LOCUS       NZ_CP127085             3180 bp    DNA     circular CON 23-NOV-2023
DEFINITION  Shigella flexneri 1b strain SF-018-002 plasmid psflex002C, complete
            sequence.
ACCESSION   NZ_CP127085
VERSION     NZ_CP127085.1
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 3180)
  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 3180)
  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
            CP127085.1.
            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..3180
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="SF-018-002"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex002C"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            join(2785..3180,1..714)
                     /gene="wzz(fepE)"
                     /locus_tag="QQS68_RS24595"
                     /old_locus_tag="QQS68_24575"
     CDS             join(2785..3180,1..714)
                     /gene="wzz(fepE)"
                     /locus_tag="QQS68_RS24595"
                     /old_locus_tag="QQS68_24575"
                     /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_025760792.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVGFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(959..1093)
                     /locus_tag="QQS68_RS24600"
     CDS             complement(959..1093)
                     /locus_tag="QQS68_RS24600"
                     /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"
     gene            complement(1739..1903)
                     /locus_tag="QQS68_RS24605"
                     /old_locus_tag="QQS68_24580"
     CDS             complement(1739..1903)
                     /locus_tag="QQS68_RS24605"
                     /old_locus_tag="QQS68_24580"
                     /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"
     Typing          1573..1659
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          1974..2072
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          2197..2454
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.402"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(1022..1548)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.139"
                     /coverage="98.0"
                     /evalue="4.86e-178"
ORIGIN
        1 attagcgctc tcgaactgca tcgtgcaatt gttgagttga gtaaaaatat gaagtcgatt
       61 gatgataatg ccagtaagaa aaacgacaag tcatcattgt atgtatcatg gactctgagt
      121 tttactgctc caacaagtaa agaagctcac gatgtgttgt ctgggtatat taattatgtt
      181 tcttcccttg ttgtaaggga tttgatggaa gatataagaa ataaactaga agttaaaact
      241 aatgttgaaa aagaaattct tgcactggat gagataaaaa ttagaaacca gctgaatgca
      301 gatattcgac gcctcaatta ttcactggag gttgctaatg cggctggaat aaaaaaacct
      361 gtatacagca atggtcagat tatgaaggat gacccagatt ttcctgtggc tctcggttct
      421 gatggtatag caactaaatt gaacatcaaa aaatcaatca aggatgtttc ggaattgagt
      481 ggggagttgc gaaatcgtca atatgttgtg aatcaattgg ttgtggcgaa agtgggggat
      541 gttgatttta tgccatttca gtatcaattg agcccaacgt taccggtcag aaaggatggg
      601 ccaagtaatg ccataattgt aattctttct tctgtcattg gagggatgct tgcatgtggc
      661 tatatacttt tacgtcatgc catggaggcc agaaagatga gtgtgattga gtaaaagttg
      721 tgctgatgca tcattttata agcaactttt ataaaaagtt caaaggatct tcttgagatc
      781 attcccttac agccgtagtc ttctactcta gaaaacgaaa aaaccacctg gggaggtggt
      841 ttttcgaagg ttcagtaagt tggggaactt ctgaaccgtg gtaacagtct tgtgcgagac
      901 atgtcaccaa atctgtcctt ctagtgtagc ctcagtaagg ctgccacttc aagaactctc
      961 aatacatctc tcgcacatcc tgtttaccag tggccgctgc caatggcgtt aagtcgtgtc
     1021 ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg
     1081 ggggttcgtg cacacagccc agcttggagc gaactgccta cccggaactg agtgtcaggc
     1141 gtggaatgag acgaacgcgg ccataacagc ggaatgacac cggtaaaccg aaaggcagga
     1201 acaggagagc gcacgaggga gccaccaggg ggaaacgcct ggtatcttta agtcctgtcg
     1261 ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc
     1321 tatggaaaaa cgccaccggc gcggcctttt ttcggggcct ctcttttgct cacatgtttt
     1381 ttctggtgtt atcccctgat tctgtggata accgtatatc cgtctttgcg tgagcagaca
     1441 ccgctcgccg cagccgaacg accgagcgca gcgagtcagt gagcgaggaa gcggaagagc
     1501 gccggaagct gcattttctc cttacgtatc tgtgcagcat ttcacacctc atatgtcgct
     1561 gttctctcac catctgctct gccgcctcat aattaagcca gtatacactc cgttatcgct
     1621 acgtgactgg gtcatggctg cgccccgaca cccgctaaaa ccccctgacg cgccctgacg
     1681 ggcttgtctg ctgacgaaaa cgcccacggg aaagccgtga ccgcctccgt cagcttcgtt
     1741 atgttcctgt ttcactttcg gcctcaaagc gaatctggat gctgttctgg agttcttctg
     1801 cgagttcgtg cagtcgtttg cacatggccg cctgttcgtc ggcatccaga gcatccagtt
     1861 tttcaagcag tgtcaggctc tggcttttga tacatcgcgc catattcagc gcagtttgtt
     1921 gttatttgtt caccttccgt tgttctccgt cagttccggg tgtcgggggg ggggaccctg
     1981 agcaggtggt aattgtaaga cgttgcgggc gatggtatta caattgcaca tcctgtcctg
     2041 tttctttagg acgtatcatg gcacagcata tcaactgata aataatccct gtgcagtgca
     2101 gccgctgttg cataaaattt cgctctgcgt cgagtgtttc ttaatcaata attccgctga
     2161 tactccggaa aaacgcgagt ctgttctcat gcctgaaatg cccacacccc acgcaaaaac
     2221 aagtttttgc tgatttttct ttataaatag agagttatga caaattagtt cttcttgctc
     2281 tctttgtgat atttaaaaaa gcggtgtcgg cgcggtgttg tagctgcgcc aacaccgctt
     2341 tttaggggtg gtactgacta ttttcataaa aaaaaacatc atcttatatt aggggtgctg
     2401 ctagcggcgc ggtgtgtttt tttacaggac gccctggggg cgctgctagg ggtgtctgtt
     2461 cagatatgta gcaatgagtc agggattcac gaactgaaaa tgtccgaaaa tgtgtctcat
     2521 gggcactgta tgcgcccaaa ccgatcgtca ttcactttca tgcatagcta tgcagtgagc
     2581 tgaaagcgat cctgacgcat ttttccggtt taccccgggg aaaacatctc tttttgcggt
     2641 gtttgcggca gaatcgcgtt cagcgcgttt tagcggtgcg cgcaataaaa tgttatgtta
     2701 aatgtctgct gaatggtttt taggtttttt cctaacatat gatagaataa aaaaaccata
     2761 tgttaatata ttgtgttttt ttcaatgaaa atctcaaagg tctctgacga acatttttct
     2821 aattacaaca tgttgccgaa tggtaatgaa gaaattgacc tttttggctt gattagcgtt
     2881 ttatgggcag caaaaataaa aattgttggg gtgattctat tttttgcttg tattggcttt
     2941 cttgtttctt ttgttttgcc acaaaaatgg actagttctg ctgtggttac tcctgctgag
     3001 tctgttcaat ggagtgaatt aaataaggag ctttccaagc ttcatgttct gggagtgggt
     3061 tttgatatca atcgtgatag cgcatttgct ctgtttatta agaaatttca gtccgttaat
     3121 tcgttgaatg agtatatgag atcatctcct tatgttatgg agattattaa aaagaataac
//
