LOCUS       NZ_CP055198             4073 bp    DNA     circular CON 01-MAY-2024
DEFINITION  Shigella flexneri strain STEFF_10 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP055198
VERSION     NZ_CP055198.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925528
            Assembly: GCF_022354325.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4073)
  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 4073)
  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_022354325.1-RS_2024_05_01
            Annotation Date                   :: 05/01/2024 05:20:57
            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)                     :: 5,075
            CDSs (total)                      :: 4,953
            Genes (coding)                    :: 4,780
            CDSs (with protein)               :: 4,780
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 173
            CDSs (without protein)            :: 173
            Pseudo Genes (ambiguous residues) :: 0 of 173
            Pseudo Genes (frameshifted)       :: 64 of 173
            Pseudo Genes (incomplete)         :: 111 of 173
            Pseudo Genes (internal stop)      :: 34 of 173
            Pseudo Genes (multiple problems)  :: 37 of 173
            Pseudo Genes (short protein)      :: 3 of 173
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP055198.1.
            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..4073
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STEFF_10"
                     /isolation_source="Shatin WWTPs_10 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(408..1322)
                     /locus_tag="HUZ40_RS25245"
                     /old_locus_tag="HUZ40_25090"
     CDS             complement(408..1322)
                     /locus_tag="HUZ40_RS25245"
                     /old_locus_tag="HUZ40_25090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001448734.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_001448734.1"
                     /translation="MPNTIHYPHVIPFISQGKINAIKSTFGNNLSDRECYGIYIWSQKA
                     SSAIYPLLQQLEVTLRNSIDKEATKLIGQKWWDNVYTDTSKSKHGDFIHNINKAKRRYE
                     NEFKKKNPSMANTKIIAPHDDIIAHTDFYTWQAVLSDAFHTQSRSEASRALWPRLTYRV
                     LKGLDRSKDEGTARIDFLNELNEIRNYRNRLSHNDCIWIKIHSKNLQSAVETIREKINK
                     IEGLIKTINPQVHLSLTKWGSFYHAKRICSQKEAELHLGKGIINSTTDEMNTILDQLYA
                     LTADGKLTGVVKRNTNNIAFHKF"
                     /name="Abi family protein"
     gene            complement(1548..1661)
                     /locus_tag="HUZ40_RS25250"
     CDS             complement(1548..1661)
                     /locus_tag="HUZ40_RS25250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071531573.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHALTPLAAATGN"
                     /name="replication initiation protein"
     gene            complement(2327..2521)
                     /locus_tag="HUZ40_RS25255"
                     /old_locus_tag="HUZ40_25095"
     CDS             complement(2327..2521)
                     /locus_tag="HUZ40_RS25255"
                     /old_locus_tag="HUZ40_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041633.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3294..3887)
                     /locus_tag="HUZ40_RS25265"
                     /old_locus_tag="HUZ40_25100"
     CDS             complement(3294..3887)
                     /locus_tag="HUZ40_RS25265"
                     /old_locus_tag="HUZ40_25100"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012537770.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_072648847.1"
                     /translation="MSGRKFGRLPNWWARNSWLVNNVRSNEIGGGIASMKCLLALSVLI
                     DFHSRTASVSFTGMERLTGLSRPMIVKGVAKLEKDGLIKIDREMFVNSYELTVQPNDDR
                     WAKVPVDTIRKKLNTISNRGMAPFVALKLYLTIISLRYQSNNTVKVTHETLRSYTGVQP
                     NQIRFGLDVLYCSRLIHLQPKEDRESNIYEIIGL"
                     /name="replication protein"
     Typing          2160..2246
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.43e-38"
     Typing          2558..2656
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2781..3036
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.411"
                     /coverage="89.0"
                     /evalue="2.67e-103"
     Typing          complement(1590..2149)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.204"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tatatacgct tattagaata aatctagata aagcaatatt tggtggctgc ttgttttccc
       61 atataaaaca tgatgttatc ttgtttttat cgttttttaa ctggtaaatg taaatttgat
      121 aatgctggtt taatcggcgt ttttagttat ttttgttgtg tgttttttga tctattggta
      181 aatggtggat ggtaagcttt ggcgtgatca tgggaaatag tttgctcttt ttcctgatga
      241 tgatgtatca tgtatggcag tgaagccttg agctttcgct ttaatgcatt gtgaaatttt
      301 tatagattca caatgacatt aaggccacgc tccaccgaaa ggtgataatg gcaagagatt
      361 tggatgaggc tcgacaggaa actgtcgggc cttttctatt ttgtgatcta aaacttgtga
      421 aatgcgatat tgttggtatt tcgttttaca acacccgtta gctttccgtc agcagttagt
      481 gcgtatagtt gatctagaat tgtgttcatc tcatctgttg tgctattgat tattcctttg
      541 cctagatgca attcggcctc tttttgagaa catattcttt tggcgtgata aaaggaaccc
      601 cacttcgtta atgataggtg tacctgtggg tttatcgttt ttatcagtcc ttctattttg
      661 tttatttttt ctcttattgt ttctactgca gattgcaaat ttttagagtg tatttttatc
      721 catatgcaat cattatgcga taacctattt ctgtagtttc tgatctcatt cagctcgttt
      781 aagaaatcaa ttctggctgt gccttcatct ttgcttctat ctaatccctt cagtactctg
      841 taggtgagcc tgggccataa ggctcttgat gcttcagatc ttgattgtgt atgaaaagca
      901 tcgctcaaaa ccgcttgcca tgtgtaaaaa tctgtgtgtg caatgatgtc atcatgaggt
      961 gcaattattt tggtatttgc cattgatggg ttttttttct tgaattcatt ctcatatctt
     1021 ctttttgctt tgtttatatt atgtatgaag tcaccgtgtt tgctttttga tgtgtcggtg
     1081 tatacattat cccaccattt ttggcctatt agttttgtcg cttctttatc aatcgagttt
     1141 ctcaaagtaa cttcgagttg ttgcagtaat ggatatatgg cagatgaggc tttctggctc
     1201 catatatata tcccgtagca ctccctatca gacaggttat taccaaacgt gctttttata
     1261 gcatttattt ttccttggga tataaatggt attacatgag ggtaatgaat tgtatttggc
     1321 atatccatct ctatcataca cttagtggtg attggatgtt gccatacacg tatggatagt
     1381 tgtagagtgt taaacgaaaa aaccgccttg gcgggcggtt tttcgaaggt tcaaagagtt
     1441 ggcgctctgt gaaccaaggt aactggcttg gaggagcgca gtcaccaaaa tctgttcttt
     1501 cagtttagcc ttaacaggtg cataacttca agacaaactc ctctaaatca gttaccagtg
     1561 gctgctgcca gtggcgttaa ggcgtgcctt accgggttgg actcaagacg atagttaccg
     1621 gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga
     1681 acgacctaca ccgaactgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc
     1741 gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg agagcgcacg
     1801 agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
     1861 tgacttgagc gtcggttttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
     1921 agcggcgcgg ccttttttcc tggctttgcc ttgttgctca catgttcttt ccggtcttat
     1981 cccctgattc tgtggataac tgtgttaccg tttttgtgtg agtcagtacc gctcgccgca
     2041 gccgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaaaagcgc ctggacgtgc
     2101 attttctcct tacgcatctg tgcggcattt cacacccggc atggggcact tttcatacaa
     2161 tccgcactga tgccgcatgg ttaagccagt atacactccg ctatcgctac gtgactgggt
     2221 catggctgcg ccccgacacc cgctaaaacc ccctgacgcg ccctgacggg cttgtctgct
     2281 gccgaaaacg ctcgcggaca agccgtgagc gcctccgtca gcttcgttat gttcctgttt
     2341 cactttcggt ctcaaagcga acctggatgc tgttctggag ttcttccgcg agttcgtgca
     2401 gtcgttcgca catggctgcc tgttcgtcgg catccagagc atccagtttt tcaagcagtg
     2461 tcaggctctg gcttttgata aatcgcgcca tattcagcgc agtttgttgt tgtttgttca
     2521 ccttccgttg ttctccgtca gttccgggtg tcggggggac cctgagcagc tggtaattgt
     2581 aagacgttgc gggcgacggt attacaattg cacatcctgt cctgtttttt taggacgtat
     2641 catggcacag catatcaact gataaataat ccctgtgcag tgcagccgct gttgcataaa
     2701 atttcgctct gcgtcgagtg tttcttaatc aataattccg ctgatactcc ggaaaaacgc
     2761 gagtctgttc tcattcctga aatgcccaca ccccacgcaa aaacaagttt ttgctgattt
     2821 ttctttataa atagagagtt atgaaaaatt agtttctctt gctctctttg cgatatttaa
     2881 aaaagcggtg ccggcgcagc tacaacaccg cgccgacacc gctttgtagg ggtggtactg
     2941 actattttta taaaaaacat cattttatat caggggtgct gctagcggcg cggtgtgttt
     3001 ttttacagga cgcccctggg ggcgctgcca ggggtgtctg ttcagatatg tagcaatgag
     3061 tcagggattc acgaactgaa aatgtccgaa aatgtgtctc atgggcaccg tatgcgccca
     3121 aaccgttcgt cattcatttt catgcatagc tatgcagtgg gctgaaaacg atcctgacgc
     3181 attttttcgg ttttcactgg gtaaaacatc tctttttgcg gtatctgcgt cagaatcgcg
     3241 ttcagtgcgt tttagcggtg cgcgtaatgc gacgttatgg taaatgcatt tcctcatagg
     3301 ccgattattt catagatgtt tgactctcta tcttcttttg gttgcagatg tatcaggcga
     3361 ctacagtaca gtacatctaa gccgaaccta atctggtttg gctggacacc tgtatagctt
     3421 ctcagtgttt catgtgtcac cttaacagta ttatttgact gataacgaag gcttataatt
     3481 gttaaatata gttttaatgc cacaaatggg gccatccccc tgttcgatat ggtgtttagt
     3541 tttttcctga tagtatctac tggtactttt gcccacctat catcatttgg ctgtactgtt
     3601 aattcatagg agttaacaaa catctctcta tctatcttta taagaccatc tttctcaagt
     3661 ttggctactc ctttcactat catggggcgg cttagtccag tcagtctttc cattccggta
     3721 aatgatactg aggctgttct tgaatggaaa tcaatcaaga cggatagagc taacaagcat
     3781 ttcattgatg caatgccgcc ccctatctca tttgaacgaa cattgtttac aagccatgag
     3841 tttcgggccc accagtttgg aagcctgcca aattttctac cgctcatttt taccccattt
     3901 tcggtcaagg agagatataa atagctttat tatcatatac atgaaaacca ttgcacctaa
     3961 agatacaaca gaaaccaaaa cctccggctt tgcggaagtt agcgttacca gcaaattgtt
     4021 gagggtttcc aattggtcct ccagtcgcat actaagttgt tgtgttttaa ctt
//
