LOCUS       NZ_CP140625             6015 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm007, complete sequence.
ACCESSION   NZ_CP140625
VERSION     NZ_CP140625.1
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 6015)
  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  JOURNAL   Unpublished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 6015)
  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
            CP140625.1.
            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..6015
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm007"
                     /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(5927..6015,1..445))
                     /locus_tag="O5Y90_RS26625"
                     /old_locus_tag="O5Y90_26620"
     CDS             complement(join(5927..6015,1..445))
                     /locus_tag="O5Y90_RS26625"
                     /old_locus_tag="O5Y90_26620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_021546188.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQRLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFSVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(448..1374)
                     /locus_tag="O5Y90_RS26630"
                     /old_locus_tag="O5Y90_26625"
     CDS             complement(448..1374)
                     /locus_tag="O5Y90_RS26630"
                     /old_locus_tag="O5Y90_26625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_001314449.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTAEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            1550..1948
                     /locus_tag="O5Y90_RS26635"
                     /old_locus_tag="O5Y90_26630"
     CDS             1550..1948
                     /locus_tag="O5Y90_RS26635"
                     /old_locus_tag="O5Y90_26630"
                     /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_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(2142..3077)
                     /locus_tag="O5Y90_RS26640"
                     /old_locus_tag="O5Y90_26635"
     CDS             complement(2142..3077)
                     /locus_tag="O5Y90_RS26640"
                     /old_locus_tag="O5Y90_26635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666805.1"
                     /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_001271369.1"
                     /translation="MSAALQYFEENLPLRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDLNAPAPNITIKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAIERALCEKLGADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSTSA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTAETFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLEVSTRTIRNWKSGK"
                     /name="replication initiation protein"
     gene            complement(3575..3718)
                     /locus_tag="O5Y90_RS26645"
                     /old_locus_tag="O5Y90_26640"
     CDS             complement(3575..3718)
                     /locus_tag="O5Y90_RS26645"
                     /old_locus_tag="O5Y90_26640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000724569.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001419703.1"
                     /translation="MKKITGIILLLLAAIILAACQANYIRDVQGGTVSPSSSAELTGVE
                     TQ"
                     /name="colicin release lysis protein"
     gene            complement(3802..4059)
                     /locus_tag="O5Y90_RS26650"
                     /old_locus_tag="O5Y90_26645"
     CDS             complement(3802..4059)
                     /locus_tag="O5Y90_RS26650"
                     /old_locus_tag="O5Y90_26645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891189.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="cloacin immunity family protein"
                     /protein_id="WP_001419702.1"
                     /translation="MGLKLHIHWFDKKNEEFKGGEYSKDFGDDGSVIERLGMPLKDNIN
                     NGWFDVEKRWVPILQPYFKNVIDISKFDYFVSFDYRDGDW"
                     /name="cloacin immunity family protein"
     gene            complement(4069..5706)
                     /locus_tag="O5Y90_RS26655"
                     /old_locus_tag="O5Y90_26650"
     CDS             complement(4069..5706)
                     /locus_tag="O5Y90_RS26655"
                     /old_locus_tag="O5Y90_26650"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000012964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like bacteriocin tRNase domain-containing
                     protein"
                     /protein_id="WP_039063724.1"
                     /translation="MSGGDGRDHNSGAHNTGGNINGGPTGLGGNGGASDGSGWSSENNP
                     WGGGSGSGVHWGGGSGNGNGGGNGNSGGGSNSSVAAVAFGFPALATPGAGTLGIAVSGE
                     ALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQV
                     STLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVP
                     SLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSV
                     TDVLTPAQVKQRQDEEKRLQQEWNDAHPVEVAERNYEQARAELNQANKDVARNQERQAK
                     AVQVYNSRKSELDAANKTLADAKAEIKQFERFAREPMAAGHRMWQMAGLKAQRAQTDVN
                     NKKAAFDAAAKEKSAADAALSSAMESRKKKEDKKRSAENKLNEEKNKRRKGTKDYGHDY
                     HPAPKTEDIKGLGELKEGRPKTPKQGGGGKRARWYGDKGRKIYEWDSQHGELEGYRASD
                     GQHLGSFDPKTGKQLKGPDPKRSIKKYL"
                     /name="colicin-like bacteriocin tRNase domain-containing
                     protein"
     BGC             1..6015
                     /name="RiPP-like"
                     /gene="RiPP-like"
                     /tool="antismash"
     Typing          complement(2143..3077)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.338"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(452..1374)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgtagttcct gtcgagaatt gttttcatcc cccatccgag cacactgaac ataaccagaa
       61 aggccactga caccccaccc agccatttcc agctataccc tttaagggtg ttgtattcct
      121 gcacgatatt gctgtgaatt gtcgcaatat ccctgttcag ggcatccgcg tttgccttca
      181 tgtttgcgac tgactcttcc agccgctgaa aatcctgact gatgcgctca cctatcagcc
      241 ctgcaacatc cagcctctgc acttcgtttc tgacttcatc cctgacctgt tttgccacac
      301 cgtcagaaat atcccgatat ccgcgaagtg tttcccttgc cacagccaga gaatcagcaa
      361 cagctttctg ttgctccatt gcggtatgtt gcagatgctc caccgataac aggagcgtga
      421 gtaatttttc ttctgtgctg gccatgttca gaatcccata gaaaatccac gtgacggtga
      481 tttaacccgt tcaggttcag ttcggttctg tctgctcact ctgtctctca tgtcaaagcc
      541 atgctcccgc gcaacatcat gttgcagcct tctgaccagt tcatgttgct taaccggagt
      601 gtccagccat tccctgatgt catgcccgac cgttcgcgcc tgttcaagat ggcgggaata
      661 gtccggttca gaccgttttt gcatgatgtc atgacgctgg gcatcatcaa gccgtccggc
      721 agcttcaaaa cccagatgca cttcgggacg tcgttcaatg ccctgttctt tcagcgtccg
      781 gcagtcaatg aagccccttt caaagccatg ctttctcata tgttcgttgt gcttcacctc
      841 ccagcgtttt cgcaattccc gcaactgctc tttttgctga gtgagagtca ggcttccgga
      901 atcctttttc gcacctcccc gctcgggata cctggcgtta tagcgccgga aatactgttc
      961 cggtgtacgt tcaatgccat cattcacacg ctggctcatc atgatatgcg catgaggctg
     1021 ttcgccgccg tcaatgctcg ctttcggatt gtgaatggca aaactccagg cgtgccgttc
     1081 gccagcttcc tgacgtacaa aatcctgcac cagttcaagg cgctgttccg ctgtcagttc
     1141 acggggtaat gcaatttcaa gttcccgata ggtcgaaccg ttcgcacgtt caaactggtc
     1201 agccgcctgc cagaaatgtg agggattatc tcgcgcccat tccggcatgt ttccgtgtgc
     1261 ggaatattcc aaatcctgac ggtcgcggta tttctctttg cgctcgatgt aatcggcgtg
     1321 gtttgcagcc tgccccttgc caccaaattt aacgctgagg tgataggttg ccacggtttc
     1381 agccctccgc aggagcgcac tgtttctcga cgaaggagag aaacatataa gtgcgcttcc
     1441 ttctaatttt acgaattagc acggaagata ccccctgcac ccaccgaccg caagcgatat
     1501 actgcacgac cacaacacac agcaaaaaac accagggagc accacgaaca tgcgcatcag
     1561 caacatcgaa tggctgaaga aacggatcgg attcatcagg aagctcggag aacagaccgc
     1621 acgacagaga cagattattg acctgctcga caacgaagca ggactcacag aacaggaacg
     1681 caaactcctc cacgtactgg caacagcgga aaaaaacgac ttacaggcac aggagagcga
     1741 acgaaaacag gcggtccaaa aacgaatcga gggaaaaaaa caacgacgag aacgcaatca
     1801 ccgactcttt ctcgcggctg ggctactgat cgaagcagga ctggtagaca caaaaacagg
     1861 cgagctatgc tataaaaaag acaggatatt acaggcactt aaggaaatta agtacgatct
     1921 ggagacatcc ccaaacccag acgcgtaagt gcctccatcc gtgttcctgt tccctggtgc
     1981 ttcctcgctc attcgctcgc tacgctcggt catgagactg cggcgagcac taccagcaca
     2041 atcatgcgga aaacagcacc attgcagggc tgaacgggga aaaacggcaa aagacctaag
     2101 gctcaaaaaa acgccagaaa ggcgctgtta tctgatatag gctattttcc gcttttccag
     2161 tttcgaatgg ttcgagtaga aacctccaac atcgccgcaa tagctttctg agaatatcca
     2221 ttctccagca tacatagcgc catgaaacgc ttgtcatcgt aggcttcgcc tttagcgatg
     2281 ccacctttcc tgcctctctt ggcctgtatt tctggcgtgt gcgtatcagc cacatactgt
     2341 gcgaaagttt ccgccgtgaa gttcctgtgc gtgtatttcg caatactctt gccaatagcc
     2401 cgacattcag gaggtgaaag cggaacggga agcgatgcgt tgtacatttc gacacgctga
     2461 atcacggcat caagccactg tgagaatgct ggccagccct gacgaatcgc cctgtaagcc
     2521 catttgcgcg tcatttcgaa cagatggcag tttctcccca ttccgtaatg tttatcgatg
     2581 ctacggcgcg ctgaagtgct caaatcgaga taatcagcca gttcatcgag ggtataggct
     2641 tcctcacgcc actccatcac ctgccattcc agatggaacg gatttttgca aatcagtccg
     2701 ctgtagttta catctgcgcc cagtttttca cacaacgcac gttcaatcgc ggcggcgtat
     2761 ttcagcgcct taaccgaagc atcaggcgcg gttctcacgg cgatattgag tgcgtagagc
     2821 aggtgggcgt gaccgttcac gggatttttt atggtgatgt tcggtgcggg ggcgttcagg
     2881 tcgctccagt caatcgcagc cccctcgcgg tcaacgtcaa aaaccagcca gaactgcgca
     2941 tgaggttggt tctgctggat ataccgtgca agaagcgcgc gccctttacc ggagatacga
     3001 aggccgaaag cgagatcatc cgtgtgatag gggcggaggg gtaaattttc ttcgaagtat
     3061 tgaagcgcgg cgctcatgtg ttacgattcc ttccaggtta tcgaccgacc tcgcccctgt
     3121 attctcgtga caatcttggc ggagagacac gaatttcagg ggcgtttgtt tttcagtcgc
     3181 ttacactaca cccaacggca aatcctgtcg atccttcccg aaaacccgat ccatttacca
     3241 taactcccgt tgtacgtacc ccttaaaacg ccctcaatcg ctttctggcg caaaaaacgc
     3301 aaaaagacaa gaaaacacca ggacaaacca gaaaaacgcg tcagaatcgt tttcagggcg
     3361 ttgcataact atgcacgaaa gcgatgtgcg atcggtttcg tgcgttctga acaccgaacg
     3421 gctcaaaacg aaaagttttc tccctccgga tggaaggttc tgcacggaga ttttagatcc
     3481 catctcccac atggaatttt tgtggcactt caacaaaaaa agcgcgtcag aatcagcctg
     3541 acacgctttg tccttgtcaa atgaggattg caggttactg cgtttccact ccggtcagtt
     3601 cagcagagga tgacggtgat acagtcccgc cctgaacatc acggatatag tttgcctgac
     3661 atgcagcaag aataatggct gcaagaagca acaaaataat ccctgttatt ttcttcatac
     3721 gattccctgt atatatggat tcaggaattc atccttgaac acctgaatca aacactttat
     3781 tactcgtccc tgatagttta attaccagtc accatcacga taatcgaaag aaacaaagta
     3841 atcgaactta ctaatatcaa taacattttt aaagtatggc tgtaatattg gcacccatct
     3901 cttttcaaca tcaaaccaac cgttattaat attatccttt aaaggcattc caagacgttc
     3961 aataaccgaa ccatcatcac cgaaatcctt tgaatactca ccacctttaa attcctcatt
     4021 cttcttatca aaccaatgaa tgtgtaattt aagtcccata acatcacctt aaagatactt
     4081 tttaatactt cgtttcggat ctggaccttt caactgctta ccggttttag ggtcaaatga
     4141 accaagatgc tgaccatcac tggctcgata gccctcaagc tcaccatgct gagagtccca
     4201 ctcataaatt ttacgcccct tatctccata ccatctggca cgcttacctc caccaccttg
     4261 ctttggagtt tttggcctcc cctcttttaa ttcccccaaa cctttaatat cctcagtttt
     4321 aggagctgga tgataatcat ggccataatc tttagtgcct tttcggcgtt tatttttctc
     4381 ttcgtttaat ttattttcag cactcctttt cttatcttct ttcttcttcc tgctttccat
     4441 cgcagaactc aatgcagcat ctgctgctga cttctctttt gcggcagcat caaatgcagc
     4501 cttcttatta tttacatccg tctgtgcccg ctgggcctta agccctgcca tttgccacat
     4561 tctgtgacca gcagccattg gttctcgggc aaatcgctcg aattgtttta tttcagcctt
     4621 tgcatcagca agagttttat tcgctgcatc aagttcactt ttacgagaat tataaacctg
     4681 aacagcttta gcctgtcgtt cctggtttct ggcaacatct ttattagcct gattcagttc
     4741 tgcgcgggcc tgttcataat tgcgttcagc cacttccacc ggatgtgcgt cattccattc
     4801 ctgctggagg cgtttttcct catcctgacg ttgttttacc tgtgctgggg taagaacatc
     4861 tgtcactgat acataaaccg gcttctgccc actttctttc ggaaagcgaa tcaccgcttc
     4921 atgtgaacca ccaccaaagg taaatcccgc aggaacggca gtccggcctt tatcctccgt
     4981 aataccacgg ggaagggttg ttgacaccgg aaggcctttg acagtgctga ctgtcagaga
     5041 agggacacca ggaaatgatg cgtgaaatac acctggagta cgtgttggtt tggcattcac
     5101 aacaggcaca ctcataggca cacctgcaac tacggcaata tgctgtcgtg tgtccttcac
     5161 aacatctgtc acacgtttcg tcacgctgac agttgcctgg tccagcggaa gtgtactgac
     5221 ctgaacattc gtcactgttt ctgccggtaa tgacgtcaca atctttgaca tcatattcgg
     5281 gtcatctttt gctatttcag atggcagaat gccgtaaagc gcaatacccc atgcgctgaa
     5341 tttaaacggg cctttcaggg ctgcaaagat atccgctatt gccgcagata aagcctcacc
     5401 agagacggcg atacccagcg ttccggcacc aggagttgcc aaagcaggaa aaccaaatgc
     5461 cactgctgct acggatgaat tgctgccacc accggaatta ccattccccc cgccattacc
     5521 attgccggag ccacctcccc agtgaacacc actaccggaa ccgccacccc atgggttatt
     5581 ttccgaactc catcctgaac cgtcagaagc cccaccattt ccaccaagcc ccgtagggcc
     5641 gccattaatg ttaccacctg tgttatgtgc gccactgttg tggtcgcgtc catctccacc
     5701 gctcataaaa attccctctt ttaagcgtta aaacaattga ttatatagtt gatactgtac
     5761 ataaaaccac tggttttatg tacagaccaa aaagtactcg ccattatttt ttctgtcaag
     5821 tcaggggggg atattttttg gcagttcgga ggaatcactc atgaaaacgg tgaacggaac
     5881 gcgaaatcct ttcgcgggtc gtgaggcgtt ggacaagcga agcgcgtcag tttttccggc
     5941 tcttacccgt gacaggtttc tccaccagtt tatcttccag tgtcacaact ttctgataca
     6001 ccgccgctgt ggcgt
//
