LOCUS       NZ_CP055046             3565 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_59 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP055046
VERSION     NZ_CP055046.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925586
            Assembly: GCF_022354025.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3565)
  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 3565)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-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_022354025.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:08:02
            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)                     :: 4,691
            CDSs (total)                      :: 4,573
            Genes (coding)                    :: 4,317
            CDSs (with protein)               :: 4,317
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 78 of 256
            Pseudo Genes (incomplete)         :: 175 of 256
            Pseudo Genes (internal stop)      :: 53 of 256
            Pseudo Genes (multiple problems)  :: 48 of 256
            Pseudo Genes (short protein)      :: 4 of 256
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055046.1.
            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..3565
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_59"
                     /isolation_source="Shek Wu Hui WWTPs_59 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(583..774)
                     /locus_tag="HUZ71_RS23305"
                     /old_locus_tag="HUZ71_23120"
     CDS             complement(583..774)
                     /locus_tag="HUZ71_RS23305"
                     /old_locus_tag="HUZ71_23120"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1193..1351
                     /locus_tag="HUZ71_RS23495"
     CDS             1193..1351
                     /locus_tag="HUZ71_RS23495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /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_071819240.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHDKTPLAAAIGIWFTERRGV
                     YKHTQSS"
                     /name="replication initiation protein"
     gene            1778..2440
                     /locus_tag="HUZ71_RS23310"
                     /old_locus_tag="HUZ71_23125"
     CDS             1778..2440
                     /locus_tag="HUZ71_RS23310"
                     /old_locus_tag="HUZ71_23125"
                     /inference="COORDINATES: protein motif:HMM:NF025179.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNVR domain-containing protein"
                     /protein_id="WP_000430080.1"
                     /translation="MENNSPDIDIIELFLFLKKKIVSIILFVVLSLILSSIFLLINKNK
                     INIKYELNMIANSPSMIINCGSDFYCKANIIQSIINNKSKSITSNIDERGKKIILSWAG
                     DDRYKPLVTAEVNAIHKAIDDWYIQDYKTYKSIVNNQDSNYINGTETYAKVALLTKINT
                     AGEKNFISINDEIVNKKYKPALIMALTLIIAVIFSFSYHIIKRSILEYKNKLNRSFY"
                     /name="GNVR domain-containing protein"
     gene            <2783..3202
                     /locus_tag="HUZ71_RS23315"
                     /old_locus_tag="HUZ71_23130"
                     /pseudo=""
     CDS             <2783..3202
                     /locus_tag="HUZ71_RS23315"
                     /old_locus_tag="HUZ71_23130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /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="IS1 family transposase"
                     /name="IS1 family transposase"
     Typing          1012..1538
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccgaaaacgg tgaacgggga cgcaatttat tgcgtggccg tgaggcgttg ccggcacagc
       61 cggaaaaacc gttttcagca cgttcaggaa ggggggcgga tgtacaaatg gcacagagga
      121 tggaactgac gtaaaagtga cgtatgagct gaaggaatga tgtaaaagtg atgtaaaagt
      181 gatgcaaaag tgttgtaaaa gtgatgtata ggctgaagga atgatgcaaa agtgatgtaa
      241 aagtgttgta aaagtgttgt atgaactgaa ggagcaatgt aattctgtag tcaggaagaa
      301 taacccgttc atgcaggcat gaacgataca gtgaggaacg ctttttttgt cacgatctcc
      361 ccttaacctg cgtaaatcac ccgccatggt tgattatttt tcaacctcaa aatggtcata
      421 cacctaacgc agctgcgatt gtcatcgcaa cttcatgaaa aataaataaa aaagaaaaaa
      481 taaagggatt ctgggtatta ccggggtaat aatattaagc gccaggacaa tgaaaattaa
      541 ggcgatgccg gtattactcc ggtaataccc agaacggagc cattacgcac cgtcctgctg
      601 ctcattcagg cgcgctgaca ggcttcggta aaggcgttcc gcatcctcat ggagtttctc
      661 gcagaaatca gcctcatgat ccagatccag ctcattaagc ctgtccagaa gaagcaggga
      721 ctgatcctgg ataaatttag ccatgttaac ggctgtcttt tgttgtttgt tcatgaaggc
      781 cccggcgcga aagtgcttac tgtacgttct gatggttttc cgcttcctcg ctcattcgct
      841 cactccgttc ggtcatgagt ctgcggcgag cggagggaag ataagcagat aacgtaacgg
      901 taagcataac gaaagctaag gacaagagcg aaaaggccac gccccgccgg ggcgtttttc
      961 cataggctcc gcccccctga caagcatcac gaaatctgac gctcaaatca gtggtggcga
     1021 aacccgacag gactataaag ataccaggcg tttccccctg atggctccct cgtgcgctct
     1081 cctgttcctg cctttcggtt taccggtgtc actccgctgt tatggccgcg tttatctcat
     1141 tccacgcctg acactcagtt ccgggtaggc agttcgctcc aagctggact gtatgcacga
     1201 accccccgtt cagtccgact gctgcgcctt atccggtaac tatcgtcttg agtccaaccc
     1261 ggaaagacac gacaaaacgc cactggcagc agccattggt atctggttta cggagcggag
     1321 aggcgtgtac aagcatacac agagttcttg aagtgttgac ctgactacgg ctacactgga
     1381 aggacagatt tggtcactgc gctccgttta agccagttac cacggttcag aaacttgccg
     1441 gtttcctgaa ccttcgaaaa accaccttgc cgggtggttt tttcgttttc agaccaagag
     1501 attacggctg taacacaagg atctcaagaa gatcttaaaa tatgtggaaa ggatacaggc
     1561 tgataacaac tctctccata gacatgaccg aacaaaaaac aaacaaaaga aattgatttt
     1621 aggagttttc tcacacctaa ataataggta aaatgttttt tatttgattg gattttaaaa
     1681 tgaaatatac taaatcggcg aaaatattca tcacggctat tttaatttta tttatttatt
     1741 taagctataa tttaataact attgttggta tataaaaatg gaaaacaatt cacctgatat
     1801 tgatatcatc gagttatttc tttttcttaa gaaaaaaatc gtgagtatta ttttgtttgt
     1861 tgttttatca ttgattttat catctatttt cttgctgata aacaaaaaca aaataaatat
     1921 aaagtacgaa ttaaacatga tcgctaattc gccaagcatg attattaact gtgggtctga
     1981 cttttattgt aaagcgaata tcatacaatc aatcataaac aataaaagca agtctataac
     2041 atcaaatata gatgaaagag gaaaaaaaat aatcctgtca tgggctggtg atgaccgtta
     2101 caaacccctg gttaccgctg aagtaaacgc tatccataaa gctattgatg actggtacat
     2161 ccaagattat aaaacttata aaagcatagt taacaaccag gacagcaact atataaatgg
     2221 cactgaaaca tatgcaaaag ttgcattatt aacaaaaata aacactgccg gagaaaaaaa
     2281 cttcatttca ataaatgatg aaatagtgaa taaaaagtat aaaccagctt taattatggc
     2341 tctaacgtta attatagccg ttatcttttc cttctcgtat catataataa aaagatctat
     2401 acttgaatat aaaaataagt taaacaggtc tttttattag cctgtaacga ttaataacct
     2461 tattctagca acatccgtta cacgccagat gcagaaaagc ccgctaatag cgggcctccc
     2521 gataaacctc aagtgaataa gggcagtcag ttctatttct tacccttcca ttgcctaact
     2581 gattctccgt ggcactgggc caactgcagc agtttttatt cccatgagga atccgattgg
     2641 tcacctcgcg atctccattt tttaagatac acacataatt tcattagacc atctacagct
     2701 gactgatgcc ataactcacc tttagcatga agattctagg tgatgactct aattagttga
     2761 atctaatgta taatacaggc tttcttcgcc tgttgcccat gctgatatgg cgcttatctg
     2821 cgagcttgat gagcaatgga gctacattgg cagtaaagcc cggcaacact ggctctggta
     2881 cgcgtacaac accaaaacag gcggtgtatt ggcctacacg tttggttccc gaaccgatta
     2941 aacgtgtcgg aagctactgg cactgcttac acccttcaac atcggcatgc tcaccagcga
     3001 tgacttgggc agctatggcc gggtggtgcc gaagaataag catctgaccg gcaaaatatt
     3061 cacccaacgc attgagcgta ataatctgac gctacgcacc cgcattaagc ggttggctcg
     3121 taaaacaatc tgcttctcac gctcagttga gatccacgaa aaagtgatcg gagcggttat
     3181 cgaaaaacac atgttctact aattggatgc actatcagat tctgaaccgt gggtatataa
     3241 gtctgcattt cagcttcatc aatcccgttt tttttgctga atccatttac caatatcctg
     3301 tccatacgtt actaaagaaa ataatatatg cggagtgagt catcatgcgc ctaatttacc
     3361 ataacatccg ttgcgtgcac cgcctgagag gcgctgaggg cgtttctgac gggaaaccgg
     3421 taaaacaggc aacaaaccac ccgaaaaccc gccagaaacg cgcaggctct gtttttacgg
     3481 catgcatgag tatgcacgca agtgcatagc gcggaaattc acgccattca gccggggtaa
     3541 gtcctgtttc cgatgttctt tttat
//
