LOCUS       NZ_CP151361             5219 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R16.1553 plasmid pR16.1553_5k, complete
            sequence.
ACCESSION   NZ_CP151361
VERSION     NZ_CP151361.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122665
            Assembly: GCF_038367175.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5219)
  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  JOURNAL   Unpublished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 5219)
  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_038367175.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:27:59
            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)                     :: 5,198
            CDSs (total)                      :: 5,067
            Genes (coding)                    :: 4,414
            CDSs (with protein)               :: 4,414
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 653
            CDSs (without protein)            :: 653
            Pseudo Genes (ambiguous residues) :: 0 of 653
            Pseudo Genes (frameshifted)       :: 180 of 653
            Pseudo Genes (incomplete)         :: 451 of 653
            Pseudo Genes (internal stop)      :: 114 of 653
            Pseudo Genes (multiple problems)  :: 88 of 653
            Pseudo Genes (short protein)      :: 3 of 653
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151361.1.
            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..5219
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R16.1553"
                     /db_xref="taxon:624"
                     /plasmid="pR16.1553_5k"
                     /collected_by="Taiwan CDC"
     gene            34..357
                     /locus_tag="AADX57_RS25915"
                     /old_locus_tag="AADX57_25895"
     CDS             34..357
                     /locus_tag="AADX57_RS25915"
                     /old_locus_tag="AADX57_25895"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            566..>997
                     /locus_tag="AADX57_RS25920"
                     /old_locus_tag="AADX57_25900"
                     /pseudo=""
     CDS             566..>997
                     /locus_tag="AADX57_RS25920"
                     /old_locus_tag="AADX57_25900"
                     /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            1035..1565
                     /locus_tag="AADX57_RS25925"
                     /old_locus_tag="AADX57_25905"
     CDS             1035..1565
                     /locus_tag="AADX57_RS25925"
                     /old_locus_tag="AADX57_25905"
                     /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            1572..1805
                     /locus_tag="AADX57_RS25930"
                     /old_locus_tag="AADX57_25910"
     CDS             1572..1805
                     /locus_tag="AADX57_RS25930"
                     /old_locus_tag="AADX57_25910"
                     /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(2350..2646)
                     /locus_tag="AADX57_RS25935"
                     /old_locus_tag="AADX57_25915"
     CDS             complement(2350..2646)
                     /locus_tag="AADX57_RS25935"
                     /old_locus_tag="AADX57_25915"
                     /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_015386304.1"
                     /translation="MSKTKSGRHRLSKTDKRLLAALIAAGYEERTARDLIQKHVYTLTQ
                     ADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKLLNGKKPEEGLNAWKGDLP"
                     /name="hypothetical protein"
     gene            2858..3055
                     /locus_tag="AADX57_RS25940"
                     /old_locus_tag="AADX57_25920"
     CDS             2858..3055
                     /locus_tag="AADX57_RS25940"
                     /old_locus_tag="AADX57_25920"
                     /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            3073..3357
                     /locus_tag="AADX57_RS25945"
                     /old_locus_tag="AADX57_25925"
     CDS             3073..3357
                     /locus_tag="AADX57_RS25945"
                     /old_locus_tag="AADX57_25925"
                     /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(3421..3810)
                     /locus_tag="AADX57_RS25950"
                     /old_locus_tag="AADX57_25930"
     CDS             complement(3421..3810)
                     /locus_tag="AADX57_RS25950"
                     /old_locus_tag="AADX57_25930"
                     /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(4216..4329)
                     /locus_tag="AADX57_RS25955"
                     /old_locus_tag="AADX57_25935"
     CDS             complement(4216..4329)
                     /locus_tag="AADX57_RS25955"
                     /old_locus_tag="AADX57_25935"
                     /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            complement(4997..5188)
                     /locus_tag="AADX57_RS25960"
                     /old_locus_tag="AADX57_25940"
     CDS             complement(4997..5188)
                     /locus_tag="AADX57_RS25960"
                     /old_locus_tag="AADX57_25940"
                     /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"
     Typing          4826..4912
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="2.47e-38"
     Typing          complement(4258..4814)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.642"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          348..1909
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggggataa tgataccgat gaaacgcgag aggatgctca caatacgggt tactgatgat
       61 gaacatgccc ggttacttga acgctgtgag ggtaaacagc tggcggtatg gatgcggcgg
      121 gtctgtctgg gtgagccggt tgcccgttcc gggaagctgc cgacactggc accgccgtta
      181 ctgcgccagc tggctgccat cgggaataac ctgaatcaga cggcgaggaa ggtgaacagc
      241 gggcagtggt cttccggtga ccgggttcag gtggtggccg cactgatggc catcgagaga
      301 gagttgcgca gcttacggca ggtcgtcagg gaacatggag cgcgggatga tagttaagtt
      361 tcatgccagg ggaaaaggcg gtggcagtgg tccggttgat tacctgctgg gaagggagcg
      421 taaccgggaa ggggcaacgg tgcttcaggg taatccggaa gaagtccggg aactcatcga
      481 tgccacgcca tttgcgaaga aatacacgtc aggtgttctg tcgttcgcgg agaaggagct
      541 gccgccggga ggacgtgaaa aggtgatggc gagctttgag cgtgtactga tgcccggtct
      601 cgaaaaaaat cagtacagca tcctgtgggt ggagcaccag gacaagggac ggcttgagct
      661 gaattttgtc attccgaaca tggagctaca gagcggaaaa cgcctccagc cgtactacga
      721 ccgggcagac aggccgagaa ttgatgcctg gcagacgctg gttaatcacc attacgggct
      781 gcatgacccc aacgccccgg agaaccgccg gatactgact ctccctgata acctgccgga
      841 aacgaaacag gcgcttgcag agagcgtcac acgcgggata gacgctcttt atcatgtcgg
      901 ggagataaaa ggccgtcagg atgtgattca ggcgctcaca gaggcagggc ttgaagtggt
      961 cagggtgacg cgaagcagta tcagcattgc agacccgaac ggtgggaaga atatcaggct
     1021 gaaaggagca ttttatgagc aatcttttac agacgggcgc ggagttcgag aaaaagctga
     1081 aagagagagc cgaatctaca gagacaatac tgaacgacga gttcaggaag ctcgaaaaat
     1141 ctgtaagcaa ggctgtgaca tcaaacgaga cgaaaatcaa agacgctata gccctgttca
     1201 cagcttcgac agaggaatca ctgaaaaaac accgggaagg ggtgaaagag gcgatgatgc
     1261 agcacaggaa ggacgtgtta aagctggcag ggaatacggg catgatgtta ctggggatgg
     1321 tcattttcct gtttaccgtg agtggcggga cgctctggta tcttggcggg atgatacagg
     1381 cgaacctgga agaaatcagg aagcagaacg agaatctgga gaagctgaac gcgaagacat
     1441 ggggcgtgcg ttatcacgag gggagcaacg gacgttttct ggtgttgccc gaggggatga
     1501 aagccgaaac gaactggacg atggaaaacg ggaaacagaa tgccgtaagg ctggtacagg
     1561 agtaacagag catgacggag ctggaaagac atttgctgaa cgcattagag caactgcaac
     1621 aggactatat gcagcggctg aacgaatggg agagcgcctt cgtggaattg cagaaaatgt
     1681 tttcgcttac gcaacgggac aacgcgatgc tgaacgagcg ggtcatgcag ttgagtcagc
     1741 aggtgcagca cttgagcgag cagacagaac gcttgagcca gttatacagc gagaacagga
     1801 gataagggac gaacggctga tacaggaacg cgaacatgcg ttatccctgg agcgtgagcg
     1861 ccagctggaa atacaggaac ggacactgga tggcccttcg ctgggatggt aatcagagac
     1921 aggctaaaat gttgtcagcg cgtttccggt gcattttttg ggataatggt tggttcgggg
     1981 gcaccgggaa cgcgcttcag tcagaccttg ctgaaaacac aggaacgcgt taaaacgcat
     2041 acgggcgcga ttctggtgtg tcttttgttg ctgtgttttg cctctattgc cagatcgcgc
     2101 tcattcccct gaacttctgt tttcccgctc cggtccccgt cttcttcgct tccgaaagca
     2161 tgaaaaaaat ccgtttcagc tgtctctggc tggcaattcc tgcatgattc acatagctgc
     2221 atagctatgc atgtggttaa aatttaccgg gtacgatcgc ggcagttttt cgggtggttt
     2281 gttgccattt ttacctgtct gctgccgtga tcgcgccgaa cgcgtttcag cggtgcgtac
     2341 aataagtgat tatggtaaat cacccttcca ggcgttcagc ccttcttccg gtttttttcc
     2401 gttcaggagt ttacgggcga gacgaatgcg tcttgcctgg taaatcgcat cgtaggcctg
     2461 tgactgtccc acaccgttac tgatttcact gaccagatgg cgcaggtcgg cctgtgtcag
     2521 tgtgtaaacg tgtttctgga tgaggtcacg ggctgtccgc tcttcgtatc cggcagcgat
     2581 aagtgcagcc agcaggcgtt tgtctgtttt gctcagtcgg tggcgaccag attttgtttt
     2641 gctcacgtta tctcctctct gttttttctc ttgatgttat ccggtgctgt ttttctgctg
     2701 cgaatcttcc cttcctgatt tttataaggg tgattcagat cacaaaaatg aaaattcata
     2761 tcattgacag gaaaaataat gcggcgtaat ttatactgta tataaaacta gtatttatat
     2821 atacagtata ttctgtgtaa ataaagggag ggataaaatg aaagaagaaa aagtattgct
     2881 tcaccgtttc ttatttgtag ttaggaataa gaatggttgt gaactatcat gttcggcaga
     2941 ccttatggga acaagggatg atgtttataa gtatttctct gattctgtta gtgggctaga
     3001 tgttgagctt atagatgttt cttgcgagag tgaatgggaa gaacattcgc attgaactaa
     3061 tcaggagatt atatgatttc tcaaaatgtt tgggctcctc ctttcttttt tggtccttgg
     3121 gttgaacttg aaaatcatac tggtgatatc gcgtacactg tctattttga tacattgtct
     3181 aatgtacccg gtccatttat tgcttttatc tggtatgccc ctaatgggcc aagaacagtt
     3241 aacgttattg gtccagcatc ttatcagatc tcttgcaagg gcgctggtgt tgataaaatt
     3301 aaatttaaaa gtgtcagtgg gacagggcag attattcatg tatacactac cttataataa
     3361 gagctgaata gatataatcc tgcctaagct ataccttaag caggattata tctattaata
     3421 ttattttgaa tatgctttta tgatttccat cactgttgtt tcatcgttca caggttgata
     3481 ataatgggtt ggatttagtg cagaatgaat gattgcaggt tgggatatta cttttccatc
     3541 aaaatatgaa atcaggggtt tccctatatt tttactagtt atttcgttta gttttttctt
     3601 acataaacta tctgtgttta cttctattat gacgcctttg tttttttctg attgggaagg
     3661 gtacatttta agtatgcaat atttattcag aatgatgctg tcaccaccaa ctttgtaaac
     3721 aatgtttttg tttgtttcag tacttgaaca tcctataagt aaggtcagta tagtactcga
     3781 tgttattgac tttactgatg atttgaacat attaactcca ttttattttg ttaaaattcc
     3841 aatctataaa tacatataca cgtaaaaata aacaatgcga acgttttcac ttatattatt
     3901 cccatgatgt gattgaatgg tggttccata taagagaggg caattatact atctttctct
     3961 cctgaactga tgggattgca gtttagagaa aaaagatcaa aggatcttct tgagatcctt
     4021 tttttctgcg cgtaatctgc tgcctgtaaa cgaaaaaacc accctggcag gtggtttttc
     4081 gaaggttagc taatcctggc agattaccta accgggtagc tggcttaagt ggagcacaga
     4141 taccaaaaga tgtcctttca gtgtagccgc tataaggctt caacttcaag agttctgcgt
     4201 atctaaatcc actttttagt taccaatggc tgctgccagt ggcgttaagt cgtgtcttac
     4261 cgggttggac tcaagacgat agttaccgga taaggcgcag cggtcgggct gaacgggggg
     4321 ttcgtgcaca cagcccagct tggagcgaac gacctacacc gaactgagat acctacagcg
     4381 tgagctatga gaaagcgcca cgcttcccga agggagaaag gcggacaggt atccggtaaa
     4441 cggtaaggtc ggaacaggag agcgcacgag ggagcttccg gggggaaacg cctggtatct
     4501 ttaagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
     4561 ggggggcgga gcctatggaa aaacgccagc ggcgcggcct tcttcctgtt cctggtcttt
     4621 tgctcacatg ttttttccgg tgttatcccc tgattctgtg gataacagca tttcgttttt
     4681 gagtgagtag ataccgctcg ccgcagtcga acgaccgagc gtagcgagtc agtgagcgag
     4741 gaagcggaaa agcggctgga cgtgcatttt ctccttacgc atctgtgcgg catttcacac
     4801 ccggtatggc gcacttttca taccatccgc actgatgccg catggttaag ccagtataca
     4861 ctccgctatc gctacgtgac tgggtcaggg ctgcgccccg acacccgcta aaacccgctg
     4921 acgtgccctg acgggcttgt cagctcccgg catccgctca cagacaagct gtgaccgtct
     4981 ccgggagctg catgtgtcag aggttttcac cgtcatcccc gaagcgagcg aggcaactgc
     5041 ggtaaagctc atcggcgtgg tcgtgaagcg attcacagat atctgcctgt tcatccgcgt
     5101 ccagttcgtt gagcttctcc agcagcgtta atgtctggct tcttataaag cgggccatgt
     5161 taagggcggt tttttcctgt ttggtcactg atgcctccgt gtaaggggga tttctgttc
//
