LOCUS       NZ_CP019694             3619 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain 75/02 plasmid p75-02_6, complete sequence.
ACCESSION   NZ_CP019694
VERSION     NZ_CP019694.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06286561
            Assembly: GCF_002150905.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3619)
  AUTHORS   Svab,D., Balint,B., Maroti,G., Vasarhelyi,B., Horvath,B. and Toth,I.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2017) NGS Platform, Seqomics Ltd., Vallakozok u.
            7., Morahalom 6782, Hungary
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: CLC Genomics Workbench v. 9.5; Geneious v. R9;
            SPAdes v. 3.0.5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140.0x
            Sequencing Technology             :: Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002150905.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 03:20:21
            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)                     :: 5,359
            CDSs (total)                      :: 5,230
            Genes (coding)                    :: 4,495
            CDSs (with protein)               :: 4,495
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 735
            CDSs (without protein)            :: 735
            Pseudo Genes (ambiguous residues) :: 0 of 735
            Pseudo Genes (frameshifted)       :: 214 of 735
            Pseudo Genes (incomplete)         :: 524 of 735
            Pseudo Genes (internal stop)      :: 123 of 735
            Pseudo Genes (multiple problems)  :: 119 of 735
            Pseudo Genes (short protein)      :: 3 of 735
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP019694.1.
            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..3619
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="75/02"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="p75-02_6"
                     /geo_loc_name="Hungary: Halimba"
                     /lat_lon="47.0335 N 17.5364 E"
                     /collection_date="2002"
                     /collected_by="National Center for Epidemiology, Budapest,
                     Hungary"
     gene            complement(join(<3619..<3619,1..128))
                     /locus_tag="BZ172_RS30180"
                     /pseudo=""
     CDS             complement(join(<3619..<3619,1..128))
                     /locus_tag="BZ172_RS30180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_858227.1"
                     /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="hypothetical protein"
                     /name="hypothetical protein"
     gene            <579..>641
                     /locus_tag="BZ172_RS29480"
                     /pseudo=""
     CDS             <579..>641
                     /locus_tag="BZ172_RS29480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001743492.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS66 family insertion sequence element accessory
                     protein TnpB"
                     /name="IS66 family insertion sequence element accessory
                     protein TnpB"
     gene            complement(710..862)
                     /locus_tag="BZ172_RS29485"
     CDS             complement(710..862)
                     /locus_tag="BZ172_RS29485"
                     /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_000994090.1"
                     /translation="MNARLRALLQTQQDTIHQMAEYNRLLSQRMAAYASEINRLKALVA
                     KLQRM"
                     /name="hypothetical protein"
     gene            complement(1033..2232)
                     /locus_tag="BZ172_RS27655"
                     /old_locus_tag="BZ172_29465"
     CDS             complement(1033..2232)
                     /locus_tag="BZ172_RS27655"
                     /old_locus_tag="BZ172_29465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558319.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /protein_id="WP_000947184.1"
                     /translation="MLSAFTPRPLKRLFTANQCWTSFLDAGGLRDIEVEAVTKMLACGT
                     RILGVKEYNCDKPECPHVRYVTNSCGSRACPSCGKKATDLWIATQLNRLPDCDWVHLVF
                     TLPDTLWPVFESNRWLLNDVCRLAVENLLYAARKRGQEPGIFCAIHTYGRRLNWHPHVH
                     VSVTCGCLNKHGQWKKLSFLKDAMRSRWMWNMRQRLLKAWSEGLAMPESLSHITTESQW
                     RSLVLKAGGKYWHVYMSKKTAGGRNTARYLGRYLKKPPIAASRLAHYNGGASLSFRYLD
                     HKTGETATETLTQRELVARLKQHIPEKFFKMVRYFGFLANRVCGEKLPQVYRALGMDKP
                     EPVAKVCYAQMVKQFLSRDPFECVLCGGRMVYRRAIAGLNVEGLKKNARDISLLRYMPA
                     "
                     /name="IS91 family transposase"
     gene            complement(2242..2430)
                     /locus_tag="BZ172_RS27660"
                     /old_locus_tag="BZ172_29470"
     CDS             complement(2242..2430)
                     /locus_tag="BZ172_RS27660"
                     /old_locus_tag="BZ172_29470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_707687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000957853.1"
                     /translation="MLTRKSIDTVLLSVGAEKLSQREWDWMKMLKPMDPPPAMVAASIL
                     ERRGDTAALTRLQDTGG"
                     /name="hypothetical protein"
     gene            2969..>3619
                     /gene="ospC2"
                     /locus_tag="BZ172_RS27665"
                     /old_locus_tag="BZ172_29475"
                     /pseudo=""
     CDS             2969..>3619
                     /gene="ospC2"
                     /locus_tag="BZ172_RS27665"
                     /old_locus_tag="BZ172_29475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_858196.1"
                     /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="type 3 secretion system effector OspC2"
                     /name="ospC2"
ORIGIN
        1 tctggcatag tttgttgtgc agcgtttcgc actgatgtca cttttggaaa caatgtatgt
       61 aatctgttat ccatagaatc tatattgcat tgggtatttg ctgagttcag tgtttctgat
      121 atattcataa aatgaacctt atatgaaaac agttttaatt aatatctttc cctacaagat
      181 atagcagggt atgaattaca atttttgagt atatatacaa tatactgcat gtaattagat
      241 aagggtgtta tatacttttg atgttatgtg atgccagata tttcaaaata tctaaaatcc
      301 gatgcttaag aactcaagtt aatctttttt gtgaaattat tttcataatt taataactat
      361 atcaatttta ttgaacagca atgaatttta ctataaaaaa acgatacttt ctctgattcc
      421 tcttatggag tgcttccagt tagtggaatg tgtattctgc aatgaaatcc tcgatgattt
      481 tttcatgaag ctcaactaag tgtgaaaaac tgatgttttt ttaatagagg ttagtttggc
      541 catatataat tattgtactt ttgcagtttt tttgttactt cccttatgag ttcaaaatcg
      601 ccttaatgga gcagtcactg caacccagag cctgtgtggc gtagatcgcc cgtgaaaatg
      661 gaatctgccg ttcggttttt gcgcgaagtt tttctgagct tttaccgaac tacatacgct
      721 gcagtttcgc aaccagcgcc ttcagtcggt tgatttcgga agcataagcc gccatccgct
      781 gtgagagcag gcggttgtat tcagccatct ggtggatagt gtcctgttgc gtctgcaaca
      841 gtgcccgcag gcgggcgttc acgtatagga aattgaaaaa ctaagcgata cccctgtccg
      901 cgccttatgc cacgtgagcc tttctgtttt tccccaccac tccggtgttt tctctctctg
      961 catggtcgat tcttataccg caacaggctg ttttttatac ttgcaccgat tcccgggcac
     1021 acttagcctg tgtcaggccg gcatatacct cagcagactg atatcccgcg cgtttttctt
     1081 cagcccctcc acattcagcc ccgcaatggc ccggcggtat accatccggc cgccacacag
     1141 cacgcattcg aacgggtcac gactcaggaa ctgtttcacc atttgtgcat agcacacttt
     1201 cgccactggt tccggtttat ccatccccag agcacggtac acctgcggca gcttctctcc
     1261 acacacccgg ttggcaagga acccgaagta cctcaccatc ttaaaaaact tctccgggat
     1321 gtgctgtttc agcctcgcga ccagctcacg ctgtgtcagc gtttccgtcg ccgtttctcc
     1381 cgttttgtgg tccaggtaac ggaagctcag gctcgcccct ccgttgtaat gtgccagccg
     1441 ggaggccgct atcggcggct tcttcagata acgacccagg tagcgcgccg tattcctccc
     1501 gccggccgtt tttttcgaca tgtacacatg ccagtatttt cctccggctt tcagcaccag
     1561 gcttctccac tgtgattccg tcgtgatatg tgacaacgac tccggcatcg ccagcccctc
     1621 tgaccacgct ttcagaagcc gttgccgcat attccacatc caccgcgaac gcatcgcgtc
     1681 tttcaggaag ctcagctttt tccactgacc atgcttattc agacatccac aggttacaga
     1741 cacatgtaca tgcggatgcc agttgagacg acggccatac gtgtggatgg cgcagaagat
     1801 accgggttcc tgcccccgtt tccgggcggc atacagcaga ttctccaccg ccagacggca
     1861 cacgtcattc agcagccacc ggttgctttc gaacaccggc cacagcgtgt ccggcagggt
     1921 gaagaccaga tgtacccagt cgcagtcagg aagacgattc agctgtgtcg ctatccacag
     1981 gtctgtggcc ttttttccgc aggacgggca ggcacggctg ccgcatgagt tagtgacgta
     2041 tctgacgtgg gggcactcag gtttatcgca gttgtattcc ttcactccca gtatccgcgt
     2101 gccgcaggcc agcatttttg tgacagcctc aacctcgata tcgcgcagac cgcccgcatc
     2161 caggaaggac gtccagcact ggttggccgt gaacagacgt ttcagcgggc ggggagtaaa
     2221 agcggacaac atgaggacgg attaaccccc ggtatcctgt agccgggtaa gggctgctgt
     2281 gtcgccacgg cgctccagga tggaggccgc gaccatcgca ggtggtgggt ccatgggttt
     2341 gagcatcttc atccagtccc attcacgttg tgagagcttc tcagcaccaa cagagagcag
     2401 aacggtatct atacttttgc gggtcaacat aagaggatga gtccttaata aaacaggtcc
     2461 tcagagcata catattctgc ggagcgtgcg gcaacaacag gacgaacagg ggcggttttc
     2521 aatttgcagc cgtcaggctg ccgtggttca atatgttgtg taaacagaca gttactataa
     2581 ctcagatgat taagggacac agcctactat tccgcgcagc tatttagctc tctttttgtt
     2641 gagcgcccat gattctttca tttattgtta ctaatttttt atgttatcat catgttatga
     2701 gcatgccctg ttctgcgtct ctattttatc tatcatattc tgagcattaa ctacataaca
     2761 aggcgcaaga tatatatcca aaaacaaata atactgttgc aataattcct ttcagtaaag
     2821 gaagtgtgat taaactcagg ggatttcaga gtgaaaatcg tacaacatat taaaatatgt
     2881 tcgttataat acatacaaga aaatattaag ttagataata ttattctaaa taactgcaga
     2941 taaaaacgca cataatgggg gatgttttat gaaaatacct gaagcagtaa atcatattaa
     3001 tgttcagaac aatattgatc ttgttgatgg aaaaataaat ccgaacaaag atacaaaagc
     3061 attacaaaaa aacatatcat gcgtaacaaa ctcatcctct tctggcataa gtgaaaaaca
     3121 tttagatcac tgtgctgata ctgtgaaaag ctttttaagg aagtctatag cagcgcaaag
     3181 ttatagtaaa atgttctctc aagggaccag tttcaaatca ttaaatcttt ctattgaagc
     3241 gccatctgga gcacggtcat catttcggtc acttgagcac ctcgataagg tgtccagaca
     3301 ctatctttct gaaataatac aaaaaactca tcctctttct tcggatgaac gtcacttgct
     3361 ctctattatt attaattctg attttaactt cagacatcaa agtaacgcta acctgtcaaa
     3421 taatactctt aatattaagt cctttgataa aattaagtct gagaatatac aaacatataa
     3481 aaacacattc tctgaggata ttgaagaaat agctaaccac gattttgttt tttttggggt
     3541 tgaaatttcc aatcatcaag aaacactccc actaaataaa acacatcata ctgtagattt
     3601 tggtgctaat gcgtatatc
//
