LOCUS       NZ_CP055203             5242 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_3 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055203
VERSION     NZ_CP055203.1
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 5242)
  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 5242)
  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
            CP055203.1.
            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..5242
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_3"
                     /isolation_source="Shatin WWTPs_3 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            complement(35..1585)
                     /locus_tag="HUZ39_RS25890"
                     /old_locus_tag="HUZ39_25720"
     CDS             complement(35..1585)
                     /locus_tag="HUZ39_RS25890"
                     /old_locus_tag="HUZ39_25720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_009440809.1"
                     /translation="MASYHCTVKTGAKGSALKHADYISRTGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGDLDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALRIQRSWAREASRSNERDQGMER"
                     /name="MobA/MobL family protein"
     gene            1757..2203
                     /locus_tag="HUZ39_RS25895"
                     /old_locus_tag="HUZ39_25725"
     CDS             1757..2203
                     /locus_tag="HUZ39_RS25895"
                     /old_locus_tag="HUZ39_25725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_089567277.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPRNHPKWQEWEKRGKELLAKNSA"
                     /name="conjugal transfer protein TraD"
     gene            complement(2464..3483)
                     /locus_tag="HUZ39_RS25900"
                     /old_locus_tag="HUZ39_25730"
     CDS             complement(2464..3483)
                     /locus_tag="HUZ39_RS25900"
                     /old_locus_tag="HUZ39_25730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            4010..5098
                     /locus_tag="HUZ39_RS25905"
                     /old_locus_tag="HUZ39_25735"
     CDS             4010..5098
                     /locus_tag="HUZ39_RS25905"
                     /old_locus_tag="HUZ39_25735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001340328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_059331889.1"
                     /translation="MNMNIKYILPLVSSFIISGCDSDGISKVKSSIDYSIDDSMTIGKA
                     FDTRSDCINGTWSEEEDSRGRTVVTYTCDISETGMKIINSEIIKGPESSLTGSIKNNNM
                     EIDNINKSIEMYKQQASLIEQTRKLMIEHVRKLENAFNEDPKISNNINIEPYLNKMLNI
                     ECHQRNEGYSCTTDEECRPYMNGLFSPNVSYDYLEESCQKHILPVYQSYIKNVLPLKSK
                     IKAISFTGMFNYCGRSSEECIKLIDDKFNGFSSYNQKQTQKISFYEDLNTRKNKTLNEC
                     KKILNISDVKLKYYWRVTDTGGVDYLSGELTYRINGENKSVAYNNNLVKYAYVNYTEKQ
                     IPSDYVNSILNQNYETIKNCSY"
                     /name="hypothetical protein"
     Typing          complement(2709..3483)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(39..1585)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggcggggt tcggggcgca gtcccgatat tgcttcaacg ctccatacct tgatcacgtt
       61 cgttactacg tgatgcctcc ctggcccagg atcgctgtat acgcagtgcc ttttcctcct
      121 gttgctgccg ttcctgcgcc atttctgcca gtaactcatg tcgcatttga gctttttcat
      181 ctccagatat actgagttca ggctccagag ataacatctg gctacgggca acggatactt
      241 cttcagcaac cttttgcctg gtattctcta aagatgccgc ggccagaatc tcacgttctc
      301 tgtacctgtc cagatcccca acgtacttat atccctcggt acgcttaaaa gcagcgtttt
      361 ctttgtccca ctcggattca gcttgctgta gcttgttcct gaattcattc ctttcatgtt
      421 cagcggtttc cagcacactt ttttgctcca gaatacgcgc atcaatctcc cttttgtcag
      481 ccccccgaaa caggccacga atcccattca aagcattgcg ttgttcctgt agctcccgca
      541 gctccctttg tgcggaaacg acattacgcc ccagtttgtc taaataccgt gctccttcat
      601 atattcgtct gctccattcg gaaagagagt cttttttagc tttcgcattc tgaagcagct
      661 tatgttcttt gagcgcattg ggattggcat cccctaaacg agcaagcctt gcctctccct
      721 gaatgaccgt tttcataacc ttgcggtact gaagcaatag ctccggtgaa cgggctgaac
      781 gaacaggctc aactgccttg attttttgct tttgctcctg ttcctgctga atggcatttg
      841 cggcatctct ggcggtcttg agttcccgct cggcattcct ccgttcctgg attgcaacaa
      901 tctgctcacc attcagactg gcggcctgaa cggggccaag atgaacttct ggcgtgcgat
      961 tgataccctg ttctttcagc gaacgatgat ctacgcgcga ctcgtgaccg tgtcgcgcaa
     1021 ggtgctcatt ctgcacatca gcccagcggg aacgcagcgc aacaagggcg gcttttcgct
     1081 ctccggcggt ctggggaata ctcgcttttt ttgcgcctcc ccgctctggt gatttgctgt
     1141 tggcacgttt aaaaaattgc tgcggatcgc gttcaatacc atcattaatc cgctcacaaa
     1201 acatgatatg cgcgtgtggc tgttcctttc cgtcgattgc acctggcgga ttgtggatcg
     1261 cgtactggta ggcatggcga tcaccaagtt ccttttgcac gaaatcttca acaagttcta
     1321 tccgttgttc gcgtgtcaac tcacgcggta atgcgatctc aatttcacgg tatgccgtcc
     1381 cgttttttcg ttcaaattca tctgcggctt tccatagctc tgcgggattt ttcttcgccc
     1441 atgatggcat gttaccagat gacgaaaatt ccagatcctc ccgcgatttg tagctcttat
     1501 attcgccggt tctggaaatg taatcagcat gttttaaggc actgcctttt gctccagttt
     1561 tgacggtgca atggtagctt gccatcagcc ttttagccct ccgcaggagc gcacagtttc
     1621 tcgatgaagt agagaaacta ctaagtgcgc atccctgaat taatcaggga tgattttacg
     1681 gtctcacacg caggcagaca aggtgatatt atgcacaata acaactcaca ttaacggcaa
     1741 aagtgcagag gtaagaatga caaatcgtga agagtggtta agtgcaaaaa ttgcctacat
     1801 caacggactg aaatcaccgt cagagcagca gagattactt gtgttactgg cagagaaaaa
     1861 aaaccgaaca acgacggatg aaaaaacgtt gtccgcactg atacgggcag aaaaaaccgc
     1921 agagaaagca gccgcagcaa aagccagggt aacggcaatc atagcggcag aacggaaggc
     1981 agccgcaagg gcagaacgaa aggcgcggga tcatgaactt tacaaggccg caggcctcat
     2041 gattgtggca ggactggtgg acagcaaaac cggaaaacca aagtttagtg ctgccgaact
     2101 ggtaggcgca ctcgcaggaa tcgcagagct accgcgcaac catcccaaat ggcaggaatg
     2161 ggaaaaacgc gggaaagagc tactcgccaa aaacagtgcg taagagcctc cgttcacatt
     2221 ccggttccct ggtgcttcct cgctcattcg ctcgctacgc tcggtcatga gactgcggcg
     2281 agcacgacca cctcaatcat gcggtaagcc gcaccattgc tgggctgaga ggagaaaacc
     2341 gccggaaagc ccgctgctca aaaagacgcc gaaaggcgct gttatctgat ataggcttgt
     2401 tcatgtccgc gaatttaacc aaccattaac aaaaaacggg gggtggtgtt gcttctttgt
     2461 taactaacat ttaattattt gtttcttggt tagccattct ccagaattat ccatccagcg
     2521 tcgaatagtc cggctgctaa caccaaccgc cactgcaata tcttccgttg acgctcccaa
     2581 gatatacata tcaagcgccc tacgacgttt gtcgtcgtta gcagtccacc gaacagcggc
     2641 gctttttttc cctttgtccg actgattttc tgacgaattg gccttcccgc ccttgcgacc
     2701 gcgtgctgcc tgaatttctg gcgtgtgcgt atcagccaca tactgtgcga aagtttccgg
     2761 cgtgaagttc ctgtgcgtgt atttcgcaat gctcttgcca atagcccgac attcagccag
     2821 tgaaagcgga acgggaagcg atgcattgta catttcgaca cgctggatca ccgcttcaag
     2881 ccactgtgag aacgctggcc agccctgacg aatcgccctg taagcccatt tgcgcgtcat
     2941 ttcgaacagg tggcagtttc gccccatccc gtaatgttta tcgatgctac gacgctctga
     3001 ggcgctcaaa tcgagataat ctgccagttc atcgagggta taggcgtcct cgcgccactc
     3061 catcacctgc cattccaggt ggaacggatt tttgcaaatc aggccgctgt agttcacatc
     3121 agcacaaagt ttctcacaca gcgaacgttc aaccgctgcg gcatatttca gcgccttaac
     3181 cgaggcatca ggcgcggttc tcacggcgat gttgagtgcg tagagcaggt gagcgtgtcc
     3241 gttcacagga tttttaacgg tgatgttcgg cgcgggggcg ttccggtcgc tccagtcaat
     3301 cgcagccccc tcgcggtcaa cgtcaaaaac cagccagaac tgcgcatgag gctggttctg
     3361 ctggatgtac cgcgcaagaa gcgcacgccc tttgccggag atgcgaaggc cgaaagcgag
     3421 atcatccgtg tgataggggc ggtggggtaa attttcttcg aagtattgaa gcgcggcgct
     3481 catgtgttac gattccttcc aggttatcga ccgacctcgc ccctgtattc tcgtgacaat
     3541 cttggcggag agacacgaat ttcaggggcg tttgtttttc agtcgcttac actaccccca
     3601 acaacaaaac ctgtcgagcc ttcccgcaaa accgatccat ttaccataac tcccgttgta
     3661 cgtaccccgt aaaacgccct caatcgctct ctgacgcaaa aaacgcaaaa agacaaggaa
     3721 acaccagggt aaaacagaaa aatgcgtcag aattgttttc attggcctgc ataactatgc
     3781 acgaaagcga tgcgcgatcg gtttcgaccg cacaaagctg cgaacgggtc aaaaagacaa
     3841 actttctcat ccagagaacg gtaaacgggc gcgaaatctt ttcgagctca atgaggcgct
     3901 gagcaccaaa tagtaagtcg gtttatacgg tatgcatgga ttccattaac atattgtttg
     3961 tattaacata tttacgttcg ttattgtcaa ataagtcaaa agtgaaaaga tgaatatgaa
     4021 catcaaatac attcttccat tagtatcttc atttattatt tcagggtgtg actctgatgg
     4081 gataagcaaa gtaaaatctt ccatagatta ttccattgac gactcaatga ctattggcaa
     4141 ggcttttgat acaaggagtg attgtattaa tggaacatgg agtgaagaag aggatagtcg
     4201 aggaagaact gttgttacat atacttgtga catcagtgaa accggcatga aaataataaa
     4261 ctcagaaata ataaaaggcc ctgagagcag cctgacaggc tctataaaaa ataacaatat
     4321 ggaaatagac aacatcaata aatcaataga gatgtacaaa cagcaagcat cattaattga
     4381 gcaaacaaga aaactcatga tcgaacacgt aaggaagtta gaaaacgcct tcaatgaaga
     4441 tcccaaaata tctaacaata ttaatattga accttacctc aataaaatgc taaacataga
     4501 atgtcatcag agaaatgaag gctatagctg cacaacagat gaagagtgca ggccatatat
     4561 gaacggcttg ttttcaccaa atgtatcata tgattactta gaagaatcat gtcaaaaaca
     4621 catattacca gtataccaat catatataaa aaatgtatta cccctaaaat ctaaaattaa
     4681 agcaataagt tttacaggta tgtttaacta ttgtgggaga agctctgagg aatgcataaa
     4741 attaatagac gataaattta atggattttc atcttacaat caaaaacaaa ctcaaaaaat
     4801 atcattctac gaagatctaa acacaagaaa aaacaaaaca ttaaatgaat gcaagaagat
     4861 attaaatatc tcggatgtta aactaaaata ttactggcgc gtaacagaca ccggaggtgt
     4921 tgactatctg agtggggagc taacatacag aattaacggg gaaaacaaat ccgtagcata
     4981 caataacaac ctagtaaaat atgcatatgt taactacaca gaaaaacaaa taccatcaga
     5041 ttatgtgaat tcaatactta accaaaacta tgagacaata aagaactgca gctattaata
     5101 ccacatctca cttactggct gtttcacata taacgcttgt taatttcatt aacacctgaa
     5161 cagtgagtga atcaaaacga taaattttct cattcagaaa acgcttcacg ggacacggaa
     5221 ttttttcgcg tcccgtgaag cg
//
