LOCUS       NZ_CP127088             1812 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri 1b strain SF-018-002 plasmid sflex002F, complete
            sequence.
ACCESSION   NZ_CP127088
VERSION     NZ_CP127088.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361129
            Assembly: GCF_033870415.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 1b
  ORGANISM  Shigella flexneri 1b
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 1812)
  AUTHORS   Neemuchwala,A., Zittermann,S., Johnson,K., Middleton,D.,
            Stapleton,P.J., Ravirajan,V., Cronin,K., Allen,V.G. and Patel,S.N.
  TITLE     Whole genome sequencing of increased number of
            azithromycin-resistant Shigella flexneri 1b isolates in Ontario
  JOURNAL   Sci Rep 13 (1), 16582 (2023)
   PUBMED   37789081
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1812)
  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 (01-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 30-MAR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: sflex002
            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 RefSeq
            Annotation Date                   :: 11/22/2023 13:22:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,929
            CDSs (total)                      :: 4,795
            Genes (coding)                    :: 4,061
            CDSs (with protein)               :: 4,061
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 105
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 734
            CDSs (without protein)            :: 734
            Pseudo Genes (ambiguous residues) :: 0 of 734
            Pseudo Genes (frameshifted)       :: 263 of 734
            Pseudo Genes (incomplete)         :: 418 of 734
            Pseudo Genes (internal stop)      :: 165 of 734
            Pseudo Genes (multiple problems)  :: 111 of 734
            Pseudo Genes (short protein)      :: 5 of 734
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP127088.1.
            Bacteria and source DNA available from Public health Ontario.
            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..1812
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="SF-018-002"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="sflex002F"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(965..1252)
                     /locus_tag="QQS68_RS24640"
                     /old_locus_tag="QQS68_24615"
     CDS             complement(965..1252)
                     /locus_tag="QQS68_RS24640"
                     /old_locus_tag="QQS68_24615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001220925.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023909281.1"
                     /translation="MRIKYESRWKLEELKLEICRSIDSLIDEYHIEYAMGINLYMNCED
                     KEFNPVDIVNEDGKNIMFVVSNNEKIQKPKKSAKKKIPAPVIELDKYRKK"
                     /name="hypothetical protein"
     gene            complement(1265..1798)
                     /locus_tag="QQS68_RS24645"
                     /old_locus_tag="QQS68_24620"
     CDS             complement(1265..1798)
                     /locus_tag="QQS68_RS24645"
                     /old_locus_tag="QQS68_24620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005707163.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000893324.1"
                     /translation="MLEQQFEDFEQQKRRDHQAQDQSKSAKQKRDRLNPPDWSQVTKAG
                     WNMLDSISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFEGSLKTSNHDLD"
                     /name="replication/maintenance protein RepL"
     Typing          473..714
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.328"
                     /coverage="97.0"
                     /evalue="1.14e-81"
ORIGIN
        1 ctgcaacgtt gtttcgtacc ttacgaaatt tatatcgtac attacgaaac aacacacgca
       61 aacatgtttg cgtatacaca tgcaaataac gtttcgtatg ttggtgtcat aatgctttga
      121 tttttaagag aatgtcgatt tttgctctaa agatctatca aagcactttt ttgctacaca
      181 agatttaatt agttcatcga acatttgggg tgtcggggcg aagccctgac ccagtcacgt
      241 agcgatagcg gagtgtatac tggcttactc ttctgcaagc ctcgccagcc gtgattttgc
      301 ccgatttcgc gctctccacg ttcaacagct cgatcatgtt tttgcagtcc gttcaccgct
      361 aaaacgcccc gcatcagtgc gtacgtgctc aatgtggttt ccggttctct tccgcttcct
      421 cgcccactcg ctcactaacg ttcggtcgct ggggctgcgg cgagcggtgc cacctctcgc
      481 atgttatcgg tgattccgct gttgttcttt cggggatgag tcgccagata gctcttcaaa
      541 cgctctcaga cgcacgaaac gggttttaaa tgcccatcag ggcatggaag gcgcgaaaaa
      601 cgcttacaga gggttttagg aggtcaggcg cgccgatacc cctaaccagg ggatttcagg
      661 tcgccaggaa ccgcgtcagc cccctgcaaa gcccatttgc acggaatagg cagccacgcg
      721 gttggtaggt ggtcgtagac cgtcgatgtt acagcgatgg gggtctgggg ttctccccag
      781 acggtttccg gttgcgctca aggcgctgcc ggaaccgtgg cggctcggtc gttctggaaa
      841 acggggagca aaaagacgca agggattttg aggcggcaaa agagcaatgc aggatagaca
      901 atcaactaga aattgcatgc aatgttctgt ggattgtccg cctgccgctg gctctgtatg
      961 gccatcactt tttccgatat ttatctaact caattacagg tgcaggaatt tttttcttcg
     1021 cacttttttt tggtttttgt attttttcat tgttgctaac aacaaacata atattctttc
     1081 catcttcatt gacaatatca acgggattaa actccttatc ttcacaattc atatatagat
     1141 ttattcccat tgcatattcg atatgatatt catcaattaa cgaatctatt gatctacata
     1201 tttctaattt tagttcttct aatttccaac gtgattcata tttaattctc atagcgcatc
     1261 atacctagtc caagtcatga ttagatgtct taagcgagcc ttcaaactct tctctcctag
     1321 agagcatgag ccgcaacttg cgatcaataa cgccatcttt ttgagttaat gtttttgcgt
     1381 taaacgctgc atatttttta gatttattat atccgcgcca tacctgatac ggatctaacg
     1441 cataagcata atagatacct actggtattt tcacgatggc accaatactt tctaaatctc
     1501 caatccaata ttggatcgtc cttaaactaa caccgaaata atcagctaag aatttttggt
     1561 cacatacaac agccccacac gatttatcta tattttgagc aaaaaaagaa tatagcctaa
     1621 atgctctggg aaccttctca gatatagagt ccaacatatt ccagcccgcc ttagtaacct
     1681 gcgaccagtc aggtggattc aaccgatctc gtttttgctt agcacttttg gattgatctt
     1741 gtgcctgatg atctcgccgt ttttgctgtt cgaaatcttc aaattgctgt tccagcatac
     1801 ttgcatcctt ac
//
