LOCUS       NZ_CP140629             4072 bp    DNA     circular CON 07-JAN-2024
DEFINITION  Shigella sonnei strain ST152 plasmid pSO87_sm011, complete sequence.
ACCESSION   NZ_CP140629
VERSION     NZ_CP140629.1
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 4072)
  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  JOURNAL   Unpublished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 4072)
  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
            CP140629.1.
            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..4072
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="ST152"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pSO87_sm011"
                     /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(4049..4072,1..2136)
                     /gene="mobQ"
                     /locus_tag="O5Y90_RS26765"
                     /old_locus_tag="O5Y90_26760"
     CDS             join(4049..4072,1..2136)
                     /gene="mobQ"
                     /locus_tag="O5Y90_RS26765"
                     /old_locus_tag="O5Y90_26760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2392..3084)
                     /locus_tag="O5Y90_RS26770"
                     /old_locus_tag="O5Y90_26765"
     CDS             complement(2392..3084)
                     /locus_tag="O5Y90_RS26770"
                     /old_locus_tag="O5Y90_26765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3616..3870)
                     /gene="mobC"
                     /locus_tag="O5Y90_RS26775"
                     /old_locus_tag="O5Y90_26770"
     CDS             complement(3616..3870)
                     /gene="mobC"
                     /locus_tag="O5Y90_RS26775"
                     /old_locus_tag="O5Y90_26770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          2..335
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.91"
                     /coverage="93.0"
                     /evalue="3.11e-163"
     Typing          complement(3872..4048)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          complement(2393..3084)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2133
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.578"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 aaaattatct ccagaagcag cggctacagc gccgtagctt ccgctgccta tcgttccggt
       61 tcactgatgc ttgatgagcg taccggactg actcacgact acacccgcaa aagcggtgtg
      121 gctgaagctg tgattctgac ccccgcgaca gcccctgcct ggtgtacgaa ccgtgccgaa
      181 ctctggaatg ccgttgagaa ggccgaatgc cggaagaact cacaacttgc gcgggaaatt
      241 gaactcgcta tcccccgtga actgccgcag gatgccgcac gggaaaccgt tctcgccttt
      301 gtcagagaaa actttgtcag tcagggcatg attgctgatg tggcgttcca tcacatggat
      361 aaaacaaatc cccatgcgca catcatgctg accacgaggg ctgtcggacc tgctgggttc
      421 ggcggaaagg tcagggactg gaacgaccgg acacatgccg agacgtggcg tgcatcatgg
      481 gctgaccatg caaacagagc actggcgaac gccggttatc aggaagagat agaccatcgt
      541 tcatacgagc gacaggggct tgagaaaacg cctggtattc acctcggaaa gtctgcctgt
      601 gcgatggaaa cacgcggtat cgaaacagaa cgcggcgaac agaatcgtct gattaacagg
      661 cttaacctgg aaatacagat ttcccgcact gaactcagga acagcgggct gacagagcct
      721 gcccgccgtg tggctgacct tctgaatatc gtgcttcctg acaacgcaac ttcgtacaca
      781 ctacgtgaca tcatcgaagc gttgccgaag gacagtaatg cggcatggaa actcaccagt
      841 aatgccatgt cgatgatggc agatatgcag gcgacgcgca gacgctggga agagctgaac
      901 accgaacgaa aggaagcgat gagccatgct gccagcctga aaaaatcatc gccgttttcg
      961 tccggttttt cccgtattcc cctgatgcaa tgggcggcac cggaataccg tagcgaacag
     1021 ggaaaaatcc agtcgctgag ccagcaaatg gaaaaattgc gacagcatta ccggaaggtg
     1081 gagaaacagg acattcccgc gagtcagacg gcatttgaaa aacagtggca gcagtggggg
     1141 gcatccggcc ttgcagctct cagagtccag ttgcttaaac gtgaagagga attgcgccgg
     1201 aaggagcagg aggatacaga acgtagtcgc gcggagcgac gagcggaaca gctcaggaaa
     1261 aatgacaatg ccgttatgga ttcaggggta ctgagcgcag tcgttacggg gtatggcgag
     1321 gcccccatgc ctggtaacgg ggaaatgacc tgttaccttc tgcttcacaa ccggaacgga
     1381 gaatacacgc tctgggggaa cgagctggag aaataccgca ccagaatctt tgagcgtgtt
     1441 gatttaatgc gtgacaggag tggttatatc tgtgaccgaa gcgaaatcgg tcaacatcca
     1501 ccactgcaac gtgtttattc ctctgcgacc tttgagcaac ttctgacgca ggtttgccag
     1561 acatggccgc aatatacccg caatctccgc cagccgaaga catggccgga gtctttctgt
     1621 cttggagaag accgccagcc agccatgcca tcactggcag caaggaaggt ggattttacg
     1681 cagggacgtc tgctaccgac gctgatgccg gtaatgagtt ctgtcgaccg ggaaacccgc
     1741 cagcttcagc ttttgctggt catgggcgtg gatgactctc tgggcggtgt tgtccggctt
     1801 aatggtacgc tgtatcccgc gtttgccgtt ccctcagccg ataacagcca gctggtcatc
     1861 agtgcactga ccgataaggg gttacggtat gcagggtatg gtgttgccgt aaatcacgat
     1921 gcagacagcc acatatcacc tgcgccggaa cttatggagt ttcatctgaa aacccgtgag
     1981 gcaccgcttt ttgctgccgt caacacacca gaaaaacagc cggatcatct gttccgctct
     2041 ctgggtttca atcgtacctg ggatgaatgg cggcgcgagg aagatgcaag aacacacacc
     2101 accgagagga gacatgatcg cggttggtca cagtgaatgt gaacaatatt ttgttttgtt
     2161 taacatcgtg ttatgttcgt cgatgttctt ctatgttcat cgacagggat gaatgcaaga
     2221 agcacacaca taatgcaagc atagttttgt ttttccgccc ccaaaaattg ggggttcttt
     2281 tttcgctgca ttagagcgct tttgacgcaa tttttcactt caatagtacc ttcgcactac
     2341 taacacaaaa aaaacgcagc agggagcgtt ttaggtgcct taaaatcgat tttagatcgt
     2401 catcttgatc tgtttgtctt ccttgaagcg aaaatgcagg gctacaaccg tgcgcccctt
     2461 tttgatcgtc tcaaccgtta cagccaggtc gctttttttg ttcagttcgt caacacaggg
     2521 ttttattagt attttattta agtctctgaa ttgtttgtat ttattttcaa tccctaacat
     2581 tgaacgaaag tcattaagag caataattct ctctcccgta ctgcggaatt gctggaggaa
     2641 ctcgtatatt cttatactgt aactacttga taaacctgat atgtttttta taacaacgcg
     2701 cgtgaattgc cccttcagtt gcgtcagata aggcattacc gcgtcagaaa aggttattcg
     2761 agccttggcc tcacctttag cgtactgtgc ccgatactgg atccagcgga actcctcacg
     2821 cttctcgtca ttcttgagaa tgatcgacct gtcccataaa cgatcgatcg cttcctgtaa
     2881 ctgaacctcg gcatttttcc gccccatgtc agggaatgaa tcaaaatatt ccgcagcggt
     2941 aatggtcatt gtcttttgca attcagcatc agcaccagat ttcaatcgac tgatacacag
     3001 caacagaaaa cgttgttcct gtagggtcaa cttgtagctg gcctcaacca aagcattcga
     3061 cttgtaggca atcaagtccg acatacaaag atcccgttca aatgtggtga tgctttaatg
     3121 tgccccacaa ataagaaatg tggaatattt ttttttatat cctcacattt ctgtgaataa
     3181 caccttaaat tcctccacct ttaccttaaa ttcctccacc taaacacctt aaattcctcc
     3241 acctttacct taaattcctc cacatatacc tctataacat attgatttta ttaatgaatt
     3301 ttgaccctaa aacaagtatt aaaaacaaga tcttaaaaac aagatctaaa aacttaacgg
     3361 cgagcctgtg gataacttgg ggcgctgaaa acaaaaaacc aataaaaaca atgtgttgca
     3421 agaaagcaga attgcaagtt ccgaatactc cccttccaac cctgtggaaa tccagtattc
     3481 atgcgggttc agcgcatatc acctaccgaa aaaccgtgcg tatgtgctca acctggcgac
     3541 ggattcactt ccgcttcctc gcccactcgc tcgctaacgc tcggtcgctg gggctgcggc
     3601 gagcggacga tacaatcact gtcctggcag cgcctccagc tcgttaatca gcggcagtat
     3661 gcgcgtcaca tcagcctgtc gtgtcacctc tgccttcagg aactggagta accaggcacg
     3721 caactgcacc tcctccggct ttctgacctt tgccagcaat gctgcaccca caacaacctt
     3781 ctgcgctgtg tccaggctcc ggctcttcgc cttcaggcgc tgtaatctcg cctcagcatc
     3841 agcaatcttc tgttcgagcg ttctgctcat gatgtaactc cgtgcgcgat gaaaaatcgc
     3901 attttagcgc gtcactggta gtttaaaaac tgagctggca taatgcgcga caaatcacaa
     3961 agtgcgcact tatacaatct ccactccgtt tcgattgtgt gcgccctgcg gggctgaaag
     4021 aaaactacaa aaaggcatta cggcagaaat ggcgatttat catctcagca tg
//
