LOCUS       NZ_CP151368             5538 bp    DNA     circular CON 18-APR-2024
DEFINITION  Shigella sonnei strain R16.0937 plasmid pR16.0937_5.5k, complete
            sequence.
ACCESSION   NZ_CP151368
VERSION     NZ_CP151368.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40122664
            Assembly: GCF_038367185.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 5538)
  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  JOURNAL   Unpublished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 5538)
  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_038367185.1-RS_2024_04_18
            Annotation Date                   :: 04/18/2024 01:38:13
            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)                     :: 5,030
            CDSs (total)                      :: 4,901
            Genes (coding)                    :: 4,266
            CDSs (with protein)               :: 4,266
            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)              :: 635
            CDSs (without protein)            :: 635
            Pseudo Genes (ambiguous residues) :: 0 of 635
            Pseudo Genes (frameshifted)       :: 172 of 635
            Pseudo Genes (incomplete)         :: 435 of 635
            Pseudo Genes (internal stop)      :: 111 of 635
            Pseudo Genes (multiple problems)  :: 81 of 635
            Pseudo Genes (short protein)      :: 3 of 635
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151368.1.
            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..5538
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="R16.0937"
                     /db_xref="taxon:624"
                     /plasmid="pR16.0937_5.5k"
                     /collected_by="Taiwan CDC"
     gene            1..537
                     /locus_tag="AADX59_RS25070"
                     /old_locus_tag="AADX59_25080"
     CDS             1..537
                     /locus_tag="AADX59_RS25070"
                     /old_locus_tag="AADX59_25080"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001555327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000654319.1"
                     /translation="MKDNKAVVVFTGKDLNIMRAEGGSGYWLAKAERLNDAKYLIAVRN
                     RRETWAVKDLEHGTGFLIAKITGCFKNPDYDDRNVITFEEYAEISVKKAWKMLTGGQRY
                     PVAYLTAEEAFSRIGITLEQLEWKKLQTSTLSQPIPSAEAPKKLSLNEAVERAKQDISN
                     ATDIDVSSITITINI"
                     /name="hypothetical protein"
     gene            593..1417
                     /locus_tag="AADX59_RS25075"
                     /old_locus_tag="AADX59_25085"
     CDS             593..1417
                     /locus_tag="AADX59_RS25075"
                     /old_locus_tag="AADX59_25085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000213997.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000213997.1"
                     /translation="MTTTIYREFEFAACDSKWSVDGHLRRDVIEKKAIHIDFKGKEAIS
                     LMCGDHPMIVLMQAMQLKVITPEQYASLMSLYMDVEDFTFGMVVLDKHSGAILVGMYTP
                     PMIAIKSKQIVYDLGSTGGEFAAHCLYYAEKRLRKKKRHRGYSTSSVGCKITSAVKYAY
                     RRDRYSGGKVYKIIWKNNGIMYNNIPLSNNSVKNHYRRILKETLKIIHSRYEEKINMRQ
                     NAQLNTAAASLSQTGQPKTQSQPHNQAPSASADKSHQMTMSRAINYARLFSD"
                     /name="hypothetical protein"
     gene            complement(1986..2219)
                     /locus_tag="AADX59_RS25080"
                     /old_locus_tag="AADX59_25090"
     CDS             complement(1986..2219)
                     /locus_tag="AADX59_RS25080"
                     /old_locus_tag="AADX59_25090"
                     /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_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(2226..2744)
                     /locus_tag="AADX59_RS25085"
                     /old_locus_tag="AADX59_25095"
     CDS             complement(2226..2744)
                     /locus_tag="AADX59_RS25085"
                     /old_locus_tag="AADX59_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_015059036.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<2782..3444)
                     /locus_tag="AADX59_RS25090"
                     /old_locus_tag="AADX59_25100"
                     /pseudo=""
     CDS             complement(<2782..3444)
                     /locus_tag="AADX59_RS25090"
                     /old_locus_tag="AADX59_25100"
                     /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            complement(3422..3745)
                     /locus_tag="AADX59_RS25095"
                     /old_locus_tag="AADX59_25105"
     CDS             complement(3422..3745)
                     /locus_tag="AADX59_RS25095"
                     /old_locus_tag="AADX59_25105"
                     /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="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_024185675.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLSEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAVLMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3810..4001
                     /locus_tag="AADX59_RS25100"
                     /old_locus_tag="AADX59_25110"
     CDS             3810..4001
                     /locus_tag="AADX59_RS25100"
                     /old_locus_tag="AADX59_25110"
                     /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          complement(4094..4175)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="95.0"
                     /evalue="1.44e-35"
     Typing          4197..4742
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.727"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1883..3432)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaaagata ataaagcagt tgtcgtattt acaggcaaag atctaaacat aatgagagct
       61 gagggaggtt caggttattg gctagcaaaa gcagaacggc ttaatgacgc caaatatctc
      121 atcgcagtaa gaaaccggag agaaacatgg gcggtgaaag acctcgaaca cggaactggc
      181 tttctgattg caaagatcac cggatgcttt aaaaaccctg attacgacga cagaaacgta
      241 attacatttg aggaatatgc tgaaatttca gtgaaaaagg catggaaaat gctaactggc
      301 ggtcagcgtt atccggttgc ttatctgaca gcagaggaag ctttttcccg tatagggata
      361 acgctagagc agctggagtg gaaaaaactc cagacttcaa cactatctca gccaatcccc
      421 tctgcagaag cgccgaaaaa actaagcctc aacgaggcag ttgaaagagc taagcaagat
      481 ataagcaatg caactgatat cgatgtatct tctattacga taactatcaa catctgattt
      541 tttcgtatat ctggtatctt aacgatagtc gaaaaagaat taagccattg atatgacaac
      601 aacaatatac agagagtttg aatttgctgc ttgtgatagc aaatggtcag ttgatggaca
      661 tcttcgaaga gatgttattg aaaaaaaagc aatacatata gatttcaaag gaaaagaagc
      721 aatatccctt atgtgtggtg atcatccgat gatcgtcctt atgcaagcta tgcagctgaa
      781 agtcataact ccagagcagt acgctagctt aatgagtctc tacatggatg tagaagactt
      841 caccttcggc atggtggtcc tcgataaaca ctcaggtgct atattagtag gtatgtatac
      901 ccccccgatg attgcgataa aaagcaaaca aatagtttac gatttaggtt caactggcgg
      961 cgaatttgca gcacattgtc tctactatgc ggaaaaaagg cttagaaaaa aaaagcgtca
     1021 tcgtggatac tctacatcgt cagtgggatg taagatcacc agcgctgtca aatatgcata
     1081 cagacgagat cgctactccg gtggtaaagt atacaaaatc atttggaaaa ataacggcat
     1141 catgtacaac aacataccgt tatctaacaa ctcggtaaaa aaccattacc ggcggatttt
     1201 aaaagaaaca ttaaagatca ttcatagcag gtacgaagag aaaataaaca tgagacagaa
     1261 tgcccagtta aatacagcgg cagcctcgct ctctcagacg ggtcagccga aaacacaaag
     1321 tcagccacat aaccaagcac ctagtgcgag tgctgataaa agccatcaga tgactatgtc
     1381 tcgagccatt aactatgctc gccttttttc tgactgatac tgtacagcta gatttaccat
     1441 aatcccttat tgcgtgcacc gcagaaacgc gttcggtgcg atcacggcag cagacaggta
     1501 aaaatggcaa caaaccaccc gaaaaactgc cgcgatcgca cccgataaat tttaaccaca
     1561 tgcatagcta tgcagccatg tgaatcacgc aggaattgcc agccagagac tgctgaaacg
     1621 gatttttttc atactttcgg aaaggcagaa gacggaaccg gagcggaaaa acagaagttc
     1681 aggggaatga gcgcgatctg gcaatagagg caaaacacag caacaaaaga cacaccagaa
     1741 tcgcgcccgt atgcgtttta acgcgttcct gtgttttcag caaggtctga ctgaagcgcg
     1801 ttcccggtgc ccccgaacca accattatcc caaaaaatgc accggaaacg cgctgacaac
     1861 attttagcct gtctctgatt accatcccag cgaagggcca tccagtgtgc gttcctgtat
     1921 ttccggctgg cgctcacgct ccagggataa cgcatgttcg cgctcctgta tcagccgttc
     1981 gtcccttatc tcctgttctc gctgtataac tggctcaagc gttctgtccg ctcgctcaag
     2041 tgctgcacct gctgactcaa ctgcatgacc tgctcgttca gcatcgcgtt gtcccgttgc
     2101 gtaagcgaaa acattttctg caattccacg aaggcgctct cccattcgct cagccgctgc
     2161 atatagtcct gttgcagttg ctctaatgcg ttcagcaaat gtctttccag ctccgtcact
     2221 ctgtgtcact ccgtcagttg tacccagtcc ttcccctgat agggaatcac cgttgccgat
     2281 ttcccgtacg gaaggaccag aaatttcctt ctcccgtcct gcacaaactc cacgccccat
     2341 gtcttcgcgt tcagtttctg caatgtttct tcctgtatcc tgatttcttc caggttcgcc
     2401 tgtatccgcc cgccaagata ccagagcgtc ccgccactcg cggtaaacag gagaaagact
     2461 atccccagca acctcatgcc cgtattccct gccagcttta acacgtcctt cctgtgctgc
     2521 atcatcgcct ctttcacccc ttcccggtgt ttttccagcg attcctctgt cgacgttgtg
     2581 aacagggcta tagcgtcttt gattttcgtc tcgtttgagg tcacagcctt gcttacagat
     2641 ttttcgagct tgctgaactc gtcgttcagc attgtctctg tagattcggc tctctctttc
     2701 agctttttct cgaactccgc gcccgtctgt aaaagattgc tcataaaatg ctcctttcag
     2761 cctgatattc ttcccgccgt tcgggtctgc aatgctgata ctgcttcgcg tcaccctgac
     2821 aacttcaagc cccgcctctg tgagcgcctg aatcacatcc tgacggcctt ttatctcccc
     2881 gacatgataa agagcgtcta tcccccgtgt aacgctctca gcaagcgcct gtttcgtttc
     2941 cggcaggtta tcagagagag tcagtatccg gcggttctcc ggggcgttgg ggtcatgcag
     3001 cccgtaatgg tgattcacca gcgtctgcca ggcatcaatt ctcggcctgt ctgcccggtc
     3061 gtagtacggc tggaggcgtt ttccgctctg tagctccatg ttcggaatga caaaattaag
     3121 ctcaagccgt cccttgtcct ggtgctccac ccacaggatg ctgtactgat tcttttcgag
     3181 accgggcatc agtacgcgct caaagctcgc catcactttt tcacgtcctc ccggcggcag
     3241 caccttctcc gcgaacgaca gaacacctga cgtgtatttc ttcgcaaatg gcgtggcatc
     3301 gatgagttcc cggacttctt ccggattacc ctgaagcacc gttgcccctt cccggttacg
     3361 ctcccttccc agcaggtaat caaccggacc actgccacca ccttttcccc tggcatgaaa
     3421 cttaactatc atcccgcgct ccatgttccc tgacgacctg ccgtaagctg cgcaactctc
     3481 tctcgatggc catcagtacg gccaccacct gaacccggtc accggaagac cactgcccgc
     3541 tgttcacctt cctcgccgtc tgattcaggt tattcccgat ggcagccagc tggcgcagta
     3601 acggcggtgc cagtgtcggc agcttcccgg aacgggcaac cggctcactc aggcagaccc
     3661 gccgcatcca taccgccagt tgtttaccct cacaacgttc cagcaaacgg gcatgttcat
     3721 catcagtaac ccgtatcgtg agcattctct cgcgtttcat cggtatcatt acccccatga
     3781 acagaaatcc cccttacacg gaggcatcag tgactaaaca ggaaaaaacc gcccttaaca
     3841 tggcccgctt tatcagaagc cagacattaa cgctgctgga gaaactcaac gaactggacg
     3901 cagatgaaca ggccgatatt tgtgaatcac ttcacgacca cgccgacgag ctttaccgca
     3961 gctgcctcgc acgcttcggg gatgacggtg aaaacctctg acacatacag ctcccggaga
     4021 cggtcactgc ttgtctgtga gcggatgccg ggagcagaca agcccgtcag ggcgcgtcag
     4081 gccgttgacc ttgcgggtgt cggggcgcag ccatgaccca gtcacgtagc gatagcggag
     4141 tgtatactgg cttaaccatg cggcatcagt gcagattata agaaaagagc accatatgcg
     4201 gtgtgaaatg ccgcacagat gcgtaaggag aaaataccgc atctggcgct cttccgcttc
     4261 ctcgctcact gactcgctac gctcggtcgt tcggctgcgg cgagcggagt cggctcactc
     4321 aaaggcggta atacggttat ccacagaatc aggggataag gccggaaaga acatgtgagc
     4381 aaaaaggcaa aggacaacaa aaggccgcgc cgctggcgtt tttccatagg ctccgccccc
     4441 ctgacgagca tcacaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata
     4501 aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc
     4561 gcttaccgga tacctgtccg cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
     4621 acgctgttgg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga
     4681 accccccgtt cagcccgacc gctgcgcctt atccggtaac tatcaacttg agtccaaccc
     4741 ggaaagacac gacaaaacgc cactggcagc ggccattggt aaacaggatg tgcgagagat
     4801 gtatcgagag ttcttgaagt ggtgccctta gtgcggctac actggaagga cagatttggt
     4861 ggcatgtctc gcacaagact gttaccacgg ttagagaatc tgccaggatt aactaacctt
     4921 cgaaaaacca cctgccaggg tggttttttc gttttcagag ctagagatta cgcgtagaaa
     4981 aaaaggatct caagaagatc ctttttgtag atagcttata gatgattccc gtgaactgaa
     5041 cgcgtatatc caatagctat attaaacatt tcagcttgac ctggattcag atagcacgtt
     5101 ctcagatcta ctctcacaag caacccatta ccttcccgct cagcatagat accacgagac
     5161 ctgcaaagat ctattgattg ctctaccagc ttttcagtaa tgcgctgtct accgggagag
     5221 cgcaggtcaa gatagaaatt actaaccatc gtaccagctt cgctagaaag acgattgatg
     5281 gtcgtttcaa tacatgaatc tatttgctgc atagatatcg acatataacc cccaaaaaga
     5341 ataacatcaa aataagatac acataaaaaa atataaaatc aaataaaaac aacttaagca
     5401 caaaataagc aaaaataaga aagagataag cacagaattt gtaggcttgc ttttatcgca
     5461 taaataaaac cacaccccta atttaatcgt atataattaa aatcatgacg ataaaaaact
     5521 aaagcatggg atttctat
//
