LOCUS       NZ_CP151297             3171 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CS14 plasmid pCS14-3, complete sequence.
ACCESSION   NZ_CP151297
VERSION     NZ_CP151297.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN40904935
            Assembly: GCF_038298665.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 3171)
  AUTHORS   Hollingshead,S., McVicker,G., Nielsen,M.R., Zhang,Y., Pilla,G.,
            Thomas,J.C., Johansen,S.E.H., Exley,R.M., Brodersen,D.E. and
            Tang,C.M.
  TITLE     Shared mechanisms mediate maintenance of the Shigella virulence
            plasmid and antibiotic tolerance
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3171)
  AUTHORS   Hollingshead,S., McVicker,G., Nielsen,M.R., Zhang,Y., Pilla,G.,
            Thomas,J.C., Johansen,S.E.H., Exley,R.M., Brodersen,D.E. and
            Tang,C.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-2024) Biosciences, Nottingham Trent University,
            Clifton Lane, Nottingham NG11 8NS, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: canu v. 2.2
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 150.4x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_038298665.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 09:59:19
            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)                     :: 5,315
            CDSs (total)                      :: 5,183
            Genes (coding)                    :: 4,447
            CDSs (with protein)               :: 4,447
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 99
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 736
            CDSs (without protein)            :: 736
            Pseudo Genes (ambiguous residues) :: 0 of 736
            Pseudo Genes (frameshifted)       :: 218 of 736
            Pseudo Genes (incomplete)         :: 520 of 736
            Pseudo Genes (internal stop)      :: 133 of 736
            Pseudo Genes (multiple problems)  :: 126 of 736
            Pseudo Genes (short protein)      :: 3 of 736
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP151297.1.
            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..3171
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CS14"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCS14-3"
                     /geo_loc_name="Brazil"
                     /collection_date="2001"
     gene            complement(join(2960..3171,1..217))
                     /locus_tag="AADR97_RS26555"
                     /old_locus_tag="AADR97_26555"
     CDS             complement(join(2960..3171,1..217))
                     /locus_tag="AADR97_RS26555"
                     /old_locus_tag="AADR97_26555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000222531.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000222531.1"
                     /translation="MTYSVKNKWKAGGLSLGWTAVPTVLFFIQNEKKLTSVAFNTLLNL
                     IVHWWSLQEWPHPSMESLAIRMGVSVRTVQRAINDLEKANLLDKKPTSKSDRRYGGRNI
                     YDLTKLVDYLDTMGPSVAEQVKKPRHKKPVYTVRKTTA"
                     /name="helix-turn-helix domain-containing protein"
     gene            375..545
                     /locus_tag="AADR97_RS26560"
                     /old_locus_tag="AADR97_26560"
     CDS             375..545
                     /locus_tag="AADR97_RS26560"
                     /old_locus_tag="AADR97_26560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001531327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001531327.1"
                     /translation="MKTEQRHDLVKDIEVFGVSLSLLISRANEKSVTMPSGLSREQRRA
                     WAAEQARKIHN"
                     /name="hypothetical protein"
     gene            509..937
                     /locus_tag="AADR97_RS26565"
                     /old_locus_tag="AADR97_26565"
     CDS             509..937
                     /locus_tag="AADR97_RS26565"
                     /old_locus_tag="AADR97_26565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000534558.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000534558.1"
                     /translation="MGSGAGAQNPQLNIVSFSETFNLYYTSRYSAKTLDKIDDFIEHFE
                     KYNLFGDPLKGYPAWTGKVSPSWKVPDHYENKEAIEKYARANKLWHAHLGDPVFKDTFH
                     GKYKVSDWVIHFQRLTPNHIKLLELGYHDPMKLPQNFE"
                     /name="hypothetical protein"
     gene            complement(1770..1964)
                     /locus_tag="AADR97_RS26570"
                     /old_locus_tag="AADR97_26570"
     CDS             complement(1770..1964)
                     /locus_tag="AADR97_RS26570"
                     /old_locus_tag="AADR97_26570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041639.1"
                     /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_001041620.1"
                     /translation="MNKQQQAVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEVENSTER"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2248..2571
                     /gene="mobA"
                     /locus_tag="AADR97_RS26575"
                     /old_locus_tag="AADR97_26575"
     CDS             2248..2571
                     /gene="mobA"
                     /locus_tag="AADR97_RS26575"
                     /old_locus_tag="AADR97_26575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_052584083.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQVIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     Typing          2000..2239
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.585"
                     /coverage="100.0"
                     /evalue="3.54e-121"
     Typing          complement(1213..1741)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.393"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          2249..2568
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.131"
                     /coverage="100.0"
                     /evalue="2.91e-61"
ORIGIN
        1 tccgtacaga aacccccata cgtatggcta gactttccat tgacggatgc ggccactctt
       61 gcaaactcca ccagtgaacg atcaggttaa gtagtgtgtt aaaggccact gaagttagct
      121 ttttctcgtt ttgtataaaa aacaatacgg taggcactgc tgtccagcca agagacaaac
      181 cgccagcttt ccatttattc ttaacggagt aagtcattga ttttcctaag ccccaaaata
      241 tttaaagtat atattatatg gtatattcat atgaataggg tgacactggc gccattattg
      301 tgcaaccaaa aaagactact ctgaaaacga ggaaaagatt ttttcctgcc tgaattagat
      361 acggagttag cgatatgaaa accgaacaac gtcatgatct tgttaaagat attgaggttt
      421 ttggcgtatc cttgtctctg ttgatttcca gagcgaatga gaagtctgtt acaatgccat
      481 ctggtctaag tcgggagcag agaagagcat gggcagcgga gcaggcgcgc aaaatccaca
      541 attgaatatt gtctcattct ctgagacctt caacctttat tacacatcca gatattctgc
      601 aaaaacactc gataaaatcg atgatttcat tgagcatttt gaaaaataca atctctttgg
      661 cgatccttta aaaggatatc cagcttggac tggcaaagta tcgccatcgt ggaaagtgcc
      721 tgatcattac gaaaacaaag aagctattga gaagtatgct agagctaaca aattatggca
      781 tgctcattta ggcgatccgg tttttaaaga tacgtttcat gggaaataca aggtttctga
      841 ctgggttatt catttccagc ggctgacacc gaaccatata aagcttttag agcttggata
      901 ccatgaccca atgaagctac ctcaaaactt tgaatgatcg agcggcaggc taaatgaaat
      961 cttgagattc attcagtctc gtcgtaatct cactattgta aaaacgaaaa aaccaccctg
     1021 gcaggtggtt tttcgaaggt tagttaatcc tggcagattc tctaaccgtg gtaacagtct
     1081 tgtgcgagac atgtcaccaa atactgtcct ttcagtgtag cctcagttag gccgccactt
     1141 caagaactct cgttacatct ctcgcacatc ctgcttacca gtggccgttg ccagtggcgt
     1201 taagtcgtgt cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc
     1261 gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct acaccgaacc
     1321 gagataccaa cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga
     1381 caggtatccg gtaagcggca gggtcggaac aggagagcgc acgagggagc ttccaggggg
     1441 aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt
     1501 tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac gccaacggcg cagccttttc
     1561 cgggttctcg ttttttgctc acatgtttct tttggcgtta tcccctgatt ctgtggataa
     1621 ccgcatctcc gcttttgagt gagccgacac cgctcgccgc agtcgaacga ccgagcgtag
     1681 cgagtcagtg agcgaggaag cggaagagcg ccttatgtga cattttctcc ttacgctctg
     1741 ttgtgccgtt cggcatcctg tcctgagagt tatctctctg tgctattttc tacttcaaag
     1801 cgtgtctgga tgctgttctg gagttcttct gcgagttcgt gcagcttctc acacatggca
     1861 gcctgttcgt cagcatcgag tgcgtccagc ttttcgagca gcgtcaggct ttggcttttt
     1921 atgaatcctg ccatgttgag tacggcttgc tgctgcttgt tcatcttttc gttttctccg
     1981 ttctgtctgt catctgcgtt gtgtgattat atcgcgtacc acttttcgac tgttttaccg
     2041 ccggtattct gccgtctgac gctttgacag gtatttctgc ctgacaatac tgtcactgcc
     2101 aaaaaactgc cgtgcctttg tcggtaattc gaacttgctg acaggacagg atgtgtaatt
     2161 gttataccgc gcatacatgc acgctattac aattaccctg gtcagggctt tgccccgaca
     2221 cccatgtcag atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg
     2281 cgggctatca gtcgccctgt tcgtctgacg gcagaagaag accaggtaat cagaaaaagg
     2341 gctgctgaat gcggcaagac cgtttccggt tttttacggg cggcagctct cggtaagaaa
     2401 gttaactcac tgactgatga tcgggtactg aaagaagtta tgagactggg ggcgttacag
     2461 aaaaaactct ttatcgacgg caagcgtgtc ggggacaggg agtatgcgga ggtgctgatc
     2521 gctattacgg agtatcaccg tgccctgtta tccaggctta tggcagatta gcttcccgga
     2581 gagaaaactg tcgaaaactg acggtatgaa caccgtaagc tcccaaagtg atcaccattc
     2641 gctttcatgc atagctatgc agcgagctga aaacgatcct gacgcatcct tcctgttttt
     2701 ccggggtaaa acatctcttt ttgcggtgtc tgcgtcagaa tcgcgttcag cgcgtttcag
     2761 tggtgcgtac aattaaggga ttatggtaaa tatatgagct atgcgataac tttaactgtg
     2821 aagcgatgaa cccattacag gcaaagccaa ttactcctga cagtggttta gccagaagca
     2881 gggctaccaa gaccaatgca ataagtaata tatcgttttg ctatcgtgca tcgctcgcgc
     2941 tcagttccat tgtgcttttt taagctgtcg tttttcttac ggtatatacc ggttttttat
     3001 ggcgtggttt cttaacttgt tcagctactg atggacccat tgtatctagg tagtcaacta
     3061 gctttgttag atcataaata ttgcgaccac catatcggcg atcactcttc gatgttggtt
     3121 tcttgtccaa gagattagct ttttcaagat cattgatagc tctctgaaca g
//
