LOCUS       NZ_CP127086             2690 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri 1b strain SF-018-002 plasmid psflex002D, complete
            sequence.
ACCESSION   NZ_CP127086
VERSION     NZ_CP127086.1
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 2690)
  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 2690)
  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
            CP127086.1.
            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..2690
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="SF-018-002"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex002D"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(join(2208..2690,1..141))
                     /locus_tag="QQS68_RS24610"
                     /old_locus_tag="QQS68_24585"
     CDS             complement(join(2208..2690,1..141))
                     /locus_tag="QQS68_RS24610"
                     /old_locus_tag="QQS68_24585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005112197.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_317811692.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKAINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(520..681)
                     /locus_tag="QQS68_RS24615"
                     /old_locus_tag="QQS68_24590"
     CDS             complement(520..681)
                     /locus_tag="QQS68_RS24615"
                     /old_locus_tag="QQS68_24590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(1179..1373)
                     /locus_tag="QQS68_RS24620"
                     /old_locus_tag="QQS68_24595"
     CDS             complement(1179..1373)
                     /locus_tag="QQS68_RS24620"
                     /old_locus_tag="QQS68_24595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1659..1982
                     /gene="mobA"
                     /locus_tag="QQS68_RS24625"
                     /old_locus_tag="QQS68_24600"
     CDS             1659..1982
                     /gene="mobA"
                     /locus_tag="QQS68_RS24625"
                     /old_locus_tag="QQS68_24600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          1412..1650
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(610..1136)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1660..1979
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 ttgacgcgtg aatagtgttt gtggatggga gatctctttc catccaccat gcgacataat
       61 gacaagttgt gttgcttttc ctgtttggct caatcctatt ccgtctttct ggaataaacg
      121 acgatgactt gttacgtcca tgtttggtga tgggtgtgtt tttatatttt tggatgatgt
      181 tagaaggtga tttcttattg ttgatgatat gtttgttatg agattcgaat tgagtatttt
      241 catttgttaa caatccattt ttgcggtgtt ttttattgtt ttttttcttt tgtttaaggg
      301 tgtgtcggtg taagtgttta ttttatgggt taaagtagga taccaagtgt gaaaaaaaat
      361 taaaggttct tcttgagatc ctttttttct gcgcgtaatc tgctgcctgt aaacgaaaaa
      421 accgccctgc aaggcggttt ttcgaaggtt ctcagagcta ccaactcttt gagccgaggt
      481 aactggcttg gaggagcgca gtcaccaaaa cttgttcttt cagtttagcc ttaacaggcg
      541 catgacttca agtcttactc ctctaattcg gttatcagtg gctgctgcca gtggcgataa
      601 ttcgtgtctt accgggttgg actcaagacg atagttaccg gataaggcgc agcggtcggg
      661 ctgaacgggg ggttcgtgca cacagcccag cttggagcga acgacctaca ccgggccgag
      721 ataccaacag cgtgagctat gagaaagcgc cacgcttccc gaagggagaa aggcggacag
      781 gtatccggta aacggcaggg tcggaacagg agagcgcacg agggagcttc cagggggaaa
      841 cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt
      901 gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc acctgcgcgg cctttgcccc
      961 tgccttcggc tttttgctca catgttcttt ccggcgttat cccctgattc tgtggataac
     1021 cgcattaccg cctttgagtg agctgacacc gctcgccgca gtcgaacgac cgagcgtagc
     1081 gagtcagtga gcgaggaagc ggaagagcgc cttatgtgac attttctcct tacgcaccgg
     1141 tataccgttc tgcatcctgt ctggagcagg atacactgtt ataccccggt gccactttcc
     1201 gcttcaaagc gtgtctgtat gctgttctgg agttcttccg cgatttcgtg cagcttctca
     1261 cacatggcgg cctgttcgtc ggcatcgagt gcgtccagct tttcgagcag cgtcaggctc
     1321 tggcttttta tgaatcccgc catgttgagt acggtttgct gctgcttgtt catctttctg
     1381 ttttctccgt tctgtctgtc atctgcgttg tgtgattata tcgcgtacca cttttcgact
     1441 gttttaccgc cggtattctg ccgtctgacg cattgacggg tatttctgcc tgacaatact
     1501 gtcactgcca aaaaaactgc cgtgcctttg tcggtaattc gaacttgctg acaggacagg
     1561 atgtgtaatt gttataccgc gcatacatgc acgctattac aattaccctg gtcagggctt
     1621 cgccccgaca ccccgtgtca gatacggagc catgttttat gacaaaacga agtggaagta
     1681 atacgcgcag gcgggctatc agtcgccctg ttcgtctgac ggcagaagaa gaccaggaaa
     1741 tcagaaaaag ggctgctgaa tgcggcaaga ccgtttctgg ttttttacgg gcggcagctc
     1801 tcggtaagaa cgttaactca ctgactgatg atcgggtgct gaaagaagtt atgagactgg
     1861 gggcgttaca gaaaaaactc tttatcgacg gcaagcgtat cggggacagg gagtatgcgg
     1921 aggtgctgat cgctattacg gagtatcacc gtgccctgtt atccaggctt atggcagatt
     1981 agcttcccgg ggagaaaact gttgaaaaca gacggtatga acacggtaag ctcccaaagt
     2041 gatctccatt cgctttcatg catagctatg cagcgagctg aaaacgatcc tgacgcatcc
     2101 ttcctgtttt tccggggtaa aacatctatt tttgtggtgt ctgcgtcaga atcgcgttca
     2161 gcgcgtttca gtggtgcgta caattaaggg attatggtaa atgatgatta tttctcctct
     2221 ctatttactc ggcaagcgcc aaagtgaatt acatcatatt ttactcctga ttcatttatt
     2281 gctttaaata tgtcagaaag gtgcttctta tgatttttat cagttataaa tgctatatca
     2341 atatttttgt ttcctaagcc atcttgatgt ctttgtataa tattttgggc ttgttcatgg
     2401 taatatagag catagttttt tatcttctca ttacttgttg cgtattcttt tctatatatg
     2461 gcttgtgaca tcatttcttc ttctaatttt gattgaggta tattgcgcgc gttcgctaga
     2521 acttttaggt catctttgct tatgtttagt gatggtgtta accctttttg agcttcagta
     2581 tggcgtttgt ttacctctga aagaacgctt agtccctttg tgaagtcgtt gtcttttgta
     2641 taaaaatcaa ttcttaggtt tttggggact acagtccatc catcgccttt
//
