LOCUS       NZ_CP055084             4062 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHIN_116 plasmid unnamed9, complete
            sequence.
ACCESSION   NZ_CP055084
VERSION     NZ_CP055084.1
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 4062)
  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 4062)
  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
            CP055084.1.
            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..4062
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_116"
                     /isolation_source="Shek Wu Hui WWTPs_116 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed9"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            complement(join(3214..4062,1..1299))
                     /gene="mobQ"
                     /locus_tag="HUZ90_RS24585"
                     /old_locus_tag="HUZ90_24350"
     CDS             complement(join(3214..4062,1..1299))
                     /gene="mobQ"
                     /locus_tag="HUZ90_RS24585"
                     /old_locus_tag="HUZ90_24350"
                     /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_070749924.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQKEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NHLINRLNLEIQISHTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKLEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQYPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRHDRGWSQ"
                     /name="mobQ"
     gene            1478..1732
                     /gene="mobC"
                     /locus_tag="HUZ90_RS24590"
                     /old_locus_tag="HUZ90_24355"
     CDS             1478..1732
                     /gene="mobC"
                     /locus_tag="HUZ90_RS24590"
                     /old_locus_tag="HUZ90_24355"
                     /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_000091744.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            2265..2966
                     /locus_tag="HUZ90_RS24595"
                     /old_locus_tag="HUZ90_24360"
     CDS             2265..2966
                     /locus_tag="HUZ90_RS24595"
                     /old_locus_tag="HUZ90_24360"
                     /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_001281396.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVEITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(942..1300)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.5"
                     /coverage="100.0"
                     /evalue="8.52e-174"
     Typing          1301..1477
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2266..2965
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(2..1299)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.339"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(3218..4062)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.227"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccctgaatcc ataacggcat tgtcattttt cctgagctgc tccgcgcgac tacgttctgt
       61 atcctccagc tccttccggc gcaattcctc ttcacgttta agcaactggg atctgagagc
      121 tgcaaggccg gattcccccc actgctgcca ctgtttttca aatgccgtct gactcgcggg
      181 aatgtcctgt ttctccagct tccggtaatg ctgtcgcaat ttttccattt gctggctcag
      241 agactggatt tttccctgct cactacggta ttccggtgca gcccattgca tcaggggaat
      301 acgggaaaaa ccggacgaaa acggcgatga ttttttcagg ctggcagcat ggctcatcgc
      361 ttcctttcgt tcggtgttca gctcttccca gcgtctgcgc gtcgcctgca tatctgccat
      421 catcgacatg gcgttactgg tgagtttcca tgccgcgtta ctgtccttcg gcaacgcttc
      481 gatgatgtca cgtagtgtgt acgaagttgc gttgtcagga agcccgatat tcagaaggtc
      541 agccacacgg cgggcaggct ctgtcagccc gctgttcctg agttcggtgt gggaaatctg
      601 tatttccagg ttaagcctgt taatcagatg attctgttcg ccgcgttctg tttcgatacc
      661 gcgtgtttcc atcgcacagg cagactttcc gaggtgaata cccggcgttt tctcaagccc
      721 ctgtcgctcg tatgaacgat ggtctatctc tttctgataa ccggcgttcg ccagtgccct
      781 gtttgcatgg tcagcccatg atgcacgcca cgtctcggca tgtgtccggt cgttccagtc
      841 cctgaccttt ccgccgaacc cagcaggccc gacagccctc gtggtcagca tgatgtgcgc
      901 atggggattt gttttatcca tgtgatggaa cgccacatca gcaatcatgc cctgactgac
      961 aaagttttct ctgacaaagg cgagaacggt ttcccgtgcg gcatcctgcg gcagttcgtg
     1021 ggggatggcg agttcaattt cccgcgcaag ttgtgagttc ttccggcgtt cggccttctc
     1081 aacggcattc cagagttcgg cacggttcgt acaccaggca ggggctgtcg cgggggtcag
     1141 aatcacagcc tcagccacac cgcttttgcg ggtgtagtcg tgagtcagtc cggtacgctc
     1201 atcaagcatt agtgaaccag aacgataggc agcagaagca acggcgctgt agccgttgct
     1261 tctggagatg attttcatac tgagatgata aatcgccatt tctgccgtaa tgcctttttg
     1321 cagttttctt tcagccccgc agggcgcaca caatcgaaac ggagtggaga ttgtataagt
     1381 gcgcacttcg tgatttgccg tgcattatgc cagctcagtt tttaaactac cagtgacgcg
     1441 ctaaaatgcg atttttcatc gcgcatggag ttacatcatg agcagaacgc tcgaacagaa
     1501 gattgctgat gctgaggcga gattacagcg cctgaaggcg aagagccgga gcctggacac
     1561 agcgcagaag gtcattgtgg gtgcagcatt gctggcaaaa gtcagaaagc cggaggaagt
     1621 gcagttgcga gcttggttac tccagttcct gaaggcagag gtgacacggc aggctgatgt
     1681 gacgcgaata ctgccgctga ttaacgagct ggaggcgctg ccagagcagt gattgtatcg
     1741 tccgctcgcc gcagcccagc gaccgagcgt tagcgagcga gtgggcgagg aagcggaagt
     1801 gaatcagtcg ccatgttgag cacatacgca cggtttttcg acaggtgata tgcgctgaac
     1861 ccgcatgaat actggatttc cacagggttg gagggggtgt attcggaatc ttcaatcctg
     1921 atttttttca acacattgtt tttattggat ttttattttc agcaccccaa gttatccaca
     1981 ggctcgccgt taagttttta agatcttatt tttagatctt tttttttaaa acctttttag
     2041 gtcttgtaac cacatgattt taaaggtgtt ctggcgagat aggtggagct tttgggggtg
     2101 ataggtggag cttttggggg tgataggtgg agcttttggg ggtgataggt ggagcttttg
     2161 ggggtgtaat ccacagaaaa aaggggttgc aaaaaaaaaa cttccaccaa tatgatgggt
     2221 ggcgtacagt aaaaaaacgc caccaatagc aacgagcaag cgaaatgtca gatctgatag
     2281 cttacaaatc aaacgccctt atcgaggcaa gctacaagct cactttgcag gaacagcgct
     2341 tcctgctggt ctgtatcagc cgcctgaaat ccggagaaga ttccccttcg ccggatgaac
     2401 aaaaaaccat gaccatcacg gctgcagagt ttcatgatgc ctttcctgac atgggacggc
     2461 agcacgctga agctaggctc aaggaagcga tagatcgcct ctgggacagg tcagtaatca
     2521 tcaagaacga ggaaaaacga gaagagttcc gctgggtgca gtaccgggcg cagtatttca
     2581 aaggtgaggc gaaagtagag atcaccttct ccgatgccat catgccgtat ctgacacagc
     2641 tcaaggggca gtttacgcgg gtagtcgtga agaacgtctc cagcctctcc agcacctaca
     2701 gcatccgcat ttacgagctg ctccagcagt tccgcagcac cggtgacaga acgatagcta
     2761 tcgatgattt ccgaaccatg cttgccgttg aagataaata tcaacaattc aaagacttga
     2821 ataagatgat aatcaagcca gccatcgccg aactgaacga aaaaagcgat ctggttgtaa
     2881 cggttgagac gatcaaaaag gggcgcacgg ttgtagccct gcattttcgc ttcaaggaag
     2941 acaaacagat caagatgacg atctagaatc gattttaagg cacctaaaac actccctgtt
     3001 gcgttttttt tgtgttagta gtgcgaaggt actattgaag tgaaaaattg cgtcaaaaac
     3061 gctctgatgc agcgaaaaaa gaacccccaa tttttggggg cggaaaaaca aaactatgct
     3121 tgcgttatgt gagtgtgctt cttgcattca tccctgtcga tgaacatcga cgaacataac
     3181 acgatgttaa acaaaacaaa atattgttca cattcactgt gaccaaccgc gatcatgtct
     3241 cctctcggtg gcgtgtgttc gtgcatcttc ctcgcgccgc cattcgtccc aggtacgatt
     3301 gaaacccagc gagcggaaca gatgatccgg ctgtttttct ggtgtgttga cggcagcaaa
     3361 aagcggtgcc tcacgggttt tcagatgaaa ctccataagt tccggcgcag gtgatatgtg
     3421 gctgtctgca tcatgattta cggcaacacc ataccctgca taccgtaacc ccttatcggt
     3481 cagtgcactg atgaccagct ggctgttatc ggctgaggga acggcaaacg cgggatacag
     3541 cgtaccatta agccggacaa caccgcccag agagtcatcc acgcccatga ccagcaaaag
     3601 ctgaagctgg cgggtttccc ggtcgacaga actcatgacc ggcatcagcg tcggtggcag
     3661 acgtccctgc gtaaaatcca ccttccttgc tgccagtgat ggcatggctg gctggcggtc
     3721 ttctccaaga cagaaagact ccggccatgt cttcggttgg cggagattgc gggtatgttg
     3781 cggccatgtc tggcaaacct gcgtcagaag ttgctcaaag gtcgcagagg aataaacacg
     3841 ttgcagtggt ggatattgac cgatttcgct tcggtcacag atataaccac tcctgtcacg
     3901 cattaaatca acactctcaa agatcctggt gcggtatttc tccagctcgt tcccccagag
     3961 cgtatattct ccgttccggt tgtgaagcag aaggtaacag gtcatttccc cgttaccagg
     4021 catgggagcc tcgccatacc ccgtaacgac tgctctcagc ac
//
