LOCUS       NZ_CP058794             3257 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_6 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP058794
VERSION     NZ_CP058794.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925576
            Assembly: GCF_022494435.1
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 (06-JUL-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. Unicycler 0.4.8
            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_022494435.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:11:09
            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)                     :: 4,890
            CDSs (total)                      :: 4,767
            Genes (coding)                    :: 4,558
            CDSs (with protein)               :: 4,558
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 209
            CDSs (without protein)            :: 209
            Pseudo Genes (ambiguous residues) :: 0 of 209
            Pseudo Genes (frameshifted)       :: 65 of 209
            Pseudo Genes (incomplete)         :: 135 of 209
            Pseudo Genes (internal stop)      :: 41 of 209
            Pseudo Genes (multiple problems)  :: 32 of 209
            Pseudo Genes (short protein)      :: 3 of 209
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058794.1.
            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="STLIN_6"
                     /isolation_source="Stanley WWTPs_6 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            296..592
                     /locus_tag="HZT08_RS24305"
                     /old_locus_tag="HZT08_24095"
     CDS             296..592
                     /locus_tag="HZT08_RS24305"
                     /old_locus_tag="HZT08_24095"
                     /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            complement(823..935)
                     /locus_tag="HZT08_RS24515"
                     /pseudo=""
     CDS             complement(823..935)
                     /locus_tag="HZT08_RS24515"
                     /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(1589..1783)
                     /locus_tag="HZT08_RS24310"
                     /old_locus_tag="HZT08_24100"
     CDS             complement(1589..1783)
                     /locus_tag="HZT08_RS24310"
                     /old_locus_tag="HZT08_24100"
                     /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            complement(2927..3208)
                     /locus_tag="HZT08_RS24320"
                     /old_locus_tag="HZT08_24105"
     CDS             complement(2927..3208)
                     /locus_tag="HZT08_RS24320"
                     /old_locus_tag="HZT08_24105"
                     /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          1434..1516
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.79e-36"
     Typing          1820..1918
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2043..2298
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.023"
                     /coverage="89.0"
                     /evalue="1.24e-101"
     Typing          complement(864..1421)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.464"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccggttcatc cgtatttcca ttgcaaaccc cttgctctat ttgaataaat gacgtaggtt
       61 ttacttaacc aagtcgcatt ttaatctgtt gacattggtt tgatgcgctg tacaatgccg
      121 gggccttgaa tttcacatca agtacccaca tcataaggaa tgattagacg caccaatgtg
      181 catcataatg tcattctttt ttttagtcaa caatgagttg cgttatgcgc aatgcgcaat
      241 ctgaaaacgc aataggccta tctttttaaa actaatatag gcttcagagg aaggtatgat
      301 taatcttgtc gatccagtac atccaggggt ttttatccgt gagatgttta tggaaccgtt
      361 tgaaatatca gccgcggacc tgtctgaaaa actgcatgta tcaccttcca ctctaagtag
      421 agtgctgaat ggaaaagctg atttaagtgt tgagatggca ttaaggcttt ctcgagttct
      481 tggtcgcagt gccgagtcgt ggataaacat gcagactcaa tacagtctta acgcgagcag
      541 gaagtcacct aatgtcatta aggaattaga tgaattggtt cctatatttt gagaaaagaa
      601 aaggccgcta tatgcggcct ttttctgtct tgactctcag gcaactggat cgtatcgttt
      661 ctcgtaaacg aaaaaaccac ccggcaaggt ggttttttcg aaggttcagt aaccggcaag
      721 tttctgaacc agggtaactg gcttggagga gcgcagtcac caaaacttgt tctttcagtt
      781 tagccttaac tggcgcataa cttcaagact aactcctcta aatcagttac cagtggctgc
      841 tgccaatggt gttttgcatg tctttccggg ttggactcaa gatgatagtt accggataag
      901 gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc
      961 tacactgaac cgagatacct acagcgtgag ctatgagaaa gcgccacgct tcccgaaggg
     1021 agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag
     1081 ccaccagggg gaaacgtctg gtatctttaa gtcctgtcgg gtttcgccac ctctgacttg
     1141 agcgtcgatt tctgtgatgc tcgtcagggg ggcggagcct atggaaaaac gcctgcggcg
     1201 cggccttctt cctgttcttg gtcttttgct cacatgttct ttccggcctt atcccctgat
     1261 tctgtggata accgtgctgc cgtttttgtg taagtcagta ccgctcgccg cagccgaacg
     1321 accgagcgta gcgagtcagt gagcgaggaa gcggaaaagc gcctggacgc gcattttctc
     1381 cttacgcatc tgtgcggaat ttcacacccg gcatggggca cttttcatac aatctgcact
     1441 gatgccgcat agttaagcca gtatacactc cgctatcgct acgtgactgg gtcagggctt
     1501 cgccccgaca cccgctgacg cgccctggcg ggcttgtctg ctgccgaaaa cgctcgcgga
     1561 caagccgtga gcgcctccgt cagcttcgtt atgttcctgt ttcactttcg gtctcaaagc
     1621 gaacctggat gctgttctgg agttcttccg cgagttcgtg cagtcgttcg cacatggccg
     1681 cctgttcgtc ggcatccaga gcatccagtt tttcaagcag tgtcaggctc tggcttttga
     1741 taaatcgcgc catattcagc gcagtttgtt gttgtttgtt caccttccgt tgttctccgt
     1801 cagttccggg tgtcgggggg accctgagca gctggtaatt gtaagacgtt gcgggcgacg
     1861 gtattacaat tgcacatcct gtcctgtttt tttaggacgt atcatggcac agcatatcaa
     1921 ctgataaata atccctgtgc agtgcagccg ctgttgcata aaatttcgct ctgcgtcgag
     1981 tgtttcttaa tcaataattc cgctgatact ccggaaaaac gcgagtctgt tctcattcct
     2041 gaaatgccca caccccacgc aaaaacaagt ttttgctgat ttttctttat aaatagagag
     2101 ttatgaaaaa ttagtttctc ttgctctctt tgcgatattt aaaaaagcgg tgccggcgca
     2161 gctacaacac cgcgccgaca ccgctttgta gggggggtac tgactatttt tataaaaaac
     2221 atcattttat atcaggggtg ctgctagcgg cgcggtgtgt ttttttacag gacgcccctg
     2281 ggggcgctgc caggggtgtc tgttcagata tgtagcaatg agtcagggat tcacgaactg
     2341 aaaatgtccg aaaatgtgtc tcatgggtac tgtatgcgcc caaaccgttc gtcattcatt
     2401 ttcatgcata gctatgcagt gggctgaaaa cgatcctgac gcattttttc ggttttcact
     2461 gggtaaaaca tctctttttg cggtatctgc gtcagaatcg cgttcagtgc gttttagcgg
     2521 tgcgcgtaat gcgacgttat ggtaaatgct gtgatttacg ggatggtttt atctatgttg
     2581 atatcaatac cacctcttat ggaggtggct tacaccgatt tttccttgtt gtctgtttca
     2641 gaacagatag aggctttttt ggcaattatc caaccactat tgatagtgtt tattactact
     2701 tagataactg agcctttact gtatctgccc ctgcaagcag gaacccaaca gttaagaacc
     2761 acccccagcc attgatacct tttagcgcta gaattgctgc gcaaatgatg gctgctatag
     2821 ggactatctg gtacagaaaa tacttcatat aacttacccc gaggttttgc ttttttatga
     2881 gaccctaaag catcgatact gtcactttga tgctttaagg accttcttag tgataatcct
     2941 cgagatccac gtcaaagacg ttaggttctt cgagcttaaa cactacgcgc cagtttccat
     3001 tgacctctaa cgaatactct ccttgacggt ctcccttcaa tggatggcag cgcaatgcct
     3061 ttaaatccat catatcctgc aagttcgtcg ctgtgcttaa ggctgttagg atcagcttca
     3121 gacgttgagt aaactgttgc ggaattcctg cgttgttacc tgtttcggca aacttacgca
     3181 aacctttatg cttgatattt atgatcatta atcaccatcc catatttgtt tagatagaaa
     3241 catcgcagtt tattttt
//
