LOCUS       NZ_CP058850             4207 bp    DNA     circular CON 30-APR-2024
DEFINITION  Shigella flexneri strain STLEFF_36 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP058850
VERSION     NZ_CP058850.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925562
            Assembly: GCF_022494155.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4207)
  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 4207)
  AUTHORS   Che,Y.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-2020) Civil Engineering, The University of Hong
            Kong, Pokfulam Road, Hong Kong 000000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: SPAdes v. Unicycler 0.4.8
            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_022494155.1-RS_2024_04_30
            Annotation Date                   :: 04/30/2024 04:10:52
            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)                     :: 4,544
            CDSs (total)                      :: 4,423
            Genes (coding)                    :: 4,231
            CDSs (with protein)               :: 4,231
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 65 of 192
            Pseudo Genes (incomplete)         :: 118 of 192
            Pseudo Genes (internal stop)      :: 39 of 192
            Pseudo Genes (multiple problems)  :: 32 of 192
            Pseudo Genes (short protein)      :: 4 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058850.1.
            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..4207
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLEFF_36"
                     /isolation_source="Stanley WWTPs_36 WWTPs effluent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed1"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            join(3382..4207,1..71)
                     /locus_tag="HZT28_RS22555"
                     /old_locus_tag="HZT28_22370"
     CDS             join(3382..4207,1..71)
                     /locus_tag="HZT28_RS22555"
                     /old_locus_tag="HZT28_22370"
                     /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_186199455.1"
                     /translation="MKKNHLIAFSQKSRKKTIYKVTSSDDKFFRNQLKEQHNGIMEYDP
                     NDRQDQSKIFFLDLSKHEGITNEIIEELKELKKSDDINTTNYKAFSASDLDGLKYMATK
                     QDQYILFQNFYKKNIIGSKVLSLKKMEVLQDGFITLNEYAEVIYDIEDKKIYFSNIVKA
                     KKILSGMEMIYKEAGIKETKHFISQDHIHLLDDFDENKVNVLNKKRIQSELDKQNKIKV
                     EKGDDYDDFYTTDISECLAEIKEYYPEMLDGNKIIIKNNKDLENYLLALDERLYTAKRS
                     QQQRVATATRKVEKSKQ"
                     /name="hypothetical protein"
     gene            complement(373..816)
                     /locus_tag="HZT28_RS22560"
                     /old_locus_tag="HZT28_22375"
     CDS             complement(373..816)
                     /locus_tag="HZT28_RS22560"
                     /old_locus_tag="HZT28_22375"
                     /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_001605388.1"
                     /translation="MTSGIFLSREDLMLLSDQAKEEVLALATGDSVSGVYEESEDGPTD
                     LSSLQAERLVRGLSDKSRTVLKAILESEDGERGFWCKSLAKELGFDVSELSGVWSGLTR
                     RTRTVSDDSEAYLISWAWDDDRDDYYGTLHPTTYRNCKKAMNF"
                     /name="hypothetical protein"
     gene            complement(1788..1979)
                     /locus_tag="HZT28_RS22565"
                     /old_locus_tag="HZT28_22380"
     CDS             complement(1788..1979)
                     /locus_tag="HZT28_RS22565"
                     /old_locus_tag="HZT28_22380"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2398..2547
                     /locus_tag="HZT28_RS22780"
     CDS             2398..2547
                     /locus_tag="HZT28_RS22780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_113419837.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPEKHAKTPLAAAIGNRNSRENYQ
                     EFLK"
                     /name="replication initiation protein"
     Typing          1855..2476
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.688"
                     /coverage="99.0"
                     /evalue="4.27e-169"
ORIGIN
        1 acacagcgaa aagaagccag caacagcgcg tagcaacagc aacaagaaaa gtagaaaaat
       61 caaaacaata gatggaaacc caacccaaat aggaagctaa aaaaaaccat gcaagactat
      121 ttttggagca aatcgatttt acgtatcacc agaacggctg ggctacggcg atttctgtac
      181 aagaaataga gcggaatcag tcgttaaatt caatcctctt agcatggttt gttttcctag
      241 tgcccacaca caaaagcctc cactgggggc ttttttatta ttcgaggatt taccataacg
      301 tctcactaca cgaaccaatg aaaaaagccc gcacatggcg ggctcacagg gaaagtatca
      361 cagcgagaac aatcaaaagt tcatagcttt cttgcagttg cgataggttg ttggatgtag
      421 cgttccatag taatcatcac ggtcatcatc ccaagcccag ctaatcaaat aagcctcaga
      481 atcatcactt accgtgcgag ttctgcgtgt aagccctgac cagacacctg aaagctcaga
      541 gacatcaaaa ccaagctcct ttgcgaggct cttgcaccag aatcctcgct caccatcctc
      601 gctttcaaga atagctttca gcactgttcg cgacttatca cttaaaccac gaacaagcct
      661 ttctgcctga agcgaggaaa gatcagtagg cccatcttcc gactcctcat aaacaccaga
      721 aaccgaatcc ccagtagcca atgccagcac ttcttctttt gcttggtctg ataacaacat
      781 caaatcttca cgggataaga aaataccact agtcatgaaa cactccattg tcttgttaag
      841 ataaaaggag aataaacata gacaagatag ttgtcaacaa gacaagtgac aagtaaatac
      901 aactaacatc aattaacagc tagttgtgtt tgatttaccg cattaactgg gttgcgatag
      961 tgagaggtca acactcaaca gcccggattt accataacgt cgcattacgc gcaccgctca
     1021 gacggcctga gcgcgtttct gacgggaaac cggtaaaaca ggcaacaaac cacccgaaaa
     1081 cccgccagaa acgcgcaggc tctgttttta cggcatgcat gagtatgcgc acaagtgcat
     1141 agcgcggaaa ttcacgccat tcagccgggg taagtcctgt ttccgatgtt cttcttaccc
     1201 gaaaacggtg aacggggacg caatttattg cgtggccgtg aggcgttgcc ggcacagccg
     1261 gaaaaaccat tttcagcacg tgcaggaggc ccaggaagag ggggcggatg tacgaatagc
     1321 tcagaggtca gatctgacgt aaaaatgatg taaaagtgat gtacttttga tgtaattctg
     1381 ttgtacaccc gcgatctgac gtaaaagtga tgtaattttg atgtactttt gatgtaattc
     1441 tgttgtacac ccgcgttctg gggtaaaagc agatgcaatt ttgtagttta tgtgtagtcg
     1501 ctgaacccat agggtcatac gagcatgacc ctttcccgga aaaggacgct ttttagccag
     1561 aatcatactt aacctgcggc gccagcactc gggagtggtc gttttatata ctaaaaaatg
     1621 acatacacct aacgcagctg cgattttcat cgcaacttca tgaaaagtaa ataaaaaata
     1681 aaaaacacag ggattctggg tattaccggg gtaataatgt taagcgctaa cacaatgaaa
     1741 attaaggcga tgccggtatt actccggtaa tacccagaac ggagccatta cgcaccgtcc
     1801 tgctgctcat tcaggcgcgc tgacaggctt cggtaaaggc gttccgcatc ctcatggagt
     1861 ttctcgcaga aatcagcctc atgatccaga tccagctcat taagcctgtc cagaagaagc
     1921 agggactgat cctggatgaa tttagccatg ttaacggcag tcttttgttg tttgttcatg
     1981 aaagccccgg cgcgaaagtg cttattgtac gttctgatgg ttttccgctt cctcgctcat
     2041 tcgctcactc cgttcggtca tgagtctgcg gcgagcggag ggaggataag cagataacgt
     2101 aacggtaagc ataacgaaag ctaaggacaa gggcgaaaag gccacgcccc gccggggcgt
     2161 ttttccatag gctccgcccc cctgacaagc atcacagaat ctgacgctca aatcagtggt
     2221 ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggtggc tccctcgtgc
     2281 gctctcctgt tcccgccttt cggtttaccg gtgtcattcc gctgttatgg ccgcgtttgt
     2341 ctcattccac gcctgacact cggttccgtt taggcagttc gctccaagct ggactgtatg
     2401 cacgaacccc ccgttcagtc cgaccgctgc gccttgtccg gtaactatcg tcttgagtcc
     2461 aacccggaaa aacacgcaaa aacgccactg gcagcagcca ttggtaacag gaattcacga
     2521 gagaattatc aggagttctt gaagtgaccg catgactacg gctacactgg tagtacgaat
     2581 ttggtgacag ttctctcgta tagttctgtt accacggtta gaacatctgc caggattttc
     2641 taacctttga aaaaaccacc ttgccgggtg gttttttctt tcaaagagaa gagtacgctg
     2701 tcactaatgc agtagtcaac atttccaagc ctacctaccc ggcatttatt tattgacata
     2761 tagcaaaatt taaaataaaa aagcctttgt cacgggagaa cactgtgtta aataaaataa
     2821 attccacaga catactcgat tatgtcttta aattattatc tacaatatca gcattaactc
     2881 cagcaatatt tgtgtacatg atcacaaact acaaaacaaa ccttaataaa gagctagtaa
     2941 ctattatctc tgataatgaa gctatgtttt tcatagccta catcatttta agcgtactca
     3001 taattctgtt tcttaattca atattcttgc gcgtagttaa caaacttgac gatgagtcaa
     3061 tgagcaatat aaatacagtg gagccggtta atgataattt tcttccgaca tacttagggt
     3121 atttttttgt ctcagttagc attacatcaa actgggtttt tggctacttt atgattctcg
     3181 ttatcctatt caaccttttc tcaaaagtat atttttttaa tccgtcacta ttaatatcag
     3241 gttttaaatt ctatcactta acatctgata aaggagtaaa aatattactt ataagtaagg
     3301 atgatctccg ttctcataaa gacatctcat cctccaacta taaaagaata aatgacttca
     3361 cattcatcaa ggtagagtaa aatgaaaaaa aaccacctta ttgcgttttc gcagaaaagc
     3421 agaaaaaaaa ccatctacaa agtaacatct tcagatgata aattctttag aaatcaacta
     3481 aaagaacaac ataatggaat tatggagtat gatccaaatg acaggcaaga tcaaagcaaa
     3541 atattctttt tagacctctc taaacacgaa ggtatcacta acgaaataat tgaagaatta
     3601 aaggaattaa aaaaatccga tgacataaac acaactaatt acaaggcatt ttccgctagt
     3661 gatcttgatg gtttaaaata catggcgaca aaacaagatc aatatatttt gttccaaaac
     3721 ttttataaaa aaaatatcat tggttcaaag gtgctgtctt taaaaaaaat ggaggtatta
     3781 caagacggat ttatcacact aaatgaatat gcagaggtaa tttatgatat agaagataaa
     3841 aaaatttatt tttcaaatat tgttaaagct aagaaaattc tatccggaat ggaaatgata
     3901 tataaagaag caggaataaa agaaacaaaa catttcatta gccaagatca cattcatcta
     3961 ttagatgatt tcgatgaaaa taaagtaaac gtattaaata aaaagagaat acaatcagaa
     4021 ttagataaac aaaataaaat aaaagttgaa aaaggtgatg attatgatga tttttacact
     4081 accgacatat cagaatgtct agctgaaata aaagaatact atccagagat gttagatggg
     4141 aataaaatta ttattaaaaa taataaagat ctagaaaact atctgttagc tttagatgaa
     4201 cgcttgt
//
