LOCUS       NZ_CP055104             3257 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain SWHIN_107 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP055104
VERSION     NZ_CP055104.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925599
            Assembly: GCF_022354645.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3257)
  AUTHORS   Che,Y., Xu,X., Yang,Y., Brinda,K., Hanage,W., Yang,C. and Zhang,T.
  TITLE     High-resolution genomic surveillance elucidates a multilayered
            hierarchical transfer of resistance between WWTP- and
            human/animal-associated bacteria
  JOURNAL   Microbiome 10 (1), 16 (2022)
   PUBMED   35078531
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3257)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-JUN-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: "Other" v. Unicycler
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200x
            Sequencing Technology :: Illumina; Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022354645.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:15:51
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,106
            CDSs (total)                      :: 4,984
            Genes (coding)                    :: 4,806
            CDSs (with protein)               :: 4,806
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 178
            CDSs (without protein)            :: 178
            Pseudo Genes (ambiguous residues) :: 0 of 178
            Pseudo Genes (frameshifted)       :: 65 of 178
            Pseudo Genes (incomplete)         :: 114 of 178
            Pseudo Genes (internal stop)      :: 25 of 178
            Pseudo Genes (multiple problems)  :: 26 of 178
            Pseudo Genes (short protein)      :: 3 of 178
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055104.1.
            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..3257
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_107"
                     /isolation_source="Shek Wu Hui WWTPs_107 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            162..356
                     /locus_tag="HUZ84_RS25420"
                     /old_locus_tag="HUZ84_25205"
     CDS             162..356
                     /locus_tag="HUZ84_RS25420"
                     /old_locus_tag="HUZ84_25205"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1010..1122
                     /locus_tag="HUZ84_RS25600"
                     /pseudo=""
     CDS             1010..1122
                     /locus_tag="HUZ84_RS25600"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(1353..1649)
                     /locus_tag="HUZ84_RS25425"
                     /old_locus_tag="HUZ84_25210"
     CDS             complement(1353..1649)
                     /locus_tag="HUZ84_RS25425"
                     /old_locus_tag="HUZ84_25210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000609270.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HigA family addiction module antitoxin"
                     /protein_id="WP_000609270.1"
                     /translation="MINLVDPVHPGVFIREMFMEPFEISAADLSEKLHVSPSTLSRVLN
                     GKADLSVEMALRLSRVLGRSAESWINMQTQYSLNASRKSPNVIKELDELVPIF"
                     /name="HigA family addiction module antitoxin"
     gene            1994..2275
                     /locus_tag="HUZ84_RS25430"
                     /old_locus_tag="HUZ84_25215"
     CDS             1994..2275
                     /locus_tag="HUZ84_RS25430"
                     /old_locus_tag="HUZ84_25215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000586174.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000586174.1"
                     /translation="MIINIKHKGLRKFAETGNNAGIPQQFTQRLKLILTALSTATNLQD
                     MMDLKALRCHPLKGDRQGEYSLEVNGNWRVVFKLEEPNVFDVDLEDYH"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     Typing          complement(28..126)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          complement(430..512)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          complement(2905..3160)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.124"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          525..1079
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.434"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cactgcacag ggattattta tcagttgata tgctgtgcca tgatacgtcc taaaaaaaca
       61 ggacaggatg tgcaattgta ataccgtcgc ccgcaacgtc ttacaattac cacctggtca
      121 gggtccaccc gacacccggt actgacggag aacaacggaa ggtgaacaaa cagcaacaaa
      181 ctgcgctgaa tatggcgcga tttatcaaaa gccagagcct gacactgctt gaaaaactgg
      241 atgctctgga tgccgacgaa caggcggcca tgtgcgaacg actgcacgaa ctcgcggaag
      301 aactccagaa cagcatccag gttcgctttg agaccgaaag tgaaacagga acataacgaa
      361 gctgacggag gcgctcacgg cttgtccgcg agcgttttcg gcagcagaca agcccgccag
      421 ggcgcgtcag cgggtgtcgg ggcgaagccc tgacccagtc acgtagcgat agcggagtgt
      481 atactggctt aactatgcgg catcagtgca gattgtatga aaagtgcccc atgccgggtg
      541 tgaaattccg cacagatgcg taaggagaaa atgcgcgtcc aggcgctttt ccgcttcctc
      601 gctcactgac tcgctacgct cggtcgttcg gctgcggcga gcggtactga cttacacaaa
      661 aacggcagca cggttatcca cagaatcagg ggataaggcc ggaaagaaca tgtgagcaaa
      721 agaccaataa caggaagaag gccgcgccgc aggcgttttt ccataggctc cgcccccctg
      781 acgagcatca cagaaatcga cgctcaagtc agaggtggcg aaacccgaca ggacttaaag
      841 ataccagacg tttccccctg gtggctccct cgtgcgctct cctgttccga ccctgccgct
      901 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
      961 ctgtaggtat ctcggttcag tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     1021 ccccgttcag cccgaccgct gcgccttatc cggtaactat catcttgagt ccaacccgga
     1081 aagacatgca aaacaccatt ggcagcagcc actggtaact gatttagagg agttagtctt
     1141 gaagttatgc gccagttaag gctaaactga aagaacaagt tttggtgact gcgctcctcc
     1201 aagccagtta ccctggttca gaaacttgcc ggttactgaa ccttcgaaaa aaccaccttg
     1261 ccgggtggtt ttttcgttta cgagaaacga tacgatccag ttgcctgaga gtcaagacag
     1321 aaaaaggccg catatagcgg ccttttcttt tctcaaaata taggaaccaa ttcatctaat
     1381 tccttaatga cattaggtga cttcctgctc gcgttaagac tgtattgagt ctgcatgttt
     1441 atccacgact cggcactgcg accaagaact cgagaaagcc ttaatgccat ctcaacactt
     1501 aaatcagctt ttccattcag cactctactt agagtggaag gtgatacatg cagtttttca
     1561 gacaggtccg cggctgatat ttcaaacggt tccataaaca tctcacggat aaaaacccct
     1621 ggatgtactg gatcgacaag attaatcata ccttcctctg aagcctatat tagttttaaa
     1681 aagataggcc tattgcgttt tcagattgcg cattgcgcat aacgcaactc attgttgact
     1741 aaaaaaaaga atgacattat gatgcacatt ggtgcgtcta atcattcctt atgatgtggg
     1801 tacttgatgt gaaattcaag gccccggcat tgtacagcgc atcaaaccaa tgtcaacaga
     1861 ttaaaatgcg acttggttaa gtaaaaccta cgtcatttat tcaaatagag caaggggttt
     1921 gcaatggaaa tacggatgaa ccggaaaaat aaactgcgat gtttctatct aaacaaatat
     1981 gggatggtga ttaatgatca taaatatcaa gcataaaggt ttgcgtaagt ttgccgaaac
     2041 aggtaacaac gcaggaattc cgcaacagtt tactcaacgt ctgaagctga tcctaacagc
     2101 cttaagcaca gcgacgaact tgcaggatat gatggattta aaggcattgc gctgccatcc
     2161 attgaaggga gaccgtcaag gagagtattc gttagaggtc aatggaaact ggcgcgtagt
     2221 gtttaagctc gaagaaccta acgtctttga cgtggatctc gaggattatc actaagaagg
     2281 tccttaaagc atcaaagtga cagtatcgat gctttagggt ctcataaaaa agcaaaacct
     2341 cggggtaagt tatatgaagt attttctgta ccagatagtc cctatagcag ccatcatttg
     2401 cgcagcaatt ctagcgctaa aaggtatcaa tggctggggg tggttcttaa ctgttgggtt
     2461 cctgcttgca ggggcagata cagtaaaggc tcagttatct aagtagtaat aaacactatc
     2521 aatagtggtt ggataattgc caaaaaagcc tctatctgtt ctgaaacaga caacaaggaa
     2581 aaatcggtgt aagccacctc cataagaggt ggtattgata tcaacataga taaaaccatc
     2641 ccgtaaatca cagcatttac cataacgtcg cattacgcgc accgccaaaa cgcgctgaac
     2701 gcgattctgc cgcgaacacc gcaaaaagag atgttttacc aagcgaaaac cggaaaaatg
     2761 cgtcaggatc gctttcagct cactgcatag ctatgcatga aagtgaatgg cgatcggttt
     2821 gggcgcatac ggtgcccatg agacacattt tcggacattt tcagttcgtg aatccctgac
     2881 tcattgctac atatctgaac agacacccct agcagcgccc ccaggggcgt cctgtaaaaa
     2941 aacacaccgc gccgctagca gcccccctaa tataaaatga tgttttttat gaaaatagtc
     3001 agtaccaccc ctaaaaagcg gtgttggcgc agctacaaca ccgcgccgac accgcttttt
     3061 taaatatcac aaagagagca agaagaacta atttgtcata actctctatt tataaagaaa
     3121 aatcagcaaa aaattgtttt tgcgtggggt gtgggcattt caggcatgag aacagactcg
     3181 cgtttttccg gagtatcagc ggaattattg attaagaaac actcgacgca gagcgaaatt
     3241 ttatgcaaca gcggctg
//
