LOCUS       NZ_CP053760             2672 bp    DNA     circular CON 17-APR-2024
DEFINITION  Shigella sonnei strain 506 plasmid pMHMC-009, complete sequence.
ACCESSION   NZ_CP053760
VERSION     NZ_CP053760.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07663113
            Assembly: GCF_013201485.1
KEYWORDS    RefSeq.
SOURCE      Shigella sonnei
  ORGANISM  Shigella sonnei
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Shigella.
REFERENCE   1  (bases 1 to 2672)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     clinical or host associated isolate for Shigella sonnei
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2672)
  AUTHORS   Hoffmann,M., Sanchez,M., Worley,J. and Bry,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-2020) CFSAN, US FDA, 5001 Campus Drive, College
            Park, MD 20740, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: MAR-2020
            Assembly Method                   :: HGAP v. 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 445.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_013201485.1-RS_2024_04_17
            Annotation Date                   :: 04/17/2024 06:48:10
            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)                     :: 5,497
            CDSs (total)                      :: 5,365
            Genes (coding)                    :: 4,629
            CDSs (with protein)               :: 4,629
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 100
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 736
            CDSs (without protein)            :: 736
            Pseudo Genes (ambiguous residues) :: 0 of 736
            Pseudo Genes (frameshifted)       :: 208 of 736
            Pseudo Genes (incomplete)         :: 523 of 736
            Pseudo Genes (internal stop)      :: 128 of 736
            Pseudo Genes (multiple problems)  :: 117 of 736
            Pseudo Genes (short protein)      :: 3 of 736
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053760.1.
            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..2672
                     /organism="Shigella sonnei"
                     /mol_type="genomic DNA"
                     /strain="506"
                     /isolation_source="stool"
                     /host="Homo sapiens"
                     /db_xref="taxon:624"
                     /plasmid="pMHMC-009"
                     /geo_loc_name="USA:Boston"
                     /collection_date="2017"
                     /collected_by="Brigham and Women's Hospital"
     gene            complement(258..452)
                     /locus_tag="COO90_RS27305"
                     /old_locus_tag="COO90_27120"
     CDS             complement(258..452)
                     /locus_tag="COO90_RS27305"
                     /old_locus_tag="COO90_27120"
                     /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"
     gene            738..1061
                     /gene="mobA"
                     /locus_tag="COO90_RS27310"
                     /old_locus_tag="COO90_27125"
     CDS             738..1061
                     /gene="mobA"
                     /locus_tag="COO90_RS27310"
                     /old_locus_tag="COO90_27125"
                     /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(1287..2012)
                     /locus_tag="COO90_RS27315"
                     /old_locus_tag="COO90_27130"
     CDS             complement(1287..2012)
                     /locus_tag="COO90_RS27315"
                     /old_locus_tag="COO90_27130"
                     /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_005112197.1"
                     /translation="MKILNSNLITNISSTIRNHLLTSSKNIKTHPSPNMDVTSHRRLFQ
                     KDGIGLSQTGKATQLVIMSHGGWKEISHPQTLFTRQKGDGWTVVPKNLRIDFYTKDNDF
                     TKGLSVLSEVNKRHTEAQKGLTPSLNISKDDLKVLANARNIPQSKLEEEMMSQAIYRKE
                     YATSNEKIKNYALYYHEQAQNIIQRHQDGLGNKNIDIAFITDKNHKKHLSDIFKVINES
                     GVKYDVIHFGACRVNREEK"
                     /name="putative adhesin"
     gene            complement(2289..2450)
                     /locus_tag="COO90_RS27320"
     CDS             complement(2289..2450)
                     /locus_tag="COO90_RS27320"
                     /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"
     Typing          491..729
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.72e-122"
     Typing          complement(2..215)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.705"
                     /coverage="92.0"
                     /evalue="5.54e-78"
     Typing          complement(2301..2670)
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.687"
                     /coverage="82.0"
                     /evalue="3.93e-168"
     Typing          739..1058
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.196"
                     /coverage="100.0"
                     /evalue="7.28e-62"
ORIGIN
        1 gagcctatgg aaaaacgcca cctgcgcggc ctttgtccct gccttcggct ttttgctcac
       61 atgttctttc cggcgttatc ccctgattct gtggataacc gcattaccgc ctttgagtga
      121 gctgacaccg ctcgccgcag tcgaacgacc gagcgtagcg agtcagtgag cgaggaagcg
      181 gaagagcgcc ttatgtgaca ttttctcctt acgcaccggt ataccgttct gcatcctgtc
      241 tggagcagga tacactgtta taccccggtg ccactttccg cttcaaagcg tgtctgtatg
      301 ctgttctgga gttcttccgc gatttcgtgc agcttctcac acatggcggc ctgttcgtcg
      361 gcatcgagtg cgtccagctt ttcgagcagc gtcaggctct ggctttttat gaatcccgcc
      421 atgttgagta cggtttgctg ctgcttgttc atctttctgt tttctccgtt ctgtctgtca
      481 tctgcgttgt gtgattatat cgcgtaccac ttttcgactg ttttaccgcc ggtattctgc
      541 cgtctgacgc attgacgggt atttctgcct gacaatactg tcactgccaa aaaaactgcc
      601 gtgcctttgt cggtaattcg aacttgctga caggacagga tgtgtaattg ttataccgcg
      661 catacatgca cgctattaca attaccctgg tcagggcttc gccccgacac cccgtgtcag
      721 atacggagcc atgttttatg acaaaacgaa gtggaagtaa tacgcgcagg cgggctatca
      781 gtcgccctgt tcgtctgacg gcagaagaag accaggaaat cagaaaaagg gctgctgaat
      841 gcggcaagac cgtttctggt tttttacggg cggcagctct cggtaagaac gttaactcac
      901 tgactgatga tcgggtgctg aaagaagtta tgagactggg ggcgttacag aaaaaactct
      961 ttatcgacgg caagcgtatc ggggacaggg agtatgcgga ggtgctgatc gctattacgg
     1021 agtatcaccg tgccctgtta tccaggctta tggcagatta gcttcccggg gagaaaactg
     1081 ttgaaaacag acggtatgaa cacggtaagc tcccaaagtg atctccattc gctttcatgc
     1141 atagctatgc agcgagctga aaacgatcct gacgcatcct tcctgttttt ccggggtaaa
     1201 acatctattt ttgtggtgtc tgcgtcagaa tcgcgttcag cgcgtttcag tggtgcgtac
     1261 aattaaggga ttatggtaaa tgatgattat ttctcctctc tatttactcg gcaagcgcca
     1321 aagtgaatta catcatattt tactcctgat tcatttatta ctttaaatat gtcagaaagg
     1381 tgcttcttat gatttttatc agttataaat gctatatcaa tatttttgtt tcctaagcca
     1441 tcttgatgtc tttgtataat attttgggct tgttcatggt aatatagagc atagtttttt
     1501 atcttctcat tacttgttgc gtattctttt ctatatatgg cttgtgacat catttcttct
     1561 tctaattttg attgaggtat attgcgcgcg ttcgctagaa cttttaggtc atctttgctt
     1621 atgtttagtg atggtgttaa ccctttttga gcttcagtat ggcgtttgtt tacctctgaa
     1681 agaacgctta gtccctttgt gaagtcgttg tcttttgtat aaaaatcaat tcttaggttt
     1741 ttggggacta cagtccatcc atcgcctttt tgacgcgtga atagtgtttg tggatgggag
     1801 atctctttcc atccaccatg cgacataatg acaagttgtg ttgcttttcc tgtttggctc
     1861 aatcctattc cgtctttctg gaataaacga cgatgacttg ttacgtccat gtttggtgat
     1921 gggtgtgttt ttatattttt ggatgatgtt agaaggtgat ttcttattgt tgatgatatg
     1981 tttgttatga gattcgaatt gagtattttc atttgttaac aatccatttt tgcggtgttt
     2041 tttattgttt tttttctttt gtttaagggt gtgtcggtgt aagtgtttat tttatgggtt
     2101 aaagtaggat accaagtgtg aaaaaaaatt aaaggttctt cttgagatcc tttttttctg
     2161 cgcgtaatct gctgcctgta aacgaaaaaa ccgccctgca aggcggtttt tcgaaggttc
     2221 tcagagctac caactctttg agccgaggta actggcttgg aggagcgcag tcaccaaaac
     2281 ttgttctttc agtttagcct taacaggcgc atgacttcaa gtcttactcc tctaattcgg
     2341 ttatcagtgg ctgctgccag tggcgataat tcgtgtctta ccgggttgga ctcaagacga
     2401 tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc
     2461 ttggagcgaa cgacctacac cgggccgaga taccaacagc gtgagctatg agaaagcgcc
     2521 acgcttcccg aagggagaaa ggcggacagg tatccggtaa acggcagggt cggaacagga
     2581 gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt
     2641 cgccacctct gacttgagcg tcgatttttg gg
//
