LOCUS       NZ_CP140630             2690 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm012, complete sequence.
ACCESSION   NZ_CP140630
VERSION     NZ_CP140630.1
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 2690)
  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  JOURNAL   Unpublished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 2690)
  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
            CP140630.1.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm012"
                     /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(207..368)
                     /locus_tag="O5Y90_RS26780"
                     /old_locus_tag="O5Y90_26775"
     CDS             complement(207..368)
                     /locus_tag="O5Y90_RS26780"
                     /old_locus_tag="O5Y90_26775"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(866..1060)
                     /locus_tag="O5Y90_RS26785"
                     /old_locus_tag="O5Y90_26780"
     CDS             complement(866..1060)
                     /locus_tag="O5Y90_RS26785"
                     /old_locus_tag="O5Y90_26780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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="WP_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1346..1669
                     /gene="mobA"
                     /locus_tag="O5Y90_RS26790"
                     /old_locus_tag="O5Y90_26785"
     CDS             1346..1669
                     /gene="mobA"
                     /locus_tag="O5Y90_RS26790"
                     /old_locus_tag="O5Y90_26785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(1895..2518)
                     /locus_tag="O5Y90_RS26795"
                     /old_locus_tag="O5Y90_26790"
     CDS             complement(1895..2518)
                     /locus_tag="O5Y90_RS26795"
                     /old_locus_tag="O5Y90_26790"
                     /inference="COORDINATES: protein motif:HMM:NF045398.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     Typing          1099..1337
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(297..823)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          1347..1666
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.599999999999999e-62"
ORIGIN
        1 gtgtttattt tatgggttaa agtaggatac caagtgtgaa aaaaaattaa aggttcttct
       61 tgagatcctt tttttctgcg cgtaatctgc tgcctgtaaa cgaaaaaacc gccctgcaag
      121 gcggtttttc gaaggttctc agagctacca actctttgag ccgaggtaac tggcttggag
      181 gagcgcagtc accaaaactt gttctttcag tttagcctta acaggcgcat gacttcaagt
      241 cttactcctc taattcggtt atcagtggct gctgccagtg gcgataattc gtgtcttacc
      301 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
      361 tcgtgcacac agcccagctt ggagcgaacg acctacaccg ggccgagata ccaacagcgt
      421 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaaac
      481 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
      541 tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
      601 ggggggcgga gcctatggaa aaacgccacc tgcgcggcct ttgtccctgc cttcggcttt
      661 ttgctcacat gttctttccg gcgttatccc ctgattctgt ggataaccgc attaccgcct
      721 ttgagtgagc tgacaccgct cgccgcagtc gaacgaccga gcgtagcgag tcagtgagcg
      781 aggaagcgga agagcgcctt atgtgacatt ttctccttac gcaccggtat accgttctgc
      841 atcctgtctg gagcaggata cactgttata ccccggtgcc actttccgct tcaaagcgtg
      901 tctgtatgct gttctggagt tcttccgcga tttcgtgcag cttctcacac atggcggcct
      961 gttcgtcggc atcgagtgcg tccagctttt cgagcagcgt caggctctgg ctttttatga
     1021 atcccgccat gttgagtacg gtttgctgct gcttgttcat ctttctgttt tctccgttct
     1081 gtctgtcatc tgcgttgtgt gattatatcg cgtaccactt ttcgactgtt ttaccgccgg
     1141 tattctgccg tctgacgcat tgacgggtat ttctgcctga caatactgtc actgccaaaa
     1201 aaactgccgt gcctttgtcg gtaattcgaa cttgctgaca ggacaggatg tgtaattgtt
     1261 ataccgcgca tacatgcacg ctattacaat taccctggtc agggcttcgc cccgacaccc
     1321 cgtgtcagat acggagccat gttttatgac aaaacgaagt ggaagtaata cgcgcaggcg
     1381 ggctatcagt cgccctgttc gtctgacggc agaagaagac caggaaatca gaaaaagggc
     1441 tgctgaatgc ggcaagaccg tttctggttt tttacgggcg gcagctctcg gtaagaacgt
     1501 taactcactg actgatgatc gggtgctgaa agaagttatg agactggggg cgttacagaa
     1561 aaaactcttt atcgacggca agcgtatcgg ggacagggag tatgcggagg tgctgatcgc
     1621 tattacggag tatcaccgtg ccctgttatc caggcttatg gcagattagc ttcccgggga
     1681 gaaaactgtt gaaaacagac ggtatgaaca cggtaagctc ccaaagtgat ctccattcgc
     1741 tttcatgcat agctatgcag cgagctgaaa acgatcctga cgcatccttc ctgtttttcc
     1801 ggggtaaaac atctattttt gtggtgtctg cgtcagaatc gcgttcagcg cgtttcagtg
     1861 gtgcgtacaa ttaagggatt atggtaaatg atgattattt ctcctctcta tttactcggc
     1921 aagcgccaaa gtgaattaca tcatatttta ctcctgattc atttattact ttaaatatgt
     1981 cagaaaggtg cttcttatga tttttatcag ttataaatgc tatatcaata tttttgtttc
     2041 ctaagccatc ttgatgtctt tgtataatat tttgggcttg ttcatggtaa tatagagcat
     2101 agttttttat cttctcatta cttgttgcgt attcttttct atatatggct tgtgacatca
     2161 tttcttcttc taattttgat tgaggtatat tgcgcgcgtt cgctagaact tttaggtcat
     2221 ctttgcttat gtttagtgat ggtgttaacc ctttttgagc ttcagtatgg cgtttgttta
     2281 cctctgaaag aacgcttagt ccctttgtga agtcgttgtc ttttgtataa aaatcaattc
     2341 ttaggttttt ggggactaca gtccatccat cgcctttttg acgcgtgaat agtgtttgtg
     2401 gatgggagat ctctttccat ccaccatgcg acataatgac aagttgtgtt gcttttcctg
     2461 tttggctcaa tcctattccg tctttctgga ataaacgacg atgacttgtt acgtccatgt
     2521 ttggtgatgg gtgtgttttt atatttttgg atgatgttag aaggtgattt cttattgttg
     2581 atgatatgtt tgttatgaga ttcgaattga gtattttcat ttgttaacaa tccatttttg
     2641 cggtgttttt tattgttttt tttcttttgt ttaagggtgt gtcggtgtaa
//
