LOCUS       NZ_CP045939             3715 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain AUSMDU00010534 plasmid pAUSMDU00010534_07,
            complete sequence.
ACCESSION   NZ_CP045939
VERSION     NZ_CP045939.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN13191651
            Assembly: GCF_009664515.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3715)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Complete microbial genomes for public health in Australia and
            Southwest Pacific
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3715)
  AUTHORS   Baines,S.L., Goncalves da Silva,A., Carter,G.P., Jennison,A.V.,
            Rathnayake,I.U., Graham,R.M.A., Sintchenko,V., Wang,Q.,
            Rockett,R.J., Timms,V.J., Martinez,E., Ballard,S., Tomita,T.,
            Isles,N., Horan,K.A., Pitchers,W., Stinear,T.P., Williamson,D.A.,
            Howden,B.P. and Seemann,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-NOV-2019) University of Melbourne, Microbiological
            Diagnostics Unit, First Floor, Building 248, Parkville, Victoria
            3010, Australia
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 22-OCT-2019
            Assembly Method                   :: Unicycler v. 0.4.8b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 103x
            Sequencing Technology :: Oxford Nanopore GridIon, Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_009664515.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 06:48:57
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,242
            CDSs (total)                      :: 5,108
            Genes (coding)                    :: 4,461
            CDSs (with protein)               :: 4,461
            Genes (RNA)                       :: 134
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 101
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 647
            CDSs (without protein)            :: 647
            Pseudo Genes (ambiguous residues) :: 0 of 647
            Pseudo Genes (frameshifted)       :: 177 of 647
            Pseudo Genes (incomplete)         :: 452 of 647
            Pseudo Genes (internal stop)      :: 106 of 647
            Pseudo Genes (multiple problems)  :: 86 of 647
            Pseudo Genes (short protein)      :: 3 of 647
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP045939.1.
            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..3715
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="AUSMDU00010534"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pAUSMDU00010534_07"
                     /geo_loc_name="Australia"
                     /collection_date="2017"
     gene            1..702
                     /locus_tag="GJE15_RS25670"
                     /old_locus_tag="GJE15_25670"
     CDS             1..702
                     /locus_tag="GJE15_RS25670"
                     /old_locus_tag="GJE15_25670"
                     /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_001281397.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(699..2750)
                     /gene="mobQ"
                     /locus_tag="GJE15_RS25675"
                     /old_locus_tag="GJE15_25675"
     CDS             complement(699..2750)
                     /gene="mobQ"
                     /locus_tag="GJE15_RS25675"
                     /old_locus_tag="GJE15_25675"
                     /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_341539940.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRIELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPD"
                     /name="mobQ"
     gene            2929..3183
                     /gene="mobC"
                     /locus_tag="GJE15_RS25680"
                     /old_locus_tag="GJE15_25680"
     CDS             2929..3183
                     /gene="mobC"
                     /locus_tag="GJE15_RS25680"
                     /old_locus_tag="GJE15_25680"
                     /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_000091745.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(2393..2751)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2752..2928
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          2..702
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(703..2837)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.719"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 atgtcggatc taattgccta taaatccaat gcgctggttg aagccagtta taaattgacc
       61 ctacaggaac agcgattttt gttactttgc atcggtcgat tgaagtctgg ggctgatgca
      121 gaatctccaa aattgcaaaa gacaatgacc attacagctg cggaatattt cgattcattc
      181 cctgacatgg ggcggaaaaa tgccgaggtt cagttacagg aagcaattga tcgtttgtgg
      241 gacaggtcaa tcattctcaa ggatgacgag aaacgtgagg agttccgctg gatccagtat
      301 cgggcacagt acgctaaagg cgaggccaga gcacaaataa cattttctga cgcagtaatg
      361 ccttatttga cacaactaca agggcaattt actagagttg taatcaagaa tatatctaga
      421 ttatcaagaa gttacagtat aaggatatac gaactcctcc agcagttccg cagtactggc
      481 gaacgtatta tcgctctcga tgattttcgc tcaatgcttg atatagagca taaatatcaa
      541 acatataaat cacttaacca gcaattatta agaccctgca ttgacgaact gaacaaaaaa
      601 agcgacctgg ctgtaacggt tgagacgatc aaaaaggggc gcacggttgt agccctgcat
      661 tttcgcttca aggaagacaa acaaatcaag atgacgatct aatccggctg tttttctggt
      721 gtgttgacgg cagcaaaaag cggtgcctca cgggttttca gatgaaactc cataagttcc
      781 ggcgcaggtg atatgtggct gtctgcatcg tgatttacgg caacaccata ccctgcatac
      841 cgtaacccct tatcggtcag tgcactgatg accagctggc tgttatcggc tgagggaacg
      901 gcaaacgcgg gatacagcgt accattaagc cggacaacac cgcccagaga gtcatccacg
      961 cccatgacca gcaaaagctg aagctggcgg gtttcccggt cgacagaact cattaccggc
     1021 atcagcgtcg gtagcagacg tccctgcgta aaatccacct tccttgctgc cagtgatggc
     1081 atggctggct ggcggtcttc tccaagacag aaagactccg gccatgtctt cggctggcgg
     1141 agattgcggg tatattgcgg ccatgtctgg caaacctgcg tcagaagttg ctcaaaggtc
     1201 gcagaggaat aaacacgttg cagtggtgga tgttgaccga tttcgcttcg gtcacagata
     1261 taaccactcc tgtcacgcat taaatcaaca cgctcaaaga ttctggtgcg gtatttctcc
     1321 agctcgttcc cccagagcgt gtattctccg ttccggttgt gaagcagaag gtaacaggtc
     1381 atttccccgt taccaggcat gggggcctcg ccataccccg taacgactgc gctcagtacc
     1441 cctgaatcca taacggcatt gtcatttttc ctgagctgtt ccgctcgtcg ctccgcgcga
     1501 ctacgttctg tatcctcctg ctccttccgg cgcaattcct cttcacgttt aagcaactgg
     1561 actctgagag ctgcaaggcc ggatgccccc cactgctgcc actgtttttc aaatgccgtc
     1621 tgactcgcgg gaatgtcctg tttctccacc ttccggtaat gctgtcgcaa tttttccatt
     1681 tgctggctca gcgactggat ttttccctgt tcgctacggt attccggtgc cgcccattgc
     1741 atcaggggaa tacgggaaaa accggacgaa aacggcgatg attttttcag gctggcagca
     1801 tggctcatcg cttcctttcg ttcggtgttc agctcttccc agcgtctgcg cgtcgcctgc
     1861 atatctgcca tcatcgacat ggcattactg gtgagtttcc atgccgcatt actgtccttc
     1921 ggcaacgctt cgatgatgtc acgtagtgtg tacgaagttg cgttgtcagg aagcacgata
     1981 ttcagaaggt cagccacacg gcgggcaggc tctgtcagcc cgctgtttct gagttcgata
     2041 cgggaaatct gtatttccag gttaagtctg ttaatcagac gattctgttc gccgcgttct
     2101 gtttcgatac cgcgtgtttc catcgcacag gcagactttc cgaggtgaat accaggcgtt
     2161 ttctcaagcc cctgtcgctc gtatgaacga tggtctatct cttcctgata accggcgttc
     2221 gccagtgccc tgttcgcatg gtcagcccat gatgcacgcc acgtctcggc atgtgtccgg
     2281 tcgttccagt ccctgacctt tccaccgaat ccagcaggtc cgacagctct cgtggtcagc
     2341 atgatgtgcg catggggatt tgttttatcc atgtgatgga acgccacatc agcaatcatg
     2401 ccctgactga caaagttttc tctgacaaag gcgagaacgg tttcccgtgc ggcatcctgc
     2461 ggtagttcgc gggggatggc gagttcaatt tcccgcgcaa gttgtgagtt cttccggcgt
     2521 tcggccttct caacggcatt ccagagttcg gcacggttcg tacaccaggc aggggctgtc
     2581 gcgggagtca gaatcacagc ttcagccaca ccgcttttgc gggtgtagtc gtgagtcagt
     2641 ccggtacgct catcaagcat cagtgaaccg gaacgatagg cagcagaagc aacggcgctg
     2701 tagccgctgt ttctggagat gattttcatg ctgagatgat aaatcgccat ttctgccgta
     2761 atgccttttt gtggttttct ttcagccccg cagggcgcac acaatcgaaa cggagtggag
     2821 attgtataag tgcgcacttc gtgattttcc gtgcattatg ccagctcagt ttttaaacta
     2881 ccagtgacgc gctaaaatgc gatttttcat cgcgcacgga gttacatcat gagcagaaca
     2941 ctcgaacaga agattgctga tgctgaggcc agattacagc gcctgaaggc gaagagcagg
     3001 agtctggaca cagcgcagaa ggtcattgtg ggtgcagcat tgctggcaaa ggtcagaaag
     3061 ccggaggagg tgcagttgcg tgcctggtta ctccagttcc tgaaggcaga ggtgacacga
     3121 caggctgatg tgacgcgcat actgccgctg attaacgagc tggaagcgct gccaggacag
     3181 tgattgtatc gtccgctcgc cgcagtccca gcgaccgagc gttagcgagc gagtgggcga
     3241 ggaagcggaa gtgaatccgt cgcctgattg agcacatacg cacggttttt cgggaggtga
     3301 tatgcgctga acccgcatga atactggatt tccacagggt tggagggggt gtattcggaa
     3361 cttgcaattc tgcttttttg caacgcattg tttttattgg ttttttgttt tcagcactcc
     3421 aagttatcca caggctcgtc gttaagtttt tagatcttgt ttttaagatc ttgtttttaa
     3481 tacttgtttt agcgccaaaa ttccttatag aaaacaaaat gttacaatgc tataggtaat
     3541 gtgatttaag gtaaaggtaa tatgatttaa ggtgtttagg tgggggaatt taaggtaaag
     3601 gcaatatgat ttaaggtaat attcacagaa aaagggatat taaaataaaa aggcattgcc
     3661 tttcgttgag ggtatgttta tcttttattc attacctttt ggggagggat gctct
//
