LOCUS       NZ_CP055118             4052 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain SWHIN_101 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP055118
VERSION     NZ_CP055118.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925596
            Assembly: GCF_022354705.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4052)
  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 4052)
  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_022354705.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:20:22
            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)                     :: 5,096
            CDSs (total)                      :: 4,977
            Genes (coding)                    :: 4,761
            CDSs (with protein)               :: 4,761
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 216
            CDSs (without protein)            :: 216
            Pseudo Genes (ambiguous residues) :: 0 of 216
            Pseudo Genes (frameshifted)       :: 80 of 216
            Pseudo Genes (incomplete)         :: 139 of 216
            Pseudo Genes (internal stop)      :: 42 of 216
            Pseudo Genes (multiple problems)  :: 44 of 216
            Pseudo Genes (short protein)      :: 2 of 216
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055118.1.
            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..4052
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="SWHIN_101"
                     /isolation_source="Shek Wu Hui WWTPs_101 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed5"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.5 N 114.1 E"
                     /collection_date="2018-12"
     gene            join(3907..4052,1..97)
                     /locus_tag="HUZ81_RS25395"
                     /old_locus_tag="HUZ81_25145"
     CDS             join(3907..4052,1..97)
                     /locus_tag="HUZ81_RS25395"
                     /old_locus_tag="HUZ81_25145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001027011.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001027012.1"
                     /translation="MNISIKNNDLKTVARFDGKTLRDAFSRKIATFDGKVLRDASLKKV
                     ATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     gene            671..1810
                     /locus_tag="HUZ81_RS25400"
                     /old_locus_tag="HUZ81_25150"
     CDS             671..1810
                     /locus_tag="HUZ81_RS25400"
                     /old_locus_tag="HUZ81_25150"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000900598.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_005761319.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            1815..2018
                     /locus_tag="HUZ81_RS25405"
                     /old_locus_tag="HUZ81_25155"
     CDS             1815..2018
                     /locus_tag="HUZ81_RS25405"
                     /old_locus_tag="HUZ81_25155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(2856..3050)
                     /locus_tag="HUZ81_RS25410"
                     /old_locus_tag="HUZ81_25160"
     CDS             complement(2856..3050)
                     /locus_tag="HUZ81_RS25410"
                     /old_locus_tag="HUZ81_25160"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3334..3657
                     /gene="mobA"
                     /locus_tag="HUZ81_RS25415"
                     /old_locus_tag="HUZ81_25165"
     CDS             3334..3657
                     /gene="mobA"
                     /locus_tag="HUZ81_RS25415"
                     /old_locus_tag="HUZ81_25165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          3086..3325
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(2300..2821)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          3335..3654
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.08e-62"
ORIGIN
        1 cggtcagaat ttaagagatg ctagttcaaa aattatcctg agtgccgatg ctgaggttgg
       61 gattgttgtt atggcctttg tagctgagtt gatttgaatc tcatgctgca taccttttag
      121 cctatcgctg gcaggataag gcgctttctt gttggtgaca gaaagataaa aaactttata
      181 ataatcagcg aagcgggcga accacgcctg gctctcgctc tttaacaaat ggttacgtgt
      241 atgttgcgca aggaaaccga tgccttgttt ttaaggcgat ctcgcatgag atcatgaccg
      301 gcctggccgc taattaatgg tgagaacgcc cctgagcgtg tatcagcact aaaagaatag
      361 cgacgattgt ctggcaatgt gagttaaaag tcccaaagag ccaatagagt ttttccttgc
      421 tttcctactg gtctggcaaa atttcataac caataggagt tgcatcatgt ttattatcaa
      481 catcaacatt aacgtaacca agagctcttc atcttgttct ggagacggtc agatgaagaa
      541 aaaaagagag gttggctctc tggaggcact gaaaaaaaca cagtttttgt tttctatgtg
      601 cttgattatg tttaaagtaa tagattacgt atcgaaactt tttaactaat cgacttttaa
      661 ctcaaacatc atgaataaac ccaggtttaa tggaactcct gttgcatctt tggattcttt
      721 atctgcgatg ttaggcatag aaagaaaaag attggactgg atagtcaagt ctgtatcgat
      781 gtcgtacaag cagtttaagg ttgaaacagg gaagaataaa aaagaaaggc aaatttttga
      841 acccaagaga tctttgaaag gaattcaaaa aaaaataaat aaagagattt ttgagaaaat
      901 tgattaccct cattatttgc atggggcgtt aagtggtcgc gattatatat ctaatgccgc
      961 tgttcatact aggaaaagaa cagttatatg tcttgatatc accaattttt atcccagcat
     1021 tagtaaaaaa gatgtttgtt ctatttttaa aaatttaatg cgtttttctc ctgatgtttc
     1081 tttatgctta acggaacttg tgacgttgaa taataaggtc cctcagggtg ggtgctgttc
     1141 tagttatatt gcaaatcttt tattttttaa tagtgagtat aatctctata atagattgaa
     1201 gtctatggga ctttcatatt caaggctttt agatgatatt actatatcct ctgataagga
     1261 tctttcatca gaggaaaaaa caaaagtaat aaaactcgtt cacggaatgg tgaatcagta
     1321 cagactttca ataaatgaaa gtaagacaac gatagagcac tcaaaagatt cgtcttctaa
     1381 acttagtgtc actgggttgt gggtaaagca tggtgttcct aagttaacaa aagaaaatag
     1441 acgttatatc aggtacttag tttatatatg taaaaaacaa ggtgcttatg aacgtcatac
     1501 gaaagagtac catgatttat ggaatagatg ctctggcaag gttgctcaaa tgtcgaggct
     1561 tgggcatgtc caggcggttg aattgagggc gattctttct gagataatgc cagtttatga
     1621 tgattacaag atatctaaat taaagttgat ggctaagcac tatctaaata agtttacgcc
     1681 gcctttaact gatgatcaga ttaggaaaat agataggatg ctctatgatt ttgatatagt
     1741 agggcggact aataagaatc ttgcaaaact atatagacgt aagctcgtgg cattacttcc
     1801 agataggtga ttatatggaa aatggatttg ttaattttta tgaccatgtt aaagggtatg
     1861 gctttataag gcgtgagcgt ggacgtgatg ttttctttcg gtatgatgat tttttgtttt
     1921 tagggcatga tgtcgatata tgtaaaggta ttttagttag gtttaaatta gaaaaaacag
     1981 ataaagggtt taaagctgta gcgattcaaa aggtataaca tcgtggatgt gtcagcttgt
     2041 ttttatgata tgagaacttg agatcctttc tatctcgtcg taatctcttg ctgtgtaaac
     2101 gaaaaaaccg ccttgcaggg cggtttttcg aaggttctca gagctaccaa ctctttgagc
     2161 cgaggtaact ggcttggagg agcgcagtca ccaaaacttg ttctttcagt ttagccttaa
     2221 caggcgcatg acttcaaggc taactcctct aattcggtta ccagtggctg ctgccagtgg
     2281 cgataagtcg tgtcttctcg gtttggattc aagtcgatag ttaccggata aggcgcagcg
     2341 gtcggactga acggggggtt cgtgcataca gtccagcttg gagcgaacga cctacaccgg
     2401 gccgagatac caacagcgtg agctatgaga aagcgccacg tttcccgaag ggagaaaggc
     2461 ggacaggtat ccggtaagcg gcagggtcgg aacaggagag cgcacgaggg agcttccagg
     2521 gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg
     2581 gtttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccatcg gcgcggcctt
     2641 tgtccctggc ttcggctttt tgctcacatg ttctttccgg cgttatcccc tgattctgtg
     2701 gataaccgta ttaccgcctt tgagtgagct gacaccgctc gccgcagtcg aacgaccgag
     2761 cgtagcgagt cagtgagcga ggaagcggaa gagcgcctta tgtgacattt tctccttacg
     2821 ctcctctatg ccgttctgca tcctgtccgg atgcgttata tcccggtgcg attttccgct
     2881 tcaaagcgtg tctgtatgct gttctgaagt tcttccgcga gttcgtgcag cttctcacac
     2941 atggcggcct gttcgtcagc atcaagtgcg tccagttttt cgagcagcgt caggctctgg
     3001 ctttttatga atcctgccat gttgagtacg gtttgctgct gcttgttcat ctttctgttt
     3061 tctccgttct gtctgtcatc tgcgttgtgt gattatatcg cgtaccactt ttcgactgtt
     3121 ttaccgtcgg tattctgctg tctgactctt tgacgggcat ttctgtcaga caacactgtc
     3181 actgccaaaa aactgccgtg cctttgtcgg taattcgagc ttgctgacag gacaggatgt
     3241 gcaattgtta taccgcgcat acatgcacgc tattacaatt accctggtca gggctttgcc
     3301 ccgacaccca tgtcagatac ggagccatgt tttatgacaa aacgaagtgg aagtaatacg
     3361 cgcaggcggg ctatcagtcg ccctgttcgt ctgacggcag aagaagacca ggaaatcaga
     3421 aaaagggctg ctgaatgcgg caagaccgtt tccggttttt tacgggcggc agctctcggt
     3481 aagaaagtta actcactgac tgatgatcgg gtactgaaag aagttatgag actgggggcg
     3541 ttacagaaaa aactctttat cgacggcaag cgtgtcgggg acagggagta tgcggaggtg
     3601 ctgatcgcta ttacggagta tcaccgtgcc ctgttatcca ggcttatggc agattagctt
     3661 ccaggggaga aaactgtcga aaacagacgg tatgaacacc gtaagctccc aaagtgatca
     3721 ccactcgctt tcatgcatag ctatgcagcg agctgaaaac gatcctgacg catttccccg
     3781 gttttcttag ggtaaaacat ctctttttgc agtgtctgtg tcagaatcgc gctcagcgcg
     3841 attctgtggt gcgtacaatt aagggattat ggtaaataca attggttaaa ttactattgg
     3901 tgagaaatga atatttcaat aaaaaacaat gacttaaaaa ccgttgctcg gtttgacggt
     3961 aaaaccttaa gagatgcctt ttcgagaaaa atagcgactt ttgatggcaa ggttttaagg
     4021 gatgcctctt taaaaaaagt agcaaccttt ga
//
