LOCUS       NZ_CP058844             2605 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_34 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP058844
VERSION     NZ_CP058844.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925560
            Assembly: GCF_022494115.1
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_022494115.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:20:03
            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)                     :: 4,960
            CDSs (total)                      :: 4,839
            Genes (coding)                    :: 4,599
            CDSs (with protein)               :: 4,599
            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)              :: 240
            CDSs (without protein)            :: 240
            Pseudo Genes (ambiguous residues) :: 0 of 240
            Pseudo Genes (frameshifted)       :: 77 of 240
            Pseudo Genes (incomplete)         :: 162 of 240
            Pseudo Genes (internal stop)      :: 45 of 240
            Pseudo Genes (multiple problems)  :: 44 of 240
            Pseudo Genes (short protein)      :: 4 of 240
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058844.1.
            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_34"
                     /isolation_source="Stanley WWTPs_34 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            629..1207
                     /locus_tag="HZT26_RS24630"
                     /old_locus_tag="HZT26_24430"
     CDS             629..1207
                     /locus_tag="HZT26_RS24630"
                     /old_locus_tag="HZT26_24430"
                     /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(1319..2311)
                     /gene="mobV"
                     /locus_tag="HZT26_RS24635"
                     /old_locus_tag="HZT26_24435"
     CDS             complement(1319..2311)
                     /gene="mobV"
                     /locus_tag="HZT26_RS24635"
                     /old_locus_tag="HZT26_24435"
                     /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 ggtcaagccg cttcgcggtc gctacgcgaa ccttgacccc ctctccactt acggaacgga
       61 gcaggggtca aggggtcgtg gaataccgga ggccgcgaag cggtcgagga tatgccgcga
      121 aagccccttg atgcctgtgc agtgacccca gcctccggct caggtgttgg cgaagaaggg
      181 agcgcagcga ccgcctgacc cagcacccga gcctcacggc ggcgagtgtg gggagtccag
      241 aggggcaacg cccctttggg cctagcgcag cggaaacaaa ccttctcgcc tctggcgagg
      301 cattactaag agagcgaagc gaacgtaaaa cggggttagg catcgcttag gggcaccgcc
      361 cctaatgaga tatagagaga aattcttaat tttaatggta tgaattggct gtaagccttg
      421 tgctgcaagg gtttcagagg agttgattat tttttgttat gtctcatgta ggtgagacat
      481 atatgtctca ccctagggct ttacataagg cggtaaaact caatcaaaaa ctggtaatgg
      541 ttaatcttga aatgattaac ggaataaagc aaaatgatta acccttaatc atgaaatgag
      601 acatgtatgt ctcatgcagg tgagacatat gacaggcaca gaacaagagg aaatatcgag
      661 attgagaagg caactggcgc aaatgtcaga ccttctagat gcagagaaag cagcgcaaag
      721 gctaccaaag aacatggact tcgttcaggt gtcacgagct gaattgagag caatagctga
      781 tctcggcgct aaaagcgcct tagctcttga tttgcttatg gtgttggctc agtcgatgga
      841 caaacaaaac gccgtcatga tttcgtttaa agctatgcag caaattcttg gtaagtcacg
      901 tcctactctc gatagagcag taagactgtt acgtgaggac aactggattc aagtagtgaa
      961 ggttggcact gccaacgctt atgttttgaa tagcgcagtc ttttggactg accgaggcga
     1021 taagcgtcac atggcaagct ttaaagcgca gatcgttacc acgttagatg aacaggacaa
     1081 agatttcaga gccaacccac acgttaagct aaaacgtgtc ccaacgttgg ttagcaaaga
     1141 tgagcgcgtg atcgttggca cagacgagct accaccacca gaccagcaag acttggatct
     1201 gaactgatgg ggtaccgccg actaacacct gacgaaatcg aggcgctacg ggttgaaatg
     1261 cgcgaggctg gcgagtggtg cagggcagag ctaaagcgcc gccgtgcggc gcgtgaagct
     1321 aacggccacg actccggtcg ttccgttcac gctcccgctt cgcctgaaac ttctcaagga
     1381 tctgagtctt cttagcctcc ttggcttgct cattttcccg ctgcatcccc accgccattt
     1441 tgagcacttc cgccatctga tccttagata gccccttaaa cggctcctga agcgtctgta
     1501 agcgtttttg ttgctctttt gcagtatctc ttagggcttt ggcgcttcgt cgctcctgag
     1561 cgctcacaga ggccttctcg atggttgccc gattcgcttg cgtgatttct ttcgacaacc
     1621 gcgccgcgac catctcagga gactcgacct ccttggtgaa taaccctttt ttgagcgttt
     1681 gaggctcgac ctgcttggga tcgactgcga tctgttgacg gtcggcggcc tccaaattcc
     1741 cgtagaactg gcgaatggtc tggtgccgtg ccttgcttcg ttcaatgcct cgttccagtc
     1801 cgtggcgttg gccgatccgg tcggcaaact cggtttgcat ctggttcaac gccttactgc
     1861 cacccaacca cttcttggcg ttcaaccgac ctgtgtcacg atctagcggc acgacatagg
     1921 cgtacatgtg gggggtggtt tcatcccgat gaacccccgc ataaaccacg ttttccgccc
     1981 cgtgtcgctc tctcagccac tccagcgagt cggcaaagta agcgtcctgc tcttcacggc
     2041 ttttgccgtg catcgcttcg ggacttgctg tgaccaggta ctcgatggcg agtaccgcat
     2101 ccttgcgccg cttctctggc aatctggcct gaacctctgc catcgcttcc gccgtcgagt
     2161 tcgccccgta gtggctgttc tccggcgtca ggctctggtc agcgttgggc gtgtcctgct
     2221 ctctgaagct gtgcttcagc gagcgccgga cactggctag atgcttcagt ttttgcgtcc
     2281 gcaggatcgc aaaattaggc gcgtcggaca tcgcatgtcc ctccgttggt tgggtgaact
     2341 ccaagggtaa gacggcggca cttgaatatc aagtggactc actacacttt acttcgtaaa
     2401 gccgtgcccg acttcgtcgg ttgcagcgtc cttcgtcctt gctctacggg ctacgccctg
     2461 cgcctccctt cggtcgttgc caagaccttg gggctttgcc ccaaacccca cgttcgccac
     2521 gtggcagggg tgcggggcat acggtcgcaa gctcccttct ttcccgcacc ccatgcggga
     2581 gcgttggtcg ttccgatggc gtcaa
//
