LOCUS       NZ_CP055083             4072 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHIN_116 plasmid unnamed8, complete
            sequence.
ACCESSION   NZ_CP055083
VERSION     NZ_CP055083.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925605
            Assembly: GCF_022354205.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4072)
  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 4072)
  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_022354205.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:17:39
            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)                     :: 4,956
            CDSs (total)                      :: 4,829
            Genes (coding)                    :: 4,546
            CDSs (with protein)               :: 4,546
            Genes (RNA)                       :: 127
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 81 of 283
            Pseudo Genes (incomplete)         :: 200 of 283
            Pseudo Genes (internal stop)      :: 45 of 283
            Pseudo Genes (multiple problems)  :: 44 of 283
            Pseudo Genes (short protein)      :: 4 of 283
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055083.1.
            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..4072
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_116"
                     /isolation_source="Shek Wu Hui WWTPs_116 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed8"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(join(3216..4072,1..1303))
                     /gene="mobQ"
                     /locus_tag="HUZ90_RS24570"
                     /old_locus_tag="HUZ90_24335"
     CDS             complement(join(3216..4072,1..1303))
                     /gene="mobQ"
                     /locus_tag="HUZ90_RS24570"
                     /old_locus_tag="HUZ90_24335"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_239635740.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRIELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1482..1736
                     /gene="mobC"
                     /locus_tag="HUZ90_RS24575"
                     /old_locus_tag="HUZ90_24340"
     CDS             1482..1736
                     /gene="mobC"
                     /locus_tag="HUZ90_RS24575"
                     /old_locus_tag="HUZ90_24340"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     gene            2269..2970
                     /locus_tag="HUZ90_RS24580"
                     /old_locus_tag="HUZ90_24345"
     CDS             2269..2970
                     /locus_tag="HUZ90_RS24580"
                     /old_locus_tag="HUZ90_24345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(946..1304)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          1305..1481
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="1.22e-84"
     Typing          2270..2970
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3..1390)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.704"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3220..4070)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.648"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccataacggc attgtcattt ttcctgagct gttccgctcg tcgctccgcg cgactacgtt
       61 ctgtatcctc ctgctccttc cggcgcaatt cctcttcacg tttaagcaac tggactctga
      121 gagctgcaag gccggatgcc ccccactgct gccactgttt ttcaaatgcc gtctgactcg
      181 cgggaatgtc ctgtttctcc accttccggt aatgctgtcg caatttttcc atttgctggc
      241 tcagcgactg gatttttccc tgttcgctac ggtattccgg tgccgcccat tgcatcaggg
      301 gaatacggga aaaaccggac gaaaacggcg atgatttttt caggctggca gcatggctca
      361 tcgcttcctt tcgttcggtg ttcagctctt cccagcgtct gcgcgtcgcc tgcatatctg
      421 ccatcatcga catggcatta ctggtgagtt tccatgccgc attactgtcc ttcggcaacg
      481 cttcgatgat gtcacgtagt gtgtacgaag ttgcgttgtc aggaagcacg atattcagaa
      541 ggtcagccac acggcgggca ggctctgtca gcccgctgtt tctgagttcg atacgggaaa
      601 tctgtatttc caggttaagt ctgttaatca gacgattctg ttcgccgcgt tctgtttcga
      661 taccgcgtgt ttccatcgca caggcagact ttccgaggtg aataccaggc gttttctcaa
      721 gcccctgtcg ctcgtatgaa cgatggtcta tctcttcctg ataaccggcg ttcgccagtg
      781 ccctgttcgc atggtcagcc catgatgcac gccacgtctc ggcatgtgtc cggtcgttcc
      841 agtccctgac ctttccaccg aatccagcag gtccgacagc tctcgtggtc agcatgatgt
      901 gcgcatgggg atttgtttta tccatgtgat ggaacgccac atcagcaatc atgccctgac
      961 tgacaaagtt ttctctgaca aaggcgagaa cggtttcccg tgcggcatcc tgcggcagtt
     1021 cgtgggggat ggcgagttca atttcccgcg caagttgtga gttcttccgg cgttcggcct
     1081 tctcaacggc attccagagt tcggcacggt tcgtacacca ggcaggggct gtcgcggggg
     1141 tcagaatcac agcctcagcc acaccgcttt tgcgggtgta gtcgtgagtc agtccggtac
     1201 gctcatcaag cattagtgaa ccagaacgat aggcagcaga agcaacggcg ctgtagccgt
     1261 tgcttctgga gatgattttc atactgagat gataaatcgc catttctgcc gtaatgcctt
     1321 tttgcagttt tctttcagcc ccgcagggcg cacacaatcg aaacggagtg gagattgtat
     1381 aagtgcgcac ttcgtgattt tccgtgcatt atgccagctc agtttttaaa ctaccagtga
     1441 cgcgctaaaa tgcgattttt catcgcgcac ggagttacat catgagcaga acactcgaac
     1501 agaagattgc tgatgctgag gccagattac agcgcctgaa ggcgaagagc aggagtctgg
     1561 acacagcgca gaaggtcatt gtgggtgcag cattgctggc aaaggtcaga aagccggagg
     1621 aggtgcagtt gcgtgcctgg ttactccagt tcctgaaggc agaggtgaca cgacaggctg
     1681 atgtgacgcg catactgccg ctgattaacg agctggaagc gctgccagga cagtgattgt
     1741 atcgtccgct cgccgcagtc ccagcgaccg agcgttagcg agcgagtggg cgaggaagcg
     1801 gaagtgaatc cgtcgcctga ttgagcacat acgcacggtt tttcgggagg tgatatgcgc
     1861 tgaacccgca tgaatactgg atttccacag ggttggaggg ggtgtattcg gaacttgcaa
     1921 ttctgctttt ttgcaacgca ttgtttttat tggttttttg ttttcagcac tccaagttat
     1981 ccacaggctc gtcgttaagt ttttagatct tgtttttaag atcttgtttt taatacttgt
     2041 tttagcgcca aaattcctta tagaaaacaa aatgttacaa tgctataggt aatgtgattt
     2101 aaggtaaagg taatatgatt taaggtgttt aggtggggga atttaaggta aaggcaatat
     2161 gatttaaggt aatattcaca gaaaaaggga tattaaaata aaaaggcatt gcctttcgtt
     2221 gagggtatgt ttatctttta ttcattacct tttggggagg gatgctctat gtcggatcta
     2281 attgcctata aatccaatgc gctggttgaa gccagttata aattgaccct acaggaacag
     2341 cgatttttgt tactttgcat cggtcgattg aagtctgggg ctgatgcaga atctccaaaa
     2401 ttgcaaaaga caatgaccat tacagctgcg gaatatttcg attcattccc tgacatgggg
     2461 cggaaaaatg ccgaggttca gttacaggaa gcaattgatc gtttgtggga caggtcaatc
     2521 attctcaagg atgacgagaa acgtgaggag ttccgctgga tccagtatcg ggcacagtac
     2581 gctaaaggcg aggccagagc acaaataaca ttttctgacg cagtaatgcc ttatttgaca
     2641 caactacaag ggcaatttac tagagttgta atcaagaata tatctagatt atcaagaagt
     2701 tacagtataa ggatatacga actcctccag cagttccgca gtactggcga acgtattatc
     2761 gctctcgatg attttcgctc aatgcttgat atagagcata aatatcaaac atataaatca
     2821 cttaaccagc aattattaag accctgcatt gacgaactga acaaaaaaag cgacctggct
     2881 gtaacggttg agacgatcaa aaaggggcgc acggttgtag ccctgcattt tcgcttcaag
     2941 gaagacaaac aaatcaagat gacgatctaa aatcgatttt aaggcaccta aaacgctccc
     3001 tgctgcgttt tttttgtgtt agtagtgcga aggtactatt gaagtgaaaa attgcgtcaa
     3061 aagcgctcta atgcagcgaa aaaagaaccc ccattttttg ggggcggaaa aacaaaacta
     3121 tgcttgcatt atgtgtgtgc ttcttgcatt catccctgtc gatgaacatc gaagaacata
     3181 acacgatgtt aaacaaaaca aaatattgtt cacattcact gtgaccaacc gcgatcatgt
     3241 ctcctctcgg tggcgtgtgt tcgtgcatct tcctcgcgcc gccattcgtc ccaggtacga
     3301 ttgaaaccca gcgagcggaa cagatgatcc ggctgttttt ctggtgtgtt gacggcagca
     3361 aaaagcggtg cctcacgggt tttcagatga aactccataa gttccggcgc aggtgatatg
     3421 tggctgtctg catcatgatt tacggcaaca ccataccctg cataccgtaa ccccttatcg
     3481 gtcagtgcac tgatgaccag ctggctgtta tcggctgagg gaacggcaaa cgcgggatac
     3541 agcgtaccat taagccggac aacaccgccc agagagtcat ccacgcccat gaccagcaaa
     3601 agctgaagct ggcgggtttc ccggtcgaca gaactcatga ccggcatcag cgtcggtggc
     3661 agacgtccct gcgtaaaatc caccttcctt gctgccagtg atggcatggc tggctggcgg
     3721 tcttctccaa gacagaaaga ctccggccat gtcttcggct ggcggagatt gcgggtatat
     3781 tgcggccatg tctggcaaac ctgcgtcaga agttgctcaa aggtcgcaga ggaataaaca
     3841 cgttgcagtg gtggatgttg accgatttcg cttcggtcac agatataacc actcctgtca
     3901 cgcattaaat caacacgctc aaagattctg gtgcggtatt tctccagctc gttcccccag
     3961 agcgtgtatt ctccgttccg gttgtgaagc agaaggtaac aggtcatttc cccgttacca
     4021 ggcatggggg cctcgccata ccccgtaacg actgcgctca gtacccctga at
//
