LOCUS       NZ_CP055044             4981 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_59 plasmid unnamed3, complete
            sequence.
ACCESSION   NZ_CP055044
VERSION     NZ_CP055044.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925586
            Assembly: GCF_022354025.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4981)
  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 4981)
  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_022354025.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:08:02
            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)                     :: 4,691
            CDSs (total)                      :: 4,573
            Genes (coding)                    :: 4,317
            CDSs (with protein)               :: 4,317
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 256
            CDSs (without protein)            :: 256
            Pseudo Genes (ambiguous residues) :: 0 of 256
            Pseudo Genes (frameshifted)       :: 78 of 256
            Pseudo Genes (incomplete)         :: 175 of 256
            Pseudo Genes (internal stop)      :: 53 of 256
            Pseudo Genes (multiple problems)  :: 48 of 256
            Pseudo Genes (short protein)      :: 4 of 256
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055044.1.
            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..4981
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_59"
                     /isolation_source="Shek Wu Hui WWTPs_59 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed3"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            868..1017
                     /locus_tag="HUZ71_RS23245"
                     /old_locus_tag="HUZ71_23065"
     CDS             868..1017
                     /locus_tag="HUZ71_RS23245"
                     /old_locus_tag="HUZ71_23065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            1257..1715
                     /locus_tag="HUZ71_RS23250"
                     /old_locus_tag="HUZ71_23070"
     CDS             1257..1715
                     /locus_tag="HUZ71_RS23250"
                     /old_locus_tag="HUZ71_23070"
                     /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_239638079.1"
                     /translation="MTKKRSSLYRSCLHERVILPDYRITSKVHQNYITFTSLIHHFYIT
                     FTSFLQLIRHFHPLCHLYITPFLNVLTAGFPAAPATLHGHAINCVPVHRFRMGRTPETG
                     LTPAEWCEFPRYALVRILMHAVKTEPARFWRVFGWFVACFTGFPSETR"
                     /name="hypothetical protein"
     gene            complement(1746..2336)
                     /locus_tag="HUZ71_RS23255"
                     /old_locus_tag="HUZ71_23075"
     CDS             complement(1746..2336)
                     /locus_tag="HUZ71_RS23255"
                     /old_locus_tag="HUZ71_23075"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_072775496.1"
                     /translation="MSTTKEKEKTDFPEALLSIWGRTILGSGWTTVPNELLKNQSHLGI
                     SNSELVLLIHLISFMHSASAKIFPSIDSLAERMNQDRRTIQRTIQRLEDKELIRKRVRS
                     TGKTDVGMSNVYDISPLMLKLINIQLPTMSPPPNTHTCPKCKKFAKSESDIERLFGYRR
                     ISAEKMVIQSWCKECRGAPKKPQSPKEGSPDLP"
                     /name="helix-turn-helix domain-containing protein"
     gene            2765..3298
                     /locus_tag="HUZ71_RS23260"
                     /old_locus_tag="HUZ71_23080"
     CDS             2765..3298
                     /locus_tag="HUZ71_RS23260"
                     /old_locus_tag="HUZ71_23080"
                     /inference="COORDINATES: protein motif:HMM:NF025323.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system YafO family toxin"
                     /protein_id="WP_072775495.1"
                     /translation="MPPHLPRIIVHIHDDLSRLPGVESVAREFETYKSYAFQIATDSEC
                     DVSNFLPTLDEEDQKAFRPDHPFFGRDRLFYGQRIRAANDPVFHVHLHHQETIKSWYDF
                     DKADVFVSQWDCVSDAALVYAYLKTESDDYHFLLLEIVAPGAHDLYQTEGKIAEWRHKT
                     RNFRYSSQNPSLRT"
                     /name="type II toxin-antitoxin system YafO family toxin"
     gene            3582..4415
                     /locus_tag="HUZ71_RS23265"
                     /old_locus_tag="HUZ71_23085"
     CDS             3582..4415
                     /locus_tag="HUZ71_RS23265"
                     /old_locus_tag="HUZ71_23085"
                     /inference="COORDINATES: protein motif:HMM:NF027299.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_072775497.1"
                     /translation="MILLAGKKMKTNYFTHRLFPSDGAVICEPLKTSFDNMIATNRNTA
                     TLANEYHVIQHVSGDVYTFIKTNSRDVFRKLDTSSNICVDLSNILNQHEKIAFASFFIL
                     KGDVIGFSNTLYSPRVGKLAEIYDAAMYSRNGNHNINFEPITNIVTEQDVMNYAHVGKI
                     TMKIEKSQGIIGGLGTLFSGNVKYDDVDSFEIKIIPKRAKDIKDTFAGLMQARPQEVSS
                     VAVSAKEHIGDVATDLNVIMSNTVYDFVNPNDTTTIEVQMEKNYNNNTTLRSLGY"
                     /name="hypothetical protein"
     gene            4426..4863
                     /locus_tag="HUZ71_RS23270"
                     /old_locus_tag="HUZ71_23090"
     CDS             4426..4863
                     /locus_tag="HUZ71_RS23270"
                     /old_locus_tag="HUZ71_23090"
                     /inference="COORDINATES: protein motif:HMM:NF027298.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046597188.1"
                     /translation="MKLKGFWLSAIVIAACNGMGFLFLYLSKTYFFPMVTFKDNLGNLG
                     SSLVTYSTAMMALLIAMVVIIFGLDGPRLHNFKKSGYLHVTYFIYMITFFELGLTMALS
                     LLCLSNISSIKVASYSLTFAFITFLLIGCLGIQLLNIKKNL"
                     /name="hypothetical protein"
     Typing          662..875
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="89.45"
                     /coverage="100.0"
                     /evalue="1.22e-70"
     Typing          complement(200..686)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.081"
                     /coverage="93.0"
                     /evalue="5.84e-177"
ORIGIN
        1 ttgctctgta aacaaaaaaa ccaccgctac caacggtggt ttgtttgccg gaagtgagag
       61 ctaccaactc tttctcccga aggtaactgg ctttcacgga gcgcagatac caaaactgtc
      121 cttttagtgt agccgtagtc aggccaccac ttcaagaact ccatagaaat actctactac
      181 tctgctccgt gaatcctctt accaatggct gctgccaatg gcgcgttgtc gtgtctttcc
      241 gggttggact caagaagaca gttaccggaa aggcgcagta gtcggactga acggggggtt
      301 cgtgcataca gtccagcttg gagcgaactg cctacccgga actgagtgtc aggcgtggaa
      361 tgagataaac gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaacagga
      421 gagcgcacga gggagctacc agggggaaac gcctgggatc tttatagtcc tgtcgggttt
      481 cgccgccact gatttgagcg tcagattttg tgatgcttgt caggggggcg gagcctatgg
      541 aaaaacggca gcgccgtatc ctttttccgg cctttcctga cttgagagcc atctttttat
      601 cttgtcattc gtgagcaggt aacgcccgcc gcagtctcac ggcaggagcg tagcgaccga
      661 gtgagcgagg aggcgtcatg tcaccgttac ctgcattttg cacttacgtc ctatagccgc
      721 attttccctt gcaacatgaa taacttccct gaattaccac tccgacctaa catattcagc
      781 ctgtatacac tccgctagcg ctacgtgact ggttcagggc tgcccccgaa acccgctaac
      841 aacctctcag ctactggata tcaccccatg ccatctgaat atgatgaaca actggattcg
      901 actgatacgc agcttcccgg cgaatatgac ctttttgatt taatggcgca ggttactgaa
      961 gagaacctgc atgcccctgt ggattttggg tcgcctgtcg gccgggaagc gttatagctt
     1021 tttcgcttgc ccgcgtacgt ggtaatactc cggtattacc ttttatttct ttattttcat
     1081 gtaattacag tggattttta atacccgggt attactcgtg aaaacgaaat attccttttt
     1141 tttcttttaa ttcatgcagt tgcgatgaaa atcgcggctg cgttaggtgt atgaccattt
     1201 tgaggttgaa aaataatcaa ccatggcggg tgatttacgc aggttaaggg gagatcgtga
     1261 caaaaaagcg ttcctcactg tatcgttcat gcctgcatga acgggttatt cttcctgact
     1321 acagaattac atcaaaagta catcaaaatt acatcacttt tacatcactt atacatcact
     1381 tttacatcac ttttacatca ttccttcagc tcatacgtca ctttcatcct ctgtgccatt
     1441 tgtacatcac ccccttcctg aacgtgctga cagcgggttt tccggctgcg ccggcaacgc
     1501 ttcacggcca cgcaataaat tgcgtccccg ttcaccgttt tcggatggga agaacgccgg
     1561 aaacaggact taccccggct gaatggtgtg aatttccgcg ctatgcactt gtgcgcatac
     1621 tcatgcatgc cgtaaaaaca gagcctgcgc gtttctggcg ggttttcggg tggtttgttg
     1681 cctgttttac cggtttcccg tcagaaacgc gctgagggcc tctgcggcgg tgcacgcaac
     1741 agatgttatg gtaaatcagg cgagccttct ttgggacttt gcggtttttt tggagcacct
     1801 ctgcattctt tacaccagct ttgtatgacc atcttttctg ccgaaatcct tcggtaacca
     1861 aataatcgtt cgatgtcaga ttcggatttt gcaaattttt tacattttgg acatgtatgt
     1921 gtgtttggag gagggctcat tgttggtagc tgtatgttga taagcttgag cattaatgga
     1981 gaaatatcat acacattact catccctaca tcggttttcc cagttgaacg tactcttttt
     2041 cttatcagct ccttatcttc gagcctttgt atggttctct gaatggtacg ccggtcttgg
     2101 ttcattcttt ctgctagaga atctattgat gggaatattt ttgcagaagc actatgcata
     2161 aatgatatca aatggataag gagaactaac tctgagttac tgatacccaa gtgagattga
     2221 ttttttagca gttcgttggg gacggttgtc catcctgaac caaggattgt cctcccccat
     2281 atggatagta aggcttcagg gaaatcagtc ttttctttct ctttagttgt actcatagcg
     2341 gttacttttt tgaatcattt atcatgacat aactactctt acatacacta tatcatagtg
     2401 tatgtaagag tagttattat tagggtggcg ttaacgccac cctaatttta ccttaaaggc
     2461 acgccttttc gtgacatgtc acgacgcttg ctcttaacat tattcgaaga ggaatagttt
     2521 gctattccta ctacgtcatt aagcgaggta ttcacatgtc tgggatgaga aaagcatcgg
     2581 aacatcgttc tccgataaaa cccgccatga gttacgctct gttccaagat tttatcaatg
     2641 cggggctggc agctcagaag agcgatgagg ctaagtctgc tgttaaaaat catcggatta
     2701 ccaatcagaa ctgatatttg tctgtgatat cattcgtact cctattttgc tcgggagtac
     2761 gtggatgccg ccgcaccttc ctcgaatcat tgttcatatt catgatgact tatctaggct
     2821 acctggagtt gagtccgtgg ctagggaatt tgaaacatat aaatcctatg cgtttcagat
     2881 agcgacagat agtgaatgtg atgtttcgaa cttccttcct acattggatg aagaagatca
     2941 aaaggcattt cgtcccgacc acccgttttt tggtcgagat cgtcttttct atggccaaag
     3001 gataagggca gcaaacgatc ctgtctttca cgttcacttg catcaccaag aaactattaa
     3061 atcttggtat gattttgata aagcagatgt ttttgttagt cagtgggatt gtgtaagtga
     3121 cgctgcattg gtctatgcat atttgaaaac agaaagtgat gattaccact ttttgttgtt
     3181 agagatcgtg gctccagggg ctcatgacct ttatcaaaca gaaggtaaaa ttgcagagtg
     3241 gagacataaa actagaaatt tccgctatag cagccagaat ccttctctga gaacttgaat
     3301 ccaattaaag cacaaaggcc cgtaaatacg ggcctttgtg ctttcacgct tcccgaaggg
     3361 aaaacggcgg gacaggtatt tggtaagcgg cagggtcgga acaagaatgc gctcgggggg
     3421 agctaccttc cgataacgga tgttatggta aatagagttg gtggcctagc tttacgacct
     3481 tcggtgacag atcatttaat atgcaaaact tggaatttta aagaagcatt gttcttccat
     3541 aagaaataga atataaaaag aagaaaatat aatgcgtttc tatgatttta ctagctggga
     3601 aaaaaatgaa aacaaattac ttcacacaca gattgtttcc ttcagatggc gctgttattt
     3661 gtgagccatt aaaaactagt tttgataata tgatcgctac taacagaaac actgcaacgc
     3721 tagccaatga gtatcatgta attcagcatg tgtctggcga tgtatatacg tttataaaaa
     3781 caaatagcag agacgttttt agaaaactag atacgagtag taatatatgt gtagatctct
     3841 caaacatctt aaatcaacat gaaaaaatag cctttgcatc ttttttcata ttgaagggtg
     3901 atgttatagg gtttagtaat acgttgtact ctcctcgtgt tgggaagttg gcagaaatat
     3961 atgatgctgc aatgtattcc cgaaatggga accacaacat aaattttgag ccgataacaa
     4021 acatagttac cgagcaagat gttatgaatt atgcccatgt tggtaaaata acgatgaaaa
     4081 tagagaagtc tcaaggcatt attggtgggc ttggtacgct tttctctggg aacgtaaagt
     4141 atgacgatgt ggattcgttt gagataaaga taatccctaa acgggctaaa gacataaagg
     4201 atacctttgc aggtttgatg caggctaggc ctcaagaggt tagctcggtc gctgtgtcag
     4261 ctaaagaaca cattggtgac gttgcaacag atttgaatgt tataatgtct aataccgtat
     4321 atgattttgt aaatccaaat gacactacta ctatcgaggt tcagatggaa aaaaattata
     4381 ataacaatac aacattaaga agtttaggtt actgaggatt gcattgtgaa gcttaagggt
     4441 ttttggttga gcgctatagt tatagctgca tgtaatggca tgggcttttt atttctatac
     4501 ctttcaaaaa cctatttctt cccgatggta acgtttaagg ataatttagg taaccttggt
     4561 tcttccttgg ttacttattc gacagcgatg atggcgttgc ttattgctat ggttgttata
     4621 atctttggct tggatggacc tcgcttgcat aactttaaaa aaagcggcta tctccatgtt
     4681 acatatttta tttatatgat aacgtttttc gagctcggct taaccatggc tctttcgtta
     4741 ctttgtttgt ccaatatctc aagtattaag gtggcttctt attcattgac ttttgcattt
     4801 attacttttt tgttgatagg atgtttaggt attcaactct taaatataaa aaagaatctt
     4861 taatcaacca aactgtgatg ttcatcacag gtgaaacggt ttgtgaccat ttttggtgag
     4921 ttgataaaat gcagaatgtg taaggatcgt cttgagattt ttgagagtgc agcgtagtct
     4981 c
//
