LOCUS       CP038000                2690 bp    DNA     circular BCT 26-MAR-2019
DEFINITION  Shigella sonnei strain FC1653 plasmid unnamed3, complete sequence.
ACCESSION   CP038000
VERSION     CP038000.1
DBLINK      BioProject: PRJNA414945
            BioSample: SAMN07811411
KEYWORDS    .
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2690)
  AUTHORS   Anandan,S., Muthuirulandi Sethuvel,D.P., Devanga Ragupathi,N.K.,
            Veeraraghavan,B., Neeravi,A., Venkatesan,M. and Vasudevan,K.
  TITLE     Complete genome sequence of S. sonnei using hybrid genome assembly
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2690)
  AUTHORS   Prabaa,D., Shalini,A., Kumar,N. and Balaji,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-OCT-2017) Clinical Microbiology, Christian Medical
            College, Ida Scudder Road, Vellore 632004, India
REFERENCE   3  (bases 1 to 2690)
  AUTHORS   Anandan,S., Muthuirulandi Sethuvel,D.P., Devanga Ragupathi,N.K.,
            Veeraraghavan,B., Neeravi,A., Venkatesan,M. and Vasudevan,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-FEB-2019) Clinical Microbiology, Christian Medical
            College, Ida Scudder Road, Vellore 632004, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method :: Canu v. 1.7; Unicycler hybrid v. 0.4.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 174.0x
            Sequencing Technology             :: Oxford Nanopore; IonTorrent
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/15/2019 14:26:40
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.7
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 4,932
            CDSs (total)                      :: 4,806
            Genes (coding)                    :: 3,949
            CDSs (with protein)               :: 3,949
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 95
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 857
            CDSs (without protein)            :: 857
            Pseudo Genes (ambiguous residues) :: 0 of 857
            Pseudo Genes (frameshifted)       :: 495 of 857
            Pseudo Genes (incomplete)         :: 335 of 857
            Pseudo Genes (internal stop)      :: 117 of 857
            Pseudo Genes (multiple problems)  :: 84 of 857
            ##Genome-Annotation-Data-END##
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="FC1653"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="unnamed3"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2017"
                     /collected_by="Christian Medical College"
     gene            451..718
                     /locus_tag="CSW73_024640"
                     /pseudo=""
     CDS             451..718
                     /locus_tag="CSW73_024640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012000844.1"
                     /note="frameshifted; 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            complement(1039..1233)
                     /locus_tag="CSW73_024645"
     CDS             complement(1039..1233)
                     /locus_tag="CSW73_024645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001712891.1"
                     /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="QBQ28141.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1519..1842
                     /locus_tag="CSW73_024650"
     CDS             1519..1842
                     /locus_tag="CSW73_024650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="nikA protein"
                     /protein_id="QBQ28142.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="nikA protein"
     gene            1862..2047
                     /locus_tag="CSW73_024655"
     CDS             1862..2047
                     /locus_tag="CSW73_024655"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001485274.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QBQ28143.1"
                     /translation="MKTDGMNTVSSQSDLHSLSCIAMQRAENDPDASFLFFRGKTSIFV
                     VSASESRSARFSGAYN"
                     /name="hypothetical protein"
     gene            complement(2068..2607)
                     /locus_tag="CSW73_024660"
     CDS             complement(2068..2607)
                     /locus_tag="CSW73_024660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015870862.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="adhesin"
                     /protein_id="QBQ28144.1"
                     /translation="MSHGGWKEISHPQTLFTRQKGDGWTVVPKNLRIDFYTKDNDFTKG
                     LSVLSEVNKRHTEAQKGLTPSLNISKDDLKVLANARNIPQSKLEEEMMSQAIYRKEYAT
                     SNEKIKNYALYYHEQAQNIIQRHQDGLGNKNIDIAFITDKNHKKHLSDIFKVINESGVK
                     YDVIHFGACRVNREEK"
                     /name="adhesin"
     Typing          1272..1510
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(470..996)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1520..1839
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 tgtttggtga tgggtgtgtt tttatatttt tggatgatgt tagaaggtga tttcttattg
       61 ttgatgatat gtttgttatg agattcgaat tgagtatttt catttgttaa caatccattt
      121 ttgcggtgtt ttttattgtt ttttttcttt tgtttaaggg tgtgtcggtg taagtgttta
      181 ttttatgggt taaagtagga taccaagtgt gaaaaaaaat taaaggttct tcttgagatc
      241 ctttttttct gcgcgtaatc tgctgcctgt aaacgaaaaa accgccctgc aaggcggttt
      301 ttcgaaggtt ctcagagcta ccaactcttt gagccgaggt aactggcttg gaggagcgca
      361 gtcaccaaaa cttgttcttt cagtttagcc ttaacaggcg catgacttca agtcttactc
      421 ctctaattcg gttatcagtg gctgctgcca gtggcgataa ttcgtgtctt accgggttgg
      481 actcaagacg atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca
      541 cacagcccag cttggagcga acgacctaca ccgggccgag ataccaacag cgtgagctat
      601 gagaaagcgc cacgcttccc gaagggagaa aggcggacag gtatccggta aacggcaggg
      661 tcggaacagg agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc
      721 ctgtcgggtt tcgccacctc tgacttgagc gtcgattttt gtgatgctcg tcaggggggc
      781 ggagcctatg gaaaaacgcc acctgcgcgg cctttgtccc tgccttcggc tttttgctca
      841 catgttcttt ccggcgttat cccctgattc tgtggataac cgcattaccg cctttgagtg
      901 agctgacacc gctcgccgca gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc
      961 ggaagagcgc cttatgtgac attttctcct tacgcaccgg tataccgttc tgcatcctgt
     1021 ctggagcagg atacactgtt ataccccggt gccactttcc gcttcaaagc gtgtctgtat
     1081 gctgttctgg agttcttccg cgatttcgtg cagcttctca cacatggcgg cctgttcgtc
     1141 ggcatcgagt gcgtccagct tttcgagcag cgtcaggctc tggcttttta tgaatcccgc
     1201 catgttgagt acggtttgct gctgcttgtt catctttctg ttttctccgt tctgtctgtc
     1261 atctgcgttg tgtgattata tcgcgtacca cttttcgact gttttaccgc cggtattctg
     1321 ccgtctgacg cattgacggg tatttctgcc tgacaatact gtcactgcca aaaaaactgc
     1381 cgtgcctttg tcggtaattc gaacttgctg acaggacagg atgtgtaatt gttataccgc
     1441 gcatacatgc acgctattac aattaccctg gtcagggctt cgccccgaca ccccgtgtca
     1501 gatacggagc catgttttat gacaaaacga agtggaagta atacgcgcag gcgggctatc
     1561 agtcgccctg ttcgtctgac ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa
     1621 tgcggcaaga ccgtttctgg ttttttacgg gcggcagctc tcggtaagaa cgttaactca
     1681 ctgactgatg atcgggtgct gaaagaagtt atgagactgg gggcgttaca gaaaaaactc
     1741 tttatcgacg gcaagcgtat cggggacagg gagtatgcgg aggtgctgat cgctattacg
     1801 gagtatcacc gtgccctgtt atccaggctt atggcagatt agcttcccgg ggagaaaact
     1861 gttgaaaaca gacggtatga acacggtaag ctcccaaagt gatctccatt cgctttcatg
     1921 catagctatg cagcgagctg aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa
     1981 aacatctatt tttgtggtgt ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta
     2041 caattaaggg attatggtaa atgatgatta tttctcctct ctatttactc ggcaagcgcc
     2101 aaagtgaatt acatcatatt ttactcctga ttcatttatt actttaaata tgtcagaaag
     2161 gtgcttctta tgatttttat cagttataaa tgctatatca atatttttgt ttcctaagcc
     2221 atcttgatgt ctttgtataa tattttgggc ttgttcatgg taatatagag catagttttt
     2281 tatcttctca ttacttgttg cgtattcttt tctatatatg gcttgtgaca tcatttcttc
     2341 ttctaatttt gattgaggta tattgcgcgc gttcgctaga acttttaggt catctttgct
     2401 tatgtttagt gatggtgtta accctttttg agcttcagta tggcgtttgt ttacctctga
     2461 aagaacgctt agtccctttg tgaagtcgtt gtcttttgta taaaaatcaa ttcttaggtt
     2521 tttggggact acagtccatc catcgccttt ttgacgcgtg aatagtgttt gtggatggga
     2581 gatctctttc catccaccat gcgacataat gacaagttgt gttgcttttc ctgtttggct
     2641 caatcctatt ccgtctttct ggaataaacg acgatgactt gttacgtcca
//
