LOCUS       NZ_CP023653             2690 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain CFSAN030807 plasmid pCFSAN030807_8, complete
            sequence.
ACCESSION   NZ_CP023653
VERSION     NZ_CP023653.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03612247
            Assembly: GCF_002442535.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2690)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Whole genome sequencing of cultured foodborne pathogen
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2690)
  AUTHORS   Hoffmann,M., Sanchez,M., Baugher,J. and Timme,R.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-SEP-2017) CFSAN-ORS-DM-MMSB, US Food and Drug
            Administration, 5100 Paint Branch Parkway, College Park, MD 20740,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v.3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 700.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002442535.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 03:16:54
            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)                     :: 5,167
            CDSs (total)                      :: 5,037
            Genes (coding)                    :: 4,336
            CDSs (with protein)               :: 4,336
            Genes (RNA)                       :: 130
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 701
            CDSs (without protein)            :: 701
            Pseudo Genes (ambiguous residues) :: 0 of 701
            Pseudo Genes (frameshifted)       :: 197 of 701
            Pseudo Genes (incomplete)         :: 506 of 701
            Pseudo Genes (internal stop)      :: 123 of 701
            Pseudo Genes (multiple problems)  :: 117 of 701
            Pseudo Genes (short protein)      :: 3 of 701
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP023653.1.
            Bacteria and source DNA available from Dwayne Roberson, US FDA.
            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..2690
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="CFSAN030807"
                     /serovar="Serotype group D"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pCFSAN030807_8"
                     /geo_loc_name="Somalia"
     gene            9..332
                     /gene="mobA"
                     /locus_tag="AT852_RS28045"
                     /old_locus_tag="AT852_28045"
     CDS             9..332
                     /gene="mobA"
                     /locus_tag="AT852_RS28045"
                     /old_locus_tag="AT852_28045"
                     /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_004988908.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKNVNSLTDDRVLKEVMRLGALQKKLFIDGKRIGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            complement(558..1181)
                     /locus_tag="AT852_RS28050"
                     /old_locus_tag="AT852_28050"
     CDS             complement(558..1181)
                     /locus_tag="AT852_RS28050"
                     /old_locus_tag="AT852_28050"
                     /inference="COORDINATES: protein motif:HMM:NF045398.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="putative adhesin"
                     /protein_id="WP_226342037.1"
                     /translation="MDVTSHRRLFQKDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFT
                     RQKGDGWTVVPKNLRIDFYTKDNDFTKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKV
                     LANARNIPQSKLEEEMMSQAIYRKEYATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKN
                     IDIAFITDKNHKKHLSDIFKVINESGVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(1560..1721)
                     /locus_tag="AT852_RS29170"
     CDS             complement(1560..1721)
                     /locus_tag="AT852_RS29170"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001318243.1"
                     /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_072007783.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHELSPLAAATDNRIRGVRLE
                     VMRLLRLN"
                     /name="replication initiation protein"
     gene            complement(2219..2413)
                     /locus_tag="AT852_RS28060"
                     /old_locus_tag="AT852_28060"
     CDS             complement(2219..2413)
                     /locus_tag="AT852_RS28060"
                     /old_locus_tag="AT852_28060"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_039059175.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHEIA
                     EELQNSIQTRFEAESGTGV"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          2452..2690
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(1650..2176)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.472"
                     /coverage="96.0"
                     /evalue="0.0"
     Typing          10..329
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="8.16e-62"
ORIGIN
        1 catgttttat gacaaaacga agtggaagta atacgcgcag gcgggctatc agtcgccctg
       61 ttcgtctgac ggcagaagaa gaccaggaaa tcagaaaaag ggctgctgaa tgcggcaaga
      121 ccgtttctgg ttttttacgg gcggcagctc tcggtaagaa cgttaactca ctgactgatg
      181 atcgggtgct gaaagaagtt atgagactgg gggcgttaca gaaaaaactc tttatcgacg
      241 gcaagcgtat cggggacagg gagtatgcgg aggtgctgat cgctattacg gagtatcacc
      301 gtgccctgtt atccaggctt atggcagatt agcttcccgg ggagaaaact gttgaaaaca
      361 gacggtatga acacggtaag ctcccaaagt gatctccatt cgctttcatg catagctatg
      421 cagcgagctg aaaacgatcc tgacgcatcc ttcctgtttt tccggggtaa aacatctatt
      481 tttgtggtgt ctgcgtcaga atcgcgttca gcgcgtttca gtggtgcgta caattaaggg
      541 attatggtaa atgatgatta tttctcctct ctatttactc ggcaagcgcc aaagtgaatt
      601 acatcatatt ttactcctga ttcatttatt actttaaata tgtcagaaag gtgcttctta
      661 tgatttttat cagttataaa tgctatatca atatttttgt ttcctaagcc atcttgatgt
      721 ctttgtataa tattttgggc ttgttcatgg taatatagag catagttttt tatcttctca
      781 ttacttgttg cgtattcttt tctatatatg gcttgtgaca tcatttcttc ttctaatttt
      841 gattgaggta tattgcgcgc gttcgctaga acttttaggt catctttgct tatgtttagt
      901 gatggtgtta accctttttg agcttcagta tggcgtttgt ttacctctga aagaacgctt
      961 agtccctttg tgaagtcgtt gtcttttgta taaaaatcaa ttcttaggtt tttggggact
     1021 acagtccatc catcgccttt ttgacgcgtg aatagtgttt gtggatggga gatctctttc
     1081 catccaccat gcgacataat gacaagttgt gttgcttttc ctgtttggct caatcctatt
     1141 ccgtctttct ggaataaacg acgatgactt gttacgtcca tgtttggtga tgggtgtgtt
     1201 tttatatttt tggatgatgt tagaaggtga tttcttattg ttgatgatat gtttgttatg
     1261 agattcgaat tgagtatttt catttgttaa caatccattt ttgcggtgtt ttttattgtt
     1321 ttttttcttt tgtttaaggg tgtgtcggtg taagtgttta ttttatgggt taaagtagga
     1381 taccaagtgt gaaaaaaaat taaaggttct tcttgagatc ctttttttct gcgcgtaatc
     1441 tgctgcctgt aaacgaaaaa accgccctgc aaggcggttt ttcgaaggtt ctcagagcta
     1501 ccaactcttt gagccgaggt aactggcttg gaggagcgca gtcaccaaaa cttgttcttt
     1561 cagtttagcc ttaacaggcg catgacttca agtcttactc ctctaattcg gttatcagtg
     1621 gctgctgcca gtggcgataa ttcgtgtctt accgggttgg actcaagacg atagttaccg
     1681 gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag cttggagcga
     1741 acgacctaca ccgggccgag ataccaacag cgtgagctat gagaaagcgc cacgcttccc
     1801 gaagggagaa aggcggacag gtatccggta aacggcaggg tcggaacagg agagcgcacg
     1861 agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt tcgccacctc
     1921 tgacttgagc gtcgattttt gtgatgctcg tcaggggggc ggagcctatg gaaaaacgcc
     1981 acctgcgcgg cctttgtccc tgccttcggc tttttgctca catgttcttt ccggcgttat
     2041 cccctgattc tgtggataac cgcattaccg cctttgagtg agctgacacc gctcgccgca
     2101 gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaagagcgc cttatgtgac
     2161 attttctcct tacgcaccgg tataccgttc tgcatcctgt ctggagcagg atacactgtt
     2221 ataccccggt gccactttcc gcttcaaagc gtgtctgtat gctgttctgg agttcttccg
     2281 cgatttcgtg cagcttctca cacatggcgg cctgttcgtc ggcatcgagt gcgtccagct
     2341 tttcgagcag cgtcaggctc tggcttttta tgaatcccgc catgttgagt acggtttgct
     2401 gctgcttgtt catctttctg ttttctccgt tctgtctgtc atctgcgttg tgtgattata
     2461 tcgcgtacca cttttcgact gttttaccgc cggtattctg ccgtctgacg cattgacggg
     2521 tatttctgcc tgacaatact gtcactgcca aaaaaactgc cgtgcctttg tcggtaattc
     2581 gaacttgctg acaggacagg atgtgtaatt gttataccgc gcatacatgc acgctattac
     2641 aattaccctg gtcagggctt cgccccgaca ccccgtgtca gatacggagc
//
