LOCUS       NZ_CP058888             4207 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_33 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP058888
VERSION     NZ_CP058888.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925559
            Assembly: GCF_022494095.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4207)
  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 4207)
  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_022494095.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:15:22
            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)                     :: 4,637
            CDSs (total)                      :: 4,516
            Genes (coding)                    :: 4,304
            CDSs (with protein)               :: 4,304
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 212
            CDSs (without protein)            :: 212
            Pseudo Genes (ambiguous residues) :: 0 of 212
            Pseudo Genes (frameshifted)       :: 71 of 212
            Pseudo Genes (incomplete)         :: 134 of 212
            Pseudo Genes (internal stop)      :: 40 of 212
            Pseudo Genes (multiple problems)  :: 34 of 212
            Pseudo Genes (short protein)      :: 4 of 212
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058888.1.
            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..4207
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_33"
                     /isolation_source="Stanley WWTPs_33 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed2"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(681..830)
                     /locus_tag="HZT25_RS23250"
     CDS             complement(681..830)
                     /locus_tag="HZT25_RS23250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_113419837.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPEKHAKTPLAAAIGNRNSRENYQ
                     EFLK"
                     /name="replication initiation protein"
     gene            1249..1440
                     /locus_tag="HZT25_RS23010"
                     /old_locus_tag="HZT25_22880"
     CDS             1249..1440
                     /locus_tag="HZT25_RS23010"
                     /old_locus_tag="HZT25_22880"
                     /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            2412..2855
                     /locus_tag="HZT25_RS23015"
                     /old_locus_tag="HZT25_22885"
     CDS             2412..2855
                     /locus_tag="HZT25_RS23015"
                     /old_locus_tag="HZT25_22885"
                     /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_001605388.1"
                     /translation="MTSGIFLSREDLMLLSDQAKEEVLALATGDSVSGVYEESEDGPTD
                     LSSLQAERLVRGLSDKSRTVLKAILESEDGERGFWCKSLAKELGFDVSELSGVWSGLTR
                     RTRTVSDDSEAYLISWAWDDDRDDYYGTLHPTTYRNCKKAMNF"
                     /name="hypothetical protein"
     gene            complement(3157..4053)
                     /locus_tag="HZT25_RS23020"
                     /old_locus_tag="HZT25_22890"
     CDS             complement(3157..4053)
                     /locus_tag="HZT25_RS23020"
                     /old_locus_tag="HZT25_22890"
                     /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_186199455.1"
                     /translation="MKKNHLIAFSQKSRKKTIYKVTSSDDKFFRNQLKEQHNGIMEYDP
                     NDRQDQSKIFFLDLSKHEGITNEIIEELKELKKSDDINTTNYKAFSASDLDGLKYMATK
                     QDQYILFQNFYKKNIIGSKVLSLKKMEVLQDGFITLNEYAEVIYDIEDKKIYFSNIVKA
                     KKILSGMEMIYKEAGIKETKHFISQDHIHLLDDFDENKVNVLNKKRIQSELDKQNKIKV
                     EKGDDYDDFYTTDISECLAEIKEYYPEMLDGNKIIIKNNKDLENYLLALDERLYTAKRS
                     QQQRVATATRKVEKSKQ"
                     /name="hypothetical protein"
     Typing          complement(753..1374)
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.688"
                     /coverage="99.0"
                     /evalue="4.27e-169"
ORIGIN
        1 tgacggatta aaaaaatata cttttgagaa aaggttgaat aggataacga gaatcataaa
       61 gtagccaaaa acccagtttg atgtaatgct aactgagaca aaaaaatacc ctaagtatgt
      121 cggaagaaaa ttatcattaa ccggctccac tgtatttata ttgctcattg actcatcgtc
      181 aagtttgtta actacgcgca agaatattga attaagaaac agaattatga gtacgcttaa
      241 aatgatgtag gctatgaaaa acatagcttc attatcagag ataatagtta ctagctcttt
      301 attaaggttt gttttgtagt ttgtgatcat gtacacaaat attgctggag ttaatgctga
      361 tattgtagat aataatttaa agacataatc gagtatgtct gtggaattta ttttatttaa
      421 cacagtgttc tcccgtgaca aaggcttttt tattttaaat tttgctatat gtcaataaat
      481 aaatgccggg taggtaggct tggaaatgtt gactactgca ttagtgacag cgtactcttc
      541 tctttgaaag aaaaaaccac ccggcaaggt ggttttttca aaggttagaa aatcctggca
      601 gatgttctaa ccgtggtaac agaactatac gagagaactg tcaccaaatt cgtactacca
      661 gtgtagccgt agtcatgcgg tcacttcaag aactcctgat aattctctcg tgaattcctg
      721 ttaccaatgg ctgctgccag tggcgttttt gcgtgttttt ccgggttgga ctcaagacga
      781 tagttaccgg acaaggcgca gcggtcggac tgaacggggg gttcgtgcat acagtccagc
      841 ttggagcgaa ctgcctaaac ggaaccgagt gtcaggcgtg gaatgagaca aacgcggcca
      901 taacagcgga atgacaccgg taaaccgaaa ggcgggaaca ggagagcgca cgagggagcc
      961 accaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc actgatttga
     1021 gcgtcagatt ctgtgatgct tgtcaggggg gcggagccta tggaaaaacg ccccggcggg
     1081 gcgtggcctt ttcgcccttg tccttagctt tcgttatgct taccgttacg ttatctgctt
     1141 atcctccctc cgctcgccgc agactcatga ccgaacggag tgagcgaatg agcgaggaag
     1201 cggaaaacca tcagaacgta caataagcac tttcgcgccg gggctttcat gaacaaacaa
     1261 caaaagactg ccgttaacat ggctaaattc atccaggatc agtccctgct tcttctggac
     1321 aggcttaatg agctggatct ggatcatgag gctgatttct gcgagaaact ccatgaggat
     1381 gcggaacgcc tttaccgaag cctgtcagcg cgcctgaatg agcagcagga cggtgcgtaa
     1441 tggctccgtt ctgggtatta ccggagtaat accggcatcg ccttaatttt cattgtgtta
     1501 gcgcttaaca ttattacccc ggtaataccc agaatccctg tgttttttat tttttattta
     1561 cttttcatga agttgcgatg aaaatcgcag ctgcgttagg tgtatgtcat tttttagtat
     1621 ataaaacgac cactcccgag tgctggcgcc gcaggttaag tatgattctg gctaaaaagc
     1681 gtccttttcc gggaaagggt catgctcgta tgaccctatg ggttcagcga ctacacataa
     1741 actacaaaat tgcatctgct tttaccccag aacgcgggtg tacaacagaa ttacatcaaa
     1801 agtacatcaa aattacatca cttttacgtc agatcgcggg tgtacaacag aattacatca
     1861 aaagtacatc acttttacat catttttacg tcagatctga cctctgagct attcgtacat
     1921 ccgccccctc ttcctgggcc tcctgcacgt gctgaaaatg gtttttccgg ctgtgccggc
     1981 aacgcctcac ggccacgcaa taaattgcgt ccccgttcac cgttttcggg taagaagaac
     2041 atcggaaaca ggacttaccc cggctgaatg gcgtgaattt ccgcgctatg cacttgtgcg
     2101 catactcatg catgccgtaa aaacagagcc tgcgcgtttc tggcgggttt tcgggtggtt
     2161 tgttgcctgt tttaccggtt tcccgtcaga aacgcgctca ggccgtctga gcggtgcgcg
     2221 taatgcgacg ttatggtaaa tccgggctgt tgagtgttga cctctcacta tcgcaaccca
     2281 gttaatgcgg taaatcaaac acaactagct gttaattgat gttagttgta tttacttgtc
     2341 acttgtcttg ttgacaacta tcttgtctat gtttattctc cttttatctt aacaagacaa
     2401 tggagtgttt catgactagt ggtattttct tatcccgtga agatttgatg ttgttatcag
     2461 accaagcaaa agaagaagtg ctggcattgg ctactgggga ttcggtttct ggtgtttatg
     2521 aggagtcgga agatgggcct actgatcttt cctcgcttca ggcagaaagg cttgttcgtg
     2581 gtttaagtga taagtcgcga acagtgctga aagctattct tgaaagcgag gatggtgagc
     2641 gaggattctg gtgcaagagc ctcgcaaagg agcttggttt tgatgtctct gagctttcag
     2701 gtgtctggtc agggcttaca cgcagaactc gcacggtaag tgatgattct gaggcttatt
     2761 tgattagctg ggcttgggat gatgaccgtg atgattacta tggaacgcta catccaacaa
     2821 cctatcgcaa ctgcaagaaa gctatgaact tttgattgtt ctcgctgtga tactttccct
     2881 gtgagcccgc catgtgcggg cttttttcat tggttcgtgt agtgagacgt tatggtaaat
     2941 cctcgaataa taaaaaagcc cccagtggag gcttttgtgt gtgggcacta ggaaaacaaa
     3001 ccatgctaag aggattgaat ttaacgactg attccgctct atttcttgta cagaaatcgc
     3061 cgtagcccag ccgttctggt gatacgtaaa atcgatttgc tccaaaaata gtcttgcatg
     3121 gtttttttta gcttcctatt tgggttgggt ttccatctat tgttttgatt tttctacttt
     3181 tcttgttgct gttgctacgc gctgttgctg gcttcttttc gctgtgtaca agcgttcatc
     3241 taaagctaac agatagtttt ctagatcttt attattttta ataataattt tattcccatc
     3301 taacatctct ggatagtatt cttttatttc agctagacat tctgatatgt cggtagtgta
     3361 aaaatcatca taatcatcac ctttttcaac ttttatttta ttttgtttat ctaattctga
     3421 ttgtattctc tttttattta atacgtttac tttattttca tcgaaatcat ctaatagatg
     3481 aatgtgatct tggctaatga aatgttttgt ttcttttatt cctgcttctt tatatatcat
     3541 ttccattccg gatagaattt tcttagcttt aacaatattt gaaaaataaa tttttttatc
     3601 ttctatatca taaattacct ctgcatattc atttagtgtg ataaatccgt cttgtaatac
     3661 ctccattttt tttaaagaca gcacctttga accaatgata ttttttttat aaaagttttg
     3721 gaacaaaata tattgatctt gttttgtcgc catgtatttt aaaccatcaa gatcactagc
     3781 ggaaaatgcc ttgtaattag ttgtgtttat gtcatcggat ttttttaatt cctttaattc
     3841 ttcaattatt tcgttagtga taccttcgtg tttagagagg tctaaaaaga atattttgct
     3901 ttgatcttgc ctgtcatttg gatcatactc cataattcca ttatgttgtt cttttagttg
     3961 atttctaaag aatttatcat ctgaagatgt tactttgtag atggtttttt ttctgctttt
     4021 ctgcgaaaac gcaataaggt ggtttttttt cattttactc taccttgatg aatgtgaagt
     4081 catttattct tttatagttg gaggatgaga tgtctttatg agaacggaga tcatccttac
     4141 ttataagtaa tatttttact cctttatcag atgttaagtg atagaattta aaacctgata
     4201 ttaatag
//
