LOCUS       NZ_CP130067             3179 bp    DNA     circular CON 21-JUL-2023
DEFINITION  Shigella flexneri 1b strain A-10383 plasmid pA-10383C, complete
            sequence.
ACCESSION   NZ_CP130067
VERSION     NZ_CP130067.1
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 3179)
  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  JOURNAL   Unpublished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 3179)
  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
            CP130067.1.
            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..3179
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="A-10383"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="pA-10383C"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            join(2786..3179,1..716)
                     /gene="wzz(fepE)"
                     /locus_tag="QS169_RS25160"
                     /old_locus_tag="QS169_25160"
     CDS             join(2786..3179,1..716)
                     /gene="wzz(fepE)"
                     /locus_tag="QS169_RS25160"
                     /old_locus_tag="QS169_25160"
                     /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(1741..1905)
                     /locus_tag="QS169_RS25165"
                     /old_locus_tag="QS169_25165"
     CDS             complement(1741..1905)
                     /locus_tag="QS169_RS25165"
                     /old_locus_tag="QS169_25165"
                     /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          1575..1661
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          1976..2074
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          2199..2455
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.769"
                     /coverage="89.0"
                     /evalue="7.31e-114"
     Typing          complement(1024..1550)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.139"
                     /coverage="98.0"
                     /evalue="4.86e-178"
ORIGIN
        1 acattagcgc tctcgaactg catcgtgcaa ttgttgagtt gagtaaaaat atgaagtcga
       61 ttgatgataa tgccagtaag aaaaacgaca agtcatcatt gtatgtatca tggactctga
      121 gttttactgc tccaacaagt aaagaagctc acgatgtgtt gtctgggtat attaattatg
      181 tttcttccct tgttgtaagg gatttgatgg aagatataag aaataaacta gaagttaaaa
      241 ctaatgttga aaaagaaatt cttgcactgg atgagataaa aattagaaac cagctgaatg
      301 cagatattcg acgcctcaat tattcactgg aggttgctaa tgcggctgga ataaaaaaac
      361 ctgtatacag caatggtcag attatgaagg atgacccaga ttttcctgtg gctctcggtt
      421 ctgatggtat agcaactaaa ttgaacatca aaaaatcaat caaggatgtt tcggaattga
      481 gtggggagtt gcgaaatcgt caatatgttg tgaatcaatt ggttgtggcg aaagtggggg
      541 atgttgattt tatgccattt cagtatcaat tgagcccaac gttaccggtc agaaaggatg
      601 ggccaagtaa tgccataatt gtaattcttt cttctgtcat tggagggatg cttgcatgtg
      661 gctatatact tttacgtcat gccatggagg ccagaaagat gagtgtgatt gagtaaaagt
      721 tgtgctgatg catcatttta taagcaactt ttataaaaag ttcaaaggat cttcttgaga
      781 tcattccctt acagccgtag tcttctactc tagaaaacga aaaaaccacc tggggaggtg
      841 gtttttcgaa ggttcagtaa gttggggaac ttctgaaccg tggtaacagt cttgtgcgag
      901 acatgtcacc aaatctgtcc ttctagtgta gcctcagtaa ggctgccact tcaagaactc
      961 tcaatacatc tctcgcacat cctgtttacc agtggccgct gccaatggcg ttaagtcgtg
     1021 tcttaccggg ttggactcaa gacgatagtt accggataag gcgcagcggt cgggctgaac
     1081 ggggggttcg tgcacacagc ccagcttgga gcgaactgcc tacccggaac tgagtgtcag
     1141 gcgtggaatg agacgaacgc ggccataaca gcggaatgac accggtaaac cgaaaggcag
     1201 gaacaggaga gcgcacgagg gagccaccag ggggaaacgc ctggtatctt taagtcctgt
     1261 cgggtttcgc cacctctgac ttgagcgtcg atttttgtga tgctcgtcag gggggcggag
     1321 cctatggaaa aacgccaccg gcgcggcctt ttttcggggc ctctcttttg ctcacatgtt
     1381 ttttctggtg ttatcccctg attctgtgga taaccgtata tccgtctttg cgtgagcaga
     1441 caccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga
     1501 gcgccggaag ctgcattttc tccttacgta tctgtgcagc atttcacacc tcatatgtcg
     1561 ctgttctctc accatctgct ctgccgcctc ataattaagc cagtatacac tccgttatcg
     1621 ctacgtgact gggtcatggc tgcgccccga cacccgctaa aaccccctga cgcgccctga
     1681 cgggcttgtc tgctgacgaa aacgcccacg ggaaagccgt gaccgcctcc gtcagcttcg
     1741 ttatgttcct gtttcacttt cggcctcaaa gcgaatctgg atgctgttct ggagttcttc
     1801 tgcgagttcg tgcagtcgtt tgcacatggc cgcctgttcg tcggcatcca gagcatccag
     1861 tttttcaagc agtgtcaggc tctggctttt gatacatcgc gccatattca gcgcagtttg
     1921 ttgttatttg ttcaccttcc gttgttctcc gtcagttccg ggtgtcgggg ggggggaccc
     1981 tgagcaggtg gtaattgtaa gacgttgcgg gcgatggtat tacaattgca catcctgtcc
     2041 tgtttcttta ggacgtatca tggcacagca tatcaactga taaataattc ctgtgcagtg
     2101 cagccgctgt tgcataaaat ttcgctctgc gtcgagtgtt tcttaatcaa taattccgct
     2161 gatactccgg aaaaacgcga gtctgttctc atgcctgaaa tgcccacacc ccacgcaaaa
     2221 acaagttttt gctgattttt ctttataaat agagagttat gacaaattag ttcttcttgc
     2281 tctctttgtg atatttaaaa aagcggtgtc ggcgcggtgt tgtagctgcg ccaacaccgc
     2341 tttttagggg tggtactgac tattttcata aaaaaaacat catcttatat taggggtgct
     2401 gctagcggcg cggtgtgttt ttttacagga cgccctgggg gcgctgctag gggtgtctgt
     2461 tcagatatgt agcaatgagt cagggattca cgaactgaaa atgtccgaaa atgtgtctca
     2521 tgggcactgt atgcgcccaa accgatcgtc attcactttc atgcatagct atgcagtgag
     2581 ctgaaagcga tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg
     2641 tgtttgcggc agaatcgcgt tcagcgcgtt ttagcggtgc gcgcaataaa atgttatgtt
     2701 aaatgtctgc tgaatggttt ttaggttttt tcctaacata tgatagaata aaaaaaccat
     2761 atgttaatat attgtgtttt tttcaatgaa aatctcaaag gtctctgacg aacatttttc
     2821 taattacaac atgttgccga atggtaatga agaaattgac ctttttggct tgattagcgt
     2881 tttatgggca gcaaaaataa aaattgttgg ggtgattcta ttttttgctt gtattggctt
     2941 tcttgtttct tttgttttgc cacaaaaatg gactagttct gctgtggtta ctcctgctga
     3001 gtctgttcaa tggagtgaat taaataagga gctttccaag cttcatgttc tgggagtggg
     3061 ttttgatatc aatcgtgata gcgcatttgc tctgtttatt aagaaatttc agtccgttaa
     3121 ttcgttgaat gagtatatga gatcatctcc ttatgttatg gagattatta aaaagaata
//
