LOCUS       CP128225                3178 bp    DNA     circular BCT 22-MAY-2024
DEFINITION  Shigella flexneri 1b strain sflex069 plasmid psflex069-D, complete
            sequence.
ACCESSION   CP128225
VERSION     CP128225.1
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 3178)
  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  JOURNAL   Unpublished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 3178)
  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..3178
                     /organism="Shigella flexneri 1b"
                     /mol_type="genomic DNA"
                     /strain="sflex069"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="psflex069-D"
                     /lat_lon="43.6 N 79.4 W"
                     /collected_by="PHO"
     gene            complement(join(3082..3178,1..68))
                     /locus_tag="QS103_25400"
     CDS             complement(join(3082..3178,1..68))
                     /locus_tag="QS103_25400"
                     /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="Rop family plasmid primer RNA-binding protein"
                     /protein_id="XBA31300.1"
                     /translation="MARCIKSQSLTLLEKLDALDADEQAAMCKRLHELAEELQNSIQIR
                     FEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            948..2057
                     /gene="wzz(fepE)"
                     /locus_tag="QS103_25405"
     CDS             948..2057
                     /gene="wzz(fepE)"
                     /locus_tag="QS103_25405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology. GO_component:
                     GO:0016020 - membrane [Evidence IEA]; GO_process:
                     GO:0009103 - lipopolysaccharide biosynthetic process
                     [Evidence IEA]"
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="XBA31301.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVGFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     Typing          139..237
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.0"
                     /coverage="100.0"
                     /evalue="6.26e-40"
     Typing          362..617
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.139"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          2916..3002
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          complement(2365..2891)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.139"
                     /coverage="98.0"
                     /evalue="4.86e-178"
ORIGIN
        1 tcgtcggcat ccagagcatc cagtttttca agcagtgtca ggctctggct tttgatacat
       61 cgcgccatat tcagcgcagt ttgttgttat ttgttcacct tccgttgttc tccgtcagtt
      121 ccgggtgtcg ggggggggga ccctgagcag gtggtaattg taagacgttg cgggcgatgg
      181 tattacaatt gcacatcctg tcctgtttct ttaggacgta tcatggcaca gcatatcaac
      241 tgataaataa ttcctgtgca gtgcagccgc tgttgcataa aatttcgctc tgcgtcgagt
      301 gtttcttaat caataattcc gctgatactc cggaaaaacg cgagtctgtt ctcatgcctg
      361 aaatgcccac accccacgca aaaacaagtt tttgctgatt tttctttata aatagagagt
      421 tatgacaaat tagttcttct tgctctcttt gtgatattta aaaaagcggt gtcggcgcgg
      481 tgttgtagct gcgccaacac cgctttttag gggtggtact gactattttc ataaaaaaac
      541 atcatcttat attaggggtg ctgctagcgg cgcggtgtgt ttttttacag gacgccctgg
      601 gggcgctgct aggggtgtct gttcagatat gtagcaatga gtcagggatt cacgaactga
      661 aaatgtccga aaatgtgtct catgggcact gtatgcgccc aaaccgatcg tcattcactt
      721 tcatgcatag ctatgcagtg agctgaaagc gatcctgacg catttttccg gtttaccccg
      781 gggaaaacat ctctttttgc ggtgtttgcg gcagaatcgc gttcagcgcg ttttagcggt
      841 gcgcgcaata aaatgttatg ttaaatgtct gctgaatggt ttttaggttt tttcctaaca
      901 tatgatagaa taaaaaaacc atatgttaat atattgtgtt tttttcaatg aaaatctcaa
      961 aggtctctga cgaacatttt tctaattaca acatgttgcc gaatggtaat gaagaaattg
     1021 acctttttgg cttgattagc gttttatggg cagcaaaaat aaaaattgtt ggggtgattc
     1081 tattttttgc ttgtattggc tttcttgttt cttttgtttt gccacaaaaa tggactagtt
     1141 ctgctgtggt tactcctgct gagtctgttc aatggagtga attaaataag gagctttcca
     1201 agcttcatgt tctgggagtg ggttttgata tcaatcgtga tagcgcattt gctctgttta
     1261 ttaagaaatt tcagtccgtt aattcgttga atgagtatat gagatcatct ccttatgtta
     1321 tggagattat taaaaagaat aacattagcg ctctcgaact gcatcgtgca attgttgagt
     1381 tgagtaaaaa tatgaagtcg attgatgata atgccagtaa gaaaaacgac aagtcatcat
     1441 tgtatgtatc atggactctg agttttactg ctccaacaag taaagaagct cacgatgtgt
     1501 tgtctgggta tattaattat gtttcttccc ttgttgtaag ggatttgatg gaagatataa
     1561 gaaataaact agaagttaaa actaatgttg aaaaagaaat tcttgcactg gatgagataa
     1621 aaattagaaa ccagctgaat gcagatattc gacgcctcaa ttattcactg gaggttgcta
     1681 atgcggctgg aataaaaaaa cctgtataca gcaatggtca gattatgaag gatgacccag
     1741 attttcctgt ggctctcggt tctgatggta tagcaactaa attgaacatc aaaaaatcaa
     1801 tcaaggatgt ttcggaattg agtggggagt tgcgaaatcg tcaatatgtt gtgaatcaat
     1861 tggttgtggc gaaagtgggg gatgttgatt ttatgccatt tcagtatcaa ttgagcccaa
     1921 cgttaccggt cagaaaggat gggccaagta atgccataat tgtaattctt tcttctgtca
     1981 ttggagggat gcttgcatgt ggctatatac ttttacgtca tgccatggag gccagaaaga
     2041 tgagtgtgat tgagtaaaag ttgtgctgat gcatcatttt ataagcaact tttataaaaa
     2101 gttcaaagga tcttcttgag atcattccct tacagccgta gtcttctact ctagaaaacg
     2161 aaaaaaccac ctggggaggt ggtttttcga aggttcagta agttggggaa cttctgaacc
     2221 gtggtaacag tcttgtgcga gacatgtcac caaatctgtc cttctagtgt agcctcagta
     2281 aggctgccac ttcaagaact ctcaatacat ctctcgcaca tcctgtttac cagtggccgc
     2341 tgccaatggc gttaagtcgt gtcttaccgg gttggactca agacgatagt taccggataa
     2401 ggcgcagcgg tcgggctgaa cggggggttc gtgcacacag cccagcttgg agcgaactgc
     2461 ctacccggaa ctgagtgtca ggcgtggaat gagacgaacg cggccataac agcggaatga
     2521 caccggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg
     2581 cctggtatct ttaagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg
     2641 atgctcgtca ggggggcgga gcctatggaa aaacgccacc ggcgcggcct tttttcgggg
     2701 cctctctttt gctcacatgt tttttctggt gttatcccct gattctgtgg ataaccgtat
     2761 atccgtcttt gcgtgagcag acaccgctcg ccgcagccga acgaccgagc gcagcgagtc
     2821 agtgagcgag gaagcggaag agcgccggaa gctgcatttt ctccttacgt atctgtgcag
     2881 catttcacac ctcatatgtc gctgttctct caccatctgc tctgccgcct cataattaag
     2941 ccagtataca ctccgttatc gctacgtgac tgggtcatgg ctgcgccccg acacccgcta
     3001 aaaccccctg acgcgccctg acgggcttgt ctgctgacga aaacgcccac gggaaagccg
     3061 tgaccgcctc cgtcagcttc gttatgttcc tgtttcactt tcggcctcaa agcgaatctg
     3121 gatgctgttc tggagttctt ctgcgagttc gtgcagtcgt ttgcacatgg ccgcctgt
//
