LOCUS       NZ_CP127087             2089 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri 1b strain SF-018-002 plasmid psflex002E, complete
            sequence.
ACCESSION   NZ_CP127087
VERSION     NZ_CP127087.1
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 2089)
  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 2089)
  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
            CP127087.1.
            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..2089
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="SF-018-002"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex002E"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            join(1637..2089,1..513)
                     /locus_tag="QQS68_RS24630"
                     /old_locus_tag="QQS68_24605"
     CDS             join(1637..2089,1..513)
                     /locus_tag="QQS68_RS24630"
                     /old_locus_tag="QQS68_24605"
                     /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            517..783
                     /locus_tag="QQS68_RS24635"
                     /old_locus_tag="QQS68_24610"
     CDS             517..783
                     /locus_tag="QQS68_RS24635"
                     /old_locus_tag="QQS68_24610"
                     /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          2..173
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-85"
ORIGIN
        1 atcagggcta cggaggtgac gcgaggtaag gatggcagcg cacatccgca ttttcactgt
       61 ctgctgatgg tgcaaccttc ttggtttaaa gggaagaact acgttaagca cgaacgttgg
      121 gtagaactct ggcgcgattg cttgcgggtg aactatgagc cgaatatcga tattcgggca
      181 gtaaaaacta agacaggtga ggttgtggcc aacgttgccg agcaactgca aagcgcggtt
      241 gctgaaacgc tgaaatactc cgttaaaccg gaagatatgg caaacgatcc tgagtggttt
      301 cttgagctga cgcggcagct tcacaagcgc cgttttatct cgaccggtgg ggcgctaaaa
      361 aacgtcctcc agttggatcg agaaaccaat gaggatcttg tcattgccga cgatgtaggg
      421 gatggcactg atgacgggaa gcggacggcg tttgtctggg attcaggtaa acggcgttac
      481 aaacgcgccc ctgagaagga taaatcggat taacgtatga atattaatat tgaatacctg
      541 aatggaaata agactattgg tttatttttt ttaagaagtg aagcggtgat tcctgacagg
      601 tttaaaaacc ttattttgct tattgatgga ttaagttttg gcacatttgg ttttcatccg
      661 cacgaaggtt ttgaggatga attaatttta tatattcaga aaacaaacga gagggtaaaa
      721 actctttttg tgaaaataga tttaaacggt atcaagtttg gatttttaag aacgcattct
      781 tagttctgga aaagagccag cggcaggctg aggtgatagg tacgagattg catgcaatct
      841 ctagtgctct gtctatcctg cattatcctc agcattatcc tcagccttgc caactcgaca
      901 ccaatgcagg atagacaatc cgatgtcaaa tgttaacact ctgcgagtgg tacattttcc
      961 ccggattatc gtcctgagcc tgccgctggc tctctttcta ccgcctcgct ttgctcgttg
     1021 ctcaacgcct cacagacacg gattaaaatc cgcatccgtt caccgttttt taaagtccgt
     1081 taaaagcatg atgccatctc cgagagttaa tctcgtcaaa tgctaaatcg tgggggtccc
     1141 ctttggggtt ccgatttagt gattgacgac accaccgatt aaaaaactta tgcggggtgg
     1201 atggtttcac gaagtgaggc catccacctg taagacaggg ttttgttttt attccctgtt
     1261 ttggtgatcg ggtgtgtgga aaaggttggg ctcagccgtt cgggggtgct tgttttgggg
     1321 ggttaaaatt gtggttattt tttgcgcaat cctcgcgcgt gatccttgta tttatactta
     1381 agggataaat ggcggatatg aaatagtggt ttagcccagt aatgacgagg ctttgagtgg
     1441 gttttgacag gtcaaagaaa atggagcaga attgaggcgt ttttaatcgg cgttggggag
     1501 tgcgtcaaca ctccccaaca tttcgaatgt gtcacctcag cggcaaactc tggtgacatg
     1561 tactggctcg caatgcacag gtacgtgatg aatataccac atcaaatcac agcctgccca
     1621 gatcggagca ggcttaatgt cagaagataa attcctttcg gactacagcc cccgtgatgc
     1681 agtttgggat acccagcgca cgcttaccga ttctgtcggg ggtatctacc agactgctgc
     1741 tgaattcgag cgctatgcac tccgtatggc ctcctgtagc ggtttgttac gttttggttg
     1801 gtctaccatc atggaaaccg gagaaacgcg cctacggctt cgtagtgcgc aattttgccg
     1861 tgtccgtcat tgccctgtct gccagtggag aagaaccctc atgtggcaag cccgttttta
     1921 tcaggctcta ccgaaaatcg ttgtggatta cccgtcttcc cgatggttgt ttctgacgtt
     1981 aactgtcagg aactgcgaga taggtgaact tggaacagtc cttacagcaa tgaatgcggc
     2041 gtttaagcga atggaaaagc gaaaggagct atcacctgtt caggggtgg
//
