LOCUS       NZ_CP055206             3577 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed7, complete
            sequence.
ACCESSION   NZ_CP055206
VERSION     NZ_CP055206.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925527
            Assembly: GCF_022354345.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3577)
  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 3577)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-JUN-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: "Other" v. Unicycler
            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_022354345.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:11
            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)                     :: 5,236
            CDSs (total)                      :: 5,112
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 84 of 252
            Pseudo Genes (incomplete)         :: 172 of 252
            Pseudo Genes (internal stop)      :: 54 of 252
            Pseudo Genes (multiple problems)  :: 51 of 252
            Pseudo Genes (short protein)      :: 2 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055206.1.
            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..3577
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed7"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(529..687)
                     /locus_tag="HUZ39_RS26235"
     CDS             complement(529..687)
                     /locus_tag="HUZ39_RS26235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(1342..1536)
                     /locus_tag="HUZ39_RS25970"
                     /old_locus_tag="HUZ39_25815"
     CDS             complement(1342..1536)
                     /locus_tag="HUZ39_RS25970"
                     /old_locus_tag="HUZ39_25815"
                     /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(2613..2909)
                     /locus_tag="HUZ39_RS25975"
                     /old_locus_tag="HUZ39_25820"
     CDS             complement(2613..2909)
                     /locus_tag="HUZ39_RS25975"
                     /old_locus_tag="HUZ39_25820"
                     /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_134723141.1"
                     /translation="MERKHKGKCPFCNSEMAPEVIEKNTIRRDKCKCTTCGEIIYKCRN
                     IFCNDYAKGGLLYDDELCPPCGERLLKAVKEFPDKYRAAIQKVVEEKNREKNN"
                     /name="hypothetical protein"
     gene            complement(2984..3139)
                     /locus_tag="HUZ39_RS25980"
                     /old_locus_tag="HUZ39_25825"
     CDS             complement(2984..3139)
                     /locus_tag="HUZ39_RS25980"
                     /old_locus_tag="HUZ39_25825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010940654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF1508 domain-containing protein"
                     /protein_id="WP_072210546.1"
                     /translation="MNDKWEFYLDNSKEWRWRRTASNGRIVGASSQGYVNKSDCIDNAR
                     RHGYNG"
                     /name="DUF1508 domain-containing protein"
     Typing          1185..1269
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          1573..1671
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.22e-45"
     Typing          1816..2071
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.124"
                     /coverage="89.0"
                     /evalue="5.65e-115"
     Typing          complement(616..1165)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.937"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 actggtccat tcgtggcggc agtttaagca tttagcccga tagatgacga tacctgccat
       61 aaaaatcccc tttttatcat acattaatgt tgatttatta tattctgaac ataataaatg
      121 taaagtatac tatgtgataa acgtaatgca ttgattttat tgatattaaa aatatttatt
      181 agagtgctaa taatggtatt ttttttgatt tttttattaa aaacaatatg ttgtatatgt
      241 gttggtgtcg tttgattacg ttcaataaat gcgtgtatca atattagata tacaaaaatg
      301 aagttagaag gtggctggga gttttaggag atttgccctc cttcagtaaa aagatcaaag
      361 gatcctcttg agatcctttt tttctgcgcg taatctgctg cctgtaaacg aaaaaaccgc
      421 ctggggaggc ggtttagtcg aaggttaagt cagttgggga ctgcttaacc gggtaactgg
      481 cttggtggag cacagatacc aaatactgtc cttctagtgt agccgcagtt aggccaccac
      541 ttcaagaact cttaatatct caatccacct tgtccagtta ccagtggctg ctgccagtgg
      601 cgctttgtcg tgtcttaccg ggttggactc aagacgatag ttaccggata aggcgcagcg
      661 gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga cctacaccga
      721 gccgagatac ctacagcgtg agctatgaga aagcgccacg cttcccgaag ggagaaaggc
      781 ggacaggtat ccggtaaacg gcagggtcgg aacaggagag cgcacgaggg agccaccagg
      841 gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc catctctgac ttgagcgtcg
      901 gtttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccatcg gcgcggcctt
      961 ttgttgctct ttgccttttt gctcacatgt tctttccggc cttatcccct gattctgtgg
     1021 ataaccgtat taccgccttt gagtgagccg acaccgctcg ccgcagtcga acgaccgagc
     1081 gtagcgagtc agtgagcgag gaagcggaag agcgtcggaa gttgcatttt ctccttacgc
     1141 atctgtgcgg catttcacac cgcatatggc gctcttttct tacaatccgc actgatgccg
     1201 catagataag ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg
     1261 acacccgctg acgcgccctg gcgggcttgt ctgctgccga aaacgctcgc ggacaagccg
     1321 tgagcgcctc cgtcagcttc gttatgttcc tgtttcactt tcggtctcaa agcgaacctg
     1381 gatgctgttc tggagttctt ccgcgagttc gtgcagtcgt tcgcacatgg ccgcctgttc
     1441 gtcggcatcc agagcatcca gtttttcaag cagtgtcagg ctctggcttt tgataaatcg
     1501 cgccatattc agcgcagttt gttgctgttt gttcaccttc cgttgttctc cgtcagtacc
     1561 gggtgtcggg tggaccctga ccaggtggta attgtaagac gttgcgggcg acggtattac
     1621 aattgcacat cctgtcctgt ttttttagga cgtatcatgg cacagcatat caactgataa
     1681 ataatccctg tgcagtgcag tgcagtgcag tgcactgcag ccgctgttgc ataaaatttc
     1741 gctctgcgtc gagtgtttct taatcaataa ttccgctgat actccggaaa aacgcgagtc
     1801 tgttctcatg cctgaaatgc ccacacccca cgcaaaaaca attttttgct gatttttctt
     1861 tataaataga gagttatgac aaattagttc ttcttgctct ctttgtgata tttaaaaaag
     1921 cggtgtcggc gcggtgttgt agctgcgcca acaccgcttt ttaggggtgg tactgactat
     1981 ttttataaaa aacatcattt tatattaggg gtgctgctag cggcgcggtg tgttttttta
     2041 caggacgccc ctgggggcgc tgctaggggt gtctgttcag atatgtagca atgagtcagg
     2101 gattcacgaa ctgaaaatgt ccgaaaatgt gtctcatggg caccgtatgc gcccaaaccg
     2161 atcgccattc actttcatgc atagctatgc agtgagctga aagcgatcct gacgcatttt
     2221 tccggttttc gcttggtaaa acatctcttt ttgcggtgtt cgcggcagaa tcgcgttcag
     2281 cgcgttttgg cggtgcgtat aattacaggg ttatgttaaa ttgatggttt gataagtgtt
     2341 ggaaataatt aattccactc ataaatatac aagatatgaa aaaaatattg ttcatatggt
     2401 agaagagcta tagggatatt tggtttcaaa atattccttt taggaaatgg attaactaaa
     2461 acaggtacta aaatacctgt taaaaataat gagagagata actctctgtt agggcgtgtg
     2521 ttggggatat agaaatattt ggtattgctt acgaaatcga ttggttttca tgataattaa
     2581 ctaatatagt tatatggttt tgtgcgctac cattaattat tcttttctct attcttctct
     2641 tctacaactt tttgaattgc tgctcgatac ttatcaggga actcttttac cgcctttaaa
     2701 agacgttcac cacatggagg gcacagttcg tcatcgtaaa gtaatccgcc ttttgcgtag
     2761 tcattacaga atatatttcg gcatttataa ataatctctc cacaagttgt acatttacat
     2821 ttatctctgc ggatagtgtt tttttctata acttctggag ccatttcgct attgcaaaaa
     2881 gggcacttac ctttgtgttt tctttccatg gtatttttct atttgtttat ctctttgcaa
     2941 ttgggattcc tacttggaat cccaacatga gaatcaattt atattagccg ttgtagccat
     3001 gacgacgtgc gttatcaata caatcagatt tattgacata tccttgagat gatgctccaa
     3061 caattcgccc gttgcttgca gttctgcgcc agcgccactc ttttgaatta tcgagataaa
     3121 actcccactt atcgttcatt caggtttcct tcttccagtt agatatttag tgatgatttg
     3181 taccagcagg taggtatcat ttcatttttt tttctaataa gcgtgttaca actgtactga
     3241 cgacgatact taaggctgtt gtccctaatg cgccgatact tctacctatg ttcgacatgc
     3301 atgacgggca taattcatca tcatataaat gaccgccctt agcgtaattc tcacatcctg
     3361 gagtacgaca tacgtaaatt attgatttac aatcagaaca ctcacactta tctcgccgta
     3421 tcttgttttc ttgaattaca cgggcattga tttccttttt acaaaaagga cacactcctt
     3481 taggttttaa gtccattagg gcttacctaa tagcactaca acttattaat tttgaacgac
     3541 atttagggca ataatcaggt gtcccaaatc cagctct
//
