LOCUS       NZ_CP046289             4698 bp    DNA     linear   CON 09-JUL-2023
DEFINITION  Shigella sonnei strain FDAARGOS_715 plasmid unnamed4.
ACCESSION   NZ_CP046289
VERSION     NZ_CP046289.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11056430
            Assembly: GCF_009729995.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4698)
  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  JOURNAL   Unpublished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 4698)
  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 (21-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                   :: SMRT v. 2.3.0, HGAP v. 3
            Genome Coverage                   :: 521.02x
            Sequencing Technology             :: Pacbio; Illumina
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 03:33:55
            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)                     :: 5,196
            CDSs (total)                      :: 5,069
            Genes (coding)                    :: 4,349
            CDSs (with protein)               :: 4,349
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 720
            CDSs (without protein)            :: 720
            Pseudo Genes (ambiguous residues) :: 0 of 720
            Pseudo Genes (frameshifted)       :: 217 of 720
            Pseudo Genes (incomplete)         :: 505 of 720
            Pseudo Genes (internal stop)      :: 128 of 720
            Pseudo Genes (multiple problems)  :: 123 of 720
            Pseudo Genes (short protein)      :: 3 of 720
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP046289.1.
            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..4698
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FDAARGOS_715"
                     /isolation_source="clinical isolate"
                     /host="Homo sapiens"
                     /culture_collection="FDA:FDAARGOS_715"
                     /db_xref="taxon:624"
                     /plasmid="unnamed4"
                     /geo_loc_name="Nigeria: Ibadan"
                     /collected_by="University of Ibadan"
     gene            <1..69
                     /locus_tag="FOC23_RS25500"
                     /old_locus_tag="FOC23_25465"
                     /pseudo=""
     CDS             <1..69
                     /locus_tag="FOC23_RS25500"
                     /old_locus_tag="FOC23_25465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /name="nikA protein"
     gene            complement(294..713)
                     /locus_tag="FOC23_RS25505"
                     /old_locus_tag="FOC23_25470"
     CDS             complement(294..713)
                     /locus_tag="FOC23_RS25505"
                     /old_locus_tag="FOC23_25470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(794..1213)
                     /locus_tag="FOC23_RS25510"
                     /old_locus_tag="FOC23_25475"
     CDS             complement(794..1213)
                     /locus_tag="FOC23_RS25510"
                     /old_locus_tag="FOC23_25475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001711305.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /protein_id="WP_156008913.1"
                     /translation="MAWHTLRDALKMTGRSRSQFYRDMRSGLVSYRTSQDGRREFETSE
                     LIRAYGELKRNETPERHTQGHSEKPHDQQIERILRELNELKQCLTLMLEDKQAQDTERR
                     RQEAERKQLQNEIAQLRQALEQEKKRGFWSRLFGH"
                     /name="entry exclusion protein 1"
     gene            1491..3056
                     /locus_tag="FOC23_RS25515"
                     /old_locus_tag="FOC23_25480"
     CDS             1491..3056
                     /locus_tag="FOC23_RS25515"
                     /old_locus_tag="FOC23_25480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_000447003.1"
                     /translation="METAVAYYKDGVPYDDKGQVIITLLNGNPDGSGSGGGGGTGGSKS
                     ESSAAIHATAKWSTAQLKKTQAEQAARAKAAAEAQAKAKANRDALTQHLKDIVNEALRH
                     NSTHPEVIDLAHANNAAMQAEAERLRLAKAEEKARKEAEAAEKAFQEAEQRRKEIEKEQ
                     AETERQLKLAEDEEKRLAALSEEARAVEVAQKNLAAAQSELAKVDEEINTLNTRLSSSI
                     HARDAETNTLSGKRNELDQASAKYKELDERVKLLSPRANDPLQSRPFFEATRLRARAGD
                     EMEEKQKQVTASETRLNQISSEINGIQEAISQANNKRSTAVSRIHDAEDNLKTAQTNLL
                     NSQIKDAVDATVSFYQTLSEKYGEKYSKMAQELADKSKGKKISNVNEALAAFEKYKDVL
                     NKKFSKADRDAIFNALEAVKYEDWAKHLDQFAKYLKITGHVSFGYDVVSDILKIKDTGD
                     WKPLFLTLEKKAVDAGVSYVVVLLFSVLAGTTLGIWGIAIVTGILCAFIDKNKLNTINE
                     VLGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(3053..3394)
                     /locus_tag="FOC23_RS25520"
                     /old_locus_tag="FOC23_25485"
     CDS             complement(3053..3394)
                     /locus_tag="FOC23_RS25520"
                     /old_locus_tag="FOC23_25485"
                     /inference="COORDINATES: protein motif:HMM:NF015489.2"
                     /GO_function="GO:0015643 - toxic substance binding
                     [Evidence IEA]"
                     /GO_process="GO:0030153 - bacteriocin immunity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin E1 family microcin immunity protein"
                     /protein_id="WP_000058755.1"
                     /translation="MSLRYYIKNILFGLYCALIYIYLITKNNEGYYFLASDKMLYAIVI
                     STILCPYSKYAIEHIFFKFIKKDFFRKRKNLNNAPVAKLNLFMLYNLLCLVLAIPFGLL
                     GLFISIKNN"
                     /name="colicin E1 family microcin immunity protein"
     gene            3442..3579
                     /locus_tag="FOC23_RS25525"
                     /old_locus_tag="FOC23_25490"
     CDS             3442..3579
                     /locus_tag="FOC23_RS25525"
                     /old_locus_tag="FOC23_25490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001329514.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTVAPSSSSKLTGISVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(4421..4615)
                     /locus_tag="FOC23_RS25535"
                     /old_locus_tag="FOC23_25500"
     CDS             complement(4421..4615)
                     /locus_tag="FOC23_RS25535"
                     /old_locus_tag="FOC23_25500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041621.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQATMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(3863..4392)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.03"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 tatgcggagg tgctgatcgc tattacggag tatcaccgtg ccctgttatc caggcttatg
       61 gcagattagc ttcccggaga gaaaactgtc gaaaactgac ggtatgaaca ccgtaagctc
      121 ccaaagtgat caccattcgc tttcatgcat agctatgcag agagctgaaa acgatcctga
      181 cgcatccttc ctgtttttcc ggggtaaaac atctcttttt gcggtgtctg cgtcagaatc
      241 gcgttcagcg cgtttcagtg gtgcgtacaa ttaagggatt atggtaaatc cacttactgt
      301 ctgccctcgt agccatcgag ataaaccgca gaaatcgtgt cagccagcag cctggatttt
      361 ttcggggtaa ggtctttgct gcggtaatca gtacccgcaa attgagttgt gccccggagt
      421 gagtttaaaa attcctggct gtgaaactgt tgaatgcgtt gttgcacatc actccgtgat
      481 tttcctgtcg ctttatcttt agctcccata tcccagaact gccgaaaaaa aggcaccatc
      541 attcgtgttg tgtcggcttt ttgggtggaa aagttgggat caaaaccgtc atcagaagca
      601 tatacgtaat gccgggtatg ttgttccacg ctgccctttg gggtacaggc tgtgagagct
      661 actgttgctg ttatcatggc gataagacaa agtttgtttc cggtacgtct catgagtgtc
      721 tccctacctt aaagtattta ttctcggtga gttattatcc gaagattatc ttatcatcag
      781 tttctgagcg cgttcagtga ccgaacagcc tggaccagaa tccccgtttc ttttcctgct
      841 ccagagcctg cctgagctgg gctatctcat tctgtagctg tttccgttct gcttcctggc
      901 gccggcgctc cgtatcctgg gcttgtttat cctcaagcat cagcgtcagg cattgtttca
      961 gctcattcag ttcccggaga atgcgttcta tctgctgatc atgaggtttt tctgagtgtc
     1021 cttgagtgtg cctttctggt gtctcattcc gctttaattc gccgtatgcc cggatcagtt
     1081 cactggtttc aaactcccgt cgtccgtcct ggctggtacg gtaactgaca agacctgagc
     1141 gcatatcacg gtaaaactgt gaacgcgatc ttccagtcat tttcagtgcg tcccggagtg
     1201 tgtgccatgc cataaagtta cagtgtccca taggtgtctc atctcatggt ttcagtaaaa
     1261 cataatgagg tctgagaacg gtaatgtttg tgctggtttt tgtggcatcg gatggaaata
     1321 gcacgtggtg tgggtggctg tttttttgat cgttttcaca aaaatgaaaa tccacagggt
     1381 tgacagggaa aatgcagcgg cgtaatttta aactgtatat aaaaccagtg attatatata
     1441 cagtatattg cttttaacta tttgttttta atgtcaaaga ggattttata atggaaacag
     1501 ctgtagcgta ctataaagat ggtgttcctt atgatgataa ggggcaggta atcattactc
     1561 ttttgaatgg taatccagac gggagtggct ctggcggtgg tggtggaact ggaggtagca
     1621 aaagtgaaag ttctgcagcc attcatgcca cagctaaatg gtctactgct caattgaaga
     1681 aaacgcaggc agaacaggct gcccgagcaa aagctgccgc agaagcacag gctaaagcaa
     1741 aagcaaaccg ggatgcgctg actcaacatc tgaaggatat tgtgaatgag gcgcttcgcc
     1801 ataattccac tcatccggag gttattgacc tggctcatgc caataatgca gcgatgcagg
     1861 cagaagcaga gcggttgcgc cttgcaaaag cagaagaaaa agcccgtaaa gaagcggaag
     1921 ctgcggaaaa ggcttttcag gaagcagaac aacgacgtaa agagatagag aaggagcagg
     1981 ctgaaacaga acgccaattg aaactggctg aggatgaaga gaaacgcctg gcagcattga
     2041 gtgaagaggc ccgggctgtg gaggtggcac aaaaaaatct tgctgctgca caatctgagc
     2101 tggcgaaagt ggatgaagag attaatacgc tcaatacccg tttaagctcc agtattcatg
     2161 cccgtgatgc agaaacgaat acgctgtccg gaaaacgaaa tgagttggat caggcatctg
     2221 ctaaatataa agaactggat gaaagggtta aacttttatc tcctagggcg aatgatccgc
     2281 ttcagagtcg tccttttttt gaggccacca gactacgggc gagagctggt gatgagatgg
     2341 aggaaaaaca aaagcaggta acagcatcag aaacgcgtct taaccaaatt agctctgaga
     2401 taaatggaat ccaagaggct atttctcagg ctaataataa gcgaagtaca gcagtttcac
     2461 gtattcatga tgctgaagat aatttgaaaa cagcacagac taatctcctg aactcgcaga
     2521 ttaaggatgc tgtggatgca acagttagct tttatcaaac gctatctgaa aaatatggtg
     2581 aaaaatattc aaaaatggca caggaacttg ctgataaatc taaaggtaag aaaatcagca
     2641 atgtgaatga agctctagct gcttttgaga aatacaagga tgtattaaat aagaaattca
     2701 gcaaagcaga ccgtgatgca attttcaatg cactggaggc ggttaagtat gaagactggg
     2761 ctaagcattt agatcagttt gccaagtact tgaagattac gggacatgtt tcttttggat
     2821 atgatgtggt atctgatatc ctaaaaatta aggatacagg tgactggaag ccgctatttc
     2881 ttacattaga gaagaaagct gtagatgctg gagttagtta tgttgttgtt ttacttttta
     2941 gtgtgcttgc tggaactaca ttaggtatct gggggattgc tattgttaca ggcattctat
     3001 gtgcctttat tgataagaat aaacttaata ctataaatga ggtgttgggt atttaattat
     3061 tctttattga tataaacagt cctagcaatc caaatgggat tgctaggacc aaacaaagta
     3121 gattgtatag cataaatagg tttaattttg ccacgggggc attatttagg ttttttcttt
     3181 ttctgaaaaa atctttcttt atgaacttaa aaaatatgtg ttcaatagca tattttgaat
     3241 atgggcatag aatagtgctt atcactattg cgtatagcat cttatctgac gctaggaaat
     3301 aatacccttc gttgtttttt gttataaggt atatatatat aagtgcgcag tataggccaa
     3361 acaaaatatt ttttatgtag tatcttaaac tcataaatta aacctcgtta tatattcttt
     3421 tcattttata aggatcgagt tatgaggaaa agattttttg tgggaatatt cgctataaac
     3481 ctccttgttg gatgtcaggc taactatata cgtgatgttc agggagggac tgtggctcca
     3541 tcatcttctt ctaaattgac ggggatctct gttcagtaga aaagatcaaa ggatcttctt
     3601 gagatccttt ttttctgcgc gtaatctgct gcctgtaaac gaaaaaaccg cctggggagg
     3661 cggtttgatc gaaggttaag tcagttgggg aactgcttaa ccgaggtaac tggcttcagc
     3721 agagcgcaga taccaaatgc tgtccttcca gtgtagccgt agtcgggcca ctacttcaag
     3781 aactctgttg caccatttgc gccatcatcg ctctgctaac caagttacca acggctgctg
     3841 ccagtggcgc taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg
     3901 cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct
     3961 acaccgggcc gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga
     4021 gaaaggcgga caggtatccg gtaaacggca gggtcggaac aggagagcgc acgagggagc
     4081 ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctggcttg
     4141 agcgtcgatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gcctgcggcg
     4201 ctggcttctt ccggtgcttt gctgtttgct cacatgttct ttccggcttt atcccctgat
     4261 tctgtggata accgtattac cgcttttgag tgagctgaca ccgctcgccg cagtcgaacg
     4321 tccgagcgta gcgagtcagt gagcgaggaa gcggaagagc gccttatgtg acattttctc
     4381 cttacgctct gttgtgccgt tcggcatcct gtcctgagcg ttatctctct gtgctatttt
     4441 ctacttcaaa gcgtgtctgg atgctgttct ggagttcttc tgcgagttcg tgcagcttct
     4501 cacacatggt agcctgttcg tcagcatcga gtgcgtccag cttttcgagc agcgtcaggc
     4561 tttggctttt tatgaatcct gccatgttga gtacggcttg ctgctgcttg ttcatctttt
     4621 cgttttctcc gttctgtctg tcatctgcgt tgtgtgatta tatcgcgtac cacttttcga
     4681 ctgttttacc gccggtat
//
