LOCUS       CP128227                1538 bp    DNA     circular BCT 22-MAY-2024
DEFINITION  Shigella flexneri 1b strain sflex069 plasmid psflex069-F, complete
            sequence.
ACCESSION   CP128227
VERSION     CP128227.1
DBLINK      BioProject: PRJNA780545
            BioSample: SAMN35361188
KEYWORDS    .
SOURCE      Shigella flexneri 1b
  ORGANISM  Shigella flexneri 1b
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1538)
  AUTHORS   Neemuchwala,A., Zittermann,S., Johnson,K., Middleton,D.,
            Stapleton,P.J., Ravirajan,V., Cronin,K., Allen,V.G. and Patel,S.N.
  TITLE     Genomic Characterization of emerging and increasing
            azithromycin-resistant Shigella flexneri 1b isolates in Ontario
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1538)
  AUTHORS   Neemuchwala,A., Zittermann,S., Johnson,K., Middleton,D.,
            Stapleton,P.J., Ravirajan,V., Cronin,K., Allen,V.G. and Patel,S.N.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 31-MAR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: SF018-069
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/15/2023 09:24:43
            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)                     :: 5,087
            CDSs (total)                      :: 4,955
            Genes (coding)                    :: 4,163
            CDSs (with protein)               :: 4,163
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 792
            CDSs (without protein)            :: 792
            Pseudo Genes (ambiguous residues) :: 0 of 792
            Pseudo Genes (frameshifted)       :: 305 of 792
            Pseudo Genes (incomplete)         :: 448 of 792
            Pseudo Genes (internal stop)      :: 173 of 792
            Pseudo Genes (multiple problems)  :: 131 of 792
            Pseudo Genes (short protein)      :: 5 of 792
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from Shigella flexneri serotype
            1b.
            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..1538
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="sflex069"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex069-F"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            1..477
                     /locus_tag="QS103_25430"
     CDS             1..477
                     /locus_tag="QS103_25430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_function:
                     GO:0003677 - DNA binding [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="XBA31307.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            896..1048
                     /locus_tag="QS103_25435"
     CDS             896..1048
                     /locus_tag="QS103_25435"
                     /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="XBA31306.1"
                     /translation="MFEGLSDDSSPKEQQRDHRQHARGDPARRKSMTERSERIDEEAEE
                     NRKLH"
                     /name="hypothetical protein"
     Typing          1082..1163
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          complement(1352..1460)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..967)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.154"
                     /coverage="99.0"
                     /evalue="3.9e-116"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaagatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcag agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaaccatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ccccagaacg
      601 accgcgccgc cacggttccg gctgcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ctgtgccgtg caaataggct ttgcagggag ctgacgcggt tcctggcgac ctgaaagccc
      781 ctggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tgacgggcat ttaaacccgt ttcgtgcgtc tgagagcttc tgagcgtgtt
      901 tgaagggcta tctgacgact catccccgaa agaacaacaa cgggatcacc gacaacatgc
      961 gagaggtgat cccgctcgcc gcaagtcgat gaccgagcgt agcgagcgaa tcgacgagga
     1021 agcggaagag aaccggaagt tacattgagc acttacgcac ggatgcgggg tgtcggggtg
     1081 aagccctgac caagtgggga atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc
     1141 tgtcccgatt tctgaggcgt tttaacggtg aacggacggc aaaaacatga tcgagcgtgg
     1201 agagcgcgaa atcgggcaaa atcacggctg acgaggcttg cagaggagta agccagtata
     1261 cactccgcta tcgctacgtg actgggtcag ggcttcgccc cgacacccca aaagggcgtt
     1321 gcgttgcgcg caacgccctt gcctagaata gatcttttac gccgatttgt aagttgttgt
     1381 ttttttagtg tgttttttgt ttacctgtcg catccagggt gacacaacgt tgtcgcatcc
     1441 aggatgcgac aacacgcaac aaggtgttgc acagatgtgt catgatggct tagatttgaa
     1501 ccaacattag tgcatgggat tttcagaggg aaaaaatc
//
