LOCUS       NZ_MW133277             6200 bp    DNA     circular CON 19-JUN-2024
DEFINITION  Shigella flexneri 1b strain 422 plasmid pSF422-2, complete sequence.
ACCESSION   NZ_MW133277
VERSION     NZ_MW133277.1
DBLINK      BioProject: PRJNA224116
KEYWORDS    RefSeq.
SOURCE      Shigella flexneri 1b
  ORGANISM  Shigella flexneri 1b
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 6200)
  AUTHORS   Nisa,I., Qasim,M. and Driessen,A.J.M.
  TITLE     Characterization of novel plasmid (pSF422-2) isolated from Shigella
            flexneri 1b 422 strain of Pakistan
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6200)
  AUTHORS   Nisa,I., Qasim,M. and Driessen,A.J.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (12-OCT-2020) Microbiology, Kohat university of science
            and technology, Kohat, Kohat, KP 26000, Pakistan
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: TopHat2 v. 2.1.1
            Coverage                          :: 3016
            Sequencing Technology             :: Illumina
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023574205.1-RS_2024_06_19
            Annotation Date                   :: 06/19/2024 10:16:40
            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)                     :: 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
            MW133277.1.
            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 1b"
                     /mol_type="genomic DNA"
                     /strain="422"
                     /serotype="1b"
                     /isolation_source="Pediatric diarrheal stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:41434"
                     /plasmid="pSF422-2"
                     /geo_loc_name="Pakistan"
                     /collection_date="2016"
                     /collected_by="Department of Microbiology, Kohat University
                     of Science and Technology, Kohat, Pakistan"
     gene            complement(123..281)
                     /locus_tag="NBT57_RS00040"
     CDS             complement(123..281)
                     /locus_tag="NBT57_RS00040"
                     /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            852..1001
                     /locus_tag="NBT57_RS00005"
     CDS             852..1001
                     /locus_tag="NBT57_RS00005"
                     /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(1746..2186)
                     /locus_tag="NBT57_RS00010"
     CDS             complement(1746..2186)
                     /locus_tag="NBT57_RS00010"
                     /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            2371..2793
                     /locus_tag="NBT57_RS00015"
     CDS             2371..2793
                     /locus_tag="NBT57_RS00015"
                     /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            2837..>3241
                     /locus_tag="NBT57_RS00020"
                     /pseudo=""
     CDS             2837..>3241
                     /locus_tag="NBT57_RS00020"
                     /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(3348..4184)
                     /locus_tag="NBT57_RS00025"
     CDS             complement(3348..4184)
                     /locus_tag="NBT57_RS00025"
                     /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"
     gene            complement(4184..4987)
                     /gene="aph(3'')-Ib"
                     /locus_tag="NBT57_RS00030"
     ARG             complement(4188..4987)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            complement(5048..5863)
                     /gene="sul2"
                     /locus_tag="NBT57_RS00035"
     ARG             complement(5052..5863)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             complement(3352..4184)
                     /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          644..817
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(115..720)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.593"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 acgaaaaaac cgcctgggga ggcggtttgt tcgaaggtta agtcagttgg ggaactgctt
       61 aacccggtaa cagggttcac gagaccgcca ttaccaaaac tgttctttca gtgtagccgc
      121 agtcaggcct ctacttcaag acctcttaat ctatcttctc gtgcactcct gttactaatg
      181 gctgctgcca gtggcgtttt gtcgtgtctt tccgggttgg actcaagttg atagttaccg
      241 gacaaggcgc agcggtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga
      301 actgccttca cggaactgag tgtcaggcgt ggaatgagaa accgcggcca taacagcgga
      361 atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca cgagggagct accaggggga
      421 aacgcctggg atctttatag tcctgtcggg tttcgccacc actgatttga gcgtcagatt
      481 ttgcgatgct tgtcaggggg gcggagccta tggaaaaacg gcttcgccgt ggccttatct
      541 cttctttgct aagtgtcttc ctggtatctt ccaggaaatt tccgtccccg tccgtaagcc
      601 ggtaccgctc gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa
      661 tatctcctgt atcgcatatt ctgctgacgc gccggtgctg ccttttttct cctgccacat
      721 gaagcacttc actgattttc gcaatcgtgg caacatagta agccagtata cactccgcta
      781 gcgctacatg actggttcag ggctgcgccc cgaaacccgc taacaacctc tcagctactg
      841 gatatcaccc catgccatct gaatatgatg aacaactgga ttcgactgat acgcagcttc
      901 ccggcgaata tgaccttttt gatttaatgg cgcaggttac tgaagagaac ctgcatgccc
      961 ctgtggattt tgggtcgcct gtcggccggg aagcgttata gctttttcgc ttgcccgcgt
     1021 acgtggtaat actccggtat taccttttat ttctttattt tcatgtaatt acagtggatt
     1081 tttaataccc gggtattact cgtgaaaacg aaatattcct tttttttctt ttaattcatg
     1141 cagttgcgat gaaaatcgcg gctgcgttag gtgtatgacc attttgaggt tgaaaaataa
     1201 tcaaccatgg cgggtgattt acgcaggtta aggggagatc gtgacaaaaa aagcgttcct
     1261 cactgtatcg ttcatgcctg catgaacggg ttattcttcc tgactacaga attacatcgc
     1321 tccttcagtt catacatcac ttttacatca cttatacatc acttttacat cattccttca
     1381 gctcatacgt cactttcatc ctctgtgcca tttgtacatc acccccttcc tgaacgtgct
     1441 gacagcgggt tttccggctg cgccggcaac gcttcacggc cacgcaataa attgcgtccc
     1501 cgttcaccgt tttcggatgg gaagaacgcc ggaaacagga cttaccccgg ctgaatggtg
     1561 tgaatttccg cgctatgcac ttgtgcgcat actcatgcat gccgtaaaaa cagagcctgc
     1621 gcgtttctgg cgggttttcg ggtggtttgt tgcctgtttt accggtttcc cgtcagaaac
     1681 gccctgaggg cctctcaggc ggtgctgata acagatgtta tggtaaatca gagtcacctg
     1741 cactgttact ctgaaccgga gcgaaacagc cgcgaccaga atccccgctt tttttcctgt
     1801 gccagcgcgt cagccagacg gctaatttcg gcctgtagtt gttccctctc ctcatttcgc
     1861 aggcggtttt ctgcttcccg cgccatcttg tcttcaagca ttagggtaac agtctgctgc
     1921 agagcgtcca gtttctgctg aatgacgtct agctgagcat tttccgcctg gctaacgaca
     1981 gatttggagt gtccctcctt gtgccttttt ggtgtctcag aagtgcgcag ctcgccatag
     2041 gcccgaatca gttcactggt ctcgaactcc cggcgatcat tttttcctgt gcgatagctg
     2101 acaaggcctt tagccatgtc acgatataat tgcgagcgcg actttcctgt taatttcagt
     2161 gtctcttgaa ctgtgtgcca tgccataaaa gtgacagtgt ctcctgtgtg taccgtattg
     2221 taacagcaga acatattact gttttaacac aaaaggtctg aggctgcccg tgaggcgtga
     2281 aaaatacaca aaaaacctgt tgacggtgtg gttttgacgg gcgtagtatt tcgaatactg
     2341 tatataaaca cattgttata aatacagttt ttgctgtttt taaaagtcaa agaggataat
     2401 tttatgagta cagagttaaa tagcggtact gtcggtggtt ttggtcacat gggaccaaat
     2461 gacccctaca atgatggtca tagcggctct ggaagttcgg gaggtagttt taacggtggt
     2521 ggtaatggtg gccatgataa tagtagtggt tcatcttata ctgcatcctt tggtctcatc
     2581 actggccgac acccgataac tgtcccaggt acgaagaata ttaattctgt cgatctttct
     2641 gctgtcatta ataacattat acatcatgaa ggtgcacgca ataacatgta cctagatact
     2701 gcgaacaatg taagagtggg agtgacgggc actggctggc aatgtctagc aacggcaggc
     2761 atttcggctg agggtaaaag aactttccgc taagcgatag actgtatgta aacacagtat
     2821 tgcaaggacg cggaacatgc ctcatgtggc ggccaggacg gccagccggg atcgggatac
     2881 tggtcgttac cagagccacc gacccgagca aacccttctc tatcagatcg ttgacgagta
     2941 ttacccggca ttcgctgcgc ttatggcaga gcagggaaag gaattgccgg gctatgtgca
     3001 acgggaattt gaagaatttc tccaatgcgg gcggctggag catggctttc tacgggttcg
     3061 ctgcgagtct tgccacgccg agcacctggt cgctttcagc tgtaagcgtc gcggtttctg
     3121 cccgagctgt ggggcgcggc ggatggccga aagtgccgcc ttgctggttg atgaagtact
     3181 gcctgaacaa cccatgcgtc agtgggtgtt gagcttcccg tttcagctgc gtttcctgtt
     3241 tggggtcgtt tgcgggaagg ggcggaatcc tacgctaagg ctttggccag cgatattctc
     3301 cggtgagatt gatgtgttcc caggggatag gagaagtcgc ttgatatcta gtatgacgtc
     3361 tgtcgcacct gcttgatcgc ggccgcgata gctagatcgc gttgctcctc ttctccatcc
     3421 gcgttccaag ctgcggaaag gcacccataa gcgtacgcct ggtcgagcag gcgacgcgga
     3481 tcgacgtcca gcgcacgaga gaatgcgtcc gccatctgtg caatgcgtct aggatcgaga
     3541 caaaggtcgt ctctgtcagc cggatcgtag aacatattgg cggcgccaaa gcccacttca
     3601 ccgaccagac cgacgggatc tatcaccagc cagccgcgac tggagaacat gatgttttca
     3661 tgatgcagat cgccatgtag cccacgcagt tccgaggcat tgctcatcat ttgatcggct
     3721 ataatcgccg cgtggacgta gtcagtttga caacctgcgt tttgatcatc gcgcgcccgc
     3781 tgaaacaaag ctgcaaagcg atcccggatc gggagaaggg cagaaggcag gggttcctca
     3841 gatgcggcat acagcttcgc cattagttcc gctgcaattt cggtcgcctg gtagtcgccg
     3901 tgctcggcaa cgatgtgaga gagcattcgc tccccggcat attcgagcaa catcagattg
     3961 ttctcacgac cgagcaaccg gactgctccc ctcccattgc gccataccag atagtcggcc
     4021 ccgcgcagtt catcagcaat gtcttctata ggtttcaatc ccttgacgat tgcaggagtc
     4081 ccgtctggca atgaaacttt ccaaacgagg ctggaaaagg tgtccgcaat gagaacaggt
     4141 tgcgaaacgt gccaatgagc aggaaaaaca ggcggcatga acatcaaccc caagtcagag
     4201 ggtccaatcg cagatagaag gcaaggcgtt cgcggtcggg ggcttcgatc cccaatacat
     4261 tgaataggac agcgaaggcg cgctctgctt catctggcgc tgcccagttc tcttcggcgt
     4321 tagcaatcat gagtgccaaa tcggcatagc gatctgctgt tccgagccgc ccaaggtcga
     4381 tcagacccgt gcattgaaga gttttagggt ccaccatgaa gttcggcatg cagggatcac
     4441 catggcaaac aaccatatcg gtgcgctctt ggtcgagccg caccggtagc tctcgttcga
     4501 cacgagccaa aagatcgagc tgcggcgtac tcttgtcctc gtccggtaag aagtcgggat
     4561 tgacggcatt gcgggacacc acatcaacgg cgcgtccgaa cattcgcgac agcctgcgct
     4621 caaacggaca ttgatcaacc gataggctgt gaacagcgcc aagttgctgc cccattgacg
     4681 gccacgcttt gagcaaatcc gctccagaca gatcagccgc cggtactccc ggaattgccg
     4741 ttatcaccaa gcatgcaccc tcctgttcct cctgccagtt gatgacctcg gggcaagcca
     4801 cacctcgacc tttgagccaa atgaggcggt cacgctctcc agcgagctca ccgcggcggg
     4861 aagcaggtgc gattttcgcg aaggcatgcc cgtcaccacg tcgaaaaaca aaatcaccag
     4921 attctccgcc tctgacaggc aaccagtcag aatgcgattc accaaaaaaa atattagttc
     4981 gattcaatgg aggttccttc agttttctga tgaagcgcga atatagagaa atatcccgaa
     5041 tgtgcagtta acgaattctt gcggtttctt tcagcgccgc caataccgcc agcccgtcgc
     5101 gcaaggggcg cggctcgtgt gtgcggatga agtcagctcc acctgcggcg gcggcaagct
     5161 ctgcagcgag tgtcgcggcc ccgacatccc ccggaccacg gcctgtgagc gcgcgcagaa
     5221 aggatttgcg cgaaacagac agaagcaccg gcaaatcgaa gcgcagccgc aattcatcga
     5281 accgcgccag caccgagagc gaggtttcgg gagcagcccc cagaaaaaac cccatgccgg
     5341 gatcaaggac aaggcggttg cgtttgatac cggcacccgt cagcgccgcg atgcgcgcgt
     5401 caaagaacgc cgcaatgtga tccatgatgt cgccagcggg tgcctcgcgc cgatctgcct
     5461 gcccgtcttg caccgaatgc ataacgacga gtttggcaga tgatttcgcc aattgcggat
     5521 agaacgcagc gtctggaaaa ccgcgaatat cattgagata ggccacacca cgcgacaagg
     5581 cataggcttg cgtcgcgggt tgataactgt cgagcgagac gggaatgcca tctgccttga
     5641 gcgcgtccag caccggcgcg atacgcgcga tttctgtgtc ggacgaaaca ggcgcggcgt
     5701 cgggattgct ggatgccgga ccgaggtcga tcacatctgc cccctcggcc atcagcttac
     5761 gcgcctgcgc aatggctgcg tctggcgcca gataccggcc tccatcggag aaactgtccg
     5821 aggttatgtt gacgatgccg aaaatgatga gcgatttatt catgggggct tctataataa
     5881 taataatcga gcatgagtct catacggatg ctcgggtcga aagggaatcc ccaggcgagt
     5941 aacctgtttg cggtgatccg tttcatgatg atgtatctgt agcattttgg aaataaatat
     6001 atcatctctc aataagtaga tatatttatc ttttttgctt ctttggtgct gcaagtcacc
     6061 aatacgaggg aaacctgtta cggagcggtt taaccgtaat caacagtgac tggtgtcatg
     6121 ttcggaagat taattgatag taatctacaa aggatcttct tgagatcctt ttcaatgaat
     6181 cgtaatctct tgctctgtaa
//
