LOCUS       NZ_CP140627             5219 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm009, complete sequence.
ACCESSION   NZ_CP140627
VERSION     NZ_CP140627.1
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 5219)
  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  JOURNAL   Unpublished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 5219)
  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
            CP140627.1.
            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..5219
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm009"
                     /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(517..750)
                     /locus_tag="O5Y90_RS26695"
                     /old_locus_tag="O5Y90_26690"
     CDS             complement(517..750)
                     /locus_tag="O5Y90_RS26695"
                     /old_locus_tag="O5Y90_26690"
                     /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_000137439.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(757..1287)
                     /locus_tag="O5Y90_RS26700"
                     /old_locus_tag="O5Y90_26695"
     CDS             complement(757..1287)
                     /locus_tag="O5Y90_RS26700"
                     /old_locus_tag="O5Y90_26695"
                     /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_015386306.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETILNDEFRKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVIFLFTVSG
                     GTLWYLGGMIQANLEEIRKQNENLEKLNAKTWGVRYHEGSNGRFLVLPEGMKAETNWTM
                     ENGKQNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<1325..2023)
                     /locus_tag="O5Y90_RS26705"
                     /old_locus_tag="O5Y90_26700"
                     /pseudo=""
     CDS             complement(<1325..2023)
                     /locus_tag="O5Y90_RS26705"
                     /old_locus_tag="O5Y90_26700"
                     /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            complement(1965..2288)
                     /locus_tag="O5Y90_RS26710"
                     /old_locus_tag="O5Y90_26705"
     CDS             complement(1965..2288)
                     /locus_tag="O5Y90_RS26710"
                     /old_locus_tag="O5Y90_26705"
                     /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_000956005.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGRLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2353..2544
                     /locus_tag="O5Y90_RS26715"
                     /old_locus_tag="O5Y90_26710"
     CDS             2353..2544
                     /locus_tag="O5Y90_RS26715"
                     /old_locus_tag="O5Y90_26710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3212..3325
                     /locus_tag="O5Y90_RS26720"
                     /old_locus_tag="O5Y90_26715"
     CDS             3212..3325
                     /locus_tag="O5Y90_RS26720"
                     /old_locus_tag="O5Y90_26715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001427889.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAAIGN"
                     /name="hypothetical protein"
     gene            3731..4120
                     /locus_tag="O5Y90_RS26725"
                     /old_locus_tag="O5Y90_26720"
     CDS             3731..4120
                     /locus_tag="O5Y90_RS26725"
                     /old_locus_tag="O5Y90_26720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679965.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000477210.1"
                     /translation="MFKSSVKSITSSTILTLLIGCSSTETNKNIVYKVGGDSIILNKYC
                     ILKMYPSQSEKNKGVIIEVNTDSLCKKKLNEITSKNIGKPLISYFDGKVISQPAIIHSA
                     LNPTHYYQPVNDETTVMEIIKAYSK"
                     /name="hypothetical protein"
     gene            complement(4184..4468)
                     /locus_tag="O5Y90_RS26730"
                     /old_locus_tag="O5Y90_26725"
     CDS             complement(4184..4468)
                     /locus_tag="O5Y90_RS26730"
                     /old_locus_tag="O5Y90_26725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000625497.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin Z C-terminal domain-related protein"
                     /protein_id="WP_000625497.1"
                     /translation="MISQNVWAPPFFFGPWVELENHTGDIAYTVYFDTLSNVPGPFIAF
                     IWYAPNGPRTVNVIGPASYQISCKGAGVDKIKFKSVSGTGQIIHVYTTL"
                     /name="colicin Z C-terminal domain-related protein"
     gene            complement(4486..4683)
                     /locus_tag="O5Y90_RS26735"
                     /old_locus_tag="O5Y90_26730"
     CDS             complement(4486..4683)
                     /locus_tag="O5Y90_RS26735"
                     /old_locus_tag="O5Y90_26730"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335786.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001335786.1"
                     /translation="MKEEKVLLHRFLFVVRNKNGCELSCSADLMGTRDDVYKYFSDSVS
                     GLDVELIDVSCESEWEEHSH"
                     /name="hypothetical protein"
     gene            4895..5191
                     /locus_tag="O5Y90_RS26740"
                     /old_locus_tag="O5Y90_26735"
     CDS             4895..5191
                     /locus_tag="O5Y90_RS26740"
                     /old_locus_tag="O5Y90_26735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001679964.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000047647.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKFLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     Typing          complement(2630..2717)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          2728..3284
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.925"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(414..1975)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.616"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gttcggcgcg atcacggcag cagacaggta aaaatggcaa caaaccaccc gaaaaactgc
       61 cgcgatcgta cccggtaaat tttaaccaca tgcatagcta tgcagctatg tgaatcatgc
      121 aggaattgcc agccagagac agctgaaacg gatttttttc atgctttcgg aagcgaagaa
      181 gacggggacc ggagcgggaa aacagaagtt caggggaatg agcgcgatct ggcaatagag
      241 gcaaaacaca gcaacaaaag acacaccaga atcgcgcccg tatgcgtttt aacgcgttcc
      301 tgtgttttca gcaaggtctg actgaagcgc gttcccggtg cccccgaacc aaccattatc
      361 ccaaaaaatg caccggaaac gcgctgacaa cattttagcc tgtctctgat taccatccca
      421 gcgaagggcc atccagtgtc cgttcctgta tttccagctg gcgctcacgc tccagggata
      481 acgcatgttc gcgttcctgt atcagccgtt cgtcccttat ctcctgttct cgctgtataa
      541 ctggctcaag cgttctgtct gctcgctcaa gtgctgcacc tgctgactca actgcatgac
      601 ccgctcgttc agcatcgcgt tgtcccgttg cgtaagcgaa aacattttct gcaattccac
      661 gaaggcgctc tcccattcgt tcagccgctg catatagtcc tgttgcagtt gctctaatgc
      721 gttcagcaaa tgtctttcca gctccgtcat gctctgttac tcctgtacca gccttacggc
      781 attctgtttc ccgttttcca tcgtccagtt cgtttcggct ttcatcccct cgggcaacac
      841 cagaaaacgt ccgttgctcc cctcgtgata acgcacgccc catgtcttcg cgttcagctt
      901 ctccagattc tcgttctgct tcctgatttc ttccaggttc gcctgtatca tcccgccaag
      961 ataccagagc gtcccgccac tcacggtaaa caggaaaatg accatcccca gtaacatcat
     1021 gcccgtattc cctgccagct ttaacacgtc cttcctgtgc tgcatcatcg cctctttcac
     1081 cccttcccgg tgttttttca gtgattcctc tgtcgaagct gtgaacaggg ctatagcgtc
     1141 tttgattttc gtctcgtttg atgtcacagc cttgcttaca gatttttcga gcttcctgaa
     1201 ctcgtcgttc agtattgtct ctgtagattc ggctctctct ttcagctttt tctcgaactc
     1261 cgcgcccgtc tgtaaaagat tgctcataaa atgctccttt cagcctgata ttcttcccac
     1321 cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct gaccacttca agccctgcct
     1381 ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc cccgacatga taaagagcgt
     1441 ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt ttccggcagg ttatcagaga
     1501 gagtcagtat ccggcggttc tccggggcgt tggggtcatg cagcccgtaa tggtgattca
     1561 ccagcgtctg ccaggcatca attctcggcc tgtctgcccg gtcgtagtac ggctggaggc
     1621 gttttccggt ctgtagctcc atgttcggaa tgacaaaatt cagctcaagc cgtcccttgt
     1681 cctggtgctc cacccacagg atgctgtact gatttttttc gagaccgggc atcagtacac
     1741 gctcaaagct cgccatcacc ttttcacgtc ctcccggtgg cagctccttc tccgcgaacg
     1801 acagcacacc ggacgtgtat ttcttcgcaa atggcgtggc atcgatgagt tcccgtactt
     1861 cttccggatt accctgaagc accgttgccc cttcccggtt acgctccctt cccagcaggt
     1921 aatcaaccgg accactgcca ccaccttttc cccgggcatg aaacttaact atcatcccgc
     1981 gtcccctgtt ccctgacggc cagacgcagc cggcgcagct catccccgat ggccatcagt
     2041 gcggccacca cctgaacccg gtcaccggaa gaccactgcc cgctgttcac cttcctcgct
     2101 gtctgattca ggttattccc gatggcggcc agctgacgca gtaacggcgg tgccagtgtc
     2161 ggcagcctcc cggaacgggc aaccggctca cccaggcaga cccgccgcat ccataccgcc
     2221 agctgtttac cctcacagcg ttcaagtaac cgggcatgtt catcatcagt aacccgtatt
     2281 gtgagcatcc tctcgcgttt catcggtatc attatcccca tgaacagaaa tcccccttac
     2341 acggaggcat cagtgaccaa acaggaaaaa accgccctta acatggcccg ctttataaga
     2401 agccagacat taacgctgct ggagaagctc aacgaactgg acgcggatga acaggcagat
     2461 atctgtgaat cgcttcacga ccacgccgat gagctttacc gcagttgcct cgctcgcttc
     2521 ggggatgacg gtgaaaacct ctgacacatg cagctcccgg agacggtcac agcttgtctg
     2581 tgagcggatg ccgggagctg acaagcccgt cagggcgcgt cagcaggttt tagcgggtgt
     2641 cggggcgcag ccctgaccca gtcacgtagc gatagcggag tgtatactgg cttaaccatg
     2701 cggcatcagt gcggattgta tgaaaagtac gccatgccgg gtgtgaaatg ccgcacagat
     2761 gcgtaaggag aaaatgcacg tccaggcgct tttccgcttc ctcgctcact gactcgctac
     2821 gctcggtcgt tcgactgcgg cgagcggtat ctactcactc aaaaacgaaa tgctgttatc
     2881 cacagaatca ggggataaca ccggaaaaaa catgtgagca aaagaccagg aacaggaaga
     2941 aggccgcgcc gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc
     3001 gacgctcaag tcagaggtgg cgaaacccga caggacttaa agataccagg cgtttccccc
     3061 cggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg cttaccggat acctgtccgc
     3121 ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgtaggt atctcagttc
     3181 ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa ccccccgttc agcccgaccg
     3241 ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg acttaacgcc
     3301 actggcagca gccattggta actaaaaagt ggatttagat acgcagaact cttgaagttg
     3361 aagccttata gcggctacac tgaaaggaca tcttttggta tctgtgctcc acttaagcca
     3421 gctacccggt taggtaatct gccaggatta gctaaccttc gaaaaaccac ctgccagggt
     3481 ggttttttcg tttacaggca gcagattacg cgcagaaaaa aaggatctca agaagatcct
     3541 ttgatctttt ttctctaaac tgcaatccca tcagttcagg agagaaagat agtataattg
     3601 ccctctctta tatggaacca ccattcaatc acatcatggg aataatataa gtgaaaacgt
     3661 tcgcattgtt tatttttacg tgtatatgta tttatagatt ggaattttaa caaaataaaa
     3721 tggagttaat atgttcaaat catcagtaaa gtcaataaca tcgagtacta tactgacctt
     3781 acttatagga tgttcaagta ctgaaacaaa caaaaacatt gtttacaaag ttggtggtga
     3841 cagcatcatt ctgaataaat attgcatact taaaatgtac ccttcccaat cagaaaaaaa
     3901 caaaggcgtc ataatagaag taaacacaga tagtttatgt aagaaaaaac taaacgaaat
     3961 aactagtaaa aatataggga aacccctgat ttcatatttt gatggaaaag taatatccca
     4021 acctgcaatc attcattctg cactaaatcc aacccattat tatcaacctg tgaacgatga
     4081 aacaacagtg atggaaatca taaaagcata ttcaaaataa tattaataga tataatcctg
     4141 cttaaggtat agcttaggca ggattatatc tattcagctc ttattataag gtagtgtata
     4201 catgaataat ctgccctgtc ccactgacac ttttaaattt aattttatca acaccagcgc
     4261 ccttgcaaga gatctgataa gatgctggac caataacgtt aactgttctt ggcccattag
     4321 gggcatacca gataaaagca ataaatggac cgggtacatt agacaatgta tcaaaataga
     4381 cagtgtacgc gatatcacca gtatgatttt caagttcaac ccaaggacca aaaaagaaag
     4441 gaggagccca aacattttga gaaatcatat aatctcctga ttagttcaat gcgaatgttc
     4501 ttcccattca ctctcgcaag aaacatctat aagctcaaca tctagcccac taacagaatc
     4561 agagaaatac ttataaacat catcccttgt tcccataagg tctgccgaac atgatagttc
     4621 acaaccattc ttattcctaa ctacaaataa gaaacggtga agcaatactt tttcttcttt
     4681 cattttatcc ctccctttat ttacacagaa tatactgtat atataaacac tagttttata
     4741 tacagtataa attacgccgc attatttttc ctgtcaatga tatgaatttt catttttgtg
     4801 atctgaatca cccttataaa aatcaggaag ggaagattcg cagcagaaaa acagcaccgg
     4861 ataacatcag gagaaaaaac agagaggaga taacgtgagc aaaacaaaat ctggtcgcca
     4921 ccgactgagc aaaacagaca aacgcctgct ggctgcactt atcgctgccg gatacgaaga
     4981 gcggacagcc cgtgacctca tccagaaaca cgtttacaca ctgacacagg ccgacctgcg
     5041 ccatctggtc agtgaaatca gtaacggtgt gggacagtca caggcctacg atgcgattta
     5101 ccaggcaaga cgcattcgtc tcgcccgtaa attcctgaac ggaaaaaaac cggaagaagg
     5161 gctgaacgcc tggaagggtg atttaccata atcacttatt gtacgcaccg ctgaaacgc
//
