LOCUS       NZ_CP140628             5114 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm010, complete sequence.
ACCESSION   NZ_CP140628
VERSION     NZ_CP140628.1
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 5114)
  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  JOURNAL   Unpublished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 5114)
  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
            CP140628.1.
            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..5114
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm010"
                     /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(4536..5114,1..972)
                     /locus_tag="O5Y90_RS26745"
                     /old_locus_tag="O5Y90_26740"
     CDS             join(4536..5114,1..972)
                     /locus_tag="O5Y90_RS26745"
                     /old_locus_tag="O5Y90_26740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001624483.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_039063720.1"
                     /translation="MASYHCTVKAGAKGSALKHADYISRSGEYKSYKSREDLEFSSSGN
                     MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIELVEDFVQKELGDRH
                     AYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRANSKSPERGGAKKASI
                     PQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGINRTPEVHLGPVQAA
                     SLNGEQIVAIQERRNAERELKTARDAANAIQQEQEQKQKIKAVEPVRSARSPELLLQYR
                     KVMKTVIQGEARLARLGDANPNALKEHKLLQNAKAKKDSLSEWSRRIYEGARYLDKLGR
                     NVVSAQRELRELQEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRNKL
                     QQAESEWDKENAAFKRTEGYKYVGELDRYREREILAAASLENTRQKVAEEVSVARSQML
                     SLEPELSISGDEKAQMRHELLAEMAQERQQQEEKALCIQRSWARGVSRSNERDQDMER"
                     /name="MobA/MobL family protein"
     gene            complement(1168..2268)
                     /locus_tag="O5Y90_RS26750"
                     /old_locus_tag="O5Y90_26745"
     CDS             complement(1168..2268)
                     /locus_tag="O5Y90_RS26750"
                     /old_locus_tag="O5Y90_26745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001569522.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024235836.1"
                     /translation="MNINFKHILPLLSSFFISGCDSDGISKVKSFVYYDIDDSMTVGKA
                     FDTRSDCINGTWSEKEDDRGRTIVTYTCDISESGLKIINSAIMQEPEDKAEYSIAQNNN
                     SIKSTNESLEEYKQKTPLVEKTKEVIIDHIRKLNSAFNEDPMIYSKLTISPYLDRMLYL
                     KDHNDNALNEICGGYEYIQSADSYSWRDVSEEYAKESCEKHIYKVYQSFKKNASPLITK
                     NFPGFYERVPPCENADECIKKTNIYFDDNFLNIYKRSQDRAPQIISDLKKHNIEIGEKL
                     NDCRKKLNISDVKLTYYWFVTDTGGVDYLDGVLTYNFQGKNRAENFHKQLLQYAYINYS
                     KNQIPRDFVTSIKNSIYYKIEDCTKF"
                     /name="hypothetical protein"
     gene            2789..3724
                     /locus_tag="O5Y90_RS26755"
                     /old_locus_tag="O5Y90_26750"
     CDS             2789..3724
                     /locus_tag="O5Y90_RS26755"
                     /old_locus_tag="O5Y90_26750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_024235833.1"
                     /translation="MSAALQYFEENLPHRPYHTDELAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNAPAPNITVKNPENGHAHLLYALNLAVRTAPDASVKA
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYALDELADYLDLRASE
                     RRSVDKHYGLGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPESFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(3918..4364)
                     /locus_tag="O5Y90_RS26760"
                     /old_locus_tag="O5Y90_26755"
     CDS             complement(3918..4364)
                     /locus_tag="O5Y90_RS26760"
                     /old_locus_tag="O5Y90_26755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_024235834.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          2790..3724
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..375
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.2"
                     /coverage="95.0"
                     /evalue="6.34e-62"
     Typing          4537..5114
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.446"
                     /coverage="100.0"
                     /evalue="3.1600000000000004e-124"
ORIGIN
        1 cacgagtcgc gcgtagatca tcgttctctg aaagaacagg gtatcaatcg cacgccggaa
       61 gttcatcttg gccccgttca ggccgccagt ctgaatgggg agcagattgt tgcaatccag
      121 gaacggagga atgccgagcg ggaactcaag accgccagag atgccgcaaa tgccattcag
      181 caggaacagg agcaaaagca aaaaatcaag gcagttgagc ctgttcgttc agcccgttca
      241 ccggagttat tgcttcagta ccgcaaggtt atgaaaacgg tcattcaggg agaggcaagg
      301 cttgctcgtt taggggatgc caatcccaat gcgctcaaag aacataagct gcttcagaat
      361 gcgaaagcta aaaaagactc tctttccgaa tggagtagac gaatatatga aggggcacgg
      421 tatttagaca aactggggcg taatgttgtt tccgcacaaa gggagctgcg ggagctacag
      481 gaacaacgca atgctttgaa tgggattcgt ggcctgtttc ggggggctga caaaagggag
      541 attgatgcgc gtattctgga gcaaaaaagt gtgctggaaa ccgctgaaca tgaaaggaat
      601 gaattcagga acaagctaca gcaagccgaa tccgagtggg acaaagaaaa cgctgctttt
      661 aagcgtaccg agggatataa gtacgttggg gagctggaca ggtacagaga acgcgagatt
      721 ctggcggcgg catctttaga gaacaccagg caaaaggttg ctgaagaggt atccgttgcc
      781 cgtagccaga tgttatctct ggagcctgaa ctcagtatat ctggagatga aaaagctcaa
      841 atgcgacatg agttactggc agaaatggcg caggaacggc agcaacagga ggaaaaagca
      901 ctgtgtatac agcgatcctg ggccaggggg gtatcacgta gtaacgaacg tgatcaagat
      961 atggagcgtt gaaaatgtag caatatcggg actgcgcccc gaaccccgcc aacgtttcac
     1021 ggaacgcgaa aaaattccgc gtcccgtgaa acgttttctg aatgagaaaa attgtcgttt
     1081 tgatttactc acagttcaga ttaatgaagt taacaggtgt taaatatttg caggtggtta
     1141 tatgtgtaac cacctgtaag ggaaggacta aaacttagtg caatcttcta ttttataata
     1201 aatactattt tttattgatg ttacaaagtc ccgaggtatt tgatttttgc tgtagttaat
     1261 gtatgcatat tgcaatagtt gtttatgaaa gttttcagct ctattctttc cctgaaaatt
     1321 atatgtcaac accccatcta aataatcaac tcctccggta tctgttacaa accagtaata
     1381 ggttaatttg acatctgaga tatttagttt tttcctacaa tcatttaact tttcacctat
     1441 ttctatattg tgttttttta aatcagaaat tatttgaggt gctctatctt ggcttctttt
     1501 gtagatattt agaaagttat catcaaagta tatatttgtt ttttttatgc attcatctgc
     1561 gttctcacag ggggggacac gttcgtagaa accggggaag tttttagtta ttaatggtga
     1621 tgcatttttc ttaaacgatt gatatacttt atatatatgc ttttcgcatg attcttttgc
     1681 atactcttca cttacatcac gccaactgta actatcggca gattgaatgt attcgtaccc
     1741 accacaaatt tcatttagcg cattgtcatt atggtccttt agatatagca ttctgtctaa
     1801 ataagggcta attgtgagtt tgctatatat cattggatct tcattaaaag cactgtttag
     1861 ctttcttata tgatctatta tgacctcttt tgttttttcc accagaggcg ttttctgttt
     1921 gtattcctct agtgattcat tggttgattt tatgctgttg ttattttgtg ctatagaata
     1981 ttcagcctta tcttcaggtt cttgcataat ggctgaattt attattttta ggccactttc
     2041 actaatatca caggtatatg tgacgatggt tcttcctcga tcatcctctt tttcactcca
     2101 tgtgccattg atgcaatcac tccttgtatc gaaggcttta ccaacagtca ttgagtcgtc
     2161 aatgtcgtaa tatacgaaag actttacctt gcttattcca tcagagtcgc atcctgaaat
     2221 aaaaaatgac gacaataaag gaaggatatg tttaaagtta atattcattt ttcccatttt
     2281 tatttctaac aataacgagg aaatattaat acaggcgata tgttaatgga atccatacat
     2341 accgataaac cgacttacta tgtttgtgct caacgtctta cgcagttcga aaagatttcg
     2401 caccagttca cctttttctg gatgagaaag tttgctgttt tgacctgttc gctgttcaaa
     2461 acgagtgaaa ccggacatga atcgctttcg tgcatagtta tgcagccccc tgaaaacaat
     2521 tctggcgcgt ttttttggtc tggcctgttg tttccctgtc tttttgcgtt ttttgcgaca
     2581 gaaagcgact gagggcgttt taaggggggc gcacaacggg agttatggta aatggatcgg
     2641 gtttgcggga agactcgaca ggttttgtcg ttgggggtag tgtaagcgac tgaaaaacaa
     2701 acgcccctga aattcgtgtc tatccggcaa gactttcacg aagatacagg ggcgatgtcg
     2761 gtcgataacc tggaaggaat cgtaacacat gagcgccgcg cttcaatact tcgaagaaaa
     2821 tttacctcac cgtccctatc acacggatga gctcgctttc ggtcttcgta tctccggcaa
     2881 agggcgtgcg ctgcttgctc gctacatcca gcaaaatcag cctcatgcgc agttctggct
     2941 ggtttttgac gttgaccgcg taggagctgc gattgactgg agcgaccgga acgcccccgc
     3001 gccgaacatc accgtaaaaa atcccgagaa cgggcacgct cacctgctct acgcgctcaa
     3061 tcttgccgtg agaaccgcgc ctgatgcgtc ggttaaggcg ctgaaatacg ccgctgcaat
     3121 tgaacgtgcg ctgtgtgaga aacttgacgc agatgtgaac tacagcggac tgatttgcaa
     3181 aaatccgttc cacctggaat ggcaggtgat ggagtggcgc gaggaagcct acgccctcga
     3241 tgaactggct gattatctcg atttgagagc ctcagagcgt cgtagcgtcg ataaacatta
     3301 cgggctgggg cgaaactgcc atctgttcga aatgacgcgc aaatgggctt acagggcgat
     3361 tcggcagggc tggccagcat tctcacagtg gcttgatgct gtgattcagc gtgtcgaaat
     3421 gtacaacgca tcgcttcccg ttccgctttc tccgcctgaa tgtcgggcta ttggcaagag
     3481 cattgcgaaa tacacgcaca ggaacttcac gccggaaagt ttcgcacagt atgtggctga
     3541 tacgcacaca ccagaaatac aggccaagag aggccggaaa ggtggcatcg ctaaaggcga
     3601 agcctacgat gacaagcgtt tcatggcgct atgtatgctg gagaatggat attctcagaa
     3661 agctattgcg gcgatgctga atgtacatcg taatacgatc cgtaattggg caatgcacaa
     3721 atagcctata tcagataaca gcgccttttc ggcgtctttt tgagcagcgg gctttccggc
     3781 ggttttctcc tttcagccca gcaatggtgc ggcttaccgt atgattgagg tggtcgtgct
     3841 cgccgcagtc tcatgaccga gcgtagcgag cgaatgagcg aggaagcacc agggaactgg
     3901 aacgtgaacg gaggctctta cgcactgtct ttggtgagta gctctttccc gcgtttttcc
     3961 cattcctgcc attttggatg gttgtgcggt agctctgcga ttcctgcgag tgcgcctacc
     4021 agttcggcag cactaaactt tggctttccg gttttgctgt ccaccagtcc tgccacaatc
     4081 atgaggcctg cggccttgta gagttcatga tcccgcgcct ttcgttccgc ccttgcggct
     4141 gccttccgtt ctgccgctat gattgccgtt actctggctt ttgctgcggc tgctttctct
     4201 gcggtttttt ctgcccgtat cagtgcggac aacgtttttt catccgtcgt tgttcggttt
     4261 tttttctctg ccagtaacac aagtaatctc tgctgctctg atggtgattt cagtccgttg
     4321 atgtaggcaa tttttgcact taaccactct tcacgatttg tcattcttac ctctgcactt
     4381 ttgccgttaa tgtgagttgt tattatgcat aatatcacct tgtttgcctg cgtgtgagac
     4441 cgtaaaatca tccatgatta attcagggat gcgcacttag tagtttctct ccttcgtcga
     4501 gaaactgtgc gctcctgcgg agggctaaaa ggcagatggc aagctaccat tgcactgtca
     4561 aagctggagc aaaaggcagt gccttaaaac atgctgatta catttccaga tccggcgaat
     4621 ataagagtta caaatcgcgg gaggatctgg aattttcgtc atccggtaac atgccatcat
     4681 gggcgaagaa aaatcccgca gagctatgga aagccgcaga tgaatttgaa cgaaaaaacg
     4741 ggactgcata ccgtgaaatt gagatcgcgt taccgcgtga actgacacgc gaacaacgga
     4801 tagaacttgt tgaagatttc gtgcaaaagg aacttggcga tcgccatgcc taccagtacg
     4861 cgatccacaa tccgccaggt gcaatcgacg gaaaggaaca gccacacgcg catatcatgt
     4921 tttgcgagcg gattaatgat ggtattgaac gcgatccaca gcaatttttt aaacgtgcca
     4981 acagcaaatc accagagcgg ggaggcgcaa aaaaagcgag tattccccag acagccggag
     5041 agcgaaaagc cgcccttgtt gcgctgcgtt cccgctgggc agatgtgcag aatgagcacc
     5101 ttgcgcgaca cggt
//
