LOCUS       NZ_CP151294             5120 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CS14 plasmid pCS14-2, complete sequence.
ACCESSION   NZ_CP151294
VERSION     NZ_CP151294.1
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 5120)
  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  JOURNAL   Unpublished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 5120)
  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
            CP151294.1.
            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..5120
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CS14"
                     /isolation_source="stool sample"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCS14-2"
                     /geo_loc_name="Brazil"
                     /collection_date="2001"
     gene            join(4716..5120,1..312)
                     /locus_tag="AADR97_RS25910"
                     /old_locus_tag="AADR97_25910"
     CDS             join(4716..5120,1..312)
                     /locus_tag="AADR97_RS25910"
                     /old_locus_tag="AADR97_25910"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_341714133.1"
                     /translation="MPSWAKKNPAELWKAADEFERKNGTAYREIEIALPRELTREQRIE
                     LVEDFVQKELGDRHAYQYAIHNPPGAIDGKEQPHAHIMFCERINDGIERDPQQFFKRAN
                     SKSPERGGAKKASIPQTAGERKAALVALRSRWADVQNEHLARHGHESRVDHRSLKEQGI
                     NRTPEVHLGPVQAASLNGRDCCNPGTAGMPSGNSRPPEMPQMPFSRNRSKSKKSRQLSL
                     FVQPFTESYCFSTARL"
                     /name="MobA/MobL family protein"
     gene            525..1094
                     /locus_tag="AADR97_RS25915"
                     /old_locus_tag="AADR97_25915"
     CDS             525..1094
                     /locus_tag="AADR97_RS25915"
                     /old_locus_tag="AADR97_25915"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_341714134.1"
                     /translation="MEQRNALNGIRGLFRGADKREIDARILEQKSVLETAEHERNEFRN
                     KLQQAESEWDKENAAFKRTEGYKYVGELDRYREREILAAASLENTRQKVAEEVSVARSQ
                     MLSLEPELSISGDEKAQMRHELLAEMAQERQQQEEKHCVYSDPGPGGYHVVTNVIKIWS
                     VENVAISGLRPEPRQRFTEREKFRVP"
                     /name="hypothetical protein"
     gene            complement(1213..2313)
                     /locus_tag="AADR97_RS25920"
                     /old_locus_tag="AADR97_25920"
     CDS             complement(1213..2313)
                     /locus_tag="AADR97_RS25920"
                     /old_locus_tag="AADR97_25920"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001569522.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_341714135.1"
                     /translation="MNINFKHILPLLSSFFISGCDSDGISKVKSFVYYDIDDSMTVGKA
                     FDTRSDCINGTWSEKEDDRGRTIVTYTCDISESGLKIINSAIMQEPEDKAEYSIAQNNN
                     SIKSTNESLEEYKQKTPLVEKTKEVIIDHIRKLNSAFNEDPMIYSKLTISPYLDRMLYL
                     KDHNDNALNEICGGYEYIQSADSYSWRDVSEEYAKESCEKHIYKVYQSFKKNASPLITK
                     KLPRFLRTCPPCENADECIKKTNIYFDDNFLNIYKRSQDRAPQIISDLKKHNIEIGEKL
                     NDCRKKLNISDVKLTYYWFVTDTGGVDYLDGVLTYNFQGKNRAENFHKQLLQYAYINYS
                     KNQIPRDFVTSIKNSIYYKIEDCTKF"
                     /name="hypothetical protein"
     gene            2834..3769
                     /locus_tag="AADR97_RS25925"
                     /old_locus_tag="AADR97_25925"
     CDS             2834..3769
                     /locus_tag="AADR97_RS25925"
                     /old_locus_tag="AADR97_25925"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_024235833.1"
                     /translation="MSAALQYFEENLPHRPYHTDELAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDRVGAAIDWSDRNAPAPNITVKNPENGHAHLLYALNLAVRTAPDASVKA
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYALDELADYLDLRASE
                     RRSVDKHYGLGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     PECRAIGKSIAKYTHRNFTPESFAQYVADTHTPEIQAKRGRKGGIAKGEAYDDKRFMAL
                     CMLENGYSQKAIAAMLNVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(3963..4409)
                     /locus_tag="AADR97_RS25930"
                     /old_locus_tag="AADR97_25930"
     CDS             complement(3963..4409)
                     /locus_tag="AADR97_RS25930"
                     /old_locus_tag="AADR97_25930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000184721.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TraD"
                     /protein_id="WP_024235834.1"
                     /translation="MTNREEWLSAKIAYINGLKSPSEQQRLLVLLAEKKNRTTTDEKTL
                     SALIRAEKTAEKAAAAKARVTAIIAAERKAAARAERKARDHELYKAAGLMIVAGLVDSK
                     TGKPKFSAAELVGALAGIAELPHNHPKWQEWEKRGKELLTKDSA"
                     /name="conjugal transfer protein TraD"
     Typing          2835..3769
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4582..5120
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.333"
                     /coverage="93.0"
                     /evalue="9.68e-114"
ORIGIN
        1 tgggcagatg tgcagaatga gcaccttgcg cgacacggtc acgagtcgcg cgtagatcat
       61 cgttctctga aagaacaggg catcaatcgc acgccggaag ttcatcttgg ccctgttcag
      121 gccgccagtc tgaatgggag agattgttgc aatccaggaa cggcaggaat gccgagcggg
      181 aactcaagac cgccagagat gccgcaaatg ccattcagca ggaacaggag caaaagcaaa
      241 aaatcaaggc agttgagcct gttcgttcag ccgttcaccg agagttattg cttcagtacc
      301 gcaaggttat gaaaaacggt cattcaggga gaggcaaggc ttgcttccgt ttaggggatg
      361 ccaatcccaa tgcgctcaaa gaacataagc tgcttccgga atcgcgaaag ctaaaaaaga
      421 ctctctttcc gaatggagta gacgaatata tgaaggggca cggtatttag acaaactggg
      481 gcgtaatgtt gtttttccgc acaaagggag ctgcgggagc tacggtggaa caacgcaatg
      541 ctttgaatgg gattcgtggc ctgtttcggg gggctgacaa aagggagatt gatgcgcgta
      601 ttctggagca aaaaagtgtg ctggaaaccg ctgaacatga aaggaatgaa ttcaggaaca
      661 agctacagca agccgaatcc gagtgggaca aagaaaacgc tgcttttaag cgtaccgagg
      721 gatataagta cgttggggag ctggacaggt acagagaacg cgagattctg gcggcggcat
      781 ctttagagaa caccaggcaa aaggttgctg aagaggtatc cgttgcccgt agccagatgt
      841 tatctctgga gcctgaactc agtatatctg gagatgaaaa agctcaaatg cgacatgagt
      901 tactggcaga aatggcgcag gaacggcagc aacaggagga aaagcactgt gtatacagcg
      961 atcctgggcc aggggggtat cacgtagtaa cgaacgtgat caagatatgg agcgttgaaa
     1021 atgtagcaat atcgggactg cgccccgaac cccgccaacg tttcacggaa cgcgaaaaat
     1081 tccgcgtccc gtgaaacgtt ttctgaatga gaaaaattgt cgttttgatt tactcacagt
     1141 tcagattaat gaagttaaca ggtgttaaat atttgcaggt ggttatatgt gtaaccacct
     1201 gtaagggaag gactaaaact tagtgcaatc ttctatttta taataaatac tattttttat
     1261 tgatgttaca aagtcccgag gtatttgatt tttgctgtag ttaatgtatg catattgcaa
     1321 tagttgttta tgaaagtttt cagctctatt ctttccctga aaattatatg tcaacacccc
     1381 atctaaataa tcaactcctc cggtatctgt tacaaaccag taataggtta atttgacatc
     1441 tgagatattt agttttttcc tacaatcatt taacttttca cctatttcta tattgtgttt
     1501 ttttaaatca gaaattattt gaggtgctct atcttggctt cttttgtaga tatttagaaa
     1561 gttatcatca aagtatatat ttgttttttt tatgcattca tctgcgttct cacagggggg
     1621 acacgttcgt agaaaccggg gaagtttttt agttattaat ggtgatgcat ttttcttaaa
     1681 cgattgatat actttatata tatgcttttc gcatgattct tttgcatact cttcacttac
     1741 atcacgccaa ctgtaactat cggcagattg aatgtattcg tacccaccac aaatttcatt
     1801 tagcgcattg tcattatggt cctttagata tagcattctg tctaaataag ggctaattgt
     1861 gagtttgcta tatatcattg gatcttcatt aaaagcactg tttagctttc ttatatgatc
     1921 tattatgacc tcttttgttt tttccaccag aggcgttttc tgtttgtatt cctctagtga
     1981 ttcattggtt gattttatgc tgttgttatt ttgtgctata gaatattcag ccttatcttc
     2041 aggttcttgc ataatggctg aatttattat ttttaggcca ctttcactaa tatcacaggt
     2101 atatgtgacg atggttcttc ctcgatcatc ctctttttca ctccatgtgc cattgatgca
     2161 atcactcctt gtatcgaagg ctttaccaac agtcattgag tcgtcaatgt cgtaatatac
     2221 gaaagacttt accttgctta ttccatcaga gtcgcatcct gaaataaaaa atgacgacaa
     2281 taaaggaagg atatgtttaa agttaatatt catttttccc atttttattt ctaacaataa
     2341 cgaggaaata ttaatacagg cgatatgtta atggaatcca tacataccga taaaccgact
     2401 tactatgttt gtgctcaacg tcttacgcag ttcgaaaaga tttcgcacca gttcaccttt
     2461 ttctggatga gaaagtttgc tgttttgacc tgttcgctgt tcaaaacgag tgaaaccgga
     2521 catgaatcgc tttcgtgcat agttatgcag ccccctgaaa acaattctgg cgcgtttttt
     2581 tggtctggcc tgttgtttcc ctgtcttttt gcgttttttg cgacagaaag cgactgaggg
     2641 cgttttaagg ggggcgcaca acgggagtta tggtaaatgg atcgggtttg cgggaagact
     2701 cgacaggttt tgtcgttggg ggtagtgtaa gcgactgaaa aacaaacgcc cctgaaattc
     2761 gtgtctatcc ggcaagactt tcacgaagat acaggggcga tgtcggtcga taacctggaa
     2821 ggaatcgtaa cacatgagcg ccgcgcttca atacttcgaa gaaaatttac ctcaccgtcc
     2881 ctatcacacg gatgagctcg ctttcggtct tcgtatctcc ggcaaagggc gtgcgctgct
     2941 tgctcgctac atccagcaaa atcagcctca tgcgcagttc tggctggttt ttgacgttga
     3001 ccgcgtagga gctgcgattg actggagcga ccggaacgcc cccgcgccga acatcaccgt
     3061 aaaaaatccc gagaacgggc acgctcacct gctctacgcg ctcaatcttg ccgtgagaac
     3121 cgcgcctgat gcgtcggtta aggcgctgaa atacgccgct gcaattgaac gtgcgctgtg
     3181 tgagaaactt gacgcagatg tgaactacag cggactgatt tgcaaaaatc cgttccacct
     3241 ggaatggcag gtgatggagt ggcgcgagga agcctacgcc ctcgatgaac tggctgatta
     3301 tctcgatttg agagcctcag agcgtcgtag cgtcgataaa cattacgggc tggggcgaaa
     3361 ctgccatctg ttcgaaatga cgcgcaaatg ggcttacagg gcgattcggc agggctggcc
     3421 agcattctca cagtggcttg atgctgtgat tcagcgtgtc gaaatgtaca acgcatcgct
     3481 tcccgttccg ctttctccgc ctgaatgtcg ggctattggc aagagcattg cgaaatacac
     3541 gcacaggaac ttcacgccgg aaagtttcgc acagtatgtg gctgatacgc acacaccaga
     3601 aatacaggcc aagagaggcc ggaaaggtgg catcgctaaa ggcgaagcct acgatgacaa
     3661 gcgtttcatg gcgctatgta tgctggagaa tggatattct cagaaagcta ttgcggcgat
     3721 gctgaatgta catcgtaata cgatccgtaa ttgggcaatg cacaaatagc ctatatcaga
     3781 taacagcgcc ttttcggcgt ctttttgagc agcgggcttt ccggcggttt tctcctttca
     3841 gcccagcaat ggtgcggctt accgtatgat tgaggtggtc gtgctcgccg cagtctcatg
     3901 accgagcgta gcgagcgaat gagcgaggaa gcaccaggga actggaacgt gaacggaggc
     3961 tcttacgcac tgtctttggt gagtagctct ttcccgcgtt tttcccattc ctgccatttt
     4021 ggatggttgt gcggtagctc tgcgattcct gcgagtgcgc ctaccagttc ggcagcacta
     4081 aactttggct ttccggtttt gctgtccacc agtcctgcca caatcatgag gcctgcggcc
     4141 ttgtagagtt catgatcccg cgcctttcgt tccgcccttg cggctgcctt ccgttctgcc
     4201 gctatgattg ccgttactct ggcttttgct gcggctgctt tctctgcggt tttttctgcc
     4261 cgtatcagtg cggacaacgt tttttcatcc gtcgttgttc ggtttttttt ctctgccagt
     4321 aacacaagta atctctgctg ctctgatggt gatttcagtc cgttgatgta ggcaattttt
     4381 gcacttaacc actcttcacg atttgtcatt cttatctctg cacttttgcc gttaatgtga
     4441 gttgttatta tgcataatat caccttgttt gcctgcgtgt gagaccgtaa aatcatccat
     4501 gattaattca gggatgcgca cttagtagtt tctctccttc gtcgagaaac tgtgcgctcc
     4561 tgcggagggc taaaaggcag atggcaagct accattgcac tgtcaaagct ggagcaaaag
     4621 gcagtgcctt aaaacatgct gattacattt ccagatccgg cgaatataag agttacaaat
     4681 cgcgggagga tctggaattt tcgtcatccg gtaacatgcc atcatgggcg aagaaaaatc
     4741 ccgcagagct atggaaagcc gcagatgaat ttgaacgaaa aaacgggact gcataccgtg
     4801 aaattgagat cgcgttaccg cgtgaactga cacgcgaaca acggatagaa cttgttgaag
     4861 atttcgtgca aaaggaactt ggcgatcgcc atgcctacca gtacgcgatc cacaatccgc
     4921 caggtgcaat cgacggaaag gaacagccac acgcgcatat catgttttgc gagcggatta
     4981 atgatggtat tgaacgcgat ccacagcaat tttttaaacg tgccaacagc aaatcaccag
     5041 agcggggagg cgcaaaaaaa gcgagtattc cccagacagc cggagagcga aaagccgccc
     5101 ttgttgcgct gcgttcccgc
//
