LOCUS       NZ_CP058775             3571 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Shigella flexneri strain STLIN_11 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP058775
VERSION     NZ_CP058775.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13925568
            Assembly: GCF_022494275.1
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri
  ORGANISM  Shigella flexneri
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3571)
  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 3571)
  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_022494275.1-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 04:41:01
            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)                     :: 5,039
            CDSs (total)                      :: 4,921
            Genes (coding)                    :: 4,537
            CDSs (with protein)               :: 4,537
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 384
            CDSs (without protein)            :: 384
            Pseudo Genes (ambiguous residues) :: 0 of 384
            Pseudo Genes (frameshifted)       :: 294 of 384
            Pseudo Genes (incomplete)         :: 94 of 384
            Pseudo Genes (internal stop)      :: 37 of 384
            Pseudo Genes (multiple problems)  :: 36 of 384
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP058775.1.
            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..3571
                     /organism="Shigella flexneri"
                     /mol_type="genomic DNA"
                     /strain="STLIN_11"
                     /isolation_source="Stanley WWTPs_11 WWTPs influent"
                     /db_xref="taxon:623"
                     /plasmid="unnamed4"
                     /geo_loc_name="Hong Kong"
                     /lat_lon="22.2 N 114.2 E"
                     /collection_date="2018-12"
     gene            105..281
                     /locus_tag="HZS97_RS25195"
                     /old_locus_tag="HZS97_24810"
     CDS             105..281
                     /locus_tag="HZS97_RS25195"
                     /old_locus_tag="HZS97_24810"
                     /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_155223322.1"
                     /translation="MASFKAQIVTTLDEQDKDFRANPHVKLKRVPTLVSKDERVIVGTD
                     ELPPPDQQDLDLN"
                     /name="hypothetical protein"
     gene            complement(393..1127)
                     /gene="mobV"
                     /locus_tag="HZS97_RS25200"
                     /old_locus_tag="HZS97_24815"
     CDS             complement(393..1127)
                     /gene="mobV"
                     /locus_tag="HZS97_RS25200"
                     /old_locus_tag="HZS97_24815"
                     /inference="COORDINATES: protein motif:HMM:NF013258.4"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobV family relaxase"
                     /protein_id="WP_284527289.1"
                     /translation="MHGKSREEQDAYFADSLEWLRERHGAENVVYAGVHRDETTPHMYA
                     YVVPLDRDTGRLNAKKWLGGSKALNQMQTEFADRIGQRHGLERGIERSKARHQTIRQFY
                     GNLEAADRQQIAVDPKQVEPQTLKKGLFTKEVESPEMVAARLSKEITQANRATIEKASV
                     SAQERRSAKALRDTAKEQQKRLQTLQEPFKGLSKDQMAEVLKMAVGMQRENEQAKEAKK
                     TQILEKFQAKRERERNDRSRGR"
                     /name="mobV"
     gene            complement(1067..1384)
                     /locus_tag="HZS97_RS25205"
                     /old_locus_tag="HZS97_24820"
     CDS             complement(1067..1384)
                     /locus_tag="HZS97_RS25205"
                     /old_locus_tag="HZS97_24820"
                     /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="plasmid recombination protein"
                     /protein_id="WP_284527291.1"
                     /translation="MSDAPNFAILRTQKLKHLASVRRSLKHSFREQDTPNADQSLTPEN
                     SHYGANSTAEAMAEVQARLPEKRRKDAVLAIEYRSQQVPKRCTAKAVKSRTLTLPTRWS
                     G"
                     /name="plasmid recombination protein"
     gene            2307..2885
                     /locus_tag="HZS97_RS25210"
                     /old_locus_tag="HZS97_24825"
     CDS             2307..2885
                     /locus_tag="HZS97_RS25210"
                     /old_locus_tag="HZS97_24825"
                     /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="plasmid replication initiation protein"
                     /protein_id="WP_240763298.1"
                     /translation="MTGTEQEEISRLRRQLAQMSDLLDAEKAAQRLPKNMDFVQVSRAE
                     LRAIADLGAKSALALDLLMVLAQSMDKQNAVMISFKAMQQILGKSRPTLDRAVRLLRED
                     NWIQVVKVGTANAYVLNSAVFWTDRGDKRHMASFKAQIVTTLDEQDKDFRANPHVKLKR
                     VPTLVSKDERVIVGTDELPPPDQQDLDLN"
                     /name="plasmid replication initiation protein"
     gene            complement(2997..3296)
                     /locus_tag="HZS97_RS25215"
                     /old_locus_tag="HZS97_24830"
     CDS             complement(2997..3296)
                     /locus_tag="HZS97_RS25215"
                     /old_locus_tag="HZS97_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001415369.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization domain protein"
                     /protein_id="WP_284527283.1"
                     /translation="MSKEITQANRATIEKASVSAQERRSAKALRDTAKEQQKRLQTLQE
                     PFKGLSKDQMAEVLKMAVGMQRENEQAKEAKKTQILEKFQAKRERERNDRSRGR"
                     /name="mobilization domain protein"
     gene            complement(3242..3502)
                     /locus_tag="HZS97_RS25220"
                     /old_locus_tag="HZS97_24835"
     CDS             complement(3242..3502)
                     /locus_tag="HZS97_RS25220"
                     /old_locus_tag="HZS97_24835"
                     /inference="COORDINATES: protein motif:HMM:NF013258.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_284527285.1"
                     /translation="MQTEFADRIGQRHGLERGIERSKARHQTIRQFYGNLEAADRQQIA
                     VDPKQVAKKASPRRSSLLRWSRRGCRKKSRKRIGQPSRRPL"
                     /name="hypothetical protein"
ORIGIN
        1 tgttacgtga ggacaactgg attcaagtag tgaaggttgg cactgccaac gcttatgttt
       61 tgaatagcgc agtcttttgg actgaccgag gcgataagcg tcacatggca agctttaaag
      121 cgcagatcgt taccacgtta gatgaacagg acaaagattt cagagccaac ccacacgtta
      181 agctaaaacg tgtcccaacg ttggttagca aagatgagcg cgtgatcgtt ggcacagacg
      241 agctaccacc accagaccag caagacttgg atctgaactg atggggtacc gccgactaac
      301 acctgacgaa atcgaggcgc tacgggttga aatgcgcgag gctggcgagt ggtgcagggc
      361 agagctaaag cgccgccgtg cggcgcgtga agctaacggc cacgactccg gtcgttccgt
      421 tcacgctccc gcttcgcctg aaacttctca aggatctgag tcttcttagc ctccttggct
      481 tgctcatttt cccgctgcat ccccaccgcc attttgagca cttccgccat ctgatcctta
      541 gatagcccct taaacggctc ctgaagcgtc tgtaagcgtt tttgttgctc ttttgcagta
      601 tctcttaggg ctttggcgct tcgtcgctcc tgagcgctca cagaggcctt ctcgatggtt
      661 gcccgattcg cttgcgtgat ttctttcgac aaccgcgccg cgaccatctc aggagactcg
      721 acctccttgg tgaataaccc ttttttgagc gtttgaggct cgacctgctt gggatcgact
      781 gcgatctgtt gacggtcggc ggcctccaaa ttcccgtaga actggcgaat ggtctggtgc
      841 cgtgccttgc ttcgttcaat gcctcgttcc agtccgtggc gttggccgat ccggtcggca
      901 aactcggttt gcatctggtt caacgcctta ctgccaccca accacttctt ggcgttcaac
      961 cgacctgtgt cacgatctag cggcacgaca taggcgtaca tgtggggggt ggtttcatcc
     1021 cgatgaaccc ccgcataaac cacgttttcc gccccgtgtc gctctctcag ccactccagc
     1081 gagtcggcaa agtaagcgtc ctgctcttca cggcttttgc cgtgcatcgc ttcgggactt
     1141 gctgtgaccg gtactcgatg gcgagtaccg catccttgcg ccgcttctct ggcaatctgg
     1201 cctgaacctc tgccatcgct tccgccgtcg agttcgcccc gtagtggctg ttctccggcg
     1261 tcaggctctg gtcagcgttg ggcgtgtcct gctctctgaa gctgtgcttc agcgagcgcc
     1321 ggacactggc tagatgcttc agtttttgcg tccgcaggat cgcaaaatta ggcgcgtcgg
     1381 acatcgcatg tccctccgtt ggttgggtga actccaaggg taagacggcg gcacttgaat
     1441 atcaagtgga ctcactacac tttacttcgt aaagccgtgc ccgacttcgt cggttgcagc
     1501 gtccttcgtc cttgctctac gggctacgcc ctgcgcctcc cttcggtcgt tgccaagacc
     1561 ttggggcttt gccccaaacc ccacgttcgc cacgtggcag gggtgcgggg catacggtcg
     1621 caagctccct tctttcccgc accccatgcg ggagcgttgg tcgttccgat ggcgtcaagg
     1681 tcaagccgct tcgcggtcgc tacgcgaacc ttgaccccct ctccacttac ggaacggagc
     1741 aggggtcaag gggtcgtgga ataccggagg ccgcgaagcg gtcgaggata tgccgcgaaa
     1801 gccccttgat gcctgtgcag tgaccccagc ctccggctca ggtgttggcg aagaagggag
     1861 cgcagcgacc gcctgaccca gcacccgagc ctcacggcgg cgagtgtggg gagtccagag
     1921 gggcaacgcc cctttgggcc tagcgcagcg gaaacaaacc ttctcgcctc tggcgaggca
     1981 ttactaagag agcgaagcga acgtaaaacg gggttaggca tcgcttaggg gcaccgcccc
     2041 taatgagata tagagagaaa ttcttaattt taatggtatg aattggctgt aagccttgtg
     2101 ctgcaagggt ttcagaggag ttgattattt tttgttatgt ctcatgtagg tgagacatat
     2161 atgtctcacc ctagggcttt acataaggcg gtaaaactca atcaaaaact ggtaatggtt
     2221 aatcttgaaa tgattaacgg aataaagcaa aatgattaac ccttaatcat gaaatgagac
     2281 atgtatgtct catgcaggtg agacatatga caggcacaga acaagaggaa atatcgagat
     2341 tgagaaggca actggcgcaa atgtcagacc ttctagatgc agagaaagca gcgcaaaggc
     2401 taccaaagaa catggacttc gttcaggtgt cacgagctga attgagagca atagctgatc
     2461 tcggcgctaa aagcgcctta gctcttgatt tgcttatggt gttggctcag tcgatggaca
     2521 aacaaaacgc cgtcatgatt tcgtttaaag ctatgcagca aattcttggt aagtcacgtc
     2581 ctactctcga tagagcagta agactgttac gtgaggacaa ctggattcaa gtagtgaagg
     2641 ttggcactgc caacgcttat gttttgaata gcgcagtctt ttggactgac cgaggcgata
     2701 agcgtcacat ggcaagcttt aaagcgcaga tcgttaccac gttagatgaa caggacaaag
     2761 atttcagagc caacccacac gttaagctaa aacgtgtccc aacgttggtt agcaaagatg
     2821 agcgcgtgat cgttggcaca gacgagctac caccaccaga ccagcaagac ttggatctga
     2881 actgatgggg taccgccgac taacacctga cgaaatcgag gcgctacggg ttgaaatgcg
     2941 cgaggctggc gagtggtgca gggcagagct aaagcgccgc cgtgcggcgc gtgaagctaa
     3001 cggccacgac tccggtcgtt ccgttcacgc tcccgcttcg cctgaaactt ctcaaggatc
     3061 tgagtcttct tagcctcctt ggcttgctca ttttcccgct gcatccccac cgccattttg
     3121 agcacttccg ccatctgatc cttagatagc cccttaaacg gctcctgaag cgtctgtaag
     3181 cgtttttgtt gctcttttgc agtatctctt agggctttgg cgcttcgtcg ctcctgagcg
     3241 ctcacagagg ccttctcgat ggttgcccga ttcgcttgcg tgatttcttt cgacaaccgc
     3301 gccgcgacca tctcaggaga ctcgacctcc ttggtgacgc ttttttggcg acctgcttgg
     3361 gatcgactgc gatctgttga cggtcggcgg cctccaaatt cccgtagaac tggcgaatgg
     3421 tctggtgccg tgccttgctt cgttcaatgc ctcgttccag tccgtggcgt tggccgatcc
     3481 ggtcggcaaa ctcggtttgc atctggttca acgccttact gccacccaac cacttcttgg
     3541 cgttcaaccg acctgtgtca cgatctagcg g
//
