LOCUS       NZ_CP151320             4065 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R21.0552 plasmid pR21.0552_4k, complete
            sequence.
ACCESSION   NZ_CP151320
VERSION     NZ_CP151320.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN39735802
            Assembly: GCF_038364745.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 4065)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W., Teng,R.-H. and Chen,B.-H.
  TITLE     WGS of Shigella
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4065)
  AUTHORS   Chiou,C.-S., Hong,Y.-P., Wang,Y.-W., Teng,R.-H. and Chen,B.-H.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-2024) Center for Diagnostics and Vaccine
            Development, Centers for Disease Control, Taiwan, No.20, Wenxin S.
            3rd Rd., Nantun Dist., Taichung City 408, Taiwan
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: flye v. v2.9.2
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038364745.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:43:35
            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)                     :: 5,428
            CDSs (total)                      :: 5,299
            Genes (coding)                    :: 4,560
            CDSs (with protein)               :: 4,560
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 96
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 739
            CDSs (without protein)            :: 739
            Pseudo Genes (ambiguous residues) :: 0 of 739
            Pseudo Genes (frameshifted)       :: 212 of 739
            Pseudo Genes (incomplete)         :: 527 of 739
            Pseudo Genes (internal stop)      :: 127 of 739
            Pseudo Genes (multiple problems)  :: 121 of 739
            Pseudo Genes (short protein)      :: 3 of 739
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151320.1.
            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..4065
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R21.0552"
                     /db_xref="taxon:624"
                     /plasmid="pR21.0552_4k"
                     /collected_by="Taiwan CDC"
     gene            1..2148
                     /gene="mobQ"
                     /locus_tag="AADX62_RS27100"
                     /old_locus_tag="AADX62_27085"
     CDS             1..2148
                     /gene="mobQ"
                     /locus_tag="AADX62_RS27100"
                     /old_locus_tag="AADX62_27085"
                     /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_124770306.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATVRRHDRGWSQ"
                     /name="mobQ"
     gene            complement(2395..3102)
                     /locus_tag="AADX62_RS27105"
                     /old_locus_tag="AADX62_27090"
     CDS             complement(2395..3102)
                     /locus_tag="AADX62_RS27105"
                     /old_locus_tag="AADX62_27090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3633..3887)
                     /gene="mobC"
                     /locus_tag="AADX62_RS27110"
                     /old_locus_tag="AADX62_27095"
     CDS             complement(3633..3887)
                     /gene="mobC"
                     /locus_tag="AADX62_RS27110"
                     /old_locus_tag="AADX62_27095"
                     /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_118998437.1"
                     /translation="MSRTLEQKIAEAEARLQRLKVKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          2..359
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.443"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3892..4065)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.857"
                     /coverage="98.0"
                     /evalue="5.65e-83"
     Typing          complement(2396..3102)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2145
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.775"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgattt atcatctcag catgaaaatc atctccagaa acagcggcta cagcgccgtt
       61 gcttctgctg cctatcgttc cggttcactg atgcttgatg agcgtaccgg actgactcac
      121 gactacaccc gcaaaagcgg tgtggctgaa gctgtgattc tgactcccgc gacagcccct
      181 gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga acgccggaag
      241 aactcacaac ttgcgcggga aattgaactc gccatccccc acgaactgcc gcaggatgcc
      301 gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct
      361 gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg
      421 agagctgtcg gacctgctgg attcggtgga aaggtcaggg actggaacga ccggacacat
      481 gccgagacgt ggcgggcatc atgggctgac catgcaaaca gggcactggc gaacgccggt
      541 tatcaggaag agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt
      601 attcacctcg gaaagtctgc ctgtgcgatg gaaacacgag gtatcgaaac agaacgcggc
      661 gaacagaatc gtctgattaa cagacttaac ctggaaatac agatttcccg taccgaactc
      721 aggaacggag ggctgacaga gcctgcccgc cgtgtggctg accttctgaa tatcgggctt
      781 cctgacaacg caacttcgta cacactacgt gacatcatcg aagcgttgcc gaaggacagt
      841 aactcggcat ggaaactcac cagtaatgcc atgtcgatga tggcagatat gcaggcgacg
      901 cgcagacgct gggaagagct gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc
      961 ctgaaaaaat catcgccgtt ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg
     1021 gcaccggaat accgtagtga gcagggaaaa atccagtctc tgagccagca aatggaaaaa
     1081 ttgcgacagc attaccggaa ggtggagaaa caggacattc ccgcgagtca gatggcattt
     1141 gaaaaacagt ggcagcagtg gggggaatcc ggccttgcag ctctcagagc ccagttgctt
     1201 aaacgtgaag aggaattgcg ccggaaggaa caggaagata ctgaacgtag tcgcgcggag
     1261 cagctcagga aaaatgacaa tgccgttatg gattcagggg tactgagcgc agtcgttacg
     1321 gggtatggcg aggcccccat gcctggtaac ggggaaatga cctgttacct tctgcttcat
     1381 aaccggaacg gagaatatac gctctggggt aacgagctgg agaaataccg caccagaatc
     1441 tttgagcgtg ttgatttaat gcgtgacagg agtggttata tctgtgaccg aagcgaaatc
     1501 ggccaacgtc cgccactgca acgtgtttat tcctctgcga cctttgagca actgctgacg
     1561 caggtttgcc agacatggcc gcaacatacc cgcaatctcc gccagccgaa gacatggccg
     1621 gagtctttct gtcttggaga agaccgccag ccagccatgc catcactggc agcaaggaag
     1681 gtggatttta cgcagggacg tctgccaccg acgctgatgc cggtcatgag ttctgtcgac
     1741 cgggaaaccc gccagcttca gcttttgctg gtcatgggcg tggatgactc tctgggcggt
     1801 gttgtccggc ttaatggtac gctgtatccc gcgtttgccg ttccctcagc cgataacagc
     1861 cagctggtca tcagtgcact aaccgataag gggttacggt atgcagggta tggtgttgcc
     1921 gtaaatcacg atgcagacag ccacatatca cctgcaccag aactgatgca gtttcatctg
     1981 aaaacccgtg aggcaccgct ttttgctgcc gtcaacacac cagaaaaaca gccggatcat
     2041 ctgttccgct cgctgggttt taatcgtacc tgggacgaat ggcggcgcga ggaagatgca
     2101 cgaacacacg ccaccgtgag gagacatgat cgcggttggt cacagtgaat gtgaacaata
     2161 ttttgttttg tgtaacatcg tgttatgttc gccgatgttc atcgacaggg atgaatgcaa
     2221 gaagcacact cacaagcgca aacatagttt tgtttttccg cccccaaaaa ttgggggttc
     2281 tttttttgct gcatcagagc gtttttgacg caacttttca cttcaatagt accttcgcat
     2341 tcctgacaca agaaaaacgc gacagtgagc gttttaggtg ccttaaaatc gattctagat
     2401 cgtcatcttg atctgtttgt cttccttgaa gcgaaaatgc agggctacaa ccgtgcgccc
     2461 ctttttgatc gtctcaaccg ttacagccag gtcgcttttt ttgttcagtt cgtcaacaca
     2521 gggttttatt agatccctgt ttaacgtttt gaaatcttta tatttaccat caagcatcag
     2581 tgatgattta aaatcatcga gggcgataat acgttcccca gtactgcgga attgctggag
     2641 aatttcgtat attcttatgc tgtaacttct tgataaatta gaaatatttt taatgacgac
     2701 tctggtgaat tgccccttca actgtgtcag ataaggcatt accgcgtcag aaaaagtgat
     2761 ttgtgctttc ccctctcccc tcgcgtactg tgcccgatac tgaatccagc ggaactcctc
     2821 gcgcttctcg tcgtccttga gaatgatcga cctgtcccac aaacgatcga tcgcttcctg
     2881 tagctgaacc tcggcatttt tccgccccat atcagggaat gaatcaaaat attccgcagc
     2941 tgtaatggtc attgtctttt gcaattcagg tgaagctacg tcagtaccgg agttaagtcg
     3001 gcttatgcag agcaataaga aacgctgttc ttgtaaagtt agcttgtaac tggcctcaac
     3061 cagcgcattg gacttatagg ctatcagagg gtttgatgtc attttaacca ccaggccaaa
     3121 gatgaggtga gataaaaacc tatcaccttt agcattggtg agcaattata ttttcacccc
     3181 ccattttcct gtgaatatta ccttaaatct cctcaccttt accttaaatt acctcaccca
     3241 agcaccttaa attatatcac ctttacctta aatcatatca cctatagcgt tgtaacattt
     3301 tgttttctat aaggaatttc gaccctaaaa caagtattaa aaacaagatc ttaaaaacaa
     3361 gatctaaaaa cttaacggcg agcctgtgga taacttgggg tgctgaaaat aaaaatccaa
     3421 taaaaacaat gtgttgcaaa aatcaggatt gaagattccg aatacccccc cctccaaccc
     3481 tgtggaaatc cagtattcat gcgggttcag cgcatatcac ctgtcgaaaa accgtgcgta
     3541 tgtgctcaac atggcgactg attcacttcc gcttcctcgc ccactcactc gctaacgctc
     3601 ggtcgctggg ctgcggcgag cggacgatac aatcactgct ctggcagcgc ctccagctcg
     3661 ttaatcagcg gcagtattcg cgtcacatca gcctgccgtg tcacctctgc cttcaggaac
     3721 tggagtaacc aagctcgcaa ctgcacttcc tccggctttc tgacctttgc cagcaatgct
     3781 gcacccacaa tgaccttctg cgctgtgtcc aggctccggc tcttcacctt caggcgctgt
     3841 aatctggcct cagcttcggc aatcttctgt tcgagtgttc tgctcatttc gtgactccgt
     3901 gcgcagtgaa aaatcgcatt ttagcgcgtc actggtagtt taaaaactga gctggcataa
     3961 tgcacggcaa atcacgaagt gcgcacttat acaatctcca ctccgtttcg attgtgtgcg
     4021 ccctgcgggg ctgaaagaaa accacaaaaa ggcattacgg cagaa
//
