LOCUS       NZ_CP045788             2101 bp    DNA     circular CON 10-JUN-2024
DEFINITION  Shigella dysenteriae strain CFSAN029786 plasmid p4CFSAN029786,
            complete sequence.
ACCESSION   NZ_CP045788
VERSION     NZ_CP045788.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN04323531
            Assembly: GCF_009662135.1
KEYWORDS    RefSeq.
SOURCE      Shigella dysenteriae
  ORGANISM  Shigella dysenteriae
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2101)
  AUTHORS   Mafiz,A., Kastanis,G. and Gonzalez Escalona,N.
  TITLE     Closed genomes of twenty-eight foodborne pathogens from the CFSAN
            verification set by a combination of long and short-reads
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2101)
  AUTHORS   Mafiz,A., Kastanis,G. and Gonzalez Escalona,N.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-NOV-2019) ORS/DM/MMSB, Food and Drug
            Administration-College Park, 5001 Campus Drive, College Park, MD
            20740-3835, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes, CANU v. 3.12.0, 1.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 176, 244, 292, 244, 227x
            Sequencing Technology :: Oxford Nanopore GridION, Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009662135.1-RS_2024_06_10
            Annotation Date                   :: 06/10/2024 03:57:13
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,212
            CDSs (total)                      :: 5,085
            Genes (coding)                    :: 4,226
            CDSs (with protein)               :: 4,226
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 99
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 859
            CDSs (without protein)            :: 859
            Pseudo Genes (ambiguous residues) :: 0 of 859
            Pseudo Genes (frameshifted)       :: 266 of 859
            Pseudo Genes (incomplete)         :: 578 of 859
            Pseudo Genes (internal stop)      :: 164 of 859
            Pseudo Genes (multiple problems)  :: 135 of 859
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045788.1.
            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..2101
                     /organism="Shigella dysenteriae"
                     /mol_type="genomic DNA"
                     /strain="CFSAN029786"
                     /serovar="Serotype 3"
                     /host="Homo sapiens"
                     /db_xref="taxon:622"
                     /plasmid="p4CFSAN029786"
                     /geo_loc_name="Somalia"
                     /collected_by="FDA"
     gene            complement(join(1437..2101,1..301))
                     /locus_tag="GH770_RS25710"
                     /old_locus_tag="GH770_25710"
     CDS             complement(join(1437..2101,1..301))
                     /locus_tag="GH770_RS25710"
                     /old_locus_tag="GH770_25710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(1167..1433)
                     /locus_tag="GH770_RS25715"
                     /old_locus_tag="GH770_25715"
     CDS             complement(1167..1433)
                     /locus_tag="GH770_RS25715"
                     /old_locus_tag="GH770_25715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(1778..2009)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ttttcggtag agcctgataa aaacgggctt gccacatgag ggttcttctc cactggcaga
       61 cagggcaatg acggacacgg caaaattgcg cactacgaag ccgtaggcgc gtttctccgg
      121 tttccatgat ggtagaccaa ccaaaacgta acaaaccgct acaggaggcc atacggagtg
      181 catagcgctc gaattcagca gcagtctggt agataccccc gacagaatcg gtaagcgtgc
      241 gctgggtatc ccaaactgca tcacgggggc tgtagtccga aaggaattta tcttctgaca
      301 ttaagcctgc tccgatctgg gcaggctgtg atttgatgtg gtatattcat cacgtacctg
      361 tgcattgcga gccagtacat gtcaccagag tttgccgctg aggtgacaca ttcgaaatgt
      421 tggggagtgt tgacgcactc cccaacgccg attaaaaacg cctcaattct gctccatttt
      481 ctttgacctg tcaaaaccca ctcaaagcct cgtcattact gggctaaacc actatttcat
      541 atccgccatt tatcccttaa gtataaatac aaggatcacg cgcgagaatt gcgcaaaaaa
      601 taaccacaat tttaaccccc caaaacaagc acccccgaac ggcttacccc aaccttttcc
      661 acacacccga tcaccaaaac agggaataaa aacaaaaccc tgtcttacag gtggatggcc
      721 tcacttcgtg aaaccatcca ccccgcataa gttttttaat cggtggtgtc gtcaatcact
      781 aaatcggaac cccaaagggg acccccacga tttagcattt gacgagatta actctcggag
      841 atggcatcat gcttttaacg gactttaaaa aacggtgaac ggatgcggat tttaatccgt
      901 gtctgtgagg cgttgagcaa cgagcaaagc gaggcggtag aaagagagcc agcggcaggc
      961 tcaggacgat aatccgggga aaatgtacca ctcgcagagt gttaacattt gacatcggat
     1021 tgtctatcct gcattggtgt cgagttggca aggctgagga taatgctgag gataatgctg
     1081 aggataatgc aggatagaca gagcactaga gattgcatgc aatctcgtac ctatcacctc
     1141 agcctgccgc tggctctttt ccagaactaa gaatgcgttc ttaaaaatcc aaacttgata
     1201 ccgtttaaat ctattttcac aaaaagagtt tttaccctct cgtttgtttt ctgaatatat
     1261 aaaattaatt catcctcaaa accttcgtgc ggatgaaaac caaatgtgcc aaaacttaat
     1321 ccatcaataa gcaaaataag gtttttaaac ctgtcaggaa tcaccgcttc acttcttaaa
     1381 aaaaataaac caatagtctt atttccattc aggtattcaa tattaatatt catacgttaa
     1441 tccgatttat ccttctcagg ggcgcgtttg taacgccgtt tacctgaatc ccagacaaac
     1501 gccgtccgct tcccgtcatc agtgccatcc cctacatcgt cggcaatgac aagatcctca
     1561 ttggtttctc gatccaactg gaggacgttt tttagcgccc caccggtcga gataaaacgg
     1621 cgcttgtgaa gctgccgcgt cagctcaaga aaccactcag gatcgtttgc catatcttcc
     1681 ggtttaacgg agtatttcag cgtttcagca accgcgcttt gcagttgctc ggcaacgttg
     1741 gccacaacct cacctgtctt agtttttact gcccgaatat cgatattcgg ctcatagttc
     1801 acccgcaagc aatcgcgcca gagttctacc caacgttcgt gcttaacgta gttcttccct
     1861 ttaaaccaag aaggttgcac catcagcaga cagtgaaaat gcggatgtgc gctgccatcc
     1921 ttacctcgcg tcacctccgt agccctgatc cacccctgaa caggtgatag ctcctttcgc
     1981 ttttccattc gcttaaacgc cgcattcatt gctgtaagga ctgttccaag ttcacctatc
     2041 tcgcagttcc tgacagttaa cgtcagaaac aaccatcggg aagacgggta atccacaacg
     2101 a
//
