LOCUS       NZ_CP140633             2089 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm015, complete sequence.
ACCESSION   NZ_CP140633
VERSION     NZ_CP140633.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32329321
            Assembly: GCF_034554795.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2089)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Complete genome assembly and description of a Shigella sonnei
            clinical strain resistant to third- and fourth-generation
            cephalosporins isolated in Northern Italy
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2089)
  AUTHORS   Gaibani,P. and Amadesi,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-DEC-2022) Microbiology, Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, Bologna, BO 40138, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 13-APR-2022
            Assembly Method                   :: Unicycler v. 0.5.0
            Assembly Name                     :: SO87
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 261.0x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina iSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 01/06/2024 22:59:22
            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)                     :: 5,368
            CDSs (total)                      :: 5,245
            Genes (coding)                    :: 4,512
            CDSs (with protein)               :: 4,512
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 733
            CDSs (without protein)            :: 733
            Pseudo Genes (ambiguous residues) :: 0 of 733
            Pseudo Genes (frameshifted)       :: 204 of 733
            Pseudo Genes (incomplete)         :: 529 of 733
            Pseudo Genes (internal stop)      :: 125 of 733
            Pseudo Genes (multiple problems)  :: 119 of 733
            Pseudo Genes (short protein)      :: 3 of 733
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP140633.1.
            Bacteria and source DNA available from Policlinico
            Sant'Orsola-Malpighi, Via Massarenti 9, 40138, Bologna (Italy).
            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..2089
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm015"
                     /geo_loc_name="Italy: Bologna"
                     /lat_lon="44.4912 N 11.3615 E"
                     /collection_date="2021-11-30"
                     /collected_by="IRCCS Policlinico S. Orsola - Malpighi"
     gene            complement(join(1603..2089,1..479))
                     /locus_tag="O5Y90_RS26825"
                     /old_locus_tag="O5Y90_26820"
     CDS             complement(join(1603..2089,1..479))
                     /locus_tag="O5Y90_RS26825"
                     /old_locus_tag="O5Y90_26820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_012421200.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQIAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(1333..1599)
                     /locus_tag="O5Y90_RS26830"
                     /old_locus_tag="O5Y90_26825"
     CDS             complement(1333..1599)
                     /locus_tag="O5Y90_RS26830"
                     /old_locus_tag="O5Y90_26825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(2..86)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
ORIGIN
        1 cctcgcgtca cctccgtagc cctgatccac ccctgaacag gtgatagctc ctttcgcttt
       61 tccattcgct taaacgccgc attcattgct gtaaggactg ttccaagttc acctatctcg
      121 cagttcctga cagttaacgt cagaaacaac catcgggaag acgggtaatc cacaacgatt
      181 ttcggtagag cctgataaaa acgggcttgc cacatgaggg ttcttctcca ctggcagaca
      241 gggcaatgac ggacacggca aaattgcgca ctacgaagcc gtaggcgcgt ttctccggtt
      301 tccatgatgg tagaccaacc aaaacgtaac aaaccgctac aggaggccat acggagtgca
      361 tagcgctcga attcagcagc aatctggtag atacccccga cagaatcggt aagcgtgcgc
      421 tgggtatccc aaactgcatc acgggggctg tagtccgaaa ggaatttatc ttctgacatt
      481 aagcctgctc cgatctgggc aggctgtgat ttgatgtggt atattcatca cgtacctgtg
      541 cattgcgagc cagtacatgt caccagagtt tgccgctgag gtgacacatt cgaaatgttg
      601 gggagtgttg acgcactccc caacgccgat taaaaacgcc tcaattctgc tccattttct
      661 ttgacctgtc aaaacccact caaagcctcg tcattactgg gctaaaccac tatttcatat
      721 ccgccattta tcccttaagt ataaatacaa ggatcacgcg cgagacttgc gcaaaaaata
      781 accacaattt taacccccca aaacaagcac tcccgaacgg ctgagcccaa ccttttccac
      841 acacccgatc accaaaacag ggaataaaaa caaaaccctg tcttacaggt ggatggcctc
      901 acttcgtgaa accatccacc ccgcataagt tttttaatcg gtggtgtcgt caatcactaa
      961 atcggaaccc caaaggggac ccccacgatt tagcatttga cgagattaac tctcggagat
     1021 ggcatcatgc ttttaacgga ctttaaaaaa cggtgaacgg atgcggattt taatccgtgt
     1081 ctgtgaggcg ttgagcaacg agcaaagcga ggcggtagaa agagagccag cggcaggctc
     1141 aggacgataa tccggggaaa atgtaccact cgcagagtgt taacatttga catcggattg
     1201 tctatcctgc attggtgtcg agttggcaag gctgaggata atgctgagga taatgcagga
     1261 tagacagagc actagagatt gcatgcaatc tcgtacctat cacctcagcc tgccgctggc
     1321 tcttttccag aactaagaat gcgttcttaa aaatccaaac ttgataccgt ttaaatctat
     1381 tttcacaaaa agagttttta ccctctcgtt tgttttctga atatataaaa ttaattcatc
     1441 ctcaaaacct tcgtgcggat gaaaaccaaa tgtgccaaaa cttaatccat caataagcaa
     1501 aataaggttt ttaaacctgt caggaatcac cgcttcactt cttaaaaaaa ataaaccaat
     1561 agtcttattt ccattcaggt attcaatatt aatattcata cgttaatccg atttatcctt
     1621 ctcaggggcg cgtttgtaac gccgtttacc tgaatcccag acaaacgccg tccgcttccc
     1681 gtcatcagtg ccatccccta catcgtcggc aatgacaaga tcctcattgg tttctcgatc
     1741 caactggagg acgtttttta gcgccccacc ggtcgagata aaacggcgct tgtgaagctg
     1801 ccgcgtcagc tcaagaaacc actcaggatc gtttgccata tcttccggtt taacggagta
     1861 tttcagcgtt tcagcaaccg cgctttgcag ttgctcggca acgttggcca caacctcacc
     1921 tgtcttagtt tttactgccc gaatatcgat attcggctca tagttcaccc gcaagcaatc
     1981 gcgccagagt tctacccaac gttcgtgctt aacgtagttc ttccctttaa accaagaagg
     2041 ttgcaccatc agcagacagt gaaaatgcgg atgtgcgctg ccatcctta
//
