LOCUS       NZ_CP151319             4072 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R21.0552 plasmid pR21.0552_4.1k, complete
            sequence.
ACCESSION   NZ_CP151319
VERSION     NZ_CP151319.1
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 4072)
  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  JOURNAL   Unpublished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 4072)
  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
            CP151319.1.
            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..4072
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R21.0552"
                     /db_xref="taxon:624"
                     /plasmid="pR21.0552_4.1k"
                     /collected_by="Taiwan CDC"
     gene            1..2160
                     /gene="mobQ"
                     /locus_tag="AADX62_RS27085"
                     /old_locus_tag="AADX62_27070"
     CDS             1..2160
                     /gene="mobQ"
                     /locus_tag="AADX62_RS27085"
                     /old_locus_tag="AADX62_27070"
                     /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(2416..3108)
                     /locus_tag="AADX62_RS27090"
                     /old_locus_tag="AADX62_27075"
     CDS             complement(2416..3108)
                     /locus_tag="AADX62_RS27090"
                     /old_locus_tag="AADX62_27075"
                     /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(3640..3894)
                     /gene="mobC"
                     /locus_tag="AADX62_RS27095"
                     /old_locus_tag="AADX62_27080"
     CDS             complement(3640..3894)
                     /gene="mobC"
                     /locus_tag="AADX62_RS27095"
                     /old_locus_tag="AADX62_27080"
                     /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..359
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.05"
                     /coverage="99.0"
                     /evalue="1.4199999999999999e-176"
     Typing          complement(3896..4072)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          complement(2417..3108)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2157
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.583"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgattt atcatctcag catgaaaatt atctccagaa gcagcggcta cagcgccgta
       61 gcttccgctg cctatcgttc cggttcactg atgcttgatg agcgtaccgg actgactcac
      121 gactacaccc gcaaaagcgg tgtggctgaa gctgtgattc tgacccccgc gacagcccct
      181 gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga atgccggaag
      241 aactcacaac ttgcgcggga aattgaactc gctatccccc gtgaactgcc gcaggatgcc
      301 gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct
      361 gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg
      421 agggctgtcg gacctgctgg gttcggcgga aaggtcaggg actggaacga ccggacacat
      481 gccgagacgt ggcgtgcatc atgggctgac catgcaaaca gagcactggc gaacgccggt
      541 tatcaggaag agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt
      601 attcacctcg gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc
      661 gaacagaatc gtctgattaa caggcttaac ctggaaatac agatttcccg cactgaactc
      721 aggaacagcg ggctgacaga gcctgcccgc cgtgtggctg accttctgaa tatcgtgctt
      781 cctgacaacg caacttcgta cacactacgt gacatcatcg aagcgttgcc gaaggacagt
      841 aatgcggcat ggaaactcac cagtaatgcc atgtcgatga tggcagatat gcaggcgacg
      901 cgcagacgct gggaagagct gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc
      961 ctgaaaaaat catcgccgtt ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg
     1021 gcaccggaat accgtagcga acagggaaaa atccagtcgc tgagccagca aatggaaaaa
     1081 ttgcgacagc attaccggaa ggtggagaaa caggacattc ccgcgagtca gacggcattt
     1141 gaaaaacagt ggcagcagtg gggggcatcc ggccttgcag ctctcagagt ccagttgctt
     1201 aaacgtgaag aggaattgcg ccggaaggag caggaggata cagaacgtag tcgcgcggag
     1261 cgacgagcgg aacagctcag gaaaaatgac aatgccgtta tggattcagg ggtactgagc
     1321 gcagtcgtta cggggtatgg cgaggccccc atgcctggta acggggaaat gacctgttac
     1381 cttctgcttc acaaccggaa cggagaatac acgctctggg ggaacgagct ggagaaatac
     1441 cgcaccagaa tctttgagcg tgttgattta atgcgtgaca ggagtggtta tatctgtgac
     1501 cgaagcgaaa tcggtcaaca tccaccactg caacgtgttt attcctctgc gacctttgag
     1561 caacttctga cgcaggtttg ccagacatgg ccgcaatata cccgcaatct ccgccagccg
     1621 aagacatggc cggagtcttt ctgtcttgga gaagaccgcc agccagccat gccatcactg
     1681 gcagcaagga aggtggattt tacgcaggga cgtctgctac cgacgctgat gccggtaatg
     1741 agttctgtcg accgggaaac ccgccagctt cagcttttgc tggtcatggg cgtggatgac
     1801 tctctgggcg gtgttgtccg gcttaatggt acgctgtatc ccgcgtttgc cgttccctca
     1861 gccgataaca gccagctggt catcagtgca ctgaccgata aggggttacg gtatgcaggg
     1921 tatggtgttg ccgtaaatca cgatgcagac agccacatat cacctgcgcc ggaacttatg
     1981 gagtttcatc tgaaaacccg tgaggcaccg ctttttgctg ccgtcaacac accagaaaaa
     2041 cagccggatc atctgttccg ctctctgggt ttcaatcgta cctgggatga atggcggcgc
     2101 gaggaagatg caagaacaca caccaccgag aggagacatg atcgcggttg gtcacagtga
     2161 atgtgaacaa tattttgttt tgtttaacat cgtgttatgt tcgtcgatgt tcttctatgt
     2221 tcatcgacag ggatgaatgc aagaagcaca cacataatgc aagcatagtt ttgtttttcc
     2281 gcccccaaaa attgggggtt cttttttcgc tgcattagag cgcttttgac gcaatttttc
     2341 acttcaatag taccttcgca ctactaacac aaaaaaaacg cagcagggag cgttttaggt
     2401 gccttaaaat cgattttaga tcgtcatctt gatctgtttg tcttccttga agcgaaaatg
     2461 cagggctaca accgtgcgcc cctttttgat cgtctcaacc gttacagcca ggtcgctttt
     2521 tttgttcagt tcgtcaacac agggttttat tagtatttta tttaagtctc tgaattgttt
     2581 gtatttattt tcaatcccta acattgaacg aaagtcatta agagcaataa ttctctctcc
     2641 cgtactgcgg aattgctgga ggaactcgta tattcttata ctgtaactac ttgataaacc
     2701 tgatatgttt tttataacaa cgcgcgtgaa ttgccccttc agttgcgtca gataaggcat
     2761 taccgcgtca gaaaaggtta ttcgagcctt ggcctcacct ttagcgtact gtgcccgata
     2821 ctggatccag cggaactcct cacgcttctc gtcattcttg agaatgatcg acctgtccca
     2881 taaacgatcg atcgcttcct gtaactgaac ctcggcattt ttccgcccca tgtcagggaa
     2941 tgaatcaaaa tattccgcag cggtaatggt cattgtcttt tgcaattcag catcagcacc
     3001 agatttcaat cgactgatac acagcaacag aaaacgttgt tcctgtaggg tcaacttgta
     3061 gctggcctca accaaagcat tcgacttgta ggcaatcaag tccgacatac aaagatcccg
     3121 ttcaaatgtg gtgatgcttt aatgtgcccc acaaataaga aatgtggaat attttttttt
     3181 atatcctcac atttctgtga ataacacctt aaattcctcc acctttacct taaattcctc
     3241 cacctaaaca ccttaaattc ctccaccttt accttaaatt cctccacata tacctctata
     3301 acatattgat tttattaatg aattttgacc ctaaaacaag tattaaaaac aagatcttaa
     3361 aaacaagatc taaaaactta acggcgagcc tgtggataac ttggggcgct gaaaacaaaa
     3421 aaccaataaa aacaatgtgt tgcaagaaag cagaattgca agttccgaat actccccttc
     3481 caaccctgtg gaaatccagt attcatgcgg gttcagcgca tatcacctac cgaaaaaccg
     3541 tgcgtatgtg ctcaacctgg cgacggattc acttccgctt cctcgcccac tcgctcgcta
     3601 acgctcggtc gctggggctg cggcgagcgg acgatacaat cactgtcctg gcagcgcctc
     3661 cagctcgtta atcagcggca gtatgcgcgt cacatcagcc tgtcgtgtca cctctgcctt
     3721 caggaactgg agtaaccagg cacgcaactg cacctcctcc ggctttctga cctttgccag
     3781 caatgctgca cccacaacaa ccttctgcgc tgtgtccagg ctccggctct tcgccttcag
     3841 gcgctgtaat ctcgcctcag catcagcaat cttctgttcg agcgttctgc tcatgatgta
     3901 actccgtgcg cgatgaaaaa tcgcatttta gcgcgtcact ggtagtttaa aaactgagct
     3961 ggcataatgc gcgacaaatc acaaagtgcg cacttataca atctccactc cgtttcgatt
     4021 gtgtgcgccc tgcggggctg aaagaaaact acaaaaaggc attacggcag aa
//
