LOCUS       NZ_CP140626             5631 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm008, complete sequence.
ACCESSION   NZ_CP140626
VERSION     NZ_CP140626.1
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 5631)
  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  JOURNAL   Unpublished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 5631)
  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
            CP140626.1.
            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..5631
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm008"
                     /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(5097..5631,1..518)
                     /locus_tag="O5Y90_RS26660"
                     /old_locus_tag="O5Y90_26655"
     CDS             join(5097..5631,1..518)
                     /locus_tag="O5Y90_RS26660"
                     /old_locus_tag="O5Y90_26655"
                     /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_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            520..1386
                     /locus_tag="O5Y90_RS26665"
                     /old_locus_tag="O5Y90_26660"
     CDS             520..1386
                     /locus_tag="O5Y90_RS26665"
                     /old_locus_tag="O5Y90_26660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(2589..2780)
                     /locus_tag="O5Y90_RS26670"
                     /old_locus_tag="O5Y90_26665"
     CDS             complement(2589..2780)
                     /locus_tag="O5Y90_RS26670"
                     /old_locus_tag="O5Y90_26665"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2845..3168
                     /locus_tag="O5Y90_RS26675"
                     /old_locus_tag="O5Y90_26670"
     CDS             2845..3168
                     /locus_tag="O5Y90_RS26675"
                     /old_locus_tag="O5Y90_26670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024192446.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     AQPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3377..>3808
                     /locus_tag="O5Y90_RS26680"
                     /old_locus_tag="O5Y90_26675"
                     /pseudo=""
     CDS             3377..>3808
                     /locus_tag="O5Y90_RS26680"
                     /old_locus_tag="O5Y90_26675"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3846..4376
                     /locus_tag="O5Y90_RS26685"
                     /old_locus_tag="O5Y90_26680"
     CDS             3846..4376
                     /locus_tag="O5Y90_RS26685"
                     /old_locus_tag="O5Y90_26680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            4383..4616
                     /locus_tag="O5Y90_RS26690"
                     /old_locus_tag="O5Y90_26685"
     CDS             4383..4616
                     /locus_tag="O5Y90_RS26690"
                     /old_locus_tag="O5Y90_26685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          2414..2495
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          1770..1957
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3159..4720
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 caagaaatca tgatagaaga ataccagggg gaatacttat ttctgtaaat gccccggggc
       61 attttatgag gctggcgata gaaaaaggtt tctataaaga tcaagaacaa gcgttagcgg
      121 atattcgtaa catgactatt cagtctgttg gtaagggtgg gtattcacat ccggaaggga
      181 tttctacaac atggcattca gaatctaatt tggatcgttt tggatgccca gtgcacaccg
      241 gtaatagttc ttattacagc ggtttttatc atactgatgt attaattcca ggagaattaa
      301 ctaaggatga aagattgctc catgaaatag aaaatagtga tccaatgatc ttcaactgga
      361 atgtattgtt ttatgtttca ttagaagagt ttcctataga tgatccttat tatggagagt
      421 ttattggtat tcctgtagat gatgcatcta tgttttttaa ctcctttcaa ccaaggaaat
      481 ttgaaaacaa acccctttat gagaaagagg atgattaata tgattaaagg aatgcttttt
      541 gcttttttag cagcgttctc atggggggca gctatcgtaa tgagcaaaaa aggagttgaa
      601 gaactagatg ccggaggggt gtttttctgg cagatttgta gtgcagtaat actatcttgg
      661 atagttcttt ttataaaaag aaaaaaactc ccattaaact caaaagcgat acttgcttat
      721 gcgacaggcg tttttgaacc attcttagcg tatactttta cactctacgg actttatttt
      781 atttcagcag gaagcgcatc aattattttt tcacttgaat cagtgtttat attggtgttg
      841 tctgttctta tttgctcagt taaaattaat tccccgcaat attttatatt gttccttata
      901 ggtgcaattg ttggcagtat tttggtagcc ttgccagaca tcagtaatgg atcgaataat
      961 attgttggat attgtcttgt tgttgccggt gtgttatcgg cagcatttta tgttgttata
     1021 tcgtctcgcc ttattaaatc gtttgagcct atcacattat tgagcggaca gttgacattc
     1081 tcccttatac tgtcatcgct ctttattttt atatctaaat catcaattta tcttccgttg
     1141 gaatccgtga ttattgtttt ttcatctgga atattacaat attttttagc tttttgtttt
     1201 tacttgaact ccttgcgttg gctcccagtt catttggcag ggataatgtt gtactttatt
     1261 ccgctagttg cattattttt gtcatggttg tttttggatg aacaattcac attcttacag
     1321 ggggtaggat ttattgtaac tgtgctaagt gtatattttc ttaacagaaa atactcagag
     1381 gagtaacatt ctgttcagga ttgccccccg gcctccatcg ataccgtgcc aaatgcacgt
     1441 aaaaaacggg agcgtttctg gtgtcggaat gtaaccaagg gggtcagagg cgcgctaaaa
     1501 cgctctcagg ggagtcaaat agagacgttt gtaacaaaaa gatcaaagga tcctcttgag
     1561 atcctttttt tctgcgcgta atctgctgcc tgtaaacgaa aaaaccgcct tgcagggcgg
     1621 tttgatcgaa ggttaagtca gcttgcagac tgcttaacca ggtaactgtc ttatgcgaga
     1681 cgagtcacca aaattgttct tctagtgtag ccgcactccg gcagccactt caagtactct
     1741 ctaaatatct cgcacatgac ttttaccaat ggctgctgcc agtggcgctt tgtggtgtct
     1801 tttccgggtt ggacccaaga gaacagttac cggagaaggc gcagcagtcg ggctgaacgg
     1861 ggggttcctg catacagccc agcccggagc gaactgccta agtcgccccg agataccaga
     1921 agacgtgagc tatgagaaag cgccacgtgt cccgtaaggg agaaaggcgg aaaaggtatc
     1981 cggtaatcga tatggcggga acgtgggggc gcaggaggga gcgattcacc ggaaacggtg
     2041 atgatcttta agccacgtcg ggtttcgcca ccgctggcgg atttcatggt tgagccgcaa
     2101 ggctcccaca gatgcaccga aaaagtgtct gttttgtgaa gtccgtcagg ggggcggagc
     2161 ctatggaaaa agcgcctccg gcgcggcctt tcccggggtt tcgttttttg cgcacatgtt
     2221 ctttcctggt ttatccccgg gttctgtgga taacagggtt agcgtttttg agaaaggaga
     2281 gtccgctcgc cgcagccgaa cgaccgagcg tagcgagtca gtgagcgagg aagcggaaga
     2341 gcgcctgaac tggcattttc tccttacgca tctgtgcggc atttcacacc ggacatggcg
     2401 cacttttcat acaatccgca ctgatgccga atggttaagc cagtatacac tccgctatcg
     2461 ctacgtgact gggtcagggc ttcgccccga caccccaaag gtcaacggcc tgacgcgccc
     2521 tggcgggctt gtctgctccc ggcatccgct cacagacaag ctgtgaccgt ctccgggagc
     2581 tgcatgtgtc agcggttttc accgtcatcc ccgaagcgtg cgaggcaact gcggtaaagc
     2641 tcatcggcgt ggtcgtgaag cgattcacag atgtctgcct gttcatccgc gtccagttcg
     2701 ttgagcttct ccagcagcgt taatgtctgg cctctgatga agcgggccat gttaagggcg
     2761 gttttttcct gtttggtcac tgatgcctcc gtgtaagggg gggttctgtt catgggggta
     2821 atgataccga tgaaacgcga gaggatgctc acgatacggg ttactgatga tgaacatgcc
     2881 cggttactgg aacgctgtga gggtaaacaa ctggcggtat ggatgcggcg ggtctgcctg
     2941 ggtgagccgg ttgcccgttc cgggaagctg ccgacactgg cacagccgtt actgcgtcag
     3001 ctggccgcca tcgggaataa ccttaaccag acagcgagga aggtgaacag cgggcagtgg
     3061 tcttccggtg accgggttca ggtggtggcc gcactgatgg ccatcgggga tgagctgcgc
     3121 cggctgcgtc tggcggtcag ggaacagggg gcgcgggatg atagttaagt ttcatgccag
     3181 gggaaaaggt ggtggcagtg gtccggttga ttacctgctg ggaagggagc gtaaccggga
     3241 aggggcaacg gtgcttcagg ggaatccgga agaggtccgg gaactcatcg atgccacgcc
     3301 atttgcgaag aaatacacgt caggtgttct gtcgttcgcg gagaaggagc tgccgcctgg
     3361 agggcgtgaa aaagtgatgg cgagctttga gcgtgtactg atgcccggtc tcgagaaaaa
     3421 tcagtacagc atcctgtggg tggagcacca ggacaaggga cggcttgagc tgaattttgt
     3481 cattccgaac atggagctac agaccggaaa acgcctccag ccgtactacg accgggcaga
     3541 caggccgaga attgatgcct ggcagacgct ggtgaatcac cattacggtc tgcatgaccc
     3601 caacgccccg gagaaccgcc ggacgctgac ccttcctgat aacctgccgg aaacgaaaca
     3661 ggcgcttgct gagggcgtca cacgcgggat agacgcgctt taccatgccg gagagataaa
     3721 aggccgtcag gatgtgattc aggcgctcac agaggcgggg cttgaagtgg tcagggtgac
     3781 gcgaagcagt atcagcattg cagacccgaa cggcgggagg aatatcagac tgaaaggagc
     3841 gttttatgag caatctttta cagacgggcg cggagttcga gaaaaagctg aaagagagag
     3901 ccgaatctac agagaaaatg ctgaacgacg agttcaggaa gctcgaagaa tctgtaaaca
     3961 gggaactgac ctcaaacgaa tctttaatca ggaacgctat caacgaccat acaacagccc
     4021 tgaaagaact gctggagagg tatcagaaaa cgaccgtcga tacgatggac gcgcactgga
     4081 aaaccgtact gaaaatgagc gtgaaacgct ggctgtggct gattatcgtc tcagtactga
     4141 tgtttgccac gaccgggagt ctgctgtggt accagggcat gaagataaac gcgaatatga
     4201 atattctccg cgagcagaaa gagagtctgg agaagctgaa cgcgaagaca tggggcgtgc
     4261 gttatcacga ggacagcaac ggacgttttc tggtgttgcc gaaggggatg aaagccgaaa
     4321 cgaactggac gaaggacaac ggcaaactga acgcagtgag actggtgcag gagtgacaga
     4381 gcatgacgga gctggaaaga catttgctga acgcattaga gcaactgcaa caggactata
     4441 tgcagcggct gaacgaatgg gagaacgcct tcgtggaatt gcagaaaatg ttttcgctta
     4501 cgcaacggga caacgcgatg ctgaacgggc gagtcatgca gttgagtcag caggtgcagc
     4561 acttgagcga gcggacagaa cgcttgagcc agttatacag cgagaacagg agataaggga
     4621 tgaacggctg atgcaggaac gcgaacatga gttatctctg gagcgggagc gtcagccgga
     4681 aatccaggag cggacactgg atggcccttc gctgggatgg tgaaaccatg aaaaatgacg
     4741 tgttcagtgg attaaggcgg gctaatgtgg cctgtagcat ctggttgcat aggtattcat
     4801 gcggttaaaa tttatcaggt gcgatcgcgg cagtttttcg ggtggtttgt tgccattttt
     4861 acctgtctgc tgccgtgatc gcaccgaacg cgttttggcg gtgcgtacaa tgcgacgtta
     4921 tggtaaatgg agcggatttt caggaaggag tgatactaac aactcgaaca ctgtgcaaat
     4981 aatgattttt ttaaaatatc ggtaacgata ataaattatt tcgttttacg ccggtaataa
     5041 atataatgta gtttcagtat ataaaaaaat atatgaggtg tcttgtggga gctttcatga
     5101 atcttcaaca acgtataaat aaactaccac aattatcatc cagtttttca tttggaaaag
     5161 atattgataa tattcattca tttatcttta acgaaacttc taaagataaa attgaagatt
     5221 tactaagaaa atgggtgtca ggcaatcagc cctgtgtatt tggtaaattg gcaagcaaga
     5281 aaattaaagg gcttgatttc catttatcta ttgtaaatag cccccaacta tataatgatg
     5341 atggtcattt gtttgatttt ttgcgtaatg aaagagttcg ttttaaagaa cgcgcaagaa
     5401 gaggagaggt cagtgcgcat ctcatttatt ttattcatcc acaacttgcc tttgctcgtc
     5461 catcagaaga gttagtggac atacaaaaat atatttgttc gctgcatatg ccagagtgct
     5521 atccaataaa agaggatgtt atttatactg aaagcgtacc atttcaggat aaagatgggc
     5581 taaaaatata taaggctggt gttaatgttt tttactcttc tgctcataga a
//
