LOCUS       NZ_CP140632             2330 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm014, complete sequence.
ACCESSION   NZ_CP140632
VERSION     NZ_CP140632.1
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 2330)
  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  JOURNAL   Unpublished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 2330)
  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
            CP140632.1.
            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..2330
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm014"
                     /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            join(1643..2330,1..311)
                     /locus_tag="O5Y90_RS26815"
                     /old_locus_tag="O5Y90_26810"
     CDS             join(1643..2330,1..311)
                     /locus_tag="O5Y90_RS26815"
                     /old_locus_tag="O5Y90_26810"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001672436.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_000795151.1"
                     /translation="MKNPELKNLTDYSPADKPWDEHRSFSDDVGGIYLRAAGFEHYGER
                     VGACSGILRFGWSTNTETGETRLRLRDARFCRVRHCPICQWRRSMMWQARFYQSLPKIV
                     TEHPGARWLFLTLTVRNCSIDALGETLTAMNAGFKRLKERKEFRHVLGWVRTTEVTRGK
                     DGSAHPHFHTLLMVPPSMLSGREYVKHARWVELWRDCLRVAYDPNVDIRVVKSRKPKDD
                     ESLPCVVAEQLRSAVVETLKYSTKPADMLADPEWFLELTRQVHKRRFVATGGALKNVLQ
                     LERETNEDLIMADGMAEGTDDGSRLAFSWVPVVKKYQRDRAKDKRQLSGED"
                     /name="protein rep"
     gene            complement(605..1039)
                     /locus_tag="O5Y90_RS26820"
                     /old_locus_tag="O5Y90_26815"
     CDS             complement(605..1039)
                     /locus_tag="O5Y90_RS26820"
                     /old_locus_tag="O5Y90_26815"
                     /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_047254555.1"
                     /translation="MAVRARLYDYTSCPDFCGFVSPEHWRNVGSFCAAPPSTEARSSGN
                     RTANHSAVFVPQLFRAIDKLAVGESHEVRTYTISTSFRLCAVCDAVKTADNRQKNPPVS
                     GGRQSQFPDDSCFEVLLYPLNLPQEHSKNNSDDGTGCVIV"
                     /name="hypothetical protein"
     Typing          complement(984..1078)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.917"
                     /coverage="100.0"
                     /evalue="2.1299999999999998e-39"
     Typing          complement(29..220)
                     /name="Col(MP18)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.83e-96"
ORIGIN
        1 cggaacagct gcgcagcgcg gtggttgaaa ctctgaaata ttccacaaag cctgctgata
       61 tgctggctga tcctgaatgg ttcctcgaat taacacggca ggtacacaag cgtcgttttg
      121 ttgctacggg gggagcgctt aagaacgttc tgcaactgga gcgggaaacg aacgaggatt
      181 taatcatggc ggatggcatg gcagagggta cagatgacgg ttcccgtctg gcgttttcgt
      241 gggtgccggt tgtcaaaaaa taccagcgag atcgggcgaa agataaacgt cagctaagtg
      301 gcgaggattg agcgcgtttc aggcgcgaac tattcatgca ctgggagaat attcagaaac
      361 gcgctcagaa gcgttctaac gtgatttttg cagacaggca aggttttgtt cgttttttcg
      421 cgtttgatgc gttcaggggt gttttaagcg cgtttctgtc gcatcccggc gctaatacca
      481 tccccatggt taacgggagc tccagaaacg cgcagatgtc tttttaacgt gtcccgggca
      541 ggttgtcgag agtgtcgggg cgcagccctg accaggtggt aatcggatgg ctgtgcgtgc
      601 gcggttatac gattacacat cctgtcccgt catcggagtt gtttttgctg tgttcctgcg
      661 gcaaattgag cgggtatagc aacacctcaa aacaactatc atcaggaaat tgactttgac
      721 ggccccctga cacaggggga tttttttgcc tgttatctgc ggttttcacc gcgtcgcaga
      781 ccgcgcacaa tcgaaacgaa gttgagattg tataagtgcg cacttcgtga gattccccga
      841 cagccagttt gtcgatcgcg cggaacagct gcggcacgaa aacggcagaa tgatttgctg
      901 tccggttgcc agaactgcgc gcttccgtgg agggcggcgc ggcgcaaaaa ctgccgacat
      961 tgcgccagtg ttccggtgac acaaacccgc agaaatcggg acaggatgtg taatcgtata
     1021 accgcgcacg cacagccatc cgattaccac ctggtcaggg ctgcgacccg acaccccgcc
     1081 aacgcttcac ggcacgcgaa aaaaaaattc tgcgtcccgc taactgttcc cgaactcgtc
     1141 aaacagaaaa tcgcgggggc ccctccgggg ttccgatttt gtgattgacg acggcacgga
     1201 aaaaaacact ggggatggtg gttggtgtca cgcagtgagg ccaaccacct gcaagacggt
     1261 ttttgttttt cacaaaatcg gtggaaaaac ctgtgagtgt tttgcgggga aaacgctttt
     1321 gtggttgttg tttttgttgt ccgaaaatca gctcagattt tgagcaaatc tcgcgcgcgt
     1381 tccttgtatt tatacttaag ggataaatgc gattttttga atcgcctcta tcccttgcca
     1441 tatctggcct gagcgcggat ttgcgtgtaa ataggtttga gagtattttg tcgggagtgg
     1501 ttataaatta gcccctgcga gtcttccacc actccagggg cgcgaccacc tagaacatga
     1561 actgatttga cgacaattgg tacaggtgat acaggaatga taacacgcaa tttcgtctgt
     1621 cgctcgcaag gggacggcag acatgaaaaa tcctgaactt aagaatctga cggattactc
     1681 tccagcagat aaaccgtggg atgaacaccg aagcttttcc gacgatgtgg gcggtattta
     1741 tctgcgtgct gccggatttg agcactacgg cgaacgtgtc ggggcttgta gtggtatttt
     1801 gcggtttggg tggtcaacaa acacagagac cggagaaacg cgcctgcggt tgcgtgatgc
     1861 acggttctgt cgcgtccggc actgtccgat ctgtcagtgg aggcgttcca tgatgtggca
     1921 agcccgtttc tatcagtccc tgccaaagat tgtgacggaa catcccggcg cgcgctggtt
     1981 gtttctcaca ctgacagtgc gcaactgttc cattgacgcg cttggtgaga cgctgaccgc
     2041 gatgaatgcg gggtttaagc ggttgaaaga gcgtaaggaa tttcggcatg tgttgggctg
     2101 ggttcgtacc acggaagtaa cgcgcggcaa ggatggtagc gcacatcccc attttcacac
     2161 tctgctgatg gttccccctt cgatgttgtc cggccgtgag tatgtgaaac atgcccgttg
     2221 ggtggaactg tggcgtgatt gtctgcgggt ggcgtatgac ccgaatgtgg atatcagagt
     2281 ggtgaagtca cggaaaccaa aagacgatga atctttacct tgtgttgttg
//
