LOCUS       NZ_CP058889             2998 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_33 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP058889
VERSION     NZ_CP058889.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925559
            Assembly: GCF_022494095.1
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_022494095.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:15:22
            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)                     :: 4,637
            CDSs (total)                      :: 4,516
            Genes (coding)                    :: 4,304
            CDSs (with protein)               :: 4,304
            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)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 71 of 212
            Pseudo Genes (incomplete)         :: 134 of 212
            Pseudo Genes (internal stop)      :: 40 of 212
            Pseudo Genes (multiple problems)  :: 34 of 212
            Pseudo Genes (short protein)      :: 4 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058889.1.
            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_33"
                     /isolation_source="Stanley WWTPs_33 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(join(1902..2998,1..10))
                     /locus_tag="HZT25_RS23025"
                     /old_locus_tag="HZT25_22895"
     CDS             complement(join(1902..2998,1..10))
                     /locus_tag="HZT25_RS23025"
                     /old_locus_tag="HZT25_22895"
                     /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            864..1055
                     /locus_tag="HZT25_RS23030"
                     /old_locus_tag="HZT25_22900"
     CDS             864..1055
                     /locus_tag="HZT25_RS23030"
                     /old_locus_tag="HZT25_22900"
                     /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(1766..>1879)
                     /locus_tag="HZT25_RS23035"
                     /old_locus_tag="HZT25_22905"
                     /pseudo=""
     CDS             complement(1766..>1879)
                     /locus_tag="HZT25_RS23035"
                     /old_locus_tag="HZT25_22905"
                     /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(369..989)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="83.463"
                     /coverage="99.0"
                     /evalue="9.37e-156"
ORIGIN
        1 ttttctgcac acaattgacc tttttggttt gttactagga tgtgaatagt attgtatttt
       61 cgaagctatc ttgaagtctt actgcttttt taagctgtac tttgaacgga gagttgaagg
      121 atcttcttga gatccttggg tgagagtcgt agtctcttaa ctaggaaacg aaaaaccacc
      181 tggggaggtg gtttttcgaa ggttcagtaa gttggggaac ttctgaaccg tggtaacagg
      241 gtgtacaaga ccgctgccac caaattcgtc ctttcagttt agccgcagtc tggctctaac
      301 tgcaagaact ctgcatcagt aatctcttgt acaccctcta ccaatggcta ccgccaatgg
      361 cgatttatcg tgccttttcg ggttggactc aagacgatag ttaccgaaaa gagcgtggta
      421 gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaactg cctacccgga
      481 actgagtgtc aggcgtggaa tgagataaac gcggccataa cagcggaatg acaccggtaa
      541 accgaaaggc aggaacagga gagcgcacga gggagccacc agggggaaac gcctggtatc
      601 tttaagtcct gtcgggtttc gccaccactg atttgagcgt ccgattctgt gatgcttgtc
      661 aggggggcgg agcctatgga aaaacgcccc ggctgggcgt ggccttttcg cccttgtcct
      721 tagctttcgt tatgcttacc gttacgttat ctgctcatct tcctccgctc gccgcagact
      781 catgaccgaa cggagtgagc gaatgagcga ggaagcggaa aaccatcaga acgtacagta
      841 agcactttcg caccggggcc ttcatgaaca aacaacaaaa gacagccgtt aacatggcta
      901 aattcatcca ggatcagtcc ctgcttcttc tggacaggct taatgagctg gatctggatc
      961 atgaggctga tttctgcgag aaactccatg aggatgcgga acgcctttac cgaagcctgt
     1021 cagcgcgcct gaatgatcag caggacggtg cgtaatggct ccgttctggg tattaccgga
     1081 gtaataccgg catcgcctta attttcattg tcttggtgct taacattatt accctggtaa
     1141 tacccagaat ccctttattt tttctttttt atttattttt catgaagttg cgataaaaat
     1201 cgcagctgcg ttaggtgtat gaccattttg aggttgaaaa ataatcaacc atggagggtg
     1261 atttacgcag gttaagggga gatcgtgaca aaaaaagcgt tcctcactgt atcgttcatg
     1321 cctgcatgaa cgggttattc ttcctgacta cagaattaca tcaaaagtac atcactttta
     1381 cgtcagatct gacctctgaa ctattcgtac atccgcccct cttcctgggc ctcctgcacg
     1441 tgctgaaaat ggtttttccg gctgtgccgg caacgcctca cggccacgca ataaattgcg
     1501 catccgttca ccgttatcgg ggtggttcgt ggtggctttc agggcgttca tcggatttta
     1561 gccgctaaaa tcccggccag gtatgtccgt gcatagccat gcagtcgcgc cagaatcatc
     1621 aggggcgttt tttctcgata tgggcacaga aaggtgtgtg tttcaggccg gaggcctcag
     1681 aaacgcactg agggcctctg cggcggtgca cgcaacggat gttatgttca atttgggtaa
     1741 cctgctgggt caccttggga tatgactaaa gaggtgagat gatttcgacc tcgtgctgga
     1801 acacgtaggg atctgaaagc aactcaaatt attcgtcatc cgggtaggta acggccacat
     1861 gatagttctc gcctgcaaat tgtgaatgct cgacacccgt tttatttatc agtcaaaagc
     1921 tggttgcagt atctaaaatt atctgctgcc ggataattag tctcttcaat tttacggcga
     1981 aagcgcttcg agaattctgg atcggttgta catcgctgta tcagatgtgc gagccgttga
     2041 ttgcgttttt ccatttcaat ttggtattcc ctttcaatct gctcctgaat ttccgcgtca
     2101 ttaaccggcg aaggtttgat tatcgctttc cagcagtaaa gcttttcccg tgatgtcgtg
     2161 actgtgccag catttttcgc ttcgattgta gccatgatat tttcgtaatt agtccgggct
     2221 aaaggatcca tggtttcaat tctcatatcg agctcgacct cagatactag cgcttcaagt
     2281 aacatctttt cagtattgat ggctgaatta aaatcagcca tagctgattg ctttccaatt
     2341 gcaatagata tgtttcgatt aaacgtcgtc agtccgtcag aaaacgcact taggtgttgt
     2401 gacagactct tccgttgtgc taaaggcttc ggtttaactg gtagggtata gtgcggcgtt
     2461 tctgcgatag ccgcttttac ctgactgata gctttatctg gggtgttgaa caccactttt
     2521 gctgggatcc gcaacaccct gtagccttgg tctacggaat attcatcccg gatacgatcg
     2581 cgttcaattt gctcatgaga tgagtgccat gccgcaccat ctatttcaat cacctggcgc
     2641 ccatttgcca gaaaatcgaa gcggtaacga ccaacattta cctgcatttc cagcgttaac
     2701 gttggagata ttaatttacc gctggcgggt ttgagattga acgctctgac cattgcgaga
     2761 agaaactgct cttccgccgg agattcgcaa ccttcgcaaa acttgctaag ccaatcgtta
     2821 tcatctgttt ttacatcacg ccaggtgggt gccggcgaga cctgggtaat gacggggcta
     2881 ttcagatcat cgtagatggt ccatataagc cagccaataa ccagtagcgt gtatggaaag
     2941 aagaagctga ctagtaacaa aaaaacgatg atccaaacac gacaccaaat agttttat
//
