LOCUS       NZ_CP058837             2605 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_27 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP058837
VERSION     NZ_CP058837.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925556
            Assembly: GCF_022494035.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2605)
  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 2605)
  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_022494035.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:32:02
            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)                     :: 4,914
            CDSs (total)                      :: 4,793
            Genes (coding)                    :: 4,554
            CDSs (with protein)               :: 4,554
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 76 of 239
            Pseudo Genes (incomplete)         :: 163 of 239
            Pseudo Genes (internal stop)      :: 44 of 239
            Pseudo Genes (multiple problems)  :: 44 of 239
            Pseudo Genes (short protein)      :: 4 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058837.1.
            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..2605
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_27"
                     /isolation_source="Stanley WWTPs_27 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(2113..2605,1..86)
                     /locus_tag="HZT22_RS24390"
                     /old_locus_tag="HZT22_24235"
     CDS             join(2113..2605,1..86)
                     /locus_tag="HZT22_RS24390"
                     /old_locus_tag="HZT22_24235"
                     /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="plasmid replication initiation protein"
                     /protein_id="WP_240763298.1"
                     /translation="MTGTEQEEISRLRRQLAQMSDLLDAEKAAQRLPKNMDFVQVSRAE
                     LRAIADLGAKSALALDLLMVLAQSMDKQNAVMISFKAMQQILGKSRPTLDRAVRLLRED
                     NWIQVVKVGTANAYVLNSAVFWTDRGDKRHMASFKAQIVTTLDEQDKDFRANPHVKLKR
                     VPTLVSKDERVIVGTDELPPPDQQDLDLN"
                     /name="plasmid replication initiation protein"
     gene            complement(198..1190)
                     /gene="mobV"
                     /locus_tag="HZT22_RS24395"
                     /old_locus_tag="HZT22_24240"
     CDS             complement(198..1190)
                     /gene="mobV"
                     /locus_tag="HZT22_RS24395"
                     /old_locus_tag="HZT22_24240"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000852935.1"
                     /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_240763297.1"
                     /translation="MSDAPNFAILRTQKLKHLASVRRSLKHSFREQDTPNADQSLTPEN
                     SHYGANSTAEAMAEVQARLPEKRRKDAVLAIEYLVTASPEAMHGKSREEQDAYFADSLE
                     WLRERHGAENVVYAGVHRDETTPHMYAYVVPLDRDTGRLNAKKWLGGSKALNQMQTEFA
                     DRIGQRHGLERGIERSKARHQTIRQFYGNLEAADRQQIAVDPKQVEPQTLKKGLFTKEV
                     ESPEMVAARLSKEITQANRATIEKASVSAQERRSAKALRDTAKEQQKRLQTLQEPFKGL
                     SKDQMAEVLKMAVGMQRENEQAKEAKKTQILEKFQAKRERERNDRSRGR"
                     /name="mobV"
ORIGIN
        1 caacgttggt tagcaaagat gagcgcgtga tcgttggcac agacgagcta ccaccaccag
       61 accagcaaga cttggatctg aactgatggg gtaccgccga ctaacacctg acgaaatcga
      121 ggcgctacgg gttgaaatgc gcgaggctgg cgagtggtgc agggcagagc taaagcgccg
      181 ccgtgcggcg cgtgaagcta acggccacga ctccggtcgt tccgttcacg ctcccgcttc
      241 gcctgaaact tctcaaggat ctgagtcttc ttagcctcct tggcttgctc attttcccgc
      301 tgcatcccca ccgccatttt gagcacttcc gccatctgat ccttagatag ccccttaaac
      361 ggctcctgaa gcgtctgtaa gcgtttttgt tgctcttttg cagtatctct tagggctttg
      421 gcgcttcgtc gctcctgagc gctcacagag gccttctcga tggttgcccg attcgcttgc
      481 gtgatttctt tcgacaaccg cgccgcgacc atctcaggag actcgacctc cttggtgaat
      541 aacccttttt tgagcgtttg aggctcgacc tgcttgggat cgactgcgat ctgttgacgg
      601 tcggcggcct ccaaattccc gtagaactgg cgaatggtct ggtgccgtgc cttgcttcgt
      661 tcaatgcctc gttccagtcc gtggcgttgg ccgatccggt cggcaaactc ggtttgcatc
      721 tggttcaacg ccttactgcc acccaaccac ttcttggcgt tcaaccgacc tgtgtcacga
      781 tctagcggca cgacataggc gtacatgtgg ggggtggttt catcccgatg aacccccgca
      841 taaaccacgt tttccgcccc gtgtcgctct ctcagccact ccagcgagtc ggcaaagtaa
      901 gcgtcctgct cttcacggct tttgccgtgc atcgcttcgg gacttgctgt gaccaggtac
      961 tcgatggcga gtaccgcatc cttgcgccgc ttctctggca atctggcctg aacctctgcc
     1021 atcgcttccg ccgtcgagtt cgccccgtag tggctgttct ccggcgtcag gctctggtca
     1081 gcgttgggcg tgtcctgctc tctgaagctg tgcttcagcg agcgccggac actggctaga
     1141 tgcttcagtt tttgcgtccg caggatcgca aaattaggcg cgtcggacat cgcatgtccc
     1201 tccgttggtt gggtgaactc caagggtaag acggcggcac ttgaatatca agtggactca
     1261 ctacacttta cttcgtaaag ccgtgcccga cttcgtcggt tgcagcgtcc ttcgtccttg
     1321 ctctacgggc tacgccctgc gcctcccttc ggtcgttgcc aagaccttgg ggctttgccc
     1381 caaaccccac gttcgccacg tggcaggggt gcggggcata cggtcgcaag ctcccttctt
     1441 tcccgcaccc catgcgggag cgttggtcgt tccgatggcg tcaaggtcaa gccgcttcgc
     1501 ggtcgctacg cgaaccttga ccccctctcc acttacggaa cggagcaggg gtcaaggggt
     1561 cgtggaatac cggaggccgc gaagcggtcg aggatatgcc gcgaaagccc cttgatgcct
     1621 gtgcagtgac cccagcctcc ggctcaggtg ttggcgaaga agggagcgca gcgaccgcct
     1681 gacccagcac ccgagcctca cggcggcgag tgtggggagt ccagaggggc aacgcccctt
     1741 tgggcctagc gcagcggaaa caaaccttct cgcctctggc gaggcattac taagagagcg
     1801 aagcgaacgt aaaacggggt taggcatcgc ttaggggcac cgcccctaat gagatataga
     1861 gagaaattct taattttaat ggtatgaatt ggctgtaagc cttgtgctgc aagggtttca
     1921 gaggagttga ttattttttg ttatgtctca tgtaggtgag acatatatgt ctcaccctag
     1981 ggctttacat aaggcggtaa aactcaatca aaaactggta atggttaatc ttgaaatgat
     2041 taacggaata aagcaaaatg attaaccctt aatcatgaaa tgagacatgt atgtctcatg
     2101 caggtgagac atatgacagg cacagaacaa gaggaaatat cgagattgag aaggcaactg
     2161 gcgcaaatgt cagaccttct agatgcagag aaagcagcgc aaaggctacc aaagaacatg
     2221 gacttcgttc aggtgtcacg agctgaattg agagcaatag ctgatctcgg cgctaaaagc
     2281 gccttagctc ttgatttgct tatggtgttg gctcagtcga tggacaaaca aaacgccgtc
     2341 atgatttcgt ttaaagctat gcagcaaatt cttggtaagt cacgtcctac tctcgataga
     2401 gcagtaagac tgttacgtga ggacaactgg attcaagtag tgaaggttgg cactgccaac
     2461 gcttatgttt tgaatagcgc agtcttttgg actgaccgag gcgataagcg tcacatggca
     2521 agctttaaag cgcagatcgt taccacgtta gatgaacagg acaaagattt cagagccaac
     2581 ccacacgtta agctaaaacg tgtcc
//
