LOCUS       NZ_CP054983             4018 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STIN_92 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP054983
VERSION     NZ_CP054983.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925548
            Assembly: GCF_022353685.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4018)
  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 4018)
  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_022353685.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:06:11
            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)                     :: 5,265
            CDSs (total)                      :: 5,144
            Genes (coding)                    :: 4,880
            CDSs (with protein)               :: 4,880
            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)              :: 264
            CDSs (without protein)            :: 264
            Pseudo Genes (ambiguous residues) :: 0 of 264
            Pseudo Genes (frameshifted)       :: 85 of 264
            Pseudo Genes (incomplete)         :: 182 of 264
            Pseudo Genes (internal stop)      :: 46 of 264
            Pseudo Genes (multiple problems)  :: 47 of 264
            Pseudo Genes (short protein)      :: 4 of 264
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054983.1.
            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..4018
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STIN_92"
                     /isolation_source="Shatin WWTPs_92 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed6"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            272..487
                     /locus_tag="HUZ60_RS26145"
                     /old_locus_tag="HUZ60_25795"
     CDS             272..487
                     /locus_tag="HUZ60_RS26145"
                     /old_locus_tag="HUZ60_25795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_072048928.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSQG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            616..1143
                     /locus_tag="HUZ60_RS26150"
                     /old_locus_tag="HUZ60_25800"
     CDS             616..1143
                     /locus_tag="HUZ60_RS26150"
                     /old_locus_tag="HUZ60_25800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883515.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_016246513.1"
                     /translation="MKCFWACSVSVVLAMSFTVAAAENNDNVTYTKPSAGRDLYLTCKG
                     YQVKGASVINVEKPSYLEGTGEQVEFAIITPVGASDGLKVFFDSWGFSSFGLIESHVMH
                     EHWSLVHVGGRASVKGEKIDYSFVDNQPQEGGSYKPKTGVFLYGCMNSDKRPSWVEKIY
                     TRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            1398..1610
                     /locus_tag="HUZ60_RS26155"
                     /old_locus_tag="HUZ60_25805"
     CDS             1398..1610
                     /locus_tag="HUZ60_RS26155"
                     /old_locus_tag="HUZ60_25805"
                     /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_034169353.1"
                     /translation="MGDFERTFGAGADFDRIIDENNSEYFREDRRKTKNSKKKFSSFQD
                     ALVWAKANPGKTIIRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(2039..2152)
                     /locus_tag="HUZ60_RS26435"
     CDS             complement(2039..2152)
                     /locus_tag="HUZ60_RS26435"
                     /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_072035093.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPERHDKTPLAAATGN"
                     /name="replication initiation protein"
     gene            2800..3123
                     /locus_tag="HUZ60_RS26160"
                     /old_locus_tag="HUZ60_25810"
     CDS             2800..3123
                     /locus_tag="HUZ60_RS26160"
                     /old_locus_tag="HUZ60_25810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024191642.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQICLDEKPSRAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGTGHDRVQVVAVLMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3332..>3766
                     /locus_tag="HUZ60_RS26165"
                     /pseudo=""
     CDS             3332..>3766
                     /locus_tag="HUZ60_RS26165"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          2510..2687
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="87.222"
                     /coverage="83.0"
                     /evalue="4.5e-50"
     Typing          complement(2040..2560)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.564"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          5..579
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.938"
                     /coverage="99.0"
                     /evalue="1.72e-97"
     Typing          3114..4018
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.351"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 gatcagccag acgtggctga ccatagtcct ggtctccgcg ctactgatcg cctcgagcgc
       61 gggcattctg tggtggcagg ggcaacagat actcgacaac tacacgacca tccaggaaca
      121 gaagagcacg caggccatgc tttcagagaa gaacaacggc gtccagctca cgacctgcgg
      181 ggaggagaga cgccgctgcg tgagggtgaa cccggaagcg ggaagattcg gagaggattc
      241 gagctggatg atactggcgg ggaaatagca catgacggaa ctggaaaaac agttgctgag
      301 cgcattagag cagctacagc aggactactc gaaaaggctg gacgagtggg agaacgcctt
      361 cgcggaatgg cggacgatgt ctgggcttat gcaacgggag aacgcggcgc tgagcgagcg
      421 cgtcacgggc ttgagcaggc aggtgcagag tttgagcgat cagctgcgcc gattgtcgca
      481 aggctgaatg gcatcgaggc gcaccgggag caggagcgcg cggcgcagca ccagaaagcg
      541 ctggagctgg aacgatcgca gcggcagaaa ggttttgagc ttggaatgta gttaatcaat
      601 gaaaagggat gcgttatgaa atgtttctgg gcttgctcag tctcggtggt tttggctatg
      661 tcatttacag tcgctgctgc ggagaataac gacaacgtta catatacaaa accgtcagcc
      721 gggagggact tatatcttac ctgtaaaggt tatcaggtga agggggcatc tgtaattaac
      781 gtcgagaaac cttcttacct tgaaggtact ggtgagcagg ttgaatttgc aatcattact
      841 cctgttggtg cgtctgacgg actcaaggtc ttttttgatt catggggttt ttcttcattt
      901 ggattgattg aaagccatgt gatgcatgag cactggtctt tagttcatgt tggggggcgt
      961 gcttcagtca aaggtgaaaa gattgattat tcatttgtag ataaccagcc acaggagggg
     1021 gggagctata aacccaaaac aggtgtgttc ctgtacggct gcatgaactc ggataaaaga
     1081 ccatcttggg tcgaaaagat ctacacaaga acaggtgtgt ttcgaggggg catagaagac
     1141 taaaatactg cttacagcat gaaaatccat tgaacagagt gtcagttcat ttccgtgcat
     1201 aactatgcat accgtaagaa cttacggggg gcatttatcg gcgtttttac gtggtaagag
     1261 gtgctctttt gcggttcatg gcgcagaacg gtgctgaggc tgtctgcggc ggtgcgaaca
     1321 agggatgtta tggtaaataa gagtgtcttt tggatatttt aaatctgttt ttttattaaa
     1381 tttaatgggg gcagaaaatg ggggattttg agcgtacctt tggagctggt gctgattttg
     1441 atcggataat tgatgagaat aacagcgaat attttcgaga agatcgccga aaaactaaaa
     1501 attcaaaaaa aaaattctct tcttttcaag atgctttggt ttgggcgaaa gctaatcctg
     1561 gcaaaacgat aataagatct ccagacggtg tggggtttat tgaaaaatga aagagtggat
     1621 tcactgtaaa acaacagtca ttttttggac aacactgtct atatacgtac tcatatgttt
     1681 cacagtgtcg tatgttggag tctatgttac gtacgttgca gggcctattt tgttagttac
     1741 aggcattctt gcatggctta cgaaacctag ctgtaatcca aagtgactgg gctagacgaa
     1801 ctttatcccc ccataaaacc cgctttttta aacggatctt cttgagatca ttcatggaga
     1861 atcgtaatct cttagcactg taaacgaaaa aaccgcccag caaggcggtt ttttcgaagg
     1921 ttctcagagc agcaactctt tgaaccgagg taactggctt ggaggagcac agtcaccaaa
     1981 acttgtcctt tcagtttagc cttaaccggc gcataacttc aagactaact cctctaaatc
     2041 agttaccagt ggctgctgcc agtggcgttt tgtcgtgtct ttccgggttg gactcaagtc
     2101 gatagttacc ggataaggcg cagcggtcgg actgaacggg gggttcgtgc atacagtcca
     2161 gcttggagcg aactgcctac ccggaactga gtgtcaggcg tggaattaga taaacgcggc
     2221 cataacagcg gaatgacacc ggtaaaccga aaggcaggaa caggagagcg cacgagggag
     2281 ctaccagggg gaaacgcctg ggatctttat agtcctgtcg ggtttcgcca ccactgattt
     2341 gagcgtcaga tttcgtgatg cttgtcaggg gggcggagcc tatggaaaaa cggcaacgcc
     2401 gcatcctttt tccgcccttt ctgattgatt tccgcttagt ctctttatcc agccattcgt
     2461 aagctggcaa cgcccgccgc agtctcacgg caggagcgca gcgaccgagt gagcgaggag
     2521 gcgtcatttc accgggatct gcatttcgca cttacgcccc acagcagcat tttctccctg
     2581 ccacatgaag cactttcctg aatccccact ccgatttacc atgttaagcc agtatacact
     2641 ccgctagcgc tacgtgactg gttcagggct gcgccccgaa acccgctgaa aagtactgcc
     2701 gcgccctgcg ggcttgccca acaccgctcc ggacaggaaa aaatttcccg cccgaaccgg
     2761 tgttatccgg aggatggttt ggcagaaaag cgcaacaaaa tgctcactat gtgggtgaca
     2821 gaagacgagc accgccgact tctggagcgc tgtgagggta aacaactcgc ggcctggatg
     2881 cgccagatat gcctggacga aaagccctcg cgtgctggca aacttccatc catctcgccg
     2941 gcgctgcttc gtcagcttgc cggcatgggt aacaacctca accagattgc ccggcaggtt
     3001 aacgccggtg gcggtactgg gcacgatcgc gtgcaggttg tcgccgtgct gatggccatt
     3061 gatgccggac tcgagcggct gcggcacgcc gtgctggaaa agggggcaga cgatgatcgt
     3121 taagtttcat cccagaggcc gcggcggtgg cggcggtccg gtggattatc tgctggggaa
     3181 agaccggcag cgcgacggcg ccagcgttct gcagggtaag ccggaggaag tgcgggagct
     3241 tattgacgcc tcgccttacg ccaagaaata cacctccggc gtgctgtctt ttgccgaaca
     3301 ggatttgccg cccggccagc gtgaaaagct gatggcgagc tttgagcggg ttctgatgcc
     3361 cggactcgat aaagaccagt acagcgtact gtgggttgag caccgggaca aagggcggct
     3421 ggagctgaac ttcctgatcc cgaacacgga gctgctgacc ggcagacgtc tccagccgta
     3481 ttacgaccgc gccgaccgtc cgcgcattga tgcctggcag accatagtga acggcagact
     3541 ggggctgcac gacccgaacg cgccggaaaa ccggcgggcg ctggttacac cgtccgcgct
     3601 gccggaagcg aagcaggaag ccgcccaggc gattacgcgc ggcctacttt cccttgcctc
     3661 atccggggag ctgaaaaccc gtcaggacgt cactgaggcg ctggaaagtg cgggttttga
     3721 ggtggtgcgc accacgaaaa gcagcatcag cattgccgac cctgacgggg ggcgaaacat
     3781 ccgactgaag ggagccatct atgaacagtc ttttaacgct ggcgaaggac ttagagcaga
     3841 aatcgaaagc gcagcagcag actaccggcg agatgctgaa agccgcattc agcgagcacg
     3901 agaagtctgt cagagcggaa ctgagcgaaa gcgagaagag aatcagcgcc gccatcctcg
     3961 accacgaccg gaagctgtcc tcagccatga gccaacgcac gaaagggatg ctgcgtat
//
