LOCUS       CP128226                2690 bp    DNA     circular BCT 22-MAY-2024
DEFINITION  Shigella flexneri 1b strain sflex069 plasmid psflex069-E, complete
            sequence.
ACCESSION   CP128226
VERSION     CP128226.1
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 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     Genomic Characterization of emerging and increasing
            azithromycin-resistant Shigella flexneri 1b isolates in Ontario
  JOURNAL   Unpublished
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 (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..2690
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="sflex069"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex069-E"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            121..282
                     /locus_tag="QS103_25410"
     CDS             121..282
                     /locus_tag="QS103_25410"
                     /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="XBA31304.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            661..1284
                     /locus_tag="QS103_25415"
     CDS             661..1284
                     /locus_tag="QS103_25415"
                     /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="XBA31305.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="hypothetical protein"
     gene            complement(1510..1833)
                     /gene="mobA"
                     /locus_tag="QS103_25420"
     CDS             complement(1510..1833)
                     /gene="mobA"
                     /locus_tag="QS103_25420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_process:
                     GO:0006355 - regulation of DNA-templated transcription
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="XBA31302.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2119..2313
                     /locus_tag="QS103_25425"
     CDS             2119..2313
                     /locus_tag="QS103_25425"
                     /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="XBA31303.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          complement(1843..2081)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(12..210)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.0"
                     /coverage="99.0"
                     /evalue="8.270000000000004e-97"
     Typing          2538..2690
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="85.0"
                     /evalue="3.1499999999999997e-69"
     Typing          complement(1514..1833)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 accctgccgt ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct
       61 catagctcac gctgttggta tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt
      121 gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag
      181 tccaacccgg taagacacga attatcgcca ctggcagcag ccactgataa ccgaattaga
      241 ggagtaagac ttgaagtcat gcgcctgtta aggctaaact gaaagaacaa gttttggtga
      301 ctgcgctcct ccaagccagt tacctcggct caaagagttg atagctctga gaaccttcga
      361 aaaaccgcct tgcagggcgg ttttttcgtt tacaggcagc agattacgcg cagaaaaaaa
      421 ggatctcaag aagaaccttt aatttttttt cacacttggt atcctacttt aacccataaa
      481 ataaacactt acaccgacac acccttaaac aaaagaaaaa aaacaataaa aaacaccgca
      541 aaaatggatt gttaacaaat gaaaatactc aattcgaatc tcataacaaa catatcatca
      601 acaataagaa atcaccttct aacatcatcc aaaaatataa aaacacaccc atcaccaaac
      661 atggacgtaa caagtcatcg tcgtttattc cagaaagacg gaataggatt gagccaaaca
      721 ggaaaagcaa cacaacttgt cattatgtcg catggtggat ggaaagagat ctcccatcca
      781 caaacactat tcacgcgtca aaaaggcgat ggatggactg tagtccccaa aaacctaaga
      841 attgattttt atacaaaaga caacgacttc acaaagggac taagcgttct ttcagaggta
      901 aacaaacgcc atactgaagc tcaaaaaggg ttaacaccat cactaaacat aagcaaagat
      961 gacctaaaag ttctagcgaa cgcgcgcaat atacctcaat caaaattaga agaagaaatg
     1021 atgtcacaag ccatatatag aaaagaatac gcaacaagta atgagaagat aaaaaactat
     1081 gctctatatt accatgaaca agcccaaaat attatacaaa gacatcaaga tggcttagga
     1141 aacaaaaata ttgatatagc atttataact gataaaaatc ataagaagca cctttctgac
     1201 atatttaaag taataaatga atcaggagta aaatatgatg taattcactt tggcgcttgc
     1261 cgagtaaata gagaggagaa ataatcatca tttaccataa tcccttaatt gtacgcacca
     1321 ctgaaacgcg ctgaacgcga ttctgacgca gacaccacaa aaatagatgt tttaccccgg
     1381 aaaaacagga aggatgcgtc aggatcgttt tcagctcgct gcatagctat gcatgaaagc
     1441 gaatggagat cactttggga gcttaccgtg ttcataccgt ctgttttcaa cagttttctc
     1501 cccgggaagc taatctgcca taagcctgga taacagggca cggtgatact ccgtaatagc
     1561 gatcagcacc tccgcatact ccctgtcccc gatacgcttg ccgtcgataa agagtttttt
     1621 ctgtaacgcc cccagtctca taacttcttt cagcacccga tcatcagtca gtgagttaac
     1681 gttcttaccg agagctgccg cccgtaaaaa accagaaacg gtcttgccgc attcagcagc
     1741 cctttttctg atttcctggt cttcttctgc cgtcagacga acagggcgac tgatagcccg
     1801 cctgcgcgta ttacttccac ttcgttttgt cataaaacat ggctccgtat ctgacacggg
     1861 gtgtcggggc gaagccctga ccagggtaat tgtaatagcg tgcatgtatg cgcggtataa
     1921 caattacaca tcctgtcctg tcagcaagtt cgaattaccg acaaaggcac ggcagttttt
     1981 ttggcagtga cagtattgtc aggcagaaat acccgtcaat gcgtcagacg gcagaatacc
     2041 ggcggtaaaa cagtcgaaaa gtggtacgcg atataatcac acaacgcaga tgacagacag
     2101 aacggagaaa acagaaagat gaacaagcag cagcaaaccg tactcaacat ggcgggattc
     2161 ataaaaagcc agagcctgac gctgctcgaa aagctggacg cactcgatgc cgacgaacag
     2221 gccgccatgt gtgagaagct gcacgaaatc gcggaagaac tccagaacag catacagaca
     2281 cgctttgaag cggaaagtgg caccggggta taacagtgta tcctgctcca gacaggatgc
     2341 agaacggtat accggtgcgt aaggagaaaa tgtcacataa ggcgctcttc cgcttcctcg
     2401 ctcactgact cgctacgctc ggtcgttcga ctgcggcgag cggtgtcagc tcactcaaag
     2461 gcggtaatgc ggttatccac agaatcaggg gataacgccg gaaagaacat gtgagcaaaa
     2521 agccgaaggc aggggcaaag gccgcgcagg tggcgttttt ccataggctc cgcccccctg
     2581 acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     2641 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg
//
