tctctggctg gcaattcctg cgtgattcac atggctgcat agctatgcat gtggttaaaa
     1081 tttaccgggt gcgatcgcgg cagtttttcg ggtggtttgt tgccattttt acctgtctgc
     1141 tgccgtgatc gcgccgaacg cgtttcagcg gtgcgtacaa ttaagatatt acgttaaatt
     1201 gtgagggaat ggtccccata tactgacttt atcataggga tagggttggt agtgggtcga
     1261 ttgggtttcg gcattgtttc cgttaatgcc aattgcattt ttgtatttga tgcaacagaa
     1321 ggcgtgagat tctcctgggc ctggaaaggc taagtgttta gaattgatgg caaaatatct
     1381 tccgtccgat ttttgaagta gttgttgttt ggctgtctcc caaagggtgc tgttacaaac
     1441 ttcttgaatt tgtagttttt gcaggactct tattactgcg ttgtcatgtt ccaattcttt
     1501 aggggagtgt attattctct cttttaataa gctgtttacc acagggttta gttgttgtct
     1561 aaagcacgca gataatgcca ttgctacaca attttgttcc cgaggaagca tgtttggcgg
     1621 ggtatgccgt gtttgatgtg atatgtctat tctcatagaa ggtctctggc ttatagcatc
     1681 aacaaatacg gctataaaac aaaattttca tagagtgatt caagatcttc ttgagatcct
     1741 tttttgcggc gcgtaatctg ctgcctgcaa acaaaaaaac caccgctacc aacggtggtt
     1801 tgtttgccgg aatctagagc taccaactct ttcttccgaa ggtaactggc ttggtggagc
     1861 acagatacca aatgctgtcc ttctagtgta gccgcagtta ggccaccact tcaagaactc
     1921 ttaatatctc aatccacctt gtccagttac caatggctgc tgccagtggc gttaagtcgt
     1981 gtcttaccgg gttggactca agacgatagt taccggataa ggcgcagcgg tcgggctgaa
     2041 cggggggttc gtgcacacag cccagcttgg agcgaacgac ctacaccgaa ctgagatacc
     2101 aacagcgtga gctatgagaa agcgccacgc ttcccgaagg gagaaaggcg gacaggtatc
     2161 cggtaagcgg cagggtcgga acaggagagc gcacgaggga gcttccaggg ggaaacgcct
     2221 ggtatcttta tagtcctgtc gggtttcgcc acctctgact tgagcgtcgg tttttgtgat
     2281 gctcgtcagg ggggcggagc ctatggaaaa acgccatcgg cgcggccttc ttcctgttcc
     2341 tggtcttttg ctcacatgtt ctttccggcg ttatcccctg attctgtgga taacagcatt
     2401 tcgtttttga gtgagtagat accgctcgcc gcagtcgaac gaccgagcgt agcgagtcag
     2461 tgagcgagga agcggaaaag cgcctggacg tgcattttct ccttacgcat ctgtgcggca
     2521 tttcacaccc ggtatggcgc acttttcata caatccgcac tgatgccgca tggttaagcc
     2581 agtatacact ccgctatcgc tacgtgactg ggtcatggct gcgccccgac acccgctaac
     2641 acccgctgac aagcccgtca gcggttttca ccgtcatccc cgaagcgagc gaggcaactg
     2701 cggtaaagct catcggcgtg gtcgtaaagc gattcacaga tgtctgcctg ttcatccgcg
     2761 tccagttcgt tgagcttctc cagcagcgtt aatgtctggc ttctgataaa gcgggccatg
     2821 ttaagggcgg ttttttcctg tttggtcact gatgcctccg tgtaaggggg atttctgttc
     2881 atgggggtaa tgataccgat gaaacgcgag aggatgctca cgatacgggt tactgatgat
     2941 gaacatgccc ggttactgga acgctgtgag ggtaaacagc tggcggtatg gatgcggcgg
     3001 gtctgcctgg gtgagccggt tgcccgttcc gggaggctgc cgacactggc accgccgtta
     3061 ctgcgtcagc tggccgccat cgggaataac ctgaatcagg cagcgaggaa ggtgaacagc
     3121 gggcagtggt cttccggtga ccgggttcag gtggtggccg cactgatggc catcggggat
     3181 gagctgcgcc ggctgcgtct ggccgtcagg gaacagggga cgcgggatga tagttaagtt
     3241 tcatgccagg ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg gaagggagcg
     3301 taaccgggaa ggggcaacgg tgcttcaggg taatccggaa gaagtccggg aactcatcga
     3361 tgccacgcca tttgcgaaga aatacacgtc cggtgttctc tcgttcgcgg agaaggagct
     3421 gccgccggga gggcgtgaaa aagtgatggc gagctttgag cgtgtactga tgcccggtct
     3481 cgaaaaaaat cagtacagca ttctgtgggt ggagcaccag gacaaggggc ggcttgagct
     3541 gaattttgtc attccgaaca tggagctaca gaccggaaaa cgcctccagc cgtactacga
     3601 ccgcgcagac aggccgagaa ttgatgcctg gcagacgctg gtgaatcacc attacgggct
     3661 gcatgacccg aacgccccgg agaaccgccg gacgctgact ctccctgata acctgccgga
     3721 aacgaaacag gcgcttgctg agagcattac acggtggata gacgctcttt atcatgtcgg
     3781 ggagataaaa ggccgtcagg atgtgattca ggcgctcaca gaggcggggc ttgaagtggt
     3841 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggcgggaaga atatcagact
     3901 gaaaggagca ttctatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga
     3961 aagagagagc cgaatctaca gagaaaatgc tgagcgacga gttcaggaag ctcgaagaat
     4021 ctgtaagcaa ggctgtgaca tc
//
