LOCUS       NZ_OR237798             6200 bp    DNA     circular CON 11-SEP-2023
DEFINITION  Shigella flexneri 2a strain CL-046 plasmid pCL046-2, complete
            sequence.
ACCESSION   NZ_OR237798
VERSION     NZ_OR237798.1
DBLINK      BioProject: PRJNA224116
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 2a
  ORGANISM  Shigella flexneri 2a
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Yassine,I., Hamze,M. and Weill,F.-X.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-JUL-2023) Enteric Bacterial Pathogens Unit, Institut
            Pasteur, 28 rue du Dr Roux, Paris 75724, France
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Sequencing Technology             :: MinION
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/11/2023 07:10:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 8
            CDSs (total)                      :: 8
            Genes (coding)                    :: 7
            CDSs (with protein)               :: 7
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            OR237798.1.
            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..6200
                     /organism="Shigella flexneri 2a"
                     /mol_type="genomic DNA"
                     /strain="CL-046"
                     /serotype="2a"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:42897"
                     /plasmid="pCL046-2"
                     /geo_loc_name="Lebanon"
                     /collection_date="2014"
     ARG             complement(2..174)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="21.72"
     ARG             complement(5572..6200)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.52"
                     /coverage="78.28"
     gene            complement(235..1050)
                     /gene="sul2"
                     /locus_tag="RI155_RS00010"
                     /old_locus_tag="pCL046-2_00001"
     ARG             complement(239..1050)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(1510..1668)
                     /locus_tag="RI155_RS00015"
     CDS             complement(1510..1668)
                     /locus_tag="RI155_RS00015"
                     /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="hypothetical protein"
                     /protein_id="WP_032287700.1"
                     /translation="MHEPPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDRL
                     RGLEVEA"
                     /name="hypothetical protein"
     gene            2239..2388
                     /locus_tag="RI155_RS00020"
                     /old_locus_tag="pCL046-2_00002"
     CDS             2239..2388
                     /locus_tag="RI155_RS00020"
                     /old_locus_tag="pCL046-2_00002"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(3133..3573)
                     /locus_tag="RI155_RS00025"
                     /old_locus_tag="pCL046-2_00003"
     CDS             complement(3133..3573)
                     /locus_tag="RI155_RS00025"
                     /old_locus_tag="pCL046-2_00003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            3758..4180
                     /locus_tag="RI155_RS00030"
                     /old_locus_tag="pCL046-2_00004"
     CDS             3758..4180
                     /locus_tag="RI155_RS00030"
                     /old_locus_tag="pCL046-2_00004"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_172684459.1"
                     /translation="MLFLKVKEDNFMSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGG
                     SFNGGGNGGHDNSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARN
                     NMYLDTANNVRVGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4224..>4628
                     /locus_tag="RI155_RS00035"
                     /old_locus_tag="pCL046-2_00005"
                     /pseudo=""
     CDS             4224..>4628
                     /locus_tag="RI155_RS00035"
                     /old_locus_tag="pCL046-2_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(4735..5571)
                     /locus_tag="RI155_RS00040"
                     /old_locus_tag="pCL046-2_00006"
     CDS             complement(4735..5571)
                     /locus_tag="RI155_RS00040"
                     /old_locus_tag="pCL046-2_00006"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     ARG             complement(4739..5571)
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          2031..2204
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.5600000000000002e-86"
     Typing          complement(1502..2107)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 gagccaaatg aggcggtcac gctctccagc gagctcaccg cggcgggaag caggtgcgat
       61 tttcgcgaag gcatgcccgt caccacgtcg aaaaacaaaa tcaccagatt ctccgcctct
      121 gacaggcaac cagtcagaat gcgattcacc aaaaaaaata ttagttcgat tcaatggagg
      181 ttccttcagt tttctgatga agcgcgaata tagagaaata tcccgaatgt gcagttaacg
      241 aattcttgcg gtttctttca gcgccgccaa taccgccagc ccgtcgcgca aggggcgcgg
      301 ctcgtgtgtg cggatgaagt cagctccacc tgcggcggcg gcaagctctg cagcgagtgt
      361 cgcggccccg acatcccccg gaccacggcc tgtgagcgcg cgcagaaagg atttgcgcga
      421 aacagacaga agcaccggca aatcgaagcg cagccgcaat tcatcgaacc gcgccagcac
      481 cgagagcgag gtttcgggag cagcccccag aaaaaacccc atgccgggat caaggacaag
      541 gcggttgcgt ttgataccgg cacccgtcag cgccgcgatg cgcgcgtcaa agaacgccgc
      601 aatgtgatcc atgatgtcgc cagcgggtgc ctcgcgccga tctgcctgcc cgtcttgcac
      661 cgaatgcata acgacgagtt tggcagatga tttcgccaat tgcggataga acgcagcgtc
      721 tggaaaaccg cgaatatcat tgagataggc cacaccacgc gacaaggcat aggcttgcgt
      781 cgcgggttga taactgtcga gcgagacggg aatgccatct gccttgagcg cgtccagcac
      841 cggcgcgata cgcgcgattt ctgtgtcgga cgaaacaggc gcggcgtcgg gattgctgga
      901 tgccggaccg aggtcgatca catctgcccc ctcggccatc agcttacgcg cctgcgcaat
      961 ggctgcgtct ggcgccagat accggcctcc atcggagaaa ctgtccgagg ttatgttgac
     1021 gatgccgaaa atgatgagcg atttattcat gggggcttct ataataataa taatcgagca
     1081 tgagtctcat acggatgctc gggtcgaaag ggaatcccca ggcgagtaac ctgtttgcgg
     1141 tgatccgttt catgatgatg tatctgtagc attttggaaa taaatatatc atctctcaat
     1201 aagtagatat atttatcttt tttgcttctt tggtgctgca agtcaccaat acgagggaaa
     1261 cctgttacgg agcggtttaa ccgtaatcaa cagtgactgg tgtcatgttc ggaagattaa
     1321 ttgatagcaa tctacaaagg atcttcttga gatccttttc aatgaatcgt aatctcttgc
     1381 tctgtaaacg aaaaaaccgc ctggggaggc ggtttgttcg aaggttaagt cagttgggga
     1441 actgcttaac ccggtaacag ggttcacgag accgccatta ccaaaactgt tctttcagtg
     1501 tagccgcagt caggcctcta cttcaagacc tcttaatcta tcttctcgtg cactcctgtt
     1561 actaatggct gctgccagtg gcgttttgtc gtgtctttcc gggttggact caagttgata
     1621 gttaccggac aaggcgcagc ggtcggactg aacggggggt tcgtgcatac agtccagctt
     1681 ggagcgaact gccttcacgg aactgagtgt caggcgtgga atgagaaacc gcggccataa
     1741 cagcggaatg acaccggtaa accgaaaggc aggaacagga gagcgcacga gggagctacc
     1801 agggggaaac gcctgggatc tttatagtcc tgtcgggttt cgccaccact gatttgagcg
     1861 tcagattttg cgatgcttgt caggggggcg gagcctatgg aaaaacggct tcgccgtggc
     1921 cttatctctt ctttgctaag tgtcttcctg gtatcttcca ggaaatttcc gtccccgtcc
     1981 gtaagccggt accgctcgcc gcagccgaac gaccgagcgt agcgagtcag tgagcgagga
     2041 agcggaatat ctcctgtatc gcatattctg ctgacgcgcc ggtgctgcct tttttctcct
     2101 gccacatgaa gcacttcact gattttcgca atcgttgcaa catagtaagc cagtatacac
     2161 tccgctagcg ctacatgact ggttcagggc tgcgccccga aacccgctaa caacctctca
     2221 gctactggat atcaccccat gccatctgaa tatgatgaac aactggattc gactgatacg
     2281 cagcttcccg gcgaatatga cctttttgat ttaatggcgc aggttactga agagaacctg
     2341 catgcccctg tggattttgg gtcgcctgtc ggccgggaag cgttatagct ttttcgcttg
     2401 cccgcgtacg tggtaatact ccggtattac cttttatttc tttattttca tgtaattaca
     2461 gtggattttt aatacccggg tattactcgt gaaaacgaaa tattcctttt ttttctttta
     2521 attcatgcag ttgcgatgaa aatcgcggct gcgttaggtg tatgaccatt ttgaggttga
     2581 aaaataatca accatggcgg gtgatttacg caggttaagg ggagatcgtg acaaaaaaag
     2641 cgttcctcac tgtatcgttc atgcctgcat gaacgggtta ttcttcctga ctacagaatt
     2701 acatcgctcc ttcagttcat acatcacttt tacatcactt atacatcact tttacatcat
     2761 tccttcagct catacgtcac tttcatcctc tgtgccattt gtacatcacc cccttcctga
     2821 acgtgctgac agcgggtttt ccggctgcgc cggcaacgct tcacggccac gcaataaatt
     2881 gcgtccccgt tcaccgtttt cggatgggaa gaacgccgga aacaggactt accccggctg
     2941 aatggtgtga atttccgcgc tatgcacttg tgcgcatact catgcatgcc gtaaaaacag
     3001 agcctgcgcg tttctggcgg gttttcgggt ggtttgttgc ctgttttacc ggtttcccgt
     3061 cagaaacgcc ctgagggcct ctcaggcggt gctgataaca gatgttatgg taaatcagag
     3121 tcacctgcac tgttactctg aaccggagcg aaacagccgc gaccagaatc cccgcttttt
     3181 ttcctgtgcc agcgcgtcag ccagacggct aatttcggcc tgtagttgtt ccctctcctc
     3241 atttcgcagg cggttttctg cttcccgcgc catcttgtct tcaagcatta gggtaacagt
     3301 ctgctgcaga gcgtccagtt tctgctgaat gacgtctagc tgagcatttt ccgcctggct
     3361 aacgacagat ttggagtgtc cctccttgtg cctttttggt gtctcagaag tgcgcagctc
     3421 gccataggcc cgaatcagtt cactggtctc gaactcccgg cgatcatttt ttcctgtgcg
     3481 atagctgaca aggcctttag ccatgtcacg atataattgc gagcgcgact ttcctgttaa
     3541 tttcagtgtc tcttgaactg tgtgccatgc cataaaagtg acagtgtctc ctgtgtgtac
     3601 cgtattgtaa cagcagaaca tattactgtt ttaacacaaa aggtctgagg ctgcccgtga
     3661 ggcgtgaaaa atacacaaaa aacctgttga cggtgtggtt ttgacgggcg tagtatttcg
     3721 aatactgtat ataaacacat tgttataaat acagtttttg ctgtttttaa aagtcaaaga
     3781 ggataatttt atgagtacag agttaaatag cggtactgtc ggtggttttg gtcacatggg
     3841 accaaatgac ccctacaatg atggtcatag cggctctgga agttcgggag gtagttttaa
     3901 cggtggtggt aatggtggcc atgataatag tagtggttca tcttatactg catcctttgg
     3961 tctcatcact ggccgacacc cgataactgt cccaggtacg aagaatatta attctgtcga
     4021 tctttctgct gtcattaata acattataca tcatgaaggt gcacgcaata acatgtacct
     4081 agatactgcg aacaatgtaa gagtgggagt gacgggcact ggctggcaat gtctagcaac
     4141 ggcaggcatt tcggctgagg gtaaaagaac tttccgctaa gcgatagact gtatgtaaac
     4201 acagtattgc aaggacgcgg aacatgcctc atgtggcggc caggacggcc agccgggatc
     4261 gggatactgg tcgttaccag agccaccgac ccgagcaaac ccttctctat cagatcgttg
     4321 acgagtatta cccggcattc gctgcgctta tggcagagca gggaaaggaa ttgccgggct
     4381 atgtgcaacg ggaatttgaa gaatttctcc aatgcgggcg gctggagcat ggctttctac
     4441 gggttcgctg cgagtcttgc cacgccgagc acctggtcgc tttcagctgt aagcgtcgcg
     4501 gtttctgccc gagctgtggg gcgcggcgga tggccgaaag tgccgccttg ctggttgatg
     4561 aagtactgcc tgaacaaccc atgcgtcagt gggtgttgag cttcccgttt cagctgcgtt
     4621 tcctgtttgg ggtcgtttgc gggaaggggc ggaatcctac gctaaggctt tggccagcga
     4681 tattctccgg tgagattgat gtgttcccag gggataggag aagtcgcttg atatctagta
     4741 tgacgtctgt cgcacctgct tgatcgcggc cgcgatagct agatcgcgtt gctcctcttc
     4801 tccatccgcg ttccaagctg cggaaaggca cccataagcg tacgcctggt cgagcaggcg
     4861 acgcggatcg acgtccagcg cacgagagaa tgcgtccgcc atctgtgcaa tgcgtctagg
     4921 atcgagacaa aggtcgtctc tgtcagccgg atcgtagaac atattggcgg cgccaaagcc
     4981 cacttcaccg accagaccga cgggatctat caccagccag ccgcgactgg agaacatgat
     5041 gttttcatga tgcagatcgc catgtagccc acgcagttcc gaggcattgc tcatcatttg
     5101 atcggctata atcgccgcgt ggacgtagtc agtttgacaa cctgcgtttt gatcatcgcg
     5161 cgcccgctga aacaaagctg caaagcgatc ccggatcggg agaagggcag aaggcagggg
     5221 ttcctcagat gcggcataca gcttcgccat tagttccgct gcaatttcgg tcgcctggta
     5281 gtcgccgtgc tcggcaacga tgtgagagag cattcgctcc ccggcatatt cgagcaacat
     5341 cagattgttc tcacgaccga gcaaccggac tgctcccctc ccattgcgcc ataccagata
     5401 gtcggccccg cgcagttcat cagcaatgtc ttctataggt ttcaatccct tgacgattgc
     5461 aggagtcccg tctggcaatg aaactttcca aacgaggctg gaaaaggtgt ccgcaatgag
     5521 aacaggttgc gaaacgtgcc aatgagcagg aaaaacaggc ggcatgaaca tcaaccccaa
     5581 gtcagagggt ccaatcgcag atagaaggca aggcgttcgc ggtcgggggc ttcgatcccc
     5641 aatacattga ataggacagc gaaggcgcgc tctgcttcat ctggcgctgc ccagttctct
     5701 tcggcgttag caatcatgag tgccaaatcg gcatagcgat ctgctgttcc gagccgccca
     5761 aggtcgatca gacccgtgca ttgaagagtt ttagggtcca ccatgaagtt cggcatgcag
     5821 ggatcaccat ggcaaacaac catatcggtg cgctcttggt cgagccgcac cggtagctct
     5881 cgttcgacac gagccaaaag atcgagctgc ggcgtactct tgtcctcgtc cggtaagaag
     5941 tcgggattga cggcattgcg ggacaccaca tcaacggcgc gtccgaacat tcgcgacagc
     6001 ctgcgctcaa acggacattg atcaaccgat aggctgtgaa cagcgccaag ttgctgcccc
     6061 attgacggcc acgctttgag caaatccgct ccagacagat cagccgccgg tactcccgga
     6121 attgccgtta tcaccaagca tgcaccctcc tgttcctctt gccagttgat gacctcgggg
     6181 caagccacac ctcgaccttt
//
