LOCUS       NZ_CP058851             2998 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_36 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP058851
VERSION     NZ_CP058851.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925562
            Assembly: GCF_022494155.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2998)
  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 2998)
  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_022494155.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:10:52
            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)                     :: 4,544
            CDSs (total)                      :: 4,423
            Genes (coding)                    :: 4,231
            CDSs (with protein)               :: 4,231
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 65 of 192
            Pseudo Genes (incomplete)         :: 118 of 192
            Pseudo Genes (internal stop)      :: 39 of 192
            Pseudo Genes (multiple problems)  :: 32 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058851.1.
            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..2998
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_36"
                     /isolation_source="Stanley WWTPs_36 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed2"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(2263..2998,1..371))
                     /locus_tag="HZT28_RS22570"
                     /old_locus_tag="HZT28_22385"
     CDS             complement(join(2263..2998,1..371))
                     /locus_tag="HZT28_RS22570"
                     /old_locus_tag="HZT28_22385"
                     /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="DUF559 domain-containing protein"
                     /protein_id="WP_112923075.1"
                     /translation="MQKNKTIWCRVWIIVFLLLVSFFFPYTLLVIGWLIWTIYDDLNSP
                     VITQVSPAPTWRDVKTDDNDWLSKFCEGCESPAEEQFLLAMVRAFNLKPASGKLISPTL
                     TLEMQVNVGRYRFDFLANGRQVIEIDGAAWHSSHEQIERDRIRDEYSVDQGYRVLRIPA
                     KVVFNTPDKAISQVKAAIAETPHYTLPVKPKPLAQRKSLSQHLSAFSDGLTTFNRNISI
                     AIGKQSAMADFNSAINTEKMLLEALVSEVELDMRIETMDPLARTNYENIMATIEAKNAG
                     TVTTSREKLYCWKAIIKPSPVNDAEIQEQIEREYQIEMEKRNQRLAHLIQRCTTDPEFS
                     KRFRRKIEETNYPAADNFRYCNQLLTDK"
                     /name="DUF559 domain-containing protein"
     gene            1225..1416
                     /locus_tag="HZT28_RS22575"
                     /old_locus_tag="HZT28_22390"
     CDS             1225..1416
                     /locus_tag="HZT28_RS22575"
                     /old_locus_tag="HZT28_22390"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_047402702.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNDQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2127..>2240)
                     /locus_tag="HZT28_RS22580"
                     /old_locus_tag="HZT28_22395"
                     /pseudo=""
     CDS             complement(2127..>2240)
                     /locus_tag="HZT28_RS22580"
                     /old_locus_tag="HZT28_22395"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005226372.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="antibiotic biosynthesis monooxygenase"
                     /name="antibiotic biosynthesis monooxygenase"
     Typing          complement(730..1350)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.463"
                     /coverage="99.0"
                     /evalue="9.37e-156"
ORIGIN
        1 cgcccatttg ccagaaaatc gaagcggtaa cgaccaacat ttacctgcat ttccagcgtt
       61 aacgttggag atattaattt accgctggcg ggtttgagat tgaacgctct gaccattgcg
      121 agaagaaact gctcttccgc cggagattcg caaccttcgc aaaacttgct aagccaatcg
      181 ttatcatctg tttttacatc acgccaggtg ggtgccggcg agacctgggt aatgacgggg
      241 ctattcagat catcgtagat ggtccatata agccagccaa taaccagtag cgtgtatgga
      301 aagaagaagc tgactagtaa caaaaaaacg atgatccaaa cacgacacca aatagtttta
      361 tttttctgca cacaattgac ctttttggtt tgttactagg atgtgaatag tattgtattt
      421 tcgaagctat cttgaagtct tactgctttt ttaagctgta ctttgaacgg agagttgaag
      481 gatcttcttg agatccttgg gtgagagtcg tagtctctta actaggaaac gaaaaaccac
      541 ctggggaggt ggtttttcga aggttcagta agttggggaa cttctgaacc gtggtaacag
      601 ggtgtacaag accgctgcca ccaaattcgt cctttcagtt tagccgcagt ctggctctaa
      661 ctgcaagaac tctgcatcag taatctcttg tacaccctct accaatggct accgccaatg
      721 gcgatttatc gtgccttttc gggttggact caagacgata gttaccgaaa agagcgtggt
      781 agtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaact gcctacccgg
      841 aactgagtgt caggcgtgga atgagataaa cgcggccata acagcggaat gacaccggta
      901 aaccgaaagg caggaacagg agagcgcacg agggagccac cagggggaaa cgcctggtat
      961 ctttaagtcc tgtcgggttt cgccaccact gatttgagcg tccgattctg tgatgcttgt
     1021 caggggggcg gagcctatgg aaaaacgccc cggctgggcg tggccttttc gcccttgtcc
     1081 ttagctttcg ttatgcttac cgttacgtta tctgctcatc ttcctccgct cgccgcagac
     1141 tcatgaccga acggagtgag cgaatgagcg aggaagcgga aaaccatcag aacgtacagt
     1201 aagcactttc gcaccggggc cttcatgaac aaacaacaaa agacagccgt taacatggct
     1261 aaattcatcc aggatcagtc cctgcttctt ctggacaggc ttaatgagct ggatctggat
     1321 catgaggctg atttctgcga gaaactccat gaggatgcgg aacgccttta ccgaagcctg
     1381 tcagcgcgcc tgaatgatca gcaggacggt gcgtaatggc tccgttctgg gtattaccgg
     1441 agtaataccg gcatcgcctt aattttcatt gtcttggtgc ttaacattat taccctggta
     1501 atacccagaa tccctttatt ttttcttttt tatttatttt tcatgaagtt gcgataaaaa
     1561 tcgcagctgc gttaggtgta tgaccatttt gaggttgaaa aataatcaac catggagggt
     1621 gatttacgca ggttaagggg agatcgtgac aaaaaaagcg ttcctcactg tatcgttcat
     1681 gcctgcatga acgggttatt cttcctgact acagaattac atcaaaagta catcactttt
     1741 acgtcagatc tgacctctga actattcgta catccgcccc tcttcctggg cctcctgcac
     1801 gtgctgaaaa tggtttttcc ggctgtgccg gcaacgcctc acggccacgc aataaattgc
     1861 gcatccgttc accgttatcg gggtggttcg tggtggcttt cagggcgttc atcggatttt
     1921 agccgctaaa atcccggcca ggtatgtccg tgcatagcca tgcagtcgcg ccagaatcat
     1981 caggggcgtt ttttctcgat atgggcacag aaaggtgtgt gtttcaggcc ggaggcctca
     2041 gaaacgcact gagggcctct gcggcggtgc acgcaacgga tgttatgttc aatttgggta
     2101 acctgctggg tcaccttggg atatgactaa agaggtgaga tgatttcgac ctcgtgctgg
     2161 aacacgtagg gatctgaaag caactcaaat tattcgtcat ccgggtaggt aacggccaca
     2221 tgatagttct cgcctgcaaa ttgtgaatgc tcgacacccg ttttatttat cagtcaaaag
     2281 ctggttgcag tatctaaaat tatctgctgc cggataatta gtctcttcaa ttttacggcg
     2341 aaagcgcttc gagaattctg gatcggttgt acatcgctgt atcagatgtg cgagccgttg
     2401 attgcgtttt tccatttcaa tttggtattc cctttcaatc tgctcctgaa tttccgcgtc
     2461 attaaccggc gaaggtttga ttatcgcttt ccagcagtaa agcttttccc gtgatgtcgt
     2521 gactgtgcca gcatttttcg cttcgattgt agccatgata ttttcgtaat tagtccgggc
     2581 taaaggatcc atggtttcaa ttctcatatc gagctcgacc tcagatacta gcgcttcaag
     2641 taacatcttt tcagtattga tggctgaatt aaaatcagcc atagctgatt gctttccaat
     2701 tgcaatagat atgtttcgat taaacgtcgt cagtccgtca gaaaacgcac ttaggtgttg
     2761 tgacagactc ttccgttgtg ctaaaggctt cggtttaact ggtagggtat agtgcggcgt
     2821 ttctgcgata gccgctttta cctgactgat agctttatct ggggtgttga acaccacttt
     2881 tgctgggatc cgcaacaccc tgtagccttg gtctacggaa tattcatccc ggatacgatc
     2941 gcgttcaatt tgctcatgag atgagtgcca tgccgcacca tctatttcaa tcacctgg
//
