LOCUS       NZ_CP055205             3877 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP055205
VERSION     NZ_CP055205.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925527
            Assembly: GCF_022354345.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3877)
  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 3877)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-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_022354345.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:11
            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)                     :: 5,236
            CDSs (total)                      :: 5,112
            Genes (coding)                    :: 4,860
            CDSs (with protein)               :: 4,860
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 252
            CDSs (without protein)            :: 252
            Pseudo Genes (ambiguous residues) :: 0 of 252
            Pseudo Genes (frameshifted)       :: 84 of 252
            Pseudo Genes (incomplete)         :: 172 of 252
            Pseudo Genes (internal stop)      :: 54 of 252
            Pseudo Genes (multiple problems)  :: 51 of 252
            Pseudo Genes (short protein)      :: 2 of 252
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055205.1.
            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..3877
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed6"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(3691..3877,1..143)
                     /locus_tag="HUZ39_RS25950"
                     /old_locus_tag="HUZ39_25785"
     CDS             join(3691..3877,1..143)
                     /locus_tag="HUZ39_RS25950"
                     /old_locus_tag="HUZ39_25785"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_094322851.1"
                     /translation="MEKRTKEIKIRLTDDEHQRLLERSQRTHLAEWLRELGLGERTPSK
                     RRKLPDVDPQLFRQIAGTSNNLNQIARKLNQMESLVAEDKIRLLSLLTSIDRQLTEILE
                     QHRDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            133..1656
                     /locus_tag="HUZ39_RS25955"
     CDS             133..1656
                     /locus_tag="HUZ39_RS25955"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_239637988.1"
                     /translation="MIVKFNSRGAGAGSGPVDYLLGKERNREQAKTLRGDPERVKTLID
                     TCDFARTYTSGVLSFEEKDLPDVDKQQLMDELEQTLLPGLDKDQYSILWVEHQDKGRLE
                     LNFVIPNIELHSGKRLQPYYDRADRPRVNAWQTLTNDRLGLSDPNDPERRRELTPGRDL
                     PKNSQKAAESITAGLSHLAMQGLVRNRQDVINVLESAGMTIARETKSSISIASPDGGKN
                     LRLKGALYERDFRFSESLRGELEAAGATYRDARESRISEAERCYQRGIELKREEYQQRY
                     PRRDPTTPTALENHLPAGNEMAVDWPVIHRPDLRRTDRGNLLVSEPATRGNTDQRTESS
                     RAEFQNGQGDRGTERDRQIPRSVLHHPAEARQQHTDLPLPETNGSELQRQITQERSPEP
                     LSDDLTHSGKESHDRDRKTLVERIRELTTRLKDTAASLTRQFQEFTGHVRENTARESSL
                     SQSLHEAEPASRGLEQASKRLEQHSESLSQTVAAKELSQLKENDRGMSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            1865..2770
                     /locus_tag="HUZ39_RS25960"
                     /old_locus_tag="HUZ39_25805"
     CDS             1865..2770
                     /locus_tag="HUZ39_RS25960"
                     /old_locus_tag="HUZ39_25805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019725130.1"
                     /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_094322853.1"
                     /translation="MSNVALKLFNDRLPHKPYFTDELQCGLRIAGKERAILAKYIQFNQ
                     PHAQYWLCFDVDRPGAAIDWSDRNAPAPTLTIMNKANGHAHLLYALKTAVRTAPDGKMK
                     PLKYAAAVESALREKLGADVGYSGLICKNPNHENWQIAVWQPELYTLDWLADSLDLNSA
                     NEKTILPDYGLGRNCTLFDKTRKWAYRAIRQGWPEYEQWLKACYERASAYNLQFISPLD
                     EKEVNGIAKSIANWTYKKFSKVKFEIYVSYTHSSEIQSRRGIASGIKRYIGSLEEQKPW
                     DKLGISRRTYFYKRKKGILK"
                     /name="replication initiation protein"
     gene            2767..3450
                     /locus_tag="HUZ39_RS25965"
                     /old_locus_tag="HUZ39_25810"
     CDS             2767..3450
                     /locus_tag="HUZ39_RS25965"
                     /old_locus_tag="HUZ39_25810"
                     /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_094322852.1"
                     /translation="MKKILPFIFMLASCGHYVDGYDGYTKAQLERMDQDIIRYYNKTPV
                     NDGTVFGYNFTKLSNRQYLNQSGFINVISDHKSVDVYEKKNISDGILKTSMIVIKNNKP
                     ITLYVAFETLNKGDIPDSFIDAINNLIANNYGVEPIVGTKIKLMTKSDYKYKYIKNRPS
                     KSDYINYKSGISNIIESISYSYDKSKSRYDFNKVVYRIDFVGFAMQQQKYLSAQERSRV
                     DFIGS"
                     /name="hypothetical protein"
ORIGIN
        1 cgagtaacaa ccttaaccag atagctcgta aacttaatca gatggagagt ctggtcgctg
       61 aggacaaaat ccggttactg agcttactca cgagtatcga tcgccagtta actgagatac
      121 tggagcagca tcgtgatcgt taaatttaat tcccgtggtg cgggtgctgg cagtggtccc
      181 gtggattatc ttctcggcaa agaacgtaat cgtgaacagg ccaaaacctt acggggtgat
      241 cccgaacggg taaaaaccct gatagacacc tgcgatttcg ctcgaaccta tacgtctggt
      301 gtcctctcgt ttgaagagaa agatctccct gacgtagaca aacagcagct gatggacgaa
      361 cttgagcaaa cgctactccc tggacttgat aaagaccaat acagcatcct ttgggttgag
      421 catcaggaca aaggccggtt agagcttaat tttgtcatcc cgaacatcga attacacagc
      481 ggtaaacgtc tacaacccta ttacgaccgt gccgaccgcc ctcgggtcaa tgcatggcaa
      541 acgctgacca atgaccgact cggattaagt gaccccaacg acccagaacg ccggcgtgaa
      601 ctcaccccgg gcagagactt gccgaaaaac agccaaaaag cggcggagtc cattacggca
      661 ggactctctc acctcgccat gcaagggctt gttcgtaacc gtcaggatgt catcaacgtc
      721 ctagaatctg ccggcatgac cattgcccga gaaaccaaat ccagcatcag catcgcctca
      781 ccggacggcg gtaaaaacct cagactcaaa ggagcactct atgagcggga tttccgattt
      841 agcgaaagcc ttcgaggaga actcgaagca gcaggcgcaa cataccgaga cgcacgtgaa
      901 agccgaattt cagaagctga acgctgctat cagcgaggaa ttgaactcaa gcgtgaagag
      961 tatcaacagc gctatccaag acgcgaccca acaacaccaa cagcacttga aaaccattta
     1021 ccggccggta atgaaatggc tgtggattgg cctgttattc atcgccctga tttgcgccgc
     1081 actgatcggg ggaacctact ggtatctgaa ccagcaactc gaggaaatac agaccaacga
     1141 acagagtcta gccgtgctga attccaaaac gggcaagggg atcgtggtac agaaagggac
     1201 aggcaaatac caaggtcagt actacatcat cctgccgaag cgcgccagca acatacagac
     1261 ttacccctac cagaaacaaa cggtagtgaa ttacagcgtc aaataaccca agagcgctca
     1321 ccagagcctc tcagcgacga tttaacccac tcaggcaaag aatcccatga ccgagacaga
     1381 aaaactcttg ttgagcgcat tagagagctt acaacacgac tcaaagacac agcagcaagc
     1441 cttactcgac agtttcagga gtttacaggc catgtacgag aaaacacggc aagagaatca
     1501 agccttagcc aatcactgca cgaggctgaa ccagcaagtc gagggcttga gcaagcaagt
     1561 aaacgacttg agcaacacag tgaatcgctt agccagactg tagccgccaa agagctgagc
     1621 cagcttaaag aaaatgaccg agggatgagc ctgtaatttg ttggtatacg gagaaattat
     1681 tcgaggaact cgacagaaac tgtcatttgc gtgtaacttt aatgccatta gaaaagacaa
     1741 cgccccgaat tcatatctca acttggcgga agggaatatg aaatcagggc gcaggtaaaa
     1801 acctaagaag gatattagca catgagacgt gcaacacaac agcccgccat aagcgcaggg
     1861 ctcattgagt aacgtagcac tcaaactttt taacgacaga ttgccccaca aaccgtactt
     1921 cacggacgaa ctgcaatgcg gtttacgtat cgcaggaaaa gagcgggcaa tccttgccaa
     1981 atatatccag tttaaccaac ctcacgctca atactggctc tgctttgacg tagacagacc
     2041 gggcgctgcc attgattgga gcgaccgtaa cgctcctgcg cccacactca ctatcatgaa
     2101 caaagccaat ggccatgcac acctacttta cgccctaaaa acagcggtac gcacggcacc
     2161 agatggaaaa atgaaaccac tcaaatatgc agcggcggtt gagagtgcgc tgcgtgaaaa
     2221 attaggcgct gacgtggggt attcggggtt aatttgcaag aatccaaacc acgaaaactg
     2281 gcaaatcgct gtttggcagc cagaactgta taccctcgac tggcttgcag actcacttga
     2341 tctgaactca gccaacgaaa aaactatcct ccccgattat ggcttaggcc gtaactgcac
     2401 actgttcgat aaaacgagaa agtgggctta ccgcgctatc cgtcaaggtt ggcctgagta
     2461 tgagcagtgg ctaaaagcct gttatgaaag agctagtgct tataatctgc aatttatatc
     2521 accactggat gaaaaagagg ttaatggaat tgctaaaagt attgcgaatt ggacttacaa
     2581 aaaatttagt aaagttaaat tcgaaattta tgtgagttat actcattctt cagaaattca
     2641 atctcgccga ggtattgctt ccggaattaa aaggtatatc ggtagtttag aagaacaaaa
     2701 accatgggat aagttaggaa ttagcaggag aacttatttc tataaaagga aaaaaggaat
     2761 attaaaatga aaaaaatact accttttata tttatgctcg catcttgcgg acattatgtt
     2821 gatggatatg acggatatac taaggctcag ctagagcgga tggatcaaga tatcattaga
     2881 tattacaata aaaccccagt gaatgatggg actgtttttg gttataattt caccaagtta
     2941 tctaacaggc aatatttgaa tcagtctggt tttataaatg tcatttccga ccataagtca
     3001 gtagatgttt acgagaaaaa aaatattagt gatggcattt tgaaaacatc catgatcgta
     3061 attaaaaata ataaaccaat tactctctac gtggcttttg aaactttaaa taaaggagat
     3121 atccctgata gttttattga tgctattaat aatctaatag ctaataatta tggtgtagaa
     3181 ccaattgtcg gaaccaaaat taaattaatg acaaaaagtg attacaaata taaatatatc
     3241 aaaaataggc catcgaagtc tgattatata aattataaat cagggataag taacattata
     3301 gaatccatct catatagcta tgataaatca aaatccaggt atgattttaa caaagtcgta
     3361 tatcgcattg attttgtcgg ttttgctatg caacaacaga agtacttgtc tgcacaggaa
     3421 aggtccagag tcgatttcat cggtagctag acttctattc tttttgcact cgaacctata
     3481 tcagataaca gcccctttat ggggcttttt tatttttccg tgacttgata ttttaagtag
     3541 ataaatatac ttataagcca gtacacacgg agtcccctct aacgagggtt caccgtgact
     3601 ggttcagggg gctcgccgcc ccccgaaacc ccgggcatcc actgcgaaac tttcgcactt
     3661 ggcgtgcaaa actttctcag cggagtcggt atggaaaagc gcaccaaaga aatcaaaatc
     3721 aggctcaccg atgatgaaca tcaacgactt cttgagcgga gtcagagaac ccatctagcg
     3781 gagtggttac gtgaacttgg attaggtgaa cggacaccct caaagcgtcg taaattaccg
     3841 gatgttgatc cgcagttatt ccgacagata gccggca
//
