LOCUS       NZ_CP055028             2845 bp    DNA     circular CON 02-MAY-2024
DEFINITION  Shigella flexneri strain SWHEFF_67 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055028
VERSION     NZ_CP055028.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925590
            Assembly: GCF_022353945.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2845)
  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 2845)
  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_022353945.1-RS_2024_05_02
            Annotation Date                   :: 05/02/2024 05:14:26
            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)                     :: 4,646
            CDSs (total)                      :: 4,527
            Genes (coding)                    :: 4,291
            CDSs (with protein)               :: 4,291
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 236
            CDSs (without protein)            :: 236
            Pseudo Genes (ambiguous residues) :: 0 of 236
            Pseudo Genes (frameshifted)       :: 70 of 236
            Pseudo Genes (incomplete)         :: 148 of 236
            Pseudo Genes (internal stop)      :: 58 of 236
            Pseudo Genes (multiple problems)  :: 35 of 236
            Pseudo Genes (short protein)      :: 3 of 236
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055028.1.
            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..2845
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHEFF_67"
                     /isolation_source="Shek Wu Hui WWTPs_67 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            382..531
                     /locus_tag="HUZ75_RS23065"
                     /old_locus_tag="HUZ75_22925"
     CDS             382..531
                     /locus_tag="HUZ75_RS23065"
                     /old_locus_tag="HUZ75_22925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_063923875.1"
                     /translation="MHEPPVQSDCCACPGNYRLESNPERHDKAPLAAATGNGLEELSLD
                     VMRL"
                     /name="hypothetical protein"
     gene            729..1382
                     /locus_tag="HUZ75_RS23070"
                     /old_locus_tag="HUZ75_22930"
     CDS             729..1382
                     /locus_tag="HUZ75_RS23070"
                     /old_locus_tag="HUZ75_22930"
                     /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_160322305.1"
                     /translation="MSFQLAIFFKQHITRPDHFFSSINDAAGNLFDRMPQIIPLPDEVP
                     PEIPRVAATNMSGTYNFNISLNRLDFTLNVSDSQFKEPEALSDFALKSKLIVKNIPNEI
                     EIIRIGIIGNYFELEKLPAIALAKKYSKKDLGNISEFNFRYNKISQEFGYSFNNVFSIS
                     NAEINTKGIVSDGIFIQKDINNNPSGLSIKKDMVMEIITKKIKELSTSGLEGIS"
                     /name="hypothetical protein"
     gene            1382..1747
                     /locus_tag="HUZ75_RS23075"
                     /old_locus_tag="HUZ75_22935"
     CDS             1382..1747
                     /locus_tag="HUZ75_RS23075"
                     /old_locus_tag="HUZ75_22935"
                     /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_112021934.1"
                     /translation="MPPQNRSSSSSSYSSPSVNSGSSSALQIDAAWASFEAMIERRLEE
                     IKPKTPAQIKANGDSRNKTIVISALVVILAIIVIYIGAIYIIDSVTGKEFTSSLMPVIT
                     AIISGVLGYLSGEKSSK"
                     /name="hypothetical protein"
     gene            complement(2452..2652)
                     /locus_tag="HUZ75_RS23080"
                     /old_locus_tag="HUZ75_22940"
     CDS             complement(2452..2652)
                     /locus_tag="HUZ75_RS23080"
                     /old_locus_tag="HUZ75_22940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166333.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="antitoxin VbhA family protein"
                     /protein_id="WP_023139298.1"
                     /translation="MARSPDPRQRTEGFRKAEASLRLEGMDPAGTPLYENIKERVISGD
                     ITYEQGRAEILAHYQKRANGH"
                     /name="antitoxin VbhA family protein"
     Typing          2..496
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.264"
                     /coverage="82.0"
                     /evalue="4.13e-174"
ORIGIN
        1 atcttccgct tcctcgctca ctgactcgct acgctcggcc gttcggctgc ggcgagcggt
       61 accggcagtc cacctggagt tacccacaga ttcgggggta gcggaaggag aaagagggga
      121 acagaaaagg ccgcggcgaa gccgtttttc cataggcttc gcccccctga caagcatcac
      181 agaatctgac gctcaaatca gtggtggcga aacccgacag gactataaag atcccaggcg
      241 tttccccctg gtagctccct cgtgcgctct cctgttcctg ccattcggtt taccggtgtc
      301 attccgctgt tatggccgcg gtttctcatt ccacgcctga cactcggttc cgggaaggca
      361 gttcgctcca agctggactg tatgcacgaa ccccccgttc agtccgactg ctgcgcctgt
      421 cccggtaact atcgtcttga gtccaacccg gaaagacacg acaaagcgcc actggcagca
      481 gccactggta acggattaga ggaattgagt cttgatgtga tgcgcctgta aaggctaaac
      541 taaaagaaca agttttggtg actgcgctcc ctctaagcca gttacctcgg ttagttagat
      601 ttcctaggtc tttctaacct ctaaaaaacc gcctgccagg gcggtttttt ttcttcgtaa
      661 gaagattacc tttcgcttta tacttcagtc aagacactaa taaaaatgga gttgaaatgg
      721 tacatgtcat gagtttccag ttggctatct tttttaagca gcatataaca agaccggatc
      781 attttttttc cagtattaat gatgccgctg gcaatttatt tgataggatg cctcaaatta
      841 tcccacttcc agatgaggta ccaccagaga tacctagagt ggcagcaaca aatatgtcgg
      901 gaacatataa ctttaacata tcactcaaca gattagattt cacattaaat gtatccgatt
      961 ctcaatttaa agagccagaa gctttaagtg actttgcact aaagtcaaaa ctaattgtaa
     1021 aaaacattcc taacgaaatt gagattatcc ggattggaat aatcggcaat tatttcgaat
     1081 tagaaaaact tccagctata gccttagcaa aaaaatactc caaaaaagat cttggaaaca
     1141 taagtgagtt taatttccga tacaataaaa tatctcagga attcggatat agttttaata
     1201 atgttttctc gattagcaat gcagagataa acaccaaggg aatagtctca gatggaatat
     1261 ttatacaaaa agacataaac aacaatccat caggattatc aataaaaaaa gacatggtaa
     1321 tggaaataat aactaagaaa atcaaggagt tgtcaacaag tggcttagag gggatatcct
     1381 aatgcctcca cagaaccgtt catcatccag ctcgtcatac agttcaccaa gtgtgaattc
     1441 tggtagctcg tctgctttgc aaatagatgc tgcatgggct tctttcgaag caatgataga
     1501 aagaagactg gaagagataa aacctaagac gccagcacaa atcaaagcaa atggtgacag
     1561 cagaaataaa accattgtca tatctgcttt agttgtaata ttagctataa tagttatata
     1621 tattggagca atatacataa ttgattctgt cactgggaag gagttcacgt cctcacttat
     1681 gcccgtaata accgcaataa taagtggcgt acttggatat ctttctggag agaaatcatc
     1741 caaataaaaa ataagcgctg ctgtattaag atatggcagc acttattatc ccaaacacaa
     1801 aactacaaat ttattaacat gtggtggaat taacttcaat ttaccataac atccgttgcg
     1861 tgcaccatct cagacgccct cagggcattt ctgcgccctc ctgcctattt ccggcatctt
     1921 tccctgtcca tatcgtgaaa aaacgcgcct gatgatttct gcgcggctgc atggctatgc
     1981 acgcaggtga atggcggtcg atttggggtg gatgctggca tgaaagcctg ctttccggcg
     2041 cataactccc ccgataacgg tgaacgggtg cacagtttac tgtgcgaccg tgaggcgttg
     2101 gccaggccgt caggcatggc agaatttact accaagcagg aggtcggatt taacgtggat
     2161 aatcagcacg cagtgatgaa cgggattcgg aaggggaacc cttgcggcgc ggcgatgtat
     2221 acatcgctaa cgtgccttac tcttttcaca gcagagggta gcaaacaagt agcaaacaga
     2281 tagcaaacag atagcaaaca agtagcaaac agacagcaaa cagacagcaa acagatagca
     2341 aacaagtagc aaacaagtag caaacagata gcaaatacag gaaaagcctg gccggagaga
     2401 ggccacgcct gtttttttga ggaagcgatg gtacctagtt tcctgtccgt gtcagtggcc
     2461 gttcgcacgc ttctggtaat gagccagaat ttctgcccgt ccctgttcgt aagtgatatc
     2521 cccggaaata acccgctcct tgatattttc gtacagcggc gttccggcgg ggtccatgcc
     2581 ttcaagcctc agcgacgctt ccgctttgcg gaaaccctca gtacgttgtc gtggatcggg
     2641 ggacctggcc atcgatgttc ctttgagctg taagcgaata aggcaggcgg taaagtaggc
     2701 ctactttaca tatcctgccc gtactctgcc gttgtttatc cgtgcagacg aatgtgtaaa
     2761 ccggaaggaa agtattgcag gaaactgtgt aatccggcgg taaagagagg gtacggcgcg
     2821 acacgagccc aatcaggcat cgcag
//
