LOCUS       NZ_CP055207             3139 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed8, complete
            sequence.
ACCESSION   NZ_CP055207
VERSION     NZ_CP055207.1
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 3139)
  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 3139)
  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
            CP055207.1.
            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..3139
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed8"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(692..1087)
                     /locus_tag="HUZ39_RS25985"
                     /old_locus_tag="HUZ39_25830"
     CDS             complement(692..1087)
                     /locus_tag="HUZ39_RS25985"
                     /old_locus_tag="HUZ39_25830"
                     /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_001222910.1"
                     /translation="MRISNIDWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNELQAQENARKQANQKRMEGKTQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELRYPKDNILQKLKAIRLDLETSPDHH"
                     /name="hypothetical protein"
     gene            1263..2189
                     /locus_tag="HUZ39_RS25990"
                     /old_locus_tag="HUZ39_25835"
     CDS             1263..2189
                     /locus_tag="HUZ39_RS25990"
                     /old_locus_tag="HUZ39_25835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001314449.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2192..2725
                     /locus_tag="HUZ39_RS25995"
                     /old_locus_tag="HUZ39_25840"
     CDS             2192..2725
                     /locus_tag="HUZ39_RS25995"
                     /old_locus_tag="HUZ39_25840"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_106509525.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNKDIATIH
                     HNVVKEYNTLNKYSLKWFIGVTVSFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPATGKSRKN"
                     /name="hypothetical protein"
     Typing          1264..2186
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caagcattac cgaccgcaca gcctccccag aatcccgaaa aaatcctgtt tttgcagatg
       61 attgcgtgtt tgcaaagacc gtttgcggtt gggggagctg tgacgacggc aaccgcacgc
      121 gtgagagttc cgctaccggc gcagagagtt tcatcgacag cggacacctg atgagttgcc
      181 acaaaaaccg tatgtagcgc ggctagattg gttgagttag accttggcgg cagttcccgg
      241 tatgtggtgg cgtgacgggt gagatggtgc ggcgaagacg catacgtcac gcaggcgcgg
      301 gttcttccac cgacgcgccc cgtgatcgat ggccttggct ccgtccggca tatcgagagc
      361 ggcaaactac ccgtcccttc actgggaggg gtgagttgtt gccgttccct ccgaccttcc
      421 accatccagc atatcgcacg atcccatgtg caccgctact cctgataact ccagtgcaaa
      481 aaaaaaaaac ggatctgcat cacaacgaga gtgatcccac cgctcgccgc agccccagcg
      541 accgaacgta gtgagcgagt gggcgaggaa gcggaagagt cacagaggca agcattgtgc
      601 acttacgcgc ctgtgccaga tccgcgcgta gcgcgtcgcg aaatcgaaaa cattgaacac
      661 cggcaggcaa acgcaccacc acgcagcgga attaatgatg atctgggctt gtttcaagat
      721 cgagcctgat tgccttaagt ttctgtaata tattgtcttt tgggtatctc agttcgcctg
      781 tttttgtgtc cactagtccg gcctcgatca gtaaccccgc cgcaagaaac aggcggtgat
      841 tgcgttcccg tcgttgtgtt ttcccctcca tccgtttttg gttggcctgt ttgcgtgcgt
      901 tctcctgtgc ctgtagctcg tttttttctg cggttgccag gacgtggagt agtttgcgct
      961 cctgttctgt tagtccggct tcgttatcga gcaggtcaat gatctgcctc tgtcgtgcgg
     1021 tctgttctcc gagcttcctg ataaagccga ttcgtttctt caaccagtcg atgttgctga
     1081 tgcgcatgtt tgggatgctc cctggtgttt tttgcggtgt gttggggttg tgcagtatat
     1141 cgcttgcggt cggtgggtgc agggggtatc ttccgtgcta attcgtaaaa ttagaaggaa
     1201 gcgcacttat atgtttctct ccttcgtcga gaaacagtgc gctcctgcgg agggctgaaa
     1261 ccgtggcaac ctatcacctc agcgttaaat ttggtggcaa ggggcaggct gcaaaccacg
     1321 ccgattacat cgagcgcaaa gagaaatacc gcgaccgtca ggatttggaa tattccgcac
     1381 acggaaacat gccggaatgg gcgcgagata atccctcaca tttctggcag gcggctgacc
     1441 agtttgaacg tgcgaacggt tcgacctatc gggaacttga aattgcatta ccccgtgaac
     1501 tgacagcgga acagcgcctt gaactggtgc aggattttgt acgtcaggaa gctggcgaac
     1561 ggcacgcctg gagttttgcc attcacaatc cgaaagcgag cattgacggc ggcgaacagc
     1621 ctcatgcgca tatcatgatg agccagcgtg tgaatgatgg cattgaacgt acaccggaac
     1681 agtatttccg gcgctataac gccaggtatc ccgagcgggg aggtgcgaaa aaggattccg
     1741 gaagcctgac tctcactcag caaaaagagc agttgcggga attgcgaaaa cgctgggagg
     1801 tgaagcacaa cgaacatatg agaaagcatg gctttgaaag gggcttcatt gactgccgga
     1861 cgctgaaaga acagggcatt gaacgacgtc ccgaagtgca tctgggtttt gaagctgccg
     1921 gacggcttga tgatgcccag cgtcatgaca tcatgcaaaa acggtctgaa ccggactatt
     1981 cccgccatct tgaacaggcg cgaacggtcg ggcatgacat cagggaatgg ctggacactc
     2041 cggttaagca acatgaactg gtcagaaggc tgcaacatga tgttgcgcgg gagcatggct
     2101 ttgacatgag agacagagtg agcagacaga accgaactga acctgaacgg gttaaatcac
     2161 cgtcacgtgg attttctatg ggattctgaa catggccagc acagaagaaa aattactcac
     2221 gctcctgtta tcggtggagc atctgcaaca taccgcaatg gagcaacaga aagctgttgc
     2281 tgattctctg gctgtggcaa gggaaacact tcgcggatat cgggatattt ctgacggtgt
     2341 ggcaaaacag gtcagggatg aagtcagaaa cgaggtgcag aagctggatg ttgcagggct
     2401 gataggtgag cgcatcagcc aggattttca gcggctggaa gagtcagtcg caaacatgaa
     2461 ggcaaacgcg gatgccctga acaaggacat tgcgacaatt catcacaatg ttgttaaaga
     2521 atacaacacg ctcaataaat acagtctgaa atggtttatc ggtgttacgg tcagttttct
     2581 ggttatgttc tgtgtgcttg gatggggaat gaaaacaatg ctcgacagga actacaacgc
     2641 cacagcggcg gtgtatcaga aagttgtgac actggaagat aaactggcgg agaaaccagc
     2701 aacagggaag agccggaaaa actgacgcgc ttcgcttgtc caacgcctca cgggacgcga
     2761 aaaaattccg cgtcccgttc accgttttct gatgagaaag tttgccattt tgacccgttc
     2821 gacggctggg gcgagcgaaa caaatcgtgt gccgtatttg tgcatagcta tgcaacatcc
     2881 tgaaaacgca tttcacgcgt ttttggggat tcagccaggg gaaaacatgg tttttttact
     2941 ttttgagcgt aaagacgtga aaaatctcgt tattgcactt gcgatctttc gtcagggagc
     3001 gtagaacgaa aaaagcccgc cgttaggcga gcttcttcgg gttcattgag gttttcgacc
     3061 tcctcaatgt tcctgtggag tctgttgcgg tgacaacgga aaccagttca ttcagtttgc
     3121 atgaaccttc tgtattctt
//
