LOCUS       NZ_CP121219             3179 bp    DNA     circular CON 29-JUN-2023
DEFINITION  Shigella flexneri 2a strain Sflex 21-42 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP121219
VERSION     NZ_CP121219.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33861938
            Assembly: GCF_029625495.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 2a
  ORGANISM  Shigella flexneri 2a
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3179)
  AUTHORS   Ritchie,G., Leung,V., Himsworth,C., Byers,K., Lee,L., Chorlton,S.,
            Stefanovic,A., Romney,M., Matic,N. and Lowe,C.
  TITLE     No isolate, no problem: Using a novel insertion sequence PCR to link
            rats to human shigellosis cases in an underserved urban community
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3179)
  AUTHORS   Ritchie,G.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-MAR-2023) Pathology and Laboratory Science, University
            of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z1Y6,
            Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 21-SEP-2021
            Assembly Method                   :: metaFlye v. SEP-2021
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 70.0x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/29/2023 08:22:13
            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)                     :: 5,088
            CDSs (total)                      :: 4,956
            Genes (coding)                    :: 4,188
            CDSs (with protein)               :: 4,188
            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)              :: 768
            CDSs (without protein)            :: 768
            Pseudo Genes (ambiguous residues) :: 0 of 768
            Pseudo Genes (frameshifted)       :: 279 of 768
            Pseudo Genes (incomplete)         :: 450 of 768
            Pseudo Genes (internal stop)      :: 173 of 768
            Pseudo Genes (multiple problems)  :: 129 of 768
            Pseudo Genes (short protein)      :: 5 of 768
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP121219.1.
            Bacteria and source DNA available from Willson Jang, St. Paul's
            Hospital Microbiology Laboratory, 1081 Burrard Street, Vancouver.
            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 2a"
                     /mol_type="genomic DNA"
                     /strain="Sflex 21-42"
                     /serotype="2a"
                     /isolation_source="fecal sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:42897"
                     /plasmid="unnamed2"
                     /geo_loc_name="Canada: Vancouver"
                     /lat_lon="49.28 N 123.12 W"
                     /collection_date="2021-03-23"
                     /collected_by="St. Paul's Hospital"
     gene            join(3018..3179,1..948)
                     /gene="wzz(fepE)"
                     /locus_tag="P5F89_RS00020"
                     /old_locus_tag="P5F89_00020"
     CDS             join(3018..3179,1..948)
                     /gene="wzz(fepE)"
                     /locus_tag="P5F89_RS00020"
                     /old_locus_tag="P5F89_00020"
                     /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_025790223.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEEIDLFGLISVLWAATIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDSAFALF
                     IKKFQSVNSLNEYMRSSPYVMEIIKKNNISALELHRAIVELSKNMKSIDDNASKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(1973..2137)
                     /locus_tag="P5F89_RS00025"
                     /old_locus_tag="P5F89_00025"
     CDS             complement(1973..2137)
                     /locus_tag="P5F89_RS00025"
                     /old_locus_tag="P5F89_00025"
                     /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          1807..1893
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2207..2305
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2430..2687
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.385"
                     /coverage="89.0"
                     /evalue="3.4e-112"
     Typing          complement(1256..1782)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 tcttttgttt tgccacaaaa atggactagt tctgctgtgg ttactcctgc tgagtctgtt
       61 caatggagtg aattaaataa ggagctttcc aagcttcatg ttctgggagt ggattttgat
      121 atcaatcgtg atagcgcatt tgctctgttt attaagaaat ttcagtccgt taattcgttg
      181 aatgagtata tgagatcatc tccttatgtt atggagatta ttaaaaagaa taacattagc
      241 gctctcgaac tgcatcgtgc aattgttgag ttgagtaaaa atatgaagtc gattgatgat
      301 aatgccagta agaaaaacga caagtcatca ttgtatgtat catggactct gagttttact
      361 gctccaacaa gtaaagaagc tcacgatgtg ttgtctgggt atattaatta tgtttcttcc
      421 cttgttgtaa gggatttgat ggaagatata agaaataaac tagaagttaa aactaatgtt
      481 gaaaaagaaa ttcttgcact ggatgagata aaaattagaa accagctgaa tgcagatatt
      541 cgacgcctca attattcact ggaggttgct aatgcggctg gaataaaaaa acctgtatac
      601 agcaatggtc agattatgaa ggatgaccca gattttcctg tggctctcgg ttctgatggt
      661 atagcaacta aattgaacat caaaaaatca atcaaggatg tttcggaatt gagtggggag
      721 ttgcgaaatc gtcaatatgt tgtgaatcaa ttggttgtgg cgaaagtggg ggatgttgat
      781 tttatgccat ttcagtatca attgagccca acgttaccgg tcagaaagga tgggccaagt
      841 aatgccataa ttgtaattct ttcttctgtc attggaggga tgcttgcatg tggctatata
      901 cttttacgtc atgccatgga ggccagaaag atgagtgtga ttgagtaaaa gttgtgctga
      961 tgcatcattt tataagcaac ttttataaaa agttcaaagg atcttcttga gatcattccc
     1021 ttacagccgt agtcttctac tctagaaaac gaaaaaacca cctggggagg tggtttttcg
     1081 aaggttcagt aagttgggga acttctgaac cgtggtaaca gtcttgtgcg agacatgtca
     1141 ccaaatctgt ccttctagtg tagcctcagt aaggctgcca cttcaagaac tctcaataca
     1201 tctctcgcac atcctgttta ccagtggccg ctgccaatgg cgttaagtcg tgtcttaccg
     1261 ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt
     1321 cgtgcacaca gcccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
     1381 tgagacgaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
     1441 gagcgcacga gggagccacc agggggaaac gcctggtatc tttaagtcct gtcgggtttc
     1501 gccacctctg acttgagcgt cgatttttgt gatgctcgtc aggggggcgg agcctatgga
     1561 aaaacgccac cggcgcggcc ttttttcggg gcctcttttt tgctcacatg ttttttctgg
     1621 tgttatcccc tgattctgtg gataaccgta tatccgtctt tgcgtgagca gacaccgctc
     1681 gccgcagccg aacgaccgag cgcagcgagt cagtgagcga ggaagcggaa gagcgccgga
     1741 agctgcattt tctccttacg tatctgtgca gcatttcaca cctcatatgt cgctgttctc
     1801 tcaccatctg ctctgccgcc tcataattaa gccagtatac actccgttat cgctacgtga
     1861 ctgggtcatg gctgcgcccc gacacccgct aaaaccccct gacgcgccct gacgggcttg
     1921 tctgctgacg aaaacgccca cgggaaagcc gtgaccgcct ccgtcagctt cgttatgttc
     1981 ctgtttcact ttcggcctca aagcgaatct ggatgctgtt ctggagttct tctgcgagtt
     2041 cgtgcagtcg tttgcacatg gccgcctgtt cgtcggcatc cagagcatcc agtttttcaa
     2101 gcagtgtcag gctctggctt ttgatacatc gcgccatatt cagcgcagtt tgttgttatt
     2161 tgttcacctt ccgttgttct ccgtcagttc cgggtgtcgg gggggggacc ctgagcaggt
     2221 ggtaattgta agacgttgcg ggcgacggta ttacaattgc acatcctgtc ctgtttcttt
     2281 aggacgtatc atggcacagc atatcaactg ataaataatc cctgtgcagt gcagccgctg
     2341 ttgcataaaa tttcgctctg cgtcgagtgt ttcttaatca ataattccgc tgatactccg
     2401 gaaaaacgcg agtctgttct catgcctgaa atgcccacac cccacgcaaa aacaagtttt
     2461 tgctgatttt tctttataaa tagagagtta tgacaaatta gttcttcttg ctctctttgt
     2521 gatatttaaa aaagcggtgt cggcgcggtg ttgtagctgc gccaacaccg ctttttaggg
     2581 gtggtactga ctattttcat aaaaaaaaca ttatcttata ttaggggtgc tgctagcggc
     2641 gcggtgtgtt tttttacagg acgcccctgg gggcgctgct aggggtgtct gttcagatat
     2701 gtagcaatga gtcagggatt cacgaactga aaatgtccga aaatgtgtct catgggcact
     2761 gtatgcgccc aaaccgatcg tcattcactt tcatgcatag ctatgcagtg agctgaaagc
     2821 gatcctgacg catttttccg gtttaccccg gggaaaacat ctctttttgc ggtgtttgcg
     2881 gcagaatcgc gttcagcgcg ttttagcggt gcgcgcaata aaatgttatg ttaaatgtct
     2941 gctgaatggt ttttaggttt tttcctaaca tatgatagaa taaaaaaacc atatgttaat
     3001 atattgtgtt tttttcaatg aaaatctcaa aggtctctga cgaacatttt tctaattaca
     3061 acatgttgcc gaatggtaat gaagaaattg acctttttgg cttgattagc gttttatggg
     3121 cagcaacaat aaaaattgtt ggggtgattc tattttttgc ttgtattggc tttcttgtt
//
