LOCUS       NZ_CP058784             2758 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_17 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP058784
VERSION     NZ_CP058784.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925572
            Assembly: GCF_022494355.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2758)
  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 2758)
  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_022494355.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:07:50
            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)                     :: 4,714
            CDSs (total)                      :: 4,591
            Genes (coding)                    :: 4,355
            CDSs (with protein)               :: 4,355
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 162 of 236
            Pseudo Genes (internal stop)      :: 43 of 236
            Pseudo Genes (multiple problems)  :: 38 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 5
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058784.1.
            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..2758
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_17"
                     /isolation_source="Stanley WWTPs_17 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            complement(join(2685..2758,1..115))
                     /locus_tag="HZT03_RS23405"
                     /old_locus_tag="HZT03_23230"
     CDS             complement(join(2685..2758,1..115))
                     /locus_tag="HZT03_RS23405"
                     /old_locus_tag="HZT03_23230"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(659..1081)
                     /locus_tag="HZT03_RS23410"
                     /old_locus_tag="HZT03_23235"
     CDS             complement(659..1081)
                     /locus_tag="HZT03_RS23410"
                     /old_locus_tag="HZT03_23235"
                     /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="hypothetical protein"
                     /protein_id="WP_080052137.1"
                     /translation="MTITYLALIFITLLTINIILKNRRSKKYLAYNICLAQFTYENEST
                     ENRARIENKAKEIIANGSSIQHMKNTIKQNNPLVIYGFYALAMDELGVPPLLYGFDRWY
                     PVRNPFLAEHGLSRHIEKAVDKIENKSKVQWEHWIN"
                     /name="hypothetical protein"
     gene            complement(1411..1557)
                     /locus_tag="HZT03_RS23415"
     CDS             complement(1411..1557)
                     /locus_tag="HZT03_RS23415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001487656.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_114456554.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAATGKRVYKRLLM
                     QSS"
                     /name="replication initiation protein"
     gene            2410..2637
                     /locus_tag="HZT03_RS23420"
                     /old_locus_tag="HZT03_23240"
     CDS             2410..2637
                     /locus_tag="HZT03_RS23420"
                     /old_locus_tag="HZT03_23240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224019247.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSYMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     Typing          complement(1389..1938)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.918"
                     /coverage="91.0"
                     /evalue="0.0"
ORIGIN
        1 cacagtcggc tgcctcgtca tcaagatcga gcacgtcgag tttttcgagc agcagcagcg
       61 actgcgcccg gataaatttt gccatgttca gtgcggctga ttcctgtttt gtcatacggc
      121 tttttcccgg ttttatggtg atcgcagact gaaatcttac ttcattcact tgagtgcata
      181 gccatgcagg tacgcagaaa tcatcagggg cgttttttct cgatatgggc acagaaaggt
      241 gtatgtttca ggccggagtc ctcagaaacg ccctgagggc gcctgaggtg gtgcgggcaa
      301 cggatgttat ggtaaatgta cctcaaggtt ggctcttttt atgtcctata gctgcttgca
      361 ggatatgagc atgtttctat tgatgactga gccagccatt aatgattgtg ggttggctgt
      421 aactaatgct ccggaatcgc catttatact aaggatgtta tatccttttg ctccacacag
      481 ttctcctgcc tttgttaaac acattcccca atcacgggcc attcctgaac aagttaaact
      541 gtacgcctcg tttccatctg ggccatagct tttgcttact gaagcacagc cggaaagtag
      601 tacaagactt aatgctgcaa ttgttatctt tttcacttca cacctacttt atataaagtt
      661 aattaatcca atgttcccat tgtacttttg atttattttc tattttgtct actgcctttt
      721 ctatatgtcg actcagccca tgttctgcaa ggaatgggtt tctaactgga taccacctat
      781 caaatccata tagtaaaggg gggactccta gctcatccat tgctaatgcg taaaagccat
      841 aaatcacaag cggattgttt tgtttgattg tatttttcat gtgttgaatg gatgaaccat
      901 tggctattat ttccttggct ttattttcta ttctggctct gttttctgta gattcatttt
      961 cataagtgaa ttgagcaagg cagatgttat atgctaaata ttttttagaa cgtctatttt
     1021 ttaatattat attgattgtt agtagggtga taaatataag agctaagtat gtgattgtca
     1081 tttttactag cttaaatggt gattgtgcat catccaacta tacgattttt tatgctttat
     1141 tttcaaaggg ttttgtcggt gtgagttttt gactggtact gttgtttggt atcggtttta
     1201 ctttgatgtc tgtcggtcat cgaagatgaa cctcttgaga tcctttccgt tgcgtcgtaa
     1261 tctcttgctc tgaaaacgaa aaaaccacct ggggaggtgg tttttcgaag gttcagtaag
     1321 ttggggaact tctgaaccgt ggtaacaggg tgtacaagac cgctgccacc aaattcgtcc
     1381 ttccagttta gccgtagttt ggctctgact tcaagaactc tgcatcagta atctcttgta
     1441 caccctctta ccagtggctg ctgccagtgg cgctttgtcg tgtctttccg ggttggactc
     1501 aagtcgatag ttaccggaac aggcgcagca gtcggactga acggggggtt cgtgcataca
     1561 gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa tgagataaac
     1621 gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga
     1681 gggagccacc agggggaaac gcctggtatc tttaagtcct gtcgggtttc gccaccactg
     1741 atttgagcgt cagatttcgt gatgcttgtc aggggggcgg agcctatgga aaaacggctt
     1801 cgccgtggcc ttcttgcttc cctgttaagc ttcttcctgg aagatgccag gaaatttccg
     1861 ccccgccagt aagccggtac cgctcgccgc agccgaacga ccgagcggag cgagtcagtg
     1921 agcgaggaag cggaatatct ccgggcttat ctttggcacc gtacgcgcca tagctgcatt
     1981 ttttaatacg atgcaggata gggcgaacgc cgcaaaatga cgtcatccga catcattccg
     2041 ccgcgttcgc ccagtgacct acagtcggct ctggggtgtc ggggctgtgc cctgaccagg
     2101 cgttttggag tatcgccacc gtggtggcgg tgctacaaaa catatcctgt cccttccttg
     2161 gcatctctga agtttagcca gtatacactc cgctagcgct acgtgactgg ttcagggctg
     2221 cgccccgaca cccgctaaaa gcactgacgc gcctgcggct tgcccaaccc cgcgccgtcc
     2281 gggaaagaat ttcccgatcg acccgacgtt tctgtttacc tgtgatgtta acgtttggat
     2341 ctttttcccg ggtttaccta ttttcttcta atgaagcgtt cacagctgac gttaatagat
     2401 gggtgcttca tgtttggttt ttcaccagga gaacttatga acctttgccc cgatgaacgt
     2461 ctgctctttg tgcggatgat ttccgctatg cttcgccgtt cgggcggtga tgcgggtgct
     2521 gttatgtttg aggcgtatcg ccatattgtg tccgatacca atcaagctcg tcgttcctac
     2581 atgctcgacc tgctcgaaag cgtcaggcat gactatgtac acggtggata tacatagttg
     2641 ccatggatac gcttttcgtc taagtgagcg ttcttttcgt ctctttattc gccgtcctgt
     2701 ataccgaagc gtgcgctcag cttctgataa agcgcttctg cctgttcgtg cattcgct
//
