LOCUS       NZ_CP130068             2690 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Shigella flexneri 1b strain A-10383 plasmid pA-10383D, complete
            sequence.
ACCESSION   NZ_CP130068
VERSION     NZ_CP130068.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN35361130
            Assembly: GCF_030506075.1
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     Genomic Characterization of Increased and Emerging
            Azithromycin-resistant Shigella flexneri 1b 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  JOURNAL   Unpublished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 (08-JUN-2023) Molecular Research, Public Health Ontario,
            661 University Ave, Toronto Ontario, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 01-APR-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: PHL-_18-A10383
            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                   :: 07/19/2023 18:07:31
            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)                     :: 5,038
            CDSs (total)                      :: 4,907
            Genes (coding)                    :: 4,136
            CDSs (with protein)               :: 4,136
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 102
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 771
            CDSs (without protein)            :: 771
            Pseudo Genes (ambiguous residues) :: 0 of 771
            Pseudo Genes (frameshifted)       :: 272 of 771
            Pseudo Genes (incomplete)         :: 452 of 771
            Pseudo Genes (internal stop)      :: 173 of 771
            Pseudo Genes (multiple problems)  :: 123 of 771
            Pseudo Genes (short protein)      :: 5 of 771
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP130068.1.
            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="A-10383"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="pA-10383D"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            join(2325..2690,1..258)
                     /locus_tag="QS169_RS25170"
                     /old_locus_tag="QS169_25170"
     CDS             join(2325..2690,1..258)
                     /locus_tag="QS169_RS25170"
                     /old_locus_tag="QS169_25170"
                     /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="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(484..807)
                     /gene="mobA"
                     /locus_tag="QS169_RS25175"
                     /old_locus_tag="QS169_25175"
     CDS             complement(484..807)
                     /gene="mobA"
                     /locus_tag="QS169_RS25175"
                     /old_locus_tag="QS169_25175"
                     /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"
     gene            1093..1287
                     /locus_tag="QS169_RS25180"
                     /old_locus_tag="QS169_25180"
     CDS             1093..1287
                     /locus_tag="QS169_RS25180"
                     /old_locus_tag="QS169_25180"
                     /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            1785..1946
                     /locus_tag="QS169_RS25185"
                     /old_locus_tag="QS169_25185"
     CDS             1785..1946
                     /locus_tag="QS169_RS25185"
                     /old_locus_tag="QS169_25185"
                     /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"
     Typing          complement(817..1055)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          1331..1857
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          complement(488..807)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 caagccatat atagaaaaga atacgcaaca agtaatgaga agataaaaaa ctatgctcta
       61 tattaccatg aacaagccca aaatattata caaagacatc aagatggctt aggaaacaaa
      121 aatattgata tagcatttat aactgataaa aatcataaga agcacctttc tgacatattt
      181 aaagtaataa atgaatcagg agtaaaatat gatgtaattc actttggcgc ttgccgagta
      241 aatagagagg agaaataatc atcatttacc ataatccctt aattgtacgc accactgaaa
      301 cgcgctgaac gcgattctga cgcagacacc acaaaaatag atgttttacc ccggaaaaac
      361 aggaaggatg cgtcaggatc gttttcagct cgctgcatag ctatgcatga aagcgaatgg
      421 agatcacttt gggagcttac cgtgttcata ccgtctgttt tcaacagttt tctccccggg
      481 aagctaatct gccataagcc tggataacag ggcacggtga tactccgtaa tagcgatcag
      541 cacctccgca tactccctgt ccccgatacg cttgccgtcg ataaagagtt ttttctgtaa
      601 cgcccccagt ctcataactt ctttcagcac ccgatcatca gtcagtgagt taacgttctt
      661 accgagagct gccgcccgta aaaaaccaga aacggtcttg ccgcattcag cagccctttt
      721 tctgatttcc tggtcttctt ctgccgtcag acgaacaggg cgactgatag cccgcctgcg
      781 cgtattactt ccacttcgtt ttgtcataaa acatggctcc gtatctgaca cggggtgtcg
      841 gggcgaagcc ctgaccaggg taattgtaat agcgtgcatg tatgcgcggt ataacaatta
      901 cacatcctgt cctgtcagca agttcgaatt accgacaaag gcacggcagt ttttttggca
      961 gtgacagtat tgtcaggcag aaatacccgt caatgcgtca gacggcagaa taccggcggt
     1021 aaaacagtcg aaaagtggta cgcgatataa tcacacaacg cagatgacag acagaacgga
     1081 gaaaacagaa agatgaacaa gcagcagcaa accgtactca acatggcggg attcataaaa
     1141 agccagagcc tgacgctgct cgaaaagctg gacgcactcg atgccgacga acaggccgcc
     1201 atgtgtgaga agctgcacga aatcgcggaa gaactccaga acagcataca gacacgcttt
     1261 gaagcggaaa gtggcaccgg ggtataacag tgtatcctgc tccagacagg atgcagaacg
     1321 gtataccggt gcgtaaggag aaaatgtcac ataaggcgct cttccgcttc ctcgctcact
     1381 gactcgctac gctcggtcgt tcgactgcgg cgagcggtgt cagctcactc aaaggcggta
     1441 atgcggttat ccacagaatc aggggataac gccggaaaga acatgtgagc aaaaagccga
     1501 aggcaggggc aaaggccgcg caggtggcgt ttttccatag gctccgcccc cctgacgagc
     1561 atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta taaagatacc
     1621 aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg ccgtttaccg
     1681 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgtt
     1741 ggtatctcgg cccggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
     1801 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac
     1861 acgaattatc gccactggca gcagccactg ataaccgaat tagaggagta agacttgaag
     1921 tcatgcgcct gttaaggcta aactgaaaga acaagttttg gtgactgcgc tcctccaagc
     1981 cagttacctc ggctcaaaga gttgatagct ctgagaacct tcgaaaaacc gccttgcagg
     2041 gcggtttttt cgtttacagg cagcagatta cgcgcagaaa aaaaggatct caagaagaac
     2101 ctttaatttt ttttcacact tggtatccta ctttaaccca taaaataaac acttacaccg
     2161 acacaccctt aaacaaaaga aaaaaaacaa taaaaaacac cgcaaaaatg gattgttaac
     2221 aaatgaaaat actcaattcg aatctcataa caaacatatc atcaacaata agaaatcacc
     2281 ttctaacatc atccaaaaat ataaaaacac acccatcacc aaacatggac gtaacaagtc
     2341 atcgtcgttt attccagaaa gacggaatag gattgagcca aacaggaaaa gcaacacaac
     2401 ttgtcattat gtcgcatggt ggatggaaag agatctccca tccacaaaca ctattcacgc
     2461 gtcaaaaagg cgatggatgg actgtagtcc ccaaaaacct aagaattgat ttttatacaa
     2521 aagacaacga cttcacaaag ggactaagcg ttctttcaga ggtaaacaaa cgccatactg
     2581 aagctcaaaa agggttaaca ccatcactaa acataagcaa agatgaccta aaagttctag
     2641 cgaacgcgcg caatatacct caatcaaaat tagaagaaga aatgatgtca
//
