LOCUS       NZ_CP055002             3788 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain STIN_80 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP055002
VERSION     NZ_CP055002.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925543
            Assembly: GCF_022353785.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3788)
  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 3788)
  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_022353785.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 04:47:53
            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)                     :: 4,894
            CDSs (total)                      :: 4,773
            Genes (coding)                    :: 4,464
            CDSs (with protein)               :: 4,464
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 309
            CDSs (without protein)            :: 309
            Pseudo Genes (ambiguous residues) :: 0 of 309
            Pseudo Genes (frameshifted)       :: 90 of 309
            Pseudo Genes (incomplete)         :: 217 of 309
            Pseudo Genes (internal stop)      :: 56 of 309
            Pseudo Genes (multiple problems)  :: 52 of 309
            Pseudo Genes (short protein)      :: 5 of 309
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055002.1.
            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..3788
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STIN_80"
                     /isolation_source="Shatin WWTPs_80 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed2"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.4 N 114.2 E"
                     /collection_date="2018-12"
     gene            702..1220
                     /locus_tag="HUZ55_RS24305"
                     /old_locus_tag="HUZ55_24115"
     CDS             702..1220
                     /locus_tag="HUZ55_RS24305"
                     /old_locus_tag="HUZ55_24115"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162676513.1"
                     /translation="MSEKAKKVGRRSLSKRRERLIKELWGDELSELNIWNRKEHDGFTT
                     IPRTLNYINRIIDYLAGAGSPVSQTYLSLWCRVFDEGFVEIRDKDALAFESGFSGQRAV
                     TTWLGRMKKLRELGLISTKPGTSGEFHYVIMLNPLYVIKKSYESNGWKRDERYNALFSR
                     MQEVGAEWE"
                     /name="hypothetical protein"
     gene            1217..1780
                     /locus_tag="HUZ55_RS24310"
                     /old_locus_tag="HUZ55_24120"
     CDS             1217..1780
                     /locus_tag="HUZ55_RS24310"
                     /old_locus_tag="HUZ55_24120"
                     /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_000999222.1"
                     /translation="MNDMKAVRHRYKQRYDFAASEVVGAFDELRSLDWSLEIASLSDVE
                     MSKRWIGAVDPNGVARLPPNGGWDWVKLYNGYLKNPSAFVCAIKSEGKLCALIGGGVSD
                     SKVVTKLHYLESAPYDTALSGYALDISVTYVVTVANAMGSEYSAIYEPNSKVREIAIND
                     YGFSEDNLFGTSKDFALYLPMSRI"
                     /name="hypothetical protein"
     gene            complement(1790..1942)
                     /locus_tag="HUZ55_RS24315"
                     /old_locus_tag="HUZ55_24125"
     CDS             complement(1790..1942)
                     /locus_tag="HUZ55_RS24315"
                     /old_locus_tag="HUZ55_24125"
                     /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_001341064.1"
                     /translation="MLAHAVELKKATEPCSSGTAGAFRQRVKARRAEQGRSNQQPEKLY
                     GVLVG"
                     /name="hypothetical protein"
     gene            complement(2238..2384)
                     /locus_tag="HUZ55_RS24320"
     CDS             complement(2238..2384)
                     /locus_tag="HUZ55_RS24320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354639.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_050863271.1"
                     /translation="MHEPPVQSDCCALSGNYHLESNPERHAKAPLAAANGKRMYKRLLT
                     QSS"
                     /name="hypothetical protein"
     gene            2944..3093
                     /locus_tag="HUZ55_RS24325"
                     /old_locus_tag="HUZ55_24130"
     CDS             2944..3093
                     /locus_tag="HUZ55_RS24325"
                     /old_locus_tag="HUZ55_24130"
                     /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_180251257.1"
                     /translation="MPSEHDEQRDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGPPVG
                     REAL"
                     /name="hypothetical protein"
     Typing          2737..2951
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.52"
                     /coverage="100.0"
                     /evalue="3.460000000000001e-56"
     Typing          complement(2276..2773)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="90.258"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 gcctgtttta ccggtttccc gtcagaaacg ccctgagggc ctctcaggcg gtgcacgcaa
       61 gagatgttat ggtaaatggt ttctgaggtg taagcgaaaa ctcgagtttt gacgccattc
      121 tgagtaggta atttgcagac ggaataaata ctggcgagca ataagctcat caacaaaaaa
      181 tggagatcct aagatggata gagaaaccct atacctactc aaaacgttag accataacaa
      241 tgccttgctt gacgatatta tccgaagaaa gatgggtagg tactacaaca cgaagatttt
      301 gcgtgattcc tgtggtgcta ttgaagccga actacgacgt cgaggaatca tttaaaaaga
      361 cgaagcccgc ttatgtgggc tttttcattg cgcattcatg gcaccccttc ctcccccctt
      421 aaacccccta agaaccccat tcagcacagc gagcacaacg attacattag agtacattga
      481 gaacagcgag tacaaaataa cgcataacta attgaaaaat aataccgtaa ccgtaaagaa
      541 tattacatct caatatttgt gttgacaaaa aaaaagaatc atatcaaatg agatgttggt
      601 taatgatgtg cttggttttt gtgttattac acataactca ttgaatataa taggtttttt
      661 gttgataata ttttcatgtt gaattgactt ttgggggata aatgtcagag aaggcaaaaa
      721 aagtaggtag gcgctctcta tcaaaaagaa gagaaagact aataaaagag ctttgggggg
      781 atgagctttc cgaactgaat atatggaaca ggaaagaaca cgatggattt acaacaatcc
      841 caagaacatt gaattatatc aataggataa tcgattacct tgctggcgct ggatctcctg
      901 tgtcacagac atacctcagt ttatggtgtc gagtttttga cgagggattc gtcgaaatta
      961 gggataaaga tgctctggca tttgagtcag ggtttagtgg gcagcgagcg gtgactactt
     1021 ggctaggaag aatgaaaaag ctacgggagc tgggactgat atcaacgaag cctggtactt
     1081 ctggcgagtt tcattatgta atcatgttga atccacttta cgtaattaaa aagtcatatg
     1141 aatcaaatgg atggaaaaga gatgagcgtt acaacgctct attttctagg atgcaggaag
     1201 tgggggcgga gtgggaatga acgacatgaa agctgttcgt caccgatata agcagagata
     1261 tgattttgct gcgtcagaag tagtgggggc gtttgatgaa cttagaagtt tggattggag
     1321 tttagaaatc gcatctttaa gtgacgtgga aatgtcaaag agatggattg gggctgttga
     1381 tcctaacggt gttgcaagat taccacctaa cggtggatgg gactgggtta agctctataa
     1441 cggctatttg aagaacccta gcgcattcgt ctgtgccatt aaatcagaag gcaagctatg
     1501 cgctctgatt ggtggcgggg tttctgatag taaagtggta actaagctgc attaccttga
     1561 atcagcccct tatgacacgg ctctttcagg atatgcactg gatatttctg ttacgtatgt
     1621 tgttactgtc gcgaatgcga tgggaagcga atactcagcc atctatgagc caaatagcaa
     1681 agtcagagag atagctataa atgattatgg atttagcgag gacaacttgt ttgggacaag
     1741 taaagatttc gctctgtatc taccaatgag ccggatttaa ccggctcatt tatcctacca
     1801 gtacgccgta gagtttttct ggctgttggt ttgatcggcc ttgctctgct cgtcttgctt
     1861 ttacgcgctg gcgaaatgct ccggctgtac cagaagagca tggttccgtc gcttttttaa
     1921 gttcgaccgc gtgagctaac atattatttc cgttttttcg tgagttagta caaagcatat
     1981 gagatgacgg atacgtcaac ttcatagtaa ctgtactgta ttgtagaaga gatgcgcaag
     2041 tcgcagaatt aatgcgaccc ttcattgacg aggcgaagag taaacgcgta tcttctttga
     2101 aaacgaaaaa accacccggc aaggtggttt ttcgaaggtt cattaaaccg gcaagtttat
     2161 gaaccgtggt aacagggtgt acaagaccac tgccaccaaa ttcgtccttc cagtttagcc
     2221 gtagttgggc tgatacttca agaactctgc gttagtaatc tcttgtacat cctcttaccg
     2281 ttggctgctg ccagtggcgc ttttgcatgt ctttccgggt tggactcaag atgatagtta
     2341 ccggataagg cgcagcagtc ggactgaacg gggggttcgt gcatacagtc cagcttggag
     2401 cgaactgcct acccggaact gagtgtcagg cgtggaatga gaaaccgcgg ccataacagc
     2461 ggagtgacac cggtaaaccg aaaggcagga acaggagagc gcacgaggga gctaccaggg
     2521 ggaaacgcct gggatcttta tagtcctgtc gggtttcgcc gccactgatt tgagcgtcag
     2581 attttgtgat gcttgtcagg ggggcggagc ctatggaaaa acggcaacgc cgcatccttt
     2641 ttccgctctt cctgatttcc gctaagtctc tttatccagc cattcgtgag ctggcaacgc
     2701 ccgccgcagt ctcacggcag gagcgcagcg accgagtgag cgaggaggcg tcatttcacc
     2761 gggatctgca tttcgcactt acacaccggt gctgcatttc ccggtaccac atgaagcact
     2821 ttcgtaaatt attactgcgt tgtagcattt taagcccgta tacactccgc tagcgctacg
     2881 tgactggttc agggcttcgc cccgaaaccc gctaacaacc tttcagctac tggatatcac
     2941 cccatgccat ctgaacatga tgaacaacgg gattcgactg atacgcagct tcccggcgaa
     3001 tatgaccttt ttgatttaat ggcgcaggtt actgaagaga acctgcacgc cccggtggat
     3061 tttggcccgc ctgtcggcag ggaagcgtta taactttttt cgctggtcag cgtacgtgta
     3121 atacgccggt attacatctt atttctttat tttcatgtga ttacaggtgg ttgtaatacg
     3181 ttgcgtatta cataaataaa cgggaaattc agtttttacc ttttaattca tgcaattgcg
     3241 atgaaaatcg cggttgcgta tggtgtatga ccatttaagg gataaaaaat catctttttt
     3301 ggtagggcgc tctccgtagg ttaaggggta tttggctaaa aagcgtccta ttctttgatg
     3361 gtcatgcaag catgaccatc tgagcaacca aaaactacag ataaactaca aaaaacgttt
     3421 tgcattagtg atggcagact acaaaaaaac tacaaaaacc gtggcggact actaatagac
     3481 tacaagaaaa ctacagataa actacaaagt aactaccgga ttacctcaga tccgttccct
     3541 gaaccattcg tacatcggcc cccttcctga acgtgctgaa aacgggtttt ccggctgtgc
     3601 cggcaacgcc tcacggccac gcaataaatt gcgtccccgt tcaccgtttt cgggtaagaa
     3661 gaacatcgga aacaggactt accccggctg aatggcgtga atttccgcgc tatgcacttg
     3721 cgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt
     3781 ggtttgtt
//
