LOCUS       NZ_CP058592             3209 bp    DNA     circular CON 23-AUG-2023
DEFINITION  Shigella flexneri strain M2901 plasmid unnamed3, complete sequence.
ACCESSION   NZ_CP058592
VERSION     NZ_CP058592.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13753499
            Assembly: GCF_013402835.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3209)
  AUTHORS   Guglielmino,C.J.D., Kakkanat,A., Forde,B.M., Rubenach,S., Merone,L.,
            Stafford,R., Graham,R.M.A., Beatson,S.A. and Jennison,A.V.
  TITLE     Outbreak of multi-drug-resistant (MDR) Shigella flexneri in northern
            Australia due to an endemic regional clone acquiring an IncFII
            plasmid
  JOURNAL   Eur J Clin Microbiol Infect Dis 40 (2), 279-286 (2021)
   PUBMED   32888117
REFERENCE   2  (bases 1 to 3209)
  AUTHORS   Forde,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUL-2020) Public Health Microbiology, Queensland
            Health Forensic and Scientific Services, PO Box 594, Archerfield,
            QLD 4108, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method                   :: Flye v. MAY-2020
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 50.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore
            PromethION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/23/2023 04:23:34
            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)                     :: 5,146
            CDSs (total)                      :: 5,014
            Genes (coding)                    :: 4,139
            CDSs (with protein)               :: 4,139
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 103
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 875
            CDSs (without protein)            :: 875
            Pseudo Genes (ambiguous residues) :: 0 of 875
            Pseudo Genes (frameshifted)       :: 369 of 875
            Pseudo Genes (incomplete)         :: 457 of 875
            Pseudo Genes (internal stop)      :: 195 of 875
            Pseudo Genes (multiple problems)  :: 143 of 875
            Pseudo Genes (short protein)      :: 5 of 875
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058592.1.
            Bacteria and source DNA available from Queensland Health Forensic
            and Scientific Services.
            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..3209
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="M2901"
                     /serotype="2b"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Australia: Queensland"
                     /lat_lon="27 S 153 E"
                     /collection_date="2019"
                     /collected_by="Queensland Health"
     gene            complement(534..698)
                     /locus_tag="HXW98_RS25595"
                     /old_locus_tag="HXW98_25405"
     CDS             complement(534..698)
                     /locus_tag="HXW98_RS25595"
                     /old_locus_tag="HXW98_25405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_000090200.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1579..2688
                     /gene="wzz(fepE)"
                     /locus_tag="HXW98_RS25600"
                     /old_locus_tag="HXW98_25410"
     CDS             1579..2688
                     /gene="wzz(fepE)"
                     /locus_tag="HXW98_RS25600"
                     /old_locus_tag="HXW98_25410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_005065596.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(2933..3067)
                     /locus_tag="HXW98_RS25795"
     CDS             complement(2933..3067)
                     /locus_tag="HXW98_RS25795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     Typing          368..454
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          768..866
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          991..1248
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(21..347)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.361"
                     /coverage="80.0"
                     /evalue="5.23e-118"
     Typing          complement(2741..3193)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.076"
                     /coverage="89.0"
                     /evalue="1.07e-119"
ORIGIN
        1 tgcctttgcg agaacagcac cagggggaaa cgcctggtat ctttaagtcc tgtcgggttt
       61 cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg
      121 aaaaacgcca ccggcgcggc cttttttcgg ggcctctttt ttgctcacat gttttttctg
      181 gtgttatccc ctgattctgt ggataaccgt atatccgtct ttgcgtgagc agacaccgct
      241 cgccgcagcc gaacgaccga gcgcagcgag tcagtgagcg aggaagcgga agagcgccgg
      301 aagctgcatt ttctccttac gtatctgtgc agcatttcac acctcatatg tcgctgttct
      361 ctcaccatct gctctgccgc ctcataatta agccagtata cactccgtta tcgctacgtg
      421 actgggtcat ggctgcgccc cgacacccgc taaaaccccc tgacgcgccc tgacgggctt
      481 gtctgctgac gaaaacgccc acgggaaagc cgtgaccgcc tccgtcagct tcgttatgtt
      541 cctgtttcac tttcggcctc aaagcgaatc tggatgctgt tctggagttc ttctgcgagt
      601 tcgtgcagtc gtttgcacat ggccgcctgt tcgtcggcat ccagagcatc cagtttttca
      661 agcagtgtca ggctctggct tttgatacat cgcgccatat tcagcgcagt ttgttgttat
      721 ttgttcacct tccgttgttc tccgtcagtt ccgggtgtcg ggggggggac cctgagcagg
      781 tggtaattgt aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttctt
      841 taggacgtat catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct
      901 gttgcataaa atttcgctct gcgtcgagtg tttcttaatc aataattccg ctgatactcc
      961 ggaaaaacgc gagtctgttc tcatgcctga aatgcccaca ccccacgcaa aaacaagttt
     1021 ttgctgattt ttctttataa atagagagtt atgacaaatt agttcttctt gctctctttg
     1081 tgatatttaa aaaagcggtg tcggcgcggt gttgtagctg cgccaacacc gctttttagg
     1141 ggtggtactg actattttca taaaaaaaac attatcttat attaggggtg ctgctagcgg
     1201 cgcggtgtgt ttttttacag gacgcccctg ggggcgctgc taggggtgtc tgttcagata
     1261 tgtagcaatg agtcagggat tcacgaactg aaaatgtccg aaaatgtgtc tcatgggcac
     1321 tgtatgcgcc caaaccgatc gtcattcact ttcatgcata gctatgcagt gagctgaaag
     1381 cgatcctgac gcatttttcc ggtttacccc ggggaaaaca tctctttttg cggtgtttgc
     1441 ggcagaatcg cgttcagcgc gttttagcgg tgcgcgcaat aaaatgttat gttaaatgtc
     1501 tgctgaatgg tttttaggtt ttttcctaac atatgataga ataaaaaaac catatgttaa
     1561 tatattgtgt ttttttcaat gaaaatctca aaggtctctg acgaacattt ttctaattac
     1621 aacatgttgc cgaatggtaa tgaagaaatt gacctttttg gcttgattag cgttttatgg
     1681 gcagcaaaaa taaaaattgt tggggtgatt ctattttttg cttgtattgg ctttcttgtt
     1741 tcttttgttt tgccacaaaa atggactagt tctgctgtgg ttactcctgc tgagtctgtt
     1801 caatggagtg aattaaataa ggagctttcc aagcttcatg ttctgggagt ggattttgat
     1861 atcaatcgtg atagcgcatt tgctctgttt attaagaaat ttcagtccgt taattcgttg
     1921 aatgagtata tgagatcatc tccttatgtt atggagatta ttaaaaagaa taacattagc
     1981 gctctcgaac tgcatcgtgc aattgttgag ttgagtaaaa atatgaagtc gattgatgat
     2041 aatgccagta agaaaaacga caagtcatca ttgtatgtat catggactct gagttttact
     2101 gctccaacaa gtaaagaagc tcacgatgtg ttgtctgggt atattaatta tgtttcttcc
     2161 cttgttgtaa gggatttgat ggaagatata agaaataaac tagaagttaa aactaatgtt
     2221 gaaaaagaaa ttcttgcact ggatgagata aaaattagaa accagctgaa tgcagatatt
     2281 cgacgcctca attattcact ggaggttgct aatgcggctg gaataaaaaa acctgtatac
     2341 agcaatggtc agattatgaa ggatgaccca gattttcctg tggctctcgg ttctgatggt
     2401 atagcaacta aattgaacat caaaaaatca atcaaggatg tttcggaatt gagtggggag
     2461 ttgcgaaatc gtcaatatgt tgtgaatcaa ttggttgtgg cgaaagtggg ggatgttgat
     2521 tttatgccat ttcagtatca attgagccca acgttaccgg tcagaaagga tgggccaagt
     2581 aatgccataa ttgtaattct ttcttctgtc attggaggga tgcttgcatg tggctatata
     2641 cttttacgtc atgccatgga ggccagaaag atgagtgtga ttgagtaaaa gttgtgctga
     2701 tgcatcattt tataagcaac ttttataaaa agttcaaagg atcttcttga gatcattccc
     2761 ttacagccgt agtcttctac tctagaaaac gaaaaaacca cctggggagg tggtttttcg
     2821 aaggttcagt aagttgggga acttctgaac cgtggtaaca gtcttgtgcg agacatgtca
     2881 ccaaatctgt ccttctagtg tagcctcagt aaggctgcca cttcaagaac tctcaataca
     2941 tctctcgcac atcctgttta ccagtggccg ctgccaatgg cgttaagtcg tgtcttaccg
     3001 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt
     3061 cgtgcacaca gcccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     3121 tgagacgaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
     3181 gagcgcacga gggtgcttcg cccggtggg
//
