LOCUS       NZ_CP058856             2028 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_38 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP058856
VERSION     NZ_CP058856.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925563
            Assembly: GCF_022494175.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2028)
  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 2028)
  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_022494175.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:19:25
            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)                     :: 4,722
            CDSs (total)                      :: 4,597
            Genes (coding)                    :: 4,347
            CDSs (with protein)               :: 4,347
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 250
            CDSs (without protein)            :: 250
            Pseudo Genes (ambiguous residues) :: 0 of 250
            Pseudo Genes (frameshifted)       :: 68 of 250
            Pseudo Genes (incomplete)         :: 166 of 250
            Pseudo Genes (internal stop)      :: 47 of 250
            Pseudo Genes (multiple problems)  :: 34 of 250
            Pseudo Genes (short protein)      :: 5 of 250
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058856.1.
            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..2028
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_38"
                     /isolation_source="Stanley WWTPs_38 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            1..441
                     /locus_tag="HZT29_RS23460"
                     /old_locus_tag="HZT29_23240"
     CDS             1..441
                     /locus_tag="HZT29_RS23460"
                     /old_locus_tag="HZT29_23240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MarR family transcriptional regulator"
                     /protein_id="WP_024192735.1"
                     /translation="MSKDTQRITQINDQGEIVGGFVAVIRPKQKSSFQRHFTMNQDALK
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIADALEMQKTHVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVSNHKKALKNGLSVIQGGRT"
                     /name="MarR family transcriptional regulator"
     gene            complement(505..1473)
                     /gene="mobV"
                     /locus_tag="HZT29_RS23465"
                     /old_locus_tag="HZT29_23245"
     CDS             complement(505..1473)
                     /gene="mobV"
                     /locus_tag="HZT29_RS23465"
                     /old_locus_tag="HZT29_23245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000024818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_000024818.1"
                     /translation="MANYAIMRCKKLTGMGSVASALQHCYRERETPNANAERTPENYCS
                     VSKSTDQAMGRVRELLPEKRRKDAVLAVEYVMTASPEWWKEATPRQQAEFFARSEQWLE
                     KKYGKDRVVAAVVHRDEATPHLSAFVVPLTQDGRLSAKEFIGGRSKMREDQSTYAESVK
                     KLGLERGIEGSRATHQTVQHYYESINRGTRSQVSISPEALEPRVLRKGIFTKDVEDQAA
                     IAKRLSHAVNDGFAGTIAMASQSAQNAKRARELQKTMDAQQKRLQSVTEPFKGLSREQM
                     TEILMMAQRFKQQNQEKEKQQRIEREKQRQTRSRGMGGMER"
                     /name="mobV"
     Typing          complement(509..1482)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.077"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 atgagcaagg acacccagag aatcacccag attaacgatc aaggtgagat tgttggcggc
       61 ttcgtcgcgg taatcagacc caagcaaaaa tcgtcatttc agaggcattt cactatgaac
      121 caagacgcat taaagatcct cgctaaggag ctaacgggcg agcaatttaa agttctaatg
      181 ctcatgctcg ctgatctgga ttacgagaat ttcatccaaa ttgcacaggc tgatatagcg
      241 gatgcattgg agatgcaaaa gacccacgta agccgcgctg ttcgtgctct tcttgatgta
      301 ggcgtgatct ttgaaggtcc gaaagtaggt agatccaaaa cctatcggtt gaacgagcaa
      361 ttcggctgga aaggaacagt aagcaatcac aaaaaagccc ttaaaaacgg cctcagcgtt
      421 atacagggcg gcagaacctg atctctggaa tgccgcaaat gacgtcactt tgcggcgtta
      481 gccctatcct gcatcgcatc aaaactaacg ctccatacca cccatgccac gcgatcgcgt
      541 ctgtcgctgt ttttcacgtt caatacgctg ctgtttttcc ttttcctggt tttgctgctt
      601 aaaccgctga gccatcatca ggatttcggt catctgctct ctggaaagcc ccttaaaagg
      661 ctctgtaacg ctctgtaggc gtttctgctg cgcatccata gtcttctgta gctcacgcgc
      721 tctttttgcg ttctgggcgc tctgagaggc catagcgatg gttcctgcaa agccatcgtt
      781 cactgcgtgg cttagacgtt tggctatggc tgcctgatct tccacgtctt tggtgaaaat
      841 gcccttccgc aatacacgcg gctccagcgc ctccggcgag atcgatacct ggctacgggt
      901 gccacggttt atcgattcgt agtagtgctg aactgtctga tgcgtggcgc ggcttccctc
      961 gatgccgcgc tcaagaccca gtttttttac tgattcagcg taggtgctct gatcttcacg
     1021 catctttgac cgcccgccaa taaactcttt cgcggacagc cgtccatcct gcgtcaatgg
     1081 caccacgaac gcagacaggt gcggggtggc ctcgtcccgg tgaaccaccg ccgccacaac
     1141 acgatccttc ccgtatttct tctccagcca ttgctcagag cgggcgaaaa actccgcctg
     1201 ctgccgtggt gtggcctctt tccaccactc agggcttgct gtcataacgt attcaacggc
     1261 cagtaccgca tctttacggc gtttttccgg cagcagctcc cgcacacgcc ccattgcctg
     1321 atccgttgat ttggacacag agcagtagtt ttctggtgtc cgttcagcgt tagcgttcgg
     1381 cgtctcacgc tctcggtagc agtgctgcaa cgcgctggcc acgctcccca tccccgtcag
     1441 ctttttgcag cgcattatcg cgtagttcgc catgttcccc cctgattccg gcattcattc
     1501 agccaggcgg gggagcgcat tgcgatacct ccggcgggcc actatcaaga tgatagtgta
     1561 ctcactagac tttgcttcgc aaaatcgttc gggcagcaag ctgccagaag gtcaaaatca
     1621 acggcggtct ggcaggtgga aggcgtcgct ccgcgccacc cccaccactg ccaagcctgt
     1681 tttatccgga gtgtcgtcaa gggtaaatgg cactcgcttc gctcgccctt gacgaaatca
     1741 ggcaatgaat atcgcttttg aaagagcagg aaccgctcgc cgcagactca tgaccgaacg
     1801 tagtgagcga atgagcgagg aagcggaatt tccactcccc gtacatagaa atccgtacac
     1861 tccgtagcta aaaaacgttg gtattcagag ctaaaccgcg cgcacgcgtt ataagataca
     1921 gaaggagcga taaaaaaacg tatgtatggc gaggggttac atttgacata gttaccaata
     1981 atggtaacac tgttaccaat aatggtaact caagataggt tattttcg
//
